Sample records for non-overlapping phenotype analyses
-
Phenotype of asthma-chronic obstructive pulmonary disease overlap syndrome.
Rhee, Chin Kook
2015-07-01
Many patients with asthma or chronic obstructive pulmonary disease (COPD) have overlapping characteristics of both diseases. By spirometric definition, patients with both fixed airflow obstruction (AO) and bronchodilator reversibility or fixed AO and bronchial hyperresponsiveness can be considered to have asthma-COPD overlap syndrome (ACOS). However, patients regarded to have ACOS by spirometric criteria alone are heterogeneous and can be classified by phenotype. Eosinophilic inflammation, a history of allergic disease, and smoke exposure are important components in the classification of ACOS. Each phenotype has a different underlying pathophysiology, set of characteristics, and prognosis. Medical treatment for ACOS should be tailored according to phenotype. A narrower definition of ACOS that includes both spirometric and clinical criteria is needed.
-
Epidemic spreading on complex networks with overlapping and non-overlapping community structure
Shang, Jiaxing; Liu, Lianchen; Li, Xin; Xie, Feng; Wu, Cheng
2015-02-01
Many real-world networks exhibit community structure where vertices belong to one or more communities. Recent studies show that community structure plays an import role in epidemic spreading. In this paper, we investigate how the extent of overlap among communities affects epidemics. In order to experiment on the characteristic of overlapping communities, we propose a rewiring algorithm that can change the community structure from overlapping to non-overlapping while maintaining the degree distribution of the network. We simulate the Susceptible-Infected-Susceptible (SIS) epidemic process on synthetic scale-free networks and real-world networks by applying our rewiring algorithm. Experiments show that epidemics spread faster on networks with higher level of overlapping communities. Furthermore, overlapping communities' effect interacts with the average degree's effect. Our work further illustrates the important role of overlapping communities in the process of epidemic spreading.
-
Paulin, Francisco; Doyle, Tracy J; Fletcher, Elaine A; Ascherman, Dana P; Rosas, Ivan O
2015-01-01
The prevalence of clinically evident interstitial lung disease in patients with rheumatoid arthritis is approximately 10%. An additional 33% of undiagnosed patients have interstitial lung abnormalities that can be detected with high-resolution computed tomography. Rheumatoid arthritis-interstitial lung disease patients have three times the risk of death compared to those with rheumatoid arthritis occurring in the absence of interstitial lung disease, and the mortality related to interstitial lung disease is rising. Rheumatoid arthritis-interstitial lung disease is most commonly classified as the usual interstitial pneumonia pattern, overlapping mechanistically and phenotypically with idiopathic pulmonary fibrosis, but can occur in a non-usual interstitial pneumonia pattern, mainly nonspecific interstitial pneumonia. Based on this, we propose two possible pathways to explain the coexistence of rheumatoid arthritis and interstitial lung disease: (i) Rheumatoid arthritis-interstitial lung disease with a non-usual interstitial pneumonia pattern may come about when an immune response against citrullinated peptides taking place in another site (e.g. the joints) subsequently affects the lungs; (ii) Rheumatoid arthritis-interstitial lung disease with a usual interstitial pneumonia pattern may represent a disease process in which idiopathic pulmonary fibrosis-like pathology triggers an immune response against citrullinated proteins that promotes articular disease indicative of rheumatoid arthritis. More studies focused on elucidating the basic mechanisms leading to different sub-phenotypes of rheumatoid arthritis-interstitial lung disease and the overlap with idiopathic pulmonary fibrosis are necessary to improve our understanding of the disease process and to define new therapeutic targets.
-
Phenotypic overlap between MMP-13 and the plasminogen activation system during wound healing in mice
DEFF Research Database (Denmark)
Juncker-Jensen, Anna; Lund, Leif R
2011-01-01
combined completely prevent wound healing. Both urokinase-type plasminogen activator and several matrix metallo proteinases (MMPs), such as MMP-3, -9 and -13, are expressed in the leading-edge keratinocytes of skin wounds, which may account for this phenotypic overlap between these classes of proteases....
-
A case study of discordant overlapping meta-analyses: vitamin d supplements and fracture.
Directory of Open Access Journals (Sweden)
Mark J Bolland
Full Text Available BACKGROUND: Overlapping meta-analyses on the same topic are now very common, and discordant results often occur. To explore why discordant results arise, we examined a common topic for overlapping meta-analyses- vitamin D supplements and fracture. METHODS AND FINDINGS: We identified 24 meta-analyses of vitamin D (with or without calcium and fracture in a PubMed search in October 2013, and analysed a sample of 7 meta-analyses in the highest ranking general medicine journals. We used the AMSTAR tool to assess the quality of the meta-analyses, and compared their methodologies, analytic techniques and results. Applying the AMSTAR tool suggested the meta-analyses were generally of high quality. Despite this, there were important differences in trial selection, data extraction, and analytical methods that were only apparent after detailed assessment. 25 trials were included in at least one meta-analysis. Four meta-analyses included all eligible trials according to the stated inclusion and exclusion criteria, but the other 3 meta-analyses "missed" between 3 and 8 trials, and 2 meta-analyses included apparently ineligible trials. The relative risks used for individual trials differed between meta-analyses for total fracture in 10 of 15 trials, and for hip fracture in 6 of 12 trials, because of different outcome definitions and analytic approaches. The majority of differences (11/16 led to more favourable estimates of vitamin D efficacy compared to estimates derived from unadjusted intention-to-treat analyses using all randomised participants. The conclusions of the meta-analyses were discordant, ranging from strong statements that vitamin D prevents fractures to equally strong statements that vitamin D without calcium does not prevent fractures. CONCLUSIONS: Substantial differences in trial selection, outcome definition and analytic methods between overlapping meta-analyses led to discordant estimates of the efficacy of vitamin D for fracture prevention
-
Hunt, E; Bornovalova, M A; Patrick, C J
2015-05-01
Previous studies have reported strong genetic and environmental overlap between antisocial-externalizing (factor 2; F2) features of psychopathy and borderline personality disorder (BPD) tendencies. However, this line of research has yet to examine etiological associations of affective-interpersonal (factor 1, F1) features of psychopathy with BPD tendencies. The current study investigated differential phenotypic and genetic overlap of psychopathy factors 1 and 2 with BPD tendencies in a sample of over 250 male and female community-recruited adult twin pairs. Consistent with previous research, biometric analyses revealed strong genetic and non-shared environmental correlations of F2 with BPD tendencies, suggesting that common genetic and non-shared environmental factors contribute to both phenotypes. In contrast, negative genetic and non-shared environmental correlations were observed between F1 and BPD tendencies, indicating that the genetic factors underlying F1 serve as protective factors against BPD. No gender differences emerged in the analyses. These findings provide further insight into associations of psychopathic features - F1 as well as F2 - and BPD tendencies. Implications for treatment and intervention are discussed, along with how psychopathic traits may differentially influence the manifestation of BPD tendencies.
-
Mõttus, René; Marioni, Riccardo; Deary, Ian J
2017-02-01
Associations between markers of ostensible psychological characteristics and social and health inequalities are pervasive but difficult to explain. In some cases, there may be causal influence flowing from social and health inequalities to psychological differences, whereas sometimes it may be the other way around. Here, we focus on the possibility that some markers that we often consider as indexing different domains of individual differences may in fact reflect at least partially overlapping genetic and/or phenotypic bases. For example, individual differences in cognitive abilities and educational attainment appear to reflect largely overlapping genetic influences, whereas cognitive abilities and health literacy may be almost identical phenomena at the phenotypic, never mind genetic, level. We make the case for employing molecular genetic data and quantitative genetic techniques to better understand the associations of psychological individual differences with social and health inequalities. We illustrate these arguments by using published findings from the Lothian Birth Cohort and the Generation Scotland studies. We also present novel findings pertaining to longitudinal stability and change in older age personality traits and some correlates of the change, molecular genetic data-based heritability estimates of Neuroticism and Extraversion, and the genetic correlations of these personality traits with markers of social and health inequalities. © 2015 The Authors. Journal of Personality published by Wiley Periodicals, Inc.
-
Perceived Non-Overlap of Objects in an Audiovisual Stream/Bounce Display
Directory of Open Access Journals (Sweden)
Yousuke Kawachi
2011-10-01
Full Text Available In a stream/bounce display in which two identical visual objects move toward each other, coincide (completely overlap, and then move apart, the objects can be perceived as either streaming through or bouncing off each other. Despite the perceptual ambiguity in this display, the streaming percept is dominant. However, a sound burst presented at the time that the objects coincide facilitates the bouncing percept. Herein, we report a perceptual phenomenon in which the overlap between objects is illusorily perceived as a non-overlap in the stream/bounce display accompanied with sound. In the experiment, the amount of overlap between two objects was systematically manipulated in the presence/absence of a sound. Observers were asked to judge whether the two objects overlapped with each other and then asked whether the objects appeared to stream through or bounce off each other. The results were consistent with those of previous studies showing that sound promoted the bouncing percept. Most importantly, the sound presentation facilitated the perception of a non-overlap between the objects instead of a physical overlap, suggesting that the momentary overlap was inadequately perceived. We discuss the possibility that an abrupt sound temporally interrupts visual processing such as the formation of dynamic object representations.
-
Individual-based analyses reveal limited functional overlap in a coral reef fish community.
Brandl, Simon J; Bellwood, David R
2014-05-01
Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on
-
Bettencourt, Conceição; Quintáns, Beatriz; Ros, Raquel; Ampuero, Israel; Yáñez, Zuleima; Pascual, Samuel Ignacio; de Yébenes, Justo García; Sobrido, María-Jesús
2012-09-01
Hereditary spastic paraplegias (HSPs) constitute a heterogeneous group of neurological disorders, characterized primarily by progressive spasticity and weakness of the lower limbs. HSPs are caused by mutations in multiple genes (at least 48 loci and 28 causative genes). The clinical spectrum of HSPs is wide and important differences have been reported between patients with distinct mutations in the same gene, or even between different family members bearing the same mutation. Many patients with HSP present clinical deficits related to the involvement of neuronal systems other than corticospinal tracts, namely, peripheral nerves, sensory, or cerebellar pathways. These cases may be difficult to differentiate from other neurological diseases (e.g., hereditary ataxias), also genetically and clinically heterogeneous. As an illustration of how overlapping this genotype-phenotype relationship is, and the difficulties that it brings upon the development of neurogenetic algorithms and databases, we review the main clinical and genetic features of HSPs, and summarize reports on cases of triplet-repeat spinocerebellar ataxias that can mimic HSP phenotypes. This complex scenario makes the necessity of high-quality, curated mutation databases even more urgent, in order to develop adequate diagnostic guidelines, correct interpretation of genetic testing, and appropriate genetic counseling. © 2012 Wiley Periodicals, Inc.
-
International Nuclear Information System (INIS)
Yuk, Seung Su; Cho, Bumhee; Cho, Nam Zin
2013-01-01
In the case of deterministic transport model, fixed-k problem formulation is necessary and the overlapping local domain is chosen. However, as mentioned in, the partial current-based Coarse Mesh Finite Difference (p-CMFD) procedure enables also non-overlapping local/global (NLG) iteration. In this paper, NLG iteration is combined with p-CMFD and with CMFD (augmented with a concept of p-CMFD), respectively, and compared to OLG iteration on a 2-D test problem. Non-overlapping local/global iteration with p-CMFD and CMFD global calculation is introduced and tested on a 2-D deterministic transport problem. The modified C5G7 problem is analyzed with both NLG and OLG methods and the solutions converge to the reference solution except for some cases of NLG with CMFD. NLG with CMFD gives the best performance if the solution converges. But if fission-source iteration in local calculation is not enough, it is prone to diverge. The p-CMFD global solver gives unconditional convergence (for both OLG and NLG). A study of switching scheme is in progress, where NLG/p-CMFD is used as 'starter' and then switched to NLG/CMFD to render the whole-core transport calculation more efficient and robust. Parallel computation is another obvious future work
-
Multiple scattering in closely packed systems of arbitrary non-overlapping shapes
International Nuclear Information System (INIS)
Keister, B.D.
1982-11-01
It has long been known that the multiple scattering of waves from a system of obstacles of finite extent can be described completely with a knowledge of the on-shell amplitudes of the individual scatterers, provided that the minimally enclosing spheres concentric with the scattering centers do not overlap. In this paper, it is shown that on-shell amplitudes alone suffice for a wider class of scattering configurations, in which the individual scatterers do not overlap, but their geometries do not satisfy the above condition. These extended geometries require a careful treatment of certain partial wave sums. An example is also discussed in which a pair of non-overlapping scatterers requires more than the on-shell amplitudes for a solution
-
Comparative Phenotypical and Molecular Analyses of Arabidopsis Grown under Fluorescent and LED Light
Directory of Open Access Journals (Sweden)
Franka Seiler
2017-06-01
Full Text Available Comparative analyses of phenotypic and molecular traits of Arabidopsis thaliana grown under standardised conditions is still a challenge using climatic devices supplied with common light sources. These are in most cases fluorescent lights, which have several disadvantages such as heat production at higher light intensities, an invariable spectral output, and relatively rapid “ageing”. This results in non-desired variations of growth conditions and lowers the comparability of data acquired over extended time periods. In this study, we investigated the growth behaviour of Arabidopsis Col0 under different light conditions, applying fluorescent compared to LED lamps, and we conducted physiological as well as gene expression analyses. By changing the spectral composition and/or light intensity of LEDs we can clearly influence the growth behaviour of Arabidopsis and thereby study phenotypic attributes under very specific light conditions that are stable and reproducible, which is not necessarily given for fluorescent lamps. By using LED lights, we can also roughly mimic the sun light emission spectrum, enabling us to study plant growth in a more natural-like light set-up. We observed distinct growth behaviour under the different light regimes which was reflected by physiological properties of the plants. In conclusion, LEDs provide variable emission spectra for studying plant growth under defined, stable light conditions.
-
ROBUST PERSON TRACKING WITH MULTIPLE NON-OVERLAPPING CAMERAS IN AN OUTDOOR ENVIRONMENT
Directory of Open Access Journals (Sweden)
S. Hellwig
2012-07-01
Full Text Available The aim of our work is to combine multiple cameras for a robust tracking of persons in an outdoor environment. Although surveillance is a well established field, many algorithms apply various constraints like overlapping fields of view or precise calibration of the cameras to improve results. An application of these developed systems in a realistic outdoor environment is often difficult. Our aim is to be widely independent from the camera setup and the observed scene, in order to use existing cameras. Thereby our algorithm needs to be capable to work with both overlapping and non-overlapping fields of views. We propose an algorithm that allows flexible combination of different static cameras with varying properties. Another requirement of a practical application is that the algorithm is able to work online. Our system is able to process the data during runtime and to provide results immediately. In addition to seeking flexibility in the camera setup, we present a specific approach that combines state of the art algorithms in order to be robust to environment influences. We present results that indicate a good performance of our introduced algorithm in different scenarios. We show its robustness to different types of image artifacts. In addition we demonstrate that our algorithm is able to match persons between cameras in a non-overlapping scenario.
-
Pre-asymptotic behavior of single-particle overlap integrals of non-Borromean two-neutron halos
International Nuclear Information System (INIS)
Timofeyuk, N.K.; Tostevin, J.A.; Blokhintsev, L.D.
2003-01-01
For non-Borromean two-neutron halo nuclei, modifications to the behavior of single-particle overlap integrals will arise due to the correlations of the two interacting nucleons in the halo. An additional contribution to the overlap integral can be obtained using the Feynman diagram approach. This additional term is modeled using a simple local potential model. We show that these modifications may play a role in detailed interpretations of experimental results from single-nucleon knockout, transfer, and other reactions that probe the single-nucleon overlap functions
-
Relative camera localisation in non-overlapping camera networks using multiple trajectories
John, V.; Englebienne, G.; Kröse, B.J.A.
2012-01-01
In this article we present an automatic camera calibration algorithm using multiple trajectories in a multiple camera network with non-overlapping field-of-views (FOV). Visible trajectories within a camera FOV are assumed to be measured with respect to the camera local co-ordinate system.
-
DEFF Research Database (Denmark)
Grosskinsky, Dominik Kilian; Svensgaard, Jesper; Christensen, Svend
2015-01-01
Plants are affected by complex genome×environment×management interactions which determine phenotypic plasticity as a result of the variability of genetic components. Whereas great advances have been made in the cost-efficient and high-throughput analyses of genetic information and non-invasive ph......Plants are affected by complex genome×environment×management interactions which determine phenotypic plasticity as a result of the variability of genetic components. Whereas great advances have been made in the cost-efficient and high-throughput analyses of genetic information and non......-invasive phenotyping, the large-scale analyses of the underlying physiological mechanisms lag behind. The external phenotype is determined by the sum of the complex interactions of metabolic pathways and intracellular regulatory networks that is reflected in an internal, physiological, and biochemical phenotype......, ultimately enabling the in silico assessment of responses under defined environments with advanced crop models. This will allow generation of robust physiological predictors also for complex traits to bridge the knowledge gap between genotype and phenotype for applications in breeding, precision farming...
-
Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.
Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav
2018-04-16
Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.
-
Diagnosis and Management of the Overlap Syndromes of Autoimmune Hepatitis
Directory of Open Access Journals (Sweden)
Albert J Czaja
2013-01-01
Full Text Available BACKGROUND: Autoimmune hepatitis may have cholestatic features that are outside the classical phenotype and that resemble findings in other immune-mediated liver diseases. These cholestatic phenotypes have been designated ‘overlap syndromes’.
-
Solving Person Re-identification in Non-overlapping Camera using Efficient Gibbs Sampling
John, V.; Englebienne, G.; Krose, B.; Burghardt, T.; Damen, D.; Mayol-Cuevas, W.; Mirmehdi, M.
2013-01-01
This paper proposes a novel probabilistic approach for appearance-based person reidentification in non-overlapping camera networks. It accounts for varying illumination, varying camera gain and has low computational complexity. More specifically, we present a graphical model where we model the
-
Clinical comparison of overlapping deletions of 19p13.3.
Risheg, Hiba; Pasion, Romela; Sacharow, Stephanie; Proud, Virginia; Immken, LaDonna; Schwartz, Stuart; Tepperberg, Jim H; Papenhausen, Peter; Tan, Tiong Y; Andrieux, Joris; Plessis, Ghislaine; Amor, David J; Keitges, Elisabeth A
2013-05-01
We present three patients with overlapping interstitial deletions of 19p13.3 identified by high resolution SNP microarray analysis. All three had a similar phenotype characterized by intellectual disability or developmental delay, structural heart abnormalities, large head relative to height and weight or macrocephaly, and minor facial anomalies. Deletion sizes ranged from 792 Kb to 1.0 Mb and included a common region arr [hg19] 19p13.3 (3,814,392-4,136,989), containing eight genes: ZFR2, ATCAY, NMRK2, DAPK3, EEF2, PIAS4, ZBTB7A, MAP2K2, and two non-coding RNA's MIR637 and SNORDU37. The patient phenotypes were compared with three previous single patient reports with similar interstitial 19p13.3 deletions and six additional patients from the DECIPHER and ISCA databases to determine if a common haploinsufficient phenotype for the region can be established. Copyright © 2013 Wiley Periodicals, Inc.
-
Generation of non-overlapping fiber architecture
DEFF Research Database (Denmark)
Chapelle, Lucie; Lévesque, M.; Brøndsted, Povl
2015-01-01
and polymer networks. The model takes into account the complex geometry of the fiber arrangement in which a fiber can be modeled with a certain degree of bending while keeping a main fiber orientation. The model is built in two steps. First, fibers are generated as a chain of overlapping spheres or as a chain......: a repulsion force to suppress the overlap between two fibers and a bending and stretching force to ensure that the fiber structure is kept unchanged. The model can be used as the geometrical basis for further finite-element modelling....
-
Expanding the genotype-phenotype spectrum in hereditary colorectal cancer by gene panel testing
DEFF Research Database (Denmark)
Rohlin, Anna; Rambech, Eva; Kvist, Anders
2017-01-01
Hereditary syndromes causing colorectal cancer include both polyposis and non-polyposis syndromes. Overlapping phenotypes between the syndromes have been recognized and this make targeted molecular testing for single genes less favorable, instead there is a gaining interest for multi-gene panel...
-
Melo, Thaise P; Takada, Luciana; Baldi, Fernando; Oliveira, Henrique N; Dias, Marina M; Neves, Haroldo H R; Schenkel, Flavio S; Albuquerque, Lucia G; Carvalheiro, Roberto
2016-06-21
QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data. Analysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping. The use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high.
-
Buxbaum, Joseph D.; Bolshakova, Nadia; Brownfeld, Jessica M.; Anney, Richard J. L.; Bender, Patrick; Bernier, Raphael; Cook, Edwin H.; Coon, Hilary; Cuccaro, Michael L.; Freitag, Christine M.; Hallmayer, Joachim; Geschwind, Daniel H.; Klauck, Sabine M.; Nurnberger, John I.; Oliveira, Guiomar
2014-01-01
Background: There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. Methods: In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC). TASC sample collection ...
-
Phenotypic plasticity or speciation? A case from a clonal marine organism
Directory of Open Access Journals (Sweden)
Yoshioka Paul M
2008-02-01
Full Text Available Abstract Background Clonal marine organisms exhibit high levels of morphological variation. Morphological differences may be a response to environmental factors but also they can be attributed to accumulated genetic differences due to disruption of gene flow among populations. In this study, we examined the extensive morphological variation (of 14 characters in natural populations observed in the gorgonian Eunicea flexuosa, a widely distributed Caribbean octocoral. Eco-phenotypic and genetic effects were evaluated by reciprocal transplants of colonies inhabiting opposite ends of the depth gradient and analysis of population genetics of mitochondrial and nuclear genes, respectively. Results Significant differences (P 17 m. A discriminant function analysis based on a priori univariate and multivariate analyses (which separated the colonies in morphotypes correctly classified 93% of the colonies for each environment. Light, water motion and sediment transport might influence the distribution of the two morphotypes. Reaction norms of morphological characters of colonies reciprocally transplanted showed gradual significant changes through the 15 months of transplantation. Sclerites of shallow water colonies became larger when transplanted to deeper environments and vice versa, but neither of the two transplanted groups overlapped with the residents' morphology. Genetic analysis of mitochondrial and nuclear genes suggested that such discrete morphology and non-overlapping phenotypic plasticity is correlated with the presence of two independent evolutionary lineages. The distribution of the lineages is non-random and may be related to adaptational responses of each lineage to the environmental demands of each habitat. Conclusion The extensive distribution and ample morphological variation of Eunicea flexuosa corresponds to two distinct genetic lineages with narrower distributions and more rigid phenotypic plasticity than the original description. The
-
Functional dyspepsia (FD) and non-erosive reflux disease (NERD): overlapping or discrete entities?
LENUS (Irish Health Repository)
Quigley, Eamonn M M
2012-02-03
As the incidence of both gastric cancer and peptic ulcer disease have declined, that of gastro-oesophageal reflux disease (GORD) and non-ulcer, or functional dyspepsia (FD) have reached virtually epidemic proportions. As we come to appreciate the expression of these disorders in the community, the real spectrum of each disease has become evident. FD and non-erosive reflux disease (NERD), the most prevalent manifestation of GORD, frequently overlap. Where then does GORD end and FD begin? Is it realistic, or even clinically relevant, to attempt a clear separation between these entities? These are more than issues of mere semantics; therapeutic options may be dictated by the classification of the patient as one or the other. Recent work indicates clearly that NERD is a heterogeneous disorder incorporating some patients who may well harbour subtle manifestations of oesophagitis and others who have entirely normal 24-hour pH studies. These differences may be crucial to the concept of NERD\\/FD overlap. While evidence in support of this concept is far from complete, it would appear that this overlap is most relevant to those NERD patients who do not exhibit abnormal esophageal acid exposure. These patients truly belong in the spectrum of functional gastrointestinal disorders rather than in GORD; attempts to shoe-horn these individuals into the spectrum of GORD will result in therapeutic disappointment and surgical disaster.
-
Relationship between endophenotype and phenotype in ADHD
Directory of Open Access Journals (Sweden)
Buitelaar Jan K
2008-01-01
Full Text Available Abstract Background It has been hypothesized that genetic and environmental factors relate to psychiatric disorders through the effect of intermediating, vulnerability traits called endophenotypes. The study had a threefold aim: to examine the predictive validity of an endophenotypic construct for the ADHD diagnosis, to test whether the magnitude of group differences at the endophenotypic and phenotypic level is comparable, and to investigate whether four factors (gender, age, IQ, rater bias have an effect (moderation or mediation on the relation between endophenotype and phenotype. Methods Ten neurocognitive tasks were administered to 143 children with ADHD, 68 non-affected siblings, and 120 control children (first-borns and 132 children with ADHD, 78 non-affected siblings, and 113 controls (second-borns (5 – 19 years. The task measures have been investigated previously for their endophenotypic viability and were combined to one component which was labeled 'the endophenotypic construct': one measure representative of endophenotypic functioning across several domains of functioning. Results The endophenotypic construct classified children with moderate accuracy (about 50% for each of the three groups. Non-affected children differed as much from controls at the endophenotypic as at the phenotypic level, but affected children displayed a more severe phenotype than endophenotype. Although a potentially moderating effect (age and several mediating effects (gender, age, IQ were found affecting the relation between endophenotypic construct and phenotype, none of the effects studied could account for the finding that affected children had a more severe phenotype than endophenotype. Conclusion Endophenotypic functioning is moderately predictive of the ADHD diagnosis, though findings suggest substantial overlap exists between endophenotypic functioning in the groups of affected children, non-affected siblings, and controls. Results suggest other
-
Extracellular vesicle-mediated phenotype switching in malignant and non-malignant colon cells
International Nuclear Information System (INIS)
Mulvey, Hillary E.; Chang, Audrey; Adler, Jason; Del Tatto, Michael; Perez, Kimberly; Quesenberry, Peter J.; Chatterjee, Devasis
2015-01-01
Extracellular vesicles (EVs) are secreted from many cells, carrying cargoes including proteins and nucleic acids. Research has shown that EVs play a role in a variety of biological processes including immunity, bone formation and recently they have been implicated in promotion of a metastatic phenotype. EVs were isolated from HCT116 colon cancer cells, 1459 non-malignant colon fibroblast cells, and tumor and normal colon tissue from a patient sample. Co-cultures were performed with 1459 cells and malignant vesicles, as well as HCT116 cells and non-malignant vesicles. Malignant phenotype was measured using soft agar colony formation assay. Co-cultures were also analyzed for protein levels using mass spectrometry. The importance of 14-3-3 zeta/delta in transfer of malignant phenotype was explored using siRNA. Additionally, luciferase reporter assay was used to measure the transcriptional activity of NF-κB. This study demonstrates the ability of EVs derived from malignant colon cancer cell line and malignant patient tissue to induce the malignant phenotype in non-malignant colon cells. Similarly, EVs derived from non-malignant colon cell lines and normal patient tissue reversed the malignant phenotype of HCT116 cells. Cells expressing an EV-induced malignant phenotype showed increased transcriptional activity of NF-κB which was inhibited by the NF--κB inhibitor, BAY117082. We also demonstrate that knock down of 14-3-3 zeta/delta reduced anchorage-independent growth of HCT116 cells and 1459 cells co-cultured with HCT derived EVs. Evidence of EV-mediated induction of malignant phenotype, and reversal of malignant phenotype, provides rational basis for further study of the role of EVs in tumorigenesis. Identification of 14-3-3 zeta/delta as up-regulated in malignancy suggests its potential as a putative drug target for the treatment of colorectal cancer
-
Directory of Open Access Journals (Sweden)
Fariba Rezaeetalab
2016-12-01
Full Text Available Overlap syndrome, which is known as the coexistence of chronic obstructive pulmonary disease (COPD and obstructive sleep apnea (OSA, was first defined by Flenley. Although it can refer to concomitant occurrence of any of the pulmonary diseases and OSA, overlap syndrome is commonly considered as the coexistence of OSA and COPD. This disease has unique adverse health consequences distinct from either condition alone. Given the high prevalence of each solitary disease, overlap syndrome is also likely to be common and clinically relevant. Despite the fact that overlap syndrome has been described in the literature for nearly 30 years, paucity of evaluations and studies limited the discussion on diagnosis, prevalence, pathophysiology, treatment, and outcomes of this disease. This review article addresses these issues by reviewing several recent studies conducted in Iran or other countries. This review suggests that overlap syndrome has worse outcomes than either disease alone. Our findings accentuated the urgent need for further studies on overlap syndrome and all overlaps between OSA and chronic pulmonary disease to provide a deeper insight into diagnosis and non-invasive treatments of this disease.
-
DEFF Research Database (Denmark)
Hyldgaard, Benita; Brix, Hans
2012-01-01
High phenotypic plasticity has been hypothesized to affect the invasiveness of plants, as high plasticity may enlarge the breath of environments in which the plants can survive and reproduce. Here we compare the phenotypic plasticity of invasive and non-invasive populations of the same species...... hypothesized that the phenotypic plasticity in fitness-related traits like growth and photosynthesis were higher in the invasive than in the non-invasive population. The invasive population acclimated to elevated temperatures through increased rates of photosynthesis (range: Pamb: 8–452 mol O2 g−1 DM h−1......-harvesting complex. Hence, the invasive population of C. demersum from New Zealand had higher phenotypic plasticity in response to temperature than the non-invasive Danish population. This might be the result of genetic evolution since its introduction to New Zealand five decades ago, but further studies are needed...
-
Zweier, Christiane; Rittinger, Olaf; Bader, Ingrid; Berland, Siren; Cole, Trevor; Degenhardt, Franziska; Di Donato, Nataliya; Graul-Neumann, Luitgard; Hoyer, Juliane; Lynch, Sally Ann; Vlasak, Ingrid; Wieczorek, Dagmar
2014-09-01
Recently, de novo aberrations in PHF6 were identified in females with intellectual disability and with a distinct phenotype including a characteristic facial gestalt with bitemporal narrowing, prominent supraorbital ridges, synophrys, a short nose and dental anomalies, tapering fingers with brachytelephalangy, clinodactyly and hypoplastic nails, short toes with hypoplastic nails, and linear skin hyperpigmentation. In adolescent or older patients, this phenotype overlaps but is not identical with Borjeson-Forssman-Lehmann syndrome in males, caused by X-linked recessive mutations in PHF6. In younger girls there seems to be a striking phenotypic overlap with Coffin-Siris syndrome, which is characterized by intellectual disability, sparse hair and hypoplastic nails. This review will summarize and characterize the female phenotype caused by de novo aberrations in PHF6 and will discuss the overlapping and distinguishing features with Coffin-Siris syndrome. © 2014 Wiley Periodicals, Inc.
-
[Asthma-COPD overlap syndrome].
Odler, Balázs; Müller, Veronika
2016-08-01
Obstructive lung diseases represent a major health problem worldwide due to their high prevalence associated with elevated socioeconomic costs. Bronchial asthma and chronic obstructive pulmonary disease are chronic obstructive ventilatory disorders with airway inflammation, however they are separate nosological entities based on thedifferent development, diagnostic and therapeutic approaches, and prognostic features. However, these diseases may coexist and can be defined as the coexistence of increased variability of airflow in a patient with incompletely reversible airway obstruction. This phenotype is called asthma - chronic obstructive pulmonary disease overlap syndrome. The syndrome is a clinical and scientific challenge as the majority of these patients have been excluded from the clinical and pharmacological trials, thus well-defined clinical characteristics and therapeutic approaches are lacking. The aim of this review is to summarize the currently available literature focusing on pathophysiological and clinical features, and discuss possible therapeutic approaches of patients with asthma - chronic obstructive pulmonary disease overlap syndrome. Orv. Hetil., 2016, 157(33), 1304-1313.
-
Crack, L R; Chan, H W; McPherson, T; Ogg, G S
2011-11-01
Accumulating evidence suggests that T cells play an important role in the pathogenesis of atopic dermatitis (AD); yet, little is known of the differentiation status of CD4+ T cells specific for common environmental allergens, such as the major cat allergen, Fel d 1. To determine the frequency, differentiation phenotype and function of circulating Fel d 1-specific CD4+ T cells in adult individuals with severe persistent AD in comparison with healthy controls. Using HLA class II tetrameric complexes based on a HLA-DPB1*0401-restricted Fel d 1 epitope, ex vivo and cultured T cell frequency and phenotype were analysed in individuals with AD and healthy controls. Cytokine secretion was measured by ex vivo and cultured IL-4 and IFN-γ ELISpots. Ex vivo Fel d 1-specific DPB1*0401-restricted CD4+ T cells in both atopics and non-atopics express high levels of CCR7, CD62L, CD27 and CD28, placing the cells largely within the central memory subgroup. However, the functional phenotype was distinct, with greater IL-4 production from the cells derived from atopics, which correlated with disease severity. Circulating Fel d 1-specific DPB1*0401-restricted CD4+ T cells in both atopic and non-atopic donors maintain a central memory phenotype; however in atopics, the cells had greater Th2 effector function, compatible with a disease model of altered antigen delivery in atopic individuals. © 2011 Blackwell Publishing Ltd.
-
Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation.
Posey, Jennifer E; Harel, Tamar; Liu, Pengfei; Rosenfeld, Jill A; James, Regis A; Coban Akdemir, Zeynep H; Walkiewicz, Magdalena; Bi, Weimin; Xiao, Rui; Ding, Yan; Xia, Fan; Beaudet, Arthur L; Muzny, Donna M; Gibbs, Richard A; Boerwinkle, Eric; Eng, Christine M; Sutton, V Reid; Shaw, Chad A; Plon, Sharon E; Yang, Yaping; Lupski, James R
2017-01-05
Whole-exome sequencing can provide insight into the relationship between observed clinical phenotypes and underlying genotypes. We conducted a retrospective analysis of data from a series of 7374 consecutive unrelated patients who had been referred to a clinical diagnostic laboratory for whole-exome sequencing; our goal was to determine the frequency and clinical characteristics of patients for whom more than one molecular diagnosis was reported. The phenotypic similarity between molecularly diagnosed pairs of diseases was calculated with the use of terms from the Human Phenotype Ontology. A molecular diagnosis was rendered for 2076 of 7374 patients (28.2%); among these patients, 101 (4.9%) had diagnoses that involved two or more disease loci. We also analyzed parental samples, when available, and found that de novo variants accounted for 67.8% (61 of 90) of pathogenic variants in autosomal dominant disease genes and 51.7% (15 of 29) of pathogenic variants in X-linked disease genes; both variants were de novo in 44.7% (17 of 38) of patients with two monoallelic variants. Causal copy-number variants were found in 12 patients (11.9%) with multiple diagnoses. Phenotypic similarity scores were significantly lower among patients in whom the phenotype resulted from two distinct mendelian disorders that affected different organ systems (50 patients) than among patients with disorders that had overlapping phenotypic features (30 patients) (median score, 0.21 vs. 0.36; P=1.77×10 -7 ). In our study, we found multiple molecular diagnoses in 4.9% of cases in which whole-exome sequencing was informative. Our results show that structured clinical ontologies can be used to determine the degree of overlap between two mendelian diseases in the same patient; the diseases can be distinct or overlapping. Distinct disease phenotypes affect different organ systems, whereas overlapping disease phenotypes are more likely to be caused by two genes encoding proteins that interact within
-
Santoro, C; Giugliano, T; Melone, M A B; Cirillo, M; Schettino, C; Bernardo, P; Cirillo, G; Perrotta, S; Piluso, G
2018-01-01
Neurofibromatosis type 1 (NF1) has long been considered a well-defined, recognizable monogenic disorder, with neurofibromas constituting a pathognomonic sign. This dogma has been challenged by recent descriptions of patients with enlarged nerves or paraspinal tumors, suggesting that neurogenic tumors and hypertrophic neuropathy may be a complication of Noonan syndrome with multiple lentigines (NSML) or RASopathy phenotype. We describe a 15-year-old boy, whose mother previously received clinical diagnosis of NF1 due to presence of bilateral cervical and lumbar spinal lesions resembling plexiform neurofibromas and features suggestive of NS. NF1 molecular analysis was negative in the mother. The boy presented with Noonan features, multiple lentigines and pectus excavatum. Next-generation sequencing analysis of all RASopathy genes identified p.Ser548Arg missense mutation in SOS1 in the boy, confirmed in his mother. Brain and spinal magnetic resonance imaging scans were negative in the boy. No heart involvement or deafness was observed in proband or mother. This is the first report of a SOS1 mutation associated with hypertrophic neuropathy resembling plexiform neurofibromas, a rare complication in Noonan phenotypes with mutations in RASopathy genes. Our results highlight the overlap between RASopathies, suggesting that NF1 diagnostic criteria need rethinking. Genetic analysis of RASopathy genes should be considered when diagnosis is uncertain. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
-
[Noonan syndrome can be diagnosed clinically and through molecular genetic analyses].
Henningsen, Marie Krab; Jelsig, Anne Marie; Andersen, Helle; Brusgaard, Klaus; Ousager, Lilian Bomme; Hertz, Jens Michael
2015-08-03
Noonan syndrome is part of the group of RASopathies caused by germ line mutations in genes involved in the RAS/MAPK pathway. There is substantial phenotypic overlap among the RASopathies. Diagnosis of Noonan syndrome is often based on clinical features including dysmorphic facial features, short stature and congenital heart disease. Rapid advances in sequencing technology have made molecular genetic analyses a helpful tool in diagnosing and distinguishing Noonan syndrome from other RASopathies.
-
Houck, Darby A; Kraeutler, Matthew J; Schuette, Hayden B; McCarty, Eric C; Bravman, Jonathan T
2017-10-01
Previous meta-analyses have been conducted to compare outcomes of early versus delayed motion after rotator cuff repair. To conduct a systematic review of overlapping meta-analyses comparing early versus delayed motion rehabilitation protocols after rotator cuff repair to determine which meta-analyses provide the best available evidence. Systematic review. A systematic review was performed by searching PubMed and Cochrane Library databases. Search terms included "rotator cuff repair," "early passive motion," "immobilization," "rehabilitation protocol," and "meta-analysis." Results were reviewed to determine study eligibility. Patient outcomes and structural healing were extracted from these meta-analyses. Meta-analysis quality was assessed using the Oxman-Guyatt and Quality of Reporting of Meta-analyses (QUOROM) systems. The Jadad decision algorithm was then used to determine which meta-analyses provided the best level of evidence. Seven meta-analyses containing a total of 5896 patients met the eligibility criteria (1 Level I evidence, 4 Level II evidence, 2 Level III evidence). None of these meta-analyses found immobilization to be superior to early motion; however, most studies suggested that early motion would increase range of motion (ROM), thereby reducing time of recovery. Three of these studies suggested that tear size contributed to the choice of rehabilitation to ensure proper healing of the shoulder. A study by Chan et al in 2014 received the highest QUOROM and Oxman-Guyatt scores, and therefore this meta-analysis appeared to have the highest level of evidence. Additionally, a study by Riboh and Garrigues in 2014 was selected as the highest quality study in this systematic review according to the Jadad decision algorithm. The current, best available evidence suggests that early motion improves ROM after rotator cuff repair but increases the risk of rotator cuff retear. Lower quality meta-analyses indicate that tear size may provide a better strategy in
-
Directory of Open Access Journals (Sweden)
E. KALOGIANNI
2014-04-01
Full Text Available Non native freshwater fish species have been long implicated in the decline of native Mediterranean ichthyofauna, through hybridization, disease transmission, competition for food and habitat, predation and/or ecosystem alteration; our knowledge, however, on the underlying mechanisms of these ecological impacts remains very limited. To explore the potential for trophic competition between the widespread Eastern mosquitofish Gambusia holbrooki and its co-occurring native toothcarp Valencia letourneuxi we compared resource use, feeding strategies, trophic selectivities and diet niche overlap. For this purpose, we studied two populations of the two species from a freshwater and a brackish habitat respectively, characterized by different food resource availabilities. In both habitats, the mosquitofish consumed a greater diversity of invertebrates and preyed on terrestrial invertebrates more frequently than the native toothcarp. Furthermore, in the less diverse and less rich brackish habitat, the non native relied heavily on plant material to balance a decrease in animal prey consumption and modified its individual feeding strategy, whereas these adaptive changes were not apparent in the native species. Their diet overlapped, indicating trophic competition, but this overlap was affected by resource availability variation; in the freshwater habitat, there was limited overlap in their diet, whereas in the brackish habitat, their diets and prey selectivities converged and there was high overlap in resource use, indicative of intense interspecific trophic competition. Overall, it appears that the underlying mechanism of the putative negative impacts of the mosquitofish on the declining Corfu toothcarp is mainly trophic competition, regulated by resource variability, though there is also evidence of larvae predation by the mosquitofish.
-
On the acoustics of overlapping laughter in conversational speech
Truong, Khiet Phuong; Trouvain, Jürgen
The social nature of laughter invites people to laugh together. This joint vocal action often results in overlapping laughter. In this paper, we show that the acoustics of overlapping laughs are different from non-overlapping laughs. We found that overlapping laughs are stronger prosodically marked
-
Differences in chronic obstructive pulmonary disease phenotypes between non-smokers and smokers.
Ji, Wonjun; Lim, Myoung Nam; Bak, So Hyeon; Hong, Seok-Ho; Han, Seon-Sook; Lee, Seung-Joon; Kim, Woo Jin; Hong, Yoonki
2018-02-01
Although tobacco smoking is a major risk factor for chronic obstructive pulmonary disease (COPD), more than one-fourth of COPD patients are non-smokers. In this cross-sectional study, the differences in COPD phenotypes between non-smokers and smokers in male subjects were investigated and were focused on structural lung changes using a quantitative assessment of computed tomography (CT) images. They divided male participants with COPD, from a Korean cohort near a cement plant, into non-smokers and smokers by a cutoff of a 5 pack-year smoking history. Clinical characteristics, including age, body mass index (BMI), spirometry results, history of biomass smoke exposure, and CT measurements, were compared between the two groups. Emphysema index (EI) and mean wall area percentage (MWA %) were used to evaluate the structural lung changes on volumetric CT scans. The non-smoker group (n = 49) had younger patients and had a greater BMI than the smoker group (n = 113) (P smokers had emphysema than non-smokers (EI 10.0 vs. 6.5, P smokers than in non-smokers (MWA 69.1 vs. 65.3, P = .03), while EI was not statistically different (EI 7.1 vs. 10.4, P = .52). Non-smoker males with COPD were younger and had a greater BMI than the smokers. Tobacco smoke exposure seemed to be associated with an emphysema-predominant phenotype, while biomass smoke exposure exhibited a significant interaction with tobacco smoking in an airway-predominant phenotype. © 2016 John Wiley & Sons Ltd.
-
Leveraging disjoint communities for detecting overlapping community structure
International Nuclear Information System (INIS)
Chakraborty, Tanmoy
2015-01-01
Network communities represent mesoscopic structure for understanding the organization of real-world networks, where nodes often belong to multiple communities and form overlapping community structure in the network. Due to non-triviality in finding the exact boundary of such overlapping communities, this problem has become challenging, and therefore huge effort has been devoted to detect overlapping communities from the network.In this paper, we present PVOC (Permanence based Vertex-replication algorithm for Overlapping Community detection), a two-stage framework to detect overlapping community structure. We build on a novel observation that non-overlapping community structure detected by a standard disjoint community detection algorithm from a network has high resemblance with its actual overlapping community structure, except the overlapping part. Based on this observation, we posit that there is perhaps no need of building yet another overlapping community finding algorithm; but one can efficiently manipulate the output of any existing disjoint community finding algorithm to obtain the required overlapping structure. We propose a new post-processing technique that by combining with any existing disjoint community detection algorithm, can suitably process each vertex using a new vertex-based metric, called permanence, and thereby finds out overlapping candidates with their community memberships. Experimental results on both synthetic and large real-world networks show that PVOC significantly outperforms six state-of-the-art overlapping community detection algorithms in terms of high similarity of the output with the ground-truth structure. Thus our framework not only finds meaningful overlapping communities from the network, but also allows us to put an end to the constant effort of building yet another overlapping community detection algorithm. (paper)
-
Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community
Directory of Open Access Journals (Sweden)
Yook Karen
2011-01-01
Full Text Available Abstract Background Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form. Results We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO. The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. Conclusions We provide a phenotype ontology (WPO that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and
-
Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping
Al-Tamimi, Nadia Ali
2016-11-17
High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.
-
Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping
Al-Tamimi, Nadia Ali; Brien, Chris; Oakey, Helena; Berger, Bettina; Saade, Stephanie; Ho, Yung Shwen; Schmö ckel, Sandra M.; Tester, Mark A.; Negrã o, Só nia
2016-01-01
High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.
-
Ashrafi, Keyhan; Valero, M Adela; Peixoto, Raquel V; Artigas, Patricio; Panova, Miroslava; Mas-Coma, Santiago
2015-04-01
Fascioliasis is a zoonotic disease emerging in numerous parts of the world. In any endemic area, the characterisation of scenarios and patterns of infection must always be considered the starting point before implementing any control measure. Fascioliasis is a parasitic disease of different epidemiological, pathological and control characteristics depending on the endemic area and the causal agent, Fasciola hepatica and Fasciolagigantica. Classically it has been accepted that F. hepatica is present worldwide, while the distribution of the two species overlaps in many areas of Africa and Asia. Fascioliasis caused by F. hepatica, F. gigantica and intermediate forms is present in Guilan province, a complicated epidemiological situation where the highest human infection rates have been described in Iran. Morphometric tools were used to analyse the possible relationship between liver-fluke metric traits and geographical and altitudinal distribution. This is the first study in which a detailed distribution of both Fasciola species is analysed in a human fascioliasis endemic area with a zonal overlap transmission pattern. An accurate analysis was conducted to phenotypically discriminate between fasciolids from naturally infected livestock (cattle, buffaloes, sheep and goats). The distribution of the % F. hepatica-like (F.h.) and F. gigantica-like (F.g.) flukes detected in each liver versus altitude (m) in each group was analysed. The presence of F.g. specimens mainly in locations below sea level (average: 11.23% F.h., 88.77% F.g.), the presence of both species with similar intensity at 1-99m (average: 56.95% F.h., 43.05% F.g.) and the presence of F.h. specimens mainly from 100 to 999m (average: 71.69% F.h., 28.31% F.g.) as well as in locations with an altitude above 1000m (average: 97.48% F.h., 2.52% F.g.) are noteworthy. A significant positive correlation was obtained between altitude and % F.h., and a significant negative correlation was obtained between altitude and
-
Parkinson Disease: The Relationship Between Non-motor Symptoms and Motor Phenotype.
Ba, Fang; Obaid, Mona; Wieler, Marguerite; Camicioli, Richard; Martin, W R Wayne
2016-03-01
Parkinson disease (PD) presents with motor and non-motor symptoms (NMS). The NMS often precede the onset of motor symptoms, but may progress throughout the disease course. Tremor dominant, postural instability gait difficulty (PIGD), and indeterminate phenotypes can be distinguished using Unified PD Rating scales (UPDRS-III). We hypothesized that the PIGD phenotype would be more likely to develop NMS, and that the non-dopamine-responsive axial signs would correlate with NMS severity. We conducted a retrospective cross-sectional chart review to assess the relationship between NMS and PD motor phenotypes. PD patients were administered the NMS Questionnaire, the UPDRS-III, and the Mini-Mental State Examination score. The relationship between NMS burden and PD subtypes was examined using linear regression models. The prevalence of each NMS among difference PD motor subtypes was analyzed using chi-square test. PD patients with more advanced disease based on their UPDRS-III had higher NMS Questionnaire scores. The axial component of UPDRS-III correlated with higher NMS. There was no correlation between NMS and tremor scores. There was a significant correlation between PIGD score and higher NMS burden. PIGD group had higher prevalence in most NMS domains when compared with tremor dominant and indeterminate groups independent of disease duration and severity. NMS profile and severity vary according to motor phenotype. We conclude that in the PD population, patients with a PIGD phenotype who have more axial involvement, associated with advanced disease and poor motor response, have a higher risk for a higher NMS burden.
-
Gasperi, Marianna; Krieger, John N; Forsberg, Christopher; Goldberg, Jack; Buchwald, Dedra; Afari, Niloofar
2017-11-01
Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is characterized by pain and voiding symptoms in the absence of an obvious infection or other cause. CP/CPPS frequently occurs with non-urological chronic overlapping pain conditions (COPCs) of unknown etiology. We conducted a co-twin control study in men discordant for chronic prostatitis (CP), an overarching diagnosis of which approximately 90% is CP/CPPS. The primary aim was to investigate the contribution of familial factors, including shared genetic and common environmental factors, to the comorbidity of CP and COPCs. Data from 6824 male twins in the Vietnam Era Twin Registry were examined to evaluate the association between self-reported lifetime physician diagnosis of CP with COPCs including fibromyalgia, chronic fatigue syndrome, irritable bowel syndrome, temporomandibular disorder, tension headaches, and migraine headaches. Random effects logistic regression models were used and within-pair analyses evaluated confounding effects of familial factors on the associations. There were significant associations between CP and all 6 examined COPCs. After adjusting for shared familial influences in within twin pair analyses, the associations for all COPCs diminished but remained significant. Familial confounding was strongest for the association of CP with fibromyalgia and temporomandibular disorder and smallest for irritable bowel syndrome. CP and COPCs are highly comorbid. These associations can be partially explained by familial factors. The mechanisms underlying these relationships are likely diverse and multifactorial. Future longitudinal research can help to further elucidate specific genetic and environmental mechanisms and determine potentially causal relationships between CP and its comorbidities. Published by Elsevier Inc.
-
Multidimensional clinical phenotyping of an adult cystic fibrosis patient population.
Directory of Open Access Journals (Sweden)
Douglas J Conrad
Full Text Available Cystic Fibrosis (CF is a multi-systemic disease resulting from mutations in the Cystic Fibrosis Transmembrane Regulator (CFTR gene and has major manifestations in the sino-pulmonary, and gastro-intestinal tracts. Clinical phenotypes were generated using 26 common clinical variables to generate classes that overlapped quantiles of lung function and were based on multiple aspects of CF systemic disease.The variables included age, gender, CFTR mutations, FEV1% predicted, FVC% predicted, height, weight, Brasfield chest xray score, pancreatic sufficiency status and clinical microbiology results. Complete datasets were compiled on 211 subjects. Phenotypes were identified using a proximity matrix generated by the unsupervised Random Forests algorithm and subsequent clustering by the Partitioning around Medoids (PAM algorithm. The final phenotypic classes were then characterized and compared to a similar dataset obtained three years earlier.Clinical phenotypes were identified using a clustering strategy that generated four and five phenotypes. Each strategy identified 1 a low lung health scores phenotype, 2 a younger, well-nourished, male-dominated class, 3 various high lung health score phenotypes that varied in terms of age, gender and nutritional status. This multidimensional clinical phenotyping strategy identified classes with expected microbiology results and low risk clinical phenotypes with pancreatic sufficiency.This study demonstrated regional adult CF clinical phenotypes using non-parametric, continuous, ordinal and categorical data with a minimal amount of subjective data to identify clinically relevant phenotypes. These studies identified the relative stability of the phenotypes, demonstrated specific phenotypes consistent with published findings and identified others needing further study.
-
Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing.
Calmels, Nadège; Greff, Géraldine; Obringer, Cathy; Kempf, Nadine; Gasnier, Claire; Tarabeux, Julien; Miguet, Marguerite; Baujat, Geneviève; Bessis, Didier; Bretones, Patricia; Cavau, Anne; Digeon, Béatrice; Doco-Fenzy, Martine; Doray, Bérénice; Feillet, François; Gardeazabal, Jesus; Gener, Blanca; Julia, Sophie; Llano-Rivas, Isabel; Mazur, Artur; Michot, Caroline; Renaldo-Robin, Florence; Rossi, Massimiliano; Sabouraud, Pascal; Keren, Boris; Depienne, Christel; Muller, Jean; Mandel, Jean-Louis; Laugel, Vincent
2016-03-22
Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). In view of the clinical overlap between NER-related disorders, as well as the existence of multiple phenotypes and the numerous genes involved, we developed a new diagnostic approach based on the enrichment of 16 NER-related genes by multiplex amplification coupled with next-generation sequencing (NGS). Our test cohort consisted of 11 DNA samples, all with known mutations and/or non pathogenic SNPs in two of the tested genes. We then used the same technique to analyse samples from a prospective cohort of 40 patients. Multiplex amplification and sequencing were performed using AmpliSeq protocol on the Ion Torrent PGM (Life Technologies). We identified causative mutations in 17 out of the 40 patients (43%). Four patients showed biallelic mutations in the ERCC6(CSB) gene, five in the ERCC8(CSA) gene: most of them had classical CS features but some had very mild and incomplete phenotypes. A small cohort of 4 unrelated classic XP patients from the Basque country (Northern Spain) revealed a common splicing mutation in POLH (XP-variant), demonstrating a new founder effect in this population. Interestingly, our results also found ERCC2(XPD), ERCC3(XPB) or ERCC5(XPG) mutations in two cases of UV-sensitive syndrome and in two cases with mixed XP/CS phenotypes. Our study confirms that NGS is an efficient technique for the analysis of NER-related disorders on a molecular level. It is particularly useful for phenotypes with combined features or unusually mild symptoms. Targeted NGS used in conjunction with DNA repair functional tests and precise clinical evaluation permits rapid and cost-effective diagnosis in patients with NER-defects.
-
Analysis of stacking overlap in nucleic acid structures: algorithm and application.
Pingali, Pavan Kumar; Halder, Sukanya; Mukherjee, Debasish; Basu, Sankar; Banerjee, Rahul; Choudhury, Devapriya; Bhattacharyya, Dhananjay
2014-08-01
RNA contains different secondary structural motifs like pseudo-helices, hairpin loops, internal loops, etc. in addition to anti-parallel double helices and random coils. The secondary structures are mainly stabilized by base-pairing and stacking interactions between the planar aromatic bases. The hydrogen bonding strength and geometries of base pairs are characterized by six intra-base pair parameters. Similarly, stacking can be represented by six local doublet parameters. These dinucleotide step parameters can describe the quality of stacking between Watson-Crick base pairs very effectively. However, it is quite difficult to understand the stacking pattern for dinucleotides consisting of non canonical base pairs from these parameters. Stacking interaction is a manifestation of the interaction between two aromatic bases or base pairs and thus can be estimated best by the overlap area between the planar aromatic moieties. We have calculated base pair overlap between two consecutive base pairs as the buried van der Waals surface between them. In general, overlap values show normal distribution for the Watson-Crick base pairs in most double helices within a range from 45 to 50 Å(2) irrespective of base sequence. The dinucleotide steps with non-canonical base pairs also are seen to have high overlap value, although their twist and few other parameters are rather unusual. We have analyzed hairpin loops of different length, bulges within double helical structures and pseudo-continuous helices using our algorithm. The overlap area analyses indicate good stacking between few looped out bases especially in GNRA tetraloop, which was difficult to quantitatively characterise from analysis of the base pair or dinucleotide step parameters. This parameter is also seen to be capable to distinguish pseudo-continuous helices from kinked helix junctions.
-
Atypical disease phenotypes in pediatric ulcerative colitis
DEFF Research Database (Denmark)
Levine, Arie; de Bie, Charlotte I; Turner, Dan
2013-01-01
Definitive diagnosis of pediatric ulcerative colitis (UC) may be particularly challenging since isolated colitis with overlapping features is common in pediatric Crohn's disease (CD), while atypical phenotypes of UC are not uncommon. The Paris classification allows more accurate phenotyping...... of atypical inflammatory bowel disease (IBD) patients. Our aim was to identify the prevalence of atypical disease patterns in new-onset pediatric UC using the Paris classification....
-
Distinct phenotype of PHF6 deletions in females.
Di Donato, N; Isidor, B; Lopez Cazaux, S; Le Caignec, C; Klink, B; Kraus, C; Schrock, E; Hackmann, K
2014-02-01
We report on two female patients carrying small overlapping Xq26.2 deletions of 100 kb and 270 kb involving the PHF6 gene. Mutations in PHF6 have been reported in individuals with Borjeson-Forssman-Lehmann syndrome, a condition present almost exclusively in males. Two very recent papers revealed de novo PHF6 defects in seven female patients with intellectual disability and a phenotype resembling Coffin-Siris syndrome (sparse hair, bitemporal narrowing, arched eyebrows, synophrys, high nasal root, bulbous nasal tip, marked clinodactyly with the hypoplastic terminal phalanges of the fifth fingers and cutaneous syndactyly of the toes, Blaschkoid linear skin hyperpigmentation, dental anomalies and occasional major malformations). The clinical presentation of these patients overlaps completely with our first patient, who carries a germline deletion involving PHF6. The second patient has a mosaic deletion and presented with a very mild phenotype of PHF6 loss in females. Our report confirms that PHF6 loss in females results in a recognizable phenotype overlapping with Coffin-Siris syndrome and distinct from Borjeson-Forssman-Lehmann syndrome. We expand the clinical spectrum and provide the first summary of the recommended medical evaluation. Copyright © 2014 Elsevier Masson SAS. All rights reserved.
-
Directory of Open Access Journals (Sweden)
Carlo Catassi
2017-11-01
Full Text Available Gluten-related disorders have recently been reclassified with an emerging scientific literature supporting the concept of non-celiac gluten sensitivity (NCGS. New research has specifically addressed prevalence, immune mechanisms, the recognition of non-immunoglobulin E (non-IgE wheat allergy and overlap of NCGS with irritable bowel syndrome (IBS-type symptoms. This review article will provide clinicians with an update that directly impacts on the management of a subgroup of their IBS patients whose symptoms are triggered by wheat ingestion.
-
The Broader Autism Phenotype and Friendships in Non-Clinical Dyads
Wainer, Allison L.; Block, Nicole; Donnellan, M. Brent; Ingersoll, Brooke
2013-01-01
The broader autism phenotype (BAP) is a set of subclinical traits qualitatively similar to those observed in autism spectrum disorders. The current study sought to elucidate the association between self- and informant-reports of the BAP and friendships, in a non-clinical sample of college student dyads. Self-informant agreement of the BAP and…
-
Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment
DEFF Research Database (Denmark)
Le Hellard, Stéphanie; Wang, Yunpeng; Witoelar, Aree
2017-01-01
. Here we investigated the shared genetic architecture between SCZ and educational attainment, which is regarded as a "proxy phenotype" for cognitive abilities, but may also reflect other traits. We applied a conditional false discovery rate (condFDR) method to GWAS of SCZ (n = 82 315), college...... completion ("College," n = 95 427), and years of education ("EduYears," n = 101 069). Variants associated with College or EduYears showed enrichment of association with SCZ, demonstrating polygenic overlap. This was confirmed by an increased replication rate in SCZ. By applying a condFDR threshold ... of these loci had effects in opposite directions. Our results provide evidence for polygenic overlap between SCZ and educational attainment, and identify novel pleiotropic loci. Other studies have reported genetic overlap between SCZ and cognition, or SCZ and educational attainment, with negative correlation...
-
An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations.
Directory of Open Access Journals (Sweden)
Arunabha Majumdar
2018-02-01
Full Text Available Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy. For a locus exhibiting overall pleiotropy, it is important to identify which specific traits underlie this association. We propose a Bayesian meta-analysis approach (termed CPBayes that uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. This method uses a unified Bayesian statistical framework based on a spike and slab prior. CPBayes performs a fully Bayesian analysis by employing the Markov Chain Monte Carlo (MCMC technique Gibbs sampling. It takes into account heterogeneity in the size and direction of the genetic effects across traits. It can be applied to both cohort data and separate studies of multiple traits having overlapping or non-overlapping subjects. Simulations show that CPBayes can produce higher accuracy in the selection of associated traits underlying a pleiotropic signal than the subset-based meta-analysis ASSET. We used CPBayes to undertake a genome-wide pleiotropic association study of 22 traits in the large Kaiser GERA cohort and detected six independent pleiotropic loci associated with at least two phenotypes. This includes a locus at chromosomal region 1q24.2 which exhibits an association simultaneously with the risk of five different diseases: Dermatophytosis, Hemorrhoids, Iron Deficiency, Osteoporosis and Peripheral Vascular Disease. We provide an R-package 'CPBayes' implementing the proposed method.
-
Active smoking and COPD phenotype: distribution and impact on prognostic factors
Directory of Open Access Journals (Sweden)
Riesco JA
2017-07-01
Full Text Available Juan Antonio Riesco,1,2 Bernardino Alcázar,3 Juan Antonio Trigueros,4 Anna Campuzano,5 Joselín Pérez,5 José Luis Lorenzo5 1Pulmonology Department, Hospital San Pedro de Alcántara, 2Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES, Cáceres, 3Pulmonology Department, Hospital La Loja, Granada, 4Centro de Salud de Menasalvas, Toledo, 5Grupo Ferrer Internacional, Barcelona, Spain Purpose: Smoking can affect both the phenotypic expression of COPD and factors such as disease severity, quality of life, and comorbidities. Our objective was to evaluate if the impact of active smoking on these factors varies according to the disease phenotype. Patients and methods: This was a Spanish, observational, cross-sectional, multicenter study of patients with a diagnosis of COPD. Smoking rates were described among four different phenotypes (non-exacerbators, asthma-COPD overlap syndrome [ACOS], exacerbators with emphysema, and exacerbators with chronic bronchitis, and correlated with disease severity (body mass index, obstruction, dyspnea and exacerbations [BODEx] index and dyspnea grade, quality of life according to the COPD assessment test (CAT, and presence of comorbidities, according to phenotypic expression. Results: In total, 1,610 patients were recruited, of whom 46.70% were classified as non-exacerbators, 14.53% as ACOS, 16.37% as exacerbators with emphysema, and 22.40% as exacerbators with chronic bronchitis. Smokers were predominant in the latter 2 groups (58.91% and 57.67%, respectively, P=0.03. Active smoking was significantly associated with better quality of life and a higher dyspnea grade, although differences were observed depending on clinical phenotype. Conclusion: Active smoking is more common among exacerbator phenotypes and appears to affect quality of life and dyspnea grade differently, depending on the clinical expression of the disease. Keywords: COPD, phenotype, smoking, prognostic factors, quality of life
-
Barth, Timothy J.; Chan, Tony F.; Tang, Wei-Pai
1998-01-01
This paper considers an algebraic preconditioning algorithm for hyperbolic-elliptic fluid flow problems. The algorithm is based on a parallel non-overlapping Schur complement domain-decomposition technique for triangulated domains. In the Schur complement technique, the triangulation is first partitioned into a number of non-overlapping subdomains and interfaces. This suggests a reordering of triangulation vertices which separates subdomain and interface solution unknowns. The reordering induces a natural 2 x 2 block partitioning of the discretization matrix. Exact LU factorization of this block system yields a Schur complement matrix which couples subdomains and the interface together. The remaining sections of this paper present a family of approximate techniques for both constructing and applying the Schur complement as a domain-decomposition preconditioner. The approximate Schur complement serves as an algebraic coarse space operator, thus avoiding the known difficulties associated with the direct formation of a coarse space discretization. In developing Schur complement approximations, particular attention has been given to improving sequential and parallel efficiency of implementations without significantly degrading the quality of the preconditioner. A computer code based on these developments has been tested on the IBM SP2 using MPI message passing protocol. A number of 2-D calculations are presented for both scalar advection-diffusion equations as well as the Euler equations governing compressible fluid flow to demonstrate performance of the preconditioning algorithm.
-
Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice
Wilson, Robert; Geyer, Stefan H.; Reissig, Lukas; Rose, Julia; Szumska, Dorota; Hardman, Emily; Prin, Fabrice; McGuire, Christina; Ramirez-Solis, Ramiro; White, Jacqui; Galli, Antonella; Tudor, Catherine; Tuck, Elizabeth; Mazzeo, Cecilia Icoresi; Smith, James C.; Robertson, Elizabeth; Adams, David J.; Mohun, Timothy; Weninger, Wolfgang J.
2017-01-01
Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates. PMID:27996060
-
The Overlap between Irritable Bowel Syndrome and Non-Celiac Gluten Sensitivity: A Clinical Dilemma
Directory of Open Access Journals (Sweden)
Archita Makharia
2015-12-01
Full Text Available The spectrum of gluten-related disorders has widened in recent times and includes celiac disease, non-celiac gluten sensitivity, and wheat allergy. The complex of symptoms associated with these diseases, such as diarrhea, constipation or abdominal pain may overlap for the gluten related diseases, and furthermore they can be similar to those caused by various other intestinal diseases, such as irritable bowel syndrome (IBS. The mechanisms underlying symptom generation are diverse for all these diseases. Some patients with celiac disease may remain asymptomatic or have only mild gastrointestinal symptoms and thus may qualify for the diagnosis of IBS in the general clinical practice. Similarly, the overlap of symptoms between IBS and non-celiac gluten sensitivity (NCGS often creates a dilemma for clinicians. While the treatment of NCGS is exclusion of gluten from the diet, some, but not all, of the patients with IBS also improve on a gluten-free diet. Both IBS and NCGS are common in the general population and both can coexist with each other independently without necessarily sharing a common pathophysiological basis. Although the pathogenesis of NCGS is not well understood, it is likely to be heterogeneous with possible contributing factors such as low-grade intestinal inflammation, increased intestinal barrier function and changes in the intestinal microbiota. Innate immunity may also play a pivotal role. One possible inducer of innate immune response has recently been reported to be amylase-trypsin inhibitor, a protein present in wheat endosperm and the source of flour, along with the gluten proteins.
-
Ford, Talitha C; Nibbs, Richard; Crewther, David P
2017-01-01
Autism and schizophrenia are multi-dimensional spectrum disorders that have substantial phenotypic overlap. This overlap is readily identified in the non-clinical population, and has been conceptualised as Social Disorganisation (SD). This study investigates the balance of excitatory glutamate and inhibitory γ -aminobutyric acid (GABA) concentrations in a non-clinical sample with high and low trait SD, as glutamate and GABA abnormalities are reported across the autism and schizophrenia spectrum disorders. Participants were 18 low (10 females) and 19 high (9 females) SD scorers aged 18 to 40 years who underwent 1 H-MRS for glutamate and GABA+macromolecule (GABA+) concentrations in right and left hemisphere superior temporal (ST) voxels. Reduced GABA+ concentration ( p = 0.03) and increased glutamate/GABA+ ratio ( p = 0.003) in the right ST voxel for the high SD group was found, and there was increased GABA+ concentration in the left compared to right ST voxel ( p = 0.047). Bilateral glutamate concentration was increased for the high SD group ( p = 0.006); there was no hemisphere by group interaction ( p = 0.772). Results suggest that a higher expression of the SD phenotype may be associated with increased glutamate/GABA+ ratio in the right ST region, which may affect speech prosody processing, and lead behavioural characteristics that are shared within the autistic and schizotypal spectra.
-
Changes in insulin-like growth factor signaling alter phenotypes in Fragile X Mice.
Wise, T L
2017-02-01
Fragile X syndrome (FXS) is an inherited form of intellectual disability that is usually caused by expansion of a polymorphic CGG repeat in the 5' untranslated region of the X-linked FMR1 gene, which leads to hypermethylation and transcriptional silencing. Two non-neurological phenotypes of FXS are enlarged testes and connective tissue dysplasia, which could be caused by alterations in a growth factor signaling pathway. FXS patients also frequently have autistic-like symptoms, suggesting that the signaling pathways affected in FXS may overlap with those affected in autism. Identifying these pathways is important for both understanding the effects of FMR1 inactivation and developing treatments for both FXS and autism. Here we show that decreasing the levels of the insulin-like growth factor (Igf) receptor 1 corrects a number of phenotypes in the mouse model of FXS, including macro-orchidism, and that increasing the levels of IGF2 exacerbates the seizure susceptibility phenotype. These results suggest that the pathways altered by the loss of the FMR1-encoded protein (FMRP) may overlap with the pathways affected by changes in Igf signaling or that one or more of the proteins that play a role in Igf signaling could interact with FMRP. They also indicate a new set of potential targets for drug treatment of FXS and autism spectrum disorders. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.
-
St Pourcain, B.; Robinson, E.; Anttila, V.; Sullivan, B.; Maller, J.; Golding, J.; Skuse, D.; Ring, S.; Evans, D.; Zammit, S.; Fisher, S.; Neale, B.; Anney, R.; Ripke, S.; Hollegaard, M.
2017-01-01
Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and\\ud schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early\\ud childhood, whereas most symptoms characteristic of schizophrenia do not appear before early adulthood. We investigated whether\\ud overlap in common genetic influences between these clinical conditions and impairments in social communication depends ...
-
Genetic Regulation of Phenotypic Plasticity and Canalisation in Yeast Growth.
Directory of Open Access Journals (Sweden)
Anupama Yadav
Full Text Available The ability of a genotype to show diverse phenotypes in different environments is called phenotypic plasticity. Phenotypic plasticity helps populations to evade extinctions in novel environments, facilitates adaptation and fuels evolution. However, most studies focus on understanding the genetic basis of phenotypic regulation in specific environments. As a result, while it's evolutionary relevance is well established, genetic mechanisms regulating phenotypic plasticity and their overlap with the environment specific regulators is not well understood. Saccharomyces cerevisiae is highly sensitive to the environment, which acts as not just external stimulus but also as signalling cue for this unicellular, sessile organism. We used a previously published dataset of a biparental yeast population grown in 34 diverse environments and mapped genetic loci regulating variation in phenotypic plasticity, plasticity QTL, and compared them with environment-specific QTL. Plasticity QTL is one whose one allele exhibits high plasticity whereas the other shows a relatively canalised behaviour. We mapped phenotypic plasticity using two parameters-environmental variance, an environmental order-independent parameter and reaction norm (slope, an environmental order-dependent parameter. Our results show a partial overlap between pleiotropic QTL and plasticity QTL such that while some plasticity QTL are also pleiotropic, others have a significant effect on phenotypic plasticity without being significant in any environment independently. Furthermore, while some plasticity QTL are revealed only in specific environmental orders, we identify large effect plasticity QTL, which are order-independent such that whatever the order of the environments, one allele is always plastic and the other is canalised. Finally, we show that the environments can be divided into two categories based on the phenotypic diversity of the population within them and the two categories have
-
Detection and Evaluation of Pre-Preg Gaps and Overlaps in Glare Laminates
Nardi, Davide; Abouhamzeh, Morteza; Leonard, Rob; Sinke, Jos
2018-03-01
Gaps and overlaps between pre-preg plies represent common flaws in composite materials that can be introduced easily in an automated fibre placement manufacturing process and are potentially detrimental for the mechanical performances of the final laminates. Whereas gaps and overlaps have been addressed for full composite material, the topic has not been extended to a hybrid composite material such as Glare, a member of the family of Fibre Metal Laminates (FMLs). In this paper/research, the manufacturing, the detection, and the optical evaluation of intraply gaps and overlaps in Glare laminates are investigated. As part of an initial assessment study on the effect of gaps and overlaps on Glare, only the most critical lay-up has been considered. The experimental investigation started with the manufacturing of specimens having gaps and overlaps with different widths, followed by a non-destructive ultrasonic-inspection. An optical evaluation of the gaps and overlaps was performed by means of microscope image analysis of the cross sections of the specimens. The results from the non-destructive evaluations show the effectiveness of the ultrasonic detection of gaps and overlaps both in position, shape, width, and severity. The optical inspections confirm the accuracy of the non-destructive evaluation also adding useful insights about the geometrical features due to the presence of gaps and overlaps in the final Glare laminates. All the results justify the need for a further investigation on the effect of gaps and overlaps on the mechanical properties.
-
Phenotypic variations in osmotic lysis of Sahel goat erythrocytes in non-ionic glucose media.
Igbokwe, Nanacha Afifi; Igbokwe, Ikechukwu Onyebuchi
2016-03-01
Erythrocyte osmotic lysis in deionised glucose media is regulated by glucose influx, cation efflux, and changes in cell volume after water diffusion. Transmembrane fluxes may be affected by varied expression of glucose transporter protein and susceptibility of membrane proteins to glucose-induced glycosylation and oxidation in various physiologic states. Variations in haemolysis of Sahel goat erythrocytes after incubation in hyposmotic non-ionic glucose media, associated with sex, age, late pregnancy, and lactation, were investigated. The osmotic fragility curve in glucose media was sigmoidal with erythrocytes from goats in late pregnancy (PRE) or lactation (LAC) or from kid (KGT) or middle-aged (MGT) goats. Non-sigmoidal phenotype occurred in yearlings (YGT) and old (OGT) goats. The composite fragility phenotype for males and non-pregnant dry (NPD) females was non-sigmoidal. Erythrocytes with non-sigmoidal curves were more stable than those with sigmoidal curves because of inflectional shift of the curve to the left. Erythrocytes tended to be more fragile with male than female sex, KGT and MGT than YGT and OGT, and LAC and PRE than NPD. Thus, sex, age, pregnancy, and lactation affected the haemolytic pattern of goat erythrocytes in glucose media. The physiologic state of the goat affected the in vitro interaction of glucose with erythrocytes, causing variations in osmotic stability with variants of fragility phenotype. Variations in the effect of high extracellular glucose concentrations on the functions of membrane-associated glucose transporter, aquaporins, and the cation cotransporter were presumed to be relevant in regulating the physical properties of goat erythrocytes under osmotic stress.
-
Bally, B.; Duguet, T.
2018-02-01
-form expression allowing its computation without any phase ambiguity. The formula is physically intuitive, accurate, and versatile. It equally applies to norm overlaps between Bogoliubov states of even or odd number parity. Numerical applications illustrate these features and provide a transparent representation of the content of the norm overlaps. Conclusions: The complex norm overlap between arbitrary Bogoliubov states is computed, without any phase ambiguity, via elementary linear algebra operations. The method can be used in any configuration mixing of orthogonal and non-orthogonal product states. Furthermore, the closed-form expression extends naturally to correlated overlaps at play in PNR-BCC and PNR-BMBPT. As such, the straight overlap between Bogoliubov states is the zero-order reduction of more involved norm kernels to be studied in a forthcoming paper.
-
Non-pulmonary vein mediated atrial fibrillation: A novel sub-phenotype.
Directory of Open Access Journals (Sweden)
Maureen Farrell
Full Text Available Atrial fibrillation (AF is a mechanistically heterogeneous disorder, and the ability to identify sub-phenotypes ("endophenotypes" of AF would assist in the delivery of personalized medicine. We used the clinical response to pulmonary vein isolation (PVI to identify a sub-group of patients with non-PV mediated AF and sought to define the clinical associations.Subjects enrolled in the Vanderbilt AF Ablation Registry who underwent a repeat AF ablation due to arrhythmia recurrence were analyzed on the basis of PV reconnection. Subjects who had no PV reconnection were defined as "non-PV mediated AF". A comparison group of subjects were identified who had AF that was treated with PVI-only and experienced no arrhythmia recurrence >12 months. They were considered a group enriched for "PV-mediated AF". Univariate and multivariable binary logistic regression analysis was performed to investigate clinical associations between the PV and non-PV mediated AF groups.Two hundred and twenty nine subjects underwent repeat AF ablation and thirty three (14% had no PV reconnection. They were compared with 91 subjects identified as having PV-mediated AF. Subjects with non-PV mediated AF were older (64 years [IQR 60,71] vs. 60 [52,67], P = 0.01, more likely to have non-paroxysmal AF (82% [N = 27] vs. 35% [N = 32], P<0.001, and had a larger left atrium (LA (4.2cm [3.6,4.8] vs. 4.0 [3.3,4.4], P = 0.04. In univariate analysis, age (per decade: OR 1.56 [95% CI: 1.04 to 2.33], P = 0.03, LA size (per cm: OR 1.8 [1.06 to 3.21], P = 0.03 and non-paroxysmal AF (OR 8.3 [3.10 to 22.19], P<0.001 were all significantly associated with non-PV mediated AF. However, in multivariable analysis only non-paroxysmal AF was independently associated with non-PV mediated AF (OR 7.47 [95% CI 2.62 to 21.29], P<0.001, when adjusted for age (per decade: OR 1.25 [0.81 to 1.94], P = 0.31, male gender (OR 0.48 [0.18 to 1.28], P = 0.14, and LA size (per 1cm: 1.24 [0.65 to 2.33], P = 0.52.Non
-
Link overlap, viability, and mutual percolation in multiplex networks
International Nuclear Information System (INIS)
Min, Byungjoon; Lee, Sangchul; Lee, Kyu-Min; Goh, K.-I.
2015-01-01
Many real-world complex systems are best modeled by multiplex networks. The multiplexity has proved to have broad impact on the system’s structure and function. Most theoretical studies on multiplex networks to date, however, have largely ignored the effect of the link overlap across layers despite strong empirical evidences for its significance. In this article, we investigate the effect of the link overlap in the viability of multiplex networks, both analytically and numerically. After a short recap of the original multiplex viability study, the distinctive role of overlapping links in viability and mutual connectivity is emphasized and exploited for setting up a proper analytic framework. A rich phase diagram for viability is obtained and greatly diversified patterns of hysteretic behavior in viability are observed in the presence of link overlap. Mutual percolation with link overlap is revisited as a limit of multiplex viability problem, and the controversy between existing results is clarified. The distinctive role of overlapping links is further demonstrated by the different responses of networks under random removals of overlapping and non-overlapping links, respectively, as well as under several link-removal strategies. Our results show that the link overlap facilitates the viability and mutual percolation; at the same time, the presence of link overlap poses a challenge in analytical approaches to the problem
-
Phenotypes of asthma revisited upon the presence of atopy.
Nieves, Ana; Magnan, Antoine; Boniface, Stéphanie; Proudhon, Hervé; Lanteaume, André; Romanet, Stéphanie; Vervloet, Daniel; Godard, Philippe
2005-03-01
Immunological studies claimed that atopic and non-atopic asthma share more similarities than differences. However, these two phenotypes of asthma are considered to be distinguishable upon distinct clinical patterns, which were not systematically assessed before in a large population. We studied characteristics discriminating atopic from non-atopic asthma among 751 asthmatic patients and 80 factors were analysed in univariate and multivariate analysis. Age, age of onset of asthma, female/male ratio were higher in non-atopic (n=200) than in atopic (n=551) asthmatics. Familial asthma, seasonal symptoms, rhinitis, conjunctivitis, allergen-triggered symptoms, improvement in altitude, exercise-induced asthma were associated with atopy. Non-atopic asthmatics displayed lower FEV(1) and FVC. Smoking was more frequent and asthma was more severe in these patients. Younger age, early onset, male sex, rhinitis and smoking were independent factors discriminating atopic from non-atopic asthma. This study establishes in a large population of asthmatics that although similarities exist between atopic and non-atopic asthma, two clinical phenotypes can still distinguish both kinds of asthma.
-
Finding overlapping communities in multilayer networks.
Liu, Weiyi; Suzumura, Toyotaro; Ji, Hongyu; Hu, Guangmin
2018-01-01
Finding communities in multilayer networks is a vital step in understanding the structure and dynamics of these layers, where each layer represents a particular type of relationship between nodes in the natural world. However, most community discovery methods for multilayer networks may ignore the interplay between layers or the unique topological structure in a layer. Moreover, most of them can only detect non-overlapping communities. In this paper, we propose a new community discovery method for multilayer networks, which leverages the interplay between layers and the unique topology in a layer to reveal overlapping communities. Through a comprehensive analysis of edge behaviors within and across layers, we first calculate the similarities for edges from the same layer and the cross layers. Then, by leveraging these similarities, we can construct a dendrogram for the multilayer networks that takes both the unique topological structure and the important interplay into consideration. Finally, by introducing a new community density metric for multilayer networks, we can cut the dendrogram to get the overlapping communities for these layers. By applying our method on both synthetic and real-world datasets, we demonstrate that our method has an accurate performance in discovering overlapping communities in multilayer networks.
-
The pion-deuteron forward elastic amplitude in the non-overlapping potentials model
International Nuclear Information System (INIS)
Butterworth, D.S.
1978-01-01
The pion-deuteron forward elastic amplitude has been calculated in the non-overlapping potentials model, which enables a description of off-shell propagation effects in terms of on-shell amplitudes. Calculations include spin, isospin and deuteron D-state probability effects. Two energy regions are considered. First the pion-nucleon P 33 resonance region, where, using a formalism developed by Agassi and Gal (Ann. Phys.; 75:56 (1973) and 94:184 (1975)), the full multiple-scattering series is summed in an approximation of P 33 wave dominance of the higher-order scatterings. Second, for the subsequent highest-energy region, the double-scattering term only is calculated. Fermi smearing effects are included in both cases. Predictions for the total cross section, its dependence on the deuteron alignment and the real part of the forward elastic amplitude are compared with those of Glauber theory, and data where available. Convergence of the multiple-scattering series is also discussed. (author)
-
Redefining Aging in HIV Infection Using Phenotypes.
Stoff, David M; Goodkin, Karl; Jeste, Dilip; Marquine, Maria
2017-10-01
This article critically reviews the utility of "phenotypes" as behavioral descriptors in aging/HIV research that inform biological underpinnings and treatment development. We adopt a phenotypic redefinition of aging conceptualized within a broader context of HIV infection and of aging. Phenotypes are defined as dimensions of behavior, closely related to fundamental mechanisms, and, thus, may be more informative than chronological age. Primary emphasis in this review is given to comorbid aging and cognitive aging, though other phenotypes (i.e., disability, frailty, accelerated aging, successful aging) are also discussed in relation to comorbid aging and cognitive aging. The main findings that emerged from this review are as follows: (1) the phenotypes, comorbid aging and cognitive aging, are distinct from each other, yet overlapping; (2) associative relationships are the rule in HIV for comorbid and cognitive aging phenotypes; and (3) HIV behavioral interventions for both comorbid aging and cognitive aging have been limited. Three paths for research progress are identified for phenotype-defined aging/HIV research (i.e., clinical and behavioral specification, biological mechanisms, intervention targets), and some important research questions are suggested within each of these research paths.
-
Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
Directory of Open Access Journals (Sweden)
Harrington Eoghan D
2008-07-01
Full Text Available Abstract Background Across the fully sequenced microbial genomes there are thousands of examples of overlapping genes. Many of these are only a few nucleotides long and are thought to function by permitting the coordinated regulation of gene expression. However, there should also be selective pressure against long overlaps, as the existence of overlapping reading frames increases the risk of deleterious mutations. Here we examine the longest overlaps and assess whether they are the product of special functional constraints or of erroneous annotation. Results We analysed the genes that overlap by 60 bps or more among 338 fully-sequenced prokaryotic genomes. The likely functional significance of an overlap was determined by comparing each of the genes to its respective orthologs. If a gene showed a significantly different length from its orthologs it was considered unlikely to be functional and therefore the result of an error either in sequencing or gene prediction. Focusing on 715 co-directional overlaps longer than 60 bps, we classified the erroneous ones into five categories: i 5'-end extension of the downstream gene due to either a mispredicted start codon or a frameshift at 5'-end of the gene (409 overlaps, ii fragmentation of a gene caused by a frameshift (163, iii 3'-end extension of the upstream gene due to either a frameshift at 3'-end of a gene or point mutation at the stop codon (68, iv Redundant gene predictions (4, v 5' & 3'-end extension which is a combination of i and iii (71. We also studied 75 divergent overlaps that could be classified as misannotations of group i. Nevertheless we found some convergent long overlaps (54 that might be true overlaps, although an important part of convergent overlaps could be classified as group iii (124. Conclusion Among the 968 overlaps larger than 60 bps which we analysed, we did not find a single real one among the co-directional and divergent orientations and concluded that there had been an
-
The overlap between cyberbullying and traditional bullying.
Waasdorp, Tracy E; Bradshaw, Catherine P
2015-05-01
Cyberbullying appears to be on the rise among adolescents due in part to increased access to electronic devices and less online supervision. Less is known about how cyberbullying differs from traditional bullying which occurs in person and the extent to which these two forms overlap. Our first aim was to examine the overlap of traditional bullying (relational, verbal, and physical) with cyberbullying. The second aim examined student- and school-level correlates of cyber victimization as compared to traditional victims. The final aim explored details of the cyberbullying experience (e.g., who sent the message, how was the message sent, and what was the message about). Data came from 28,104 adolescents (grades, 9-12) attending 58 high schools. Approximately 23% of the youth reported being victims of any form of bullying (cyber, relational, physical, and verbal) within the last month, with 25.6% of those victims reporting being cyberbullied. The largest proportion (50.3%) of victims reported they were victimized by all four forms, whereas only 4.6% reported being only cyberbullied. Multilevel analyses indicated that as compared to those who were only traditionally bullied, those who were cyberbullied were more likely to have externalizing (odds ratio = 1.44) and internalizing symptoms (odds ratio = 1.25). Additional analyses examined detailed characteristics of the cyberbullying experiences, indicating a relatively high level of overlap between cyber and traditional bullying. Implications for preventive interventions targeting youth involved with cyberbullying and its overlap with other forms of bullying are discussed. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.
-
A non overlapping parallel domain decomposition method applied to the simplified transport equations
International Nuclear Information System (INIS)
Lathuiliere, B.; Barrault, M.; Ramet, P.; Roman, J.
2009-01-01
A reactivity computation requires to compute the highest eigenvalue of a generalized eigenvalue problem. An inverse power algorithm is used commonly. Very fine modelizations are difficult to tackle for our sequential solver, based on the simplified transport equations, in terms of memory consumption and computational time. So, we propose a non-overlapping domain decomposition method for the approximate resolution of the linear system to solve at each inverse power iteration. Our method brings to a low development effort as the inner multigroup solver can be re-use without modification, and allows us to adapt locally the numerical resolution (mesh, finite element order). Numerical results are obtained by a parallel implementation of the method on two different cases with a pin by pin discretization. This results are analyzed in terms of memory consumption and parallel efficiency. (authors)
-
Genetic overlap between impulsivity and alcohol dependence: a large-scale national twin study.
Khemiri, L; Kuja-Halkola, R; Larsson, H; Jayaram-Lindström, N
2016-04-01
Alcohol dependence is associated with increased levels of impulsivity, but the genetic and environmental underpinnings of this overlap remain unclear. The purpose of the current study was to investigate the degree to which genetic and environmental factors contribute to the overlap between alcohol dependence and impulsivity. Univariate and bivariate twin model fitting was conducted for alcohol dependence and impulsivity in a national sample of 16 819 twins born in Sweden from 1959 to 1985. The heritability estimate for alcohol dependence was 44% [95% confidence interval (CI) 31-57%] for males and 62% (95% CI 52-72%) for females. For impulsivity, the heritability was 33% (95% CI 30-36%) in males and females. The bivariate twin analysis indicated a statistically significant genetic correlation between alcohol dependence and impulsivity of 0.40 (95% CI 0.23-0.58) in males and 0.20 (95% CI 0.07-0.33) in females. The phenotypic correlation between alcohol dependence and impulsivity was 0.20 and 0.17 for males and females, respectively, and the bivariate heritability was 80% (95% CI 47-117%) for males and 53% (95% CI 19-86%) for females. The remaining variance in all models was accounted for by non-shared environmental factors. The association between alcohol dependence and impulsivity can be partially accounted for by shared genetic factors. The genetic correlation was greater in men compared with women, which may indicate different pathways to the development of alcohol dependence between sexes. The observed genetic overlap has clinical implications regarding treatment and prevention, and partially explains the substantial co-morbidity between alcohol dependence and psychiatric disorders characterized by impulsive behaviour.
-
3D Maize Plant Reconstruction Based on Georeferenced Overlapping LiDAR Point Clouds
Directory of Open Access Journals (Sweden)
Miguel Garrido
2015-12-01
Full Text Available 3D crop reconstruction with a high temporal resolution and by the use of non-destructive measuring technologies can support the automation of plant phenotyping processes. Thereby, the availability of such 3D data can give valuable information about the plant development and the interaction of the plant genotype with the environment. This article presents a new methodology for georeferenced 3D reconstruction of maize plant structure. For this purpose a total station, an IMU, and several 2D LiDARs with different orientations were mounted on an autonomous vehicle. By the multistep methodology presented, based on the application of the ICP algorithm for point cloud fusion, it was possible to perform the georeferenced point clouds overlapping. The overlapping point cloud algorithm showed that the aerial points (corresponding mainly to plant parts were reduced to 1.5%–9% of the total registered data. The remaining were redundant or ground points. Through the inclusion of different LiDAR point of views of the scene, a more realistic representation of the surrounding is obtained by the incorporation of new useful information but also of noise. The use of georeferenced 3D maize plant reconstruction at different growth stages, combined with the total station accuracy could be highly useful when performing precision agriculture at the crop plant level.
-
Gong, Jing-Bo; Wang, Ya; Lui, Simon S Y; Cheung, Eric F C; Chan, Raymond C K
2017-11-01
Childhood trauma has been shown to be a robust risk factor for mental disorders, and may exacerbate schizotypal traits or contribute to autistic trait severity. However, little is known whether childhood trauma confounds the overlap between schizotypal traits and autistic traits. This study examined whether childhood trauma acts as a confounding variable in the overlap between autistic and schizotypal traits in a large non-clinical adult sample. A total of 2469 participants completed the Autism Spectrum Quotient (AQ), the Schizotypal Personality Questionnaire (SPQ), and the Childhood Trauma Questionnaire-Short Form. Correlation analysis showed that the majority of associations between AQ variables and SPQ variables were significant (p autistic and schizotypal traits could not be explained by shared variance in terms of exposure to childhood trauma. The findings point to important overlaps in the conceptualization of ASD and SSD, independent of childhood trauma. Copyright © 2017 Elsevier B.V. All rights reserved.
-
Non-specific filtering of beta-distributed data.
Wang, Xinhui; Laird, Peter W; Hinoue, Toshinori; Groshen, Susan; Siegmund, Kimberly D
2014-06-19
Non-specific feature selection is a dimension reduction procedure performed prior to cluster analysis of high dimensional molecular data. Not all measured features are expected to show biological variation, so only the most varying are selected for analysis. In DNA methylation studies, DNA methylation is measured as a proportion, bounded between 0 and 1, with variance a function of the mean. Filtering on standard deviation biases the selection of probes to those with mean values near 0.5. We explore the effect this has on clustering, and develop alternate filter methods that utilize a variance stabilizing transformation for Beta distributed data and do not share this bias. We compared results for 11 different non-specific filters on eight Infinium HumanMethylation data sets, selected to span a variety of biological conditions. We found that for data sets having a small fraction of samples showing abnormal methylation of a subset of normally unmethylated CpGs, a characteristic of the CpG island methylator phenotype in cancer, a novel filter statistic that utilized a variance-stabilizing transformation for Beta distributed data outperformed the common filter of using standard deviation of the DNA methylation proportion, or its log-transformed M-value, in its ability to detect the cancer subtype in a cluster analysis. However, the standard deviation filter always performed among the best for distinguishing subgroups of normal tissue. The novel filter and standard deviation filter tended to favour features in different genome contexts; for the same data set, the novel filter always selected more features from CpG island promoters and the standard deviation filter always selected more features from non-CpG island intergenic regions. Interestingly, despite selecting largely non-overlapping sets of features, the two filters did find sample subsets that overlapped for some real data sets. We found two different filter statistics that tended to prioritize features with
-
Targeting mitochondrial phenotypes for non-communicable diseases
Directory of Open Access Journals (Sweden)
Zhengtang Qi
2016-06-01
Full Text Available The concept that “Exercise is Medicine” has been challenged by the rising prevalence of non-communicable chronic diseases (NCDs. This is partly due to the fact that the underlying mechanisms of how exercise influences energy homeostasis and counteracts high-fat diets and physical inactivity is complex and remains relatively poorly understood on a molecular level. In addition to genetic polymorphisms in humans that lead to gross variations in responsiveness to exercise, adaptation in mitochondrial networks is central to physical activity, inactivity, and diet. To harness the benefits of exercise for NCDs, much work still needs to be done to improve health effectively on a societal level such as developing personalized exercise interventions aided by advances in high-throughput genomics, proteomics, and metabolomics. We propose that understanding the mitochondrial phenotype according to the molecular information of genotypes, lifestyles, and exercise responsiveness in individuals will optimize exercise effects for prevention of NCDs.
-
PAXX Is an Accessory c-NHEJ Factor that Associates with Ku70 and Has Overlapping Functions with XLF
Directory of Open Access Journals (Sweden)
Satish K. Tadi
2016-10-01
Full Text Available In mammalian cells, classical non-homologous end joining (c-NHEJ is critical for DNA double-strand break repair induced by ionizing radiation and during V(DJ recombination in developing B and T lymphocytes. Recently, PAXX was identified as a c-NHEJ core component. We report here that PAXX-deficient cells exhibit a cellular phenotype uncharacteristic of a deficiency in c-NHEJ core components. PAXX-deficient cells display normal sensitivity to radiomimetic drugs, are proficient in transient V(DJ recombination assays, and do not shift toward higher micro-homology usage in plasmid repair assays. Although PAXX-deficient cells lack c-NHEJ phenotypes, PAXX forms a stable ternary complex with Ku bound to DNA. Formation of this complex involves an interaction with Ku70 and requires a bare DNA extension for stability. Moreover, the relatively weak Ku-dependent stimulation of LIG4/XRCC4 activity by PAXX is unmasked by XLF ablation. Thus, PAXX plays an accessory role during c-NHEJ that is largely overlapped by XLF’s function.
-
Overlapping bio-absorbable scaffolds: Aim for D2D technique?
Khan, Asaad A; Dangas, George D
2018-06-01
The results of overlapping metallic stents have been concerning but this practice is often unavoidable in the setting of long or tortuous lesions, diameter discrepancy of proximal and distal vessel, and for residual dissections. Theoretically, bio-absorbable scaffolds may carry an advantage over metallic stents due to the progressive resorption of the scaffold theoretically rendering the overlap a non-issue; this has not been clinically evident. Since stent/scaffold overlap cannot be entirely avoided, improved stent delivery/deployment and scaffold design modification may reduce complications in this complex patient subset. © 2018 Wiley Periodicals, Inc.
-
The uses of overlap: carer-child interaction involving a nine-year-old boy with auditory neuropathy.
Anstey, Julie; Wells, Bill
2013-01-01
The subject of this single case study, Ricky, is a nine-year-old boy with a profound hearing loss arising from auditory neuropathy. Despite cochlear implantation at the age of two, his receptive language skills remain very restricted and his speech is unintelligible. Techniques of interactional linguistics are used to analyse recordings of Ricky and his mother during shared book reading. Both participants display competences in managing turn-taking and overlapping talk that enable them to progress the book-reading activity, to talk spontaneously on topically related matters and also to handle issues of phonetic and linguistic repair. Instances of both competitive and non-competitive overlap reveal that Ricky has access to interactionally important prosodic skills. The study thus reinforces the need, when assessing a child's potential to understand and use spoken language, to examine the child's talk from an interactional perspective. It further indicates that overlapping talk is not necessarily a problem; indeed it can be part of a solution to issues of interpersonal understanding that routinely arise in the course of talk-in-interaction.
-
Emergence of cooperation in phenotypically heterogeneous populations: a replicator dynamics analysis
International Nuclear Information System (INIS)
Barreira da Silva Rocha, A; Escobedo, R; Laruelle, A
2015-01-01
The emergence of cooperation is analyzed in heterogeneous populations where two kinds of individuals exist according to their phenotypic appearance. Phenotype recognition is assumed for all individuals: individuals are able to identify the type of every other individual, but fail to recognize their own type. Individuals thus behave under partial information conditions. The interactions between individuals are described by the snowdrift game, where individuals can either cooperate or defect. The evolution of such populations is studied in the framework of evolutionary game theory by means of the replicator dynamics. Overlapping generations are considered, so the replicator equations are formulated in discrete-time form. The stability analysis of the dynamical system is carried out and a detailed description of the behavior of trajectories starting from the interior of the state-space is given. We find that the four monomorphic states are unstable and that a polymorphic state exists which is a global attractor for non-degenerate initial states of the population. The result for the discrete-time replicator coincides with the one of the continuous case. (paper)
-
Cerebral and non-cerebral coenurosis: on the genotypic and phenotypic diversity of Taenia multiceps.
Christodoulopoulos, Georgios; Dinkel, Anke; Romig, Thomas; Ebi, Dennis; Mackenstedt, Ute; Loos-Frank, Brigitte
2016-12-01
We characterised the causative agents of cerebral and non-cerebral coenurosis in livestock by determining the mitochondrial genotypes and morphological phenotypes of 52 Taenia multiceps isolates from a wide geographical range in Europe, Africa, and western Asia. Three studies were conducted: (1) a morphological comparison of the rostellar hooks of cerebral and non-cerebral cysts of sheep and goats, (2) a morphological comparison of adult worms experimentally produced in dogs, and (3) a molecular analysis of three partial mitochondrial genes (nad1, cox1, and 12S rRNA) of the same isolates. No significant morphological or genetic differences were associated with the species of the intermediate host. Adult parasites originating from cerebral and non-cerebral cysts differed morphologically, e.g. the shape of the small hooks and the distribution of the testes in the mature proglottids. The phylogenetic analysis of the mitochondrial haplotypes produced three distinct clusters: one cluster including both cerebral isolates from Greece and non-cerebral isolates from tropical and subtropical countries, and two clusters including cerebral isolates from Greece. The majority of the non-cerebral specimens clustered together but did not form a monophyletic group. No monophyletic groups were observed based on geography, although specimens from the same region tended to cluster. The clustering indicates high intraspecific diversity. The phylogenetic analysis suggests that all variants of T. multiceps can cause cerebral coenurosis in sheep (which may be the ancestral phenotype), and some variants, predominantly from one genetic cluster, acquired the additional capacity to produce non-cerebral forms in goats and more rarely in sheep.
-
The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes.
Colombo, Marco; Diepeveen, Eveline T; Muschick, Moritz; Santos, M Emilia; Indermaur, Adrian; Boileau, Nicolas; Barluenga, Marta; Salzburger, Walter
2013-02-01
The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick-lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick-lipped phenotype also occurs elsewhere, for example in the Central American Midas Cichlid assemblage. Here, we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick-lipped species. We found that similar morphological adaptations occur in both thick-lipped species and that the 'fleshy' lips are associated with hard-shelled prey in the form of molluscs and invertebrates. We then used comparative Illumina RNA sequencing of thick vs. normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick-lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages. © 2012 Blackwell Publishing Ltd.
-
Trisomy 2p: Analysis of unusual phenotypic findings
Energy Technology Data Exchange (ETDEWEB)
Lurie, I.W.; Ilyina, H.G.; Gurevich, D.B. [Belorussian Research Institute of Hereditary Disease, Minsk (Russian Federation)] [and others
1995-01-16
We present three probands with partial trisomies 2p21-23 due to ins(4;2)(q21;p21p23) pat, 2p23-pter due to t(2;4)(p23;q35)mat, and 2p21-pter due to t(2;11)(p21;q23.3)mat. More than 50 cases of partial trisomy 2p have been reviewed and some abnormalities, unusual for most other types of structural autosomal imbalance, have been found in patients with inherited forms of 2p trisomy and in their non-karyotyped sibs. Neural tube defects (anencephaly, occipital encephalocele, and spina bifida) were found in five probands and 4/6 affected non-karyotyped sibs. The only triplicated segment common to all was 2p24. Different forms of {open_quotes}broncho-pulmonary a/hypoplasia{close_quotes} (including two cases of lung agenesis) were described in four patients (overlapping triplicated segment was 2p21-p25). Three patients (with overlapping triplicated segment 2p23-p25) had diaphragmatic hernia. Abnormal rotation of the heart or L-transposition of large vessels (with or without visceral heterotaxia) was found in two infants (overlapping triplicated segment 2p23-p24). In two patients with common triplicated segment 2p22.3-p25, neuroblastoma has been described. The occurrence of all these defects may be explained either by the action of the same gene(s) mapped to 2p24 or by action of some independent factors located in different segments of the short arm. Although the latter hypothesis is much less probable, it can not be rejected at the present time. We propose the existence of a genetic system controlling surveillance of an abnormal embryo to explain the phenotypic differences between patients with the same imbalance within a family. In some {open_quotes}restrictive{close_quotes} combinations the abnormal embryos will die, although in {open_quotes}permissive{close_quotes} combinations they can survive. 47 refs., 2 figs., 3 tabs.
-
Directory of Open Access Journals (Sweden)
Mohit Kumar Jolly
2018-03-01
Full Text Available It is well known that genetic mutations can drive drug resistance and lead to tumor relapse. Here, we focus on alternate mechanisms—those without mutations, such as phenotypic plasticity and stochastic cell-to-cell variability that can also evade drug attacks by giving rise to drug-tolerant persisters. The phenomenon of persistence has been well-studied in bacteria and has also recently garnered attention in cancer. We draw a parallel between bacterial persistence and resistance against androgen deprivation therapy in prostate cancer (PCa, the primary standard care for metastatic disease. We illustrate how phenotypic plasticity and consequent mutation-independent or non-genetic heterogeneity possibly driven by protein conformational dynamics can stochastically give rise to androgen independence in PCa, and suggest that dynamic phenotypic plasticity should be considered in devising therapeutic dosing strategies designed to treat and manage PCa.
-
Futamura, Hiroshi
2015-01-01
An overlapping generations model is an applied dynamic general equilibrium model for which the lifecycle models are employed as main analytical tools. At any point in time, there are overlapping generations consisting of individuals born this year, individuals born last year, individuals born two years ago, and so on. As we saw in the analysis of lifecycle models, each individual makes an optimal consumption-saving plan to maximize lifetime utility over her/his lifecycle. For example, an indi...
-
Czech Academy of Sciences Publication Activity Database
Bustince, H.; Fernández, J.; Mesiar, Radko; Montero, J.; Orduna, R.
2010-01-01
Roč. 72, 3-4 (2010), s. 1488-1499 ISSN 0362-546X R&D Projects: GA ČR GA402/08/0618 Institutional research plan: CEZ:AV0Z10750506 Keywords : t-norm * Migrative property * Homogeneity property * Overlap function Subject RIV: BA - General Mathematics Impact factor: 1.279, year: 2010 http://library.utia.cas.cz/separaty/2009/E/mesiar-overlap functions.pdf
-
Olar, Adriana; Wani, Khalida; Mansouri, Alireza; Zadeh, Gelareh; Wilson, Charmaine; DeMonte, Franco; Fuller, Gregory; Jones, David; Pfister, Stefan; von Deimling, Andreas; Sulman, Erik; Aldape, Kenneth
2014-01-01
BACKGROUND: Methylation profiling of solid tumors has revealed biologic subtypes, often with clinical implications. Methylation profiles of meningioma and their clinical implications are not well understood. METHODS: Ninety-two meningioma samples (n = 44 test set and n = 48 validation set) were profiled using the Illumina HumanMethylation450 BeadChip. Unsupervised clustering and analyses for recurrence-free survival (RFS) were performed. RESULTS: Unsupervised clustering of the test set using approximately 900 highly variable markers identified two clearly defined methylation subgroups. One of the groups (n = 19) showed global hypermethylation of a set of markers, analogous to CpG island methylator phenotype (CIMP). These findings were reproducible in the validation set, with 18/48 samples showing the CIMP-positive phenotype. Importantly, of 347 highly variable markers common to both the test and validation set analyses, 107 defined CIMP in the test set and 94 defined CIMP in the validation set, with an overlap of 83 markers between the two datasets. This number is much greater than expected by chance indicating reproducibly of the hypermethylated markers that define CIMP in meningioma. With respect to clinical correlation, the 37 CIMP-positive cases displayed significantly shorter RFS compared to the 55 non-CIMP cases (hazard ratio 2.9, p = 0.013). In an effort to develop a preliminary outcome predictor, a 155-marker subset correlated with RFS was identified in the test dataset. When interrogated in the validation dataset, this 155-marker subset showed a statistical trend (p < 0.1) towards distinguishing survival groups. CONCLUSIONS: This study defines the existence of a CIMP phenotype in meningioma, which involves a substantial proportion (37/92, 40%) of samples with clinical implications. Ongoing work will expand this cohort and examine identification of additional biologic differences (mutational and DNA copy number analysis) to further characterize the aberrant
-
Directory of Open Access Journals (Sweden)
Borja G Cosio
Full Text Available The Spanish guideline for COPD (GesEPOC recommends COPD treatment according to four clinical phenotypes: non-exacerbator phenotype with either chronic bronchitis or emphysema (NE, asthma-COPD overlap syndrome (ACOS, frequent exacerbator phenotype with emphysema (FEE or frequent exacerbator phenotype with chronic bronchitis (FECB. However, little is known on the distribution and outcomes of the four suggested phenotypes.We aimed to determine the distribution of these COPD phenotypes, and their relation with one-year clinical outcomes.We followed a cohort of well-characterized patients with COPD up to one-year. Baseline characteristics, health status (CAT, BODE index, rate of exacerbations and mortality up to one year of follow-up were compared between the four phenotypes.Overall, 831 stable COPD patients were evaluated. They were distributed as NE, 550 (66.2%; ACOS, 125 (15.0%; FEE, 38 (4.6%; and FECB, 99 (11.9%; additionally 19 (2.3% COPD patients with frequent exacerbations did not fulfill the criteria for neither FEE nor FECB. At baseline, there were significant differences in symptoms, FEV1 and BODE index (all p<0.05. The FECB phenotype had the highest CAT score (17.1±8.2, p<0.05 compared to the other phenotypes. Frequent exacerbator groups (FEE and FECB were receiving more pharmacological treatment at baseline, and also experienced more exacerbations the year after (all p<0.05 with no differences in one-year mortality. Most of NE (93% and half of exacerbators were stable after one year.There is an uneven distribution of COPD phenotypes in stable COPD patients, with significant differences in demographics, patient-centered outcomes and health care resources use.
-
A Bayesian Approach to the Overlap Analysis of Epidemiologically Linked Traits.
Asimit, Jennifer L; Panoutsopoulou, Kalliope; Wheeler, Eleanor; Berndt, Sonja I; Cordell, Heather J; Morris, Andrew P; Zeggini, Eleftheria; Barroso, Inês
2015-12-01
Diseases often cooccur in individuals more often than expected by chance, and may be explained by shared underlying genetic etiology. A common approach to genetic overlap analyses is to use summary genome-wide association study data to identify single-nucleotide polymorphisms (SNPs) that are associated with multiple traits at a selected P-value threshold. However, P-values do not account for differences in power, whereas Bayes' factors (BFs) do, and may be approximated using summary statistics. We use simulation studies to compare the power of frequentist and Bayesian approaches with overlap analyses, and to decide on appropriate thresholds for comparison between the two methods. It is empirically illustrated that BFs have the advantage over P-values of a decreasing type I error rate as study size increases for single-disease associations. Consequently, the overlap analysis of traits from different-sized studies encounters issues in fair P-value threshold selection, whereas BFs are adjusted automatically. Extensive simulations show that Bayesian overlap analyses tend to have higher power than those that assess association strength with P-values, particularly in low-power scenarios. Calibration tables between BFs and P-values are provided for a range of sample sizes, as well as an approximation approach for sample sizes that are not in the calibration table. Although P-values are sometimes thought more intuitive, these tables assist in removing the opaqueness of Bayesian thresholds and may also be used in the selection of a BF threshold to meet a certain type I error rate. An application of our methods is used to identify variants associated with both obesity and osteoarthritis. © 2015 The Authors. *Genetic Epidemiology published by Wiley Periodicals, Inc.
-
Exploring overlapping functional units with various structure in protein interaction networks.
Directory of Open Access Journals (Sweden)
Xiao-Fei Zhang
Full Text Available Revealing functional units in protein-protein interaction (PPI networks are important for understanding cellular functional organization. Current algorithms for identifying functional units mainly focus on cohesive protein complexes which have more internal interactions than external interactions. Most of these approaches do not handle overlaps among complexes since they usually allow a protein to belong to only one complex. Moreover, recent studies have shown that other non-cohesive structural functional units beyond complexes also exist in PPI networks. Thus previous algorithms that just focus on non-overlapping cohesive complexes are not able to present the biological reality fully. Here, we develop a new regularized sparse random graph model (RSRGM to explore overlapping and various structural functional units in PPI networks. RSRGM is principally dominated by two model parameters. One is used to define the functional units as groups of proteins that have similar patterns of connections to others, which allows RSRGM to detect non-cohesive structural functional units. The other one is used to represent the degree of proteins belonging to the units, which supports a protein belonging to more than one revealed unit. We also propose a regularizer to control the smoothness between the estimators of these two parameters. Experimental results on four S. cerevisiae PPI networks show that the performance of RSRGM on detecting cohesive complexes and overlapping complexes is superior to that of previous competing algorithms. Moreover, RSRGM has the ability to discover biological significant functional units besides complexes.
-
Directory of Open Access Journals (Sweden)
Buxbaum Joseph D
2012-02-01
Full Text Available Abstract Background There is interest in defining mouse neurobiological phenotypes useful for studying autism spectrum disorders (ASD in both forward and reverse genetic approaches. A recurrent focus has been on high-order behavioral analyses, including learning and memory paradigms and social paradigms. However, well-studied mouse models, including for example Fmr1 knockout mice, do not show dramatic deficits in such high-order phenotypes, raising a question as to what constitutes useful phenotypes in ASD models. Methods To address this, we made use of a list of 112 disease genes etiologically involved in ASD to survey, on a large scale and with unbiased methods as well as expert review, phenotypes associated with a targeted disruption of these genes in mice, using the Mammalian Phenotype Ontology database. In addition, we compared the results with similar analyses for human phenotypes. Findings We observed four classes of neurobiological phenotypes associated with disruption of a large proportion of ASD genes, including: (1 Changes in brain and neuronal morphology; (2 electrophysiological changes; (3 neurological changes; and (4 higher-order behavioral changes. Alterations in brain and neuronal morphology represent quantitative measures that can be more widely adopted in models of ASD to understand cellular and network changes. Interestingly, the electrophysiological changes differed across different genes, indicating that excitation/inhibition imbalance hypotheses for ASD would either have to be so non-specific as to be not falsifiable, or, if specific, would not be supported by the data. Finally, it was significant that in analyses of both mouse and human databases, many of the behavioral alterations were neurological changes, encompassing sensory alterations, motor abnormalities, and seizures, as opposed to higher-order behavioral changes in learning and memory and social behavior paradigms. Conclusions The results indicated that mutations
-
Circadian polymorphisms in night owls, in bipolars, and in non-24-hour sleep cycles.
Kripke, Daniel F; Klimecki, Walter T; Nievergelt, Caroline M; Rex, Katharine M; Murray, Sarah S; Shekhtman, Tatyana; Tranah, Gregory J; Loving, Richard T; Lee, Heon-Jeong; Rhee, Min Kyu; Shadan, Farhad F; Poceta, J Steven; Jamil, Shazia M; Kline, Lawrence E; Kelsoe, John R
2014-10-01
People called night owls habitually have late bedtimes and late times of arising, sometimes suffering a heritable circadian disturbance called delayed sleep phase syndrome (DSPS). Those with DSPS, those with more severe progressively-late non-24-hour sleep-wake cycles, and those with bipolar disorder may share genetic tendencies for slowed or delayed circadian cycles. We searched for polymorphisms associated with DSPS in a case-control study of DSPS research participants and a separate study of Sleep Center patients undergoing polysomnography. In 45 participants, we resequenced portions of 15 circadian genes to identify unknown polymorphisms that might be associated with DSPS, non-24-hour rhythms, or bipolar comorbidities. We then genotyped single nucleotide polymorphisms (SNPs) in both larger samples, using Illumina Golden Gate assays. Associations of SNPs with the DSPS phenotype and with the morningness-eveningness parametric phenotype were computed for both samples, then combined for meta-analyses. Delayed sleep and "eveningness" were inversely associated with loci in circadian genes NFIL3 (rs2482705) and RORC (rs3828057). A group of haplotypes overlapping BHLHE40 was associated with non-24-hour sleep-wake cycles, and less robustly, with delayed sleep and bipolar disorder (e.g., rs34883305, rs34870629, rs74439275, and rs3750275 were associated with n=37, p=4.58E-09, Bonferroni p=2.95E-06). Bright light and melatonin can palliate circadian disorders, and genetics may clarify the underlying circadian photoperiodic mechanisms. After further replication and identification of the causal polymorphisms, these findings may point to future treatments for DSPS, non-24-hour rhythms, and possibly bipolar disorder or depression.
-
Directory of Open Access Journals (Sweden)
Christian Peeters
Full Text Available The South American seed-harvester ant Pogonomyrmex laticeps has dimorphic queens: ergatoid (permanently wingless and brachypterous (short, non-functional wings. Surveys in western Argentina indicated that colonies near Chilecito, La Rioja Province, produced only ergatoid queens, while those near Punta Balasto, Catamarca Province (263 km away, produced only brachypterous queens. Brachypterous queens were significantly larger than ergatoid queens for 10 of 11 external characters, but both phenotypes had comparable reproductive potential, i.e., a spermatheca and a similar number of ovarioles. Using normal winged queens of the closely related P. uruguayensis for comparison, we determined that both queen phenotypes in P. laticeps had a full set of dorsal thoracic sclerites, albeit each sclerite was much reduced, whereas workers had a thorax without distinct dorsal sclerites. Sclerites were fused and immobile in ergatoid queens, while they were separable and fully articulated in brachypterous queens. Both phenotypes lacked the big indirect flight muscles, but brachypterous queens retained the tiny direct flight muscles. Overall, this dimorphism across populations indicates that there are alternative solutions to selective pressures against flying queens. We lack field data about colony founding strategy (independent or dependent for either queen phenotype, but colonies at both sites produced numerous gynes, and we infer that all foundresses initiate colonies independently and are obligate foragers.
-
Savic, Sinisa; Mistry, Anoop; Wilson, Anthony G; Barcenas-Morales, Gabriela; Doffinger, Rainer; Emery, Paul; McGonagle, Dennis
2017-01-01
At the population level, rheumatoid arthritis (RA) is generally viewed as autoimmune in nature with a small subgroup of cases having a palindromic form or systemic autoinflammatory disorder (SAID) phenotype. Herein, we describe resistant cases of classical autoantibody associated RA that had clinical, genetic and therapeutic responses indicative of coexistent autoinflammatory disease. Five patients with clinically overlapping features between RA and SAID including polysynovitis and autoantibody/shared epitope positivity, and who had abrupt severe self-limiting attacks including fevers and serositis, are described. Mutations or single nucleotide polymorphisms in recognised autoinflammatory pathways were evident. Generally, these cases responded poorly to conventional Disease-modifying anti-rheumatic drugs (DMARD) treatment with some excellent responses to colchicine or interleukin 1 pathway blockade. A subgroup of RA cases have a mixed autoimmune-autoinflammatory phenotype and genotype with therapeutic implications.
-
Directory of Open Access Journals (Sweden)
Javan M Bauder
Full Text Available Understanding the factors influencing the degree of spatial overlap among conspecifics is important for understanding multiple ecological processes. Compared to terrestrial carnivores, relatively little is known about the factors influencing conspecific spatial overlap in snakes, although across snake taxa there appears to be substantial variation in conspecific spatial overlap. In this study, we described conspecific spatial overlap of eastern indigo snakes (Drymarchon couperi in peninsular Florida and examined how conspecific spatial overlap varied by sex and season (breeding season vs. non-breeding season. We calculated multiple indices of spatial overlap using 6- and 3-month utilization distributions (UD of dyads of simultaneously adjacent telemetered snakes. We also measured conspecific UD density values at each telemetry fix and modeled the distribution of those values as a function of overlap type, sex, and season using generalized Pareto distributions. Home range overlap between males and females was significantly greater than overlap between individuals of the same sex and male home ranges often completely contained female home ranges. Male home ranges overlapped little during both seasons, whereas females had higher levels of overlap during the non-breeding season. The spatial patterns observed in our study are consistent with those seen in many mammalian carnivores, in which low male-male overlap and high inter-sexual overlap provides males with greater access to females. We encourage additional research on the influence of prey availability on conspecific spatial overlap in snakes as well as the behavioral mechanisms responsible for maintaining the low levels of overlap we observed.
-
Candidate gene analyses of 3-dimensional dentoalveolar phenotypes in subjects with malocclusion.
Weaver, Cole A; Miller, Steven F; da Fontoura, Clarissa S G; Wehby, George L; Amendt, Brad A; Holton, Nathan E; Allareddy, Veeratrishul; Southard, Thomas E; Moreno Uribe, Lina M
2017-03-01
Genetic studies of malocclusion etiology have identified 4 deleterious mutations in genes DUSP6,ARHGAP21, FGF23, and ADAMTS1 in familial Class III cases. Although these variants may have large impacts on Class III phenotypic expression, their low frequency (common genetic variations in craniofacial candidate genes and 3-dimensional dentoalveolar phenotypes in patients with malocclusion. Pretreatment dental casts or cone-beam computed tomographic images from 300 healthy subjects were digitized with 48 landmarks. The 3-dimensional coordinate data were submitted to a geometric morphometric approach along with principal component analysis to generate continuous phenotypes including symmetric and asymmetric components of dentoalveolar shape variation, fluctuating asymmetry, and size. The subjects were genotyped for 222 single-nucleotide polymorphisms in 82 genes/loci, and phenotpye-genotype associations were tested via multivariate linear regression. Principal component analysis of symmetric variation identified 4 components that explained 68% of the total variance and depicted anteroposterior, vertical, and transverse dentoalveolar discrepancies. Suggestive associations (P centroid size, a proxy for dentoalveolar size variation with 4p16.1 and SNAI1. Specific genetic pathways associated with 3-dimensional dentoalveolar phenotypic variation in malocclusions were identified. Copyright © 2016 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.
-
Phenotypic and genetic associations between the big five and trait emotional intelligence.
Vernon, Philip A; Villani, Vanessa C; Schermer, Julie Aitken; Petrides, K V
2008-10-01
This study reports the first behavioral genetic investigation of the extent to which genetic and/or environmental factors contribute to the relationship between the Big Five personality factors and trait emotional intelligence. 213 pairs of adult monozygotic twins and 103 pairs of same-sex dizygotic twins completed the NEO-PI-R and the Trait Emotional Intelligence Questionnaire (TEIQue). Replicating previous non-twin studies, many significant phenotypic correlations were found between the Big Five factors - especially Neuroticism, Extraversion, and Conscientiousness - and the facets, factors, and global scores derived from the TEIQue. Bivariate behavioral genetic model-fitting analyses revealed that these phenotypic correlations were primarily attributable to correlated genetic factors and secondarily to correlated non-shared environmental factors. The results support the feasibility of incorporating EI as a trait within existing personality taxonomies.
-
Overlap and distinction between measures of insight and self-stigma.
Hasson-Ohayon, Ilanit
2018-05-24
Multiple studies on insight into one's illness and self-stigma among patients with serious mental illness and their relatives have shown that these constructs are related to one another and that they affect outcome. However, a critical exploration of the items used to assess both constructs raises questions with regard to the possible overlapping and centrality of items. The current study used five different samples to explore the possible overlap and distinction between insight and self-stigma, and to identify central items, via network analyses and principal component factor analysis. Findings from the network analyses showed overlap between insight and self-stigma exist with a relatively clearer observational distinction between the constructs among the two parent samples in comparison to the patient samples. Principal component factor analysis constrained to two factors showed that a relatively high percentage of items were not loaded on either factor, and in a few datasets, several insight items were loaded on the self-stigma scale and vice versa. The author discusses implications for research and calls for rethinking the way insight is assessed. Clinical implications are also discussed in reference to central items of social isolation, future worries and stereotype endorsement among the different study groups. Copyright © 2018 Elsevier B.V. All rights reserved.
-
Directory of Open Access Journals (Sweden)
Pari Basharat
2016-07-01
Full Text Available Idiopathic inflammatory myopathies (IIM are traditionally identified as a group of disorders that target skeletal muscle due to autoimmune dysfunction. The IIM can be divided into subtypes based on certain clinical characteristics, and several classification schemes have been proposed. The predominant diagnostic criteria for IIM is the Bohan and Peter criteria, which subdivides IIM into primary polymyositis (PM, primary dermatomyositis (DM, myositis with another connective tissue disease, and myositis associated with cancer. However, this measure has been criticised for several reasons including lack of specific criteria to help distinguish between muscle biopsy findings of PM, DM, and immune-mediated necrotising myopathy, as well as the lack of identification of cases of overlap myositis (OM. Because of this issue, other classification criteria for IIM have been proposed, which include utilising myositis-associated antibodies and myositis-specific antibodies, as well as overlap features such as Raynaud’s phenomenon, polyarthritis, oesophageal abnormalities, interstitial lung disease, small bowel abnormalities such as hypomotility and malabsorption, and renal crises, amongst others. Indeed, the identification of autoantibodies associated with certain clinical phenotypes of myositis, in particular connective tissue disease-myositis overlap, has further helped divide IIM into distinct clinical subsets, which include OM and overlap syndromes (OS. This paper reviews the concepts of OM and OS as they pertain to IIM, including definitions in the literature, clinical characteristics, and overlap autoantibodies.
-
Manolov, Rumen; Losada, José L; Chacón-Moscoso, Salvador; Sanduvete-Chaves, Susana
2016-01-01
Two-phase single-case designs, including baseline evaluation followed by an intervention, represent the most clinically straightforward option for combining professional practice and research. However, unless they are part of a multiple-baseline schedule, such designs do not allow demonstrating a causal relation between the intervention and the behavior. Although the statistical options reviewed here cannot help overcoming this methodological limitation, we aim to make practitioners and applied researchers aware of the available appropriate options for extracting maximum information from the data. In the current paper, we suggest that the evaluation of behavioral change should include visual and quantitative analyses, complementing the substantive criteria regarding the practical importance of the behavioral change. Specifically, we emphasize the need to use structured criteria for visual analysis, such as the ones summarized in the What Works Clearinghouse Standards, especially if such criteria are complemented by visual aids, as illustrated here. For quantitative analysis, we focus on the non-overlap of all pairs and the slope and level change procedure, as they offer straightforward information and have shown reasonable performance. An illustration is provided of the use of these three pieces of information: visual, quantitative, and substantive. To make the use of visual and quantitative analysis feasible, open source software is referred to and demonstrated. In order to provide practitioners and applied researchers with a more complete guide, several analytical alternatives are commented on pointing out the situations (aims, data patterns) for which these are potentially useful.
-
Directory of Open Access Journals (Sweden)
Verhoeven W
2018-03-01
Full Text Available Willem Verhoeven,1,2 Jos Egger,1,3 Emmy Räkers,4 Arjen van Erkelens,5 Rolph Pfundt,5 Marjolein H Willemsen5 1Vincent van Gogh Institute for Psychiatry, Centre of Excellence for Neuropsychiatry, Venray, the Netherlands; 2Department of Psychiatry, Erasmus University Medical Centre, Rotterdam, the Netherlands; 3Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands; 4ASVZ, Centre for People with Intellectual Disabilities, Sliedrecht, the Netherlands; 5Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands Abstract: The additional sex combs like 3 gene is considered to be causative for the rare Bainbridge-Ropers syndrome (BRPS, which is characterized by severe intellectual disability, neonatal hypotonia, nearly absent development of speech and language as well as several facial dysmorphisms. Apart from disruptive autistiform behaviors, sleep disturbances and epileptic phenomena may be present. Here, a 47-year-old severely intellectually disabled male is described in whom exome sequencing disclosed a novel heterozygous frameshift mutation in the ASXL3 gene leading to a premature stopcodon in the last part of the last exon. Mutations in this very end 3' of the gene have not been reported before in BRPS. The phenotypical presentation of the patient including partially therapy-resistant epilepsy starting in later adulthood shows overlap with BRPS, and it was therefore concluded that the phenotype is likely explained by the identified mutation in ASXL3. Keywords: Bainbridge-Ropers syndrome, ASLX3, frameshift mutation, epilepsy, intellectual disability, array analysis, whole exome sequencing, autism spectrum disorder
-
Directory of Open Access Journals (Sweden)
Kostikas K
2016-06-01
Full Text Available Konstantinos Kostikas, Andreas Clemens, Francesco Patalano Novartis Pharma AG, Basel, Switzerland Abstract: The term asthma–COPD overlap syndrome (ACOS is one of multiple terms used to describe patients with characteristics of both COPD and asthma, representing ~20% of patients with obstructive airway diseases. The recognition of both sets of morbidities in patients is important to guide practical treatment decisions. It is widely recognized that patients with COPD and coexisting asthma present with a higher disease burden, despite the conceptual expectation that the “reversible” or “treatable” component of asthma would allow for more effective management and better outcomes. However, subcategorization into terms such as ACOS is complicated by the vast spectrum of heterogeneity that is encapsulated by asthma and COPD, resulting in different clinical clusters. In this review, we discuss the possibility that these different clusters are suboptimally described by the umbrella term “ACOS”, as this additional categorization may lead to clinical confusion and potential inappropriate use of resources. We suggest that a more clinically relevant approach would be to recognize the extreme variability and the numerous phenotypes encompassed within obstructive airway diseases, with various degrees of overlapping in individual patients. In addition, we discuss some of the evidence to be considered when making practical decisions on the treatment of patients with overlapping characteristics between COPD and asthma, as well as the potential options for phenotype and biomarker-driven management of airway disease with the aim of providing more personalized treatment for patients. Finally, we highlight the need for more evidence in patients with overlapping disease characteristics and to facilitate better characterization of potential treatment responders. Keywords: emphysema, chronic bronchitis, COPD, asthma, ACOS, overlap syndrome
-
Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLalphas/ALEX Relay.
Directory of Open Access Journals (Sweden)
2005-08-01
Full Text Available XLalphas and ALEX are structurally unrelated mammalian proteins translated from alternative overlapping reading frames of a single transcript. Not only are they encoded by the same locus, but a specific XLalphas/ALEX interaction is essential for G-protein signaling in neuroendocrine cells. A disruption of this interaction leads to abnormal human phenotypes, including mental retardation and growth deficiency. The region of overlap between the two reading frames evolves at a remarkable speed: the divergence between human and mouse ALEX polypeptides makes them virtually unalignable. To trace the evolution of this puzzling locus, we sequenced it in apes, Old World monkeys, and a New World monkey. We show that the overlap between the two reading frames and the physical interaction between the two proteins force the locus to evolve in an unprecedented way. Namely, to maintain two overlapping protein-coding regions the locus is forced to have high GC content, which significantly elevates its intrinsic evolutionary rate. However, the two encoded proteins cannot afford to change too quickly relative to each other as this may impair their interaction and lead to severe physiological consequences. As a result XLalphas and ALEX evolve in an oscillating fashion constantly balancing the rates of amino acid replacements. This is the first example of a rapidly evolving locus encoding interacting proteins via overlapping reading frames, with a possible link to the origin of species-specific neurological differences.
-
OVERLAPPING VIRTUAL CADASTRAL DOCUMENTATION
Directory of Open Access Journals (Sweden)
Madalina - Cristina Marian
2013-12-01
Full Text Available Two cadastrale plans of buildings, can overlap virtual. Overlap is highlighted when digital reception. According to Law no. 7/1996 as amended and supplemented, to solve these problems is by updating the database graphs, the repositioning. This paper addresses the issue of overlapping virtual cadastre in the history of the period 1999-2012.
-
Unique presentation of LHON/MELAS overlap syndrome caused by m.13046T>C in MTND5.
Kolarova, Hana; Liskova, Petra; Tesarova, Marketa; Kucerova Vidrova, Vendula; Forgac, Martin; Zamecnik, Josef; Hansikova, Hana; Honzik, Tomas
2016-12-01
Leber hereditary optic neuropathy (LHON) and mitochondrial encephalopathy, myopathy, lactic acidosis and stroke-like episodes (MELAS) syndromes are mitochondrially inherited disorders characterized by acute visual failure and variable multiorgan system presentation, respectively. A 12-year-old girl with otherwise unremarkable medical history presented with abrupt, painless loss of vision. Over the next few months, she developed moderate sensorineural hearing loss, vertigo, migraines, anhedonia and thyroiditis. Ocular examination confirmed bilateral optic nerve atrophy. Metabolic workup documented elevated cerebrospinal fluid lactate. Initial genetic analyses excluded the three most common LHON mutations. Subsequently, Sanger sequencing of the entire mitochondrial DNA (mtDNA) genome was performed. Whole mtDNA sequencing revealed a pathogenic heteroplasmic mutation m.13046T>C in MTND5 encoding the ND5 subunit of complex I. This particular variant has previously been described in a single case report of MELAS/Leigh syndrome (subacute necrotizing encephalopathy). Based on the constellation of clinical symptoms in our patient, we diagnose the condition as LHON/MELAS overlap syndrome. We describe a unique presentation of LHON/MELAS overlap syndrome resulting from a m.13046T>C mutation in a 12-year-old girl. In patients with sudden vision loss in which three of the most prevalent LHON mitochondrial mutations have been ruled out, molecular genetic examination should be extended to other mtDNA-encoded subunits of MTND5 complex I. Furthermore, atypical clinical presentations must be considered, even in well-described phenotypes.
-
Headache and temporomandibular disorders: evidence for diagnostic and behavioural overlap.
Glaros, A G; Urban, D; Locke, J
2007-06-01
To assess the diagnostic and behavioural overlap of headache patients with temporomandibular disorders (TMD), individuals recruited from the general population with self-described headaches were compared with non-headache controls. The examination and diagnostic procedures in the Research Diagnostic Criteria (RDC) for TMD were applied to both sets of subjects by a blinded examiner. Following their examination, subjects used experience sampling methods to obtain data on pain, tooth contact, masticatory muscle tension, emotional states and stress. Results showed that a significantly higher proportion of the headache patients received an RDC/TMD diagnosis of myofascial pain than non-headache controls. Headache patients also reported significantly more frequent and intense tooth contact, more masticatory muscle tension, more stress and more pain in the face/head and other parts of the body than non-headache controls. These results are similar to those reported for TMD patients and they suggest that headache patients and TMD patients overlap considerably in diagnosis and oral parafunctional behaviours.
-
Asthma phenotypes in childhood.
Reddy, Monica B; Covar, Ronina A
2016-04-01
This review describes the literature over the past 18 months that evaluated childhood asthma phenotypes, highlighting the key aspects of these studies, and comparing these studies to previous ones in this area. Recent studies on asthma phenotypes have identified new phenotypes on the basis of statistical analyses (using cluster analysis and latent class analysis methodology) and have evaluated the outcomes and associated risk factors of previously established early childhood asthma phenotypes that are based on asthma onset and patterns of wheezing illness. There have also been investigations focusing on immunologic, physiologic, and genetic correlates of various phenotypes, as well as identification of subphenotypes of severe childhood asthma. Childhood asthma remains a heterogeneous condition, and investigations into these various presentations, risk factors, and outcomes are important since they can offer therapeutic and prognostic relevance. Further investigation into the immunopathology and genetic basis underlying childhood phenotypes is important so therapy can be tailored accordingly.
-
Directory of Open Access Journals (Sweden)
Robert Wilson
2017-02-01
Full Text Available Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates.
-
Effect of overlapping on location of peaks in qualitative X-ray fluorescent analysis
International Nuclear Information System (INIS)
Jordanov, J.; Stefanov, R.; Tsanov, T.; Jordanov, N.
1982-01-01
To determine the location of the maxima in spectra without resorting to the comparatively complex Fourier-analysis apparatus it is proposed to take into account the overlapping of two adjacent peaks. A formula for the correction of the locations of overlapping maxima with an infinitely small step has been obtained and it is recommended when using X-ray apparatus with great resolution. With flat crystal-analyser apparata, which has a comparatively small resolution, a considerable number of maxima are obtained from the overlapping of at least two adjacent peaks. For that case another formula for the estimation of the shift of the maxima's location from their tabular values is proposed. (authors)
-
Calculational framework for safety analyses of non-reactor nuclear facilities
International Nuclear Information System (INIS)
Coleman, J.R.
1994-01-01
A calculational framework for the consequences analysis of non-reactor nuclear facilities is presented. The analysis framework starts with accident scenarios which are developed through a traditional hazard analysis and continues with a probabilistic framework for the consequences analysis. The framework encourages the use of response continua derived from engineering judgment and traditional deterministic engineering analyses. The general approach consists of dividing the overall problem into a series of interrelated analysis cells and then devising Markov chain like probability transition matrices for each of the cells. An advantage of this division of the problem is that intermediate output (as probability state vectors) are generated at each calculational interface. The series of analyses when combined yield risk analysis output. The analysis approach is illustrated through application to two non-reactor nuclear analyses: the Ulysses Space Mission, and a hydrogen burn in the Hanford waste storage tanks
-
Effects of icotinib on advanced non-small cell lung cancer with different EGFR phenotypes.
Pan, Huiyun; Liu, Rong; Li, Shengjie; Fang, Hui; Wang, Ziwei; Huang, Sheng; Zhou, Jianying
2014-09-01
Icotinib is the first oral epidermal growth factor receptor (EGFR) tyrosine kinase receptor inhibitor, which has been proven to exert significant inhibitory effects on non-small cell lung cancer in vitro. Clinical evidence has showed that the efficacy of Icotinib on retreating advanced non-small cell lung cancer is comparable to Gefitinib. However, different phenotypes of EGFR can affect the therapeutic outcomes of EGFR tyrosine kinase receptor inhibitor. Therefore, our study focused on efficacy and safety of Icotinib in patients with advanced non-small cell lung cancer of different EGPR phenotypes. Clinical data of patients with advanced non-small cell lung cancer who received Icotinib treatment from August, 2011 to May, 2013 were retrospectively analyzed. Kaplan-Meier analysis was used for survival analysis and comparison. 18 wild-type EGFR and 51 mutant type were found in a total of 69 patients. Objective response rate of patients with mutant type EGFR was 54.9 % and disease control rate was 86.3 %. Objective response rate of wild-type patients was 11.1 % (P = 0.0013 vs mutant type), disease control rate was 50.0 % (P = 0.0017). Median progression-free survival (PFS) of mutant type and wild-type patients were 9.7 and 2.6 months, respectively (P Icotinib included rash, diarrhea, itching skin with occurrence rates of 24.6 % (17/69), 13.0 % (9/69), and 11.6 % (8/69), respectively. Most adverse reactions were grade I-II. Icotinib has great efficacy in EGFR mutated patients, making it an optimal regimen to treat EGFR mutated patients. Furthermore, most of adverse reactions associated with Icotinib treatment were tolerable.
-
Candidate gene analyses of 3-dimensional dentoalveolar phenotypes in subjects with malocclusion
Weaver, Cole A.; Miller, Steven F.; da Fontoura, Clarissa S. G.; Wehby, George L.; Amendt, Brad A.; Holton, Nathan E.; Allareddy, Veeratrishul; Southard, Thomas E.; Moreno Uribe, Lina M.
2017-01-01
Introduction Genetic studies of malocclusion etiology have identified 4 deleterious mutations in genes, DUSP6, ARHGAP21, FGF23, and ADAMTS1 in familial Class III cases. Although these variants may have large impacts on Class III phenotypic expression, their low frequency (malocclusions. Thus, much of the genetic variation underlying the dentofacial phenotypic variation associated with malocclusion remains unknown. In this study, we evaluated associations between common genetic variations in craniofacial candidate genes and 3-dimensional dentoalveolar phenotypes in patients with malocclusion. Methods Pretreatment dental casts or cone-beam computed tomographic images from 300 healthy subjects were digitized with 48 landmarks. The 3-dimensional coordinate data were submitted to a geometric morphometric approach along with principal component analysis to generate continuous phenotypes including symmetric and asymmetric components of dentoalveolar shape variation, fluctuating asymmetry, and size. The subjects were genotyped for 222 single-nucleotide polymorphisms in 82 genes/loci, and phenotpye-genotype associations were tested via multivariate linear regression. Results Principal component analysis of symmetric variation identified 4 components that explained 68% of the total variance and depicted anteroposterior, vertical, and transverse dentoalveolar discrepancies. Suggestive associations (P eruptions. Suggestive associations were found with TBX1 AJUBA, SNAI3 SATB2, TP63, and 1p22.1. Fluctuating asymmetry was associated with BMP3 and LATS1. Associations for SATB2 and BMP3 with asymmetric variations remained significant after the Bonferroni correction (P malocclusions were identified. PMID:28257739
-
Further delineation of the KAT6B molecular and phenotypic spectrum.
LENUS (Irish Health Repository)
Gannon, Tamsin
2015-09-01
KAT6B sequence variants have been identified previously in both patients with the Say-Barber-Biesecker type of blepharophimosis mental retardation syndromes (SBBS) and in the more severe genitopatellar syndrome (GPS). We report on the findings in a previously unreported group of 57 individuals with suggestive features of SBBS or GPS. Likely causative variants have been identified in 34\\/57 patients and were commonly located in the terminal exons of KAT6B. Of those where parental samples could be tested, all occurred de novo. Thirty out of thirty-four had truncating variants, one had a missense variant and the remaining three had the same synonymous change predicted to affect splicing. Variants in GPS tended to occur more proximally to those in SBBS patients, and genotype\\/phenotype analysis demonstrated significant clinical overlap between SBBS and GPS. The de novo synonymous change seen in three patients with features of SBBS occurred more proximally in exon 16. Statistical analysis of clinical features demonstrated that KAT6B variant-positive patients were more likely to display hypotonia, feeding difficulties, long thumbs\\/great toes and dental, thyroid and patella abnormalities than KAT6B variant-negative patients. The few reported patients with KAT6B haploinsufficiency had a much milder phenotype, though with some features overlapping those of SBBS. We report the findings in a previously unreported patient with a deletion of the KAT6B gene to further delineate the haploinsufficiency phenotype. The molecular mechanisms giving rise to the SBBS and GPS phenotypes are discussed.
-
Directory of Open Access Journals (Sweden)
Jessica Duong
Full Text Available Epidemic strains of Pseudomonas aeruginosa have been found worldwide among the cystic fibrosis (CF patient population. Using pulse-field gel electrophoresis, the Prairie Epidemic Strain (PES has recently been found in one-third of patients attending the Calgary Adult CF Clinic in Canada. Using multi-locus sequence typing, PES isolates from unrelated patients were found to consistently have ST192. Though most patients acquired PES prior to enrolling in the clinic, some patients were observed to experience strain replacement upon transitioning to the clinic whereby local non-epidemic P. aeruginosa isolates were displaced by PES. Here we genotypically and phenotypically compared PES to other P. aeruginosa epidemic strains (OES found around the world as well as local non-epidemic CF P. aeruginosa isolates in order to characterize PES. Since some epidemic strains are associated with worse clinical outcomes, we assessed the pathogenic potential of PES to determine if these isolates are virulent, shared properties with OES, and if its phenotypic properties may offer a competitive advantage in displacing local non-epidemic isolates during strain replacement. As such, we conducted a comparative analysis using fourteen phenotypic traits, including virulence factor production, biofilm formation, planktonic growth, mucoidy, and antibiotic susceptibility to characterize PES, OES, and local non-epidemic isolates. We observed that PES and OES could be differentiated from local non-epidemic isolates based on biofilm growth with PES isolates being more mucoid. Pairwise comparisons indicated that PES produced significantly higher levels of proteases and formed better biofilms than OES but were more susceptible to antibiotic treatment. Amongst five patients experiencing strain replacement, we found that super-infecting PES produced lower levels of proteases and elastases but were more resistant to antibiotics compared to the displaced non-epidemic isolates. This
-
PairWise Neighbours database: overlaps and spacers among prokaryote genomes
Directory of Open Access Journals (Sweden)
Garcia-Vallvé Santiago
2009-06-01
Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.
-
Phenotypically non-suppressive cells predominate among FoxP3-positive cells in oral lichen planus.
Schreurs, Olav; Karatsaidis, Andreas; Schenck, Karl
2016-11-01
Oral lichen planus (OLP) is a common T-cell-dominated oral chronic inflammatory disease occurring in periods of remission, quiescence, activity with pronounced inflammation, and acute ulceration. Cell infiltrates in OLP contain varying numbers of CD4 + T cells expressing the transcription factor FoxP3. FoxP3 + CD4 + T cells are, however, a heterogeneous cell population containing suppressive and non-suppressive cells, and their distribution in infiltrates from OLP is unknown. Biopsies were taken from normal oral mucosa (n = 8) and OLP lesions (n = 19), and a set of in situ methods for the determination of the functional phenotype of FoxP3 + CD4 + T cells was applied. Numbers of FoxP3 + CD4 + T cells were highest in the atrophic form of the disease, yet low in the ulcerative form. The main FoxP3 + CD4 + T-cell population observed was FoxP3 + CD45RA - CD25 + CD45RO + and CD15s - , a phenotype delineating a non-suppressive subset. Numbers of cells with an actively suppressing phenotype (FoxP3 + CD45RA - CD25 + CD45RO + and CD15s + ) were, however, about twice as high in reticular lesions as compared with the atrophic form. Many FoxP3 + CD4 + T cells expressed T-bet, the hallmark transcription factor for IFN-γ-producing T cells, indicating that they may enhance immune and inflammatory responses rather than suppress them. The absence of actively suppressing FoxP3 + CD4 + T cells may in part explain why OLP is a remarkably persisting condition, in spite of the presence of substantially high numbers of FoxP3 + CD4 + T cells. The findings emphasize that it is crucial to examine not only numbers but also functional phenotype of FoxP3 + CD4 + T cells in human tissues. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
-
Overlapping clusters for distributed computation.
Energy Technology Data Exchange (ETDEWEB)
Mirrokni, Vahab (Google Research, New York, NY); Andersen, Reid (Microsoft Corporation, Redmond, WA); Gleich, David F.
2010-11-01
Scalable, distributed algorithms must address communication problems. We investigate overlapping clusters, or vertex partitions that intersect, for graph computations. This setup stores more of the graph than required but then affords the ease of implementation of vertex partitioned algorithms. Our hope is that this technique allows us to reduce communication in a computation on a distributed graph. The motivation above draws on recent work in communication avoiding algorithms. Mohiyuddin et al. (SC09) design a matrix-powers kernel that gives rise to an overlapping partition. Fritzsche et al. (CSC2009) develop an overlapping clustering for a Schwarz method. Both techniques extend an initial partitioning with overlap. Our procedure generates overlap directly. Indeed, Schwarz methods are commonly used to capitalize on overlap. Elsewhere, overlapping communities (Ahn et al, Nature 2009; Mishra et al. WAW2007) are now a popular model of structure in social networks. These have long been studied in statistics (Cole and Wishart, CompJ 1970). We present two types of results: (i) an estimated swapping probability {rho}{infinity}; and (ii) the communication volume of a parallel PageRank solution (link-following {alpha} = 0.85) using an additive Schwarz method. The volume ratio is the amount of extra storage for the overlap (2 means we store the graph twice). Below, as the ratio increases, the swapping probability and PageRank communication volume decreases.
-
Same Phenotype in Children with Growth Hormone Deficiency and Resistance
Ioimo, Irene; Guarracino, Carmen; Meazza, Cristina; Domené, Horacio M.
2018-01-01
By definition, about 2.5% of children show a short stature due to several causes. Two clinical conditions are characterized by serum IGF-I low levels, idiopathic GH deficiency (IGHD), and GH insensitivity (GHI), and the phenotypic appearance of these patients may be very similar. We studied two children with short stature and similar phenotypes. The first case showed frontal bossing, doll face, acromicria, and truncal obesity, with a GH peak Laron syndrome was confirmed after the molecular analysis of the GH receptor (GHR) gene. IGHD type IA and Laron syndrome is characterized by opposite circulating levels of GH, while both have reduced levels of IGF-I, with an overlapping clinical phenotype, lacking the effects of IGF-I on cartilage. These classical cases show the importance of differential diagnosis in children with severe short stature. PMID:29850346
-
Phenotypic equilibrium as probabilistic convergence in multi-phenotype cell population dynamics.
Directory of Open Access Journals (Sweden)
Da-Quan Jiang
Full Text Available We consider the cell population dynamics with n different phenotypes. Both the Markovian branching process model (stochastic model and the ordinary differential equation (ODE system model (deterministic model are presented, and exploited to investigate the dynamics of the phenotypic proportions. We will prove that in both models, these proportions will tend to constants regardless of initial population states ("phenotypic equilibrium" under weak conditions, which explains the experimental phenomenon in Gupta et al.'s paper. We also prove that Gupta et al.'s explanation is the ODE model under a special assumption. As an application, we will give sufficient and necessary conditions under which the proportion of one phenotype tends to 0 (die out or 1 (dominate. We also extend our results to non-Markovian cases.
-
Non-random mating for selection with restricted rates of inbreeding and overlapping generations
Sonesson, A.K.; Meuwissen, T.H.E.
2002-01-01
Minimum coancestry mating with a maximum of one offspring per mating pair (MC1) is compared with random mating schemes for populations with overlapping generations. Optimum contribution selection is used, whereby $\\\\\\\\Delta F$ is restricted. For schemes with $\\\\\\\\Delta F$ restricted to 0.25% per
-
Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice
Hairmansis, Aris
2014-08-14
Background Soil salinity is an abiotic stress wide spread in rice producing areas, limiting both plant growth and yield. The development of salt-tolerant rice requires efficient and high-throughput screening techniques to identify promising lines for salt affected areas. Advances made in image-based phenotyping techniques provide an opportunity to use non-destructive imaging to screen for salinity tolerance traits in a wide range of germplasm in a reliable, quantitative and efficient way. However, the application of image-based phenotyping in the development of salt-tolerant rice remains limited. Results A non-destructive image-based phenotyping protocol to assess salinity tolerance traits of two rice cultivars (IR64 and Fatmawati) has been established in this study. The response of rice to different levels of salt stress was quantified over time based on total shoot area and senescent shoot area, calculated from visible red-green-blue (RGB) and fluorescence images. The response of rice to salt stress (50, 75 and 100 mM NaCl) could be clearly distinguished from the control as indicated by the reduced increase of shoot area. The salt concentrations used had only a small effect on the growth of rice during the initial phase of stress, the shoot Na+ accumulation independent phase termed the ‘osmotic stress’ phase. However, after 20 d of treatment, the shoot area of salt stressed plants was reduced compared with non-stressed plants. This was accompanied by a significant increase in the concentration of Na+ in the shoot. Variation in the senescent area of the cultivars IR64 and Fatmawati in response to a high concentration of Na+ in the shoot indicates variation in tissue tolerance mechanisms between the cultivars. Conclusions Image analysis has the potential to be used for high-throughput screening procedures in the development of salt-tolerant rice. The ability of image analysis to discriminate between the different aspects of salt stress (shoot ion
-
Modeling of chromosome intermingling by partially overlapping uniform random polygons.
Blackstone, T; Scharein, R; Borgo, B; Varela, R; Diao, Y; Arsuaga, J
2011-03-01
During the early phase of the cell cycle the eukaryotic genome is organized into chromosome territories. The geometry of the interface between any two chromosomes remains a matter of debate and may have important functional consequences. The Interchromosomal Network model (introduced by Branco and Pombo) proposes that territories intermingle along their periphery. In order to partially quantify this concept we here investigate the probability that two chromosomes form an unsplittable link. We use the uniform random polygon as a crude model for chromosome territories and we model the interchromosomal network as the common spatial region of two overlapping uniform random polygons. This simple model allows us to derive some rigorous mathematical results as well as to perform computer simulations easily. We find that the probability that one uniform random polygon of length n that partially overlaps a fixed polygon is bounded below by 1 − O(1/√n). We use numerical simulations to estimate the dependence of the linking probability of two uniform random polygons (of lengths n and m, respectively) on the amount of overlapping. The degree of overlapping is parametrized by a parameter [Formula: see text] such that [Formula: see text] indicates no overlapping and [Formula: see text] indicates total overlapping. We propose that this dependence relation may be modeled as f (ε, m, n) = [Formula: see text]. Numerical evidence shows that this model works well when [Formula: see text] is relatively large (ε ≥ 0.5). We then use these results to model the data published by Branco and Pombo and observe that for the amount of overlapping observed experimentally the URPs have a non-zero probability of forming an unsplittable link.
-
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease
Groza, Tudor; Köhler, Sebastian; Moldenhauer, Dawid; Vasilevsky, Nicole; Baynam, Gareth; Zemojtel, Tomasz; Schriml, Lynn Marie; Kibbe, Warren Alden; Schofield, Paul N.; Beck, Tim; Vasant, Drashtti; Brookes, Anthony J.; Zankl, Andreas; Washington, Nicole L.; Mungall, Christopher J.; Lewis, Suzanna E.; Haendel, Melissa A.; Parkinson, Helen; Robinson, Peter N.
2015-01-01
The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available. PMID:26119816
-
Božić-Antić, Ivana; Ilić, Dušan; Bjekić-Macut, Jelica; Bogavac, Tamara; Vojnović-Milutinović, Danijela; Kastratovic-Kotlica, Biljana; Milić, Nataša; Stanojlović, Olivera; Andrić, Zoran; Macut, Djuro
2016-12-01
There are limited data on cardiometabolic risk factors and the prevalence of metabolic syndrome (MetS) across the different PCOS phenotypes in Caucasian population. Lipid accumulation product (LAP) is a clinical surrogate marker that could be used for evaluation of MetS in clinical practice. The aim of the study was to analyze metabolic characteristics and the ability of LAP to predict MetS in different PCOS phenotypes. Cross-sectional clinical study analyzing 365 women with PCOS divided into four phenotypes according to the ESHRE/ASRM criteria, and 125 healthy BMI-matched controls. In all subjects, LAP was determined and MetS was diagnosed according to the National Cholesterol Education Program/Adult Treatment Panel III (NCEP-ATP III), the International Diabetes Federation (IDF) and the Joint Interim Statement (JIS) criteria. Logistic regression and ROC curve analyses were used to determine predictors of MetS in each PCOS phenotype. All analyses were performed with age and BMI adjustment. All PCOS phenotypes in comparison to controls had higher prevalence of MetS assessed by NCEP-ATP III criteria, and only classic phenotypes when IDF and JIS criteria were used. All phenotypes had the same prevalence of MetS irrespective of used definition. LAP and exhibited the highest diagnostic accuracy and was an independent predictor of MetS in all phenotypes. LAP is an independent and accurate clinical determinant of MetS in all PCOS phenotypes in our Caucasian population. All PCOS phenotypes, including non-classic ones, are metabolically challenged and with cardiovascular risk, particularly phenotype B. © 2016 European Society of Endocrinology.
-
Emerging semantics to link phenotype and environment
Directory of Open Access Journals (Sweden)
Anne E. Thessen
2015-12-01
Full Text Available Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1 use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2 two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3 two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE and the Biological Collections Ontology (BCO; these provide a starting point for the development of a data model linking phenotypes and environments.
-
Illusion induced overlapped optics.
Zang, XiaoFei; Shi, Cheng; Li, Zhou; Chen, Lin; Cai, Bin; Zhu, YiMing; Zhu, HaiBin
2014-01-13
The traditional transformation-based cloak seems like it can only hide objects by bending the incident electromagnetic waves around the hidden region. In this paper, we prove that invisible cloaks can be applied to realize the overlapped optics. No matter how many in-phase point sources are located in the hidden region, all of them can overlap each other (this can be considered as illusion effect), leading to the perfect optical interference effect. In addition, a singular parameter-independent cloak is also designed to obtain quasi-overlapped optics. Even more amazing of overlapped optics is that if N identical separated in-phase point sources covered with the illusion media, the total power outside the transformation region is N2I0 (not NI0) (I0 is the power of just one point source, and N is the number point sources), which seems violating the law of conservation of energy. A theoretical model based on interference effect is proposed to interpret the total power of these two kinds of overlapped optics effects. Our investigation may have wide applications in high power coherent laser beams, and multiple laser diodes, and so on.
-
Genome-wide association analyses of expression phenotypes.
Chen, Gary K; Zheng, Tian; Witte, John S; Goode, Ellen L; Gao, Lei; Hu, Pingzhao; Suh, Young Ju; Suktitipat, Bhoom; Szymczak, Silke; Woo, Jung Hoon; Zhang, Wei
2007-01-01
A number of issues arise when analyzing the large amount of data from high-throughput genotype and expression microarray experiments, including design and interpretation of genome-wide association studies of expression phenotypes. These issues were considered by contributions submitted to Group 1 of the Genetic Analysis Workshop 15 (GAW15), which focused on the association of quantitative expression data. These contributions evaluated diverse hypotheses, including those relevant to cancer and obesity research, and used various analytic techniques, many of which were derived from information theory. Several observations from these reports stand out. First, one needs to consider the genetic model of the trait of interest and carefully select which single nucleotide polymorphisms and individuals are included early in the design stage of a study. Second, by targeting specific pathways when analyzing genome-wide data, one can generate more interpretable results than agnostic approaches. Finally, for datasets with small sample sizes but a large number of features like the Genetic Analysis Workshop 15 dataset, machine learning approaches may be more practical than traditional parametric approaches. (c) 2007 Wiley-Liss, Inc.
-
Hirschtritt, M. E.; Darrow, S. M.; Illmann, C.; Osiecki, L.; Grados, M.; Sandor, P.; Dion, Y.; King, R. A.; Pauls, D.; Budman, C. L.; Cath, D. C.; Greenberg, E.; Lyon, G. J.; Yu, D.; McGrath, L. M.; McMahon, W. M.; Lee, P. C.; Delucchi, K. L.; Scharf, J. M.; Mathews, C. A.
Background. The unique phenotypic and genetic aspects of obsessive-compulsive (OCD) and attention-deficit/hyperactivity disorder (ADHD) among individuals with Tourette syndrome (TS) are not well characterized. Here, we examine symptom patterns and heritability of OCD and ADHD in TS families. Method.
-
Awlia, Mariam
2016-09-28
Reproducible and efficient high-throughput phenotyping approaches, combined with advances in genome sequencing, are facilitating the discovery of genes affecting plant performance. Salinity tolerance is a desirable trait that can be achieved through breeding, where most have aimed at selecting for plants that perform effective ion exclusion from the shoots. To determine overall plant performance under salt stress, it is helpful to investigate several plant traits collectively in one experimental setup. Hence, we developed a quantitative phenotyping protocol using a high-throughput phenotyping system, with RGB and chlorophyll fluorescence (ChlF) imaging, which captures the growth, morphology, color and photosynthetic performance of Arabidopsis thaliana plants in response to salt stress. We optimized our salt treatment by controlling the soil-water content prior to introducing salt stress. We investigated these traits over time in two accessions in soil at 150, 100, or 50 mM NaCl to find that the plants subjected to 100 mM NaCl showed the most prominent responses in the absence of symptoms of severe stress. In these plants, salt stress induced significant changes in rosette area and morphology, but less prominent changes in rosette coloring and photosystem II efficiency. Clustering of ChlF traits with plant growth of nine accessions maintained at 100 mM NaCl revealed that in the early stage of salt stress, salinity tolerance correlated with non-photochemical quenching processes and during the later stage, plant performance correlated with quantum yield. This integrative approach allows the simultaneous analysis of several phenotypic traits. In combination with various genetic resources, the phenotyping protocol described here is expected to increase our understanding of plant performance and stress responses, ultimately identifying genes that improve plant performance in salt stress conditions.
-
Overlapping structures in sensory-motor mappings.
Directory of Open Access Journals (Sweden)
Kevin Earland
Full Text Available This paper examines a biologically-inspired representation technique designed for the support of sensory-motor learning in developmental robotics. An interesting feature of the many topographic neural sheets in the brain is that closely packed receptive fields must overlap in order to fully cover a spatial region. This raises interesting scientific questions with engineering implications: e.g. is overlap detrimental? does it have any benefits? This paper examines the effects and properties of overlap between elements arranged in arrays or maps. In particular we investigate how overlap affects the representation and transmission of spatial location information on and between topographic maps. Through a series of experiments we determine the conditions under which overlap offers advantages and identify useful ranges of overlap for building mappings in cognitive robotic systems. Our motivation is to understand the phenomena of overlap in order to provide guidance for application in sensory-motor learning robots.
-
International Nuclear Information System (INIS)
Sciurano, R.; Rodriguero, M.; Gomez Cendra, P.; Vilardi, J.; Segura, D.; Cladera, J.L.; Allinghi, Armando
2007-01-01
Despite the interest in applying environmentally friendly control methods such as sterile insect technique (SIT) against Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae), information about its biology, taxonomy, and behavior is still insufficient. To increase this information, the present study aims to evaluate the performance of wild flies under field cage conditions through the study of sexual competitiveness among males (sexual selection). A wild population from Horco Molle, Tucuman, Argentina was sampled. Mature virgin males and females were released into outdoor field cages to compete for mating. Morphometric analyses were applied to determine the relationship between the multivariate phenotype and copulatory success. Successful and unsuccessful males were measured for 8 traits: head width (HW), face width (FW), eye length (EL), thorax length (THL), wing length (WL), wing width (WW), femur length (FL), and tibia length (TIL). Combinations of different multivariate statistical methods and graphical analyses were used to evaluate sexual selection on male phenotype. The results indicated that wing width and thorax length would be the most probable targets of sexual selection. They describe a non-linear association between expected fitness and each of these 2 traits. This non-linear relation suggests that observed selection could maintain the diversity related to body size. (author) [es
-
Pinto, Rebecca; Rijsdijk, Fruhling; Ronald, Angelica; Asherson, Philip; Kuntsi, Jonna
2016-02-01
Attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorders (ASDs) frequently co-occur. However, due to previous exclusionary diagnostic criteria, little is known about the underlying causes of this covariation. Twin studies assessing ADHD symptoms and autistic-like traits (ALTs) suggest substantial genetic overlap, but have largely failed to take into account the genetic heterogeneity of symptom subscales. This study aimed to clarify the phenotypic and genetic relations between ADHD and ASD by distinguishing between symptom subscales that characterise the two disorders. Moreover, we aimed to investigate whether ADHD-related cognitive impairments show a relationship with ALT symptom subscales; and whether potential shared cognitive impairments underlie the genetic risk shared between the ADHD and ALT symptoms. Multivariate structural equation modelling was conducted on a population-based sample of 1312 twins aged 7-10. Social-communication ALTs correlated moderately with both ADHD symptom domains (phenotypic correlations around 0.30) and showed substantial genetic overlap with both inattention and hyperactivity-impulsivity (genetic correlation = 0.52 and 0.44, respectively). In addition to previously reported associations with ADHD traits, reaction time variability (RTV) showed significant phenotypic (0.18) and genetic (0.32) association with social-communication ALTs. RTV captured a significant proportion (24 %) of the genetic influences shared between inattention and social-communication ALTs. Our findings suggest that social-communication ALTs underlie the previously observed phenotypic and genetic covariation between ALTs and ADHD symptoms. RTV is not specific to ADHD symptoms, but is also associated with social-communication ALTs and can, in part, contribute to an explanation of the co-occurrence of ASD and ADHD.
-
Colorectal Cancer "Methylator Phenotype": Fact or Artifact?
Directory of Open Access Journals (Sweden)
Charles Anacleto
2005-04-01
Full Text Available It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI. We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.
-
[Symptom overlaps between functional heartburn, functional dyspepsia, and irritable bowel syndrome].
2014-05-01
To determine symptom overlaps between functional heartburn (FH), functional dyspepsia (FD), and irritable bowel syndrome (IBS). One hundred and ten patients with frequent heartburn but no mucosa breakage under endoscopy were enrolled consecutively. They were required to fill out a questionnaire. The overlapped symptoms of FD and IBS symptoms were screened using Rome ill criteria. The participants were also examined using Hamilton anxiety scale/Hamilton depression scale. All of the participants were followed with 24 h esophageal multichannel intra-luminal impedance monitoring with pH sensor (MII-pH) monitoring and proton pump inhibitor (PPI) trials. The participants were divided into non-erosive reflux disease (NERD) and FH groups. The prevalence of symptom overlaps FD and IBS, between NERD and FH groups was analyzed. Women were more likely to present with FH than with NERD (P heartburn symptom had FD symptoms; 31 (28.2%) had IBS symptoms, and 10 (9.09%) had both FD and IBS symptoms. Patients with FH were more likely to have symptom overlaps of FD and IBS than those with NERD (62% vs. 35%, 48% vs. 11.7%, respectively; P 0.05). IBS-diarrhea was also slightly more likely to have overlapped NERD and FH symptoms than IBS-constipation. Again, the difference was not significant (16.4% vs. 11.8%, P > 0.05). Female, higher prevalence of anxiety and depression, overlapped FD and IBS symptoms are more likely to appear in FH patients than in NERD patients.
-
Non-Rutherford backscattering microscopy using 25 MeV protons
Energy Technology Data Exchange (ETDEWEB)
Peeper, Katrin, E-mail: katrin.peeper@unibw.de [Universitaet der Bundeswehr, Angewandte Physik und Messtechnik, Werner-Heisenberg-Weg 39, 85577 Neubiberg (Germany); Moser, Marcus; Reichart, Patrick; Dollinger, Guenther [Universitaet der Bundeswehr, Angewandte Physik und Messtechnik, Werner-Heisenberg-Weg 39, 85577 Neubiberg (Germany)
2012-02-15
Protons at energies between 10 and 25 MeV are a very sensitive probe for hydrogen using coincident proton-proton scattering with the possibility for depth profiling samples up to several 100 {mu}m thickness. At the Munich microprobe SNAKE we have developed this method for sensitive 3D hydrogen microscopy . In parallel to sensitive 3D hydrogen microscopy by proton-proton scattering we introduce a non-Rutherford backscattering analysis utilizing 25 MeV protons in order to obtain 3D depth profiles of all major elements. We present energy spectra of backscattered protons at various thin and thick film samples of pure elements which we use as fingerprints to analyse more complex materials like minerals or metals. It is due to the low stopping power of the high energy protons that the depth profiles of several elements do not or do only partially overlap when analysing freestanding samples with thicknesses in the 100 {mu}m range. The merit of our method is that signals of the light elements may not be affected by heavier matrix elements. Analysing thin films smaller than 5 {mu}m we have achieved a mass resolution of {Delta}A/A{<=}1/28 for non-overlapping mass signals utilizing a 5 mm thick Si(Li)-detector.
-
Advanced phenotyping and phenotype data analysis for the plant growth and development study
Directory of Open Access Journals (Sweden)
Md. Matiur eRahaman
2015-08-01
Full Text Available Due to increase in the consumption of food, feed, fuel and to ensure global food security for rapidly growing human population, there is need to breed high yielding crops that can adapt to future climate. To solve these global issues, novel approaches are required to provide quantitative phenotypes to elucidate the genetic basis of agriculturally import traits and to screen germplasm with super performance in function under resource-limited environment. At present, plant phenomics has offered and integrated suite technologies for understanding the complete set of phenotypes of plants, towards the progression of the full characteristics of plants with whole sequenced genomes. In this aspect, high-throughput phenotyping platforms have been developed that enables to capture extensive and intensive phenotype data from non-destructive imaging over time. These developments advance our view on plant growth and performance with responses to the changing climate and environment. In this paper, we present a brief review on currently developed high-throughput plant phenotyping infrastructures based on imaging techniques and corresponding principles for phenotype data analysis.
-
Accurate phenotyping: Reconciling approaches through Bayesian model averaging.
Directory of Open Access Journals (Sweden)
Carla Chia-Ming Chen
Full Text Available Genetic research into complex diseases is frequently hindered by a lack of clear biomarkers for phenotype ascertainment. Phenotypes for such diseases are often identified on the basis of clinically defined criteria; however such criteria may not be suitable for understanding the genetic composition of the diseases. Various statistical approaches have been proposed for phenotype definition; however our previous studies have shown that differences in phenotypes estimated using different approaches have substantial impact on subsequent analyses. Instead of obtaining results based upon a single model, we propose a new method, using Bayesian model averaging to overcome problems associated with phenotype definition. Although Bayesian model averaging has been used in other fields of research, this is the first study that uses Bayesian model averaging to reconcile phenotypes obtained using multiple models. We illustrate the new method by applying it to simulated genetic and phenotypic data for Kofendred personality disorder-an imaginary disease with several sub-types. Two separate statistical methods were used to identify clusters of individuals with distinct phenotypes: latent class analysis and grade of membership. Bayesian model averaging was then used to combine the two clusterings for the purpose of subsequent linkage analyses. We found that causative genetic loci for the disease produced higher LOD scores using model averaging than under either individual model separately. We attribute this improvement to consolidation of the cores of phenotype clusters identified using each individual method.
-
Efficient methods for overlapping group lasso.
Yuan, Lei; Liu, Jun; Ye, Jieping
2013-09-01
The group Lasso is an extension of the Lasso for feature selection on (predefined) nonoverlapping groups of features. The nonoverlapping group structure limits its applicability in practice. There have been several recent attempts to study a more general formulation where groups of features are given, potentially with overlaps between the groups. The resulting optimization is, however, much more challenging to solve due to the group overlaps. In this paper, we consider the efficient optimization of the overlapping group Lasso penalized problem. We reveal several key properties of the proximal operator associated with the overlapping group Lasso, and compute the proximal operator by solving the smooth and convex dual problem, which allows the use of the gradient descent type of algorithms for the optimization. Our methods and theoretical results are then generalized to tackle the general overlapping group Lasso formulation based on the l(q) norm. We further extend our algorithm to solve a nonconvex overlapping group Lasso formulation based on the capped norm regularization, which reduces the estimation bias introduced by the convex penalty. We have performed empirical evaluations using both a synthetic and the breast cancer gene expression dataset, which consists of 8,141 genes organized into (overlapping) gene sets. Experimental results show that the proposed algorithm is more efficient than existing state-of-the-art algorithms. Results also demonstrate the effectiveness of the nonconvex formulation for overlapping group Lasso.
-
Infra-red thermography for high throughput field phenotyping in Solanum tuberosum.
Directory of Open Access Journals (Sweden)
Ankush Prashar
Full Text Available The rapid development of genomic technology has made high throughput genotyping widely accessible but the associated high throughput phenotyping is now the major limiting factor in genetic analysis of traits. This paper evaluates the use of thermal imaging for the high throughput field phenotyping of Solanum tuberosum for differences in stomatal behaviour. A large multi-replicated trial of a potato mapping population was used to investigate the consistency in genotypic rankings across different trials and across measurements made at different times of day and on different days. The results confirmed a high degree of consistency between the genotypic rankings based on relative canopy temperature on different occasions. Genotype discrimination was enhanced both through normalising data by expressing genotype temperatures as differences from image means and through the enhanced replication obtained by using overlapping images. A Monte Carlo simulation approach was used to confirm the magnitude of genotypic differences that it is possible to discriminate. The results showed a clear negative association between canopy temperature and final tuber yield for this population, when grown under ample moisture supply. We have therefore established infrared thermography as an easy, rapid and non-destructive screening method for evaluating large population trials for genetic analysis. We also envisage this approach as having great potential for evaluating plant response to stress under field conditions.
-
Depression, anxiety and somatization in primary care: syndrome overlap and functional impairment.
Löwe, Bernd; Spitzer, Robert L; Williams, Janet B W; Mussell, Monika; Schellberg, Dieter; Kroenke, Kurt
2008-01-01
To determine diagnostic overlap of depression, anxiety and somatization as well as their unique and overlapping contribution to functional impairment. Two thousand ninety-one consecutive primary care clinic patients participated in a multicenter cross-sectional survey in 15 primary care clinics in the United States (participation rate, 92%). Depression, anxiety, somatization and functional impairment were assessed using validated scales from the Patient Health Questionnaire (PHQ) (PHQ-8, eight-item depression module; GAD-7, seven-item Generalized Anxiety Disorder Scale; and PHQ-15, 15-item somatic symptom scale) and the Short-Form General Health Survey (SF-20). Multiple linear regression analyses were used to investigate unique and overlapping associations of depression, anxiety and somatization with functional impairment. In over 50% of cases, comorbidities existed between depression, anxiety and somatization. The contribution of the commonalities of depression, anxiety and somatization to functional impairment substantially exceeded the contribution of their independent parts. Nevertheless, depression, anxiety and somatization did have important and individual effects (i.e., separate from their overlap effect) on certain areas of functional impairment. Given the large syndrome overlap, a potential consideration for future diagnostic classification would be to describe basic diagnostic criteria for a single overarching disorder and to optionally code additional diagnostic features that allow a more detailed classification into specific depressive, anxiety and somatoform subtypes.
-
Zheng, Ling; Chen, Yan; Elhanan, Gai; Perl, Yehoshua; Geller, James; Ochs, Christopher
2018-05-28
In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of "complex") in an ontology are more likely to exhibit errors than other concepts. Thus, such complex concepts often become fertile ground for quality assurance (QA) in ontologies. They should be audited first. One example of complex concepts is given by "overlapping concepts" (to be defined below.) Historically, a different auditing methodology had to be developed for every single ontology. For better scalability and efficiency, it is desirable to identify family-wide QA methodologies. Each such methodology would be applicable to a whole family of similar ontologies. In past research, we had divided the 685 ontologies of BioPortal into families of structurally similar ontologies. We showed for four ontologies of the same large family in BioPortal that "overlapping concepts" are indeed statistically significantly more likely to exhibit errors. In order to make an authoritative statement concerning the success of "overlapping concepts" as a methodology for a whole family of similar ontologies (or of large subhierarchies of ontologies), it is necessary to show that "overlapping concepts" have a higher likelihood of errors for six out of six ontologies of the family. In this paper, we are demonstrating for two more ontologies that "overlapping concepts" can successfully predict groups of concepts with a higher error rate than concepts from a control group. The fifth ontology is the Neoplasm subhierarchy of the National Cancer Institute thesaurus (NCIt). The sixth ontology is the Infectious Disease subhierarchy of SNOMED CT. We demonstrate quality assurance results for both of them. Furthermore, in this paper we observe two novel, important, and useful phenomena during quality assurance of "overlapping concepts." First, an erroneous "overlapping concept" can help with discovering other erroneous "non-overlapping concepts" in its vicinity
-
Weatherhead, Elizabeth C.; Harder, Jerald; Araujo-Pradere, Eduardo A.; Bodeker, Greg; English, Jason M.; Flynn, Lawrence E.; Frith, Stacey M.; Lazo, Jeffrey K.; Pilewskie, Peter; Weber, Mark; Woods, Thomas N.
2017-12-01
Sensors on satellites provide unprecedented understanding of the Earth's climate system by measuring incoming solar radiation, as well as both passive and active observations of the entire Earth with outstanding spatial and temporal coverage. A common challenge with satellite observations is to quantify their ability to provide well-calibrated, long-term, stable records of the parameters they measure. Ground-based intercomparisons offer some insight, while reference observations and internal calibrations give further assistance for understanding long-term stability. A valuable tool for evaluating and developing long-term records from satellites is the examination of data from overlapping satellite missions. This paper addresses how the length of overlap affects the ability to identify an offset or a drift in the overlap of data between two sensors. Ozone and temperature data sets are used as examples showing that overlap data can differ by latitude and can change over time. New results are presented for the general case of sensor overlap by using Solar Radiation and Climate Experiment (SORCE) Spectral Irradiance Monitor (SIM) and Solar Stellar Irradiance Comparison Experiment (SOLSTICE) solar irradiance data as an example. To achieve a 1 % uncertainty in estimating the offset for these two instruments' measurement of the Mg II core (280 nm) requires approximately 5 months of overlap. For relative drift to be identified within 0.1 % yr-1 uncertainty (0.00008 W m-2 nm-1 yr-1), the overlap for these two satellites would need to be 2.5 years. Additional overlap of satellite measurements is needed if, as is the case for solar monitoring, unexpected jumps occur adding uncertainty to both offsets and drifts; the additional length of time needed to account for a single jump in the overlap data may be as large as 50 % of the original overlap period in order to achieve the same desired confidence in the stability of the merged data set. Results presented here are directly
-
Diet composition, quality and overlap of sympatric American pronghorn and gemsbok
Cain, James W.; Avery, Mindi M.; Caldwell, Colleen A.; Abbott, Laurie B.; Holechek, Jerry L.
2017-01-01
Species with a long evolutionary history of sympatry often have mechanisms for resource partitioning that reduce competition. However, introduced non-native ungulates often compete with native ungulates and competitive effects can be exacerbated in arid regions due to low primary productivity. Our objectives were to characterize diet composition, quality, and overlap between American pronghorn Antilocapra americana and introduced non-native gemsbok Oryx gazella in southcentral New Mexico, USA. Severe drought occurred between 2010 and 2011, which allowed us to evaluate drought impacts on diet composition, quality, and overlap. Using feces collected from each species, we assessed diet composition and overlap with microhistological analysis and diet quality using fecal nitrogen (FN) and fecal 2,6-diaminopimelic acid (FDAPA). Pronghorn diet was primarily composed of shrubs in the cool—dry season (64.5%) then shifted to forbs in the warm—dry (64.7%) and warm—wet (54.1%) seasons. Pronghorn diet also shifted to shrubs during drought (50.7%). Gemsbok diets were evenly distributed across forage types. Fifty-three percent of the species of plants consumed by pronghorn and gemsbok were shared; diet overlap averaged 0.44 ± 0.06 (SE) and 0.49 ± 0.06 during the warm—dry seasons of 2010 and 2011, respectively. During drought, key forage species shared between pronghorn and gemsbok included yucca Yucca spp., prickly pear Opuntia spp., globemallow Sphaeralcea coccinea and horsenettle Solanum elaeagnifolium, comprising 50% of the pronghorn and 40% of the gemsbok diets. Fecal nitrogen and FDAPA decreased in pronghorn by 26% and 27% between the warm—dry season of 2010 (non-drought) and the warm—dry season of 2011 (drought), respectively. Drought had little effect on dietary quality for gemsbok. Gemsbok can use forage with lower nutritional content giving them an advantage over pronghorn, particularly during drought periods. Pronghorn are more dependent upon
-
Overlap between functional abdominal pain disorders and organic diseases in children.
Langshaw, A H; Rosen, J M; Pensabene, L; Borrelli, O; Salvatore, S; Thapar, N; Concolino, D; Saps, M
2018-04-02
Functional abdominal pain disorders are highly prevalent in children. These disorders can be present in isolation or combined with organic diseases, such as celiac disease and inflammatory bowel diseases. Intestinal inflammation (infectious and non-infectious) predisposes children to the development of visceral hypersensitivity that can manifest as functional abdominal pain disorders, including irritable bowel syndrome. The new onset of irritable bowel syndrome symptoms in a patient with an underlying organic disease, such as inflammatory bowel disease, is clinically challenging, given that the same symptomatology may represent a flare-up of the inflammatory bowel disease or an overlapping functional abdominal pain disorder. Similarly, irritable bowel syndrome symptoms in a child previously diagnosed with celiac disease may occur due to poorly controlled celiac disease or the overlap with a functional abdominal pain disorder. There is little research on the overlap of functional abdominal disorders with organic diseases in children. Studies suggest that the overlap between functional abdominal pain disorders and inflammatory bowel disease is more common in adults than in children. The causes for these differences in prevalence are unknown. Only a handful of studies have been published on the overlap between celiac disease and functional abdominal pain disorders in children. The present article provides a review of the literature on the overlap between celiac disease, inflammatory bowel disease, and functional abdominal pain disorders in children and establish comparisons with studies conducted on adults. Copyright © 2018 Asociación Mexicana de Gastroenterología. Publicado por Masson Doyma México S.A. All rights reserved.
-
Technology initiatives with government/business overlap
Knapp, Robert H., Jr.
2015-03-01
Three important present-day technology development settings involve significant overlap between government and private sectors. The Advanced Research Project Agency for Energy (ARPA-E) supports a wide range of "high risk, high return" projects carried out in academic, non-profit or private business settings. The Materials Genome Initiative (MGI), based in the White House, aims at radical acceleration of the development process for advanced materials. California public utilities such as Pacific Gas & Electric operate under a structure of financial returns and political program mandates that make them arms of public policy as much as independent businesses.
-
Ripple artifact reduction using slice overlap in slice encoding for metal artifact correction.
den Harder, J Chiel; van Yperen, Gert H; Blume, Ulrike A; Bos, Clemens
2015-01-01
Multispectral imaging (MSI) significantly reduces metal artifacts. Yet, especially in techniques that use gradient selection, such as slice encoding for metal artifact correction (SEMAC), a residual ripple artifact may be prominent. Here, an analysis is presented of the ripple artifact and of slice overlap as an approach to reduce the artifact. The ripple artifact was analyzed theoretically to clarify its cause. Slice overlap, conceptually similar to spectral bin overlap in multi-acquisition with variable resonances image combination (MAVRIC), was achieved by reducing the selection gradient and, thus, increasing the slice profile width. Time domain simulations and phantom experiments were performed to validate the analyses and proposed solution. Discontinuities between slices are aggravated by signal displacement in the frequency encoding direction in areas with deviating B0. Specifically, it was demonstrated that ripple artifacts appear only where B0 varies both in-plane and through-plane. Simulations and phantom studies of metal implants confirmed the efficacy of slice overlap to reduce the artifact. The ripple artifact is an important limitation of gradient selection based MSI techniques, and can be understood using the presented simulations. At a scan-time penalty, slice overlap effectively addressed the artifact, thereby improving image quality near metal implants. © 2014 Wiley Periodicals, Inc.
-
Phenotypic spectrum associated with mutations of the mitochondrial polymerase gamma gene.
Horvath, Rita; Hudson, Gavin; Ferrari, Gianfrancesco; Fütterer, Nancy; Ahola, Sofia; Lamantea, Eleonora; Prokisch, Holger; Lochmüller, Hanns; McFarland, Robert; Ramesh, V; Klopstock, Thomas; Freisinger, Peter; Salvi, Fabrizio; Mayr, Johannes A; Santer, Rene; Tesarova, Marketa; Zeman, Jiri; Udd, Bjarne; Taylor, Robert W; Turnbull, Douglass; Hanna, Michael; Fialho, Doreen; Suomalainen, Anu; Zeviani, Massimo; Chinnery, Patrick F
2006-07-01
Mutations in the gene coding for the catalytic subunit of the mitochondrial DNA (mtDNA) polymerase gamma (POLG1) have recently been described in patients with diverse clinical presentations, revealing a complex relationship between genotype and phenotype in patients and their families. POLG1 was sequenced in patients from different European diagnostic and research centres to define the phenotypic spectrum and advance understanding of the recurrence risks. Mutations were identified in 38 cases, with the majority being sporadic compound heterozygotes. Eighty-nine DNA sequence changes were identified, including 2 predicted to alter a splice site, 1 predicted to cause a premature stop codon and 13 predicted to cause novel amino acid substitutions. The majority of children had a mutation in the linker region, often 1399G-->A (A467T), and a mutation affecting the polymerase domain. Others had mutations throughout the gene, and 11 had 3 or more substitutions. The clinical presentation ranged from the neonatal period to late adult life, with an overlapping phenotypic spectrum from severe encephalopathy and liver failure to late-onset external ophthalmoplegia, ataxia, myopathy and isolated muscle pain or epilepsy. There was a strong gender bias in children, with evidence of an environmental interaction with sodium valproate. POLG1 mutations cause an overlapping clinical spectrum of disease with both dominant and recessive modes of inheritance. 1399G-->A (A467T) is common in children, but complete POLG1 sequencing is required to identify multiple mutations that can have complex implications for genetic counselling.
-
A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks
Directory of Open Access Journals (Sweden)
Xuezhong Zhou
2018-05-01
Full Text Available The International Classification of Diseases (ICD relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. Keywords: Disease taxonomy, Network medicine, Disease phenotypes, Molecular profiles, Precision medicine
-
DEFF Research Database (Denmark)
St Pourcain, B; Robinson, E B; Anttila, V
2017-01-01
Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early childhood, whereas most symptoms characteristic......-developing youth (Avon Longitudinal Study of Parents and Children, N⩽5553, longitudinal assessments at 8, 11, 14 and 17 years) using the Social Communication Disorder Checklist. Data on clinical ASD (PGC-ASD: 5305 cases, 5305 pseudo-controls; iPSYCH-ASD: 7783 cases, 11 359 controls) and schizophrenia (PGC-SCZ2: 34...... 241 cases, 45 604 controls, 1235 trios) were either obtained through the Psychiatric Genomics Consortium (PGC) or the Danish iPSYCH project. Overlap in genetic influences between ASD and social communication difficulties during development decreased with age, both in the PGC-ASD and the iPSYCH-ASD...
-
Hsu, Chi-Pin; Lin, Shang-Chih; Shih, Kao-Shang; Huang, Chang-Hung; Lee, Chian-Her
2014-12-01
After total knee replacement, the model-based Roentgen stereophotogrammetric analysis (RSA) technique has been used to monitor the status of prosthetic wear, misalignment, and even failure. However, the overlap of the prosthetic outlines inevitably increases errors in the estimation of prosthetic poses due to the limited amount of available outlines. In the literature, quite a few studies have investigated the problems induced by the overlapped outlines, and manual adjustment is still the mainstream. This study proposes two methods to automate the image processing of overlapped outlines prior to the pose registration of prosthetic models. The outline-separated method defines the intersected points and segments the overlapped outlines. The feature-recognized method uses the point and line features of the remaining outlines to initiate registration. Overlap percentage is defined as the ratio of overlapped to non-overlapped outlines. The simulated images with five overlapping percentages are used to evaluate the robustness and accuracy of the proposed methods. Compared with non-overlapped images, overlapped images reduce the number of outlines available for model-based RSA calculation. The maximum and root mean square errors for a prosthetic outline are 0.35 and 0.04 mm, respectively. The mean translation and rotation errors are 0.11 mm and 0.18°, respectively. The errors of the model-based RSA results are increased when the overlap percentage is beyond about 9%. In conclusion, both outline-separated and feature-recognized methods can be seamlessly integrated to automate the calculation of rough registration. This can significantly increase the clinical practicability of the model-based RSA technique.
-
Koblizek, Vladimir; Chlumsky, Jan; Zindr, Vladimir; Neumannova, Katerina; Zatloukal, Jakub; Zak, Jaroslav; Sedlak, Vratislav; Kocianova, Jana; Zatloukal, Jaromir; Hejduk, Karel; Pracharova, Sarka
2013-06-01
COPD is a global concern. Currently, several sets of guidelines, statements and strategies to managing COPD exist around the world. The Czech Pneumological and Phthisiological Society (CPPS) has commissioned an Expert group to draft recommended guidelines for the management of stable COPD. Subsequent revisions were further discussed at the National Consensus Conference (NCC). Reviewers' comments contributed to the establishment of the document's final version. The hallmark of the novel approach to COPD is the integrated evaluation of the patient's lung functions, symptoms, exacerbations and identifications of clinical phenotype(s). The CPPS defines 6 clinically relevant phenotypes: frequent exacerbator, COPD-asthma overlap, COPD-bronchiectasis overlap, emphysematic phenotype, bronchitic phenotype and pulmonary cachexia phenotype. Treatment recommendations can be divided into four steps. 1(st) step = Risk exposure elimination: reduction of smoking and environmental tobacco smoke (ETS), decrease of home and occupational exposure risks. 2(nd) step = Standard treatment: inhaled bronchodilators, regular physical activity, pulmonary rehabilitation, education, inhalation training, comorbidity treatment, vaccination. 3(rd) step = Phenotype-specific therapy: PDE4i, ICS+LABA, LVRS, BVR, AAT augmentation, physiotherapy, mucolytic, ABT. 4(th) step = Care for respiratory insufficiency and terminal COPD: LTOT, lung transplantation, high intensity-NIV and palliative care. Optimal treatment of COPD patients requires an individualised, multidisciplinary approach to the patient's symptoms, clinical phenotypes, needs and wishes. The new Czech COPD guideline reflects and covers these requirements.
-
Procopio, V; Manti, S; Bianco, G; Conti, G; Romeo, A; Maimone, F; Arrigo, T; Cutrupi, M C; Salpietro, C; Cuppari, C
2018-01-30
Uncertainty remains on the pathogenetic mechanisms, model of inheritance as well as genotype-phenotype correlation of FMF disease. To investigate the impact of genetic factors on the FMF phenotype and the disease inheritance model. A total of 107 FMF patients were enrolled. Patients were diagnosed clinically. All patients underwent genetic analysis of the FMF locus on 16p13.3. 9 distinct mutations were detected. Specifically, the 85.98% of patients showed a heterozygous genotype. The most common genotypes were p.Met680Ile/wt and p.Met694Val/wt. The most frequent clinical findings were fever, abdominal pain, joint pain, thoracic pain, and erysipelas-like erythema. Analysis of clinical data did not detect any significant difference in clinical phenotype among heterozygous, homozygous as well as compound homozygous subjects, further supporting the evidence that, contrary to the recessive autosomal inheritance, heterozygous patients fulfilled the criteria of clinical FMF. Moreover, subjects with p.Met694Val/wt and p.Met680Ile/wt genotype reported the most severe clinical phenotype. p.Ala744Ser/wt, p.Glu148Gln/Met680Ile, p.Met680Ile/Met680Ile, p.Met680Ile/Met694Val, p.Pro369Ser/wt, p.Met694Ile/wt, p.Glu148Gln/Glu148Gln, p.Lys695Arg/wt resulted in 100% pathogenicity. The existence of a "non classic" autosomal recessive inheritance as well as of an "atypical" dominant autosomal inheritance with incomplete penetrance and variable expressivity cannot be excluded in FMF. Copyright © 2017 Elsevier B.V. All rights reserved.
-
Birth and death of gene overlaps in vertebrates
Directory of Open Access Journals (Sweden)
Makałowska Izabela
2007-10-01
Full Text Available Abstract Background Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the evolutionary basis of these phenomenon are still not well understood. Here, we present results of the comparative analysis of several vertebrate genomes. The purpose of this study was to examine overlapping genes in the context of their evolution and mechanisms leading to their origin. Results Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution. Analysis of these theoretical scenarios and close examination of genomic sequences revealed new mechanisms leading to the overlaps evolution and confirmed that many of the vertebrate gene overlaps are not conserved. This study also demonstrates that repetitive elements contribute to the overlapping genes origination and, for the first time, that evolutionary events could lead to the loss of an ancient overlap. Conclusion Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes evolution. The major forces in the gene overlaps origination are transposition and exaptation. Our results also imply that origin of overlapping genes is not an issue of saving space and contracting genomes size.
-
Abd El Ghany, Moataz
2016-05-25
Human infections with Salmonella enterica subspecies enterica serovar Senftenberg are often associated with exposure to poultry flocks, farm environments, or contaminated food. The recent emergence of multidrug-resistant isolates has raised public health concerns. In this study, comparative genomics and phenotypic analysis were used to characterize 14 Salmonella Senftenberg clinical isolates recovered from multiple outbreaks in Shenzhen and Shanghai, China, between 2002 and 2011. Single-nucleotide polymorphism analyses identified two phylogenetically distinct clades of S. Senftenberg, designated SC1 and SC2, harboring variations in Salmonella pathogenicity island 1 (SPI-1) and SPI-2 and exhibiting distinct biochemical and phenotypic signatures. Although the two variants shared the same serotype, the SC2 isolates of sequence type 14 (ST14) harbored intact SPI-1 and -2 and hence were characterized by possessing efficient invasion capabilities. In contrast, the SC1 isolates had structural deletion patterns in both SPI-1 and -2 that correlated with an impaired capacity to invade cultured human cells and also the year of their isolation. These atypical SC1 isolates also lacked the capacity to produce hydrogen sulfide. These findings highlight the emergence of atypical Salmonella Senftenberg variants in China and provide genetic validation that variants lacking SPI-1 and regions of SPI-2, which leads to impaired invasion capacity, can still cause clinical disease. These data have identified an emerging public health concern and highlight the need to strengthen surveillance to detect the prevalence and transmission of nontyphoidal Salmonella species.
-
Liu, Jiang-Bo; Feng, Chen-Yi; Deng, Miao; Ge, Dong-Feng; Liu, De-Chun; Mi, Jian-Qiang; Feng, Xiao-Shan
2017-08-01
This retrospective study and meta-analysis was designed to explore the relationship between E-cadherin (E-cad) expression and the molecular subtypes of invasive non-lobular breast cancer, especially in early-stage invasive ductal carcinoma (IDC). A total of 156 post-operative cases of early-stage IDCs were retrospectively collected for the immunohistochemistry (IHC) detection of E-cad expression. The association of E-cad expression with molecular subtypes of early-stage IDCs was analyzed. A literature search was conducted in March 2016 to retrieve publications on E-cad expression in association with molecular subtypes of invasive non-lobular breast cancer, and a meta-analysis was performed to estimate the relational statistics. E-cad was expressed in 82.7% (129/156) of early-stage IDCs. E-cad expression was closely associated with the molecular types of early-stage IDCs (P cancer (TNBC) than in other molecular subtypes (TNBC vs. luminal A: RR = 3.45, 95% CI = 2.79-4.26; TNBC vs. luminal B: RR = 2.41, 95% CI = 1.49-3.90; TNBC vs. HER2-enriched: RR = 1.95, 95% CI = 1.24-3.07). Early-stage IDCs or invasive non-lobular breast cancers with the TNBC molecular phenotype have a higher risk for the loss of E-cad expression than do tumors with non-TNBC molecular phenotypes, suggesting that E-cad expression phenotypes were closely related to molecular subtypes and further studies are needed to clarify the underlying mechanism.
-
Experimental apparatus for overlapping a ground-state cooled ion with ultracold atoms
Meir, Ziv; Sikorsky, Tomas; Ben-shlomi, Ruti; Akerman, Nitzan; Pinkas, Meirav; Dallal, Yehonatan; Ozeri, Roee
2018-03-01
Experimental realizations of charged ions and neutral atoms in overlapping traps are gaining increasing interest due to their wide research application ranging from chemistry at the quantum level to quantum simulations of solid state systems. In this paper, we describe our experimental system in which we overlap a single ground-state cooled ion trapped in a linear Paul trap with a cloud of ultracold atoms such that both constituents are in the ?K regime. Excess micromotion (EMM) currently limits atom-ion interaction energy to the mK energy scale and above. We demonstrate spectroscopy methods and compensation techniques which characterize and reduce the ion's parasitic EMM energy to the ?K regime even for ion crystals of several ions. We further give a substantial review on the non-equilibrium dynamics which governs atom-ion systems. The non-equilibrium dynamics is manifested by a power law distribution of the ion's energy. We also give an overview on the coherent and non-coherent thermometry tools which can be used to characterize the ion's energy distribution after single to many atom-ion collisions.
-
Neuert, Saskia; Nair, Satheesh; Day, Martin R; Doumith, Michel; Ashton, Philip M; Mellor, Kate C; Jenkins, Claire; Hopkins, Katie L; Woodford, Neil; de Pinna, Elizabeth; Godbole, Gauri; Dallman, Timothy J
2018-01-01
Surveillance of antimicrobial resistance (AMR) in non-typhoidal Salmonella enterica (NTS), is essential for monitoring transmission of resistance from the food chain to humans, and for establishing effective treatment protocols. We evaluated the prediction of phenotypic resistance in NTS from genotypic profiles derived from whole genome sequencing (WGS). Genes and chromosomal mutations responsible for phenotypic resistance were sought in WGS data from 3,491 NTS isolates received by Public Health England's Gastrointestinal Bacteria Reference Unit between April 2014 and March 2015. Inferred genotypic AMR profiles were compared with phenotypic susceptibilities determined for fifteen antimicrobials using EUCAST guidelines. Discrepancies between phenotypic and genotypic profiles for one or more antimicrobials were detected for 76 isolates (2.18%) although only 88/52,365 (0.17%) isolate/antimicrobial combinations were discordant. Of the discrepant results, the largest number were associated with streptomycin (67.05%, n = 59). Pan-susceptibility was observed in 2,190 isolates (62.73%). Overall, resistance to tetracyclines was most common (26.27% of isolates, n = 917) followed by sulphonamides (23.72%, n = 828) and ampicillin (21.43%, n = 748). Multidrug resistance (MDR), i.e., resistance to three or more antimicrobial classes, was detected in 848 isolates (24.29%) with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines being the most common MDR profile ( n = 231; 27.24%). For isolates with this profile, all but one were S . Typhimurium and 94.81% ( n = 219) had the resistance determinants bla TEM-1, strA-strB, sul2 and tet (A). Extended-spectrum β-lactamase genes were identified in 41 isolates (1.17%) and multiple mutations in chromosomal genes associated with ciprofloxacin resistance in 82 isolates (2.35%). This study showed that WGS is suitable as a rapid means of determining AMR patterns of NTS for public health surveillance.
-
Krieger, Nancy; Chen, Jarvis T; Waterman, Pamela D; Kosheleva, Anna; Beckfield, Jason
2013-02-01
Most public health literature on trends in population health and health inequities pertains to observed or targeted changes in rates or proportions per year or decade. We explore, in novel analyses, whether additional insight can be gained by using the 'haldane', a metric developed by evolutionary biologists to measure change in traits in standard deviations per generation, thereby enabling meaningful comparisons across species and time periods. We analysed the phenotypic embodied traits of body height, weight and body mass index of US-born White and Black non-Hispanic adults ages 20 to 44 as measured in six large nationally representative population samples spanning from the 1959-1962 National Health Examination Survey I to the 2005-2008 National Health and Nutrition Examination Survey. Setting the former as baseline, we computed the haldane for each outcome for each racial/ethnic group for each survey, overall and stratified by family income quintile. For height, high rates of phenotypic change (haldane ≥ 0.3) occurred chiefly between 1960 and 1980, especially for the Black population in the higher income quintiles. By contrast, for weight, high rates of phenotypic change became evident for both the White and Black populations in the late 1980s and increased thereafter; for body mass index, the shift to high rates of change started in both groups in the late 1990s, especially in the middle income quintiles. Our results support use of the haldane as a supplemental metric to place changes in population health and health inequities in a larger biological and historical context.
-
An extension to artifact-free projection overlaps
International Nuclear Information System (INIS)
Lin, Jianyu
2015-01-01
Purpose: In multipinhole single photon emission computed tomography, the overlapping of projections has been used to increase sensitivity. Avoiding artifacts in the reconstructed image associated with projection overlaps (multiplexing) is a critical issue. In our previous report, two types of artifact-free projection overlaps, i.e., projection overlaps that do not lead to artifacts in the reconstructed image, were formally defined and proved, and were validated via simulations. In this work, a new proposition is introduced to extend the previously defined type-II artifact-free projection overlaps so that a broader range of artifact-free overlaps is accommodated. One practical purpose of the new extension is to design a baffle window multipinhole system with artifact-free projection overlaps. Methods: First, the extended type-II artifact-free overlap was theoretically defined and proved. The new proposition accommodates the situation where the extended type-II artifact-free projection overlaps can be produced with incorrectly reconstructed portions in the reconstructed image. Next, to validate the theory, the extended-type-II artifact-free overlaps were employed in designing the multiplexing multipinhole spiral orbit imaging systems with a baffle window. Numerical validations were performed via simulations, where the corresponding 1-pinhole nonmultiplexing reconstruction results were used as the benchmark for artifact-free reconstructions. The mean square error (MSE) was the metric used for comparisons of noise-free reconstructed images. Noisy reconstructions were also performed as part of the validations. Results: Simulation results show that for noise-free reconstructions, the MSEs of the reconstructed images of the artifact-free multiplexing systems are very similar to those of the corresponding 1-pinhole systems. No artifacts were observed in the reconstructed images. Therefore, the testing results for artifact-free multiplexing systems designed using the
-
Self, D Mitchell; Ilyas, Adeel; Stetler, William R
2018-04-27
Overlapping surgery, a long-standing practice within academic neurosurgery centers nationwide, has recently come under scrutiny from the government and media as potentially harmful to patients. Therefore, the objective of this systematic review and meta-analysis is to determine the safety of overlapping neurosurgical procedures. The authors performed a systematic review and meta-analysis in accordance with PRISMA guidelines. A review of PubMed and Medline databases was undertaken with the search phrase "overlapping surgery AND neurosurgery AND outcomes." Data regarding patient demographics, type of neurosurgical procedure, and outcomes and complications were extracted from each study. The principle summary measure was odds ratio (OR) of the association of overlapping versus non-overlapping surgery with outcomes. The literature search yielded a total of 36 studies, of which 5 studies met inclusion criteria and were included in this study. These studies included a total of 25,764 patients undergoing neurosurgical procedures. Overlapping surgery was associated with an increased likelihood of being discharged home (OR = 1.32; 95% CI 1.20 to 1.44; P < 0.001) and a reduced 30-day unexpected return to the operating room (OR = 0.79; 95% CI 0.72 to 0.87; P < 0.001). Overlapping surgery did not significantly affect OR of length of surgery, 30-day mortality, or 30-day readmission. Overlapping neurosurgical procedures were not associated with worse patient outcomes. Additional, prospective studies are needed to further assess the safety overlapping procedures. Copyright © 2018. Published by Elsevier Inc.
-
Sumner, Emma; Leonard, Hayley C.; Hill, Elisabeth L.
2016-01-01
Motor and social difficulties are often found in children with an autism spectrum disorder (ASD) and with developmental coordination disorder (DCD), to varying degrees. This study investigated the extent of overlap of these problems in children aged 7-10 years who had a diagnosis of either ASD or DCD, compared to typically-developing controls.…
-
Comparative Analyses of Phenotypic Trait Covariation within and among Populations.
Peiman, Kathryn S; Robinson, Beren W
2017-10-01
Many morphological, behavioral, physiological, and life-history traits covary across the biological scales of individuals, populations, and species. However, the processes that cause traits to covary also change over these scales, challenging our ability to use patterns of trait covariance to infer process. Trait relationships are also widely assumed to have generic functional relationships with similar evolutionary potentials, and even though many different trait relationships are now identified, there is little appreciation that these may influence trait covariation and evolution in unique ways. We use a trait-performance-fitness framework to classify and organize trait relationships into three general classes, address which ones more likely generate trait covariation among individuals in a population, and review how selection shapes phenotypic covariation. We generate predictions about how trait covariance changes within and among populations as a result of trait relationships and in response to selection and consider how these can be tested with comparative data. Careful comparisons of covariation patterns can narrow the set of hypothesized processes that cause trait covariation when the form of the trait relationship and how it responds to selection yield clear predictions about patterns of trait covariation. We discuss the opportunities and limitations of comparative approaches to evaluate hypotheses about the evolutionary causes and consequences of trait covariation and highlight the importance of evaluating patterns within populations replicated in the same and in different selective environments. Explicit hypotheses about trait relationships are key to generating effective predictions about phenotype and its evolution using covariance data.
-
Inflation expectations and stability in an overlapping generations experiment with money creation
Heemeijer, P.; Hommes, C.; Sonnemans, J.; Tuinstra, J.
2009-01-01
We investigate how non-specialists form inflation expectations by running an experiment using a basic Overlapping Generations (OLG) model. The participants of the experiment are students of the University of Amsterdam, who predict inflation during 50 successive periods and are rewarded based on
-
Directory of Open Access Journals (Sweden)
Lino Guimarães Marujo
2009-07-01
Full Text Available This work aims to explore a novel framework to analyze the planning concepts in product development projects employing techniques to reduce the lead-time of activities, such as overlapping of a pair of each. With the System Dynamics methodology a model to evaluate the rework fraction needed to accommodate the deviations proportional to the overlapping grade of the activities. A numerical example is provided to demonstrate the validity of the model. Although problems encountered during the project management are dynamic, they have been treated on a static basis, what has as result, chronic schedules delays, overruns and cost overspent persist in follow the managers’ (reactions. In this work, we have addressed this known problem by introducing and reviewing some characteristics of the concept of rework in overlapped schedules. This consists in observe and capture the relations feedbacks among the original planned project schedule, the overlapping strategy and the inherent uncertainty in a work being done with poor information. To realize this concept, we have faced with many behaviors patterns (e.g. rework, new duration, non-conformity, and analyze the output behavior pattern, produced by the proposed model.
-
Directory of Open Access Journals (Sweden)
Sheila K Patterson
Full Text Available Salmonella enterica serovar Typhimurium strain 798 has previously been shown to undergo phenotypic phase variation. One of the phenotypes expresses virulence traits such as adhesion, while the other phenotype does not. Phenotypic phase variation appears to correlate with the ability of this strain to cause persistent, asymptomatic infections of swine. A new method to detect cells in either phenotypic phase was developed using Evans Blue-Uranine agar plates. Using this new assay, rates of phenotypic phase variation were obtained. The rate of phase variation from non-adhesive to adhesive phenotype was approximately 10(-4 per cell per generation while phase variation from the adhesive to the non-adhesive phenotype was approximately 10(-6 per cell per generation. Two highly virulent S. Typhimurium strains, SL1344 and ATCC 14028, were also shown to undergo phase variation. However, while the rate from adhesive to non-adhesive phenotype was approximately the same as for strain 798, the non-adhesive to adhesive phenotype shift was 37-fold higher. Differential gene expression was measured using RNA-Seq. Eighty-three genes were more highly expressed by 798 cells in the adhesive phenotype compared to the non-adhesive cells. Most of the up-regulated genes were in virulence genes and in particular all genes in the Salmonella pathogenicity island 1 were up-regulated. When compared to the virulent strain SL1344, expression of the virulence genes was approximately equal to those up-regulated in the adhesive phenotype of strain 798. A comparison of invasive ability demonstrated that strain SL1344 was the most invasive followed by the adhesive phenotype of strain 798, then the non-adhesive phenotype of strain 798. The least invasive strain was ATCC 14028. The genome of strain 798 was sequenced and compared to SL1344. Both strains had very similar genome sequences and gene deletions could not readily explain differences in the rates of phase variation from non
-
Optimization of control bank overlap for SMART
International Nuclear Information System (INIS)
Song, Jae Seung; Cho, Byung Oh; Zee, Sung Quun
1998-07-01
In the pressurized water reactor, control banks are operated by 40% effective core height overlap to avoid decrease of differential rod worth. This overlap does not effect on the core depletion history because the pressurized water reactor core operated at all rod out condition for the most of the operation time. For the boron free reactor SMART, however, one or more control banks are always inserted in the core to maintain critical condition, and the control bank overlap effects on the core depletion history. Since the cycle length of SMART is limited by three-dimensional core peaking factor at EOC, at which the control bank located at the core center is withdrawn, the cycle length of SMART is affected by the control bank overlap. In this report, the effect of control bank overlap on the core depletion history was evaluated. It is concluded that 60 cm control bank overlap corresponding to 30% effective core height was selected not to increase maximum peaking factor at EOC so that the control bank overlap does not affect the cycle length of the core. (author). 8 refs., 2 tabs., 19 figs
-
Léger, Sandy; Balguerie, Xavier; Goldenberg, Alice; Drouin-Garraud, Valérie; Cabot, Annick; Amstutz-Montadert, Isabelle; Young, Paul; Joly, Pascal; Bodereau, Virginie; Holder-Espinasse, Muriel; Jamieson, Robyn V; Krause, Amanda; Chen, Hongsheng; Baumann, Clarisse; Nunes, Luis; Dollfus, Hélène; Goossens, Michel; Pingault, Véronique
2012-01-01
The microphthalmia-associated transcription factor (MITF) is a basic helix-loop-helix leucine zipper transcription factor, which regulates melanocyte development and the biosynthetic melanin pathway. A notable relationship has been described between non-truncating mutations of its basic domain and Tietz syndrome, which is characterized by albinoid-like hypopigmentation of the skin and hair, rather than the patchy depigmentation seen in Waardenburg syndrome, and severe hearing loss. Twelve patients with new or recurrent non-truncating mutations of the MITF basic domain from six families were enrolled in this study. We observed a wide range of phenotypes and some unexpected features. All the patients had blue irides and pigmentation abnormalities that ranged from diffuse hypopigmentation to Waardenburg-like patches. In addition, they showed congenital complete hearing loss, diffuse hypopigmentation of the skin, freckling and ocular abnormalities, more frequently than patients with MITF mutations outside the basic domain. In conclusion, the non-truncating mutations of the basic domain do not always lead to Tietz syndrome but rather to a large range of phenotypes. Sun-exposed freckles are interestingly observed more frequently in Asian populations. This variability argues for the possible interaction with modifier loci. PMID:22258527
-
[The Overlap Syndrome: association of COPD and Obstructive Sleep Apnoea].
Weitzenblum, E; Chaouat, A; Kessler, R; Canuet, M; Hirschi, S
2010-04-01
Chronic obstructive pulmonary disease (COPD) and the obstructive sleep apnoea-hypopnoea syndrome (OSAHS) are both common diseases affecting respectively 10 and 5% of the adult population over 40 years of age. Their coexistence, which is denominated "Overlap Syndrome", can be expected to occur in about 0.5% of this population. Two recent epidemiologic studies have shown that the prevalence of OSAHS is not higher in COPD than in the general population, and that the coexistence of the two conditions is due to chance and not through a pathophysiological linkage. Patients with "overlap" have a higher risk of sleep-related O(2) desaturation than do patients with COPD alone and the same degree of bronchial obstruction. They have an increased risk of developing hypercapnic respiratory failure and pulmonary hypertension when compared with patients with OSAHS alone and with patients with "usual" COPD. In patients with overlap, hypoxaemia, hypercapnia, and pulmonary hypertension can be observed in the presence of mild to moderate bronchial obstruction, which is different from "usual" COPD. Treatment of the overlap syndrome consists of nasal continuous positive airway pressure or nocturnal non-invasive ventilation (NIV), with or without nocturnal O(2). Patients who are markedly hypoxaemic during the daytime (PaO(2)<55-60 mmHg) should be given conventional long-term O(2) therapy in addition to nocturnal ventilation. Copyright 2010 SPLF. Published by Elsevier Masson SAS. All rights reserved.
-
Sakai, Joseph T; Boardman, Jason D; Gelhorn, Heather L; Smolen, Andrew; Corley, Robin P; Huizinga, David; Menard, Scott; Hewitt, John K; Stallings, Michael C
2010-10-01
Conduct disorder is a serious, relatively common disorder of childhood and adolescence. Findings from genetic association studies searching for genetic determinants of the liability toward such behaviors have been inconsistent. One possible explanation for differential results is that most studies define phenotype from a single assessment; for many adolescents conduct problems decrease in severity over time, whereas for others such behaviors persist. Therefore, longitudinal datasets offer the opportunity to refine phenotype. We used Caucasians that were first assessed during adolescence from the National Youth Survey Family Study. Nine waves of data were used to create latent growth trajectories and test for associations between trajectory class and 5HTTLPR genotype. For the full sample, 5HTTLPR was not associated with conduct problem phenotypes. However, the short (s) allele was associated with chronic conduct problems in females; a nominally significant sex by 5HTTLPR genotype interaction was noted. Longitudinal studies provide unique opportunities for phenotypic refinement and such techniques, with large samples, may be useful for phenotypic definition with other study designs, such as whole genome association studies.
-
Topological susceptibility from the overlap
International Nuclear Information System (INIS)
Del Debbio, Luigi; Pica, Claudio
2004-01-01
The chiral symmetry at finite lattice spacing of Ginsparg-Wilson fermionic actions constrains the renormalization of the lattice operators; in particular, the topological susceptibility does not require any renormalization, when using a fermionic estimator to define the topological charge. Therefore, the overlap formalism appears as an appealing candidate to study the continuum limit of the topological susceptibility while keeping the systematic errors under theoretical control. We present results for the SU(3) pure gauge theory using the index of the overlap Dirac operator to study the topology of the gauge configurations. The topological charge is obtained from the zero modes of the overlap and using a new algorithm for the spectral flow analysis. A detailed comparison with cooling techniques is presented. Particular care is taken in assessing the systematic errors. Relatively high statistics (500 to 1000 independent configurations) yield an extrapolated continuum limit with errors that are comparable with other methods. Our current value from the overlap is χ 1/4 = 188±12±5MeV (author)
-
Prediction of peak overlap in NMR spectra
International Nuclear Information System (INIS)
Hefke, Frederik; Schmucki, Roland; Güntert, Peter
2013-01-01
Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.
-
Detecting overlapping community structure of networks based on vertex–vertex correlations
International Nuclear Information System (INIS)
Zarei, Mina; Izadi, Dena; Samani, Keivan Aghababaei
2009-01-01
Using the NMF (non-negative matrix factorization) method, the structure of overlapping communities in complex networks is investigated. For the feature matrix of the NMF method we introduce a vertex–vertex correlation matrix. The method is applied to some computer-generated and real-world networks. Simulations show that this feature matrix gives more reasonable results
-
Directory of Open Access Journals (Sweden)
Sillence David
2011-06-01
Full Text Available Abstract Background The TRPV4 gene encodes a calcium-permeable ion-channel that is widely expressed, responds to many different stimuli and participates in an extraordinarily wide range of physiologic processes. Autosomal dominant brachyolmia, spondylometaphyseal dysplasia Kozlowski type (SMDK and metatropic dysplasia (MD are currently considered three distinct skeletal dysplasias with some shared clinical features, including short stature, platyspondyly, and progressive scoliosis. Recently, TRPV4 mutations have been found in patients diagnosed with these skeletal phenotypes. Methods and Results We critically analysed the clinical and radiographic data on 26 subjects from 21 families, all of whom had a clinical diagnosis of one of the conditions described above: 15 with MD; 9 with SMDK; and 2 with brachyolmia. We sequenced TRPV4 and identified 9 different mutations in 22 patients, 4 previously described, and 5 novel. There were 4 mutation-negative cases: one with MD and one with SMDK, both displaying atypical clinical and radiographic features for these diagnoses; and two with brachyolmia, who had isolated spine changes and no metaphyseal involvement. Conclusions Our data suggest the TRPV4 skeletal dysplasias represent a continuum of severity with areas of phenotypic overlap, even within the same family. We propose that AD brachyolmia lies at the mildest end of this spectrum and, since all cases described with this diagnosis and TRPV4 mutations display metaphyseal changes, we suggest that it is not a distinct entity but represents the mildest phenotypic expression of SMDK.
-
Vetro, Annalisa; Iascone, Maria; Limongelli, Ivan; Ameziane, Najim; Gana, Simone; Della Mina, Erika; Giussani, Ursula; Ciccone, Roberto; Forlino, Antonella; Pezzoli, Laura; Rooimans, Martin A; van Essen, Antoni J; Messa, Jole; Rizzuti, Tommaso; Bianchi, Paolo; Dorsman, Josephine; de Winter, Johan P; Lalatta, Faustina; Zuffardi, Orsetta
2015-05-01
The diagnosis of VACTERL syndrome can be elusive, especially in the prenatal life, due to the presence of malformations that overlap those present in other genetic conditions, including the Fanconi anemia (FA). We report on three VACTERL cases within two families, where the two who arrived to be born died shortly after birth due to severe organs' malformations. The suspicion of VACTERL association was based on prenatal ultrasound assessment and postnatal features. Subsequent chromosome breakage analysis suggested the diagnosis of FA. Finally, by next-generation sequencing based on the analysis of the exome in one family and of a panel of Fanconi genes in the second one, we identified novel FANCL truncating mutations in both families. We used ectopic expression of wild-type FANCL to functionally correct the cellular FA phenotype for both mutations. Our study emphasizes that the diagnosis of FA should be considered when VACTERL association is suspected. Furthermore, we show that loss-of-function mutations in FANCL result in a severe clinical phenotype characterized by early postnatal death. © 2015 WILEY PERIODICALS, INC.
-
Palomares, María; Delicado, Alicia; Mansilla, Elena; de Torres, María Luisa; Vallespín, Elena; Fernandez, Luis; Martinez-Glez, Victor; García-Miñaur, Sixto; Nevado, Julián; Simarro, Fernando Santos; Ruiz-Perez, Victor L.; Lynch, Sally Ann; Sharkey, Freddie H.; Thuresson, Ann-Charlotte; Annerén, Göran; Belligni, Elga F.; Martínez-Fernández, María Luisa; Bermejo, Eva; Nowakowska, Beata; Kutkowska-Kazmierczak, Anna; Bocian, Ewa; Obersztyn, Ewa; Martínez-Frías, María Luisa; Hennekam, Raoul C. M.; Lapunzina, Pablo
2011-01-01
We report eight unrelated individuals with intellectual disability and overlapping submicroscopic deletions of 8q21.11 (0.66-13.55 Mb in size). The deletion was familial in one and simplex in seven individuals. The phenotype was remarkably similar and consisted of a round face with full cheeks, a
-
Menegola, Milena; Clark, Eliana; Trimmer, James S
2012-06-01
To gain insights into the phenotype of voltage-gated potassium (Kv)1.1 and Kv4.2 knockout mice, we used immunohistochemistry to analyze the expression of component principal or α subunits and auxiliary subunits of neuronal Kv channels in knockout mouse brains. Genetic ablation of the Kv1.1 α subunit did not result in compensatory changes in the expression levels or subcellular distribution of related ion channel subunits in hippocampal medial perforant path and mossy fiber nerve terminals, where high levels of Kv1.1 are normally expressed. Genetic ablation of the Kv4.2 α subunit did not result in altered neuronal cytoarchitecture of the hippocampus. Although Kv4.2 knockout mice did not exhibit compensatory changes in the expression levels or subcellular distribution of the related Kv4.3 α subunit, we found dramatic decreases in the cellular and subcellular expression of specific Kv channel interacting proteins (KChIPs) that reflected their degree of association and colocalization with Kv4.2 in wild-type mouse and rat brains. These studies highlight the insights that can be gained by performing detailed immunohistochemical analyses of Kv channel knockout mouse brains. Wiley Periodicals, Inc. © 2012 International League Against Epilepsy.
-
Liu, Jin-kang; Wang, Xiao-yi; Xiong, Zeng; Zhou, Hui; Zhou, Jian-hua; Fu, Chun-yan; Li, Bo
2008-08-01
To construct a technological platform of 2-dimensional tumor microvascular architecture phenotype (2D-TAMP) expression. Thirty samples of non-small cell lung cancer (NSCLC) were collected after surgery. The corresponding sections of tumor tissue specimens to the slice of CT perfusion imaging were selected. Immunohistochemical staining,Gomori methenamine silver stain, and electron microscope observation were performed to build a technological platform of 2D-TMAP expression by detecting the morphology and the integrity of basement membrane of microvasculature, microvascular density, various microvascular subtype, the degree of the maturity and lumenization of microvasculature, and the characteristics of immunogenetics of microvasculature. The technological platform of 2D-TMAP expression was constructed successfully. There was heterogeneity in 2D-TMAP expression of non-small cell lung cancer. The microvascular of NSCLC had certain characteristics. 2D-TMAP is a key technology that can be used to observe the overall state of micro-environment in tumor growth.
-
Integrating phenotype ontologies with PhenomeNET
Rodriguez-Garcia, Miguel Angel
2017-12-19
Background Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast. Results Here, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies. Conclusions PhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.
-
Ouchene-Khelifi, Nadjet-Amina; Ouchene, Nassim; Maftah, Abderrahman; Da Silva, Anne Blondeau; Lafri, Mohamed
2015-10-01
In Algeria, goat research has been largely neglected, in spite of the economic importance of this domestic species for rural livelihoods. Goat farming is traditional and cross-breeding practices are current. The phenotypic variability of the four main native breeds (Arabia, Makatia, M'zabite and Kabyle), and of two exotic breeds (Alpine and Saanen), was investigated for the first time, using multivariate discriminant analysis. A total of 892 females were sampled in a large area, including the cradle of the native breeds, and phenotyped with 23 quantitative measures and 10 qualitative traits. Our results suggested that cross-breeding practices have ever led to critical consequences, particularly for Makatia and M'zabite. The information reported in this study has to be carefully considered in order to establish governmental plan able to prevent the genetic dilution of the Algerian goat livestock.
-
Leng, Yinglin; Liu, Yuhe; Fang, Xiaojing; Li, Yao; Yu, Lei; Yuan, Yun; Wang, Zhaoxia
2015-04-01
Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes/Leigh (MELAS/LS) overlap syndrome is a mitochondrial disorder subtype with clinical and magnetic resonance imaging (MRI) features that are characteristic of both MELAS and Leigh syndrome (LS). Here, we report an MELAS/LS case presenting with cortical deafness and seizures. Cranial MRI revealed multiple lesions involving bilateral temporal lobes, the basal ganglia and the brainstem, which conformed to neuroimaging features of both MELAS and LS. Whole mitochondrial DNA (mtDNA) sequencing and PCR-RFLP revealed a de novo heteroplasmic m.10197 G > A mutation in the NADH dehydrogenase subunit 3 gene (ND3), which was predicted to cause an alanine to threonine substitution at amino acid 47. Although the mtDNA m.10197 G > A mutation has been reported in association with LS, Leber hereditary optic neuropathy and dystonia, it has never been linked with MELAS/LS overlap syndrome. Our patient therefore expands the phenotypic spectrum of the mtDNA m.10197 G > A mutation.
-
Peshnina, I.; Sinitsina, O.
2017-11-01
The study relevance is determined by the increasing interest in reconstruction of city historical centers and located in the area of industrial buildings the functional profile of which needs to be changed. The problem of obtaining extra usable spaces in the historical centers of cities is solved by raising the number of storeys in the buildings which can be achieved by the construction of additional built-in inter-floor overlaps. The article is dedicated to the analysis of the recent years’ experience in reconstruction design involving this method in our country and abroad, in the Netherlands, in particular. The article presents the results of the analysis of the experience in reconstruction of the objects by constructing additional inter-floor overlaps and aims to define the optimum construction solution for built-in inter-floor overlapping and to develop non-existing solutions for wide application of this method in the reconstruction of a building with non-unified and unmodulated parameters. It was determined as expedient to apply a monolith reinforced concrete slab with the use of steel profiled flooring as a formwork and reinforcement and steel beams designed as “Built-in Beams” for the construction of built-in inter-floor overlaps in reconstruction. The article will be useful for specialists doing research in the sphere of reconstruction of the buildings and for the practical activity of design engineers.
-
The macroevolutionary consequences of phenotypic integration: from development to deep time.
Goswami, A; Smaers, J B; Soligo, C; Polly, P D
2014-08-19
Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution.
-
Villaseñor-Sierra, Alberto; Katahira, Eva; Jaramillo-Valdivia, Abril N.; de los Angeles Barajas-García, María; Bryant, Amy; Morfín-Otero, Rayo; Márquez-Díaz, Francisco; Tinoco, Juan Carlos; Sánchez-Corona, José; Stevens, Dennis L.
2012-01-01
Summary Objective To compare the prevalence, phenotypes, and genes responsible for erythromycin resistance among Streptococcus pyogenes isolates from Mexico and the USA. Methods Eighty-nine invasive and 378 non-invasive isolates from Mexico, plus 148 invasive, 21 non-invasive, and five unclassified isolates from the USA were studied. Susceptibilities to penicillin, erythromycin, clindamycin, ceftriaxone, and vancomycin were evaluated according to Clinical and Laboratory Standards Institute (CLSI) standards. Phenotypes of erythromycin resistance were identified by triple disk test, and screening for mefA, ermTR, and ermB genes was carried out by PCR. Results All isolates were susceptible to penicillin, ceftriaxone, and vancomycin. Erythromycin resistance was found in 4.9% of Mexican strains and 5.2% of USA strains. Phenotypes in Mexican strains were 95% M and 5% cMLS; in strains from the USA, phenotypes were 33.3% iMLS, 33.3% iMLS-D, and 33.3% M. Erythromycin resistance genes in strains from Mexico were mefA (95%) and ermB (5%); USA strains harbored ermTR (56%), mefA (33%), and none (11%). In Mexico, all erythromycin-resistant strains were non-invasive, whereas 89% of strains from the USA were invasive. Conclusions Erythromycin resistance continues to exist at low levels in both Mexico and the USA, although the genetic mechanisms responsible differ between the two nations. These genetic differences may be related to the invasive character of the S. pyogenes isolated. PMID:22217469
-
Trajectories of the healthy ageing phenotype among middle-aged and older Britons, 2004-2013.
Tampubolon, Gindo
2016-06-01
Since the ageing population demands a response to ensure older people remain healthy and active, we studied the dynamics of a recently proposed healthy ageing phenotype. We drew the phenotype's trajectories and tested whether their levels and rates of change are influenced by health behaviours, comorbidities and socioeconomic positions earlier in the life course. The English Longitudinal Ageing Study, a prospective, nationally representative sample of people aged ≥50 years, measured a set of eight biomarkers which make up the outcome of the healthy ageing phenotype three times over nearly a decade (N2004=5009, N2008=5301, N2013=4455). A cluster of health behaviours, comorbidities and socioeconomic positions were also measured repeatedly. We assessed the phenotype's distribution non-parametrically, then fitted linear mixed models to phenotypic change and further examined time interactions with gender and socioeconomic position. We ran additional analyses to test robustness. Women had a wider distribution of the healthy ageing phenotype than men had. The phenotype declined annually by -0.242 (95% confidence interval [CI]: -0.352, -0.131). However, there was considerable heterogeneity in the levels and rates of phenotypic change. Women started at higher levels, then declined more steeply by -0.293 (CI: -0.403, -0.183) annually, leading to crossover in the trajectories. Smoking and physical activity assessed on the Allied Dunbar scale were strongly associated with the trajectories. Though marked by secular decline, the trajectories of the healthy ageing phenotype showed distinct socioeconomic gradients. The trajectories were also susceptible to variations in health behaviours, strengthening the case for serial interventions to attain healthy and active ageing. Copyright © 2016 The Author. Published by Elsevier Ireland Ltd.. All rights reserved.
-
Influences of overlap index on Fourier ptychography imaging
Wang, Honghong; Rong, Lu; Wang, Dayong; Zhang, Xu; Zhai, Changchao; Panezai, Spozmai; Wang, Yunxin; Zhao, Jie
2018-01-01
Fourier ptychography is a new type of synthetic aperture imaging technique based on phase retrieval method which can improve microscopeic imaging performance beyond the diffraction limit of the employed optical components by illuminating the object with oblique waves of different incident angles where the field of view remains unchanged. illumination angle and the overlap rate of spectrum will have a certain impact on the quality of reconstruction. In this paper, we study the effects of illumination angle and spectral overlap rate on the image quality of Fourier ptychography. The simulation results show that increasing the illumination angle and spectral overlap can improve the resolution, but there is a threshold for the key parameters of spectral overlap rate. The convergence rate decreases when the overlap rate exceeds 70%, and the reconstruction process is more time-consuming due to the high overlap rate. However the results of proposed study shows that an overlap of 60% is the optimal choice to acquire a high-quality recovery with high speed.
-
Phenotypic and Genotypic Analysis of Newly Obtained Interspecific Hybrids in the Campanula Genus.
Directory of Open Access Journals (Sweden)
Anna-Catharina Röper
Full Text Available Interspecific hybridisation creates new phenotypes within several ornamental plant species including the Campanula genus. We have employed phenotypic and genotypic methods to analyse and evaluate interspecific hybridisation among cultivars of four Campanula species, i.e. C. cochleariifolia, C. isophylla, C. medium and C. formanekiana. Hybrids were analysed using amplified fragment length polymorphism (AFLP, flow cytometry and biometrical measurements. Results of correlation matrices demonstrated heterogeneous phenotypes for the parental species, which confirmed our basic premise for new phenotypes of interspecific hybrids. AFLP assays confirmed the hybridity and identified self-pollinated plants. Limitation of flow cytometry analysis detection was observed while detecting the hybridity status of two closely related parents, e.g. C. cochleariiafolia × C. isophylla. Phenotypic characteristics such as shoot habitus and flower colour were strongly influenced by one of the parental species in most crosses. Rooting analysis revealed that inferior rooting quality occurred more often in interspecific hybrids than in the parental species. Only interspecific hybrid lines of C. formanekiana 'White' × C. medium 'Pink' showed a high rooting level. Phenotype analyses demonstrated a separation from the interspecific hybrid lines of C. formanekiana 'White' × C. medium 'Pink' to the other clustered hybrids of C. formanekiana and C. medium. In our study we demonstrated that the use of correlation matrices is a suitable tool for identifying suitable cross material. This study presents a comprehensive overview for analysing newly obtained interspecific hybrids. The chosen methods can be used as guidance for analyses for further interspecific hybrids in Campanula, as well as in other ornamental species.
-
International Nuclear Information System (INIS)
Mattes, Malcolm D.; Lee, Jennifer C.; Einaiem, Sara; Guirguis, Adel; Ikoro, N. C.; Ashamalla Hani
2013-01-01
The goal of this study is to determine whether the magnitude of overlap between planning target volume (PTV) and rectum (Rectum overlap ) or PTV and bladder (Bladder overlap ) in prostate cancer volumetric-modulated arc therapy (VMAT) is predictive of the dose-volume relationships achieved after optimization, and to identify predictive equations and cutoff values using these overlap volumes beyond which the Quantitative Analyses of Normal Tissue Effects in the Clinic (QUANTEC) dose-volume constraints are unlikely to be met. Fifty-seven patients with prostate cancer underwent VMAT planning using identical optimization conditions and normalization. The PTV (for the 50.4 Gy primary plan and 30.6 Gy boost plan) included 5 to 10 mm margins around the prostate and seminal vesicles. Pearson correlations, linear regression analyses, and receiver operating characteristic (ROC) curves were used to correlate the percentage overlap with dose-volume parameters. The percentage Rectum overlap and Bladder overlap correlated with sparing of that organ but minimally impacted other dose-volume parameters, predicted the primary plan rectum V 45 and bladder V 50 with R 2 = 0.78 and R 2 = 0.83, respectively, and predicted the boost plan rectum V 30 and bladder V 30 with R 2 = 0.53 and R 2 = 0.81, respectively. The optimal cutoff value of boost Rectumoverlap to predict rectum V75 >15% was 3.5% (sensitivity 100%, specificity 94%, p overlap to predict bladder V 80 >10% was 5.0% (sensitivity 83%, specificity 100%, p < 0.01). The degree of overlap between PTV and bladder or rectum can be used to accurately guide physicians on the use of interventions to limit the extent of the overlap region prior to optimization.
-
Heritability of tic disorders: a twin-family study.
Zilhão, N R; Olthof, M C; Smit, D J A; Cath, D C; Ligthart, L; Mathews, C A; Delucchi, K; Boomsma, D I; Dolan, C V
2017-04-01
Genetic-epidemiological studies that estimate the contributions of genetic factors to variation in tic symptoms are scarce. We estimated the extent to which genetic and environmental influences contribute to tics, employing various phenotypic definitions ranging between mild and severe symptomatology, in a large population-based adult twin-family sample. In an extended twin-family design, we analysed lifetime tic data reported by adult mono- and dizygotic twins (n = 8323) and their family members (n = 7164; parents and siblings) from 7311 families in the Netherlands Twin Register. We measured tics by the abbreviated version of the Schedule for Tourette and Other Behavioral Syndromes. Heritability was estimated by genetic structural equation modeling for four tic disorder definitions: three dichotomous and one trichotomous phenotype, characterized by increasingly strictly defined criteria. Prevalence rates of the different tic disorders in our sample varied between 0.3 and 4.5% depending on tic disorder definition. Tic frequencies decreased with increasing age. Heritability estimates varied between 0.25 and 0.37, depending on phenotypic definitions. None of the phenotypes showed evidence of assortative mating, effects of shared environment or non-additive genetic effects. Heritabilities of mild and severe tic phenotypes were estimated to be moderate. Overlapping confidence intervals of the heritability estimates suggest overlapping genetic liabilities between the various tic phenotypes. The most lenient phenotype (defined only by tic characteristics, excluding criteria B, C and D of DSM-IV) rendered sufficiently reliable heritability estimates. These findings have implications in phenotypic definitions for future genetic studies.
-
Neural overlap in processing music and speech
Peretz, Isabelle; Vuvan, Dominique; Lagrois, Marie-Élaine; Armony, Jorge L.
2015-01-01
Neural overlap in processing music and speech, as measured by the co-activation of brain regions in neuroimaging studies, may suggest that parts of the neural circuitries established for language may have been recycled during evolution for musicality, or vice versa that musicality served as a springboard for language emergence. Such a perspective has important implications for several topics of general interest besides evolutionary origins. For instance, neural overlap is an important premise for the possibility of music training to influence language acquisition and literacy. However, neural overlap in processing music and speech does not entail sharing neural circuitries. Neural separability between music and speech may occur in overlapping brain regions. In this paper, we review the evidence and outline the issues faced in interpreting such neural data, and argue that converging evidence from several methodologies is needed before neural overlap is taken as evidence of sharing. PMID:25646513
-
Phenotypes of COPD patients with a smoking history in Central and Eastern Europe: the POPE Study
Koblizek, Vladimir; Milenkovic, Branislava; Barczyk, Adam; Tkacova, Ruzena; Somfay, Attila; Zykov, Kirill; Tudoric, Neven; Kostov, Kosta; Zbozinkova, Zuzana; Svancara, Jan; Sorli, Jurij; Krams, Alvils; Miravitlles, Marc
2017-01-01
Chronic obstructive pulmonary disease (COPD) represents a major health problem in Central and Eastern European (CEE) countries; however, there are no data regarding clinical phenotypes of these patients in this region. Participation in the Phenotypes of COPD in Central and Eastern Europe (POPE) study was offered to stable patients with COPD in a real-life setting. The primary aim of this study was to assess the prevalence of phenotypes according to predefined criteria. Secondary aims included analysis of differences in symptom load, comorbidities and pharmacological treatment. 3362 patients with COPD were recruited in 10 CEE countries. 63% of the population were nonexacerbators, 20.4% frequent exacerbators with chronic bronchitis, 9.5% frequent exacerbators without chronic bronchitis and 6.9% were classified as asthma–COPD overlap. Differences in the distribution of phenotypes between countries were observed, with the highest heterogeneity observed in the nonexacerbator cohort and the lowest heterogeneity observed in the asthma–COPD cohort. There were statistically significant differences in symptom load, lung function, comorbidities and treatment between these phenotypes. The majority of patients with stable COPD in CEE are nonexacerbators; however, there are distinct differences in surrogates of disease severity and therapy between predefined COPD phenotypes. PMID:28495687
-
Spotted phenotypes in horses lost attractiveness in the Middle Ages
DEFF Research Database (Denmark)
Wutke, Saskia; Benecke, Norbert; Sandoval-Castellanos, Edson
2016-01-01
were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant...
-
Comparison of various HFB overlap formulae
International Nuclear Information System (INIS)
Oi, M.
2015-01-01
The nuclear many-body approach beyond the mean-field approximation demands overlap calculations of different many-body states. Norm overlaps between two different Hartree-Fock-Bogoliubov states can be calculated by means of the Onishi formula. However, the formula leaves the sign of the norm overlap undetermined. Several approaches have been proposed by Hara-Hayashi-Ring, Neergård-Wüst, and Robledo. In the present paper, the Neergård-Wüst formula is examined whether it is applicable to practical numerical calculations, although the formula was dismissed by many nuclear theoreticians so far for unknown reasons
-
Energy Technology Data Exchange (ETDEWEB)
Barja, P R; Coelho, C C; Paiva, R F [Research and Development Institute, UNIVAP, Av. Shishima Hifumi 2911, Sao Jose dos Campos, SP (Brazil); Barboza, M A; Matos, L C; Matos, C C B [Faculty of Medicine of Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, SP (Brazil); Oliveira, L V F, E-mail: barja@univap.b [Rehabilitation Sciences Master' s Program, Nove de Julho University (UNINOVE), Sao Paulo, SP (Brazil)
2010-03-01
Cystic fibrosis (CF) is an autosomal recessive inherited disease that increases viscoelasticity of pulmonary secretions. Affected patients are required to use therapeutic aerosols continuously. The expression of ABH glycoconjugates in exocrine secretions determines the nature of part of the carbohydrates present in these secretions, allowing the classification of individuals into the so-called 'secretor' and 'non secretor' phenotypes. The aim of this work was to employ photoacoustic (PA) measurements to monitor the solubilization kinetics of pulmonary secretions from CF patients, analyzing the influence of the secretor status in the solubilization kinetics of samples nebulized with different therapeutic aerosols. Sputum samples were obtained by spontaneous expectoration from positive and negative secretor CF patients. Each sample was nebulized with i) tobramycin, ii) alpha dornase, and iii) N-acetylcysteine in a PA cell; fitting of the data with the Boltzmann equation led to the determination of t{sub 0} (typical interaction time) and {Delta}t (solubilization interval) for each curve. Differences between the secretor and non-secretor phenotypes were statistically significant in the groups for tobramycin and alpha dornase, but not for N-acetylcysteine. Results show that the secretor status influences the solubilization of pulmonary mucus of CF patients nebulized with tobramycin and alpha dornase.
-
SAGE: String-overlap Assembly of GEnomes.
Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto
2014-09-15
De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.
-
Wong, J C; Alon, N; Norga, K; Kruyt, F A; Youssoufian, H; Buchwald, M
2000-08-01
Despite the cloning of four disease-associated genes for Fanconi anemia (FA), the molecular pathogenesis of FA remains largely unknown. To study FA complementation group A using the mouse as a model system, we cloned and characterized the mouse homolog of the human FANCA cDNA. The mouse cDNA (Fanca) encodes a 161-kDa protein that shares 65% amino acid sequence identity with human FANCA. Fanca is located at the distal region of mouse chromosome 8 and has a ubiquitous pattern of expression in embryonic and adult tissues. Expression of the mouse cDNA in human FA-A cells restores the cellular drug sensitivity to normal levels. Thus, the expression pattern, protein structure, chromosomal location, and function of FANCA are conserved in the mouse. We also isolated a novel zinc finger protein, Zfp276, which has five C(2)H(2) domains. Interestingly, Zfp276 is situated in the Fanca locus, and the 3'UTR of its cDNA overlaps with the last four exons of Fanca in a tail-to-tail manner. Zfp276 is expressed in the same tissues as Fanca, but does not complement the mitomycin C (MMC)-sensitive phenotype of FA-A cells. The overlapping genomic organization between Zfp276 and Fanca may have relevance to the disease phenotype of FA. Copyright 2000 Academic Press.
-
Neural overlap in processing music and speech.
Peretz, Isabelle; Vuvan, Dominique; Lagrois, Marie-Élaine; Armony, Jorge L
2015-03-19
Neural overlap in processing music and speech, as measured by the co-activation of brain regions in neuroimaging studies, may suggest that parts of the neural circuitries established for language may have been recycled during evolution for musicality, or vice versa that musicality served as a springboard for language emergence. Such a perspective has important implications for several topics of general interest besides evolutionary origins. For instance, neural overlap is an important premise for the possibility of music training to influence language acquisition and literacy. However, neural overlap in processing music and speech does not entail sharing neural circuitries. Neural separability between music and speech may occur in overlapping brain regions. In this paper, we review the evidence and outline the issues faced in interpreting such neural data, and argue that converging evidence from several methodologies is needed before neural overlap is taken as evidence of sharing. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
-
Post-Irradiation Non-Destructive Analyses of the AFIP-7 Experiment
Williams, W. J.; Robinson, A. B.; Rabin, B. H.
2017-12-01
This article reports the results and interpretation of post-irradiation non-destructive examinations performed on four curved full-size fuel plates that comprise the AFIP-7 experiment. These fuel plates, having a U-10 wt.%Mo monolithic design, were irradiated under moderate operating conditions in the Advanced Test Reactor to assess fuel performance for geometries that are prototypic of research reactor fuel assemblies. Non-destructive examinations include visual examination, neutron radiography, profilometry, and precision gamma scanning. This article evaluates the qualitative and quantitative data taken for each plate, compares corresponding data sets, and presents the results of swelling analyses. These characterization results demonstrate that the fuel meets established irradiation performance requirements for mechanical integrity, geometric stability, and stable and predictable behavior.
-
Guan, Guobo; Dai, Yu; Nobile, Clarissa J.; Liang, Weihong; Cao, Chengjun; Zhang, Qiuyu; Zhong, Jin; Huang, Guanghua
2014-01-01
Non-genetic phenotypic variations play a critical role in the adaption to environmental changes in microbial organisms. Candida albicans, a major human fungal pathogen, can switch between several morphological phenotypes. This ability is critical for its commensal lifestyle and for its ability to cause infections. Here, we report the discovery of a novel morphological form in C. albicans, referred to as the “gray” phenotype, which forms a tristable phenotypic switching system with the previously reported white and opaque phenotypes. White, gray, and opaque cell types differ in a number of aspects including cellular and colony appearances, mating competency, secreted aspartyl proteinase (Sap) activities, and virulence. Of the three cell types, gray cells exhibit the highest Sap activity and the highest ability to cause cutaneous infections. The three phenotypes form a tristable phenotypic switching system, which is independent of the regulation of the mating type locus (MTL). Gray cells mate over 1,000 times more efficiently than do white cells, but less efficiently than do opaque cells. We further demonstrate that the master regulator of white-opaque switching, Wor1, is essential for opaque cell formation, but is not required for white-gray transitions. The Efg1 regulator is required for maintenance of the white phenotype, but is not required for gray-opaque transitions. Interestingly, the wor1/wor1 efg1/efg1 double mutant is locked in the gray phenotype, suggesting that Wor1 and Efg1 could function coordinately and play a central role in the regulation of gray cell formation. Global transcriptional analysis indicates that white, gray, and opaque cells exhibit distinct gene expression profiles, which partly explain their differences in causing infections, adaptation ability to diverse host niches, metabolic profiles, and stress responses. Therefore, the white-gray-opaque tristable phenotypic switching system in C. albicans may play a significant role in a wide
-
Tang, Weijuan; Hazebroek, Jan; Zhong, Cathy; Harp, Teresa; Vlahakis, Chris; Baumhover, Brian; Asiago, Vincent
2017-06-28
We evaluated the variability of metabolites in various maize hybrids due to the effect of environment, genotype, phenotype as well as the interaction of the first two factors. We analyzed 480 forage and the same number of grain samples from 21 genetically diverse non-GM Pioneer brand maize hybrids, including some with drought tolerance and viral resistance phenotypes, grown at eight North American locations. As complementary platforms, both GC/MS and LC/MS were utilized to detect a wide diversity of metabolites. GC/MS revealed 166 and 137 metabolites in forage and grain samples, respectively, while LC/MS captured 1341 and 635 metabolites in forage and grain samples, respectively. Univariate and multivariate analyses were utilized to investigate the response of the maize metabolome to the environment, genotype, phenotype, and their interaction. Based on combined percentages from GC/MS and LC/MS datasets, the environment affected 36% to 84% of forage metabolites, while less than 7% were affected by genotype. The environment affected 12% to 90% of grain metabolites, whereas less than 27% were affected by genotype. Less than 10% and 11% of the metabolites were affected by phenotype in forage and grain, respectively. Unsupervised PCA and HCA analyses revealed similar trends, i.e., environmental effect was much stronger than genotype or phenotype effects. On the basis of comparisons of disease tolerant and disease susceptible hybrids, neither forage nor grain samples originating from different locations showed obvious phenotype effects. Our findings demonstrate that the combination of GC/MS and LC/MS based metabolite profiling followed by broad statistical analysis is an effective approach to identify the relative impact of environmental, genetic and phenotypic effects on the forage and grain composition of maize hybrids.
-
Inflammatory biomarkers in asthma-COPD overlap syndrome
Directory of Open Access Journals (Sweden)
Kobayashi S
2016-09-01
Full Text Available Seiichi Kobayashi, Masakazu Hanagama, Shinsuke Yamanda, Masatsugu Ishida, Masaru YanaiDepartment of Respiratory Medicine, Japanese Red Cross Ishinomaki Hospital, Ishinomaki, JapanBackground: The clinical phenotypes and underlying mechanisms of asthma-COPD overlap syndrome (ACOS remain elusive. This study aimed to investigate a comparison of COPD patients with and without ACOS, focusing on inflammatory biomarkers, in an outpatient COPD cohort.Methods: We conducted a cross-sectional study analyzing prospectively collected data from the Ishinomaki COPD Network registry. All participants were diagnosed with COPD, confirmed by using spirometry, and were aged 40–90 years and former smokers. Patients with features of asthma including both variable respiratory symptoms and variable expiratory airflow limitation were identified and defined as having ACOS. Then, the inflammatory biomarkers such as fractional exhaled nitric oxide level, blood eosinophil count and percentage, total immunoglobulin E (IgE level, and presence of antigen-specific IgE were evaluated.Results: A total of 257 patients with COPD were identified, including 37 (14.4% with ACOS. Patients with ACOS tended to be younger, have a shorter smoking history, and use more respiratory medications, especially inhaled corticosteroids and theophylline. Mean fractional exhaled nitric oxide level was significantly higher in those with ACOS than in those without ACOS (38.5 parts per billion [ppb] vs 20.3 ppb, P<0.001. Blood eosinophil count and percentage were significantly increased in those with ACOS (295/mm3 vs 212/mm3, P=0.032; 4.7% vs 3.2%, P=0.003, respectively. Total IgE level was also significantly higher, and presence of antigen-specific IgE was observed more frequently in patients with ACOS. Receiver operating characteristic curve analysis indicated that the sensitivity and specificity of these biomarkers were relatively low, but combinations of these biomarkers showed high specificity for
-
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism
Parikshak, Neelroop N.; Luo, Rui; Zhang, Alice; Won, Hyejung; Lowe, Jennifer K.; Chandran, Vijayendran; Horvath, Steve; Geschwind, Daniel H.
2013-01-01
Genetic studies have identified dozens of autism spectrum disorder (ASD) susceptibility genes, raising two critical questions: 1) do these genetic loci converge on specific biological processes, and 2) where does the phenotypic specificity of ASD arise, given its genetic overlap with intellectual disability (ID)? To address this, we mapped ASD and ID risk genes onto co-expression networks representing developmental trajectories and transcriptional profiles representing fetal and adult cortica...
-
DEFF Research Database (Denmark)
Barco, L.; Mancin, M.; Ruffa, M.
2012-01-01
in Italy, particularly as far as veterinary isolates are concerned. For this reason, a data set of 877 strains isolated in the north-east of Italy from foodstuffs, animals and environment was analysed during 2005-2010. The Random Forests (RF) method was used to identify the most important epidemiological...... and phenotypic variables to show the difference between the two serovars. Both descriptive analysis and RF revealed that S. 4,[5],12:i:- is less heterogeneous than S. Typhimurium. RF highlighted that phage type was the most important variable to differentiate the two serovars. The most common phage types...
-
Therapeutic approaches to asthma-chronic obstructive pulmonary disease overlap syndromes.
Barnes, Peter J
2015-09-01
The recognition that there are some patients with features of asthma and chronic obstructive pulmonary disease (COPD) has highlighted the need to develop more specific treatments for these clinical phenotypes. Some patients with COPD have predominantly eosinophilic inflammation and might respond to high doses of inhaled corticosteroids and newly developed specific antieosinophil therapies, including blocking antibodies against IL-5, IL-13, IL-33, and thymic stromal lymphopoietin, as well as oral chemoattractant receptor-homologous molecule expressed on TH2 cells antagonists. Other patients have severe asthma or are asthmatic patients who smoke with features of COPD-induced inflammation and might benefit from treatments targeting neutrophils, including macrolides, CXCR2 antagonists, phosphodiesterase 4 inhibitors, p38 mitogen-activating protein kinase inhibitors, and antibodies against IL-1 and IL-17. Other patients appear to have largely fixed obstruction with little inflammation and might respond to long-acting bronchodilators, including long-acting muscarinic antagonists, to reduce hyperinflation. Highly selected patients with severe asthma might benefit from bronchial thermoplasty. Some patients with overlap syndromes can be conveniently treated with triple fixed-dose combination inhaler therapy with an inhaled corticosteroid, long-acting β2-agonist, and long-acting muscarinic antagonist, several of which are now in development. Corticosteroid resistance is a feature of asthma-COPD overlap syndrome, and understanding the various molecular mechanisms of this resistance has identified novel therapeutic targets and presented the prospect of therapies that can restore corticosteroid responsiveness. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.
-
The phenotypic manifestations of rare genic CNVs in autism spectrum disorder.
Merikangas, A K; Segurado, R; Heron, E A; Anney, R J L; Paterson, A D; Cook, E H; Pinto, D; Scherer, S W; Szatmari, P; Gill, M; Corvin, A P; Gallagher, L
2015-11-01
Significant evidence exists for the association between copy number variants (CNVs) and Autism Spectrum Disorder (ASD); however, most of this work has focused solely on the diagnosis of ASD. There is limited understanding of the impact of CNVs on the 'sub-phenotypes' of ASD. The objective of this paper is to evaluate associations between CNVs in differentially brain expressed (DBE) genes or genes previously implicated in ASD/intellectual disability (ASD/ID) and specific sub-phenotypes of ASD. The sample consisted of 1590 cases of European ancestry from the Autism Genome Project (AGP) with a diagnosis of an ASD and at least one rare CNV impacting any gene and a core set of phenotypic measures, including symptom severity, language impairments, seizures, gait disturbances, intelligence quotient (IQ) and adaptive function, as well as paternal and maternal age. Classification analyses using a non-parametric recursive partitioning method (random forests) were employed to define sets of phenotypic characteristics that best classify the CNV-defined groups. There was substantial variation in the classification accuracy of the two sets of genes. The best variables for classification were verbal IQ for the ASD/ID genes, paternal age at birth for the DBE genes and adaptive function for de novo CNVs. CNVs in the ASD/ID list were primarily associated with communication and language domains, whereas CNVs in DBE genes were related to broader manifestations of adaptive function. To our knowledge, this is the first study to examine the associations between sub-phenotypes and CNVs genome-wide in ASD. This work highlights the importance of examining the diverse sub-phenotypic manifestations of CNVs in ASD, including the specific features, comorbid conditions and clinical correlates of ASD that comprise underlying characteristics of the disorder.
-
Directory of Open Access Journals (Sweden)
Umar Twahir
2011-05-01
Full Text Available In this work, the retarding influence of a gel on the rotational motion of a macromolecule is investigated within the framework of the Effective Medium (EM model. This is an extension of an earlier study that considered the effect of a gel on the translational motion of a macromolecule [Allison, S. et al. J. Phys. Chem. B 2008, 112, 5858-5866]. The macromolecule is modeled as an array of non-overlapping spherical beads with no restriction placed on their size or configuration. Specific applications include the rotational motion of right circular cylinders and wormlike chains modeled as strings of identical touching beads. The procedure is then used to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. At low gel concentration (M £ 0.010 gm/mL, good agreement between theory and experiment is achieved if the persistence length of DNA is taken to be 65 nm and the gel fiber radius of agarose is taken to be 2.5 nm. At higher gel concentrations, the EM model substantially underestimates the rotational relaxation time of DNA and this can be attributed to the onset of direct interactions that become significant when the effective particle size becomes comparable to the mean gel fiber spacing.
-
Energy Technology Data Exchange (ETDEWEB)
Mattes, Malcolm D.; Lee, Jennifer C.; Einaiem, Sara; Guirguis, Adel; Ikoro, N. C.; Ashamalla Hani [Dept. of Radiation Oncology, New York Methodist Hospital, Brooklyn (United States)
2013-12-15
The goal of this study is to determine whether the magnitude of overlap between planning target volume (PTV) and rectum (Rectum{sub overlap}) or PTV and bladder (Bladder{sub overlap}) in prostate cancer volumetric-modulated arc therapy (VMAT) is predictive of the dose-volume relationships achieved after optimization, and to identify predictive equations and cutoff values using these overlap volumes beyond which the Quantitative Analyses of Normal Tissue Effects in the Clinic (QUANTEC) dose-volume constraints are unlikely to be met. Fifty-seven patients with prostate cancer underwent VMAT planning using identical optimization conditions and normalization. The PTV (for the 50.4 Gy primary plan and 30.6 Gy boost plan) included 5 to 10 mm margins around the prostate and seminal vesicles. Pearson correlations, linear regression analyses, and receiver operating characteristic (ROC) curves were used to correlate the percentage overlap with dose-volume parameters. The percentage Rectum{sub overlap} and Bladder{sub overlap} correlated with sparing of that organ but minimally impacted other dose-volume parameters, predicted the primary plan rectum V{sub 45} and bladder V{sub 50} with R{sup 2} = 0.78 and R{sup 2} = 0.83, respectively, and predicted the boost plan rectum V{sub 30} and bladder V{sub 30} with R{sup 2} = 0.53 and R{sup 2} = 0.81, respectively. The optimal cutoff value of boost Rectumoverlap to predict rectum V75 >15% was 3.5% (sensitivity 100%, specificity 94%, p < 0.01), and the optimal cutoff value of boost Bladder{sub overlap} to predict bladder V{sub 80} >10% was 5.0% (sensitivity 83%, specificity 100%, p < 0.01). The degree of overlap between PTV and bladder or rectum can be used to accurately guide physicians on the use of interventions to limit the extent of the overlap region prior to optimization.
-
Material model for non-linear finite element analyses of large concrete structures
Engen, Morten; Hendriks, M.A.N.; Øverli, Jan Arve; Åldstedt, Erik; Beushausen, H.
2016-01-01
A fully triaxial material model for concrete was implemented in a commercial finite element code. The only required input parameter was the cylinder compressive strength. The material model was suitable for non-linear finite element analyses of large concrete structures. The importance of including
-
Influence of slice overlap on positron emission tomography image quality
International Nuclear Information System (INIS)
McKeown, Clare; Gillen, Gerry; Dempsey, Mary Frances; Findlay, Caroline
2016-01-01
PET scans use overlapping acquisition beds to correct for reduced sensitivity at bed edges. The optimum overlap size for the General Electric (GE) Discovery 690 has not been established. This study assesses how image quality is affected by slice overlap. Efficacy of 23% overlaps (recommended by GE) and 49% overlaps (maximum possible overlap) were specifically assessed. European Association of Nuclear Medicine (EANM) guidelines for calculating minimum injected activities based on overlap size were also reviewed. A uniform flood phantom was used to assess noise (coefficient of variation, (COV)) and voxel accuracy (activity concentrations, Bq ml −1 ). A NEMA (National Electrical Manufacturers Association) body phantom with hot/cold spheres in a background activity was used to assess contrast recovery coefficients (CRCs) and signal to noise ratios (SNR). Different overlap sizes and sphere-to-background ratios were assessed. COVs for 49% and 23% overlaps were 9% and 13% respectively. This increased noise was difficult to visualise on the 23% overlap images. Mean voxel activity concentrations were not affected by overlap size. No clinically significant differences in CRCs were observed. However, visibility and SNR of small, low contrast spheres (⩽13 mm diameter, 2:1 sphere to background ratio) may be affected by overlap size in low count studies if they are located in the overlap area. There was minimal detectable influence on image quality in terms of noise, mean activity concentrations or mean CRCs when comparing 23% overlap with 49% overlap. Detectability of small, low contrast lesions may be affected in low count studies—however, this is a worst-case scenario. The marginal benefits of increasing overlap from 23% to 49% are likely to be offset by increased patient scan times. A 23% overlap is therefore appropriate for clinical use. An amendment to EANM guidelines for calculating injected activities is also proposed which better reflects the effect overlap size
-
Iterative Overlap FDE for Multicode DS-CDMA
Takeda, Kazuaki; Tomeba, Hiromichi; Adachi, Fumiyuki
Recently, a new frequency-domain equalization (FDE) technique, called overlap FDE, that requires no GI insertion was proposed. However, the residual inter/intra-block interference (IBI) cannot completely be removed. In addition to this, for multicode direct sequence code division multiple access (DS-CDMA), the presence of residual interchip interference (ICI) after FDE distorts orthogonality among the spreading codes. In this paper, we propose an iterative overlap FDE for multicode DS-CDMA to suppress both the residual IBI and the residual ICI. In the iterative overlap FDE, joint minimum mean square error (MMSE)-FDE and ICI cancellation is repeated a sufficient number of times. The bit error rate (BER) performance with the iterative overlap FDE is evaluated by computer simulation.
-
FLIC-overlap fermions and topology
International Nuclear Information System (INIS)
Kamleh, W.; Kusterer, D.J.; Leinweber, D.B.; Williams, A.G.
2003-01-01
APE smearing the links in the irrelevant operators of clover fermions (Fat-Link Irrelevant Clover (FLIC) fermions) provides significant improvement in the condition number of the Hermitian-Dirac operator and gives rise to a factor of two savings in computing the overlap operator. This report investigates the effects of using a highly-improved definition of the lattice field-strength tensor F μν in the fermion action, made possible through the use of APE-smeared fat links in the construction of the irrelevant operators. Spurious double-zero crossings in the spectral flow of the Hermitian-Wilson Dirac operator associated with lattice artifacts at the scale of the lattice spacing are removed with FLIC fermions composed with an O(α 4 )-improved lattice field strength tensor. Hence, FLIC-Overlap fermions provide an additional benefit to the overlap formalism: a correct realization of topology in the fermion sector on the lattice
-
Masino, Aaron J; Dechene, Elizabeth T; Dulik, Matthew C; Wilkens, Alisha; Spinner, Nancy B; Krantz, Ian D; Pennington, Jeffrey W; Robinson, Peter N; White, Peter S
2014-07-21
Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging variants that must be individually assessed to establish clear association with patient phenotype. To assist interpretation, we implemented an algorithm that ranks a given set of genes relative to patient phenotype. The algorithm orders genes by the semantic similarity computed between phenotypic descriptors associated with each gene and those describing the patient. Phenotypic descriptor terms are taken from the Human Phenotype Ontology (HPO) and semantic similarity is derived from each term's information content. Model validation was performed via simulation and with clinical data. We simulated 33 Mendelian diseases with 100 patients per disease. We modeled clinical conditions by adding noise and imprecision, i.e. phenotypic terms unrelated to the disease and terms less specific than the actual disease terms. We ranked the causative gene against all 2488 HPO annotated genes. The median causative gene rank was 1 for the optimal and noise cases, 12 for the imprecision case, and 60 for the imprecision with noise case. Additionally, we examined a clinical cohort of subjects with hearing impairment. The disease gene median rank was 22. However, when also considering the patient's exome data and filtering non-exomic and common variants, the median rank improved to 3. Semantic similarity can rank a causative gene highly within a gene list relative to patient phenotype characteristics, provided that imprecision is mitigated. The clinical case results suggest that phenotype rank combined with variant analysis provides significant improvement over the individual approaches. We expect that this combined prioritization approach may increase accuracy and decrease effort for
-
Directory of Open Access Journals (Sweden)
Avijit Podder
2017-06-01
Full Text Available Intercommunication of Dopamine Receptors (DRs with their associate protein partners is crucial to maintain regular brain function in human. Majority of the brain disorders arise due to malfunctioning of such communication process. Hence, contributions of genetic factors, as well as phenotypic indications for various neurological and psychiatric disorders are often attributed as sharing in nature. In our earlier research article entitled “Human Dopamine Receptors Interaction Network (DRIN: a systems biology perspective on topology, stability and functionality of the network” (Podder et al., 2014 [1], we had depicted a holistic interaction map of human Dopamine Receptors. Given emphasis on the topological parameters, we had characterized the functionality along with the vulnerable properties of the network. In support of this, we hereby provide an additional data highlighting the genetic overlapping of various brain disorders in the network. The data indicates the sharing nature of disease genes for various neurological and psychiatric disorders in dopamine receptors connecting protein-protein interactions network. The data also indicates toward an alternative approach to prioritize proteins for overlapping brain disorders as valuable drug targets in the network.
-
Borderline Personality Disorder as a Female Phenotypic Expression of Psychopathy?
Sprague, Jenessa; Javdani, Shabnam; Sadeh, Naomi; Newman, Joseph P.; Verona, Edelyn
2011-01-01
Evidence suggests that the combination of the interpersonal-affective (F1) and impulsive-antisocial (F2) features of psychopathy may be associated with borderline personality disorder (BPD), specifically among women (e.g., Coid, 1993; Hicks, Vaidyana-than, & Patrick, 2010). However, empirical research explicitly examining gendered relationships between BPD and psychopathy factors is lacking. To further inform this area of research, we investigated the hypothesis that the interplay between the two psychopathy factors is associated with BPD among women across two studies. Study 1 consisted of a college sample of 318 adults (51% women), and Study 2 consisted of a large sample of 488 female prisoners. The interpersonal-affective (F1) and impulsiveantisocial psychopathy (F2) scores, measured with self-report and clinician-rated indices, respectively, were entered as explanatory variables in regression analyses to investigate their unique contributions to BPD traits. Across two independent samples, results indicated that the interaction of high F1 and F2 psychopathy scores was associated with BPD in women. This association was found to be specific to women in Study 1. These results suggest that BPD and psychopathy, at least as they are measured by current instruments, overlap in women and, accordingly, may reflect gender-differentiated phenotypic expressions of similar dispositional vulnerabilities. PMID:22452756
-
Tordjman, S; Cohen, D; Coulon, N; Anderson, G M; Botbol, M; Canitano, R; Roubertoux, P L
2017-01-30
Clinical and molecular genetics have advanced current knowledge on genetic disorders associated with autism. A review of diverse genetic disorders associated with autism is presented and for the first time discussed extensively with regard to possible common underlying mechanisms leading to a similar cognitive-behavioral phenotype of autism. The possible role of interactions between genetic and environmental factors, including epigenetic mechanisms, is in particular examined. Finally, the pertinence of distinguishing non-syndromic autism (isolated autism) from syndromic autism (autism associated with genetic disorders) will be reconsidered. Given the high genetic and etiological heterogeneity of autism, autism can be viewed as a behavioral syndrome related to known genetic disorders (syndromic autism) or currently unknown disorders (apparent non-syndromic autism), rather than a specific categorical mental disorder. It highlights the need to study autism phenotype and developmental trajectory through a multidimensional, non-categorical approach with multivariate analyses within autism spectrum disorder but also across mental disorders, and to conduct systematically clinical genetic examination searching for genetic disorders in all individuals (children but also adults) with autism. Copyright © 2017. Published by Elsevier Ltd.
-
Directory of Open Access Journals (Sweden)
Benjamin Cocanougher
2015-06-01
Full Text Available Galactosemia is a metabolic disorder caused by mutations in the GALT gene [1,2]. We encountered a patient heterozygous for a known pathogenic H132Q mutation and a novel S222N variant of unknown significance [3]. Reminiscent of patients with the S135L mutation, our patient had loss of GALT enzyme activity in erythrocytes but a very mild clinical phenotype [3–8]. We performed splicing experiments and computational structural analyses to investigate the role of the novel S222N variant. Alamut software data predicted loss of splicing enhancers for the S222N and S135L mutations [9,10]. A cDNA library was generated from our patient׳s RNA to investigate for splicing errors, but no change in transcript length was seen [3]. In silico structural analysis was performed to investigate enzyme stability and attempt to understand the mechanism of the atypical galactosemia phenotype. Stability results are publicly available in the GALT Protein Database 2.0 [11–14]. Animations were created to give the reader a dynamic view of the enzyme structure and mutation locations. Protein database files and python scripts are included for further investigation.
-
International Nuclear Information System (INIS)
Samaraweera, Leleesha; Grandinetti, Kathryn B; Huang, Ruojun; Spengler, Barbara A; Ross, Robert A
2014-01-01
Neuroblastoma (NB) is the most common extracranial solid tumor in children. NB tumors and derived cell lines are phenotypically heterogeneous. Cell lines are classified by phenotype, each having distinct differentiation and tumorigenic properties. The neuroblastic phenotype is tumorigenic, has neuronal features and includes stem cells (I-cells) and neuronal cells (N-cells). The non-neuronal phenotype (S-cell) comprises cells that are non-tumorigenic with features of glial/smooth muscle precursor cells. This study identified miRNAs associated with each distinct cell phenotypes and investigated their role in regulating associated differentiation and tumorigenic properties. A miRNA microarray was performed on the three cell phenotypes and expression verified by qRT-PCR. miRNAs specific for certain cell phenotypes were modulated using miRNA inhibitors or stable transfection. Neuronal differentiation was induced by RA; non-neuronal differentiation by BrdU. Changes in tumorigenicity were assayed by soft agar colony forming ability. N-myc binding to miR-375 promoter was assayed by chromatin-immunoprecipitation. Unsupervised hierarchical clustering of miRNA microarray data segregated neuroblastic and non-neuronal cell lines and showed that specific miRNAs define each phenotype. qRT-PCR validation confirmed that increased levels of miR-21, miR-221 and miR-335 are associated with the non-neuronal phenotype, whereas increased levels of miR-124 and miR-375 are exclusive to neuroblastic cells. Downregulation of miR-335 in non-neuronal cells modulates expression levels of HAND1 and JAG1, known modulators of neuronal differentiation. Overexpression of miR-124 in stem cells induces terminal neuronal differentiation with reduced malignancy. Expression of miR-375 is exclusive for N-myc-expressing neuroblastic cells and is regulated by N-myc. Moreover, miR-375 downregulates expression of the neuronal-specific RNA binding protein HuD. Thus, miRNAs define distinct NB cell phenotypes
-
Piles, tabs and overlaps in navigation among documents
DEFF Research Database (Denmark)
Jakobsen, Mikkel Rønne; Hornbæk, Kasper
2010-01-01
Navigation among documents is a frequent, but ill supported activity. Overlapping or tabbed documents are widespread, but they offer limited visibility of their content. We explore variations on navigation support: arranging documents with tabs, as overlapping windows, and in piles. In an experim......Navigation among documents is a frequent, but ill supported activity. Overlapping or tabbed documents are widespread, but they offer limited visibility of their content. We explore variations on navigation support: arranging documents with tabs, as overlapping windows, and in piles....... In an experiment we compared 11 participants’ navigation with these variations and found strong task effects. Overall, overlapping windows were preferred and their structured layout worked well with some tasks. Surprisingly, tabbed documents were efficient in tasks requiring simply finding a document. Piled...... on document navigation and its support by piling....
-
Bootstrap inference for pre-averaged realized volatility based on non-overlapping returns
DEFF Research Database (Denmark)
Gonçalves, Sílvia; Hounyo, Ulrich; Meddahi, Nour
The main contribution of this paper is to propose bootstrap methods for realized volatility-like estimators defined on pre-averaged returns. In particular, we focus on the pre-averaged realized volatility estimator proposed by Podolskij and Vetter (2009). This statistic can be written (up to a bias......-overlapping nature of the pre-averaged returns implies that these are asymptotically independent, but possibly heteroskedastic. This motivates the application of the wild bootstrap in this context. We provide a proof of the first order asymptotic validity of this method for percentile and percentile-t intervals. Our...... Monte Carlo simulations show that the wild bootstrap can improve the finite sample properties of the existing first order asymptotic theory provided we choose the external random variable appropriately. We use empirical work to illustrate its use in practice....
-
Prader-Willi-like phenotypes: a systematic review of their chromosomal abnormalities.
Rocha, C F; Paiva, C L A
2014-03-31
Prader-Willi syndrome (PWS) is caused by the lack of expression of genes located on paternal chromosome 15q11-q13. This lack of gene expression may be due to a deletion in this chromosomal segment, to maternal uniparental disomy of chromosome 15, or to a defect in the imprinting center on 15q11-q13. PWS is characterized by hypotonia during the neonatal stage and in childhood, accompanied by a delay in neuropsychomotor development. Overeating, obesity, and mental deficiency arise later on. The syndrome has a clinical overlap with other diseases, which makes it difficult to accurately diagnose. The purpose of this article is to review the Prader-Willi-like phenotype in the scientific literature from 2000 to 2013, i.e., to review the cases of PWS caused by chromosomal abnormalities different from those found on chromosome 15. A search was carried out using the "National Center for Biotechnology Information" (www.pubmed.com) and "Scientific Electronic Library Online (www.scielo.br) databases and combinations of key words such as "Prader-Willi-like phenotype" and "Prader-Willi syndrome phenotype". Editorials, letters, reviews, and guidelines were excluded. Articles chosen contained descriptions of patients diagnosed with the PWS phenotype but who were negative for alterations on 15q11-q13. Our search found 643 articles about PWS, but only 14 of these matched with the Prader-Willi-like phenotype and with the selected years of publication (2000-2013). If two or more articles reported the same chromosomal alterations for Prader-Willi-like phenotype, the most recent was chosen. Twelve articles of 14 were case reports and 2 reported series of cases.
-
Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.
Directory of Open Access Journals (Sweden)
Kristina Kirschner
2015-03-01
Full Text Available The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage and chronically activated (in senescent or pro-apoptotic conditions p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.
-
St Pourcain, B; Robinson, E B; Anttila, V; Sullivan, B B; Maller, J; Golding, J; Skuse, D; Ring, S; Evans, D M; Zammit, S; Fisher, S E; Neale, B M; Anney, R J L; Ripke, S; Hollegaard, M V; Werge, T; Ronald, A; Grove, J; Hougaard, D M; Børglum, A D; Mortensen, P B; Daly, M J; Davey Smith, G
2018-02-01
Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early childhood, whereas most symptoms characteristic of schizophrenia do not appear before early adulthood. We investigated whether overlap in common genetic influences between these clinical conditions and impairments in social communication depends on the developmental stage of the assessed trait. Social communication difficulties were measured in typically-developing youth (Avon Longitudinal Study of Parents and Children, N⩽5553, longitudinal assessments at 8, 11, 14 and 17 years) using the Social Communication Disorder Checklist. Data on clinical ASD (PGC-ASD: 5305 cases, 5305 pseudo-controls; iPSYCH-ASD: 7783 cases, 11 359 controls) and schizophrenia (PGC-SCZ2: 34 241 cases, 45 604 controls, 1235 trios) were either obtained through the Psychiatric Genomics Consortium (PGC) or the Danish iPSYCH project. Overlap in genetic influences between ASD and social communication difficulties during development decreased with age, both in the PGC-ASD and the iPSYCH-ASD sample. Genetic overlap between schizophrenia and social communication difficulties, by contrast, persisted across age, as observed within two independent PGC-SCZ2 subsamples, and showed an increase in magnitude for traits assessed during later adolescence. ASD- and schizophrenia-related polygenic effects were unrelated to each other and changes in trait-disorder links reflect the heterogeneity of genetic factors influencing social communication difficulties during childhood versus later adolescence. Thus, both clinical ASD and schizophrenia share some genetic influences with impairments in social communication, but reveal distinct developmental profiles in their genetic links, consistent with the onset of clinical symptoms.
-
Cardio-facio-cutaneous syndrome: does genotype predict phenotype?
Allanson, Judith E; Annerén, Göran; Aoki, Yoki; Armour, Christine M; Bondeson, Marie-Louise; Cave, Helene; Gripp, Karen W; Kerr, Bronwyn; Nystrom, Anna-Maja; Sol-Church, Katia; Verloes, Alain; Zenker, Martin
2011-05-15
Cardio-facio-cutaneous (CFC) syndrome is a sporadic multiple congenital anomalies/mental retardation condition principally caused by mutations in BRAF, MEK1, and MEK2. Mutations in KRAS and SHOC2 lead to a phenotype with overlapping features. In approximately 10–30% of individuals with a clinical diagnosis of CFC, a mutation in one of these causative genes is not found. Cardinal features of CFC include congenital heart defects, a characteristic facial appearance, and ectodermal abnormalities. Additional features include failure to thrive with severe feeding problems, moderate to severe intellectual disability and short stature with relative macrocephaly. First described in 1986, more than 100 affected individuals are reported. Following the discovery of the causative genes, more information has emerged on the breadth of clinical features. Little, however, has been published on genotype–phenotype correlations. This clinical study of 186 children and young adults with mutation-proven CFC syndrome is the largest reported to date. BRAF mutations are documented in 140 individuals (approximately 75%), while 46 (approximately 25%) have a mutation in MEK 1 or MEK 2. The age range is 6 months to 32 years, the oldest individual being a female from the original report [Reynolds et al. (1986); Am J Med Genet 25:413–427]. While some clinical data on 136 are in the literature, 50 are not previously published. We provide new details of the breadth of phenotype and discuss the frequency of particular features in each genotypic group. Pulmonary stenosis is the only anomaly that demonstrates a statistically significant genotype–phenotype correlation, being more common in individuals with a BRAF mutation.
-
Topological susceptibility from the overlap
DEFF Research Database (Denmark)
Del Debbio, Luigi; Pica, Claudio
2003-01-01
The chiral symmetry at finite lattice spacing of Ginsparg-Wilson fermionic actions constrains the renormalization of the lattice operators; in particular, the topological susceptibility does not require any renormalization, when using a fermionic estimator to define the topological charge....... Therefore, the overlap formalism appears as an appealing candidate to study the continuum limit of the topological susceptibility while keeping the systematic errors under theoretical control. We present results for the SU(3) pure gauge theory using the index of the overlap Dirac operator to study...
-
Baxter, Melissa; Withey, Sarah; Harrison, Sean; Segeritz, Charis-Patricia; Zhang, Fang; Atkinson-Dell, Rebecca; Rowe, Cliff; Gerrard, Dave T; Sison-Young, Rowena; Jenkins, Roz; Henry, Joanne; Berry, Andrew A; Mohamet, Lisa; Best, Marie; Fenwick, Stephen W; Malik, Hassan; Kitteringham, Neil R; Goldring, Chris E; Piper Hanley, Karen; Vallier, Ludovic; Hanley, Neil A
2015-03-01
Hepatocyte-like cells (HLCs), differentiated from pluripotent stem cells by the use of soluble factors, can model human liver function and toxicity. However, at present HLC maturity and whether any deficit represents a true fetal state or aberrant differentiation is unclear and compounded by comparison to potentially deteriorated adult hepatocytes. Therefore, we generated HLCs from multiple lineages, using two different protocols, for direct comparison with fresh fetal and adult hepatocytes. Protocols were developed for robust differentiation. Multiple transcript, protein and functional analyses compared HLCs to fresh human fetal and adult hepatocytes. HLCs were comparable to those of other laboratories by multiple parameters. Transcriptional changes during differentiation mimicked human embryogenesis and showed more similarity to pericentral than periportal hepatocytes. Unbiased proteomics demonstrated greater proximity to liver than 30 other human organs or tissues. However, by comparison to fresh material, HLC maturity was proven by transcript, protein and function to be fetal-like and short of the adult phenotype. The expression of 81% phase 1 enzymes in HLCs was significantly upregulated and half were statistically not different from fetal hepatocytes. HLCs secreted albumin and metabolized testosterone (CYP3A) and dextrorphan (CYP2D6) like fetal hepatocytes. In seven bespoke tests, devised by principal components analysis to distinguish fetal from adult hepatocytes, HLCs from two different source laboratories consistently demonstrated fetal characteristics. HLCs from different sources are broadly comparable with unbiased proteomic evidence for faithful differentiation down the liver lineage. This current phenotype mimics human fetal rather than adult hepatocytes. Copyright © 2014 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.
-
Racial Identity, Phenotype, and Self-Esteem among Biracial Polynesian/White Individuals
Allen, G. E. Kawika; Garriott, Patton O.; Reyes, Carla J.; Hsieh, Catherine
2013-01-01
This study examined racial identity, self-esteem, and phenotype among biracial Polynesian/White adults. Eighty-four Polynesian/White persons completed the Biracial Identity Attitude Scale, the Rosenberg Self-Esteem Inventory, and a Polynesian phenotype scale. Profile analyses showed participants identified more with their Polynesian parent. A…
-
Hanel, A.; Stilla, U.
2017-05-01
Vehicle environment cameras observing traffic participants in the area around a car and interior cameras observing the car driver are important data sources for driver intention recognition algorithms. To combine information from both camera groups, a camera system calibration can be performed. Typically, there is no overlapping field-of-view between environment and interior cameras. Often no marked reference points are available in environments, which are a large enough to cover a car for the system calibration. In this contribution, a calibration method for a vehicle camera system with non-overlapping camera groups in an urban environment is described. A-priori images of an urban calibration environment taken with an external camera are processed with the structure-frommotion method to obtain an environment point cloud. Images of the vehicle interior, taken also with an external camera, are processed to obtain an interior point cloud. Both point clouds are tied to each other with images of both image sets showing the same real-world objects. The point clouds are transformed into a self-defined vehicle coordinate system describing the vehicle movement. On demand, videos can be recorded with the vehicle cameras in a calibration drive. Poses of vehicle environment cameras and interior cameras are estimated separately using ground control points from the respective point cloud. All poses of a vehicle camera estimated for different video frames are optimized in a bundle adjustment. In an experiment, a point cloud is created from images of an underground car park, as well as a point cloud of the interior of a Volkswagen test car is created. Videos of two environment and one interior cameras are recorded. Results show, that the vehicle camera poses are estimated successfully especially when the car is not moving. Position standard deviations in the centimeter range can be achieved for all vehicle cameras. Relative distances between the vehicle cameras deviate between
-
Directory of Open Access Journals (Sweden)
Jonathan D Mosley
Full Text Available A single mutation can alter cellular and global homeostatic mechanisms and give rise to multiple clinical diseases. We hypothesized that these disease mechanisms could be identified using low minor allele frequency (MAF<0.1 non-synonymous SNPs (nsSNPs associated with "mechanistic phenotypes", comprised of collections of related diagnoses. We studied two mechanistic phenotypes: (1 thrombosis, evaluated in a population of 1,655 African Americans; and (2 four groupings of cancer diagnoses, evaluated in 3,009 white European Americans. We tested associations between nsSNPs represented on GWAS platforms and mechanistic phenotypes ascertained from electronic medical records (EMRs, and sought enrichment in functional ontologies across the top-ranked associations. We used a two-step analytic approach whereby nsSNPs were first sorted by the strength of their association with a phenotype. We tested associations using two reverse genetic models and standard additive and recessive models. In the second step, we employed a hypothesis-free ontological enrichment analysis using the sorted nsSNPs to identify functional mechanisms underlying the diagnoses comprising the mechanistic phenotypes. The thrombosis phenotype was solely associated with ontologies related to blood coagulation (Fisher's p = 0.0001, FDR p = 0.03, driven by the F5, P2RY12 and F2RL2 genes. For the cancer phenotypes, the reverse genetics models were enriched in DNA repair functions (p = 2×10-5, FDR p = 0.03 (POLG/FANCI, SLX4/FANCP, XRCC1, BRCA1, FANCA, CHD1L while the additive model showed enrichment related to chromatid segregation (p = 4×10-6, FDR p = 0.005 (KIF25, PINX1. We were able to replicate nsSNP associations for POLG/FANCI, BRCA1, FANCA and CHD1L in independent data sets. Mechanism-oriented phenotyping using collections of EMR-derived diagnoses can elucidate fundamental disease mechanisms.
-
Same Phenotype in Children with Growth Hormone Deficiency and Resistance
Directory of Open Access Journals (Sweden)
Irene Ioimo
2018-01-01
Full Text Available By definition, about 2.5% of children show a short stature due to several causes. Two clinical conditions are characterized by serum IGF-I low levels, idiopathic GH deficiency (IGHD, and GH insensitivity (GHI, and the phenotypic appearance of these patients may be very similar. We studied two children with short stature and similar phenotypes. The first case showed frontal bossing, doll face, acromicria, and truncal obesity, with a GH peak <0.05 ng/ml after stimuli and undetectable serum IGF-I levels. After PCR amplification of the whole GH1 gene, type IA idiopathic GHD was diagnosed. The second case had cranium hypoplasia, a large head, protruding forehead, saddle nose, underdeveloped mandible, and a micropenis. Basal GH levels were high (28.4 ng/ml while serum IGF-I levels were low and unchangeable during the IGF-I generation test. Laron syndrome was confirmed after the molecular analysis of the GH receptor (GHR gene. IGHD type IA and Laron syndrome is characterized by opposite circulating levels of GH, while both have reduced levels of IGF-I, with an overlapping clinical phenotype, lacking the effects of IGF-I on cartilage. These classical cases show the importance of differential diagnosis in children with severe short stature.
-
The phenotypes of podocytes and parietal epithelial cells may overlap in diabetic nephropathy.
Andeen, Nicole K; Nguyen, Tri Q; Steegh, Floor; Hudkins, Kelly L; Najafian, Behzad; Alpers, Charles E
2015-11-01
Reversal of diabetic nephropathy (DN) has been achieved in humans and mice, but only rarely and under special circumstances. As progression of DN is related to podocyte loss, reversal of DN requires restoration of podocytes. Here, we identified and quantified potential glomerular progenitor cells that could be a source for restored podocytes. DN was identified in 31 human renal biopsy cases and separated into morphologically early or advanced lesions. Markers of podocytes (WT-1, p57), parietal epithelial cells (PECs) (claudin-1), and cell proliferation (Ki-67) were identified by immunohistochemistry. Podocyte density was progressively reduced with DN. Cells marking as podocytes (p57) were present infrequently on Bowman's capsule in controls, but significantly increased in histologically early DN. Ki-67-expressing cells were identified on the glomerular tuft and Bowman's capsule in DN, but rarely in controls. Cells marking as PECs were present on the glomerular tuft, particularly in morphologically advanced DN. These findings show evidence of phenotypic plasticity in podocyte and PEC populations and are consistent with studies in the BTBR ob/ob murine model in which reversibility of DN occurs with podocytes potentially regenerating from PEC precursors. Thus, our findings support, but do not prove, that podocytes may regenerate from PEC progenitors in human DN. If so, progression of DN may represent a modifiable net balance between podocyte loss and regeneration.
-
Genotype-phenotype associations in obesity dependent on definition of the obesity phenotype.
Kring, Sofia Inez Iqbal; Larsen, Lesli Hingstrup; Holst, Claus; Toubro, Søren; Hansen, Torben; Astrup, Arne; Pedersen, Oluf; Sørensen, Thorkild I A
2008-01-01
In previous studies of associations of variants in the genes UCP2, UCP3, PPARG2, CART, GRL, MC4R, MKKS, SHP, GHRL, and MCHR1 with obesity, we have used a case-control approach with cases defined by a threshold for BMI. In the present study, we assess the association of seven abdominal, peripheral, and overall obesity phenotypes, which were analyzed quantitatively, and thirteen candidate gene polymorphisms in these ten genes in the same cohort. Obese Caucasian men (n = 234, BMI >or= 31.0 kg/m(2)) and a randomly sampled non-obese group (n = 323), originally identified at the draft board examinations, were re-examined at median ages of 47.0 or 49.0 years by anthropometry and DEXA scanning. Obesity phenotypes included BMI, fat body mass index, waist circumference, waist for given BMI, intra-abdominal adipose tissue, hip circumference and lower body fat mass (%). Using logistic regression models, we estimated the odds for defined genotypes (dominant or recessive genetic transmission) in relation to z-scores of the phenotypes. The minor (rare) allele for SHP 512G>C (rs6659176) was associated with increased hip circumference. The minor allele for UCP2 Ins45bp was associated with increased BMI, increased abdominal obesity, and increased hip circumference. The minor allele for UCP2 -866G>A (rs6593669) was associated with borderline increased fat body mass index. The minor allele for MCHR1 100213G>A (rs133072) was associated with reduced abdominal obesity. None of the other genotype-phenotype combinations showed appreciable associations. If replicated in independent studies with focus on the specific phenotypes, our explorative studies suggest significant associations between some candidate gene polymorphisms and distinct obesity phenotypes, predicting beneficial and detrimental effects, depending on compartments for body fat accumulation. Copyright 2008 S. Karger AG, Basel.
-
Simplicity of state and overlap structure in finite-volume realistic spin glasses
International Nuclear Information System (INIS)
Newman, C.M.; Stein, D.L.
1998-01-01
We present a combination of heuristic and rigorous arguments indicating that both the pure state structure and the overlap structure of realistic spin glasses should be relatively simple: in a large finite volume with coupling-independent boundary conditions, such as periodic, at most a pair of flip-related (or the appropriate number of symmetry-related in the non-Ising case) states appear, and the Parisi overlap distribution correspondingly exhibits at most a pair of δ functions at ±q EA . This rules out the nonstandard mean-field picture introduced by us earlier, and when combined with our previous elimination of more standard versions of the mean-field picture, argues against the possibility of even limited versions of mean-field ordering in realistic spin glasses. If broken spin-flip symmetry should occur, this leaves open two main possibilities for ordering in the spin glass phase: the droplet-scaling two-state picture, and the chaotic pairs many-state picture introduced by us earlier. We present scaling arguments which provide a possible physical basis for the latter picture, and discuss possible reasons behind numerical observations of more complicated overlap structures in finite volumes. copyright 1998 The American Physical Society
-
Directory of Open Access Journals (Sweden)
Tallulah Andrews
2015-03-01
Full Text Available Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51% groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects.
-
Andrews, Tallulah; Meader, Stephen; Vulto-van Silfhout, Anneke; Taylor, Avigail; Steinberg, Julia; Hehir-Kwa, Jayne; Pfundt, Rolph; de Leeuw, Nicole; de Vries, Bert B A; Webber, Caleb
2015-03-01
Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51%) groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i) this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii) that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects.
-
Cattle phenotypes can disguise their maternal ancestry.
Srirattana, Kanokwan; McCosker, Kieren; Schatz, Tim; St John, Justin C
2017-06-26
Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments. A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P cattle with a Bos taurus phenotype. The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.
-
Recurrent mutations in the CDKL5 gene: genotype-phenotype relationships.
Bahi-Buisson, Nadia; Villeneuve, Nathalie; Caietta, Emilie; Jacquette, Aurélia; Maurey, Helene; Matthijs, Gert; Van Esch, Hilde; Delahaye, Andrée; Moncla, Anne; Milh, Mathieu; Zufferey, Flore; Diebold, Bertrand; Bienvenu, Thierry
2012-07-01
Mutations in the cyclin-dependent kinase-like 5 gene (CDKL5) have been described in epileptic encephalopathies in females with infantile spasms with features that overlap with Rett syndrome. With more than 80 reported patients, the phenotype of CDKL5-related encephalopathy is well-defined. The main features consist of seizures starting before 6 months of age, severe intellectual disability with absent speech and hand stereotypies and deceleration of head growth, which resembles Rett syndrome. However, some clinical discrepancies suggested the influence of genetics and/or environmental factors. No genotype-phenotype correlation has been defined and thus there is a need to examine individual mutations. In this study, we analyzed eight recurrent CDKL5 mutations to test whether the clinical phenotype of patients with the same mutation is similar and whether patients with specific CDKL5 mutations have a milder phenotype than those with other CDKL5 mutations. Patients bearing missense mutations in the ATP binding site such as the p.Ala40Val mutation typically walked unaided, had normocephaly, better hand use ability, and less frequent refractory epilepsy when compared to girls with other CDKL5 mutations. In contrast, patients with mutations in the kinase domain (such as p.Arg59X, p.Arg134X, p.Arg178Trp/Pro/Gln, or c.145 + 2T > C) and frameshift mutations in the C-terminal region (such as c.2635_2636delCT) had a more severe phenotype with infantile spasms, refractory epileptic encephalopathy, absolute microcephaly, and inability to walk. It is important for clinicians to have this information when such patients are diagnosed. Copyright © 2012 Wiley Periodicals, Inc.
-
Phenotypic Resistance to Antibiotics
Directory of Open Access Journals (Sweden)
Jose L. Martinez
2013-04-01
Full Text Available The development of antibiotic resistance is usually associated with genetic changes, either to the acquisition of resistance genes, or to mutations in elements relevant for the activity of the antibiotic. However, in some situations resistance can be achieved without any genetic alteration; this is called phenotypic resistance. Non-inherited resistance is associated to specific processes such as growth in biofilms, a stationary growth phase or persistence. These situations might occur during infection but they are not usually considered in classical susceptibility tests at the clinical microbiology laboratories. Recent work has also shown that the susceptibility to antibiotics is highly dependent on the bacterial metabolism and that global metabolic regulators can modulate this phenotype. This modulation includes situations in which bacteria can be more resistant or more susceptible to antibiotics. Understanding these processes will thus help in establishing novel therapeutic approaches based on the actual susceptibility shown by bacteria during infection, which might differ from that determined in the laboratory. In this review, we discuss different examples of phenotypic resistance and the mechanisms that regulate the crosstalk between bacterial metabolism and the susceptibility to antibiotics. Finally, information on strategies currently under development for diminishing the phenotypic resistance to antibiotics of bacterial pathogens is presented.
-
The spatial patterns of directional phenotypic selection
Siepielski, Adam M.; Gotanda, Kiyoko M.; Morrissey, Michael B.; Diamond, Sarah E.; DiBattista, Joseph; Carlson, Stephanie Marie
2013-01-01
the spatial patterns of selection, namely the extent of variation among populations in the strength and direction of selection. Here, we analyse a data set of spatially replicated studies of directional phenotypic selection from natural populations. The data
-
BreedVision — A Multi-Sensor Platform for Non-Destructive Field-Based Phenotyping in Plant Breeding
Busemeyer, Lucas; Mentrup, Daniel; Möller, Kim; Wunder, Erik; Alheit, Katharina; Hahn, Volker; Maurer, Hans Peter; Reif, Jochen C.; Würschum, Tobias; Müller, Joachim; Rahe, Florian; Ruckelshausen, Arno
2013-01-01
To achieve the food and energy security of an increasing World population likely to exceed nine billion by 2050 represents a major challenge for plant breeding. Our ability to measure traits under field conditions has improved little over the last decades and currently constitutes a major bottleneck in crop improvement. This work describes the development of a tractor-pulled multi-sensor phenotyping platform for small grain cereals with a focus on the technological development of the system. Various optical sensors like light curtain imaging, 3D Time-of-Flight cameras, laser distance sensors, hyperspectral imaging as well as color imaging are integrated into the system to collect spectral and morphological information of the plants. The study specifies: the mechanical design, the system architecture for data collection and data processing, the phenotyping procedure of the integrated system, results from field trials for data quality evaluation, as well as calibration results for plant height determination as a quantified example for a platform application. Repeated measurements were taken at three developmental stages of the plants in the years 2011 and 2012 employing triticale (×Triticosecale Wittmack L.) as a model species. The technical repeatability of measurement results was high for nearly all different types of sensors which confirmed the high suitability of the platform under field conditions. The developed platform constitutes a robust basis for the development and calibration of further sensor and multi-sensor fusion models to measure various agronomic traits like plant moisture content, lodging, tiller density or biomass yield, and thus, represents a major step towards widening the bottleneck of non-destructive phenotyping for crop improvement and plant genetic studies. PMID:23447014
-
Distinct genetic architectures for phenotype means and plasticities in Zea mays.
Kusmec, Aaron; Srinivasan, Srikant; Nettleton, Dan; Schnable, Patrick S
2017-09-01
Phenotypic plasticity describes the phenotypic variation of a trait when a genotype is exposed to different environments. Understanding the genetic control of phenotypic plasticity in crops such as maize is of paramount importance for maintaining and increasing yields in a world experiencing climate change. Here, we report the results of genome-wide association analyses of multiple phenotypes and two measures of phenotypic plasticity in a maize nested association mapping (US-NAM) population grown in multiple environments and genotyped with ~2.5 million single-nucleotide polymorphisms. We show that across all traits the candidate genes for mean phenotype values and plasticity measures form structurally and functionally distinct groups. Such independent genetic control suggests that breeders will be able to select semi-independently for mean phenotype values and plasticity, thereby generating varieties with both high mean phenotype values and levels of plasticity that are appropriate for the target performance environments.
-
The fluid linguistic zone of causalities: areas of contrast and overlap
Directory of Open Access Journals (Sweden)
Andre Vinicius Lopes Coneglian
2015-01-01
Full Text Available The fluid linguistic zone of causalities: areas of contrast and overlap Abstract: This article is an investigation of the fluid linguistic adverbial zone of causalities. By conjugating functional and cognitive premisses in order to analyze language in use, we analyze the adverbial relations of cause, condition and concession aiming at identifying the semantic and pragmatic parameters through which we observe areas of contrast and overlap between these categories. The treatment given these adverbial relations presupposes that they be considered categories which present more prototypical members, that is, exemplar members, and more peripheral members, that may be allocated in areas of transition between categories. Ultimately, we argue in favor of a view a non-rigid grammatical categories, in this case, the category of adverbial relations, giving continuity to a trend of studies in functional and cognitive linguistics such as Dancygier and Sweetser (2005 and Neves (2010, 2012.
-
The impact of nectar chemical features on phenotypic variation in two related nectar yeasts.
Pozo, María I; Herrera, Carlos M; Van den Ende, Wim; Verstrepen, Kevin; Lievens, Bart; Jacquemyn, Hans
2015-06-01
Floral nectars become easily colonized by microbes, most often species of the ascomycetous yeast genus Metschnikowia. Although it is known that nectar composition can vary tremendously among plant species, most probably corresponding to the nutritional requirements of their main pollinators, far less is known about how variation in nectar chemistry affects intraspecific variation in nectarivorous yeasts. Because variation in nectar traits probably affects growth and abundance of nectar yeasts, nectar yeasts can be expected to display large phenotypic variation in order to cope with varying nectar conditions. To test this hypothesis, we related variation in the phenotypic landscape of a vast collection of nectar-living yeast isolates from two Metschnikowia species (M. reukaufii and M. gruessii) to nectar chemical traits using non-linear redundancy analyses. Nectar yeasts were collected from 19 plant species from different plant families to include as much variation in nectar chemical traits as possible. As expected, nectar yeasts displayed large variation in phenotypic traits, particularly in traits related to growth performance in carbon sources and inhibitors, which was significantly related to the host plant from which they were isolated. Total sugar concentration and relative fructose content significantly explained the observed variation in the phenotypic profile of the investigated yeast species, indicating that sugar concentration and composition are the key traits that affect phenotypic variation in nectarivorous yeasts. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
-
Structural Dynamic Analyses And Test Predictions For Spacecraft Structures With Non-Linearities
Vergniaud, Jean-Baptiste; Soula, Laurent; Newerla, Alfred
2012-07-01
The overall objective of the mechanical development and verification process is to ensure that the spacecraft structure is able to sustain the mechanical environments encountered during launch. In general the spacecraft structures are a-priori assumed to behave linear, i.e. the responses to a static load or dynamic excitation, respectively, will increase or decrease proportionally to the amplitude of the load or excitation induced. However, past experiences have shown that various non-linearities might exist in spacecraft structures and the consequences of their dynamic effects can significantly affect the development and verification process. Current processes are mainly adapted to linear spacecraft structure behaviour. No clear rules exist for dealing with major structure non-linearities. They are handled outside the process by individual analysis and margin policy, and analyses after tests to justify the CLA coverage. Non-linearities can primarily affect the current spacecraft development and verification process on two aspects. Prediction of flights loads by launcher/satellite coupled loads analyses (CLA): only linear satellite models are delivered for performing CLA and no well-established rules exist how to properly linearize a model when non- linearities are present. The potential impact of the linearization on the results of the CLA has not yet been properly analyzed. There are thus difficulties to assess that CLA results will cover actual flight levels. Management of satellite verification tests: the CLA results generated with a linear satellite FEM are assumed flight representative. If the internal non- linearities are present in the tested satellite then there might be difficulties to determine which input level must be passed to cover satellite internal loads. The non-linear behaviour can also disturb the shaker control, putting the satellite at risk by potentially imposing too high levels. This paper presents the results of a test campaign performed in
-
Directory of Open Access Journals (Sweden)
Calle Rubio M
2017-08-01
Full Text Available Myriam Calle Rubio,1,2 Ricard Casamor,3 Marc Miravitlles4 On behalf of the FENEPOC study group1Pulmonary Department, Hospital Clínico San Carlos, 2Department of Medicine, Faculty of Medicine, University Complutense of Madrid, Research Institute of Hospital Clínico San Carlos (IdISSC, Madrid, 3Medical Department, Novartis Farmaceutica, Barcelona, 4Pneumology Department, University Hospital Vall d’Hebron, CIBER de Enfermedades Respiratorias (CIBERES, Barcelona, SpainBackground: The Spanish Guidelines for COPD (GesEPOC describe four clinical phenotypes: non-exacerbator (NE, asthma-COPD overlap syndrome (ACO, frequent exacerbator with emphysema (EE, and exacerbator with chronic bronchitis (ECB. The objective of this study was to determine the frequency of COPD phenotypes, their clinical characteristics, and the availability of diagnostic tools to classify COPD phenotypes in clinical practice.Materials and methods: This study was an epidemiological, cross-sectional, and multicentered study. Patients ≥40 years old with a post-bronchodilator forced expiratory volume in 1 s (FEV1/forced vital capacity ratio of <0.7 and who were smokers or former smokers (with at least 10 pack-years were included. The availability of diagnostic tools to classify COPD phenotypes was assessed by an ad hoc questionnaire.Results: A total of 647 patients (294 primary care [PC], 353 pulmonology centers were included. Most patients were male (80.8%, with a mean age (SD of 68.2 (9.2 years, mean post-bronchodilator FEV1 was 53.2% (18.9% and they suffered a mean of 2.2 (2.1 exacerbations in the last year. NE was the most frequent phenotype (47.5% found, followed by ECB (29.1%, EE (17.0%, and ACO (6.5%. Significant differences between the four phenotypes were found regarding age; sex; body mass index; FEV1; body mass index, airflow obstruction, dyspnea, and exercise capacity (BODE/body mass index, airflow obstruction, dyspnea and exacerbations (BODEx index; modified Medical
-
Delineating SPTAN1 associated phenotypes
DEFF Research Database (Denmark)
Syrbe, Steffen; Harms, Frederike L; Parrini, Elena
2017-01-01
De novo in-frame deletions and duplications in the SPTAN1 gene, encoding the non-erythrocyte αII spectrin, have been associated with severe West syndrome with hypomyelination and pontocerebellar atrophy. We aimed at comprehensively delineating the phenotypic spectrum associated with SPTAN1 mutati...
-
Nfatc2 and Tob1 have non-overlapping function in T cell negative regulation and tumorigenesis.
Directory of Open Access Journals (Sweden)
Sarah L May
Full Text Available Nfatc2 and Tob1 are intrinsic negative regulators of T cell activation. Nfatc2-deficient and Tob1-deficient T cells show reduced thresholds of activation; however, whether these factors have independent or overlapping roles in negative regulation of T cell responses has not been previously examined. Here, we show that Nfatc2 knockout (KO but not Tob1 KO mice have age-associated accumulation of persistently activated T cells in vivo and expansion of the CD44+ memory cell compartment and age-associated lymphocytic infiltrates in visceral organs, without significant changes in numbers of CD4+CD25+Foxp3+ regulatory T cells (Treg. In vitro, CD4+CD25- "conventional" T cells (Tconvs from both KO strains showed greater proliferation than wild type (WT Tconvs. However, while Tregs from Nfatc2 KO mice retained normal suppressive function, Tregs from Tob1 KOs had enhanced suppressive activity. Nfatc2 KO Tconvs expanded somewhat more rapidly than WT Tconvs under conditions of homeostatic proliferation, but their accelerated growth capacity was negated, at least acutely, in a lymphoreplete environment. Finally, Nfatc2 KO mice developed a previously uncharacterized increase in B-cell malignancies, which was not accelerated by the absence of Tob1. The data thus support the prevailing hypothesis that Nfatc2 and Tob1 are non-redundant regulators of lymphocyte homeostasis.
-
Xeroderma Pigmentosum-Trichothiodystrophy overlap patient with novel XPD/ERCC2 mutation
Kralund, Henrik H.; Ousager, Lilian; Jaspers, Nicolaas G.; Raams, Anja; Pedersen, Erling B.; Gade, Else; Bygum, Anette
2013-01-01
Xeroderma Pigmentosum (XP), Trichothiodystrophy (TTD) and Cockayne Syndrome (CS) are rare, recessive disorders caused by mutational defects in the Nucleotide Excision Repair (NER) pathway and/or disruption of basic cellular DNA transcription. To date, a multitude of mutations in the XPD/ERCC2 gene have been described, many of which give rise to NER- and DNA transcription related diseases, which share certain diagnostic features and few overlap patients have been described. Despite increasing understanding of the roles of XPD/ERCC2 in mammalian cells, there is still weak predictability of somatic outcome from many of these mutations. We demonstrate a patient, believed to represent an overlap between XP and TTD/CS. In addition to other organ dysfunctions, the young man presented with Photosensitivity, Ichthyosis, Brittle hair, Impaired physical and mental development, Decreased fertility and Short stature (PIBIDS) suggestive of TTD, but lacking the almost patognomonic “tiger tail” banding of the hair under polarized light. Additionally, he developed basal cell carcinoma aged 28, as well as adult onset kidney failure, features normally not associated with TTD but rather XP/CS. His freckled appearance also suggested XP, but fibroblast cultures only demonstrated x2 UV-sensitivity with expected NER and TFIIH-activity decrease. Genetic sequencing of the XPD/ERCC2 gene established the patient as heterozygote compound with a novel, N-terminal Y18H mutation and a known C-terminal (TTD) mutation, A725P. The possible interplay between gene products and the patient phenotype is discussed. PMID:25002996
-
Gollasch, Benjamin; Basmanav, Fitnat Buket; Nanda, Arti; Fritz, Günter; Mahmoudi, Hassnaa; Thiele, Holger; Wehner, Maria; Wolf, Sabrina; Altmüller, Janine; Nürnberg, Peter; Frank, Jorge; Betz, Regina C
2015-11-01
Three children from an expanded consanguineous Kuwaiti kindred presented with ankyloblepharon, sparse and curly hair, and hypoplastic nails, suggestive of CHAND syndrome (OMIM 214350) that belongs to the heterogeneous spectrum of ectodermal dysplasias. After exclusion of pathogenic mutations in TP63 we performed homozygosity mapping, followed by exome sequencing of one affected individual. We initially identified three homozygous mutations in the linked region, located in PWP2, MX2 and RIPK4. Recently, mutations in RIPK4 have been reported in Bartsocas-Papas syndrome (OMIM 263650) that shows overlapping clinical symptoms with the phenotype observed in the affected individuals studied here. Subsequent analysis of affected and non-affected family members showed that mutation c.850G>A (p.Glu284Lys) in RIPK4 was in complete segregation with the disease phenotype, in accordance with an autosomal recessive inheritance pattern, thus supporting pathogenicity of this variant. Interestingly, however, our patients did not have cleft lip/palate, a common feature encountered in Bartsocas-Papas syndrome. Whereas in Bartsocas-Papas syndromes missense mutations are usually located within the serin/threonin kinase of RIPK4, the mutation detected in our family resides just outside of the kinase domain, which could explain the milder phenotype. Our data raise the question if CHAND syndrome indeed is a distinct entity. Alternatively, CHAND and Bartsocas-Papas syndrome might be allelic disorders or RIPK4 mutations could confer varying degrees of phenotypic severity, depending on their localization within or outside functionally important domains. Our findings indicate that making an accurate diagnosis based only on the prevailing clinical symptoms is challenging. © 2015 Wiley Periodicals, Inc.
-
Interleaved neuromuscular electrical stimulation: Motor unit recruitment overlap.
Wiest, Matheus J; Bergquist, Austin J; Schimidt, Helen L; Jones, Kelvin E; Collins, David F
2017-04-01
In this study, we quantified the "overlap" between motor units recruited by single pulses of neuromuscular electrical stimulation (NMES) delivered over the tibialis anterior muscle (mNMES) and the common peroneal nerve (nNMES). We then quantified the torque produced when pulses were alternated between the mNMES and nNMES sites at 40 Hz ("interleaved" NMES; iNMES). Overlap was assessed by comparing torque produced by twitches evoked by mNMES, nNMES, and both delivered together, over a range of stimulus intensities. Trains of iNMES were delivered at the intensity that produced the lowest overlap. Overlap was lowest (5%) when twitches evoked by both mNMES and nNMES produced 10% peak twitch torque. iNMES delivered at this intensity generated 25% of maximal voluntary dorsiflexion torque (11 Nm). Low intensity iNMES leads to low overlap and produces torque that is functionally relevant to evoke dorsiflexion during walking. Muscle Nerve 55: 490-499, 2017. © 2016 Wiley Periodicals, Inc.
-
Application of a latent class analysis to empirically define eating disorder phenotypes.
Keel, Pamela K; Fichter, Manfred; Quadflieg, Norbert; Bulik, Cynthia M; Baxter, Mark G; Thornton, Laura; Halmi, Katherine A; Kaplan, Allan S; Strober, Michael; Woodside, D Blake; Crow, Scott J; Mitchell, James E; Rotondo, Alessandro; Mauri, Mauro; Cassano, Giovanni; Treasure, Janet; Goldman, David; Berrettini, Wade H; Kaye, Walter H
2004-02-01
Diagnostic criteria for eating disorders influence how we recognize, research, and treat eating disorders, and empirically valid phenotypes are required for revealing their genetic bases. To empirically define eating disorder phenotypes. Data regarding eating disorder symptoms and features from 1179 individuals with clinically significant eating disorders were submitted to a latent class analysis. The resulting latent classes were compared on non-eating disorder variables in a series of validation analyses. Multinational, collaborative study with cases ascertained through diverse clinical settings (inpatient, outpatient, and community). Members of affected relative pairs recruited for participation in genetic studies of eating disorders in which probands met DSM-IV-TR criteria for anorexia nervosa (AN) or bulimia nervosa and had at least 1 biological relative with a clinically significant eating disorder. Main Outcome Measure Number and clinical characterization of latent classes. A 4-class solution provided the best fit. Latent class 1 (LC1) resembled restricting AN; LC2, AN and bulimia nervosa with the use of multiple methods of purging; LC3, restricting AN without obsessive-compulsive features; and LC4, bulimia nervosa with self-induced vomiting as the sole form of purging. Biological relatives were significantly likely to belong to the same latent class. Across validation analyses, LC2 demonstrated the highest levels of psychological disturbance, and LC3 demonstrated the lowest. The presence of obsessive-compulsive features differentiates among individuals with restricting AN. Similarly, the combination of low weight and multiple methods of purging distinguishes among individuals with binge eating and purging behaviors. These results support some of the distinctions drawn within the DSM-IV-TR among eating disorder subtypes, while introducing new features to define phenotypes.
-
A simple algorithm for the identification of clinical COPD phenotypes
Burgel, Pierre-Régis; Paillasseur, Jean-Louis; Janssens, Wim; Piquet, Jacques; ter Riet, Gerben; Garcia-Aymerich, Judith; Cosio, Borja; Bakke, Per; Puhan, Milo A.; Langhammer, Arnulf; Alfageme, Inmaculada; Almagro, Pere; Ancochea, Julio; Celli, Bartolome R.; Casanova, Ciro; de-Torres, Juan P.; Decramer, Marc; Echazarreta, Andrés; Esteban, Cristobal; Gomez Punter, Rosa Mar; Han, MeiLan K.; Johannessen, Ane; Kaiser, Bernhard; Lamprecht, Bernd; Lange, Peter; Leivseth, Linda; Marin, Jose M.; Martin, Francis; Martinez-Camblor, Pablo; Miravitlles, Marc; Oga, Toru; Sofia Ramírez, Ana; Sin, Don D.; Sobradillo, Patricia; Soler-Cataluña, Juan J.; Turner, Alice M.; Verdu Rivera, Francisco Javier; Soriano, Joan B.; Roche, Nicolas
2017-01-01
This study aimed to identify simple rules for allocating chronic obstructive pulmonary disease (COPD) patients to clinical phenotypes identified by cluster analyses. Data from 2409 COPD patients of French/Belgian COPD cohorts were analysed using cluster analysis resulting in the identification of
-
Dalzell, Johnathan J; McMaster, Steven; Johnston, Michael J; Kerr, Rachel; Fleming, Colin C; Maule, Aaron G
2009-11-01
Nine non-nematode-derived double-stranded RNAs (dsRNAs), designed for use as controls in RNA interference (RNAi) screens of neuropeptide targets, were found to induce aberrant phenotypes and an unexpected inhibitory effect on motility of root knot nematode Meloidogyne incognita J2s following 24h soaks in 0.1 mg/ml dsRNA; a simple soaking procedure which we have found to elicit profound knockdown of neuronal targets in Globodera pallida J2s. We have established that this inhibitory phenomenon is both time- and concentration-dependent, as shorter 4h soaks in 0.1 mg/ml dsRNA had no negative impact on M. incognita J2 stage worms, yet a 10-fold increase in concentration to 1 mg/ml for the same 4h time period had an even greater qualitative and quantitative impact on worm phenotype and motility. Further, a 10-fold increase of J2s soaked in 0.1 mg/ml dsRNA did not significantly alter the observed phenotypic aberration, which suggests that dsRNA uptake of the soaked J2s is not saturated under these conditions. This phenomenon was not initially observed in potato cyst nematode G. pallida J2s, which displayed no aberrant phenotype, or diminution of migratory activity in response to the same 0.1 mg/ml dsRNA 24h soaks. However, a 10-fold increase in dsRNA to 1mg/ml was found to elicit comparable irregularity of phenotype and inhibition of motility in G. pallida, to that initially observed in M. incognita following a 24h soak in 0.1 mg/ml dsRNA. Again, a 10-fold increase in the number of G. pallida J2s soaked in the same volume of 1 mg/ml dsRNA preparation did not significantly affect the observed phenotypic deviation. We do not observe any global impact on transcript abundance in either M. incognita or G. pallida J2s following 0.1 mg/ml dsRNA soaks, as revealed by reverse transcriptase-PCR and quantitative PCR data. This study aims to raise awareness of a phenomenon which we observe consistently and which we believe signifies a more expansive deficiency in our knowledge and
-
Transiting topological sectors with the overlap
International Nuclear Information System (INIS)
Creutz, Michael
2003-01-01
The overlap operator provides an elegant definition for the winding number of lattice gauge field configurations. Only for a set of configurations of measure zero is this procedure undefined. Without restrictions on the lattice fields, however, the space of gauge fields is simply connected. I present a simple low dimensional illustration of how the eigenvalues of a truncated overlap operator flow as one travels between different topological sectors
-
Non-Cell Autonomous Effects of the Senescence-Associated Secretory Phenotype in Cancer Therapy
Directory of Open Access Journals (Sweden)
Tareq Saleh
2018-05-01
Full Text Available In addition to promoting various forms of cell death, most conventional anti-tumor therapies also promote senescence. There is now extensive evidence that therapy-induced senescence (TIS might be transient, raising the concern that TIS could represent an undesirable outcome of therapy by providing a mechanism for tumor dormancy and eventual disease recurrence. The senescence-associated secretory phenotype (SASP is a hallmark of TIS and may contribute to aberrant effects of cancer therapy. Here, we propose that the SASP may also serve as a major driver of escape from senescence and the re-emergence of proliferating tumor cells, wherein factors secreted from the senescent cells contribute to the restoration of tumor growth in a non-cell autonomous fashion. Accordingly, anti-SASP therapies might serve to mitigate the deleterious outcomes of TIS. In addition to providing an overview of the putative actions of the SASP, we discuss recent efforts to identify and eliminate senescent tumor cells.
-
Tordjman, S; Cohen, D; Anderson, G M; Botbol, M; Canitano, R; Coulon, N; Roubertoux, P L
2018-06-01
Clinical and molecular genetics have advanced current knowledge on genetic disorders associated with autism. A review of diverse genetic disorders associated with autism is presented and for the first time discussed extensively with regard to possible common underlying mechanisms leading to a similar cognitive-behavioral phenotype of autism. The possible role of interactions between genetic and environmental factors, including epigenetic mechanisms, is in particular examined. Finally, the pertinence of distinguishing non-syndromic autism (isolated autism) from syndromic autism (autism associated with genetic disorders) will be reconsidered. Given the high genetic and etiological heterogeneity of autism, autism can be viewed as a behavioral syndrome related to known genetic disorders (syndromic autism) or currently unknown disorders (apparent non-syndromic autism), rather than a specific categorical mental disorder. It highlights the need to study autism phenotype and developmental trajectory through a multidimensional, non-categorical approach with multivariate analyses within autism spectrum disorder but also across mental disorders, and to conduct systematically clinical genetic examination searching for genetic disorders in all individuals (children but also adults) with autism. Copyright © 2018. Published by Elsevier Ltd.
-
Pierson, Tyler Mark; Simeonov, Dimitre R; Sincan, Murat; Adams, David A; Markello, Thomas; Golas, Gretchen; Fuentes-Fajardo, Karin; Hansen, Nancy F; Cherukuri, Praveen F; Cruz, Pedro; Blackstone, Craig; Tifft, Cynthia; Boerkoel, Cornelius F; Gahl, William A
2012-01-01
Fatty acid hydroxylase-associated neurodegeneration due to fatty acid 2-hydroxylase deficiency presents with a wide range of phenotypes including spastic paraplegia, leukodystrophy, and/or brain iron deposition. All previously described families with this disorder were consanguineous, with homozygous mutations in the probands. We describe a 10-year-old male, from a non-consanguineous family, with progressive spastic paraplegia, dystonia, ataxia, and cognitive decline associated with a sural axonal neuropathy. The use of high-throughput sequencing techniques combined with SNP array analyses revealed a novel paternally derived missense mutation and an overlapping novel maternally derived ∼28-kb genomic deletion in FA2H. This patient provides further insight into the consistent features of this disorder and expands our understanding of its phenotypic presentation. The presence of a sural nerve axonal neuropathy had not been previously associated with this disorder and so may extend the phenotype. PMID:22146942
-
Prevalence of sexual dimorphism in mammalian phenotypic traits
Karp, Natasha A.; Mason, Jeremy; Beaudet, Arthur L.; Benjamini, Yoav; Bower, Lynette; Braun, Robert E.; Brown, Steve D.M.; Chesler, Elissa J.; Dickinson, Mary E.; Flenniken, Ann M.; Fuchs, Helmut; Angelis, Martin Hrabe de; Gao, Xiang; Guo, Shiying; Greenaway, Simon; Heller, Ruth; Herault, Yann; Justice, Monica J.; Kurbatova, Natalja; Lelliott, Christopher J.; Lloyd, K.C. Kent; Mallon, Ann-Marie; Mank, Judith E.; Masuya, Hiroshi; McKerlie, Colin; Meehan, Terrence F.; Mott, Richard F.; Murray, Stephen A.; Parkinson, Helen; Ramirez-Solis, Ramiro; Santos, Luis; Seavitt, John R.; Smedley, Damian; Sorg, Tania; Speak, Anneliese O.; Steel, Karen P.; Svenson, Karen L.; Obata, Yuichi; Suzuki, Tomohiro; Tamura, Masaru; Kaneda, Hideki; Furuse, Tamio; Kobayashi, Kimio; Miura, Ikuo; Yamada, Ikuko; Tanaka, Nobuhiko; Yoshiki, Atsushi; Ayabe, Shinya; Clary, David A.; Tolentino, Heather A.; Schuchbauer, Michael A.; Tolentino, Todd; Aprile, Joseph Anthony; Pedroia, Sheryl M.; Kelsey, Lois; Vukobradovic, Igor; Berberovic, Zorana; Owen, Celeste; Qu, Dawei; Guo, Ruolin; Newbigging, Susan; Morikawa, Lily; Law, Napoleon; Shang, Xueyuan; Feugas, Patricia; Wang, Yanchun; Eskandarian, Mohammad; Zhu, Yingchun; Nutter, Lauryl M. J.; Penton, Patricia; Laurin, Valerie; Clarke, Shannon; Lan, Qing; Sohel, Khondoker; Miller, David; Clark, Greg; Hunter, Jane; Cabezas, Jorge; Bubshait, Mohammed; Carroll, Tracy; Tondat, Sandra; MacMaster, Suzanne; Pereira, Monica; Gertsenstein, Marina; Danisment, Ozge; Jacob, Elsa; Creighton, Amie; Sleep, Gillian; Clark, James; Teboul, Lydia; Fray, Martin; Caulder, Adam; Loeffler, Jorik; Codner, Gemma; Cleak, James; Johnson, Sara; Szoke-Kovacs, Zsombor; Radage, Adam; Maritati, Marina; Mianne, Joffrey; Gardiner, Wendy; Allen, Susan; Cater, Heather; Stewart, Michelle; Keskivali-Bond, Piia; Sinclair, Caroline; Brown, Ellen; Doe, Brendan; Wardle-Jones, Hannah; Grau, Evelyn; Griggs, Nicola; Woods, Mike; Kundi, Helen; Griffiths, Mark N. D.; Kipp, Christian; Melvin, David G.; Raj, Navis P. S.; Holroyd, Simon A.; Gannon, David J.; Alcantara, Rafael; Galli, Antonella; Hooks, Yvette E.; Tudor, Catherine L.; Green, Angela L.; Kussy, Fiona L.; Tuck, Elizabeth J.; Siragher, Emma J.; Maguire, Simon A.; Lafont, David T.; Vancollie, Valerie E.; Pearson, Selina A.; Gates, Amy S.; Sanderson, Mark; Shannon, Carl; Anthony, Lauren F. E.; Sumowski, Maksymilian T.; McLaren, Robbie S. B.; Swiatkowska, Agnieszka; Isherwood, Christopher M.; Cambridge, Emma L; Wilson, Heather M.; Caetano, Susana S.; Mazzeo, Cecilia Icoresi; Dabrowska, Monika H.; Lillistone, Charlotte; Estabel, Jeanne; Maguire, Anna Karin B.; Roberson, Laura-Anne; Pavlovic, Guillaume; Birling, Marie-Christine; Marie, Wattenhofer-Donze; Jacquot, Sylvie; Ayadi, Abdel; Ali-Hadji, Dalila; Charles, Philippe; André, Philippe; Le Marchand, Elise; El Amri, Amal; Vasseur, Laurent; Aguilar-Pimentel, Antonio; Becker, Lore; Treise, Irina; Moreth, Kristin; Stoeger, Tobias; Amarie, Oana V.; Neff, Frauke; Wurst, Wolfgang; Bekeredjian, Raffi; Ollert, Markus; Klopstock, Thomas; Calzada-Wack, Julia; Marschall, Susan; Brommage, Robert; Steinkamp, Ralph; Lengger, Christoph; Östereicher, Manuela A.; Maier, Holger; Stoeger, Claudia; Leuchtenberger, Stefanie; Yildrim, AliÖ; Garrett, Lillian; Hölter, Sabine M; Zimprich, Annemarie; Seisenberger, Claudia; Bürger, Antje; Graw, Jochen; Eickelberg, Oliver; Zimmer, Andreas; Wolf, Eckhard; Busch, Dirk H; Klingenspor, Martin; Schmidt-Weber, Carsten; Gailus-Durner, Valérie; Beckers, Johannes; Rathkolb, Birgit; Rozman, Jan; Wakana, Shigeharu; West, David; Wells, Sara; Westerberg, Henrik; Yaacoby, Shay; White, Jacqueline K.
2017-01-01
The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both in wildtype and mutants are influenced by sex. This result has implications for interpreting disease phenotypes in animal models and humans. PMID:28650954
-
Directory of Open Access Journals (Sweden)
Charles Onyutha
2017-10-01
Full Text Available Some of the problems in drought assessments are that: analyses tend to focus on coarse temporal scales, many of the methods yield skewed indices, a few terminologies are ambiguously used, and analyses comprise an implicit assumption that the observations come from a stationary process. To solve these problems, this paper introduces non-stationary frequency analyses of quantiles. How to use non-parametric rescaling to obtain robust indices that are not (or minimally skewed is also introduced. To avoid ambiguity, some concepts on, e.g., incidence, extremity, etc., were revisited through shift from monthly to daily time scale. Demonstrations on the introduced methods were made using daily flow and precipitation insufficiency (precipitation minus potential evapotranspiration from the Blue Nile basin in Africa. Results show that, when a significant trend exists in extreme events, stationarity-based quantiles can be far different from those when non-stationarity is considered. The introduced non-parametric indices were found to closely agree with the well-known standardized precipitation evapotranspiration indices in many aspects but skewness. Apart from revisiting some concepts, the advantages of the use of fine instead of coarse time scales in drought assessment were given. The links for obtaining freely downloadable tools on how to implement the introduced methods were provided.
-
Camarero, J J; Palacio, S; Montserrat-Martí, G
2013-09-01
Whole-plant approaches allow quantification of the temporal overlap between primary and secondary growth. If the amount of time available to grow is short, there may be a high temporal overlap between shoot growth and wood formation. We hypothesise that such overlap depends on the duration of the growing season and relates to wood anatomy. We evaluated wood anatomy, shoot longitudinal and radial growth rates, fine root production and the concentrations of non-structural carbohydrates (NSC) in the wood of six sub-shrub species growing in sites with contrasting climatic conditions (Lepidium subulatum, Linum suffruticosum, Salvia lavandulifolia, Satureja montana, Ononis fruticosa, Echinospartum horridum). Sub-shrub species living in sites with a short growing season displayed a high overlap between aboveground primary and secondary growth and formed wide vessels, whereas species from the warmest and driest sites presented the reverse characteristics. The highest overlap was linked to a rapid shoot extension and thickening through the enhanced hydraulic conductivity provided by wide vessels. The reductions in NSC concentrations when growth peaked were low or moderate, indicating that sub-shrubs accumulate NSC in excess, as do trees. The temporal overlap among primary and secondary growth in woody plants may be connected to the duration and rates of shoot and wood growth, which in turn depend on the vessel lumen area. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.
-
Directory of Open Access Journals (Sweden)
De Molfetta Greice Andreotti
2002-01-01
Full Text Available Angelman syndrome (AS and Prader-Willi syndrome (PWS are distinct human neurogenetic disorders; however, a clinical overlap between AS and PWS has been identified. We report on a further case of a patient showing the PWS phenotype with the AS molecular defect. Despite the PWS phenotype, the DNA methylation analysis of SNRPN revealed an AS pattern. Cytogenetic and FISH analysis showed normal chromosomes 15 and microsatellite analysis showed heterozygous loci inside and outside the 15q11-13 region. The presence of these atypical cases could be more frequent than previously expected and we reinforce that the DNA methylation analysis is important for the correct diagnosis of severe mental deficiency, congenital hypotonia and obesity.
-
Sprovieri, T; Conforti, F L; Fiumara, A; Mazzei, R; Ungaro, C; Citrigno, L; Muglia, M; Arena, A; Quattrone, A
2009-02-15
Mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have recently been reported in patients with severe neurodevelopmental disorder characterized by early-onset seizures, infantile spasms, severe psychomotor impairment and very recently, in patients with Rett syndrome (RTT)-like phenotype. Although the involvement of CDKL5 in specific biological pathways and its neurodevelopmental role have not been completely elucidated, the CDKL5 appears to be physiologically related to the MECP2 gene. Here we report on the clinical and CDKL5 molecular investigation in a very unusual RTT case, with severe, early-neurological involvement in which we have shown in a previous report, a novel P388S MECP2 mutation [Conforti et al. (2003); Am J Med Genet A 117A: 184-187]. The patient has had severe psychomotor delay since the first month of life and infantile spasms since age 5 months. Moreover, at age 5 years the patient suddenly presented with renal failure. The severe pattern of symptoms in our patient, similar to a CDKL5 phenotype, prompted us to perform an analysis of the CDKL5, which revealed a novel missense mutation never previously described. The X-inactivation assay was non-informative. In conclusion, this report reinforces the observation that the CDKL5 phenotype overlaps with RTT and that CDKL5 analysis is recommended in patients with a seizure disorder commencing during the first months of life.
-
Numerical properties of staggered overlap fermions
de Forcrand, Philippe; Panero, Marco
2010-01-01
We report the results of a numerical study of staggered overlap fermions, following the construction of Adams which reduces the number of tastes from 4 to 2 without fine-tuning. We study the sensitivity of the operator to the topology of the gauge field, its locality and its robustness to fluctuations of the gauge field. We make a first estimate of the computing cost of a quark propagator calculation, and compare with Neuberger's overlap.
-
Bergamo, Pedro Joaquim; Wolowski, Marina; Maruyama, Pietro Kiyoshi; Vizentin-Bugoni, Jeferson; Carvalheiro, Luísa G; Sazima, Marlies
2017-07-01
Plant species within communities may overlap in pollinators' use and influence visitation patterns of shared pollinators, potentially engaging in indirect interactions (e.g., facilitation or competition). While several studies have explored the mechanisms regulating insect-pollination networks, there is a lack of studies on bird-pollination systems, particularly in species-rich tropical areas. Here, we evaluated if phenotypic similarity, resource availability (floral abundance), evolutionary relatedness and flowering phenology affect the potential for indirect effects via shared pollinators in hummingbird-pollinated plant species within four communities in the Brazilian Atlantic forest. Among the evaluated factors, phenotypic similarity (corolla length and anther height) was the most important variable, while resource availability (floral abundance) had a secondary importance. On the other hand, evolutionary relatedness and flowering phenology were less important, which altogether highlights the relevance of convergent evolution and that the contribution of a plant to the diet of the pollinators of another plant is independent of the level of temporal overlap in flowering in this tropical system. Interestingly, our findings contrast with results from multiple insect-pollinated plant communities, mostly from temperate regions, in which floral abundance was the most important driver, followed by evolutionary relatedness and phenotypic similarity. We propose that these contrasting results are due to high level of specialization inherent to tropical hummingbird-pollination systems. Moreover, our results demonstrated that factors defining linkage rules of plant-hummingbird networks also determinate plant-plant potential indirect effects. Future studies are needed to test if these findings can be generalized to other highly specialized systems. Overall, our results have important implications for the understanding of ecological processes due resource sharing in
-
Directory of Open Access Journals (Sweden)
Rivka Colen
2014-10-01
Full Text Available The National Cancer Institute (NCI Cancer Imaging Program organized two related workshops on June 26–27, 2013, entitled “Correlating Imaging Phenotypes with Genomics Signatures Research” and “Scalable Computational Resources as Required for Imaging-Genomics Decision Support Systems.” The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently advanced to correlate with imaging phenotypes that underpin genomics and clinical outcomes, and exploring new scientific methods to extract phenotypic features from medical images and relate them to genomics analyses. The second workshop focused on computational methods that explore informatics and computational requirements to extract phenotypic features from medical images and relate them to genomics analyses and improve the accessibility and speed of dissemination of existing NIH resources. These workshops linked clinical and scientific requirements of currently known phenotypic and genotypic cancer biology characteristics with imaging phenotypes that underpin genomics and clinical outcomes. The group generated a set of recommendations to NCI leadership and the research community that encourage and support development of the emerging radiogenomics research field to address short-and longer-term goals in cancer research.
-
DEFF Research Database (Denmark)
Witt, S H; Streit, F; Jungkunz, M
2017-01-01
Borderline personality disorder (BOR) is determined by environmental and genetic factors, and characterized by affective instability and impulsivity, diagnostic symptoms also observed in manic phases of bipolar disorder (BIP). Up to 20% of BIP patients show comorbidity with BOR. This report...... describes the first case-control genome-wide association study (GWAS) of BOR, performed in one of the largest BOR patient samples worldwide. The focus of our analysis was (i) to detect genes and gene sets involved in BOR and (ii) to investigate the genetic overlap with BIP. As there is considerable genetic...... overlap between BIP, major depression (MDD) and schizophrenia (SCZ) and a high comorbidity of BOR and MDD, we also analyzed the genetic overlap of BOR with SCZ and MDD. GWAS, gene-based tests and gene-set analyses were performed in 998 BOR patients and 1545 controls. Linkage disequilibrium score...
-
Automatic and controlled processing and the Broad Autism Phenotype.
Camodeca, Amy; Voelker, Sylvia
2016-01-30
Research related to verbal fluency in the Broad Autism Phenotype (BAP) is limited and dated, but generally suggests intact abilities in the context of weaknesses in other areas of executive function (Hughes et al., 1999; Wong et al., 2006; Delorme et al., 2007). Controlled processing, the generation of search strategies after initial, automated responses are exhausted (Spat, 2013), has yet to be investigated in the BAP, and may be evidenced in verbal fluency tasks. One hundred twenty-nine participants completed the Delis-Kaplan Executive Function System Verbal Fluency test (D-KEFS; Delis et al., 2001) and the Broad Autism Phenotype Questionnaire (BAPQ; Hurley et al., 2007). The BAP group (n=53) produced significantly fewer total words during the 2nd 15" interval compared to the Non-BAP (n=76) group. Partial correlations indicated similar relations between verbal fluency variables for each group. Regression analyses predicting 2nd 15" interval scores suggested differentiation between controlled and automatic processing skills in both groups. Results suggest adequate automatic processing, but slowed development of controlled processing strategies in the BAP, and provide evidence for similar underlying cognitive constructs for both groups. Controlled processing was predictive of Block Design score for Non-BAP participants, and was predictive of Pragmatic Language score on the BAPQ for BAP participants. These results are similar to past research related to strengths and weaknesses in the BAP, respectively, and suggest that controlled processing strategy use may be required in instances of weak lower-level skills. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
-
Mealey, Alex; Abbott, Gavin; Byrne, Linda K; McGillivray, Jane
2014-10-30
Autism spectrum and schizophrenia spectrum disorders are classified separately in the DSM-5, yet research indicates that these two disorders share overlapping features. The aim of the present study was to examine the overlap between autistic and schizotypal personality traits and whether anxiety and depression act as confounding variables in this relationship within a non-clinical population. One hundred and forty-four adults completed the Autism Spectrum Quotient and the Schizotypal Personality Questionnaire and the Depression Anxiety Stress Scales-21. A number of associations were seen between autistic and schizotypal personality traits. However, negative traits were the only schizotypal feature to uniquely predict global autistic traits, thus highlighting the importance of interpersonal qualities in the overlap of autistic and schizotypal characteristics. The inclusion of anxiety and depression did not alter relationships between autistic and schizotypal traits, indicating that anxiety and depression are not confounders of this relationship. These findings have important implications for the conceptualisation of both disorders. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
-
International Nuclear Information System (INIS)
Dimitrova, S.S.; Gaidarov, M.K.; Antonov, A.N.; Stoitsov, M.V.; Hodgson, P.E; Lukyanov, V.K.; Zemlyanaya, E.V.; Krumova, G.Z.
1997-01-01
Overlap functions and spectroscopic factors extracted from a model one-body density matrix (OBDM) accounting for short-range nucleon-nucleon correlations are used to calculate differential cross sections of (p, d) reactions and the momentum distributions of transitions to single-particle states in 16 O and 40 Ca. A comparison between the experimental (p, d) and (e, e'p) data, their DWBA and CDWIA analyses and the OBDM calculations is made. Our theoretical predictions for the spectroscopic factors are compared with the empirically extracted ones. It is shown that the overlap functions obtained within the Jastrow correlation method are applicable to the description of the quantities considered. (author)
-
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
Dierks, C; Mömke, S; Philipp, U; Distl, O
2013-08-01
Hitherto, the only known mutant gene leading to the long-hair phenotype in mammals is the fibroblast growth factor 5 (FGF5). In many dog breeds, the previously discovered FGF5:p.Cys95Phe mutation appeared completely concordant with the long-hair phenotype, but for some breeds, the long-hair phenotype could not be resolved. First, we studied the role of the FGF5:p.Cys95Phe and FGF5:g.145_150dupACCAGC mutations in 268 dogs descending from 27 breeds and seven wolves. As these mutations did not explain all the long-hair phenotypes, all exons and their neighbouring regions of FGF5 were re-sequenced. We detected three novel mutations in the coding sequence and one novel non-coding splice-site mutation in FGF5 associated with the long-hair phenotype. The FGF5:p.Ala193Val polymorphism was perfectly consistent with long hair in Akitas and probably in Siberian huskies, too. Dogs of the long-hair breed Samoyed were either homozygous or compound heterozygous for the FGF5:p.Ala193Val or the FGF5:p.Cys95Phe polymorphisms respectively. The two newly detected polymorphisms FGF5:c.559_560dupGG and FGF5:g.8193T>A and the known mutation FGF5:p.Cys95Phe explained the long-hair phenotype of all Afghan hounds analysed. An FGF5:c.556_571del16 mutation was found in one longhaired Eurasier. All long-hair-associated mutations follow a recessive mode of inheritance, and allelic heterogeneity was a common finding in breeds other than Akita. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.
-
Directory of Open Access Journals (Sweden)
Nadia Tinto
Full Text Available BACKGROUND: Maturity onset diabetes of the young type 2 (or GCK MODY is a genetic form of diabetes mellitus provoked by mutations in the glucokinase gene (GCK. METHODOLOGY/PRINCIPAL FINDINGS: We screened the GCK gene by direct sequencing in 30 patients from South Italy with suspected MODY. The mutation-induced structural alterations in the protein were analyzed by molecular modeling. The patients' biochemical, clinical and anamnestic data were obtained. Mutations were detected in 16/30 patients (53%; 9 of the 12 mutations identified were novel (p.Glu70Asp, p.Phe123Leu, p.Asp132Asn, p.His137Asp, p.Gly162Asp, p.Thr168Ala, p.Arg392Ser, p.Glu290X, p.Gln106_Met107delinsLeu and are in regions involved in structural rearrangements required for catalysis. The prevalence of mutation sites was higher in the small domain (7/12: approximately 59% than in the large (4/12: 33% domain or in the connection (1/12: 8% region of the protein. Mild diabetic phenotypes were detected in almost all patients [mean (SD OGTT = 7.8 mMol/L (1.8] and mean triglyceride levels were lower in mutated than in unmutated GCK patients (p = 0.04. CONCLUSIONS: The prevalence of GCK MODY is high in southern Italy, and the GCK small domain is a hot spot for MODY mutations. Both the severity of the GCK mutation and the genetic background seem to play a relevant role in the GCK MODY phenotype. Indeed, a partial genotype-phenotype correlation was identified in related patients (3 pairs of siblings but not in two unrelated children bearing the same mutation. Thus, the molecular approach allows the physician to confirm the diagnosis and to predict severity of the mutation.
-
Awlia, Mariam Sahal Abdulaziz; Nigro, Arianna; Fajkus, Jiří
; Schmoeckel, Sandra Manuela; Negrã o, Só nia; Santelia, Diana; Trtí lek, Martin; Tester, Mark A.; Julkowska, Magdalena; Panzarová , Klá ra 2016-01-01
stage, plant performance correlated with quantum yield. This integrative approach allows the simultaneous analysis of several phenotypic traits. In combination with various genetic resources, the phenotyping protocol described here is expected
-
Non-dystrophic myotonia: prospective study of objective and patient reported outcomes.
Trivedi, Jaya R; Bundy, Brian; Statland, Jeffrey; Salajegheh, Mohammad; Rayan, Dipa Raja; Venance, Shannon L; Wang, Yunxia; Fialho, Doreen; Matthews, Emma; Cleland, James; Gorham, Nina; Herbelin, Laura; Cannon, Stephen; Amato, Anthony; Griggs, Robert C; Hanna, Michael G; Barohn, Richard J
2013-07-01
Non-dystrophic myotonias are rare diseases caused by mutations in skeletal muscle chloride and sodium ion channels with considerable phenotypic overlap between diseases. Few prospective studies have evaluated the sensitivity of symptoms and signs of myotonia in a large cohort of patients. We performed a prospective observational study of 95 participants with definite or clinically suspected non-dystrophic myotonia recruited from six sites in the USA, UK and Canada between March 2006 and March 2009. We used the common infrastructure and data elements provided by the NIH-funded Rare Disease Clinical Research Network. Outcomes included a standardized symptom interview and physical exam; the Short Form-36 and the Individualized Neuromuscular Quality of Life instruments; electrophysiological short and prolonged exercise tests; manual muscle testing; and a modified get-up-and-go test. Thirty-two participants had chloride channel mutations, 34 had sodium channel mutations, nine had myotonic dystrophy type 2, one had myotonic dystrophy type 1, and 17 had no identified mutation. Phenotype comparisons were restricted to those with sodium channel mutations, chloride channel mutations, and myotonic dystrophy type 2. Muscle stiffness was the most prominent symptom overall, seen in 66.7% to 100% of participants. In comparison with chloride channel mutations, participants with sodium mutations had an earlier age of onset of stiffness (5 years versus 10 years), frequent eye closure myotonia (73.5% versus 25%), more impairment on the Individualized Neuromuscular Quality of Life summary score (20.0 versus 9.44), and paradoxical eye closure myotonia (50% versus 0%). Handgrip myotonia was seen in three-quarters of participants, with warm up of myotonia in 75% chloride channel mutations, but also 35.3% of sodium channel mutations. The short exercise test showed ≥10% decrement in the compound muscle action potential amplitude in 59.3% of chloride channel participants compared with 27
-
Directory of Open Access Journals (Sweden)
Kenkichi Takase
Full Text Available The demand for meta-analyses in basic biomedical research has been increasing because the phenotyping of genetically modified mice does not always produce consistent results. Melanin-concentrating hormone (MCH has been reported to be involved in a variety of behaviors that include feeding, body-weight regulation, anxiety, sleep, and reward behavior. However, the reported behavioral and metabolic characteristics of MCH signaling-deficient mice, such as MCH-deficient mice and MCH receptor 1 (MCHR1-deficient mice, are not consistent with each other. In the present study, we performed a meta-analysis of the published data related to MCH-deficient and MCHR1-deficient mice to obtain robust conclusions about the role of MCH signaling. Overall, the meta-analysis revealed that the deletion of MCH signaling enhanced wakefulness, locomotor activity, aggression, and male sexual behavior and that MCH signaling deficiency suppressed non-REM sleep, anxiety, responses to novelty, startle responses, and conditioned place preferences. In contrast to the acute orexigenic effect of MCH, MCH signaling deficiency significantly increased food intake. Overall, the meta-analysis also revealed that the deletion of MCH signaling suppressed the body weight, fat mass, and plasma leptin, while MCH signaling deficiency increased the body temperature, oxygen consumption, heart rate, and mean arterial pressure. The lean phenotype of the MCH signaling-deficient mice was also confirmed in separate meta-analyses that were specific to sex and background strain (i.e., C57BL/6 and 129Sv. MCH signaling deficiency caused a weak anxiolytic effect as assessed with the elevated plus maze and the open field test but also caused a weak anxiogenic effect as assessed with the emergence test. MCH signaling-deficient mice also exhibited increased plasma corticosterone under non-stressed conditions, which suggests enhanced activity of the hypothalamic-pituitary-adrenal axis. To the best of our
-
Craig, Francesco; Lamanna, Anna Linda; Margari, Francesco; Matera, Emilia; Simone, Marta; Margari, Lucia
2015-06-01
Recent studies support several overlapping traits between autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD), assuming the existence of a combined phenotype. The aim of our study was to evaluate the common or distinctive clinical features between ASD and ADHD in order to identify possible different phenotypes that could have a clinical value. We enrolled 181 subjects divided into four diagnostic groups: ADHD group, ASD group, ASD+ADHD group (that met diagnostic criteria for both ASD and ADHD), and control group. Intelligent quotient (IQ), emotional and behavior problems, ADHD symptoms, ASD symptoms, and adaptive behaviors were investigated through the following test: Wechsler Intelligence Scale for Children, Wechsler Preschool and Primary Scale of Intelligence or Leiter International Performances Scale Revised, Child Behavior Checklist, Conners' Rating Scales-Revised, SNAP-IV Rating Scale, the Social Communication Questionnaire, Vineland Adaptive Behavior Scales. The ASD+ADHD group differs from ADHD or ASD in some domains such as lower IQ mean level and a higher autistic symptoms severity. However, the ASD+ADHD group shares inattention and hyperactivity deficit and some emotional and behavior problems with the ADHD group, while it shares adaptive behavior impairment with ASD group. These findings provide a new understanding of clinical manifestation of ASD+ADHD phenotype, they may also inform a novel treatment target. © 2015 The Authors Autism Research published by Wiley Periodicals, Inc. on behalf of International Society for Autism Research.
-
Body Temperature Measurements for Metabolic Phenotyping in Mice
Meyer, Carola W.; Ootsuka, Youichirou; Romanovsky, Andrej A.
2017-01-01
Endothermic organisms rely on tightly balanced energy budgets to maintain a regulated body temperature and body mass. Metabolic phenotyping of mice, therefore, often includes the recording of body temperature. Thermometry in mice is conducted at various sites, using various devices and measurement practices, ranging from single-time probing to continuous temperature imaging. Whilst there is broad agreement that body temperature data is of value, procedural considerations of body temperature measurements in the context of metabolic phenotyping are missing. Here, we provide an overview of the various methods currently available for gathering body temperature data from mice. We explore the scope and limitations of thermometry in mice, with the hope of assisting researchers in the selection of appropriate approaches, and conditions, for comprehensive mouse phenotypic analyses. PMID:28824441
-
Directory of Open Access Journals (Sweden)
Cinar Nese
2012-12-01
Full Text Available Abstract Background Adrenal androgen excess is frequently observed in PCOS. The aim of the study was to determine whether adrenal gland function varies among PCOS phenotypes, women with hyperandrogenism (H only and healthy women. Methods The study included 119 non-obese patients with PCOS (age: 22.2 ± 4.1y, BMI:22.5 ± 3.1 kg/m2, 24 women with H only and 39 age and BMI- matched controls. Among women with PCOS, 50 had H, oligo-anovulation (O, and polycystic ovaries (P (PHO, 32 had O and H (OH, 23 had P and H (PH, and 14 had P and O (PO. Total testosterone (T, SHBG and DHEAS levels at basal and serum 17-hydroxprogesterone (17-OHP, androstenedione (A4, DHEA and cortisol levels after ACTH stimulation were measured. Results T, FAI and DHEAS, and basal and AUC values for 17-OHP and A4 were significantly and similarly higher in PCOS and H groups than controls (p Conclusion PCOS patients and women with H only have similar and higher basal and stimulated adrenal androgen levels than controls. All three hyperandrogenic subphenotypes of PCOS exhibit similar and higher basal and stimulated adrenal androgen secretion patterns compared to non-hyperandrogenic subphenotype.
-
A non-equilibrium neutral model for analysing cultural change.
Kandler, Anne; Shennan, Stephen
2013-08-07
Neutral evolution is a frequently used model to analyse changes in frequencies of cultural variants over time. Variants are chosen to be copied according to their relative frequency and new variants are introduced by a process of random mutation. Here we present a non-equilibrium neutral model which accounts for temporally varying population sizes and mutation rates and makes it possible to analyse the cultural system under consideration at any point in time. This framework gives an indication whether observed changes in the frequency distributions of a set of cultural variants between two time points are consistent with the random copying hypothesis. We find that the likelihood of the existence of the observed assemblage at the end of the considered time period (expressed by the probability of the observed number of cultural variants present in the population during the whole period under neutral evolution) is a powerful indicator of departures from neutrality. Further, we study the effects of frequency-dependent selection on the evolutionary trajectories and present a case study of change in the decoration of pottery in early Neolithic Central Europe. Based on the framework developed we show that neutral evolution is not an adequate description of the observed changes in frequency. Copyright © 2013 Elsevier Ltd. All rights reserved.
-
Neurological and endocrine phenotypes of fragile X carrier women.
Hall, D; Todorova-Koteva, K; Pandya, S; Bernard, B; Ouyang, B; Walsh, M; Pounardjian, T; Deburghraeve, C; Zhou, L; Losh, M; Leehey, M; Berry-Kravis, E
2016-01-01
Women who carry fragile X mental retardation 1 (FMR1)gene premutation expansions frequently report neurological or endocrine symptoms and prior studies have predominantly focused on questionnaire report of medical issues. Premutation carrier (PMC) women (n = 33) and non-carrier controls (n = 13) were recruited and evaluated by a neurologist, neuropsychologist, and endocrinologist. Blood and skin biopsies were collected for molecular measures. Scales for movement disorders, neuropathy, cognitive function, psychiatric symptoms, sleep, and quality of life were completed. The average age of the women was 51 years (n = 46) and average CGG repeat size was 91 ± 24.9 in the FMR1 PMC women. Seventy percent of the PMC women had an abnormal neurological examination. PMC women had significantly higher scores on the Fragile X-Associated Tremor Ataxia Syndrome (FXTAS) rating scale, more neuropathy, and difficulty with tandem gait compared to controls. Central sensitivity syndromes, a neuroticism profile on the NEO Personality Profile, and sleep disorders were also prevalent. Discrepancies between subject report and examination findings were also seen. This pilot study suggests that women with the FMR1 premutation may have a phenotype that overlaps with that seen in FXTAS. Additional research with larger sample sizes is warranted to better delineate the clinical features. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
-
Transcriptional Analyses of Barrett's Metaplasia and Normal Upper GI Mucosae
Directory of Open Access Journals (Sweden)
Michael T. Barrett
2002-01-01
Full Text Available Over the last two decades, the incidence of esophageal adenocarcinoma (EA has increased dramatically in the US and Western Europe. It has been shown that EAs evolve from premalignant Barrett's esophagus (BE tissue by a process of clonal expansion and evolution. However, the molecular phenotype of the premalignant metaplasia, and its relationship to those of the normal upper gastrointestinal (GI mucosae, including gastric, duodenal, and squamous epithelium of the esophagus, has not been systematically characterized. Therefore, we used oligonucleotide-based microarrays to characterize gene expression profiles in each of these tissues. The similarity of BE to each of the normal tissues was compared using a series of computational approaches. Our analyses included esophageal squamous epithelium, which is present at the same anatomic site and exposed to similar conditions as Barrett's epithelium, duodenum that shares morphologic similarity to Barrett's epithelium, and adjacent gastric epithelium. There was a clear distinction among the expression profiles of gastric, duodenal, and squamous epithelium whereas the BE profiles showed considerable overlap with normal tissues. Furthermore, we identified clusters of genes that are specific to each of the tissues, to the Barrett's metaplastic epithelia, and a cluster of genes that was distinct between squamous and nonsquamous epithelia.
-
New tools to analyze overlapping coding regions.
Bayegan, Amir H; Garcia-Martin, Juan Antonio; Clote, Peter
2016-12-13
Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We
-
Zhou, Hui; Liu, Jinkang; Chen, Shengxi; Xiong, Zeng; Zhou, Jianhua; Tong, Shiyu; Chen, Hao; Zhou, Moling
2012-06-01
To explore the degree, mechanism and clinical significance of three-dimensional tumor microvascular architecture phenotype heterogeneity (3D-TMAPH) in non-small cell carcinoma (NSCLC). Twenty-one samples of solitary pulmonary nodules were collected integrally. To establish two-dimensional tumor microvascular architecture phenotype (2D-TMAP) and three-dimensional tumor microvascular architecture phenotype (3D-TMAP), five layers of each nodule were selected and embedded in paraffin. Test indices included the expressions of vascular endothelial growth factor (VEGF), proliferating cell nuclear antigen (PCNA), EphB4, ephfinB2 and microvascular density marked by anti-CD34 (CD34-MVD). The degrees of 3D-TMAPH were evaluated by the coefficient of variation and extend of heterogeneity. Spearman rank correlation analysis was used to investigate the relationships between 2D-TMAP, 3D-TMAP and clinicopathological features. 3D-TMAPH showed that 2D-TMAP heterogeneity was expressed in the tissues of NSCLC. The heterogeneities in the malignant nodules were significantly higher than those in the active inflammatory nodules and tubercular nodules. In addition, different degrees of heterogeneity of CD34-MVD and PCNA were found in NSCLC tissues. The coefficients of variation of CD34- MVD and PCNA were positively related to the degree of differentiation (all P0.05). The level of heterogeneity of various expression indexes (ephrinB2, EphB4, VEGF) in NSCLC tissues were inconsistent, but there were no significant differences in heterogeneity in NSCLC tissues with different histological types (P>0.05). 3D-TMAPH exists widely in the microenvironment during the genesis and development of NSCLC and has a significant impact on its biological complexity.
-
MERRF/MELAS overlap syndrome due to the m.3291T>C mutation.
Liu, Kaiming; Zhao, Hui; Ji, Kunqian; Yan, Chuanzhu
2014-03-01
We report the case of a 19-year-old Chinese female harboring the m.3291T>C mutation in the MT-TL1 gene encoding the mitochondrial transfer RNA for leucine. She presented with a complex phenotype characterized by progressive cerebellar ataxia, frequent myoclonus seizures, recurrent stroke-like episodes, migraine-like headaches with nausea and vomiting, and elevated resting lactate blood level. It is known that the myoclonus epilepsy with ragged-red fibers (MERRF) is characterized by cerebellar ataxia and myoclonus epilepsy, while that the mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is characterized by recurrent stroke-like episodes, migraine-like headaches, and elevated resting lactate blood level. So the patient's clinical manifestations suggest the presence of a MERRF/MELAS overlap syndrome. Muscle biopsy of the patient showed the presence of numerous scattered ragged-red fibers, some cytochrome c oxidase-deficient fibers, and several strongly succinate dehygrogenase-reactive vessels, suggestive of a mitochondrial disorder. Direct sequencing of the complete mitochondrial genome of the proband revealed no mutations other than the T-to-C transition at nucleotide position 3291. Restriction fragment length polymorphism analysis of the proband and her family revealed maternal inheritance of the mutation in a heteroplasmic manner. The analysis of aerobic respiration and glycolysis demonstrated that the fibroblasts from the patient had mitochondrial dysfunction. Our results suggest that the m.3291T>C is pathogenic. This study is the first to describe the m.3291T>C mutation in association with the MERRF/MELAS overlap syndrome.
-
DEFF Research Database (Denmark)
Andersen, Birgitte; Hansen, Michael Edberg; Smedsgaard, Jørn
2005-01-01
often has been broadly applied to various morphologically and chemically distinct groups of isolates from different hosts. The purpose of this study was to develop and evaluate automated and unbiased image analysis systems that will analyze different phenotypic characters and facilitate testing...
-
Directory of Open Access Journals (Sweden)
Lee DW
2017-08-01
Full Text Available Dong-Won Lee,1 Hyun-Jung Jin,2 Kyeong-Cheol Shin,2 Jin-Hong Chung,2 Hyoung-Woo Lee,3 Kwan-Ho Lee2 1Division of Pulmonology, Department of Internal Medicine, Andong Sungso Hospital, Andong, 2Division of Pulmonology and Allergy, 3Division of Endocrinology, Department of Internal Medicine, Yeungnam University Hospital, Daegu, South Korea Background: Sarcopenia and decreased bone-mineral density (BMD are common in elderly people, and are major comorbidities of obstructive airway disease (OAD. However, the relationship between sarcopenia and BMD in each OAD phenotype, especially asthma–COPD overlap syndrome (ACOS, is not yet clear. We aimed to evaluate differences in BMD according to the presence of sarcopenia in each OAD phenotype. Materials and methods: Among the research subjects in KNHANES IV and V (2008–2011, 5,562 were ≥50 years old and underwent qualified spirometry and dual-energy X-ray absorptiometry. A total of 947 subjects were included in the study: 89 had asthma, 748 COPD, and 110 ACOS. Results: In the COPD and ACOS phenotypes, T-scores were lower in the sarcopenia group than the nonsarcopenia group. Prevalence rates of osteopenia and osteoporosis were higher in the sarcopenia group than the nonsarcopenia group. (P<0.001 and P=0.017, respectively. The sarcopenia group had higher risks of developing osteopenia, osteoporosis, and low BMD than the nonsarcopenia group in the ACOS phenotype (OR 6.620, 95% CI 1.129–38.828 [P=0.036], OR 9.611, 95% CI 1.133–81.544 [P=0.038], and OR 6.935, 95% CI 1.194–40.272 [P=0.031], respectively. However, in the asthma phenotype, the sarcopenia group showed no increased risk compared with the nonsarcopenia group. Conclusion: In the ACOS phenotype, individuals with sarcopenia had a higher prevalence rate and higher risks of osteopenia and osteoporosis than those without sarcopenia among all OAD phenotypes. Keywords: asthma, chronic obstructive pulmonary disease, asthma–COPD overlap syndrome
-
Directory of Open Access Journals (Sweden)
McCallion Andrew S
2009-01-01
Full Text Available Abstract Background Transcriptional regulatory elements are central to development and interspecific phenotypic variation. Current regulatory element prediction tools rely heavily upon conservation for prediction of putative elements. Recent in vitro observations from the ENCODE project combined with in vivo analyses at the zebrafish phox2b locus suggests that a significant fraction of regulatory elements may fall below commonly applied metrics of conservation. We propose to explore these observations in vivo at the human PHOX2B locus, and also evaluate the potential evidence for genome-wide applicability of these observations through a novel analysis of extant data. Results Transposon-based transgenic analysis utilizing a tiling path proximal to human PHOX2B in zebrafish recapitulates the observations at the zebrafish phox2b locus of both conserved and non-conserved regulatory elements. Analysis of human sequences conserved with previously identified zebrafish phox2b regulatory elements demonstrates that the orthologous sequences exhibit overlapping regulatory control. Additionally, analysis of non-conserved sequences scattered over 135 kb 5' to PHOX2B, provides evidence of non-conserved regulatory elements positively biased with close proximity to the gene. Furthermore, we provide a novel analysis of data from the ENCODE project, finding a non-uniform distribution of regulatory elements consistent with our in vivo observations at PHOX2B. These observations remain largely unchanged when one accounts for the sequence repeat content of the assayed intervals, when the intervals are sub-classified by biological role (developmental versus non-developmental, or by gene density (gene desert versus non-gene desert. Conclusion While regulatory elements frequently display evidence of evolutionary conservation, a fraction appears to be undetected by current metrics of conservation. In vivo observations at the PHOX2B locus, supported by our analyses of in
-
Phenotypic and immunohistochemical characterization of sarcoglycanopathies
Directory of Open Access Journals (Sweden)
Ana F. B. Ferreira
2011-01-01
Full Text Available INTRODUCTION: Limb-girdle muscular dystrophy presents with heterogeneous clinical and molecular features. The primary characteristic of this disorder is proximal muscular weakness with variable age of onset, speed of progression, and intensity of symptoms. Sarcoglycanopathies, which are a subgroup of the limb-girdle muscular dystrophies, are caused by mutations in sarcoglycan genes. Mutations in these genes cause secondary deficiencies in other proteins, due to the instability of the dystrophin-glycoprotein complex. Therefore, determining the etiology of a given sarcoglycanopathy requires costly and occasionally inaccessible molecular methods. OBJECTIVE: The aim of this study was to identify phenotypic differences among limb-girdle muscular dystrophy patients who were grouped according to the immunohistochemical phenotypes for the four sarcoglycans. METHODS: To identify phenotypic differences among patients with different types of sarcoglycanopathies, a questionnaire was used and the muscle strength and range of motion of nine joints in 45 patients recruited from the Department of Neurology - HC-FMUSP (Clinics Hospital of the Faculty of Medicine of the University of São Paulo were evaluated. The findings obtained from these analyses were compared with the results of the immunohistochemical findings. RESULTS: The patients were divided into the following groups based on the immunohistochemical findings: a-sarcoglycanopathies (16 patients, b-sarcoglycanopathies (1 patient, y-sarcoglycanopathies (5 patients, and nonsarcoglycanopathies (23 patients. The muscle strength analysis revealed significant differences for both upper and lower limb muscles, particularly the shoulder and hip muscles, as expected. No pattern of joint contractures was found among the four groups analyzed, even within the same family. However, a high frequency of tiptoe gait was observed in patients with a-sarcoglycanopathies, while calf pseudo-hypertrophy was most common in
-
Pattern overlap implies runaway growth in hierarchical tile systems
Directory of Open Access Journals (Sweden)
David Doty
2015-11-01
Full Text Available We show that in the hierarchical tile assembly model, if there is a producible assembly that overlaps a nontrivial translation of itself consistently (i.e., the pattern of tile types in the overlap region is identical in both translations, then arbitrarily large assemblies are producible. The significance of this result is that tile systems intended to controllably produce finite structures must avoid pattern repetition in their producible assemblies that would lead to such overlap.This answers an open question of Chen and Doty (SODA 2012, who showed that so-called "partial-order" systems producing a unique finite assembly and avoiding such overlaps must require time linear in the assembly diameter. An application of our main result is that any system producing a unique finite assembly is automatically guaranteed to avoid such overlaps, simplifying the hypothesis of Chen and Doty's main theorem.
-
Dietary patterns and the insulin resistance phenotype among non-diabetic adults
Background: Information on the relation between dietary patterns derived by cluster analysis and insulin resistance is scarce. Objective: To compare insulin resistance phenotypes, including waist circumference, body mass index, fasting and 2-hour post-challenge insulin, insulin sensitivity index (I...
-
Tohya, Mari; Watanabe, Takayasu; Maruyama, Fumito; Arai, Sakura; Ota, Atsushi; Athey, Taryn B T; Fittipaldi, Nahuel; Nakagawa, Ichiro; Sekizaki, Tsutomu
2016-01-01
Many bacterial species coexist in the same niche as heterogeneous clones with different phenotypes; however, understanding of infectious diseases by polyphenotypic bacteria is still limited. In the present study, encapsulation in isolates of the porcine pathogen Streptococcus suis from persistent endocarditis lesions was examined. Coexistence of both encapsulated and unencapsulated S. suis isolates was found in 26 out of 59 endocarditis samples. The isolates were serotype 2, and belonged to two different sequence types (STs), ST1 and ST28. The genomes of each of the 26 pairs of encapsulated and unencapsulated isolates from the 26 samples were sequenced. The data showed that each pair of isolates had one or more unique nonsynonymous mutations in the cps gene, and the encapsulated and unencapsulated isolates from the same samples were closest to each other. Pairwise comparisons of the sequences of cps genes in 7 pairs of encapsulated and unencapsulated isolates identified insertion/deletions (indels) ranging from one to 104 bp in different cps genes of unencapsulated isolates. Capsule expression was restored in a subset of unencapsulated isolates by complementation in trans with cps expression vectors. Examination of gene content common to isolates indicated that mutation frequency was higher in ST28 pairs than in ST1 pairs. Genes within mobile genetic elements were mutation hot spots among ST28 isolates. Taken all together, our results demonstrate the coexistence of dual phenotype (encapsulated and unencapsulated) bacterial clones and suggest that the dual phenotypes arose independently in each farm by means of spontaneous mutations in cps genes.
-
Directory of Open Access Journals (Sweden)
Mari Tohya
Full Text Available Many bacterial species coexist in the same niche as heterogeneous clones with different phenotypes; however, understanding of infectious diseases by polyphenotypic bacteria is still limited. In the present study, encapsulation in isolates of the porcine pathogen Streptococcus suis from persistent endocarditis lesions was examined. Coexistence of both encapsulated and unencapsulated S. suis isolates was found in 26 out of 59 endocarditis samples. The isolates were serotype 2, and belonged to two different sequence types (STs, ST1 and ST28. The genomes of each of the 26 pairs of encapsulated and unencapsulated isolates from the 26 samples were sequenced. The data showed that each pair of isolates had one or more unique nonsynonymous mutations in the cps gene, and the encapsulated and unencapsulated isolates from the same samples were closest to each other. Pairwise comparisons of the sequences of cps genes in 7 pairs of encapsulated and unencapsulated isolates identified insertion/deletions (indels ranging from one to 104 bp in different cps genes of unencapsulated isolates. Capsule expression was restored in a subset of unencapsulated isolates by complementation in trans with cps expression vectors. Examination of gene content common to isolates indicated that mutation frequency was higher in ST28 pairs than in ST1 pairs. Genes within mobile genetic elements were mutation hot spots among ST28 isolates. Taken all together, our results demonstrate the coexistence of dual phenotype (encapsulated and unencapsulated bacterial clones and suggest that the dual phenotypes arose independently in each farm by means of spontaneous mutations in cps genes.
-
Tohya, Mari; Watanabe, Takayasu; Maruyama, Fumito; Arai, Sakura; Ota, Atsushi; Athey, Taryn B. T.; Fittipaldi, Nahuel; Nakagawa, Ichiro; Sekizaki, Tsutomu
2016-01-01
Many bacterial species coexist in the same niche as heterogeneous clones with different phenotypes; however, understanding of infectious diseases by polyphenotypic bacteria is still limited. In the present study, encapsulation in isolates of the porcine pathogen Streptococcus suis from persistent endocarditis lesions was examined. Coexistence of both encapsulated and unencapsulated S. suis isolates was found in 26 out of 59 endocarditis samples. The isolates were serotype 2, and belonged to two different sequence types (STs), ST1 and ST28. The genomes of each of the 26 pairs of encapsulated and unencapsulated isolates from the 26 samples were sequenced. The data showed that each pair of isolates had one or more unique nonsynonymous mutations in the cps gene, and the encapsulated and unencapsulated isolates from the same samples were closest to each other. Pairwise comparisons of the sequences of cps genes in 7 pairs of encapsulated and unencapsulated isolates identified insertion/deletions (indels) ranging from one to 104 bp in different cps genes of unencapsulated isolates. Capsule expression was restored in a subset of unencapsulated isolates by complementation in trans with cps expression vectors. Examination of gene content common to isolates indicated that mutation frequency was higher in ST28 pairs than in ST1 pairs. Genes within mobile genetic elements were mutation hot spots among ST28 isolates. Taken all together, our results demonstrate the coexistence of dual phenotype (encapsulated and unencapsulated) bacterial clones and suggest that the dual phenotypes arose independently in each farm by means of spontaneous mutations in cps genes. PMID:27433935
-
Campbell, M. T.; Walia, H.; Grondin, A.; Knecht, A.
2017-12-01
The development of abiotic stress tolerant crops (i.e. drought, salinity, or heat stress) requires the discovery of DNA sequence variants associated with stress tolerance-related traits. However, many traits underlying adaptation to abiotic stress involve a suite of physiological pathways that may be induced at different times throughout the duration of stress. Conventional single-point phenotyping approaches fail to fully capture these temporal responses, and thus downstream genetic analysis may only identify a subset of the genetic variants that are important for adaptation to sub-optimal environments. Although genomic resources for crops have advanced tremendously, the collection of phenotypic data for morphological and physiological traits is laborious and remains a significant bottleneck in bridging the phenotype-genotype gap. In recent years, the availability of automated, image-based phenotyping platforms has provided researchers with an opportunity to collect morphological and physiological traits non-destructively in a highly controlled environment. Moreover, these platforms allow abiotic stress responses to be recorded throughout the duration of the experiment, and have facilitated the use of function-valued traits for genetic analyses in major crops. We will present our approaches for addressing abiotic stress tolerance in cereals. This talk will focus on novel open-source software to process and extract biological meaningful data from images generated from these phenomics platforms. In addition, we will discuss the statistical approaches to model longitudinal phenotypes and dissect the genetic basis of dynamic responses to these abiotic stresses throughout development.
-
Lekberg, Ylva; Roskilly, Beth; Hendrick, Margaret F; Zabinski, Catherine A; Barr, Camille M; Fishman, Lila
2012-09-01
In flowering plants, soil heterogeneity can generate divergent natural selection over fine spatial scales, and thus promote local adaptation in the absence of geographic barriers to gene flow. Here, we investigate phenotypic and genetic differentiation in one of the few flowering plants that thrives in both geothermal and non-thermal soils in Yellowstone National Park (YNP). Yellow monkeyflowers (Mimulus guttatus) growing at two geothermal ("thermal") sites in YNP were distinct in growth form and phenology from paired populations growing nearby ( 0.34), which were only weakly differentiated from each other (all F (ST) geothermal gradient in Yellowstone.
-
Common neural substrates support speech and non-speech vocal tract gestures.
Chang, Soo-Eun; Kenney, Mary Kay; Loucks, Torrey M J; Poletto, Christopher J; Ludlow, Christy L
2009-08-01
The issue of whether speech is supported by the same neural substrates as non-speech vocal tract gestures has been contentious. In this fMRI study we tested whether producing non-speech vocal tract gestures in humans shares the same functional neuroanatomy as non-sense speech syllables. Production of non-speech vocal tract gestures, devoid of phonological content but similar to speech in that they had familiar acoustic and somatosensory targets, was compared to the production of speech syllables without meaning. Brain activation related to overt production was captured with BOLD fMRI using a sparse sampling design for both conditions. Speech and non-speech were compared using voxel-wise whole brain analyses, and ROI analyses focused on frontal and temporoparietal structures previously reported to support speech production. Results showed substantial activation overlap between speech and non-speech function in regions. Although non-speech gesture production showed greater extent and amplitude of activation in the regions examined, both speech and non-speech showed comparable left laterality in activation for both target perception and production. These findings posit a more general role of the previously proposed "auditory dorsal stream" in the left hemisphere--to support the production of vocal tract gestures that are not limited to speech processing.
-
Rosser, Neil; Kozak, Krzysztof M; Phillimore, Albert B; Mallet, James
2015-06-30
Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry. Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32%-95% of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved. Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on "strict and " "relaxed" biological species concepts (BSC), as well as on a surrogate for the widely-used "diagnostic" version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two
-
Necka, Elizabeth A; Sokolowski, H Moriah; Lyons, Ian M
2015-01-01
Recent work has demonstrated that math anxiety is more than just the product of poor math skills. Psychosocial factors may play a key role in understanding what it means to be math anxious, and hence may aid in attempts to sever the link between math anxiety and poor math performance. One such factor may be the extent to which individuals integrate math into their sense of self. We adapted a well-established measure of this degree of integration (i.e., self-other overlap) to assess individuals' self-math overlap. This non-verbal single-item measure showed that identifying oneself with math (having higher self-math overlap) was strongly associated with lower math anxiety (r = -0.610). We also expected that having higher self-math overlap would leave one especially susceptible to the threat of poor math performance to the self. We identified two competing hypotheses regarding how this plays out in terms of math anxiety. Those higher in self-math overlap might be more likely to worry about poor math performance, exacerbating the negative relation between math anxiety and math ability. Alternatively, those higher in self-math overlap might exhibit self-serving biases regarding their math ability, which would instead predict a decoupling of the relation between their perceived and actual math ability, and in turn the relation between their math ability and math anxiety. Results clearly favored the latter hypothesis: those higher in self-math overlap exhibited almost no relation between math anxiety and math ability, whereas those lower in self-math overlap showed a strong negative relation between math anxiety and math ability. This was partially explained by greater self-serving biases among those higher in self-math overlap. In sum, these results reveal that the degree to which one integrates math into one's self - self-math overlap - may provide insight into how the pernicious negative relation between math anxiety and math ability may be ameliorated.
-
Necka, Elizabeth A.; Sokolowski, H. Moriah; Lyons, Ian M.
2015-01-01
Recent work has demonstrated that math anxiety is more than just the product of poor math skills. Psychosocial factors may play a key role in understanding what it means to be math anxious, and hence may aid in attempts to sever the link between math anxiety and poor math performance. One such factor may be the extent to which individuals integrate math into their sense of self. We adapted a well-established measure of this degree of integration (i.e., self-other overlap) to assess individuals’ self-math overlap. This non-verbal single-item measure showed that identifying oneself with math (having higher self-math overlap) was strongly associated with lower math anxiety (r = -0.610). We also expected that having higher self-math overlap would leave one especially susceptible to the threat of poor math performance to the self. We identified two competing hypotheses regarding how this plays out in terms of math anxiety. Those higher in self-math overlap might be more likely to worry about poor math performance, exacerbating the negative relation between math anxiety and math ability. Alternatively, those higher in self-math overlap might exhibit self-serving biases regarding their math ability, which would instead predict a decoupling of the relation between their perceived and actual math ability, and in turn the relation between their math ability and math anxiety. Results clearly favored the latter hypothesis: those higher in self-math overlap exhibited almost no relation between math anxiety and math ability, whereas those lower in self-math overlap showed a strong negative relation between math anxiety and math ability. This was partially explained by greater self-serving biases among those higher in self-math overlap. In sum, these results reveal that the degree to which one integrates math into one’s self – self-math overlap – may provide insight into how the pernicious negative relation between math anxiety and math ability may be ameliorated. PMID
-
Detecting highly overlapping community structure by greedy clique expansion
Lee, Conrad; Reid, Fergal; McDaid, Aaron; Hurley, Neil
2010-01-01
In complex networks it is common for each node to belong to several communities, implying a highly overlapping community structure. Recent advances in benchmarking indicate that existing community assignment algorithms that are capable of detecting overlapping communities perform well only when the extent of community overlap is kept to modest levels. To overcome this limitation, we introduce a new community assignment algorithm called Greedy Clique Expansion (GCE). The algorithm identifies d...
-
Obesity Differentially Affects Phenotypes of Polycystic Ovary Syndrome
Moran, Carlos; Arriaga, Monica; Rodriguez, Gustavo; Moran, Segundo
2012-01-01
Obesity or overweight affect most of patients with polycystic ovary syndrome (PCOS). Phenotypes are the clinical characteristics produced by the interaction of heredity and environment in a disease or syndrome. Phenotypes of PCOS have been described on the presence of clinical hyperandrogenism, oligoovulation and polycystic ovaries. The insulin resistance is present in the majority of patients with obesity and/or PCOS and it is more frequent and of greater magnitude in obese than in non obese PCOS patients. Levels of sexual hormone binding globulin are decreased, and levels of free androgens are increased in obese PCOS patients. Weight loss treatment is important for overweight or obese PCOS patients, but not necessary for normal weight PCOS patients, who only need to avoid increasing their body weight. Obesity decreases or delays several infertility treatments. The differences in the hormonal and metabolic profile, as well as the different focus and response to treatment between obese and non obese PCOS patients suggest that obesity has to be considered as a characteristic for classification of PCOS phenotypes. PMID:22829818
-
Obesity Differentially Affects Phenotypes of Polycystic Ovary Syndrome
Directory of Open Access Journals (Sweden)
Carlos Moran
2012-01-01
Full Text Available Obesity or overweight affect most of patients with polycystic ovary syndrome (PCOS. Phenotypes are the clinical characteristics produced by the interaction of heredity and environment in a disease or syndrome. Phenotypes of PCOS have been described on the presence of clinical hyperandrogenism, oligoovulation and polycystic ovaries. The insulin resistance is present in the majority of patients with obesity and/or PCOS and it is more frequent and of greater magnitude in obese than in non obese PCOS patients. Levels of sexual hormone binding globulin are decreased, and levels of free androgens are increased in obese PCOS patients. Weight loss treatment is important for overweight or obese PCOS patients, but not necessary for normal weight PCOS patients, who only need to avoid increasing their body weight. Obesity decreases or delays several infertility treatments. The differences in the hormonal and metabolic profile, as well as the different focus and response to treatment between obese and non obese PCOS patients suggest that obesity has to be considered as a characteristic for classification of PCOS phenotypes.
-
Covariant extension of the GPD overlap representation at low Fock states
Energy Technology Data Exchange (ETDEWEB)
Chouika, N.; Moutarde, H. [Univ. Paris-Saclay, Gif-sur-Yvette (France). IRFU, CEA; Mezrag, C. [Argonne National Laboratory, Argonne, IL (United States). Physics Div.; Istituto Nazionale di Fisica Nucleare, Rome (Italy); Rodriguez-Quintero, J. [Huelva Univ. (Spain). Dept. Ciencias Integradas
2017-12-15
We present a novel approach to compute generalized parton distributions within the lightfront wave function overlap framework. We show how to systematically extend generalized parton distributions computed within the DGLAP region to the ERBL one, fulfilling at the same time both the polynomiality and positivity conditions. We exemplify our method using pion lightfront wave functions inspired by recent results of non-perturbative continuum techniques and algebraic nucleon lightfront wave functions. We also test the robustness of our algorithm on reggeized phenomenological parameterizations. This approach paves the way to a better understanding of the nucleon structure from non-perturbative techniques and to a unification of generalized parton distributions and transverse momentum dependent parton distribution functions phenomenology through lightfront wave functions. (orig.)
-
Directory of Open Access Journals (Sweden)
Michela Traglia
2009-10-01
Full Text Available Isolated populations are a useful resource for mapping complex traits due to shared stable environment, reduced genetic complexity and extended Linkage Disequilibrium (LD compared to the general population. Here we describe a large genetic isolate from the North West Apennines, the mountain range that runs through Italy from the North West Alps to the South.The study involved 1,803 people living in 7 villages of the upper Borbera Valley. For this large population cohort, data from genealogy reconstruction, medical questionnaires, blood, anthropometric and bone status QUS parameters were evaluated. Demographic and epidemiological analyses indicated a substantial genetic component contributing to each trait variation as well as overlapping genetic determinants and family clustering for some traits.The data provide evidence for significant heritability of medical relevant traits that will be important in mapping quantitative traits. We suggest that this population isolate is suitable to identify rare variants associated with complex phenotypes that may be difficult to study in larger but more heterogeneous populations.
-
Obesity Differentially Affects Phenotypes of Polycystic Ovary Syndrome
Moran, Carlos; Arriaga, Monica; Rodriguez, Gustavo; Moran, Segundo
2012-01-01
Obesity or overweight affect most of patients with polycystic ovary syndrome (PCOS). Phenotypes are the clinical characteristics produced by the interaction of heredity and environment in a disease or syndrome. Phenotypes of PCOS have been described on the presence of clinical hyperandrogenism, oligoovulation and polycystic ovaries. The insulin resistance is present in the majority of patients with obesity and/or PCOS and it is more frequent and of greater magnitude in obese than in non obese...
-
Directory of Open Access Journals (Sweden)
Henrik Bjørn Nielsen
2007-08-01
Full Text Available The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between experimental factors affecting a biological system. Unfortunately, direct comparisons of gene expression profiles obtained in independent, publicly available microarray experiments are typically compromised by substantial, experiment-specific biases. Here we suggest a novel yet conceptually simple approach for deriving 'Functional Association(s by Response Overlap' (FARO between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability between studies that is typical for methods that rely on correlation in gene expression. We apply FARO to a compendium of 242 diverse Arabidopsis microarray experimental factors, including phyto-hormones, stresses and pathogens, growth conditions/stages, tissue types and mutants. We also use FARO to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates the usefulness of our approach for exploiting public microarray data to derive biologically meaningful associations between experimental factors. Finally, our
-
Non-linear finite element analyses applicable for the design of large reinforced concrete structures
Engen, M; Hendriks, M.A.N.; Øverli, Jan Arve; Åldstedt, Erik
2017-01-01
In order to make non-linear finite element analyses applicable during assessments of the ultimate load capacity or the structural reliability of large reinforced concrete structures, there is need for an efficient solution strategy with a low modelling uncertainty. A solution strategy comprises
-
Directory of Open Access Journals (Sweden)
Umma A. Ibrahim
2018-07-01
Full Text Available Haemophilia-A is an X-linked recessive bleeding disorder characterized by deficiency of FVIII. Although severity of haemophilia is largely determined by the extent to which different mutations abolish FVIII production, the overall phenotypic variations among haemophiliacs is determined by a combination of several other factors, which range from general to tropical factors on the one hand, and from genetic to immunologic and infective factors on the other hand. Determinants and modifiers of haemophilic bleeding phenotypes are important predictors of prognosis. However, tropical determinants of haemophilic bleeding phenotypes are virtually ignored because majority of haemophilia research originated from developed non-tropical countries. The aim of this paper is to present a balanced review of the haemophilic bleeding phenotypes from general and tropical perspectives. Hence, we present a concisely updated comprehensive review of the pathophysiologic and clinical significance of general vis-à-vis tropical determinants and modifiers of haemophilic bleeding phenotypes from genetic, immunologic and infective perspectives. Understanding of general phenotypic determinants such as FVIII gene mutations, immunological (inhibitors and infective (e.g. hepatitis and HIV complications, classical thrombophilias (e.g. FV-Leiden and non-classical thrombophilias (e.g. non-O blood groups will throw more light into the mechanisms by which some tropical prothrombotic gene mutations (such as sickle β-globin gene and certain chronic tropical pro-haemorrhagic parasitic infections (such as urinary and gastrointestinal helminthiasis may modify frequency, intensity and pattern of bleeding among haemophiliacs in the tropics. The clinical significance of iron deficiency within the context of helminthiasis and haemophilia is also reviewed. More research is needed to determine the precise effect of non-classical thrombophilias such as sickling disorders and ABO blood groups
-
A non-dispersive infrared analyser for analysis of HF in the PPM range
International Nuclear Information System (INIS)
Kartha, V.B.; Patel, N.D.; Venkateswaran, S.
1985-01-01
The determination of trace amounts of HF is of importance in many industrial processes, and in nuclear industry in the production of UF 6 . Mass spectrometric and gas chromatographic methods are difficult to use for this purpose, because of the highly corrosive nature of the samples. Infrared Spectroscopy can be conveniently used with the required sensitivity and it has the added advantage that continuous non-destructive on-line monitoring can be conveniently done. A non-dispersive infrared analyser for determination of HF in UF 6 in the concentration range of 50-2000 ppm has been fabricated and tested. The instrument has been shown to possess high sensitivity and good long term stability, so that it can be used as on-line monitor for non-destructive, continuous analysis. (author)
-
Hall, Barry G
2014-01-01
SNP-association studies are a starting point for identifying genes that may be responsible for specific phenotypes, such as disease traits. The vast bulk of tools for SNP-association studies are directed toward SNPs in the human genome, and I am unaware of any tools designed specifically for such studies in bacterial or viral genomes. The PPFS (Predict Phenotypes From SNPs) package described here is an add-on to kSNP , a program that can identify SNPs in a data set of hundreds of microbial genomes. PPFS identifies those SNPs that are non-randomly associated with a phenotype based on the χ² probability, then uses those diagnostic SNPs for two distinct, but related, purposes: (1) to predict the phenotypes of strains whose phenotypes are unknown, and (2) to identify those diagnostic SNPs that are most likely to be causally related to the phenotype. In the example illustrated here, from a set of 68 E. coli genomes, for 67 of which the pathogenicity phenotype was known, there were 418,500 SNPs. Using the phenotypes of 36 of those strains, PPFS identified 207 diagnostic SNPs. The diagnostic SNPs predicted the phenotypes of all of the genomes with 97% accuracy. It then identified 97 SNPs whose probability of being causally related to the pathogenic phenotype was >0.999. In a second example, from a set of 116 E. coli genome sequences, using the phenotypes of 65 strains PPFS identified 101 SNPs that predicted the source host (human or non-human) with 90% accuracy.
-
International Nuclear Information System (INIS)
Ilgenfritz, E.M.; Leinweber, D.; Moran, P.; Koller, K.; Weinberg, V.; Freie Univ. Berlin
2008-01-01
A detailed comparison is made between the topological structure of quenched QCD as revealed by the recently proposed over-improved stout-link smearing in conjunction with an improved gluonic definition of the topological density on one hand and a similar analysis made possible by the overlap-fermionic topological charge density both with and without variable ultraviolet cutoff λ cut . The matching is twofold, provided by fitting the density-density two-point functions on one hand and by a point-by-point fitting of the topological densities according to the two methods. We point out the similar cluster structure of the topological density for moderate smearing and 200 MeV cut <600 MeV, respectively. We demonstrate the relation of the gluonic topological density for extensive smearing to the location of the overlap zero modes and the lowest overlap non-zero mode as found for the unsmeared configurations. (orig.)
-
Energy Technology Data Exchange (ETDEWEB)
Ilgenfritz, E.M.; Leinweber, D.; Moran, P. [Adelaide Univ., SA (AU). Special Research Centre for the Subatomic Structure of Matter (CSSM); Koller, K. [Muenchen Univ. (Germany). Sektion Physik; Schierholz, G. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Weinberg, V. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Freie Univ. Berlin (Germany). Inst. fuer Theoretische Physik
2008-01-11
A detailed comparison is made between the topological structure of quenched QCD as revealed by the recently proposed over-improved stout-link smearing in conjunction with an improved gluonic definition of the topological density on one hand and a similar analysis made possible by the overlap-fermionic topological charge density both with and without variable ultraviolet cutoff {lambda}{sub cut}. The matching is twofold, provided by fitting the density-density two-point functions on one hand and by a point-by-point fitting of the topological densities according to the two methods. We point out the similar cluster structure of the topological density for moderate smearing and 200 MeV<{lambda}{sub cut}<600 MeV, respectively. We demonstrate the relation of the gluonic topological density for extensive smearing to the location of the overlap zero modes and the lowest overlap non-zero mode as found for the unsmeared configurations. (orig.)
-
GenomeRNAi: a database for cell-based RNAi phenotypes.
Horn, Thomas; Arziman, Zeynep; Berger, Juerg; Boutros, Michael
2007-01-01
RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated gene in the genome. As increasing large datasets of RNAi-induced phenotypes become available, an important challenge remains the systematic integration and annotation of functional information. Genome-wide RNAi screens have been performed both in Caenorhabditis elegans and Drosophila for a variety of phenotypes and several RNAi libraries have become available to assess phenotypes for almost every gene in the genome. These screens were performed using different types of assays from visible phenotypes to focused transcriptional readouts and provide a rich data source for functional annotation across different species. The GenomeRNAi database provides access to published RNAi phenotypes obtained from cell-based screens and maps them to their genomic locus, including possible non-specific regions. The database also gives access to sequence information of RNAi probes used in various screens. It can be searched by phenotype, by gene, by RNAi probe or by sequence and is accessible at http://rnai.dkfz.de.
-
Lee, Junghee; Rizzo, Shemra; Altshuler, Lori; Glahn, David C; Miklowitz, David J; Sugar, Catherine A; Wynn, Jonathan K; Green, Michael F
2017-02-01
Bipolar disorder (BD) and schizophrenia (SZ) show substantial overlap. It has been suggested that a subgroup of patients might contribute to these overlapping features. This study employed a cross-diagnostic cluster analysis to identify subgroups of individuals with shared cognitive phenotypes. 143 participants (68 BD patients, 39 SZ patients and 36 healthy controls) completed a battery of EEG and performance assessments on perception, nonsocial cognition and social cognition. A K-means cluster analysis was conducted with all participants across diagnostic groups. Clinical symptoms, functional capacity, and functional outcome were assessed in patients. A two-cluster solution across 3 groups was the most stable. One cluster including 44 BD patients, 31 controls and 5 SZ patients showed better cognition (High cluster) than the other cluster with 24 BD patients, 35 SZ patients and 5 controls (Low cluster). BD patients in the High cluster performed better than BD patients in the Low cluster across cognitive domains. Within each cluster, participants with different clinical diagnoses showed different profiles across cognitive domains. All patients are in the chronic phase and out of mood episode at the time of assessment and most of the assessment were behavioral measures. This study identified two clusters with shared cognitive phenotype profiles that were not proxies for clinical diagnoses. The finding of better social cognitive performance of BD patients than SZ patients in the Lowe cluster suggest that relatively preserved social cognition may be important to identify disease process distinct to each disorder. Copyright © 2016 Elsevier B.V. All rights reserved.
-
Schunter, Celia; Vollmer, Steven V; Macpherson, Enrique; Pascual, Marta
2014-02-28
Social dominance is important for the reproductive success of males in many species. In the black-faced blenny (Tripterygion delaisi) during the reproductive season, some males change color and invest in nest making and defending a territory, whereas others do not change color and 'sneak' reproductions when females lay their eggs. Using RNAseq, we profiled differential gene expression between the brains of territorial males, sneaker males, and females to study the molecular signatures of male dimorphism. We found that more genes were differentially expressed between the two male phenotypes than between males and females, suggesting that during the reproductive period phenotypic plasticity is a more important factor in differential gene expression than sexual dimorphism. The territorial male overexpresses genes related to synaptic plasticity and the sneaker male overexpresses genes involved in differentiation and development. Previously suggested candidate genes for social dominance in the context of alternative mating strategies seem to be predominantly species-specific. We present a list of novel genes which are differentially expressed in Tripterygion delaisi. This is the first genome-wide study for a molecular non-model species in the context of alternative mating strategies and provides essential information for further studies investigating the molecular basis of social dominance.
-
Plant Phenotyping through the Eyes of Complex Systems: Theoretical Considerations
Kim, J.
2017-12-01
Plant phenotyping is an emerging transdisciplinary research which necessitates not only the communication and collaboration of scientists from different disciplines but also the paradigm shift to a holistic approach. Complex system is defined as a system having a large number of interacting parts (or particles, agents), whose interactions give rise to non-trivial properties like self-organization and emergence. Plant ecosystems are complex systems which are continually morphing dynamical systems, i.e. self-organizing hierarchical open systems. Such systems are composed of many subunits/subsystems with nonlinear interactions and feedback. The throughput such as the flow of energy, matter and information is the key control parameter in complex systems. Information theoretic approaches can be used to understand and identify such interactions, structures and dynamics through reductions in uncertainty (i.e. entropy). The theoretical considerations based on network and thermodynamic thinking and exemplary analyses (e.g. dynamic process network, spectral entropy) of the throughput time series will be presented. These can be used as a framework to develop more discipline-specific fundamental approaches to provide tools for the transferability of traits between measurement scales in plant phenotyping. Acknowledgment: This work was funded by the Weather Information Service Engine Program of the Korea Meteorological Administration under Grant KMIPA-2012-0001.
-
Troyanov, Yves; Targoff, Ira N; Payette, Marie-Pier; Raynauld, Jean-Pierre; Chartier, Suzanne; Goulet, Jean-Richard; Bourré-Tessier, Josiane; Rich, Eric; Grodzicky, Tamara; Fritzler, Marvin J; Joyal, France; Koenig, Martial; Senécal, Jean-Luc
2014-11-01
Dermatomyositis (DM) is a major clinical subset of autoimmune myositis (AIM). The characteristic DM rash (Gottron papules, heliotrope rash) and perifascicular atrophy at skeletal muscle biopsy are regarded as specific features for this diagnosis. However, new concepts are challenging the current definition of DM. A modified Bohan and Peter classification of AIM was proposed in which the core concept was the inclusion of the diagnostic significance of overlap connective tissue disease features. In this clinical classification, a DM rash in association with myositis in the absence of overlap features indicates a diagnosis of pure DM. However, overlap features in association with myositis allow a diagnosis of overlap myositis (OM), irrespective of the presence or absence of the DM rash. Perifascicular atrophy may be present in both pure DM and OM. Recently, the presence of perifascicular atrophy in myositis without a DM rash was proposed as diagnostic of a novel entity, adermatopathic DM. We conducted the present study to evaluate these new concepts to further differentiate pure DM from OM.Using the modified Bohan and Peter classification, we performed a follow-up study of a longitudinal cohort of 100 consecutive adult French Canadian patients with AIM, including 44 patients with a DM phenotype, defined as a DM rash, and/or DM-type calcinosis, and/or the presence of perifascicular atrophy on muscle biopsy. A detailed evaluation was performed for overlap features, the extent and natural history of the DM rash, adermatopathic DM, DM-specific and overlap autoantibodies by protein A immunoprecipitation on coded serum samples, and associations with cancer and survival.Two distinct subsets were identified in patients with a DM phenotype: pure DM (n = 24) and OM with DM features, or OMDM (n = 20). In pure DM, the DM rash was a dominant finding. It was the first disease manifestation, was always present at the time of myositis diagnosis, and was associated with a high
-
Nam, Soon Woo; Bae, Si Hyun; Lee, Seung Woo; Kim, Yeon Soo; Kang, Sang Bum; Choi, Jong Young; Cho, Se Hyun; Yoon, Seung Kew; Han, Joon-Yeol; Yang, Jin Mo; Lee, Young Suk
2008-01-01
AIM: To evaluate the efficacy of short-term overlap lamivudine therapy with adefovir in patients with lamivudine-resistant and naïve chronic hepatitis B, we compared patients receiving overlap therapy with those receiving adefovir alone. METHODS: Eighty patients who had received lamivudine treatment for various periods and had a lamivudine-resistant liver function abnormality were enrolled. Forty of these patients received adefovir treatment combined with lamivudine treatment for ≥ 2 mo, while the other 40 received adefovir alone. We assessed the levels of hepatitis B virus (HBV) DNA at 0, 12 and 48 wk and serum alanine aminotransferase (ALT) levels after 0, 12, 24 and 48 wk of adefovir treatment in each group. RESULTS: We found serum ALT became normalized in 72 (87.5%) of the 80 patients, and HBV DNA decreased by ≥ 2 log10 copies/mL in 60 (75%) of the 80 patients at the end of a 48-wk treatment. HBV DNA levels were not significantly different between the groups. The improvements in serum ALT were also not significantly different between the two groups. CONCLUSION: These findings suggest short-term overlap lamivudine treatment results in no better virological and biological outcomes than non-overlap adefovir monotherapy. PMID:18350610
-
Non-Statistical Methods of Analysing of Bankruptcy Risk
Directory of Open Access Journals (Sweden)
Pisula Tomasz
2015-06-01
Full Text Available The article focuses on assessing the effectiveness of a non-statistical approach to bankruptcy modelling in enterprises operating in the logistics sector. In order to describe the issue more comprehensively, the aforementioned prediction of the possible negative results of business operations was carried out for companies functioning in the Polish region of Podkarpacie, and in Slovakia. The bankruptcy predictors selected for the assessment of companies operating in the logistics sector included 28 financial indicators characterizing these enterprises in terms of their financial standing and management effectiveness. The purpose of the study was to identify factors (models describing the bankruptcy risk in enterprises in the context of their forecasting effectiveness in a one-year and two-year time horizon. In order to assess their practical applicability the models were carefully analysed and validated. The usefulness of the models was assessed in terms of their classification properties, and the capacity to accurately identify enterprises at risk of bankruptcy and healthy companies as well as proper calibration of the models to the data from training sample sets.
-
Dutra Filho, J A; Junior, T C; Simões Neto, D E
2015-10-05
In the present study, we assessed the agro-industrial performance of 22 sugarcane genotypes adaptable to edaphoclimatic conditions in production microregions in the State of Pernambuco, Brazil, and we recommended the commercial cultivation of select genotypes. The variables analyzed were as follows: sucrose percentage in cane juice, tonnage of saccharose per hectare (TPH), sugarcane tonnage per hectare (TCH), fiber, solid soluble contents, total recoverable sugar tonnage (ATR), and total recoverable sugar tonnage per hectare (ATR t/ha). A randomized block design with 4 repeats was used. Combined variance of the experiments, genetic parameter estimates, and environment stratification were analyzed. Phenotypic adaptability and stability were analyzed using the Annicchiarico and Wricke methods and analysis of variance. Genetic gain was estimated using the classic index and sum of ranks. Genotype selection was efficient for TPH, TCH, and ATR t/ha. Genotypes presented a great potential for improvement and a similar response pattern in Litoral Norte and Mata Sul microregions for TPH and TCH and Litoral Norte and Litoral Sul microregions for ATR t/ha. Genotypes SP78-4764, RB813804, and SP79-101 showed better productivity and phenotypic adaptability and stability, according to the Wricke and Annicchiarico methods. These genotypes can be recommended for cultivation in the sugarcane belt in the State of Pernambuco.
-
Davidson, Julie; Goin-Kochel, Robin P.; Green-Snyder, Lee Anne; Hundley, Rachel J.; Warren, Zachary; Peters, Sarika U.
2014-01-01
The broad autism phenotype (BAP) refers to the phenotypic expression of an underlying genetic liability to autism, manifest in non-autistic relatives. This study examined the relationship among the "Broad Autism Phenotype Questionnaire" (BAPQ), "Social Responsiveness Scale: Adult Research Version" (SRS:ARV), and "Family…
-
How Phenotypic Screening Influenced Drug Discovery: Lessons from Five Years of Practice.
Haasen, Dorothea; Schopfer, Ulrich; Antczak, Christophe; Guy, Chantale; Fuchs, Florian; Selzer, Paul
Since 2011, phenotypic screening has been a trend in the pharmaceutical industry as well as in academia. This renaissance was triggered by analyses that suggested that phenotypic screening is a superior strategy to discover first-in-class drugs. Despite these promises and considerable investments, pharmaceutical research organizations have encountered considerable challenges with the approach. Few success stories have emerged in the past 5 years and companies are questioning their investment in this area. In this contribution, we outline what we have learned about success factors and challenges of phenotypic screening. We then describe how our efforts in phenotypic screening have influenced our approach to drug discovery in general. We predict that concepts from phenotypic screening will be incorporated into target-based approaches and will thus remain influential beyond the current trend.
-
Tung, Wan-Ping; Chen, Yi-Huey; Cheng, Wei-Chun; Chuang, Ming-Feng; Hsu, Wan-Tso; Kam, Yeong-Choy; Lehtinen, Richard M
2015-01-01
Overlapping offspring occurs when eggs are laid in a nest containing offspring from earlier reproduction. Earlier studies showed that the parentage is not always obvious due to difficulties in field observation and/or alternative breeding tactics. To unveil the parentage between overlapping offspring and parents is critical in understanding oviposition site selection and the reproductive strategies of parents. Amplectant pairs of an arboreal-breeding frog, Kurixalus eiffingeri, lay eggs in tadpole-occupied nests where offspring of different life stages (embryos and tadpoles) coexist. We used five microsatellite DNA markers to assess the parentage between parents and overlapping offspring. We also tested the hypothesis that the male or female frog would breed in the same breeding site because of the scarcity of nest sites. Results showed varied parentage patterns, which may differ from the phenomenon of overlapping egg clutches reported earlier. Parentage analyses showed that only 58 and 25% of the tadpole-occupied stumps were reused by the same male and female respectively, partially confirming our prediction. Re-nesting by the same individual was more common in males than females, which is most likely related to the cost of tadpole feeding and/or feeding schemes of females. On the other hand, results of parentage analyses showed that about 42 and 75% of male and female respectively bred in tadpole-occupied stumps where tadpoles were genetically unrelated. Results of a nest-choice experiment revealed that 40% of frogs chose tadpole-occupied bamboo cups when we presented identical stumps, without or with tadpoles, suggesting that the habitat saturation hypothesis does not fully explain why frogs used the tadpole-occupied stumps. Several possible benefits of overlapping offspring with different life stages were proposed. Our study highlights the importance of integrating molecular data with field observations to better understand the reproductive biology and nest
-
Di Dalmazi, Guido; Vicennati, Valentina; Garelli, Silvia; Casadio, Elena; Rinaldi, Eleonora; Giampalma, Emanuela; Mosconi, Cristina; Golfieri, Rita; Paccapelo, Alexandro; Pagotto, Uberto; Pasquali, Renato
2014-05-01
Incidental discovery of adrenal masses has increased over the past few years. Mild alterations in cortisol secretion without clinical signs of overt hypercortisolism (subclinical Cushing's syndrome) are a common finding in patients with these tumours. Although metabolic alterations and increased cardiovascular risk have been noted in patients with subclinical Cushing's syndrome, incidence of cardiovascular events and mortality in the long term have not been assessed. We aimed to ascertain the frequency of new cardiovascular events and mortality in patients with non-secreting adrenal incidentalomas, tumours of intermediate phenotype, or those causing subclinical Cushing's syndrome. From January, 1995, to September, 2010, consecutive outpatients with adrenal incidentalomas who were referred to the endocrinology unit of S Orsola-Malpighi Hospital, Bologna, Italy, were enrolled into our study. Individuals were assessed every 18-30 months for the first 5 years (mean follow-up 7·5 [SD 3·2] years, range 26 months to 15 years). Cortisol concentrations after the 1 mg dexamethasone suppression test (DST) were used to define non-secreting (+50 nmol/L) and intermediate phenotype (50-138 nmol/L) adrenal incidentalomas and subclinical Cushing's syndrome (+138 nmol/L). At the end of follow-up, patients were reclassified as having either unchanged or worsened secreting patterns from baseline. 198 outpatients were assessed; at the end of follow-up, 114 patients had stable non-secreting adrenal incidentalomas, 61 had either a stable intermediate phenotype or subclinical Cushing's syndrome, and 23 had a pattern of secretion that had worsened. By comparison with patients with stable non-secreting adrenal incidentalomas, the incidence of cardiovascular events was higher in individuals with a stable intermediate phenotype or subclinical Cushing's syndrome (6·7% vs 16·7%; p=0·04) and in those with worsened secreting patterns (6·7% vs 28·4%; p=0·02). Cardiovascular events were
-
Overlap of autistic and schizotypal traits in adolescents with Autism Spectrum Disorders.
Barneveld, Petra S; Pieterse, Jolijn; de Sonneville, Leo; van Rijn, Sophie; Lahuis, Bertine; van Engeland, Herman; Swaab, Hanna
2011-03-01
This study addresses the unraveling of the relationship between autism spectrum and schizophrenia spectrum traits in a population of adolescents with Autism Spectrum Disorders (ASD). Recent studies comparing isolated symptoms of both spectrum disorders as well as diagnostic criteria for each (DSM-IV-TR) suggest resemblances in the clinical phenotype. A group of 27 adolescents with ASD (11 to 18 years) and 30 typically developing adolescents, matched for age and gender, participated in this study. Within the ASD group 11 adolescents satisfied DSM-IV-TR criteria for schizotypal personality disorders. Autistic and schizotypal traits were identified by means of well validated questionnaires (Autism Questionnaire, AQ and Schizotypal Personality Questionnaire-Revised, SPQ). Significantly more schizotypal traits in adolescents with ASD were found than in typically developing controls. Besides high levels of negative symptoms, adolescents with ASD also displayed high levels of positive and disorganized symptoms. There appeared to be a relationship between the mean level of autistic symptoms and schizotypal traits, as well as specific associations between autistic symptoms and negative, disorganized and positive schizotypal symptoms within individuals. Schizotypal symptomatology in all sub dimensions that are reflected by the SPQ scores, was most prominently associated with attention switching problems of the autism symptoms from the AQ. These findings indicate that patients diagnosed with an ASD show schizophrenia spectrum traits in adolescence. Although other studies have provided empirical support for this overlap in diagnostic criteria between both spectrum disorders, the present findings add to the literature that behavioral overlap is not limited to negative schizotypal symptoms, but extends to disorganized and positive symptoms as well. Copyright © 2010 Elsevier B.V. All rights reserved.
-
Jaouannet, Maëlle; Morris, Jenny A.; Hedley, Peter E.; Bos, Jorunn I. B.
2015-01-01
Aphids are economically important pests that display exceptional variation in host range. The determinants of diverse aphid host ranges are not well understood, but it is likely that molecular interactions are involved. With significant progress being made towards understanding host responses upon aphid attack, the mechanisms underlying non-host resistance remain to be elucidated. Here, we investigated and compared Arabidopsis thaliana host and non-host responses to aphids at the transcriptional level using three different aphid species, Myzus persicae, Myzus cerasi and Rhopalosiphum pisum. Gene expression analyses revealed a high level of overlap in the overall gene expression changes during the host and non-host interactions with regards to the sets of genes differentially expressed and the direction of expression changes. Despite this overlap in transcriptional responses across interactions, there was a stronger repression of genes involved in metabolism and oxidative responses specifically during the host interaction with M. persicae. In addition, we identified a set of genes with opposite gene expression patterns during the host versus non-host interactions. Aphid performance assays on Arabidopsis mutants that were selected based on our transcriptome analyses identified novel genes contributing to host susceptibility, host defences during interactions with M. persicae as well to non-host resistance against R. padi. Understanding how plants respond to aphid species that differ in their ability to infest plant species, and identifying the genes and signaling pathways involved, is essential for the development of novel and durable aphid control in crop plants. PMID:25993686
-
Overlap syndrome of COPD and OSA in Koreans.
Choi, Kyung-Mee; Thomas, Robert J; Kim, Jinkwan; Lee, Seung Ku; Yoon, Dae Wui; Shin, Chol
2017-07-01
Overlap syndrome of chronic obstructive pulmonary disease (COPD) and obstructive sleep apnea (OSA) leads to increased morbidity and mortality. There have been no reports available on the overlap syndrome for Koreans. Our primary aim was to identify prevalence and predictors of the overlap syndrome in Koreans.This is a cross-sectional study with a community-based sample of 1298 participants (mean age, 59.7 ± 6.7) from the cohort of Korean Genomic and Epidemiologic Study during 2013 to 2014. OSA and COPD were assessed by apnea-hypopnea index (AHI) and the ratio of forced expiratory volume in 1 s to forced vital capacity (FEV1/FVC syndrome. The prevalence of COPD remained the same as 10.8% regardless of the presence of OSA. The mean ratio of FEV1/FVC for those with COPD was 0.77, regardless of OSA. The OR increased for age (OR, 1.1; 95% CI, 1.0-1.1) and smokers (OR, 3.6; 95% CI, 2.0-6.4), but decreased for body mass index (BMI) (OR, 0.84; 95% CI, 0.8-0.9) and overweight state (OR, 0.4; 95% CI, 0.2-0.7). Risk factors of the overlap syndrome differed by OSA severity, that is, BMI in those with moderate-to-severe OSA, whereas sex (OR, 4.7; 95% CI, 2.1-10.6) and age (OR, 1.1; 95% CI, 1.0-1.1) in those with mild OSA.In a population study from Korea, 10.8% of OSA patients had an overlap syndrome with COPD. Although BMI is a well-known risk factor of OSA, it is likely that being overweight may be protective for moderate-to-severe OSA patients from the risk of COPD (i.e., overlap syndrome).
-
Noori, Hamid R; Cosa Linan, Alejandro; Spanagel, Rainer
2016-09-01
Cue reactivity to natural and social rewards is essential for motivational behavior. However, cue reactivity to drug rewards can also elicit craving in addicted subjects. The degree to which drug and natural rewards share neural substrates is not known. The objective of this study is to conduct a comprehensive meta-analysis of neuroimaging studies on drug, gambling and natural stimuli (food and sex) to identify the common and distinct neural substrates of cue reactivity to drug and natural rewards. Neural cue reactivity studies were selected for the meta-analysis by means of activation likelihood estimations, followed by sensitivity and clustering analyses of averaged neuronal response patterns. Data from 176 studies (5573 individuals) suggests largely overlapping neural response patterns towards all tested reward modalities. Common cue reactivity to natural and drug rewards was expressed by bilateral neural responses within anterior cingulate gyrus, insula, caudate head, inferior frontal gyrus, middle frontal gyrus and cerebellum. However, drug cues also generated distinct activation patterns in medial frontal gyrus, middle temporal gyrus, posterior cingulate gyrus, caudate body and putamen. Natural (sexual) reward cues induced unique activation of the pulvinar in thalamus. Neural substrates of cue reactivity to alcohol, drugs of abuse, food, sex and gambling are largely overlapping and comprise a network that processes reward, emotional responses and habit formation. This suggests that cue-mediated craving involves mechanisms that are not exclusive for addictive disorders but rather resemble the intersection of information pathways for processing reward, emotional responses, non-declarative memory and obsessive-compulsive behavior. Copyright © 2016 Elsevier B.V. and ECNP. All rights reserved.
-
Comparative analysis of distinct phenotypes in gambling disorder based on gambling preferences.
Moragas, Laura; Granero, Roser; Stinchfield, Randy; Fernández-Aranda, Fernando; Fröberg, Frida; Aymamí, Neus; Gómez-Peña, Mónica; Fagundo, Ana B; Islam, Mohammed A; Del Pino-Gutiérrez, Amparo; Agüera, Zaida; Savvidou, Lamprini G; Arcelus, Jon; Witcomb, Gemma L; Sauchelli, Sarah; Menchón, José M; Jiménez-Murcia, Susana
2015-04-15
Studies examining gambling preferences have identified the importance of the type of gambling practiced on distinct individual profiles. The objectives were to compare clinical, psychopathological and personality variables between two different groups of individuals with a gambling disorder (strategic and non-strategic gamblers) and to evaluate the statistical prediction capacity of these preferences with respect to the severity of the disorder. A total sample of 2010 treatment-seeking patients with a gambling disorder participated in this stand-alone study. All were recruited from a single Pathological Gambling Unit in Spain (1709 strategic and 301 non-strategic gamblers). The design of the study was cross-sectional and data were collected at the start of treatment. Data was analysed using logistic regression for binary outcomes and analysis of variance (ANOVA) for quantitative responses. There were significant differences in several socio-demographic and clinical variables, as well as in personality traits (novelty seeking and cooperativeness). Multiple regression analysis showed harm avoidance and self-directedness were the main predictors of gambling severity and psychopathology, while age at assessment and age of onset of gambling behaviour were predictive of gambling severity. Strategic gambling (as opposed to non-strategic) was significantly associated with clinical outcomes, but the effect size of the relationships was small. It is possible to identify distinct phenotypes depending on the preference of gambling. While these phenotypes differ in relation to the severity of the gambling disorder, psychopathology and personality traits, they can be useful from a clinical and therapeutic perspective in enabling risk factors to be identified and prevention programs targeting specific individual profiles to be developed.
-
Novel R pipeline for analyzing Biolog Phenotypic MicroArray data.
Directory of Open Access Journals (Sweden)
Minna Vehkala
Full Text Available Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells' respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, respectively. We expand existing solutions by introducing an important assumption that active and non-active bacteria manifest completely different metabolism and thus should be treated separately. Effect identification, in turn, provides new insights into detecting differing respiration patterns between experimental conditions, e.g. between different combinations of strains and temperatures, as not only the main effects but also their interactions can be evaluated. In the effect identification, the multilevel data are effectively processed by a hierarchical model in the Bayesian framework. The pipeline is tested on a data set of 12 phenotypic plates with bacterium Yersinia enterocolitica. Our pipeline is implemented in R language on the top of opm R package and is freely available for research purposes.
-
Chironomidae larvae (Diptera) of Neotropical floodplain: overlap niche in different habitats.
Butakka, C M M; Ragonha, F H; Takeda, A M
2014-05-01
The niche overlap between trophic groups of Chironomidae larvae in different habitats was observed between trophic groups and between different environments in Neotropical floodplain. For the evaluation we used the index of niche overlap (CXY) and analysis of trophic networks, both from the types and amount of food items identified in the larval alimentary canal. In all environments, the larvae fed on mainly organic matter such as plants fragments and algae, but there were many omnivore larvae. Species that have high values of food items occurred in diverse environments as generalists with great overlap niche and those with a low amount of food items with less overlap niche were classified as specialists. The largest number of trophic niche overlap was observed among collector-gatherers in connected floodplain lakes. The lower values of index niche overlap were predators. The similarity in the diet of different taxa in the same niche does not necessarily imply competition between them, but coexistence when the food resource is not scarce in the environment even in partially overlapping niches.
-
Research on Some Bus Transport Networks with Random Overlapping Clique Structure
International Nuclear Information System (INIS)
Yang Xuhua; Sun Youxian; Wang Bo; Wang Wanliang
2008-01-01
On the basis of investigating the statistical data of bus transport networks of three big cities in China, we propose that each bus route is a clique (maximal complete subgraph) and a bus transport network (BTN) consists of a lot of cliques, which intensively connect and overlap with each other. We study the network properties, which include the degree distribution, multiple edges' overlapping time distribution, distribution of the overlap size between any two overlapping cliques, distribution of the number of cliques that a node belongs to. Naturally, the cliques also constitute a network, with the overlapping nodes being their multiple links. We also research its network properties such as degree distribution, clustering, average path length, and so on. We propose that a BTN has the properties of random clique increment and random overlapping clique, at the same time, a BTN is a small-world network with highly clique-clustered and highly clique-overlapped. Finally, we introduce a BTN evolution model, whose simulation results agree well with the statistical laws that emerge in real BTNs
-
Iterative methods for overlap and twisted mass fermions
International Nuclear Information System (INIS)
Chiarappa, T.; Jansen, K.; Shindler, A.; Wetzorke, I.; Scorzato, L.; Urbach, C.; Wenger, U.
2006-09-01
We present a comparison of a number of iterative solvers of linear systems of equations for obtaining the fermion propagator in lattice QCD. In particular, we consider chirally invariant overlap and chirally improved Wilson (maximally) twisted mass fermions. The comparison of both formulations of lattice QCD is performed at four fixed values of the pion mass between 230 MeV and 720 MeV. For overlap fermions we address adaptive precision and low mode preconditioning while for twisted mass fermions we discuss even/odd preconditioning. Taking the best available algorithms in each case we find that calculations with the overlap operator are by a factor of 30-120 more expensive than with the twisted mass operator. (orig.)
-
Iterative methods for overlap and twisted mass fermions
Energy Technology Data Exchange (ETDEWEB)
Chiarappa, T. [Univ. di Milano Bicocca (Italy); Jansen, K.; Shindler, A.; Wetzorke, I. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Nagai, K.I. [Wuppertal Univ. (Gesamthochschule) (Germany). Fachbereich Physik; Papinutto, M. [INFN Sezione di Roma Tre, Rome (Italy); Scorzato, L. [European Centre for Theoretical Studies in Nuclear Physics and Related Areas (ECT), Villazzano (Italy); Urbach, C. [Liverpool Univ. (United Kingdom). Dept. of Mathematical Sciences; Wenger, U. [ETH Zuerich (Switzerland). Inst. fuer Theoretische Physik
2006-09-15
We present a comparison of a number of iterative solvers of linear systems of equations for obtaining the fermion propagator in lattice QCD. In particular, we consider chirally invariant overlap and chirally improved Wilson (maximally) twisted mass fermions. The comparison of both formulations of lattice QCD is performed at four fixed values of the pion mass between 230 MeV and 720 MeV. For overlap fermions we address adaptive precision and low mode preconditioning while for twisted mass fermions we discuss even/odd preconditioning. Taking the best available algorithms in each case we find that calculations with the overlap operator are by a factor of 30-120 more expensive than with the twisted mass operator. (orig.)
-
Interference Management in Full-Duplex Cellular Networks with Partial Spectrum Overlap
Randrianantenaina, Itsikiantsoa
2017-03-31
Full-duplex (FD) communication is promoted to double the spectral efficiency when compared to the halfduplex (HD) counterpart. In the context of cellular networks, however, FD communication exacerbates the aggregate uplink and downlink interference, which diminishes the foreseen FD gains. This paper considers a flexible duplex system, denoted by -duplex (-D) system, wherein a fine-grained bandwidth control for each uplink/downlink channel pair in each base station (BS) is allowed, which also leads to partial spectrum overlap between the uplink and downlink channels. The paper addresses the resulting interference management problem by maximizing a network-wide rate-based utility function subject to uplink/downlink power constraints, so as to determine userto- BS association, user-to-channel scheduling, the UL and DL transmit powers, and the fraction of spectrum overlap between UL and DL for every user, under the assumption that the number of available channels and users are equal. The paper solves such a non-convex mixed-integer optimization problem in an iterative way by decoupling the problem into several subproblems. Particularly, the user-to-BS association problem is solved using a matching algorithm that is a generalization of the stable marriage problem. The scheduling problem is solved by iterative Hungarian algorithm. The power and spectrum overlap problem is solved by successive convex approximation. The proposed iterative strategy guarantees an efficient one-toone user to BS and channel assignment. It further provides optimized flexible duplexing and power allocation schemes for all transceivers. Simulations results show appreciable gains when comparing the proposed solution to different schemes from the literature.
-
Interference Management in Full-Duplex Cellular Networks with Partial Spectrum Overlap
Randrianantenaina, Itsikiantsoa; Dahrouj, Hayssam; Elsawy, Hesham; Alouini, Mohamed-Slim
2017-01-01
Full-duplex (FD) communication is promoted to double the spectral efficiency when compared to the halfduplex (HD) counterpart. In the context of cellular networks, however, FD communication exacerbates the aggregate uplink and downlink interference, which diminishes the foreseen FD gains. This paper considers a flexible duplex system, denoted by -duplex (-D) system, wherein a fine-grained bandwidth control for each uplink/downlink channel pair in each base station (BS) is allowed, which also leads to partial spectrum overlap between the uplink and downlink channels. The paper addresses the resulting interference management problem by maximizing a network-wide rate-based utility function subject to uplink/downlink power constraints, so as to determine userto- BS association, user-to-channel scheduling, the UL and DL transmit powers, and the fraction of spectrum overlap between UL and DL for every user, under the assumption that the number of available channels and users are equal. The paper solves such a non-convex mixed-integer optimization problem in an iterative way by decoupling the problem into several subproblems. Particularly, the user-to-BS association problem is solved using a matching algorithm that is a generalization of the stable marriage problem. The scheduling problem is solved by iterative Hungarian algorithm. The power and spectrum overlap problem is solved by successive convex approximation. The proposed iterative strategy guarantees an efficient one-toone user to BS and channel assignment. It further provides optimized flexible duplexing and power allocation schemes for all transceivers. Simulations results show appreciable gains when comparing the proposed solution to different schemes from the literature.
-
Non-invasive PGAA, PIXE and ToF-ND analyses on Hungarian Bronze Age defensive armour
International Nuclear Information System (INIS)
Marianne Moedlinger; Imre Kovacs; Zoltan Szoekefalvi-Nagy; Ziad El Morr
2014-01-01
Non-invasive, archaeometric analyses on selected Hungarian Bronze Age defensive armour is presented here: three greaves, three helmets two shields as well as one vessel fragment were analysed with PIXE, PGAA and TOF-ND. The detected alloy elemental and phase composition as well as its intergranular or spatial concentration distribution reveals important insights into the alloys used and the manufacturing techniques applied c. 1200-950 BC, and allows to reconstruct the production techniques used during the Late Bronze Age. (author)
-
Poussier, Stéphane; Thoquet, Philippe; Trigalet-Demery, Danièle; Barthet, Séverine; Meyer, Damien; Arlat, Matthieu; Trigalet, André
2003-08-01
Ralstonia solanacearum is a plant pathogenic bacterium that undergoes a spontaneous phenotypic conversion (PC) from a wild-type pathogenic to a non-pathogenic form. PC is often associated with mutations in phcA, which is a key virulence regulatory gene. Until now, reversion to the wild-type pathogenic form has not been observed for PC variants and the biological significance of PC has been questioned. In this study, we characterized various alterations in phcA (eight IS element insertions, three tandem duplications, seven deletions and a base substitution) in 19 PC mutants from the model strain GMI1000. In five of these variants, reversion to the pathogenic form was observed in planta, while no reversion was ever noticed in vitro whatever culture media used. However, reversion was observed for a 64 bp tandem duplication in vitro in the presence of tomato root exudate. This is the first report showing a complete cycle of phenotypic conversion/reversion in a plant pathogenic bacterium.
-
Directory of Open Access Journals (Sweden)
J. Li
2018-05-01
Full Text Available Studies have shown that changes in cloud cover are responsible for the rapid climate warming over the Tibetan Plateau (TP in the past 3 decades. To simulate the total cloud cover, atmospheric models have to reasonably represent the characteristics of vertical overlap between cloud layers. Until now, however, this subject has received little attention due to the limited availability of observations, especially over the TP. Based on the above information, the main aim of this study is to examine the properties of cloud overlaps over the TP region and to build an empirical relationship between cloud overlap properties and large-scale atmospheric dynamics using 4 years (2007–2010 of data from the CloudSat cloud product and collocated ERA-Interim reanalysis data. To do this, the cloud overlap parameter α, which is an inverse exponential function of the cloud layer separation D and decorrelation length scale L, is calculated using CloudSat and is discussed. The parameters α and L are both widely used to characterize the transition from the maximum to random overlap assumption with increasing layer separations. For those non-adjacent layers without clear sky between them (that is, contiguous cloud layers, it is found that the overlap parameter α is sensitive to the unique thermodynamic and dynamic environment over the TP, i.e., the unstable atmospheric stratification and corresponding weak wind shear, which leads to maximum overlap (that is, greater α values. This finding agrees well with the previous studies. Finally, we parameterize the decorrelation length scale L as a function of the wind shear and atmospheric stability based on a multiple linear regression. Compared with previous parameterizations, this new scheme can improve the simulation of total cloud cover over the TP when the separations between cloud layers are greater than 1 km. This study thus suggests that the effects of both wind shear and atmospheric stability on cloud overlap
-
Li, Jiming; Lv, Qiaoyi; Jian, Bida; Zhang, Min; Zhao, Chuanfeng; Fu, Qiang; Kawamoto, Kazuaki; Zhang, Hua
2018-05-01
Studies have shown that changes in cloud cover are responsible for the rapid climate warming over the Tibetan Plateau (TP) in the past 3 decades. To simulate the total cloud cover, atmospheric models have to reasonably represent the characteristics of vertical overlap between cloud layers. Until now, however, this subject has received little attention due to the limited availability of observations, especially over the TP. Based on the above information, the main aim of this study is to examine the properties of cloud overlaps over the TP region and to build an empirical relationship between cloud overlap properties and large-scale atmospheric dynamics using 4 years (2007-2010) of data from the CloudSat cloud product and collocated ERA-Interim reanalysis data. To do this, the cloud overlap parameter α, which is an inverse exponential function of the cloud layer separation D and decorrelation length scale L, is calculated using CloudSat and is discussed. The parameters α and L are both widely used to characterize the transition from the maximum to random overlap assumption with increasing layer separations. For those non-adjacent layers without clear sky between them (that is, contiguous cloud layers), it is found that the overlap parameter α is sensitive to the unique thermodynamic and dynamic environment over the TP, i.e., the unstable atmospheric stratification and corresponding weak wind shear, which leads to maximum overlap (that is, greater α values). This finding agrees well with the previous studies. Finally, we parameterize the decorrelation length scale L as a function of the wind shear and atmospheric stability based on a multiple linear regression. Compared with previous parameterizations, this new scheme can improve the simulation of total cloud cover over the TP when the separations between cloud layers are greater than 1 km. This study thus suggests that the effects of both wind shear and atmospheric stability on cloud overlap should be taken into
-
Presentation of dynamically overlapping auditory messages in user interfaces
Energy Technology Data Exchange (ETDEWEB)
Papp, III, Albert Louis [Univ. of California, Davis, CA (United States)
1997-09-01
This dissertation describes a methodology and example implementation for the dynamic regulation of temporally overlapping auditory messages in computer-user interfaces. The regulation mechanism exists to schedule numerous overlapping auditory messages in such a way that each individual message remains perceptually distinct from all others. The method is based on the research conducted in the area of auditory scene analysis. While numerous applications have been engineered to present the user with temporally overlapped auditory output, they have generally been designed without any structured method of controlling the perceptual aspects of the sound. The method of scheduling temporally overlapping sounds has been extended to function in an environment where numerous applications can present sound independently of each other. The Centralized Audio Presentation System is a global regulation mechanism that controls all audio output requests made from all currently running applications. The notion of multimodal objects is explored in this system as well. Each audio request that represents a particular message can include numerous auditory representations, such as musical motives and voice. The Presentation System scheduling algorithm selects the best representation according to the current global auditory system state, and presents it to the user within the request constraints of priority and maximum acceptable latency. The perceptual conflicts between temporally overlapping audio messages are examined in depth through the Computational Auditory Scene Synthesizer. At the heart of this system is a heuristic-based auditory scene synthesis scheduling method. Different schedules of overlapped sounds are evaluated and assigned penalty scores. High scores represent presentations that include perceptual conflicts between over-lapping sounds. Low scores indicate fewer and less serious conflicts. A user study was conducted to validate that the perceptual difficulties predicted by
-
Monzani, Benedetta; Rijsdijk, Fruhling; Iervolino, Alessandra C; Anson, Martin; Cherkas, Lynn; Mataix-Cols, David
2012-06-01
Body dysmorphic disorder (BDD) is thought to be etiologically related to obsessive-compulsive disorder (OCD) but the available evidence is incomplete. The current study examined the genetic and environmental sources of covariance between body dysmorphic and obsessive-compulsive symptoms in a community sample of adult twins. A total of 2,148 female twins (1,074 pairs) completed valid and reliable measures of body dysmorphic concerns and obsessive-compulsive symptoms. The data were analyzed using bivariate twin modeling methods and the statistical programme Mx. In the best-fitting model, the covariation between body dysmorphic and obsessive-compulsive traits was largely accounted for by genetic influences common to both phenotypes (64%; 95% CI: 0.50-0.80). This genetic overlap was even higher when specific obsessive-compulsive symptom dimensions were considered, with up to 82% of the phenotypic correlation between the obsessing and symmetry/ordering symptom dimensions and dysmorphic concerns being attributable to common genetic factors. Unique environmental factors, although influencing these traits individually, did not substantially contribute to their covariation. The results remained unchanged when excluding individuals reporting an objective medical condition/injury accounting for their concern in physical appearance. The association between body dysmorphic concerns and obsessive-compulsive symptoms is largely explained by shared genetic factors. Environmental risk factors were largely unique to each phenotype. These results support current recommendations to group BDD together with OCD in the same DSM-5 chapter, although comparison with other phenotypes such as somatoform disorders and social phobia is needed. Copyright © 2012 Wiley Periodicals, Inc.
-
Xia, Renbo; Hu, Maobang; Zhao, Jibin; Chen, Songlin; Chen, Yueling
2018-06-01
Multi-camera vision systems are often needed to achieve large-scale and high-precision measurement because these systems have larger fields of view (FOV) than a single camera. Multiple cameras may have no or narrow overlapping FOVs in many applications, which pose a huge challenge to global calibration. This paper presents a global calibration method for multi-cameras without overlapping FOVs based on photogrammetry technology and a reconfigurable target. Firstly, two planar targets are fixed together and made into a long target according to the distance between the two cameras to be calibrated. The relative positions of the two planar targets can be obtained by photogrammetric methods and used as invariant constraints in global calibration. Then, the reprojection errors of target feature points in the two cameras’ coordinate systems are calculated at the same time and optimized by the Levenberg–Marquardt algorithm to find the optimal solution of the transformation matrix between the two cameras. Finally, all the camera coordinate systems are converted to the reference coordinate system in order to achieve global calibration. Experiments show that the proposed method has the advantages of high accuracy (the RMS error is 0.04 mm) and low cost and is especially suitable for on-site calibration.
-
Do plants and animals differ in phenotypic plasticity?
Indian Academy of Sciences (India)
Unknown
fits, of a plastic versus non-plastic phenotype in plants and animals. [Renee M Borges ... polyphenol oxidase and other oxidative enzymes in the defence repertoire of .... males in response to environmental stress (Cremer and. Heinze 2003).
-
Measures for interoperability of phenotypic data: minimum information requirements and formatting.
Ćwiek-Kupczyńska, Hanna; Altmann, Thomas; Arend, Daniel; Arnaud, Elizabeth; Chen, Dijun; Cornut, Guillaume; Fiorani, Fabio; Frohmberg, Wojciech; Junker, Astrid; Klukas, Christian; Lange, Matthias; Mazurek, Cezary; Nafissi, Anahita; Neveu, Pascal; van Oeveren, Jan; Pommier, Cyril; Poorter, Hendrik; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Scholz, Uwe; van Schriek, Marco; Seren, Ümit; Usadel, Björn; Weise, Stephan; Kersey, Paul; Krajewski, Paweł
2016-01-01
Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a document called "Minimum Information About a Plant Phenotyping Experiment", which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA-Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA-Tab-formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.
-
Le, Duc-Hau; Dao, Lan T M
2018-05-23
Recently, many long non-coding RNAs (lncRNAs) have been identified and their biological function has been characterized; however, our understanding of their underlying molecular mechanisms related to disease is still limited. To overcome the limitation in experimentally identifying disease-lncRNA associations, computational methods have been proposed as a powerful tool to predict such associations. These methods are usually based on the similarities between diseases or lncRNAs since it was reported that similar diseases are associated with functionally similar lncRNAs. Therefore, prediction performance is highly dependent on how well the similarities can be captured. Previous studies have calculated the similarity between two diseases by mapping exactly each disease to a single Disease Ontology (DO) term, and then use a semantic similarity measure to calculate the similarity between them. However, the problem of this approach is that a disease can be described by more than one DO terms. Until now, there is no annotation database of DO terms for diseases except for genes. In contrast, Human Phenotype Ontology (HPO) is designed to fully annotate human disease phenotypes. Therefore, in this study, we constructed disease similarity networks/matrices using HPO instead of DO. Then, we used these networks/matrices as inputs of two representative machine learning-based and network-based ranking algorithms, that is, regularized least square and heterogeneous graph-based inference, respectively. The results showed that the prediction performance of the two algorithms on HPO-based is better than that on DO-based networks/matrices. In addition, our method can predict 11 novel cancer-associated lncRNAs, which are supported by literature evidence. Copyright © 2018 Elsevier Ltd. All rights reserved.
-
DEFF Research Database (Denmark)
Ansari-Mahyari, S; Berg, P; Lund, M S
2009-01-01
disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...
-
International Nuclear Information System (INIS)
Marsit, C. J.; Kelsey, K. T.; Houseman, E. A.; Kelsey, K. T.; Houseman, E. A.; Nelson, H. H.
2008-01-01
Both genetic and epigenetic alterations characterize human non small cell lung cancer (NSCLC), but the biological processes that create or select these alterations remain incompletely investigated. Our hypothesis posits that a roughly reciprocal relationship between the propensity for promoter hyper methylation and a propensity for genetic deletion leads to distinct molecular phenotypes of lung cancer. To test this hypothesis, we examined promoter hyper methylation of 17 tumor suppressor genes, as a marker of epigenetic alteration propensity, and deletion events at the 3p21 region, as a marker of genetic alteration. To model the complex biology between these somatic alterations, we utilized an item response theory model. We demonstrated that tumors exhibiting LOH at greater than 30% of informative alleles in the 3p21 region have a significantly reduced propensity for hyper methylation. At the same time, tumors with activating KRAS mutations showed a significantly increased propensity for hyper methylation of the loci examined, a result similar to what has been observed in colon cancer. These data suggest that NSCLCs have distinct epigenetic or genetic alteration phenotypes acting upon tumor suppressor genes and that mutation of oncogenic growth promoting genes, such as KRAS, is associated with the epigenetic phenotype.
-
PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models.
Glueck, Michael; Naeini, Mahdi Pakdaman; Doshi-Velez, Finale; Chevalier, Fanny; Khan, Azam; Wigdor, Daniel; Brudno, Michael
2018-01-01
PhenoLines is a visual analysis tool for the interpretation of disease subtypes, derived from the application of topic models to clinical data. Topic models enable one to mine cross-sectional patient comorbidity data (e.g., electronic health records) and construct disease subtypes-each with its own temporally evolving prevalence and co-occurrence of phenotypes-without requiring aligned longitudinal phenotype data for all patients. However, the dimensionality of topic models makes interpretation challenging, and de facto analyses provide little intuition regarding phenotype relevance or phenotype interrelationships. PhenoLines enables one to compare phenotype prevalence within and across disease subtype topics, thus supporting subtype characterization, a task that involves identifying a proposed subtype's dominant phenotypes, ages of effect, and clinical validity. We contribute a data transformation workflow that employs the Human Phenotype Ontology to hierarchically organize phenotypes and aggregate the evolving probabilities produced by topic models. We introduce a novel measure of phenotype relevance that can be used to simplify the resulting topology. The design of PhenoLines was motivated by formative interviews with machine learning and clinical experts. We describe the collaborative design process, distill high-level tasks, and report on initial evaluations with machine learning experts and a medical domain expert. These results suggest that PhenoLines demonstrates promising approaches to support the characterization and optimization of topic models.
-
Analyses of non-fatal accidents in an opencast mine by logistic regression model - a case study.
Onder, Seyhan; Mutlu, Mert
2017-09-01
Accidents cause major damage for both workers and enterprises in the mining industry. To reduce the number of occupational accidents, these incidents should be properly registered and carefully analysed. This study efficiently examines the Aegean Lignite Enterprise (ELI) of Turkish Coal Enterprises (TKI) in Soma between 2006 and 2011, and opencast coal mine occupational accident records were used for statistical analyses. A total of 231 occupational accidents were analysed for this study. The accident records were categorized into seven groups: area, reason, occupation, part of body, age, shift hour and lost days. The SPSS package program was used in this study for logistic regression analyses, which predicted the probability of accidents resulting in greater or less than 3 lost workdays for non-fatal injuries. Social facilities-area of surface installations, workshops and opencast mining areas are the areas with the highest probability for accidents with greater than 3 lost workdays for non-fatal injuries, while the reasons with the highest probability for these types of accidents are transporting and manual handling. Additionally, the model was tested for such reported accidents that occurred in 2012 for the ELI in Soma and estimated the probability of exposure to accidents with lost workdays correctly by 70%.
-
The Fragile X Syndrome: Behavioral Phenotype and Learning Disabilities
Directory of Open Access Journals (Sweden)
Claudia GRAU RUBIO
2016-04-01
Full Text Available In this article, we describe the behavioral phenotype of individuals with Fragile X Syndrome and its impact in the educational scope. This syndrome is characterized by difficulties in sensory integration, cognitive deficits (verbal reasoning, abstract/ visual and cuantitative skills, short term memory, sequential processing, attention and executive processes, language disorders (phonetic-phonologicals, semanticals, morphosyntacticals and pragmaticals and communication disorders, social anxiety, general hyperarousal, autism, non autistic social difficulties, attention deficit and hyperactivity, and learning disabilities. The behavioral phenotype is highly variable and depends on sex, age, and mutation status (full mutation or premutation. The behavioural phenotype has important repercussions in education, as it enables us to understand the learning disabilities and to develop specific intervention strategies.
-
Lande, Russell
2009-07-01
Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.
-
Diagnostic Challenges in Retinitis Pigmentosa: Genotypic Multiplicity and Phenotypic Variability
Chang, Susie; Vaccarella, Leah; Olatunji, Sunday; Cebulla, Colleen; Christoforidis, John
2011-01-01
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal disorders. Diagnosis can be challenging as more than 40 genes are known to cause non-syndromic RP and phenotypic expression can differ significantly resulting in variations in disease severity, age of onset, rate of progression, and clinical findings. We describe the clinical manifestations of RP, the more commonly known causative gene mutations, and the genotypic-phenotypic correlation of RP. PMID:22131872
-
Otto, Benjamin; Misra, Supriya; Prasad, Aditya; McRae, Kateri
2014-09-01
One factor that influences the success of emotion regulation is the manner in which the regulated emotion was generated. Recent research has suggested that reappraisal, a top-down emotion regulation strategy, is more effective in decreasing self-reported negative affect when emotions were generated from the top-down, versus the bottom-up. On the basis of a process overlap framework, we hypothesized that the neural regions active during reappraisal would overlap more with emotions that were generated from the top-down, rather than from the bottom-up. In addition, we hypothesized that increased neural overlap between reappraisal and the history effects of top-down emotion generation would be associated with increased reappraisal success. The results of several analyses suggested that reappraisal and emotions that were generated from the top-down share a core network of prefrontal, temporal, and cingulate regions. This overlap is specific; no such overlap was observed between reappraisal and emotions that were generated in a bottom-up fashion. This network consists of regions previously implicated in linguistic processing, cognitive control, and self-relevant appraisals, which are processes thought to be crucial to both reappraisal and top-down emotion generation. Furthermore, individuals with high reappraisal success demonstrated greater neural overlap between reappraisal and the history of top-down emotion generation than did those with low reappraisal success. The overlap of these key regions, reflecting overlapping processes, provides an initial insight into the mechanism by which generation history may facilitate emotion regulation.
-
A dynamic model for managing overlapped iterative product development
Lin, J.; Chai, K.H.; Wong, Y.S.; Brombacher, A.C.
2008-01-01
Intense competition in many industries impels firms to develop more products in less time. Overlapping of development activities is regarded as one of the most promising strategies to reduce project cycle time. However, the gain from overlapping must be weighed against the additional resource and
-
Optimization of overlap uniformness for ptychography.
Huang, Xiaojing; Yan, Hanfei; Harder, Ross; Hwu, Yeukuang; Robinson, Ian K; Chu, Yong S
2014-05-19
We demonstrate the advantages of imaging with ptychography scans that follow a Fermat spiral trajectory. This scan pattern provides a more uniform coverage and a higher overlap ratio with the same number of scan points over the same area than the presently used mesh and concentric [13] patterns. Under realistically imperfect measurement conditions, numerical simulations show that the quality of the reconstructed image is improved significantly with a Fermat spiral compared with a concentric scan pattern. The result is confirmed by the performance enhancement with experimental data, especially under low-overlap conditions. These results suggest that the Fermat spiral pattern increases the quality of the reconstructed image and tolerance to data with imperfections.
-
Communication Avoiding and Overlapping for Numerical Linear Algebra
2012-05-08
future exascale systems, communication cost must be avoided or overlapped. Communication-avoiding 2.5D algorithms improve scalability by reducing...linear algebra problems to future exascale systems, communication cost must be avoided or overlapped. Communication-avoiding 2.5D algorithms improve...will continue to grow relative to the cost of computation. With exascale computing as the long-term goal, the community needs to develop techniques
-
Mahdieh, Nejat; Mikaeeli, Sahar; Tavasoli, Ali Reza; Rezaei, Zahra; Maleki, Majid; Rabbani, Bahareh
2018-04-01
Gangliosidosis is an inherited metabolic disorder causing neurodegeneration and motor regression. Preventive diagnosis is the first choice for the affected families due to lack of straightforward therapy. Genetic studies could confirm the diagnosis and help families for carrier screening and prenatal diagnosis. An update of HEXB gene variants concerning genotype, phenotype and in silico analysis are presented. Panel based next generation sequencing and direct sequencing of four cases were performed to confirm the clinical diagnosis and for reproductive planning. Bioinformatic analyses of the HEXB mutation database were also performed. Direct sequencing of HEXA and HEXB genes showed recurrent homozygous variants at c.509G>A (p.Arg170Gln) and c.850C>T (p.Arg284Ter), respectively. A novel variant at c.416T>A (p.Leu139Gln) was identified in the GLB1 gene. Panel based next generation sequencing was performed for an undiagnosed patient which showed a novel mutation at c.1602C>A (p.Cys534Ter) of HEXB gene. Bioinformatic analysis of the HEXB mutation database showed 97% consistency of in silico genotype analysis with the phenotype. Bioinformatic analysis of the novel variants predicted to be disease causing. In silico structural and functional analysis of the novel variants showed structural effect of HEXB and functional effect of GLB1 variants which would provide fast analysis of novel variants. Panel based studies could be performed for overlapping symptomatic patients. Consequently, genetic testing would help affected families for patients' management, carrier detection, and family planning's. Copyright © 2018 Elsevier B.V. All rights reserved.
-
Querin, Giorgia; Bertolin, Cinzia; Da Re, Elisa; Volpe, Marco; Zara, Gabriella; Pegoraro, Elena; Caretta, Nicola; Foresta, Carlo; Silvano, Maria; Corrado, Domenico; Iafrate, Massimo; Angelini, Lorenzo; Sartori, Leonardo; Pennuto, Maria; Gaiani, Alessandra; Bello, Luca; Semplicini, Claudio; Pareyson, Davide; Silani, Vincenzo; Ermani, Mario; Ferlin, Alberto; Sorarù, Gianni
2016-08-01
To carry out a deep characterisation of the main androgen-responsive tissues involved in spinal and bulbar muscular atrophy (SBMA). 73 consecutive Italian patients underwent a full clinical protocol including biochemical and hormonal analyses, genitourinary examination, bone metabolism and densitometry, cardiological evaluation and muscle pathology. Creatine kinase levels were slightly to markedly elevated in almost all cases (68 of the 73; 94%). 30 (41%) patients had fasting glucose above the reference limit, and many patients had total cholesterol (40; 54.7%), low-density lipoproteins cholesterol (29; 39.7%) and triglyceride (35; 48%) levels above the recommended values. Although testosterone, luteinising hormone and follicle-stimulating hormone values were generally normal, in one-third of cases we calculated an increased Androgen Sensitivity Index reflecting the presence of androgen resistance in these patients. According to the International Prostate Symptom Score (IPSS), 7/70 (10%) patients reported severe lower urinal tract symptoms (IPSS score >19), and 21/73 (30%) patients were moderately symptomatic (IPSS score from 8 to 19). In addition, 3 patients were carriers of an indwelling bladder catheter. Videourodynamic evaluation indicated that 4 of the 7 patients reporting severe urinary symptoms had an overt prostate-unrelated bladder outlet obstruction. Dual-energy X-ray absorptiometry scan data were consistent with low bone mass in 25/61 (41%) patients. Low bone mass was more frequent at the femoral than at the lumbar level. Skeletal muscle biopsy was carried out in 20 patients and myogenic changes in addition to the neurogenic atrophy were mostly observed. Our study provides evidence of a wide non-neural clinical phenotype in SBMA, suggesting the need for comprehensive multidisciplinary protocols for these patients. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
-
Metformin treatment in different phenotypes of polycystic ovary syndrome.
Hosseini, Marzieh Agha; Alleyassin, Ashraf; Sarvi, Fatemeh; Safdarian, Leila; Kokab, Abas; Fanisalek, Mehran
2013-11-01
The aim of this study was to evaluate the effectiveness of Metformin on ovulation and eventual clinical pregnancy in different phenotypes of polycystic ovary syndrome (PCOS). A total of 359 subjects who had proven PCOS according to Rotterdam criteria were prospectively selected. Patients' PCOS phenotypes were determined and recorded. All patients were younger than 35 years. Clinical and biochemical assays in all patients were initially obtained. Then patients were divided into two separate groups. One group received both 1,500 mg of Metformin and 1 mg of folic acid per day and the other group received only 1 mg of folic acid for a total of 2 months. Subsequently, all patients underwent ovulation stimulation with 5 mg of Letrozole per day for 5 days followed by an intra-uterine insemination. Finally, ovulation and pregnancy rates were evaluated for all four PCOS phenotypes. Effect of Metformin therapy was evaluated for each group and each phenotype. The pregnancy rate in Metformin and non-Metformin groups were, respectively, as follows: in phenotype A (39.2 vs. 33.7 %, p = 0.270), phenotype B (43.8 vs. 20 %, p = 0.210), phenotype C (44 vs. 20 %, p = 0.064), and phenotype D (36.5 vs. 28.6 %, p = 0.279). Although there was a little improvement in ovulation and pregnancy rates among patients with B and C phenotypes, there was not a statistically significant difference between the two groups. Based on our study, Metformin therapy does not change the ovulation and pregnancy rate.
-
Non-LTE spectral analyses of the lately discovered DB-gap white dwarfs from the SDSS
International Nuclear Information System (INIS)
Huegelmeyer, S D; Dreizler, S
2009-01-01
For a long time, no hydrogen-deficient white dwarfs have been known that have effective temperature between 30 kK and eff < 45 kK (Eisenstein et al. 2006). It has been shown for DO white dwarfs that the relaxation of LTE is necessary to account for non local effects in the atmosphere caused by the intense radiation field. Therefore, we calculated a non-LTE model grid and re-analysed the aforementioned set of SDSS spectra. Our results confirm the existence of DB-gap white dwarfs.
-
Usefulness of non-linear input-output models for economic impact analyses in tourism and recreation
Klijs, J.; Peerlings, J.H.M.; Heijman, W.J.M.
2015-01-01
In tourism and recreation management it is still common practice to apply traditional input–output (IO) economic impact models, despite their well-known limitations. In this study the authors analyse the usefulness of applying a non-linear input–output (NLIO) model, in which price-induced input
-
Deng, Fan; Dong, Hangming; Zou, Mengchen; Zhao, Haijin; Cai, Chunqing; Cai, Shaoxi
2014-12-30
To explore the polarization of migration dynamics of neutrophils isolated from patients with asthma, chronic obstructive pulmonary disease (COPD) and asthma-COPD overlap syndrome (ACOS) compared with healthy smoking and non-smoking controls. Recruited volunteers were classified as healthy controls, healthy smokers, asthma, COPD and ACOS at Nanfang Hospital from April 2013 to June 2014 according to the Global Strategy for the Diagnosis, Management and Prevention of COPD 2011, Global Strategy for Asthma Management and Prevention 2011 and Consensus on Overlap Phenotype COPD-asthma in COPD 2012. Neutrophils were freshly isolated from whole blood with density gradient technique. The proportion of polarized cells with gradient concentration of formyl-Met-Leu-Phe (fMLP) in Zigmond chamber and vital component of Store Operated Calcium Entry (SOCE) (stromal interaction molecule (STIM) 1, 2 and Orai1) in neutrophils was detected by Western blot. Asthma, COPD and ACOS neutrophils demonstrated a higher spontaneous polarization rate versus healthy controls and healthy smokers ((25.05 ± 4.06)%, (16.20 ± 4.46)%, (29.43 ± 5.53)% vs (7.27 ± 0.99)%, (7.06 ± 3.12)%, all P polarization rate ((14.62 ± 2.26)%, (8.00 ± 1.75)%, all P polarization rate than healthy controls and healthy smokers ((2.45 ± 0.54)% vs (5.12 ± 1.28)%, (5.24 ± 1.34)%, all P vs 0.26 ± 0.14, 0.38 ± 0.12; STIM2: 0.52 ± 0.19, 0.22 ± 0.13, 0.24 ± 0.10 vs 0.05 ± 0.03, 0.10 ± 0.06; Orai1: 0.56 ± 0.04, 0.39 ± 0.05, 0.48 ± 0.05 vs 0.13 ± 0.04, 0.13 ± 0.03) (all P < 0.01). Asthma, COPD and ACOS neutrophils are intrinsically different than counterparts from healthy control subjects and healthy smokers. And vital components of SOCE from patient neutrophils are intrinsically up-regulated.
-
Some considerations on disciplinary liability overlapping criminal liability
Directory of Open Access Journals (Sweden)
Ştefania DUMITRACHE
2011-12-01
Full Text Available Among the various forms of legal liability there are many points of contact reflected in their common goal - the encouragement of active members of society. Starting from the statement - the independent nature of the various forms of legal liability does not mean they are excluded - in what follows, given the legal autonomy of spheres of social relations protected by various laws, we will consider disciplinary overlapping with other forms of legal liability - criminal liability. Of course, this is possible only if the act committed by the employee is both disciplinary and criminal. This form of accumulation are possible without violating the principle of non bis in idem that since each of the envisaged legal rules protect different social relations. In addition of this applying the same principle prohibits two or more same kind sanctions for an unlawful action
-
A novel 3D imaging system for strawberry phenotyping
Directory of Open Access Journals (Sweden)
Joe Q. He
2017-11-01
Full Text Available Abstract Background Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. Results A low cost multi-view stereo (MVS imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. Conclusion This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique.
-
A novel 3D imaging system for strawberry phenotyping.
He, Joe Q; Harrison, Richard J; Li, Bo
2017-01-01
Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. A low cost multi-view stereo (MVS) imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique.
-
Some new results on the central overlap problem in astrometry
Rapaport, M.
1998-07-01
The central overlap problem in astrometry has been revisited in the recent last years by Eichhorn (1988) who explicitly inverted the matrix of a constrained least squares problem. In this paper, the general explicit solution of the unconstrained central overlap problem is given. We also give the explicit solution for an other set of constraints; this result is a confirmation of a conjecture expressed by Eichhorn (1988). We also consider the use of iterative methods to solve the central overlap problem. A surprising result is obtained when the classical Gauss Seidel method is used; the iterations converge immediately to the general solution of the equations; we explain this property writing the central overlap problem in a new set of variables.
-
Directory of Open Access Journals (Sweden)
Druka Arnis
2008-11-01
Full Text Available Abstract Background A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community. Description Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits. Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them. Conclusion By
-
International Nuclear Information System (INIS)
Rutten, A.; Isgum, I.; Prokop, M.
2011-01-01
Objective: To examine the feasibility of reducing the inter-scan variability of prospectively ECG-triggered calcium-scoring scans by using overlapping 3-mm datasets generated from multiplanar reformation (MPR) instead of non-overlapping 3-mm or 1.5-mm datasets. Patients and methods: Seventy-five women (59-79 years old) underwent two sequential prospectively ECG-triggered calcium-scoring scans with 16 mm x 1.5 mm collimation in one session. Between the two scans patients got off and on the table. We performed calcium scoring (Agatston and mass scores) on the following datasets: contiguous 3-mm sections reconstructed from the raw data (A), contiguous 3-mm sections from MPR (B), overlapping 3-mm sections from MPR (C) and contiguous 1.5-mm sections from the raw data (D). To determine the feasibility of the MPR approach, we compared MPR (B) with direct raw data reconstruction (A). Inter-scan variability was calculated for each type of dataset (A-D). Results: Calcium scores ranged from 0 to 1455 (Agatston) and 0 to 279 mg (mass) for overlapping 3-mm sections (C). Calcium scores (both Agatston and mass) were nearly identical for MPR (B) and raw data approaches (A), with inter-quartile ranges of 0-1% for inter-scan variability. Median inter-scan variability with contiguous 3-mm sections (B) was 13% (Agatston) and 11% (mass). Median variability was reduced to 10% (Agatston and mass) with contiguous 1.5-mm sections (D) and to 8% (Agatston) and 7% (mass) with overlapping 3-mm MPR (A). Conclusion: Calcium scoring on MPR yields nearly identical results to calcium scoring on images directly reconstructed from raw data. Overlapping MPR from prospectively ECG-triggered scans improve inter-scan variability of calcium scoring without increasing patient radiation dose.
-
GAB2 Amplification in Squamous Cell Lung Cancer of Non-Smokers.
Park, Yu Rang; Bae, Soo Hyeon; Ji, Wonjun; Seo, Eul Ju; Lee, Jae Cheol; Kim, Hyeong Ryul; Jang, Se Jin; Choi, Chang Min
2017-11-01
Lung squamous cell cancer (SCC) is typically found in smokers and has a very low incidence in non-smokers, indicating differences in the tumor biology of lung SCC in smokers and non-smokers. However, the specific mutations that drive tumor growth in non-smokers have not been identified. To identify mutations in lung SCC of non-smokers, we performed a genetic analysis using arrays comparative genomic hybridization (ArrayCGH). We analyzed 19 patients with lung SCC who underwent surgical treatment between April 2005 and April 2015. Clinical characteristics were reviewed, and DNA was extracted from fresh frozen lung cancer specimens. All of copy number alterations from ArrayCGH were validated using The Cancer Genome Atlas (TCGA) copy number variation (CNV) data of lung SCC. We examined the frequency of copy number changes according to the smoking status (non-smoker [n = 8] or smoker [n = 11]). We identified 16 significantly altered regions from ArrayCGH data, three gain and four loss regions overlapped with the TCGA lung squamous cell carcinoma (LUSC) patients. Within these overlapped significant regions, we detected 15 genes that have been reported in the Cancer Gene census. We also found that the proto-oncogene GAB2 (11q14.1) was significantly amplified in non-smokers patients and vice versa in both ArrayCGH and TCGA data. Immunohistochemical analyses showed that GAB2 protein was relatively upregulated in non-smoker than smoker tissues (37.5% vs. 9.0%, P = 0.007). GAB2 amplification may have an important role in the development of lung SCC in non-smokers. GAB2 may represent a potential biomarker for lung SCC in non-smokers. © 2017 The Korean Academy of Medical Sciences.
-
Directory of Open Access Journals (Sweden)
Pasquale Tripodi
2018-04-01
Full Text Available Increasing the ability to investigate plant functions and structure through non-invasive methods with high accuracy has become a major target in plant breeding and precision agriculture. Emerging approaches in plant phenotyping play a key role in unraveling quantitative traits responsible for growth, production, quality, and resistance to various stresses. Beyond fully automatic phenotyping systems, several promising technologies can help accurately characterize a wide range of plant traits at affordable costs and with high-throughput. In this review, we revisit the principles of proximal and remote sensing, describing the application of non-invasive devices for precision phenotyping applied to the protected horticulture. Potentiality and constraints of big data management and integration with “omics” disciplines will also be discussed.
-
The overlap Dirac operator as a continued fraction
International Nuclear Information System (INIS)
Wenger, U.; Deutsches Elektronen-Synchrotron
2004-03-01
We use a continued fraction expansion of the sign-function in order to obtain a five dimensional formulation of the overlap lattice Dirac operator. Within this formulation the inverse of the overlap operator can be calculated by a single Krylov space method and nested conjugate gradient procedures are avoided. We point out that the five dimensional linear system can be made well conditioned using equivalence transformations on the continued fractions. (orig.)
-
The interrelation between hypothyroidism and glaucoma: a critical review and meta-analyses.
Thvilum, Marianne; Brandt, Frans; Brix, Thomas Heiberg; Hegedüs, Laszlo
2017-12-01
Data on the association between hypothyroidism and glaucoma are conflicting. We sought to shed light on this by conducting a critical review and meta-analyses. The meta-analyses were conducted in adherence with the widely accepted MOOSE guidelines. Using the Medical Subject Heading (MeSH) terms: hypothyroidism, myxoedema and glaucoma or intraocular pressure, case-control studies, cohort studies and cross-sectional studies were identified (PubMed) and reviewed. Using meta-analysis, the relative risk (RR) of coexistence of glaucoma and hypothyroidism was calculated. Based on the literature search, thirteen studies fulfilled the inclusion criteria and could be categorized into two groups based on the exposure. The designs of the studies varied considerably, and there was heterogeneity related to lack of power, weak phenotype classifications and length of follow-up. Eight studies had glaucoma (5757 patients) as exposure and hypothyroidism as outcome. Among these, we found a non-significantly increased risk of hypothyroidism associated with glaucoma (RR 1.65; 95% confidence interval [CI]: 0.97-2.82). Based on five studies (168 006 patients) with hypothyroidism as exposure and glaucoma as outcome, we found the risk of glaucoma to be significantly increased (RR 1.33; 95% CI: 1.13-1.58). Based on these meta-analyses, there seems to be an association between hypothyroidism and glaucoma, which does not seem to be the case between glaucoma and hypothyroidism. However, larger scale studies with better phenotype classification, longer follow-up and taking comorbidity and other biases into consideration are needed to address a potential causal relationship. © 2017 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.
-
Conserved regulators of nucleolar size revealed by global phenotypic analyses.
Neumüller, Ralph A; Gross, Thomas; Samsonova, Anastasia A; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P; Andrews, Brenda; Winston, Fred; Perrimon, Norbert
2013-08-20
Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I-mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I-mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry-based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules.
-
Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses
Neumüller, Ralph A.; Gross, Thomas; Samsonova, Anastasia A.; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P.; Andrews, Brenda; Winston, Fred; Perrimon, Norbert
2014-01-01
Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I–mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I–mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry–based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules. PMID:23962978
-
The ecology of white-handed and pileated gibbons in a zone of overlap and hybridization in Thailand.
Asensio, Norberto; José-Domínguez, Juan Manuel; Kongrit, Chalita; Brockelman, Warren Y
2017-08-01
The study of related species in contact zones can elucidate what factors mediate species coexistence and geographical distributions. We investigated niche overlap and group interactions of two gibbon species and their hybrids co-occurring in a zone of overlap and hybridization. The location, composition and behavior of white-handed, pileated, and mixed-species gibbon groups were studied by following them during 31 consecutive months in a relatively large part of the contact zone. Twenty groups of white-handed gibbon were mapped followed by nine groups of pileated gibbons and five mixed-species groups. White-handed, pileated and mixed-species groups had similar sizes and composition, ate a high proportion of fruits, shared a large number of species in their diets, and presented similar habitat preferences. Group home range sizes did not differ between species and overlapped little with neighboring groups irrespective of species, and intraspecific and interspecific encounter rates were similar. Ecological similarities support that competition between the gibbon species exists and takes the form of interspecific territoriality. However, we could not find any clear mechanism of niche partitioning favoring coexistence between species. Our findings suggest that the contact zone is unstable and is maintained by dispersal inward from groups of the parental species. The relatively low numbers of mixed-species groups and hybrids found suggests a high degree of premating reproductive isolation, perhaps mediated by interspecific miscommunication. The existence of hybrids and backcrosses potentially undetectable from phenotypic characters alone raises the possibility of more widespread introgression than has been evident. Hence, while interspecific territoriality should reduce the rate of gene transfer, it would not necessarily present a barrier to introgression into contiguous populations of the opposite species. © 2017 Wiley Periodicals, Inc.
-
Song, Chao; Wang, Qian; Zhang, Ruilei; Sun, Bingjiao; Wang, Xinhua
2016-02-16
In this study, we tested the utility of the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) as the barcode region to deal with taxonomical problems of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae). The 114 DNA barcodes representing 27 morphospecies are divided into 33 well separated clusters based on both Neighbor Joining and Maximum Likelihood methods. DNA barcodes revealed an 82% success rate in matching with morphospecies. The selected DNA barcode data support 37-64 operational taxonomic units (OTUs) based on the methods of Automatic Barcode Gap Discovery (ABGD) and Poisson Tree Process (PTP). Furthermore, a priori species based on consistent phenotypic variations were attested by molecular analysis, and a taxonomical misidentification of barcode sequences from GenBank was found. We could not observe a distinct barcode gap but an overlap ranged from 9-12%. Our results supported DNA barcoding as an ideal method to detect cryptic species, delimit sibling species, and associate different life stages in non-biting midges.
-
Interference management with partial uplink/downlink spectrum overlap
Randrianantenaina, Itsikiantsoa
2016-07-26
Simultaneous reuse of spectral resources by uplink and downlink, denoted as in-band full duplex (FD) communication, is promoted to double the spectral efficiency when compared to its half-duplex (HD) counterpart. Interference management, however, remains challenging in FD cellular networks, especially when high disparity between uplink and downlink transmission powers exists. The uplink performance can be particularly deteriorated when operating on channels that are simultaneously occupied with downlink transmission. This paper considers a cellular wireless system with partial spectrum overlap between the downlink and uplink. The performance of the system becomes, therefore, a function of the overlap fraction, as well as the power levels of both the uplink and downlink transmissions. The paper considers the problem of maximizing an overall network utility to find the uplink/downlink transmission powers and the spectrum overlap fraction between the uplink and downlink spectrum in each cell, and proposes solving the problem using interior point method. Simulations results confirm the vulnerability of the uplink performance to the FD operation, and show the superiority of the proposed scheme over the FD and HD schemes. The results further show that explicit uplink and downlink performance should be considered for efficient design of cellular networks with overlapping uplink/downlink resources. © 2016 IEEE.
-
Comparison of Patient Outcomes and Cost of Overlapping Versus Nonoverlapping Spine Surgery.
Zygourakis, Corinna C; Sizdahkhani, Saman; Keefe, Malla; Lee, Janelle; Chou, Dean; Mummaneni, Praveen V; Ames, Christopher P
2017-04-01
Overlapping surgery recently has gained significant media attention, but there are limited data on its safety and efficacy. To date, there has been no analysis of overlapping surgery in the field of spine. Our goal was to compare overlapping versus nonoverlapping spine surgery patient outcomes and cost. A retrospective review was undertaken of 2319 spine surgeries (n = 848 overlapping; 1471 nonoverlapping) performed by 3 neurosurgery attendings from 2012 to 2015 at the University of California San Francisco. Collected variables included patient age, sex, insurance, American Society of Anesthesiology score, severity of illness, risk of mortality, procedure type, surgeon, day of surgery, source of transfer, admission type, overlapping versus nonoverlapping surgery (≥1 minute of overlapping procedure time), Medicare-Severity Diagnosis-Related Group, osteotomy, and presence of another attending/fellow/resident. Univariate, then multivariate mixed-effect models were used to evaluate the effect of the collected variables on the following outcomes: procedure time, estimated blood loss, length of stay, discharge status, 30-day mortality, 30-day unplanned readmission, unplanned return to OR, and total hospital cost. Urgent spine cases were more likely to be done in an overlapping fashion (all P return to the operating room, estimated blood loss, length of stay, and total hospital cost (all P = ns). Overlapping spine surgery may be performed safely at our institution, although continued monitoring of patient outcomes is necessary. Overlapping surgery does not lead to greater hospital costs. Copyright © 2017 Elsevier Inc. All rights reserved.
-
Directory of Open Access Journals (Sweden)
Irfan Ismail Ayub
2018-01-01
Full Text Available Background: There is dearth of literature on asthma-chronic obstructive pulmonary disease overlap syndrome (ACOS in India. The aim was to compare clinical characteristics between patients with ACOS and non-ACOS COPD and to identify clinical predictors of ACOS in patients with COPD. Methods: We conducted a retrospective study by reviewing data collected from patients performing spirometry at our hospital. Those with postbronchodilator FEV1/FVC <70% were included in the study. Among them, those with significant reversibility (change in FEV1or FVC by 12% and 200 ml postbronchodilator were diagnosed with ACOS and the rest were considered to have non-ACOS COPD. Data on the 2 groups were compared and statistical analysis was performed. Results: Out of a total of 324 patients, 100 of them had postbronchodilator FEV1/FVC <70%. Of them, 45 and 55 were diagnosed with ACOS and non-ACOS COPD, respectively. Patients with ACOS had significantly higher postbronchodilator FVC volumes and FVC % predicted values (P < 0.05, had higher reported wheeze (P = 0.02 and ankle edema (P < 0.05, were more likely to be smokers (P = 0.01 with lower smoking index (P = 0.03, and had frequent (≥2 ER visits (P = 0.04. However, very frequent (≥3 per year hospital admissions (P < 0.01 with higher rates of invasive mechanical ventilation (P = 0.02, and pulmonary hypertension diagnosed by two-dimensional echocardiography (P < 0.01 were significantly higher in the non-ACOS group. The two groups did not differ with respect to history of atopy, family history of wheeze, compliance to inhaler therapy, or blood absolute eosinophil counts. Conclusion: Our study highlights how the ACOS phenotype may clinically differ from their counterparts elsewhere, making it a clinical challenge to identify them in India.
-
Guerrero-Berroa, Elizabeth; Ravona-Springer, Ramit; Heymann, Anthony; Schmeidler, James; Hoffman, Hadas; Preiss, Rachel; Koifmann, Keren; Greenbaum, Lior; Levy, Andrew; Silverman, Jeremy M; Leroith, Derek; Sano, Mary; Schnaider-Beeri, Michal
2016-05-01
The haptoglobin (Hp) genotype has been associated with cognitive function in type 2 diabetes. Because ethnicity/culture has been associated with both cognitive function and Hp genotype frequencies, we examined whether it modulates the association of Hp with cognitive function. This cross-sectional study evaluated 787 cognitively normal older individuals (>65 years of age) with type 2 diabetes participating in the Israel Diabetes and Cognitive Decline study. Interactions in two-way analyses of covariance compared Group (Non-Ashkenazi versus Ashkenazi Jews) on the associations of Hp phenotype (Hp 1-1 versus non- Hp 1-1) with five cognitive outcome measures. The primary control variables were age, gender, and education. Compared with Ashkenazi Jews, non-Ashkenazi Jews with the Hp 1-1 phenotype had significantly poorer cognitive function than non-Hp 1-1 in the domains of Attention/Working Memory (p = 0.035) and Executive Function (p = 0.023), but not in Language/Semantic Categorization (p = 0.432), Episodic Memory (p = 0.268), or Overall Cognition (p = 0.082). After controlling for additional covariates (type 2 diabetes-related characteristics, cardiovascular risk factors, Mini-mental State Examination, and extent of depressive symptoms), Attention/Working Memory (p = 0.038) and Executive Function (p = 0.013) remained significant. Older individuals from specific ethnic/cultural backgrounds with the Hp 1-1 phenotype may benefit more from treatment targeted at decreasing or halting the detrimental effects of Hp 1-1 on the brain. Future studies should examine differential associations of Hp 1-1 and cognitive impairment, especially for groups with high prevalence of both, such as African-Americans and Hispanics. Copyright © 2015 John Wiley & Sons, Ltd.
-
International Nuclear Information System (INIS)
Boess, Franziska; Lenz, Barbara; Funk, Juergen; Niederhauser, Urs; Bassett, Simon; Zhang, Jitao David; Singer, Thomas; Roth, Adrian B.
2017-01-01
Highlights: • RG3487 induced foci of altered hepatocytes and subsequent liver tumors in rats. • Early phenotypic markers preceding foci appearance in rats were identified. • These early foci markers could be recapitulated in cellular rat liver models. • A species comparison using rat, mouse and dog liver cell models qualified the approach. • In vitro human data support non-human-relevance for RG3487 induced foci formation. - Abstract: Foci of altered hepatocytes (FAH) are considered putative, pre-neoplastic lesions that can occur spontaneously in aging rodents, but can also be induced by chemicals or drugs. Progression of FAH to hepatocellular neoplasms has been reported repeatedly but increases in foci in rodents do not necessarily lead to tumors in carcinogenicity studies and the relevance for humans often remains unclear. Here we present the case of RG3487, a molecule which induced FAH and, later on, tumors in rats. Because the molecule was negative in genotoxicity assays it was classified as a non-genotoxic carcinogen. In order to assess the potential for liver tumor formation in humans, we analyzed treatment-induced changes in vivo to establish a possible mode of action (MoA). In vivo and in vitro gene expression analysis revealed that nuclear receptor signaling was unlikely to be the relevant MoA and no other known mechanism could be established. We therefore took an approach comparing phenotypic markers, including mRNA changes, proliferation and glycogen accumulation, in vitro using cells of different species to assess the human relevance of this finding. Since the alterations observed in rats were not seen in the liver of mice or dogs in vivo, we could validate the relevance of the cell models chosen by use of hepatocytes from these species in vitro. This ultimately allowed for a cross-species comparison, which suggested that the formation of FAH and liver tumors was rat specific and unlikely to translate to human. Our work showed that phenotypic
-
Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye
Morrison, Carolyn A.; Chen, Hao; Cook, Tiffany; Brown, Stuart
2018-01-01
Transcriptional regulators can specify different cell types from a pool of equivalent progenitors by activating distinct developmental programs. The Glass transcription factor is expressed in all progenitors in the developing Drosophila eye, and is maintained in both neuronal and non-neuronal cell types. Glass is required for neuronal progenitors to differentiate as photoreceptors, but its role in non-neuronal cone and pigment cells is unknown. To determine whether Glass activity is limited to neuronal lineages, we compared the effects of misexpressing it in neuroblasts of the larval brain and in epithelial cells of the wing disc. Glass activated overlapping but distinct sets of genes in these neuronal and non-neuronal contexts, including markers of photoreceptors, cone cells and pigment cells. Coexpression of other transcription factors such as Pax2, Eyes absent, Lozenge and Escargot enabled Glass to induce additional genes characteristic of the non-neuronal cell types. Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. These results indicate that Glass is a determinant of organ identity that acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye. PMID:29324767
-
Holistic and component plant phenotyping using temporal image sequence.
Das Choudhury, Sruti; Bashyam, Srinidhi; Qiu, Yumou; Samal, Ashok; Awada, Tala
2018-01-01
automated detection of individual leaves and the stem to compute new component phenotypes along with a public release of a benchmark dataset, i.e., UNL-CPPD. Detailed experimental analyses are performed to demonstrate the temporal variation of the holistic and component phenotypes in maize regulated by environment and genetic variation with a discussion on their significance in the context of plant science.
-
Red blood cell phenotype prevalence in blood donors who self-identify as Hispanic
DEFF Research Database (Denmark)
Sheppard, Chelsea A; Bolen, Nicole L; Eades, Beth
2017-01-01
CONCLUSIONS: Molecular genotyping platforms provide a quick, high-throughput method for identifying red blood cell units for patients on extended phenotype-matching protocols, such as those with sickle cell disease or thalassemia. Most of the antigen prevalence data reported are for non-Hispanic ......CONCLUSIONS: Molecular genotyping platforms provide a quick, high-throughput method for identifying red blood cell units for patients on extended phenotype-matching protocols, such as those with sickle cell disease or thalassemia. Most of the antigen prevalence data reported are for non...
-
Noordman, Iris; Duijnhouwer, Anthonie; Kapusta, Livia; Kempers, Marlies; Roeleveld, Nel; Schokking, Michiel; Smeets, Dominique; Freriks, Kim; Timmers, Henri; van Alfen-van der Velden, Janiëlle
2018-06-01
Turner syndrome (TS) is a genetic disorder characterized by the (partial) absence or a structural aberration of the second sex chromosome and is associated with a variety of phenotypes with specific physical features and cardio-aortic malformations. The objective of this study was to gain a better insight into the differences in dysmorphic features between girls and women with TS and to explore the association between these features, karyotype and cardio-aortic malformations. This prospective study investigated 14 dysmorphic features of TS girls and women using a checklist. Three major phenotypic patterns were recognized (severe phenotype, lymphatic phenotype and skeletal phenotype). Patient data including karyotype and cardio-aortic malformations (bicuspid aortic valve (BAV) and aortic coarctation (COA)) were collected. Associations between the prevalence of dysmorphic features, karyotype and cardio-aortic malformations were analysed using chi 2 -test and odds ratios. A total of 202 patients (84 girls and 118 women) were analysed prospectively. Differences in prevalence of dysmorphic features were found between girls and women. A strong association was found between monosomy 45,X and the phenotypic patterns. Furthermore, an association was found between COA and lymphatic phenotype, but no association was found between karyotype and cardio-aortic malformations. This study uncovered a difference in dysmorphic features between girls and women. Monosomy 45,X is associated with a more severe phenotype, lymphatic phenotype and skeletal phenotype. All patients with TS should be screened for cardio-aortic malformations, because in contrast to previous reports, karyotype and cardio-aortic malformations showed no significant association. Copyright © 2018 Elsevier Masson SAS. All rights reserved.
-
Umoh, Mfon E; Dammer, Eric B; Dai, Jingting; Duong, Duc M; Lah, James J; Levey, Allan I; Gearing, Marla; Glass, Jonathan D; Seyfried, Nicholas T
2018-01-01
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases with overlap in clinical presentation, neuropathology, and genetic underpinnings. The molecular basis for the overlap of these disorders is not well established. We performed a comparative unbiased mass spectrometry-based proteomic analysis of frontal cortical tissues from postmortem cases clinically defined as ALS, FTD, ALS and FTD (ALS/FTD), and controls. We also included a subset of patients with the C9orf72 expansion mutation, the most common genetic cause of both ALS and FTD Our systems-level analysis of the brain proteome integrated both differential expression and co-expression approaches to assess the relationship of these differences to clinical and pathological phenotypes. Weighted co-expression network analysis revealed 15 modules of co-expressed proteins, eight of which were significantly different across the ALS-FTD disease spectrum. These included modules associated with RNA binding proteins, synaptic transmission, and inflammation with cell-type specificity that showed correlation with TDP-43 pathology and cognitive dysfunction. Modules were also examined for their overlap with TDP-43 protein-protein interactions, revealing one module enriched with RNA-binding proteins and other causal ALS genes that increased in FTD/ALS and FTD cases. A module enriched with astrocyte and microglia proteins was significantly increased in ALS cases carrying the C9orf72 mutation compared to sporadic ALS cases, suggesting that the genetic expansion is associated with inflammation in the brain even without clinical evidence of dementia. Together, these findings highlight the utility of integrative systems-level proteomic approaches to resolve clinical phenotypes and genetic mechanisms underlying the ALS-FTD disease spectrum in human brain. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.
-
LINEAR AND NON-LINEAR ANALYSES OF CABLE-STAYED STEEL FRAME SUBJECTED TO SEISMIC ACTIONS
Directory of Open Access Journals (Sweden)
Marko Đuran
2017-01-01
Full Text Available In this study, linear and non-linear dynamic analyses of a cable-stayed steel frame subjected to seismic actions are performed. The analyzed cable-stayed frame is the main supporting structure of a wide-span sports hall. Since the complex dynamic behavior of cable-stayed structures results in significant geometric nonlinearity, a nonlinear time history analysis is conducted. As a reference, an analysis using the European standard approach, the so-called linear modal response spectrum method, is also performed. The analyses are conducted for different seismic actions considering dependence on the response spectrums for various ground types and the corresponding artificially generated accelerograms. Despite fundamental differences between the two analyses, results indicate that the modal response spectrum analysis is surprisingly consistent with the internal forces and bending moment distributions of the nonlinear time history analysis. However, significantly smaller values of bending moments, internal forces, and displacements are obtained with the response spectrum analysis.
-
Pestel, G; Fukui, K; Higashi, M; Schmidtmann, I; Werner, C
2018-06-01
An ideal non-invasive monitoring system should provide accurate and reproducible measurements of clinically relevant variables that enables clinicians to guide therapy accordingly. The monitor should be rapid, easy to use, readily available at the bedside, operator-independent, cost-effective and should have a minimal risk and side effect profile for patients. An example is the introduction of pulse oximetry, which has become established for non-invasive monitoring of oxygenation worldwide. A corresponding non-invasive monitoring of hemodynamics and perfusion could optimize the anesthesiological treatment to the needs in individual cases. In recent years several non-invasive technologies to monitor hemodynamics in the perioperative setting have been introduced: suprasternal Doppler ultrasound, modified windkessel function, pulse wave transit time, radial artery tonometry, thoracic bioimpedance, endotracheal bioimpedance, bioreactance, and partial CO 2 rebreathing have been tested for monitoring cardiac output or stroke volume. The photoelectric finger blood volume clamp technique and respiratory variation of the plethysmography curve have been assessed for monitoring fluid responsiveness. In this manuscript meta-analyses of non-invasive monitoring technologies were performed when non-invasive monitoring technology and reference technology were comparable. The primary evaluation criterion for all studies screened was a Bland-Altman analysis. Experimental and pediatric studies were excluded, as were all studies without a non-invasive monitoring technique or studies without evaluation of cardiac output/stroke volume or fluid responsiveness. Most studies found an acceptable bias with wide limits of agreement. Thus, most non-invasive hemodynamic monitoring technologies cannot be considered to be equivalent to the respective reference method. Studies testing the impact of non-invasive hemodynamic monitoring technologies as a trend evaluation on outcome, as well as
-
Location of frame overlap choppers on pulsed source instruments
International Nuclear Information System (INIS)
Narehood, D.G.; Pearce, J.V.; Sokol, P.E.
2002-01-01
A detailed study has been performed to investigate the effect of frame overlap in a cold neutron chopper spectrometer. The basic spectrometer is defined by two high-speed choppers, one near the moderator to shape the pulse from the moderator, and one near the sample to define energy resolution. Using ray-tracing timing diagrams, we have observed that there are regions along the guide where the trajectories of neutrons with different velocities converge temporally at characteristic points along the spectrometer. At these points of convergence, a frame overlap chopper would be totally ineffective, allowing neutrons of all velocities to pass through. Conversely, at points where trajectories of different velocity neutrons are divergent, a frame overlap chopper is most effective. An analytical model to describe this behaviour has been developed, and leads us to the counterintuitive conclusion that the optimum position for a frame overlap chopper is as close to the initial chopper as possible. We further demonstrate that detailed Monte Carlo simulations produce results which are consistent with this model
-
Segmenting overlapping nano-objects in atomic force microscopy image
Wang, Qian; Han, Yuexing; Li, Qing; Wang, Bing; Konagaya, Akihiko
2018-01-01
Recently, techniques for nanoparticles have rapidly been developed for various fields, such as material science, medical, and biology. In particular, methods of image processing have widely been used to automatically analyze nanoparticles. A technique to automatically segment overlapping nanoparticles with image processing and machine learning is proposed. Here, two tasks are necessary: elimination of image noises and action of the overlapping shapes. For the first task, mean square error and the seed fill algorithm are adopted to remove noises and improve the quality of the original image. For the second task, four steps are needed to segment the overlapping nanoparticles. First, possibility split lines are obtained by connecting the high curvature pixels on the contours. Second, the candidate split lines are classified with a machine learning algorithm. Third, the overlapping regions are detected with the method of density-based spatial clustering of applications with noise (DBSCAN). Finally, the best split lines are selected with a constrained minimum value. We give some experimental examples and compare our technique with two other methods. The results can show the effectiveness of the proposed technique.
-
Of overlapping Cantor sets and earthquakes: analysis of the discrete Chakrabarti-Stinchcombe model
Bhattacharyya, Pratip
2005-03-01
We report an exact analysis of a discrete form of the Chakrabarti-Stinchcombe model for earthquakes (Physica A 270 (1999) 27), which considers a pair of dynamically overlapping finite generations of the Cantor set as a prototype of geological faults. In this model the nth generation of the Cantor set shifts on its replica in discrete steps of the length of a line segment in that generation and periodic boundary conditions are assumed. We determine the general form of time sequences for the constant magnitude overlaps and, hence, obtain the complete time-series of overlaps by the superposition of these sequences for all overlap magnitudes. From the time-series we derive the exact frequency distribution of the overlap magnitudes. The corresponding probability distribution of the logarithm of overlap magnitudes for the nth generation is found to assume the form of the binomial distribution for n Bernoulli trials with probability {1}/{3} for the success of each trial. For an arbitrary pair of consecutive overlaps in the time-series where the magnitude of the earlier overlap is known, we find that the magnitude of the later overlap can be determined with a definite probability; the conditional probability for each possible magnitude of the later overlap follows the binomial distribution for k Bernoulli trials with probability {1}/{2} for the success of each trial and the number k is determined by the magnitude of the earlier overlap. Although this model does not produce the Gutenberg-Richter law for earthquakes, our results indicate that the fractal structure of faults admits a probabilistic prediction of earthquake magnitudes.
-
Directory of Open Access Journals (Sweden)
Atkins John F
2009-03-01
Full Text Available Abstract The plant-infecting members of the genus Fijivirus (family Reoviridae have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these – namely segment 5 – contains a second long ORF (~200+ codons that overlaps the 3' end of the major ORF (~920–940 codons in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed.
-
Overlapping communities detection based on spectral analysis of line graphs
Gui, Chun; Zhang, Ruisheng; Hu, Rongjing; Huang, Guoming; Wei, Jiaxuan
2018-05-01
Community in networks are often overlapping where one vertex belongs to several clusters. Meanwhile, many networks show hierarchical structure such that community is recursively grouped into hierarchical organization. In order to obtain overlapping communities from a global hierarchy of vertices, a new algorithm (named SAoLG) is proposed to build the hierarchical organization along with detecting the overlap of community structure. SAoLG applies the spectral analysis into line graphs to unify the overlap and hierarchical structure of the communities. In order to avoid the limitation of absolute distance such as Euclidean distance, SAoLG employs Angular distance to compute the similarity between vertices. Furthermore, we make a micro-improvement partition density to evaluate the quality of community structure and use it to obtain the more reasonable and sensible community numbers. The proposed SAoLG algorithm achieves a balance between overlap and hierarchy by applying spectral analysis to edge community detection. The experimental results on one standard network and six real-world networks show that the SAoLG algorithm achieves higher modularity and reasonable community number values than those generated by Ahn's algorithm, the classical CPM and GN ones.
-
Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.
Directory of Open Access Journals (Sweden)
Ruzianisra Mohamed
Full Text Available Protein-protein interactions (PPIs play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP complexes, and 161 protein-ligand (PL complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.
-
Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji
2015-12-01
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.
-
Energy Technology Data Exchange (ETDEWEB)
Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)
2015-12-15
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.
-
Emergent properties of gene evolution: Species as attractors in phenotypic space
Reuveni, Eli; Giuliani, Alessandro
2012-02-01
The question how the observed discrete character of the phenotype emerges from a continuous genetic distance metrics is the core argument of two contrasted evolutionary theories: punctuated equilibrium (stable evolution scattered with saltations in the phenotype) and phyletic gradualism (smooth and linear evolution of the phenotype). Identifying phenotypic saltation on the molecular levels is critical to support the first model of evolution. We have used DNA sequences of ∼1300 genes from 6 isolated populations of the budding yeast Saccharomyces cerevisiae. We demonstrate that while the equivalent measure of the genetic distance show a continuum between lineage distance with no evidence of discrete states, the phenotypic space illustrates only two (discrete) possible states that can be associated with a saltation of the species phenotype. The fact that such saltation spans large fraction of the genome and follows by continuous genetic distance is a proof of the concept that the genotype-phenotype relation is not univocal and may have severe implication when looking for disease related genes and mutations. We used this finding with analogy to attractor-like dynamics and show that punctuated equilibrium could be explained in the framework of non-linear dynamics systems.
-
On the interpretation of wave function overlaps in quantum dots
DEFF Research Database (Denmark)
Stobbe, Søren; Hvam, Jørn Märcher; Lodahl, Peter
2011-01-01
The spontaneous emission rate of excitons strongly confined in quantum dots (QDs) is proportional to the overlap integral of electron and hole envelope wave functions. A common and intuitive interpretation of this result is that the spontaneous emission rate is proportional to the probability...... that the electron and the hole are located at the same point or region in space, i.e., they must coincide spatially to recombine. Here, we show that this interpretation is not correct even loosely speaking. By general mathematical considerations we compare the envelope wave function overlap, the exchange overlap...... integral, and the probability of electrons and holes coinciding, and find that the frequency dependence of the envelope wave function overlap integral is very different from that expected from the common interpretation. We show that these theoretical considerations lead to predictions for measurements. We...
-
Same-strand overlapping genes in bacteria: compositional determinants of phase bias
Directory of Open Access Journals (Sweden)
Landan Giddy
2008-08-01
Full Text Available Abstract Background Same-strand overlapping genes may occur in frameshifts of one (phase 1 or two nucleotides (phase 2. In previous studies of bacterial genomes, long phase-1 overlaps were found to be more numerous than long phase-2 overlaps. This bias was explained by either genomic location or an unspecified selection advantage. Models that focused on the ability of the two genes to evolve independently did not predict this phase bias. Here, we propose that a purely compositional model explains the phase bias in a more parsimonious manner. Same-strand overlapping genes may arise through either a mutation at the termination codon of the upstream gene or a mutation at the initiation codon of the downstream gene. We hypothesized that given these two scenarios, the frequencies of initiation and termination codons in the two phases may determine the number for overlapping genes. Results We examined the frequencies of initiation- and termination-codons in the two phases, and found that termination codons do not significantly differ between the two phases, whereas initiation codons are more abundant in phase 1. We found that the primary factors explaining the phase inequality are the frequencies of amino acids whose codons may combine to form start codons in the two phases. We show that the frequencies of start codons in each of the two phases, and, hence, the potential for the creation of overlapping genes, are determined by a universal amino-acid frequency and species-specific codon usage, leading to a correlation between long phase-1 overlaps and genomic GC content. Conclusion Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection. Therefore, it can be used as a null model of neutral evolution to test selection hypotheses concerning the evolution of overlapping genes. Reviewers This article was reviewed by Bill Martin, Itai Yanai, and Mikhail Gelfand.
-
Semantic integration to identify overlapping functional modules in protein interaction networks
Directory of Open Access Journals (Sweden)
Ramanathan Murali
2007-07-01
Full Text Available Abstract Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification.
-
Mutations in PIGY: expanding the phenotype of inherited glycosylphosphatidylinositol deficiencies.
Ilkovski, Biljana; Pagnamenta, Alistair T; O'Grady, Gina L; Kinoshita, Taroh; Howard, Malcolm F; Lek, Monkol; Thomas, Brett; Turner, Anne; Christodoulou, John; Sillence, David; Knight, Samantha J L; Popitsch, Niko; Keays, David A; Anzilotti, Consuelo; Goriely, Anne; Waddell, Leigh B; Brilot, Fabienne; North, Kathryn N; Kanzawa, Noriyuki; Macarthur, Daniel G; Taylor, Jenny C; Kini, Usha; Murakami, Yoshiko; Clarke, Nigel F
2015-11-01
Glycosylphosphatidylinositol (GPI)-anchored proteins are ubiquitously expressed in the human body and are important for various functions at the cell surface. Mutations in many GPI biosynthesis genes have been described to date in patients with multi-system disease and together these constitute a subtype of congenital disorders of glycosylation. We used whole exome sequencing in two families to investigate the genetic basis of disease and used RNA and cellular studies to investigate the functional consequences of sequence variants in the PIGY gene. Two families with different phenotypes had homozygous recessive sequence variants in the GPI biosynthesis gene PIGY. Two sisters with c.137T>C (p.Leu46Pro) PIGY variants had multi-system disease including dysmorphism, seizures, severe developmental delay, cataracts and early death. There were significantly reduced levels of GPI-anchored proteins (CD55 and CD59) on the surface of patient-derived skin fibroblasts (∼20-50% compared with controls). In a second, consanguineous family, two siblings had moderate development delay and microcephaly. A homozygous PIGY promoter variant (c.-540G>A) was detected within a 7.7 Mb region of autozygosity. This variant was predicted to disrupt a SP1 consensus binding site and was shown to be associated with reduced gene expression. Mutations in PIGY can occur in coding and non-coding regions of the gene and cause variable phenotypes. This article contributes to understanding of the range of disease phenotypes and disease genes associated with deficiencies of the GPI-anchor biosynthesis pathway and also serves to highlight the potential importance of analysing variants detected in 5'-UTR regions despite their typically low coverage in exome data. © The Author 2015. Published by Oxford University Press.
-
Phenotypic and Transcriptomic Analyses of Autotetraploid and Diploid Mulberry (Morus alba L.).
Dai, Fanwei; Wang, Zhenjiang; Luo, Guoqing; Tang, Cuiming
2015-09-22
Autopolyploid plants and their organs are often larger than their diploid counterparts, which makes them attractive to plant breeders. Mulberry (Morus alba L.) is an important commercial woody plant in many tropical and subtropical areas. In this study, we obtained a series of autotetraploid mulberry plants resulting from a colchicine treatment. To evaluate the effects of genome duplications in mulberry, we compared the phenotypes and transcriptomes of autotetraploid and diploid mulberry trees. In the autotetraploids, the height, breast-height diameter, leaf size, and fruit size were larger than those of diploids. Transcriptome data revealed that of 21,229 expressed genes only 609 (2.87%) were differentially expressed between diploids and autotetraploids. Among them, 30 genes were associated with the biosynthesis and signal transduction of plant hormones, including cytokinin, gibberellins, ethylene, and auxin. In addition, 41 differentially expressed genes were involved in photosynthesis. These results enhance our understanding of the variations that occur in mulberry autotetraploids and will benefit future breeding work.
-
Riis, Tenna; Lambertini, Carla; Olesen, Birgit; Clayton, John S.; Brix, Hans; Sorrell, Brian K.
2010-01-01
Background and Aims The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions. Methods Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified. Key Results For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics. Conclusions The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained
-
Raas-Rothschild, Annick; Wanders, Ronald J A; Mooijer, Petra A W; Gootjes, Jeannette; Waterham, Hans R; Gutman, Alisa; Suzuki, Yasuyuki; Shimozawa, Nobuyuki; Kondo, Naomi; Eshel, Gideon; Espeel, Marc; Roels, Frank; Korman, Stanley H
2002-04-01
Sensorineural deafness and retinitis pigmentosa (RP) are the hallmarks of Usher syndrome (USH) but are also prominent features in peroxisomal biogenesis defects (PBDs); both are autosomal recessively inherited. The firstborn son of unrelated parents, who both had sensorineural deafness and RP diagnosed as USH, presented with sensorineural deafness, RP, dysmorphism, developmental delay, hepatomegaly, and hypsarrhythmia and died at age 17 mo. The infant was shown to have a PBD, on the basis of elevated plasma levels of very-long- and branched-chain fatty acids (VLCFAs and BCFAs), deficiency of multiple peroxisomal functions in fibroblasts, and complete absence of peroxisomes in fibroblasts and liver. Surprisingly, both parents had elevated plasma levels of VLCFAs and BCFAs. Fibroblast studies confirmed that both parents had a PBD. The parents' milder phenotypes correlated with relatively mild peroxisomal biochemical dysfunction and with catalase immunofluorescence microscopy demonstrating mosaicism and temperature sensitivity in fibroblasts. The infant and both of his parents belonged to complementation group C. PEX6 gene sequencing revealed mutations on both alleles, in the infant and in his parents. This unique family is the first report of a PBD with which the parents are themselves affected individuals rather than asymptomatic carriers. Because of considerable overlap between USH and milder PBD phenotypes, individuals suspected to have USH should be screened for peroxisomal dysfunction.
-
Castiglia, Daniela; Battaglia, Salvatore; Benfante, Alida; Sorino, Claudio; Scichilone, Nicola
2016-06-01
Asthma and chronic obstructive pulmonary disease (COPD) are two distinct diseases that share a condition of chronic inflammation of the airways and bronchial obstruction. In clinical settings, it is not rare to come across patients who present with clinical and functional features of both diseases, posing a diagnostic dilemma. The overlap condition has been termed asthma-COPD overlap syndrome (ACOS), and mainly occurs in individuals with long-standing asthma, especially if they are also current or former smokers. Patients with ACOS have poorer health-related quality of life and a higher exacerbation rate than subjects with asthma or COPD alone. Whether ACOS is a distinct nosological entity with genetic variants or rather a condition of concomitant diseases that overlap is still a matter of debate. However, there is no doubt that extended life expectancy has increased the prevalence of asthma and COPD in older ages, and thus the probability that overlap conditions occur in clinical settings. In addition, age-associated changes of the lung create the basis for the two entities to converge on the same subject. ACOS patients may benefit from a stepwise treatment similar to that of asthma and COPD; however, the proposed therapeutic algorithms are only speculative and extrapolated from studies that are not representative of the ACOS population. Inhaled corticosteroids are the mainstay of therapy, and always in conjunction with long-acting bronchodilators. The potential heterogeneity of the overlap syndrome in terms of inflammatory features (T helper-1 vs. T helper-2 pathways) may be responsible for the different responses to treatments. The interaction between respiratory drugs and concomitant diseases should be carefully evaluated. Similarly, the effect of non-respiratory drugs, such as aspirin, statins, and β-blockers, on lung function needs to be properly assessed.
-
Tissue-specific functional networks for prioritizing phenotype and disease genes.
Directory of Open Access Journals (Sweden)
Yuanfang Guan
Full Text Available Integrated analyses of functional genomics data have enormous potential for identifying phenotype-associated genes. Tissue-specificity is an important aspect of many genetic diseases, reflecting the potentially different roles of proteins and pathways in diverse cell lineages. Accounting for tissue specificity in global integration of functional genomics data is challenging, as "functionality" and "functional relationships" are often not resolved for specific tissue types. We address this challenge by generating tissue-specific functional networks, which can effectively represent the diversity of protein function for more accurate identification of phenotype-associated genes in the laboratory mouse. Specifically, we created 107 tissue-specific functional relationship networks through integration of genomic data utilizing knowledge of tissue-specific gene expression patterns. Cross-network comparison revealed significantly changed genes enriched for functions related to specific tissue development. We then utilized these tissue-specific networks to predict genes associated with different phenotypes. Our results demonstrate that prediction performance is significantly improved through using the tissue-specific networks as compared to the global functional network. We used a testis-specific functional relationship network to predict genes associated with male fertility and spermatogenesis phenotypes, and experimentally confirmed one top prediction, Mbyl1. We then focused on a less-common genetic disease, ataxia, and identified candidates uniquely predicted by the cerebellum network, which are supported by both literature and experimental evidence. Our systems-level, tissue-specific scheme advances over traditional global integration and analyses and establishes a prototype to address the tissue-specific effects of genetic perturbations, diseases and drugs.
-
Specific surface area of overlapping spheres in the presence of obstructions.
Jenkins, D R
2013-02-21
This study considers the random placement of uniform sized spheres, which may overlap, in the presence of another set of randomly placed (hard) spheres, which do not overlap. The overlapping spheres do not intersect the hard spheres. It is shown that the specific surface area of the collection of overlapping spheres is affected by the hard spheres, such that there is a minimum in the specific surface area as a function of the relative size of the two sets of spheres. The occurrence of the minimum is explained in terms of the break-up of pore connectivity. The configuration can be considered to be a simple model of the structure of a porous composite material. In particular, the overlapping particles represent voids while the hard particles represent fillers. Example materials are pervious concrete, metallurgical coke, ice cream, and polymer composites. We also show how the material properties of such composites are affected by the void structure.
-
Directory of Open Access Journals (Sweden)
Udi E Ghitza
2016-05-01
Full Text Available Over the past two decades, a steeply growing number of persons with chronic non-cancer pain have been using opioid analgesics chronically to treat it, accompanied by a markedly increased prevalence of individuals with opioid-related misuse, opioid use disorders, emergency department visits, hospitalizations, admissions to drug treatment programs, and drug overdose deaths. This opioid misuse and overdose epidemic calls for well-designed randomized-controlled clinical trials into more skillful and appropriate pain management and for developing effective analgesics which have lower abuse liability and are protective against stress induced by chronic non-cancer pain. However, incomplete knowledge regarding effective approaches to treat various types of pain has been worsened by an under-appreciation of overlapping neurobiological mechanisms of stress, stress-induced relapse to opioid use, and chronic non-cancer pain in patients presenting for care for these conditions. This insufficient knowledge base has unfortunately encouraged common prescription of conveniently-available opioid pain-relieving drugs with abuse liability, as opposed to treating underlying problems using team-based multidisciplinary, patient-centered, collaborative-care approaches for addressing pain and co-occurring stress and risk for opioid use disorder. This paper reviews recent neurobiological findings regarding overlapping mechanisms of stress-induced relapse to opioid misuse and chronic non-cancer pain, and then discusses these in the context of key outstanding evidence gaps and clinical-treatment research directions which may be pursued to fill these gaps. Such research directions, if conducted through well-designed randomized controlled trials, may substantively inform clinical practice in general medical settings on how to effectively care for patients presenting with pain-related distress and these common co-occurring conditions.
-
Non-overlapped P- and S-wave Poynting vectors and its solution on Grid Method
Lu, Yong Ming; Liu, Qiancheng
2017-01-01
Poynting vector represents the local directional energy flux density of seismic waves in geophysics. It is widely used in elastic reverse time migration (RTM) to analyze source illumination, suppress low-wavenumber noise, correct for image polarity and extract angle-domain common imaging gather (ADCIG). However, the P and S waves are mixed together during wavefield propagation such that the P and S energy fluxes are not clean everywhere, especially at the overlapped points. In this paper, we use a modified elastic wave equation in which the P and S vector wavefields are naturally separated. Then, we develop an efficient method to evaluate the separable P and S poynting vectors, respectively, based on the view that the group velocity and phase velocity have the same direction in isotropic elastic media. We furthermore formulate our method using an unstructured mesh based modeling method named the grid method. Finally, we verify our method using two numerical examples.
-
Non-overlapped P- and S-wave Poynting vectors and its solution on Grid Method
Lu, Yong Ming
2017-12-12
Poynting vector represents the local directional energy flux density of seismic waves in geophysics. It is widely used in elastic reverse time migration (RTM) to analyze source illumination, suppress low-wavenumber noise, correct for image polarity and extract angle-domain common imaging gather (ADCIG). However, the P and S waves are mixed together during wavefield propagation such that the P and S energy fluxes are not clean everywhere, especially at the overlapped points. In this paper, we use a modified elastic wave equation in which the P and S vector wavefields are naturally separated. Then, we develop an efficient method to evaluate the separable P and S poynting vectors, respectively, based on the view that the group velocity and phase velocity have the same direction in isotropic elastic media. We furthermore formulate our method using an unstructured mesh based modeling method named the grid method. Finally, we verify our method using two numerical examples.
-
Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.
Funk, W Chris; Murphy, Melanie A
2010-02-01
Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.
-
Overlapping community detection using weighted consensus ...
Indian Academy of Sciences (India)
2016-09-21
Sep 21, 2016 ... Complex networks; overlapping community; consensus clustering. PACS Nos 89.75 ... networks, a person may be in several social groups like family, friends ..... the social interactions between individuals in a karate club in an.
-
Overlapping ETF: Pair trading between two gold stocks
Bell, Peter N; Lui, Brian; Brekke, Alex
2012-01-01
The purpose of this paper is to propose a trading strategy for overlapping ETF and calculate the profitability using real price data. For two overlapping ETF that are designed to provide the same intraday percentage change, the difference in percentage changes is a measure of mispricing. This mispricing is the central focus of the paper. The premise of the paper is that mispricing can take large positive or negative values, but it will always come back to zero. This assumption reflects ou...
-
Optimal overlapping of waveform relaxation method for linear differential equations
International Nuclear Information System (INIS)
Yamada, Susumu; Ozawa, Kazufumi
2000-01-01
Waveform relaxation (WR) method is extremely suitable for solving large systems of ordinary differential equations (ODEs) on parallel computers, but the convergence of the method is generally slow. In order to accelerate the convergence, the methods which decouple the system into many subsystems with overlaps some of the components between the adjacent subsystems have been proposed. The methods, in general, converge much faster than the ones without overlapping, but the computational cost per iteration becomes larger due to the increase of the dimension of each subsystem. In this research, the convergence of the WR method for solving constant coefficients linear ODEs is investigated and the strategy to determine the number of overlapped components which minimizes the cost of the parallel computations is proposed. Numerical experiments on an SR2201 parallel computer show that the estimated number of the overlapped components by the proposed strategy is reasonable. (author)
-
Resolution enhancement of holographic printer using a hogel overlapping method.
Hong, Keehoon; Park, Soon-gi; Yeom, Jiwoon; Kim, Jonghyun; Chen, Ni; Pyun, Kyungsuk; Choi, Chilsung; Kim, Sunil; An, Jungkwuen; Lee, Hong-Seok; Chung, U-in; Lee, Byoungho
2013-06-17
We propose a hogel overlapping method for the holographic printer to enhance the lateral resolution of holographic stereograms. The hogel size is directly related to the lateral resolution of the holographic stereogram. Our analysis by computer simulation shows that there is a limit to decreasing the hogel size while printing holographic stereograms. Instead of reducing the size of hogel, the lateral resolution of holographic stereograms can be enhanced by printing overlapped hogels, which makes it possible to take advantage of multiplexing property of the volume hologram. We built a holographic printer, and recorded two holographic stereograms using the conventional and proposed overlapping methods. The images and movies of the holographic stereograms experimentally captured were compared between the conventional and proposed methods. The experimental results confirm that the proposed hogel overlapping method improves the lateral resolution of holographic stereograms compared to the conventional holographic printing method.
-
The overlapping community structure of structural brain network in young healthy individuals.
Directory of Open Access Journals (Sweden)
Kai Wu
2011-05-01
Full Text Available Community structure is a universal and significant feature of many complex networks in biology, society, and economics. Community structure has also been revealed in human brain structural and functional networks in previous studies. However, communities overlap and share many edges and nodes. Uncovering the overlapping community structure of complex networks remains largely unknown in human brain networks. Here, using regional gray matter volume, we investigated the structural brain network among 90 brain regions (according to a predefined anatomical atlas in 462 young, healthy individuals. Overlapped nodes between communities were defined by assuming that nodes (brain regions can belong to more than one community. We demonstrated that 90 brain regions were organized into 5 overlapping communities associated with several well-known brain systems, such as the auditory/language, visuospatial, emotion, decision-making, social, control of action, memory/learning, and visual systems. The overlapped nodes were mostly involved in an inferior-posterior pattern and were primarily related to auditory and visual perception. The overlapped nodes were mainly attributed to brain regions with higher node degrees and nodal efficiency and played a pivotal role in the flow of information through the structural brain network. Our results revealed fuzzy boundaries between communities by identifying overlapped nodes and provided new insights into the understanding of the relationship between the structure and function of the human brain. This study provides the first report of the overlapping community structure of the structural network of the human brain.
-
Growth Modeling with Non-Ignorable Dropout: Alternative Analyses of the STAR*D Antidepressant Trial
Muthén, Bengt; Asparouhov, Tihomir; Hunter, Aimee; Leuchter, Andrew
2011-01-01
This paper uses a general latent variable framework to study a series of models for non-ignorable missingness due to dropout. Non-ignorable missing data modeling acknowledges that missingness may depend on not only covariates and observed outcomes at previous time points as with the standard missing at random (MAR) assumption, but also on latent variables such as values that would have been observed (missing outcomes), developmental trends (growth factors), and qualitatively different types of development (latent trajectory classes). These alternative predictors of missing data can be explored in a general latent variable framework using the Mplus program. A flexible new model uses an extended pattern-mixture approach where missingness is a function of latent dropout classes in combination with growth mixture modeling using latent trajectory classes. A new selection model allows not only an influence of the outcomes on missingness, but allows this influence to vary across latent trajectory classes. Recommendations are given for choosing models. The missing data models are applied to longitudinal data from STAR*D, the largest antidepressant clinical trial in the U.S. to date. Despite the importance of this trial, STAR*D growth model analyses using non-ignorable missing data techniques have not been explored until now. The STAR*D data are shown to feature distinct trajectory classes, including a low class corresponding to substantial improvement in depression, a minority class with a U-shaped curve corresponding to transient improvement, and a high class corresponding to no improvement. The analyses provide a new way to assess drug efficiency in the presence of dropout. PMID:21381817
-
Directory of Open Access Journals (Sweden)
D. Araújo
2017-03-01
Full Text Available Introduction: Phenotypic overlap between the two main chronic airway pulmonary diseases, asthma and chronic obstructive pulmonary disease (COPD, has been the subject of debate for decades, and recently the nomenclature of asthma-COPD overlap syndrome (ACOS was adopted for this condition. The definition of this entity in the literature is, however, very heterogeneous, it is therefore important to define how it applies to Portugal. Methods: A literature review of ACOS was made in a first phase resulting in the drawing up of a document that was later submitted for discussion among a panel of chronic lung diseases experts, resulting in reflexions about diagnosis, treatment and clinical guidance for ACOS patients. Results: There was a consensus among the experts that the diagnosis of ACOS should be considered in the concomitant presence of: clinical manifestations characteristic of both asthma and COPD, persistent airway obstruction (post-bronchodilator FEV1/FVC 300 eosinophils/μL or >5% of leukocytes and previous history of atopy should also be considered. The recommended first line pharmacological treatment in these patients is the ICS/LABA association; if symptomatic control is not achieved or in case of clinical severity, triple therapy with ICS/LABA/LAMA may be used. An effective control of the exposure to risk factors, vaccination, respiratory rehabilitation and treatment of comorbidities is also important. Conclusions: The creation of initial guidelines on ACOS, which can be applied in the Portuguese context, has an important role in the generation of a broad nationwide consensus. This will give, in the near future, a far better clinical, functional and epidemiological characterization of ACOS patients, with the ultimate goal of achieving better therapeutic guidance. Keywords: Asthma, Chronic obstructive pulmonary disease, Overlap syndrome, Portuguese consensus
-
Overlapped flowers yield detection using computer-based interface
Directory of Open Access Journals (Sweden)
Anuradha Sharma
2016-09-01
Full Text Available Precision agriculture has always dealt with the accuracy and timely information about agricultural products. With the help of computer hardware and software technology designing a decision support system that could generate flower yield information and serve as base for management and planning of flower marketing is made so easy. Despite such technologies, some problem still arise, for example, a colour homogeneity of a specimen which cannot be obtained similar to actual colour of image and overlapping of image. In this paper implementing a new ‘counting algorithm’ for overlapped flower is being discussed. For implementing this algorithm, some techniques and operations such as colour image segmentation technique, image segmentation, using HSV colour space and morphological operations have been used. In this paper used two most popular colour space; those are RGB and HSV. HSV colour space decouples brightness from a chromatic component in the image, by which it provides better result in case for occlusion and overlapping.
-
An Economical Analytical Equation for the Integrated Vertical Overlap of Cumulus and Stratus
Park, Sungsu
2018-03-01
By extending the previously proposed heuristic parameterization, the author derived an analytical equation computing the overlap areas between the precipitation (or radiation) areas and the cloud areas in a cloud system consisting of cumulus and stratus. The new analytical equation is accurate and much more efficient than the previous heuristic equation, which suffers from the truncation error in association with the digitalization of the overlap areas. Global test simulations with the new analytical formula in an offline mode showed that the maximum cumulus overlap simulates more surface precipitation flux than the random cumulus overlap. On the other hand, the maximum stratus overlap simulates less surface precipitation flux than random stratus overlap, which is due to the increase in the evaporation rate of convective precipitation from the random to maximum stratus overlap. The independent precipitation approximation (IPA) marginally decreases the surface precipitation flux, implying that IPA works well with other parameterizations. In contrast to the net production rate of precipitation and surface precipitation flux that increase when the cumulus and stratus are maximally and randomly overlapped, respectively, the global mean net radiative cooling and longwave cloud radiative forcing (LWCF) increase when the cumulus and stratus are randomly overlapped. On the global average, the vertical cloud overlap exerts larger impacts on the precipitation flux than on the radiation flux. The radiation scheme taking the subgrid variability of water vapor between the cloud and clear portions into account substantially increases the global mean LWCF in tropical deep convection and midlatitude storm track regions.
-
Overlapping sphincteroplasty and posterior repair.
Crane, Andrea K; Myers, Erinn M; Lippmann, Quinn K; Matthews, Catherine A
2014-12-01
Knowledge of how to anatomically reconstruct extensive posterior-compartment defects is variable among gynecologists. The objective of this video is to demonstrate an effective technique of overlapping sphincteroplasty and posterior repair. In this video, a scripted storyboard was constructed that outlines the key surgical steps of a comprehensive posterior compartment repair: (1) surgical incision that permits access to posterior compartment and perineal body, (2) dissection of the rectovaginal space up to the level of the cervix, (3) plication of the rectovaginal muscularis, (4) repair of internal and external anal sphincters, and (5) reconstruction of the perineal body. Using a combination of graphic illustrations and live video footage, tips on repair are highlighted. The goals at the end of repair are to: (1) have improved vaginal caliber, (2) increase rectal tone along the entire posterior vaginal wall, (3) have the posterior vaginal wall at a perpendicular plane to the perineal body, (4) reform the hymenal ring, and (5) not have an overly elongated perineal body. This video provides a step-by-step guide on how to perform an overlapping sphincteroplasty and posterior repair.
-
The puzzle of immune phenotypes of childhood asthma.
Landgraf-Rauf, Katja; Anselm, Bettina; Schaub, Bianca
2016-12-01
Asthma represents the most common chronic childhood disease worldwide. Whereas preschool children present with wheezing triggered by different factors (multitrigger and viral wheeze), clinical asthma manifestation in school children has previously been classified as allergic and non-allergic asthma. For both, the underlying immunological mechanisms are not yet understood in depth in children. Treatment is still prescribed regardless of underlying mechanisms, and children are not always treated successfully. This review summarizes recent key findings on the complex mechanisms of the development and manifestation of childhood asthma. Whereas traditional classification of childhood asthma is primarily based on clinical symptoms like wheezing and atopy, novel approaches to specify asthma phenotypes are under way and face challenges such as including the stability of phenotypes over time and transition into adulthood. Epidemiological studies enclose more information on the patient's disease history and environmental influences. Latest studies define endotypes based on molecular and cellular mechanisms, for example defining risk and protective single nucleotide polymorphisms (SNPs) and new immune phenotypes, showing promising results. Also, regulatory T cells and recently discovered T helper cell subtypes such as Th9 and Th17 cells were shown to be important for the development of asthma. Innate lymphoid cells (ILC) could play a critical role in asthma patients as they produce different cytokines associated with asthma. Epigenetic findings showed different acetylation and methylation patterns for children with allergic and non-allergic asthma. On a posttranscriptional level, miRNAs are regulating factors identified to differ between asthma patients and healthy controls and also indicate differences within asthma phenotypes. Metabolomics is another exciting chapter important for endotyping asthmatic children. Despite the development of new biomarkers and the discovery of
-
Overlapping Chronic Pain Conditions: Implications for Diagnosis and Classification.
Maixner, William; Fillingim, Roger B; Williams, David A; Smith, Shad B; Slade, Gary D
2016-09-01
There is increasing recognition that many if not most common chronic pain conditions are heterogeneous with a high degree of overlap or coprevalence of other common pain conditions along with influences from biopsychosocial factors. At present, very little attention is given to the high degree of overlap of many common pain conditions when recruiting for clinical trials. As such, many if not most patients enrolled into clinical studies are not representative of most chronic pain patients. The failure to account for the heterogeneous and overlapping nature of most common pain conditions may result in treatment responses of small effect size when these treatments are administered to patients with chronic overlapping pain conditions (COPCs) represented in the general population. In this brief review we describe the concept of COPCs and the putative mechanisms underlying COPCs. Finally, we present a series of recommendations that will advance our understanding of COPCs. This brief review describes the concept of COPCs. A mechanism-based heuristic model is presented and current knowledge and evidence for COPCs are presented. Finally, a set of recommendations is provided to advance our understanding of COPCs. Copyright © 2016 American Pain Society. Published by Elsevier Inc. All rights reserved.
-
Hoshino, Tomonori; Fujiwara, Taku; Kilian, Mogens
2005-12-01
The aim of this study was to evaluate molecular and phenotypic methods for the identification of nonhemolytic streptococci. A collection of 148 strains consisting of 115 clinical isolates from cases of infective endocarditis, septicemia, and meningitis and 33 reference strains, including type strains of all relevant Streptococcus species, were examined. Identification was performed by phylogenetic analysis of nucleotide sequences of four housekeeping genes, ddl, gdh, rpoB, and sodA; by PCR analysis of the glucosyltransferase (gtf) gene; and by conventional phenotypic characterization and identification using two commercial kits, Rapid ID 32 STREP and STREPTOGRAM and the associated databases. A phylogenetic tree based on concatenated sequences of the four housekeeping genes allowed unequivocal differentiation of recognized species and was used as the reference. Analysis of single gene sequences revealed deviation clustering in eight strains (5.4%) due to homologous recombination with other species. This was particularly evident in S. sanguinis and in members of the anginosus group of streptococci. The rate of correct identification of the strains by both commercial identification kits was below 50% but varied significantly between species. The most significant problems were observed with S. mitis and S. oralis and 11 Streptococcus species described since 1991. Our data indicate that identification based on multilocus sequence analysis is optimal. As a more practical alternative we recommend identification based on sodA sequences with reference to a comprehensive set of sequences that is available for downloading from our server. An analysis of the species distribution of 107 nonhemolytic streptococci from bacteremic patients showed a predominance of S. oralis and S. anginosus with various underlying infections.
-
Genetic and phenotypic variation of some reproductive traits in ...
African Journals Online (AJOL)
Unknown
sasas.co.za/Sajas.html. 195. Genetic and phenotypic variation of some reproductive traits in Egyptian buffalo ..... Mourad, Kawthar A., Khattab, A.S. & Ibrahim, M.A.R., 1989. Effect of genetic and non-genetic factors on reproductive traits in Egyptian ...
-
Treatment of Oral Mucosal Lesions Associated With Overlapping Psychodermatologic Disorders.
Alfaris, Sausan; France, Katherine; Sollecito, Thomas P; Stoopler, Eric T
2018-04-01
Delusional infestations are psychodermatologic disorders in which those affected have a false belief they are infested by parasites and/or "growing" inanimate objects from cutaneous surfaces. Individuals with delusional parasitosis (DP) believe parasites, bacteria, worms, mites, or other living organisms are the source of cutaneous symptoms, while those with Morgellons disease (MD) attribute their symptoms to growth of small fibers or inorganic material. In both DP and MD, self-inflicted, non-healing cutaneous lesions caused by scratching at the affected areas to alleviate symptoms are commonly observed. This report describes a case of oral mucosal lesions in a patient demonstrating overlapping symptoms of DP and MD. It is important for oral healthcare providers to recognize oral signs and symptoms that may be associated with psychodermatologic disorders.
-
McGoey, Brechann V; Stinchcombe, John R
2009-08-01
Shade avoidance syndrome is a known adaptive response for Impatiens capensis growing in dense intraspecific competition. However, I. capensis also grow with dominant interspecific competitors in marshes. Here, we compare the I. capensis shade-avoidance phenotypes produced in the absence and presence of heterospecific competitors, as well as selection on those traits. Two treatments were established in a marsh; in one treatment all heterospecifics were removed, while in the other, all competitors remained. We compared morphological traits, light parameters, seed output and, using phenotypic selection analysis, examined directional and nonlinear selection operating in the different competitive treatments. Average phenotypes, light parameters and seed production all varied depending on competitive treatment. Phenotypic selection analyses revealed different directional, disruptive, stabilizing and correlational selection. The disparities seen in both phenotypes and selection between the treatments related to the important differences in elongation timing depending on the presence of heterospecifics, although environmental covariances between traits and fitness could also contribute. Phenotypes produced by I. capensis depend on their competitive environment, and differing selection on shade-avoidance traits between competitive environments could indirectly select for increased plasticity given gene flow between populations in different competitive contexts.
-
Directory of Open Access Journals (Sweden)
Albert Goday
2016-04-01
Full Text Available Abstract Background Metabolically healthy obese (MHO phenotype may present with distinct characteristics compared with those with a metabolically unhealthy obese phenotype. Epidemiologic data on the distribution of these conditions in the working population are lacking. We aimed to evaluate the prevalence and clinical characteristics of MHO and other obese/non-obese metabolic phenotypes in a working population. Methods Cross-sectional analysis of all subjects who had undergone a medical examination with Ibermutuamur Prevention Society from May 2004 to December 2007. Participants were classified into 5 categories according to their body mass index (BMI; within each of these categories, participants were further classified as metabolically healthy (MH or metabolically unhealthy (MUH according to the modified NCEP-ATPIII criteria. A logistic regression analysis was performed to evaluate some clinically relevant factors associated with a MH status. Results In the overall population, the prevalence of the MHO phenotype was 8.6 %. The proportions of MH individuals in the overweight and obese categories were: 87.1 % (overweight and 55.5 % (obese I-III [58.8, 40.0, and 38.7 % of the obese I, II, and III categories, respectively]. When the overweight and obese categories were considered, compared with individuals who were MUH, those who were MH tended to be younger and more likely to be female or participate in physical exercise; they were also less likely to smoke, or to be a heavy drinker. In the underweight and normal weight categories, compared with individuals who were MH, those who were MUH were more likely to be older, male, manual (blue collar workers, smokers and heavy drinkers. Among participants in the MUH, normal weight group, the proportion of individuals with a sedentary lifestyle was higher relative to those in the MH, normal weight group. The factors more strongly associated with the MUH phenotype were BMI and age, followed by the
-
Angular overlap model in actinides
International Nuclear Information System (INIS)
Gajek, Z.; Mulak, J.
1991-01-01
Quantitative foundations of the Angular Overlap Model in actinides based on ab initio calculations of the crystal field effect in the uranium (III) (IV) and (V) ions in various crystals are presented. The calculations justify some common simplifications of the model and fix up the relations between the AOM parameters. Traps and limitations of the AOM phenomenology are discussed
-
Angular overlap model in actinides
Energy Technology Data Exchange (ETDEWEB)
Gajek, Z.; Mulak, J. (Polska Akademia Nauk, Wroclaw (PL). Inst. Niskich Temperatur i Badan Strukturalnych)
1991-01-01
Quantitative foundations of the Angular Overlap Model in actinides based on ab initio calculations of the crystal field effect in the uranium (III) (IV) and (V) ions in various crystals are presented. The calculations justify some common simplifications of the model and fix up the relations between the AOM parameters. Traps and limitations of the AOM phenomenology are discussed.
-
Maroofian, Reza; Riemersma, Moniek; Jae, Lucas T; Zhianabed, Narges; Willemsen, Marjolein H; Wissink-Lindhout, Willemijn M; Willemsen, Michèl A; de Brouwer, Arjan P M; Mehrjardi, Mohammad Yahya Vahidi; Ashrafi, Mahmoud Reza; Kusters, Benno; Kleefstra, Tjitske; Jamshidi, Yalda; Nasseri, Mojila; Pfundt, Rolph; Brummelkamp, Thijn R; Abbaszadegan, Mohammad Reza; Lefeber, Dirk J; van Bokhoven, Hans
2017-12-22
The phenotypic severity of congenital muscular dystrophy-dystroglycanopathy (MDDG) syndromes associated with aberrant glycosylation of α-dystroglycan ranges from the severe Walker-Warburg syndrome or muscle-eye-brain disease to mild, late-onset, isolated limb-girdle muscular dystrophy without neural involvement. However, muscular dystrophy is invariably found across the spectrum of MDDG patients. Using linkage mapping and whole-exome sequencing in two families with an unexplained neurodevelopmental disorder, we have identified homozygous and compound heterozygous mutations in B3GALNT2. The first family comprises two brothers of Dutch non-consanguineous parents presenting with mild ID and behavioral problems. Immunohistochemical analysis of muscle biopsy revealed no significant aberrations, in line with the absence of a muscular phenotype in the affected siblings. The second family includes five affected individuals from an Iranian consanguineous kindred with mild-to-moderate intellectual disability (ID) and epilepsy without any notable neuroimaging, muscle, or eye abnormalities. Complementation assays of the compound heterozygous mutations identified in the two brothers had a comparable effect on the O-glycosylation of α-dystroglycan as previously reported mutations that are associated with severe muscular phenotypes. In conclusion, we show that mutations in B3GALNT2 can give rise to a novel MDDG syndrome presentation, characterized by ID associated variably with seizure, but without any apparent muscular involvement. Importantly, B3GALNT2 activity does not fully correlate with the severity of the phenotype as assessed by the complementation assay.
-
Headaches and myofascial temporomandibular disorders: overlapping entities, separate managements?
Conti, P C R; Costa, Y M; Gonçalves, D A; Svensson, P
2016-09-01
There are relevant clinical overlaps between some of the painful temporomandibular disorders (TMD) and headache conditions that may hamper the diagnostic process and treatment. A non-systematic search for studies on the relationship between TMD and headaches was carried out in the following databases: PubMed, Cochrane Library and Embase. Important pain mechanisms contributing to the close association and complex relationship between TMD and headache disorders are as follows: processes of peripheral and central sensitisation which take place in similar anatomical areas, the possible impairment of the descending modulatory pain pathways and the processes of referred pain. In addition, the clinical examination does not always provide distinguishing information to differentiate between headaches and TMD. So, considering the pathophysiology and the clinical presentation of some types of headache and myofascial TMD, such overlap can be considered not only a matter of comorbid relationship, but rather a question of disorders where the distinction lines are sometimes hard to identify. These concerns are certainly reflected in the current classification systems of both TMD and headache where the clinical consequences of diagnosis such as headache attributed to or associated with TMD are uncertain. There are several similarities in terms of therapeutic strategies used to manage myofascial TMD and headaches. Considering all these possible levels of interaction, we reinforce the recommendation for multidisciplinary approaches, by a team of oro-facial pain specialists and a neurologist (headache specialist), to attain the most precise differential diagnosis and initiate the best and most efficient treatment. © 2016 John Wiley & Sons Ltd.
-
Lee, Dong-Won; Jin, Hyun-Jung; Shin, Kyeong-Cheol; Chung, Jin-Hong; Lee, Hyoung-Woo; Lee, Kwan-Ho
2017-01-01
Sarcopenia and decreased bone-mineral density (BMD) are common in elderly people, and are major comorbidities of obstructive airway disease (OAD). However, the relationship between sarcopenia and BMD in each OAD phenotype, especially asthma-COPD overlap syndrome (ACOS), is not yet clear. We aimed to evaluate differences in BMD according to the presence of sarcopenia in each OAD phenotype. Among the research subjects in KNHANES IV and V (2008-2011), 5,562 were ≥50 years old and underwent qualified spirometry and dual-energy X-ray absorptiometry. A total of 947 subjects were included in the study: 89 had asthma, 748 COPD, and 110 ACOS. In the COPD and ACOS phenotypes, T-scores were lower in the sarcopenia group than the nonsarcopenia group. Prevalence rates of osteopenia and osteoporosis were higher in the sarcopenia group than the nonsarcopenia group. ( P sarcopenia group had higher risks of developing osteopenia, osteoporosis, and low BMD than the nonsarcopenia group in the ACOS phenotype (OR 6.620, 95% CI 1.129-38.828 [ P =0.036], OR 9.611, 95% CI 1.133-81.544 [ P =0.038], and OR 6.935, 95% CI 1.194-40.272 [ P =0.031], respectively). However, in the asthma phenotype, the sarcopenia group showed no increased risk compared with the nonsarcopenia group. In the ACOS phenotype, individuals with sarcopenia had a higher prevalence rate and higher risks of osteopenia and osteoporosis than those without sarcopenia among all OAD phenotypes.
-
Astuto, L M; Bork, J M; Weston, M D; Askew, J W; Fields, R R; Orten, D J; Ohliger, S J; Riazuddin, S; Morell, R J; Khan, S; Riazuddin, S; Kremer, H; van Hauwe, P; Moller, C G; Cremers, C W R J; Ayuso, C; Heckenlively, J R; Rohrschneider, K; Spandau, U; Greenberg, J; Ramesar, R; Reardon, W; Bitoun, P; Millan, J; Legge, R; Friedman, T B; Kimberling, W J
2002-08-01
Usher syndrome type I is characterized by congenital hearing loss, retinitis pigmentosa (RP), and variable vestibular areflexia. Usher syndrome type ID, one of seven Usher syndrome type I genetic localizations, have been mapped to a chromosomal interval that overlaps with a nonsyndromic-deafness localization, DFNB12. Mutations in CDH23, a gene that encodes a putative cell-adhesion protein with multiple cadherin-like domains, are responsible for both Usher syndrome and DFNB12 nonsyndromic deafness. Specific CDH23 mutational defects have been identified that differentiate these two phenotypes. Only missense mutations of CDH23 have been observed in families with nonsyndromic deafness, whereas nonsense, frameshift, splice-site, and missense mutations have been identified in families with Usher syndrome. In the present study, a panel of 69 probands with Usher syndrome and 38 probands with recessive nonsyndromic deafness were screened for the presence of mutations in the entire coding region of CDH23, by heteroduplex, single-strand conformation polymorphism, and direct sequence analyses. A total of 36 different CDH23 mutations were detected in 45 families; 33 of these mutations were novel, including 18 missense, 3 nonsense, 5 splicing defects, 5 microdeletions, and 2 insertions. A total of seven mutations were common to more than one family. Numerous exonic and intronic polymorphisms also were detected. Results of ophthalmologic examinations of the patients with nonsyndromic deafness have found asymptomatic RP-like manifestations, indicating that missense mutations may have a subtle effect in the retina. Furthermore, patients with mutations in CDH23 display a wide range of hearing loss and RP phenotypes, differing in severity, age at onset, type, and the presence or absence of vestibular areflexia.
-
Astuto, L. M.; Bork, J. M.; Weston, M. D.; Askew, J. W.; Fields, R. R.; Orten, D. J.; Ohliger, S. J.; Riazuddin, S.; Morell, R. J.; Khan, S.; Riazuddin, S.; Kremer, H.; van Hauwe, P.; Moller, C. G.; Cremers, C. W. R. J.; Ayuso, C.; Heckenlively, J. R.; Rohrschneider, K.; Spandau, U.; Greenberg, J.; Ramesar, R.; Reardon, W.; Bitoun, P.; Millan, J.; Legge, R.; Friedman, T. B.; Kimberling, W. J.
2002-01-01
Usher syndrome type I is characterized by congenital hearing loss, retinitis pigmentosa (RP), and variable vestibular areflexia. Usher syndrome type ID, one of seven Usher syndrome type I genetic localizations, have been mapped to a chromosomal interval that overlaps with a nonsyndromic-deafness localization, DFNB12. Mutations in CDH23, a gene that encodes a putative cell-adhesion protein with multiple cadherin-like domains, are responsible for both Usher syndrome and DFNB12 nonsyndromic deafness. Specific CDH23 mutational defects have been identified that differentiate these two phenotypes. Only missense mutations of CDH23 have been observed in families with nonsyndromic deafness, whereas nonsense, frameshift, splice-site, and missense mutations have been identified in families with Usher syndrome. In the present study, a panel of 69 probands with Usher syndrome and 38 probands with recessive nonsyndromic deafness were screened for the presence of mutations in the entire coding region of CDH23, by heteroduplex, single-strand conformation polymorphism, and direct sequence analyses. A total of 36 different CDH23 mutations were detected in 45 families; 33 of these mutations were novel, including 18 missense, 3 nonsense, 5 splicing defects, 5 microdeletions, and 2 insertions. A total of seven mutations were common to more than one family. Numerous exonic and intronic polymorphisms also were detected. Results of ophthalmologic examinations of the patients with nonsyndromic deafness have found asymptomatic RP–like manifestations, indicating that missense mutations may have a subtle effect in the retina. Furthermore, patients with mutations in CDH23 display a wide range of hearing loss and RP phenotypes, differing in severity, age at onset, type, and the presence or absence of vestibular areflexia. PMID:12075507
-
Sładek, Małgorzata; Wasilewska, Agata; Swiat, Agnieszka; Cmiel, Adam
2014-01-01
Antibodies reacting with various microbial epitopes have been described in inflammatory bowel disease (IBD) and are associated with a specific diagnosis and clinical presentation. To evaluate the profile of new anti-glycan antibodies, their potential association with disease phenotype and diagnostic accuracy in paediatric Crohn's disease (CD). Blood samples from 134 paediatric IBD patients (109 CD, 25 ulcerative colitis (UC)) and 67 controls were blindly analysed for anti-Saccharomyces cerevisiae (ASCA), anti-chitobioside carbohydrate (ACCA), anti-laminaribioside carbohydrate (ALCA), and anti-mannobioside carbohydrate (AMCA) antibodies using commercially available assays. The serological response to glycans was correlated with clinical disease characteristics. At least one of the tested anti-glycan antibodies was present in 75% of CD patients. Despite the high frequency of reactivity to glycan epitopes, a limited overlap of serological markers was observed. In total, 49% of ASCA-negative patients presented with one of the following: ACCA, ALCA, or AMCA. The occurrence of one antibody from the anti-glycan panel was independently associated with complicated disease phenotype and ileocolonic disease location. A higher level of immune response as assessed by the quartile sum scores for ACCA, ALCA, and AMCA was linked with older age at diagnosis (10-17 years) and ileocolonic disease location. The ASCA had the greatest accuracy for diagnosis and differentiation of CD. Qualitative and quantitative serologicalal response to glycan epitopes was associated with distinct clinical presentation in paediatric CD patients. This raises the possibility for the use of these markers to differentiate subgroups of CD patients with more sever clinical presentation. The ASCA was the most accurate serological marker for CD; however, testing for the new anti-glycan antibodies may constitute an adjunctive tool in a specific group of patients to aid in the differentiation of CD with absent
-
AlShahrani, Mona; Hoehndorf, Robert
2018-01-01
In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease's (or patient's) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.
-
Alshahrani, Mona
2018-04-30
In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease\\'s (or patient\\'s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.
-
Guided Classification System for Conceptual Overlapping Classes in OpenStreetMap
Directory of Open Access Journals (Sweden)
Ahmed Loai Ali
2016-06-01
Full Text Available The increased development of Volunteered Geographic Information (VGI and its potential role in GIScience studies raises questions about the resulting data quality. Several studies address VGI quality from various perspectives like completeness, positional accuracy, consistency, etc. They mostly have consensus on the heterogeneity of data quality. The problem may be due to the lack of standard procedures for data collection and absence of quality control feedback for voluntary participants. In our research, we are concerned with data quality from the classification perspective. Particularly in VGI-mapping projects, the limited expertise of participants and the non-strict definition of geographic features lead to conceptual overlapping classes, where an entity could plausibly belong to multiple classes, e.g., lake or pond, park or garden, marsh or swamp, etc. Usually, quantitative and/or qualitative characteristics exist that distinguish between classes. Nevertheless, these characteristics might not be recognizable for non-expert participants. In previous work, we developed the rule-guided classification approach that guides participants to the most appropriate classes. As exemplification, we tackle the conceptual overlapping of some grass-related classes. For a given data set, our approach presents the most highly recommended classes for each entity. In this paper, we present the validation of our approach. We implement a web-based application called Grass&Green that presents recommendations for crowdsourcing validation. The findings show the applicability of the proposed approach. In four months, the application attracted 212 participants from more than 35 countries who checked 2,865 entities. The results indicate that 89% of the contributions fully/partially agree with our recommendations. We then carried out a detailed analysis that demonstrates the potential of this enhanced data classification. This research encourages the development of
-
Melis, Melania; Yousaf, Neeta Y; Mattes, Mitchell Z; Cabras, Tiziana; Messana, Irene; Crnjar, Roberto; Tomassini Barbarossa, Iole; Tepper, Beverly J
2017-05-01
Individual differences in astringency perception are poorly understood. Astringency from tannins stimulates the release of specific classes of salivary proteins. These proteins form complexes with tannins, altering their perceived astringency and reducing their bioavailability. We studied the bitter compound, 6-n-propylthioural (PROP), as a phenotypic marker for variation in astringency perception and salivary protein responses. Seventy-nine subjects classified by PROP taster status rated cranberry juice cocktail (CJC; with added sugar) supplemented with 0, 1.5 or 2.0g/L tannic acid (TA). Saliva for protein analyses was collected at rest, or after stimulation with TA or cranberry juice (CJ; without added sugar). CJC with 1.5g/L tannic acid was found to be less astringent, and was liked more by PROP non-taster males than PROP taster males, consistent with the expectation that non-tasters are less sensitive to astringency. Levels of acidic Proline Rich Proteins (aPRPs) and basic Proline Rich Proteins (bPRPs) decreased after TA, while levels of aPRPs, bPRPs and Cystatins unexpectedly rose after CJ. Increases in bPRPs and Cystatins were only observed in PROP tasters. The PROP phenotype plays a gender-specific, but somewhat limited role in the perceived astringency of tannic-acid supplemented, cranberry juice cocktail. The PROP phenotype (regardless of gender) may also be involved in the release of salivary proteins previously implicated in oral health. Copyright © 2017 Elsevier Inc. All rights reserved.
-
Symmetry and symmetry restoration of lattice chiral fermions in the overlap formalism
International Nuclear Information System (INIS)
Kikukawa, Y.
1999-01-01
Three aspects of the symmetry structure of lattice chiral fermions in the overlap formalism are discussed. By the weak coupling expansion of the overlap Dirac operator, the axial anomaly associated to the chiral transformation proposed by Luescher is evaluated and is shown to have the correct form of the topological charge density for perturbative backgrounds. Next we discuss the exponential suppression of the self-energy correction of the lightest mode in the domain-wall fermion/truncated overlap. Finally, we consider a supersymmetric extension of the overlap formula in the case of the chiral multiplet and examine the symmetry structure of the action
-
An assessment of the overlap between morale and work engagement in a nonoperational military sample.
Ivey, Gary W; Blanc, J-R Sébastien; Mantler, Janet
2015-07-01
The degree of overlap between two positive motivational constructs-morale and work engagement-was assessed in a random sample of Canadian Armed Forces personnel stationed across Canada (N = 1,224). Based on self-determination theory and past research, job-specific self-efficacy, trust in teammates, and job significance were expected to be associated with morale and work engagement. Structural equation modeling analyses revealed that morale and work engagement were highly positively correlated, but had different patterns of association with predictor and outcome variables. Although trust in teammates and job significance predicted both morale and work engagement, job-specific self-efficacy predicted morale but not work engagement. Willingness to deploy on operations, turnover intentions, and psychological distress were predicted by both morale and work engagement, but morale was a better predictor of psychological distress and work engagement was a stronger predictor of turnover intentions. Together, the results suggest that, despite their overlap, morale and work engagement, as defined and measured herein, are not interchangeable. (c) 2015 APA, all rights reserved).
-
Angel, Jordan B.; Banks, Jeffrey W.; Henshaw, William D.
2018-01-01
High-order accurate upwind approximations for the wave equation in second-order form on overlapping grids are developed. Although upwind schemes are well established for first-order hyperbolic systems, it was only recently shown by Banks and Henshaw [1] how upwinding could be incorporated into the second-order form of the wave equation. This new upwind approach is extended here to solve the time-domain Maxwell's equations in second-order form; schemes of arbitrary order of accuracy are formulated for general curvilinear grids. Taylor time-stepping is used to develop single-step space-time schemes, and the upwind dissipation is incorporated by embedding the exact solution of a local Riemann problem into the discretization. Second-order and fourth-order accurate schemes are implemented for problems in two and three space dimensions, and overlapping grids are used to treat complex geometry and problems with multiple materials. Stability analysis of the upwind-scheme on overlapping grids is performed using normal mode theory. The stability analysis and computations confirm that the upwind scheme remains stable on overlapping grids, including the difficult case of thin boundary grids when the traditional non-dissipative scheme becomes unstable. The accuracy properties of the scheme are carefully evaluated on a series of classical scattering problems for both perfect conductors and dielectric materials in two and three space dimensions. The upwind scheme is shown to be robust and provide high-order accuracy.
-
Improving Phrap-based assembly of the rat using "reliable" overlaps.
Directory of Open Access Journals (Sweden)
Michael Roberts
2008-03-01
Full Text Available The assembly methods used for whole-genome shotgun (WGS data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our "reliable-overlap" algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.
-
Segmentation of Overlapping Shapes using Test Ray Intersections
DEFF Research Database (Denmark)
Rasmusson, Allan
As the use of digital images have become standard in everyday bioimaging, people are naturally trying to utilize computer algorithms for automating laborious and repetetive image analysis tasks. A preliminary task is the segmentation of structures of interest from digital images. This may in itself....... This may, however, quickly lead to the implementation of complex descriptions of any possible configuration the overlapping shapes may appear in. Presented here is a new approach to segment overlapping shapes which utilizes information gained from probing the image with test rays. Test rays intersections...
-
Genotypic and phenotypic analysis of 396 individuals with mutations in Sonic Hedgehog.
Solomon, Benjamin D; Bear, Kelly A; Wyllie, Adrian; Keaton, Amelia A; Dubourg, Christele; David, Veronique; Mercier, Sandra; Odent, Sylvie; Hehr, Ute; Paulussen, Aimee; Clegg, Nancy J; Delgado, Mauricio R; Bale, Sherri J; Lacbawan, Felicitas; Ardinger, Holly H; Aylsworth, Arthur S; Bhengu, Ntombenhle Louisa; Braddock, Stephen; Brookhyser, Karen; Burton, Barbara; Gaspar, Harald; Grix, Art; Horovitz, Dafne; Kanetzke, Erin; Kayserili, Hulya; Lev, Dorit; Nikkel, Sarah M; Norton, Mary; Roberts, Richard; Saal, Howard; Schaefer, G B; Schneider, Adele; Smith, Erika K; Sowry, Ellen; Spence, M Anne; Shalev, Stavit A; Steiner, Carlos E; Thompson, Elizabeth M; Winder, Thomas L; Balog, Joan Z; Hadley, Donald W; Zhou, Nan; Pineda-Alvarez, Daniel E; Roessler, Erich; Muenke, Maximilian
2012-07-01
Holoprosencephaly (HPE), the most common malformation of the human forebrain, may result from mutations in over 12 genes. Sonic Hedgehog (SHH) was the first such gene discovered; mutations in SHH remain the most common cause of non-chromosomal HPE. The severity spectrum is wide, ranging from incompatibility with extrauterine life to isolated midline facial differences. To characterise genetic and clinical findings in individuals with SHH mutations. Through the National Institutes of Health and collaborating centres, DNA from approximately 2000 individuals with HPE spectrum disorders were analysed for SHH variations. Clinical details were examined and combined with published cases. This study describes 396 individuals, representing 157 unrelated kindreds, with SHH mutations; 141 (36%) have not been previously reported. SHH mutations more commonly resulted in non-HPE (64%) than frank HPE (36%), and non-HPE was significantly more common in patients with SHH than in those with mutations in the other common HPE related genes (pC-terminus (including accounting for the relative size of the coding regions, p=0.00010), no specific genotype-phenotype correlations could be established regarding mutation location. SHH mutations overall result in milder disease than mutations in other common HPE related genes. HPE is more frequent in individuals with truncating mutations, but clinical predictions at the individual level remain elusive.
-
Becker muscular dystrophy with widespread muscle hypertrophy and a non-sense mutation of exon 2.
Witting, N; Duno, M; Vissing, J
2013-01-01
Becker muscular dystrophy features progressive proximal weakness, wasting and often focal hypertrophy. We present a patient with pain and cramps from adolescence. Widespread muscle hypertrophy, preserved muscle strength and a 10-20-fold raised CPK were noted. Muscle biopsy was dystrophic, and Western blot showed a 95% reduction of dystrophin levels. Genetic analyses revealed a non-sense mutation in exon 2 of the dystrophin gene. This mutation is predicted to result in a Duchenne phenotype, but resulted in a mild Becker muscular dystrophy with widespread muscle hypertrophy. We suggest that this unusual phenotype is caused by translation re-initiation downstream from the mutation site. Copyright © 2012 Elsevier B.V. All rights reserved.
-
Reijnders, Margot R F; Miller, Kerry A; Alvi, Mohsan; Goos, Jacqueline A C; Lees, Melissa M; de Burca, Anna; Henderson, Alex; Kraus, Alison; Mikat, Barbara; de Vries, Bert B A; Isidor, Bertrand; Kerr, Bronwyn; Marcelis, Carlo; Schluth-Bolard, Caroline; Deshpande, Charu; Ruivenkamp, Claudia A L; Wieczorek, Dagmar; Baralle, Diana; Blair, Edward M; Engels, Hartmut; Lüdecke, Hermann-Josef; Eason, Jacqueline; Santen, Gijs W E; Clayton-Smith, Jill; Chandler, Kate; Tatton-Brown, Katrina; Payne, Katelyn; Helbig, Katherine; Radtke, Kelly; Nugent, Kimberly M; Cremer, Kirsten; Strom, Tim M; Bird, Lynne M; Sinnema, Margje; Bitner-Glindzicz, Maria; van Dooren, Marieke F; Alders, Marielle; Koopmans, Marije; Brick, Lauren; Kozenko, Mariya; Harline, Megan L; Klaassens, Merel; Steinraths, Michelle; Cooper, Nicola S; Edery, Patrick; Yap, Patrick; Terhal, Paulien A; van der Spek, Peter J; Lakeman, Phillis; Taylor, Rachel L; Littlejohn, Rebecca O; Pfundt, Rolph; Mercimek-Andrews, Saadet; Stegmann, Alexander P A; Kant, Sarina G; McLean, Scott; Joss, Shelagh; Swagemakers, Sigrid M A; Douzgou, Sofia; Wall, Steven A; Küry, Sébastien; Calpena, Eduardo; Koelling, Nils; McGowan, Simon J; Twigg, Stephen R F; Mathijssen, Irene M J; Nellaker, Christoffer; Brunner, Han G; Wilkie, Andrew O M
2018-06-07
Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.
-
Overlaps of partial Néel states and Bethe states
International Nuclear Information System (INIS)
Foda, O; Zarembo, K
2016-01-01
Partial Néel states are generalizations of the ordinary Néel (classical anti-ferromagnet) state that can have arbitrary integer spin. We study overlaps of these states with Bethe states. We first identify this overlap with a partial version of reflecting-boundary domain-wall partition function, and then derive various determinant representations for off-shell and on-shell Bethe states. (paper: quantum statistical physics, condensed matter, integrable systems)
-
Improving Inversions of the Overlap Operator
International Nuclear Information System (INIS)
Krieg, S.; Cundy, N.; Eshof, J. van den; Frommer, A.; Lippert, Th.; Schaefer, K.
2005-01-01
We present relaxation and preconditioning techniques which accelerate the inversion of the overlap operator by a factor of four on small lattices, with larger gains as the lattice size increases. These improvements can be used in both propagator calculations and dynamical simulations
-
Low Self-Control and the Victim-Offender Overlap: A Gendered Analysis.
Flexon, Jamie L; Meldrum, Ryan C; Piquero, Alex R
2016-07-01
The overlap between victimization and offending is well documented. Yet, there have been fewer investigations of the reasons underlying this relationship. One possible, but understudied, explanation lies with Gottfredson and Hirschi's arguments regarding self-control. The current study adds to this line of inquiry by assessing whether low self-control accounts for the victim-offender overlap in a sample of young adults and whether self-control accounts for the observed overlap similarly across gender. Results from a series of bivariate probit regression models indicate that low self-control is positively related to both victimization and offending. However, only among males does low self-control account for a substantive portion of the victim-offender overlap. Limitations of the study and implications and directions for future research are discussed. © The Author(s) 2015.
-
Non Linear Analyses for the Evaluation of Seismic Behavior of Mixed R.C.-Masonry Structures
International Nuclear Information System (INIS)
Liberatore, Laura; Tocci, Cesare; Masiani, Renato
2008-01-01
In this work the seismic behavior of masonry buildings with mixed structural system, consisting of perimeter masonry walls and internal r.c. frames, is studied by means of non linear static (pushover) analyses. Several aspects, like the distribution of seismic action between masonry and r.c. elements, the local and global behavior of the structure, the crisis of the connections and the attainment of the ultimate strength of the whole structure are examined. The influence of some parameters, such as the masonry compressive and tensile strength, on the structural behavior is investigated. The numerical analyses are also repeated on a building in which the r.c. internal frames are replaced with masonry walls
-
Phenotypic plasticity, costs of phenotypes, and costs of plasticity
DEFF Research Database (Denmark)
Callahan, Hilary S; Maughan, Heather; Steiner, Uli
2008-01-01
Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns...... of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both...... types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic...
-
Monin, Marie-Lorraine; Mignot, Cyril; De Lonlay, Pascale; Héron, Bénédicte; Masurel, Alice; Mathieu-Dramard, Michèle; Lenaerts, Catherine; Thauvin, Christel; Gérard, Marion; Roze, Emmanuel; Jacquette, Aurélia; Charles, Perrine; de Baracé, Claire; Drouin-Garraud, Valérie; Khau Van Kien, Philippe; Cormier-Daire, Valérie; Mayer, Michèle; Ogier, Hélène; Brice, Alexis; Seta, Nathalie; Héron, Delphine
2014-12-11
PMM2-CDG (formerly known as CDG Ia) a deficiency in phosphomannomutase, is the most frequent congenital disorder of glycosylation. The phenotype encompasses a wide range of neurological and non-neurological manifestations comprising cerebellar atrophy and intellectual deficiency. The phenotype of the disorder is well characterized in children but the long term course of the disease is unknown and the phenotype of late onset forms has not been comprehensively described. We thus retrospectively collected the clinical, biological and radiological data of 29 French PMM2-CDG patients aged 15 years or more with a proven molecular diagnosis (16 females and 13 males). In addition, thirteen of these patients were reexamined at the time of the study to obtain detailed information. 27 of the 29 patients had a typical PMM2-CDG phenotype, with infantile hypotonia, strabismus, developmental delay followed by intellectual deficiency, epilepsy, retinitis pigmentosa and/or visceral manifestations. The main health problems for these patients as teenagers and in adulthood were primary ovarian insufficiency, growth retardation, coagulation anomalies and thrombotic events, skeletal deformities and osteopenia/osteoporosis, retinitis pigmentosa, as well as peripheral neuropathy. Three patients had never walked and three lost their ability to walk. The two remaining patients had a late-onset phenotype unreported to date. All patients (n = 29) had stable cerebellar atrophy. Our findings are in line with those of previous adult PMM2-CDG cohorts and points to the need for a multidisciplinary approach to the follow up of PMM2-CDG patients to prevent late complications. Additionally, our findings add weight to the view that PMM2-CDG may be diagnosed in teenage/adult patients with cerebellar atrophy, even in the absence of intellectual deficiency or non-neurological involvement.
-
Population genomic analyses based on 1 million SNPs in commercial egg layers.
Directory of Open Access Journals (Sweden)
Mahmood Gholami
Full Text Available Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise FST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for FST calculation. Averages of FST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were NCOA1, SREBF2 and RALGAPA1 associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 and IGFBP2. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection.
-
Brown, Thackery I.; Hasselmo, Michael E.; Stern, Chantal E.
2015-01-01
When navigating our world we often first plan or retrieve an ideal route to our goal, avoiding alternative paths that lead to other destinations. The medial temporal lobe (MTL) has been implicated in processing contextual information, sequence memory, and uniquely retrieving routes that overlap or “cross paths.” However, the identity of subregions of the hippocampus and neighboring cortex that support these functions in humans remains unclear. The present study used high-resolution functional magnetic resonance imaging (hr-fMRI) in humans to test whether the CA3/DG hippocampal subfield and para-hippocampal cortex are important for processing spatial context and route retrieval, and whether the CA1 subfield facilitates prospective planning of mazes that must be distinguished from alternative overlapping routes. During hr-fMRI scanning, participants navigated virtual mazes that were well-learned from prior training while also learning new mazes. Some routes learned during scanning shared hallways with those learned during pre-scan training, requiring participants to select between alternative paths. Critically, each maze began with a distinct spatial contextual Cue period. Our analysis targeted activity from the Cue period, during which participants identified the current navigational episode, facilitating retrieval of upcoming route components and distinguishing mazes that overlap. Results demonstrated that multiple MTL regions were predominantly active for the contextual Cue period of the task, with specific regions of CA3/DG, parahippocampal cortex, and perirhinal cortex being consistently recruited across trials for Cue periods of both novel and familiar mazes. During early trials of the task, both CA3/DG and CA1 were more active for overlapping than non-overlapping Cue periods. Trial-by-trial Cue period responses in CA1 tracked subsequent overlapping maze performance across runs. Together, our findings provide novel insight into the contributions of MTL
-
Stinchcombe, John R; Kirkpatrick, Mark
2012-11-01
Many central questions in ecology and evolutionary biology require characterizing phenotypes that change with time and environmental conditions. Such traits are inherently functions, and new 'function-valued' methods use the order, spacing, and functional nature of the data typically ignored by traditional univariate and multivariate analyses. These rapidly developing methods account for the continuous change in traits of interest in response to other variables, and are superior to traditional summary-based analyses for growth trajectories, morphological shapes, and environmentally sensitive phenotypes. Here, we explain how function-valued methods make flexible use of data and lead to new biological insights. These approaches frequently offer enhanced statistical power, a natural basis of interpretation, and are applicable to many existing data sets. We also illustrate applications of function-valued methods to address ecological, evolutionary, and behavioral hypotheses, and highlight future directions. Copyright © 2012 Elsevier Ltd. All rights reserved.
-
Speech overlap detection in a two-pass speaker diarization system
Huijbregts, M.A.H.; Leeuwen, D.A. van; Jong, F. M. G de
2009-01-01
In this paper we present the two-pass speaker diarization system that we developed for the NIST RT09s evaluation. In the first pass of our system a model for speech overlap detection is gen- erated automatically. This model is used in two ways to reduce the diarization errors due to overlapping
-
Speech overlap detection in a two-pass speaker diarization system
Huijbregts, M.; Leeuwen, D.A. van; Jong, F.M.G. de
2009-01-01
In this paper we present the two-pass speaker diarization system that we developed for the NIST RT09s evaluation. In the first pass of our system a model for speech overlap detection is generated automatically. This model is used in two ways to reduce the diarization errors due to overlapping
-
Comparisons of Satellite-Deduced Overlapping Cloud Properties and CALIPSO CloudSat Data
Chang, Fu-Lung; Minnis, Patrick; Lin, Bing; Sun-Mack, Sunny
2010-01-01
Introduction to the overlapped cloud properties derived from polar-orbiting (MODIS) and geostationary (GOES-12, -13, Meteosat-8, -9, etc.) meteorological satellites, which are produced at the NASA Langley Research Center (LaRC) cloud research & development team (NASA lead scientist: Dr. Patrick Minnis). Comparison of the LaRC CERES MODIS Edition-3 overlapped cloud properties to the CALIPSO and the CloudSat active sensing data. High clouds and overlapped clouds occur frequently as deduced by CALIPSO (44 & 25%), CloudSat (25 & 4%), and MODIS (37 & 6%). Large fractions of optically-thin cirrus and overlapped clouds are deduced from CALIPSO, but much smaller fractions are from CloudSat and MODIS. For overlapped clouds, the averaged upper-layer CTHs are about 12.8 (CALIPSO), 10.9 (CloudSat) and 10 km (MODIS), and the averaged lower-layer CTHs are about 3.6 (CALIPSO), 3.2 (CloudSat) and 3.9 km (MODIS). Based on comparisons of upper and lower-layer cloud properties as deduced from the MODIS, CALIPSO and CloudSat data, more enhanced passive satellite methods for retrieving thin cirrus and overlapped cloud properties are needed and are under development.
-
METALLOPROTEINS DURING DEVELOPMENT OF WALKER-256 CARCINOSARCOMA RESISTANT PHENOTYPE.
Chekhun, V F; Lozovska, Yu V; Burlaka, A P; Ganusevich, I I; Shvets, Yu V; Lukianova, N Yu; Todor, I M; Demash, D V; Pavlova, A A; Naleskina, L A
2015-01-01
The study was focused on the detection of changes in serum and tumor metal-containing proteins in animals during development ofdoxorubicin-resistant phenotype in malignant cells after 12 courses of chemotherapy. We found that on every stage of resistance development there was a significant increase in content of ferritin and transferrin proteins (which take part in iron traffick and storage) in Walker-256 carc'inosarcoma tissue. We observed decreased serumferritin levels at the beginning stage of the resistance development and significant elevation of this protein levels in the cases withfully developed resistance phenotype. Transferrin content showed changes opposite to that offerritin. During the development of resistance phenotype the tumor tissue also exhibited increased 'free iron' concentration that putatively correlate with elevation of ROS generation and levels of MMP-2 and MMP-9 active forms. The tumor non-protein thiol content increases gradually as well. The serum of animals with early stages of resistance phenotype development showed high ceruloplasmin activity and its significant reduction after loss of tumor sensitivity to doxorubicin. Therefore, the development of resistance phenotype in Walker-256 carcinosarcoma is accompanied by both the deregulation of metal-containing proteins in serum and tumor tissue and by the changes in activity of antioxidant defense system. Thus, the results of this study allow us to determine the spectrum of metal-containing proteins that are involved in the development of resistant tumor phenotype and that may be targeted for methods for doxorubicin sensitivity correction therapy.
-
Directory of Open Access Journals (Sweden)
Conceição Bettencourt
2017-11-01
Full Text Available Abstract Background Autosomal recessive hereditary spastic paraplegia (HSP due to AP4M1 mutations is a very rare neurodevelopmental disorder reported for only a few patients. Methods We investigated a Greek HSP family using whole exome sequencing (WES. Results A novel AP4M1A frameshift insertion, and a very rare missense variant were identified in all three affected siblings in the compound heterozygous state (p.V174fs and p.C319R; the unaffected parents were carriers of only one variant. Patients were affected with a combination of: (a febrile seizures with onset in the first year of life (followed by epileptic non-febrile seizures; (b distinctive facial appearance (e.g., coarse features, bulbous nose and hypomimia; (c developmental delay and intellectual disability; (d early-onset spastic weakness of the lower limbs; and (e cerebellar hypoplasia/atrophy on brain MRI. Conclusions We review genotype-phenotype correlations and discuss clinical overlaps between different AP4-related diseases. The AP4M1 belongs to a complex that mediates vesicle trafficking of glutamate receptors, being likely involved in brain development and neurotransmission.
-
Spatial overlap links seemingly unconnected genotype-matched TB cases in rural Uganda
Kato-Maeda, Midori; Emperador, Devy M.; Wandera, Bonnie; Mugagga, Olive; Crandall, John; Janes, Michael; Marquez, Carina; Kamya, Moses R.; Charlebois, Edwin D.; Havlir, Diane V.
2018-01-01
Introduction Incomplete understanding of TB transmission dynamics in high HIV prevalence settings remains an obstacle for prevention. Understanding where transmission occurs could provide a platform for case finding and interrupting transmission. Methods From 2012–2015, we sought to recruit all adults starting TB treatment in a Ugandan community. Participants underwent household (HH) contact investigation, and provided names of social contacts, sites of work, healthcare and socializing, and two sputum samples. Mycobacterium tuberculosis culture-positive specimens underwent 24-loci MIRU-VNTR and spoligotyping. We sought to identify epidemiologic links between genotype-matched cases by analyzing social networks and mapping locations where cases reported spending ≥12 hours over the one-month pre-treatment. Sites of spatial overlap (≤100m) between genotype-matched cases were considered potential transmission sites. We analyzed social networks stratified by genotype clustering status, with cases linked by shared locations, and compared network density by location type between clustered vs. non-clustered cases. Results Of 173 adults with TB, 131 (76%) were enrolled, 108 provided sputum, and 84/131 (78%) were MTB culture-positive: 52% (66/131) tested HIV-positive. Of 118 adult HH contacts, 105 (89%) were screened and 3 (2.5%) diagnosed with active TB. Overall, 33 TB cases (39%) belonged to 15 distinct MTB genotype-matched clusters. Within each cluster, no cases shared a HH or reported shared non-HH contacts. In 6/15 (40%) clusters, potential epidemiologic links were identified by spatial overlap at specific locations: 5/6 involved health care settings. Genotype-clustered TB social networks had significantly greater network density based on shared clinics (p<0.001) and decreased density based on shared marketplaces (p<0.001), compared to non-clustered networks. Conclusions In this molecular epidemiologic study, links between MTB genotype-matched cases were only
-
Shahrami, Seyedeh Hajar; Abbasi Ranjbar, Zahra; Milani, Forozan; Kezem-Nejad, Ehsan; Hassanzadeh Rad, Afagh; Dalil Heirat, Seyedeh Fatemeh
2016-02-01
Critical issue regarding to variation of findings based on different phenotypes led investigators to define whether they are distinct features or overlapping ones. Therefore, we aimed to investigate the association between diverse phenotypes of PCOS (Poly Cystic Ovary Syndrome) with clinical manifestations, anthropometric indices, and metabolic characteristics. This was a descriptive cross-sectional study conducted in 15-39 years old women with PCOS referred to infertility clinics in the north part of Iran, Rasht during 2010-2011. Data were gathered through an interview by a form consisted of demographic characteristics, laboratory findings, ovarian volume and anthropometric indices. A total of 214 patients consisted of 161 PCOS (cases) and 53 normal women (controls) participated in this study. The most prevalent phenotype in PCOS population was IM/PCO/HA (54%), followed by IM/HA (28%) and IM/PCO (13%). PCO/HA was present only in 6 PCOS patients (5%). PCOS patients were significantly younger than controls (P=0.07). Results showed that increased ovarian volume were higher in PCOS group in comparison with controls and IM/PCO/HA, and IM/PCO had respectively the largest ovarian volumes. Also, a significant relation was observed based on Cholesterol, 17OHP, LH, TG, 2hpp, and LH/FSH between patients with PCOS and control groups. There were significant differences in demographic, anthropometric, hormonal and ultrasound findings between PCOS and controls. Therefore, it seems that classification of the characteristics of each phenotype could offer an appropriate guide for screening risks of PCOS and may facilitate performing most favorable treatment for these complications.
-
Genotypic and phenotypic diversity of Alicyclobacillus acidocaldarius isolates.
Félix-Valenzuela, L; Guardiola-Avila, I; Burgara-Estrella, A; Ibarra-Zavala, M; Mata-Haro, V
2015-10-01
The fruit juice industry recognizes Alicyclobacillus as a major quality control target micro-organism. In this study, we analysed 19 bacterial isolates to identify Alicyclobacillus species by polymerase chain reaction (PCR) and sequencing analyses. Phenotypic and genomic diversity among isolates were investigated by API 50CHB system and ERIC-PCR (enterobacterial repetitive intergenic consensus-PCR) respectively. All bacterial isolates were identified as Alicyclobacillus acidocaldarius, and almost all showed identical DNA sequences according to their 16S rRNA (rDNA) gene partial sequences. Only few carbohydrates were fermented by A. acidocaldarius isolates, and there was little variability in the biochemical profile. Genotypic fingerprinting of the A. acidocaldarius isolates showed high diversity, and clusters by ERIC-PCR were distinct to those obtained from the 16S rRNA gene phylogenetic tree. There was no correlation between phenotypic and genotypic variability in the A. acidocaldarius isolates analysed in this study. Detection of Alicyclobacillus strains is imperative in fruit concentrates and juices due to the production of guaiacol. Identification of the genera originates rejection of the product by processing industry. However, not all the Alicyclobacillus species are deteriorative and hence the importance to differentiate among them. In this study, partial 16S ribosomal RNA sequence alignment allowed the differentiation of species. In addition, ERIC-PCR was introduced for the genotypic characterization of Alicyclobacillus, as an alternative for differentiation among isolates from the same species. © 2015 The Society for Applied Microbiology.
-
Kamal, Muna; Tamana, Sukhpreet K; Smithson, Lisa; Ding, Linda; Lau, Amanda; Chikuma, Joyce; Mariasine, Jennifer; Lefebvre, Diana L; Subbarao, Padmaja; Becker, Allan B; Turvey, Stuart E; Sears, Malcolm R; Pei, Jacqueline; Mandhane, Piush J
2018-05-03
Childhood sleep-disordered breathing (SDB) symptoms may comprise multiple phenotypes depending on craniofacial anatomy, tonsil and adenoid growth, body habitus, and rhinitis symptoms. The primary objective of this study is to identify and characterize the different SDB phenotypes to two years of age. Data from 770 infants in the Edmonton sub-cohort of the Canadian Healthy Infant Longitudinal Study (CHILD) were analyzed to identify SDB phenotypes based on age of onset and duration of symptoms. Parents completed the 22-item sleep-related breathing disorder (SRBD) scale. Children with a SRBD ratio greater than 0.33 were considered positive for SDB at each quarterly assessment between three months and two years. The STATA Proc trajectory extension identified SDB phenotypes based on their age of onset and duration of symptoms and attributed the percentage chance of a participant being assigned to each phenotype. Multivariate linear regression identified factors associated with increased risk of being assigned to each SDB phenotype. Trajectory analysis identified four phenotypes: no SDB (65.7%), early-onset SDB (15.7%) with peak symptoms at nine months, late-onset SDB (14.2%) with peak symptoms at 18 months, and persistent SDB (5.3%) with symptoms from 3 to 24 months. Rhinitis was associated with all three SDB symptom trajectories (p sleep apnea syndrome (OSAS) was associated with persistent (p = 0.01) and late SDB (p < 0.001). Atopy (positive skin prick test at one year) was associated with persistent SDB (p = 0.04). Infants born prior to 36.5 weeks gestational age were more likely to present with late SDB (p = 0.03). Childhood SDB symptoms, rather than being a homogenous disorder, may comprise multiple overlapping phenotypes each with unique risk factors. Copyright © 2018 Elsevier B.V. All rights reserved.
-
Kasper, Marta L; Reeson, Andrew F; Cooper, Steven J B; Perry, Kym D; Austin, Andrew D
2004-07-01
Abstract In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.
-
Phenotypic variability in Meesmann's dystrophy
DEFF Research Database (Denmark)
Ehlers, Niels; Hjortdal, Jesper; Nielsen, Kim
2008-01-01
symptoms often include blurred vision and ocular irritation. Typical cases may be entirely free of complaints. Intermittent pain episodes, such as occur in recurrent erosion syndrome, are not the rule. Genetic sequencing indicated a familial relationship with the originally described Meesmann family......'s dystrophy occurs worldwide. The largest family described is the original German one, now supplemented with a Danish branch. Despite the presence of an identical genetic defect, the clinical phenotype varies. This suggests that non-KRT12-related mechanisms are responsible for the variation....
-
International Nuclear Information System (INIS)
Morrow, A; Rangaraj, D; Perez-Andujar, A; Krishnamurthy, N
2016-01-01
Purpose: This work’s objective is to determine the overlap of processes, in terms of sub-processes and time, between acceptance testing and commissioning of a conventional medical linear accelerator and to evaluate the time saved by consolidating the two processes. Method: A process map for acceptance testing for medical linear accelerators was created from vendor documentation (Varian and Elekta). Using AAPM TG-106 and inhouse commissioning procedures, a process map was created for commissioning of said accelerators. The time to complete each sub-process in each process map was evaluated. Redundancies in the processes were found and the time spent on each were calculated. Results: Mechanical testing significantly overlaps between the two processes - redundant work here amounts to 9.5 hours. Many beam non-scanning dosimetry tests overlap resulting in another 6 hours of overlap. Beam scanning overlaps somewhat - acceptance tests include evaluating PDDs and multiple profiles but for only one field size while commissioning beam scanning includes multiple field sizes and depths of profiles. This overlap results in another 6 hours of rework. Absolute dosimetry, field outputs, and end to end tests are not done at all in acceptance testing. Finally, all imaging tests done in acceptance are repeated in commissioning, resulting in about 8 hours of rework. The total time overlap between the two processes is about 30 hours. Conclusion: The process mapping done in this study shows that there are no tests done in acceptance testing that are not also recommended to do for commissioning. This results in about 30 hours of redundant work when preparing a conventional linear accelerator for clinical use. Considering these findings in the context of the 5000 linacs in the United states, consolidating acceptance testing and commissioning would have allowed for the treatment of an additional 25000 patients using no additional resources.
-
Energy Technology Data Exchange (ETDEWEB)
Morrow, A [Scott & White Hospital Temple, TX (United States); Rangaraj, D [Baylor Scott & White Health, Temple, TX (United States); Perez-Andujar, A [University of California San Francisco, San Francisco, CA (United States); Krishnamurthy, N [Baylor Scott & White Healthcare, Temple, TX (United States)
2016-06-15
Purpose: This work’s objective is to determine the overlap of processes, in terms of sub-processes and time, between acceptance testing and commissioning of a conventional medical linear accelerator and to evaluate the time saved by consolidating the two processes. Method: A process map for acceptance testing for medical linear accelerators was created from vendor documentation (Varian and Elekta). Using AAPM TG-106 and inhouse commissioning procedures, a process map was created for commissioning of said accelerators. The time to complete each sub-process in each process map was evaluated. Redundancies in the processes were found and the time spent on each were calculated. Results: Mechanical testing significantly overlaps between the two processes - redundant work here amounts to 9.5 hours. Many beam non-scanning dosimetry tests overlap resulting in another 6 hours of overlap. Beam scanning overlaps somewhat - acceptance tests include evaluating PDDs and multiple profiles but for only one field size while commissioning beam scanning includes multiple field sizes and depths of profiles. This overlap results in another 6 hours of rework. Absolute dosimetry, field outputs, and end to end tests are not done at all in acceptance testing. Finally, all imaging tests done in acceptance are repeated in commissioning, resulting in about 8 hours of rework. The total time overlap between the two processes is about 30 hours. Conclusion: The process mapping done in this study shows that there are no tests done in acceptance testing that are not also recommended to do for commissioning. This results in about 30 hours of redundant work when preparing a conventional linear accelerator for clinical use. Considering these findings in the context of the 5000 linacs in the United states, consolidating acceptance testing and commissioning would have allowed for the treatment of an additional 25000 patients using no additional resources.
-
Tsay, Ming-Yueh; Wu, Tai-Luan; Tseng, Ling-Li
2017-01-01
This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic), two aggregate institutional repositories (OAIster and OpenDOAR), and two physics-related open sources (arXiv.org and Astrophysics Data System). The 2001-2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations. Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems. The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system.
-
Cell and small animal models for phenotypic drug discovery
Directory of Open Access Journals (Sweden)
Szabo M
2017-06-01
Full Text Available Mihaly Szabo,1 Sara Svensson Akusjärvi,1 Ankur Saxena,1 Jianping Liu,2 Gayathri Chandrasekar,1 Satish S Kitambi1 1Department of Microbiology Tumor, and Cell Biology, 2Department of Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden Abstract: The phenotype-based drug discovery (PDD approach is re-emerging as an alternative platform for drug discovery. This review provides an overview of the various model systems and technical advances in imaging and image analyses that strengthen the PDD platform. In PDD screens, compounds of therapeutic value are identified based on the phenotypic perturbations produced irrespective of target(s or mechanism of action. In this article, examples of phenotypic changes that can be detected and quantified with relative ease in a cell-based setup are discussed. In addition, a higher order of PDD screening setup using small animal models is also explored. As PDD screens integrate physiology and multiple signaling mechanisms during the screening process, the identified hits have higher biomedical applicability. Taken together, this review highlights the advantages gained by adopting a PDD approach in drug discovery. Such a PDD platform can complement target-based systems that are currently in practice to accelerate drug discovery. Keywords: phenotype, screening, PDD, discovery, zebrafish, drug
-
International Nuclear Information System (INIS)
Milani, Gabriele; Valente, Marco
2015-01-01
This study presents some FE results regarding the behavior under horizontal loads of eight existing masonry towers located in the North-East of Italy. The towers, albeit unique for geometric and architectural features, show some affinities which justify a comparative analysis, as for instance the location and the similar masonry material. Their structural behavior under horizontal loads is therefore influenced by geometrical issues, such as slenderness, walls thickness, perforations, irregularities, presence of internal vaults, etc., all features which may be responsible for a peculiar output. The geometry of the towers is deduced from both existing available documentation and in-situ surveys. On the basis of such geometrical data, a detailed 3D realistic mesh is conceived, with a point by point characterization of each single geometric element. The FE models are analysed under seismic loads acting along geometric axes of the plan section, both under non-linear static (pushover) and non-linear dynamic excitation assumptions. A damage-plasticity material model exhibiting softening in both tension and compression, already available in the commercial code Abaqus, is used for masonry. Pushover analyses are performed with both G1 and G2 horizontal loads distribution, according to Italian code requirements, along X+/− and Y+/− directions. Non-linear dynamic analyses are performed along both X and Y directions with a real accelerogram scaled to different peak ground accelerations. Some few results are presented in this paper. It is found that the results obtained with pushover analyses reasonably well fit expensive non-linear dynamic simulations, with a slightly less conservative trend
-
Energy Technology Data Exchange (ETDEWEB)
Milani, Gabriele, E-mail: milani@stru.polimi.it, E-mail: gabriele.milani@polimi.it; Valente, Marco [Department of Architecture, Built Environment and Construction Engineering (ABC), Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan (Italy)
2015-12-31
This study presents some FE results regarding the behavior under horizontal loads of eight existing masonry towers located in the North-East of Italy. The towers, albeit unique for geometric and architectural features, show some affinities which justify a comparative analysis, as for instance the location and the similar masonry material. Their structural behavior under horizontal loads is therefore influenced by geometrical issues, such as slenderness, walls thickness, perforations, irregularities, presence of internal vaults, etc., all features which may be responsible for a peculiar output. The geometry of the towers is deduced from both existing available documentation and in-situ surveys. On the basis of such geometrical data, a detailed 3D realistic mesh is conceived, with a point by point characterization of each single geometric element. The FE models are analysed under seismic loads acting along geometric axes of the plan section, both under non-linear static (pushover) and non-linear dynamic excitation assumptions. A damage-plasticity material model exhibiting softening in both tension and compression, already available in the commercial code Abaqus, is used for masonry. Pushover analyses are performed with both G1 and G2 horizontal loads distribution, according to Italian code requirements, along X+/− and Y+/− directions. Non-linear dynamic analyses are performed along both X and Y directions with a real accelerogram scaled to different peak ground accelerations. Some few results are presented in this paper. It is found that the results obtained with pushover analyses reasonably well fit expensive non-linear dynamic simulations, with a slightly less conservative trend.
-
The Phenotype/Genotype Correlation of Lactase Persistence among Omani Adults
Directory of Open Access Journals (Sweden)
Abdulrahim Al-Abri
2013-09-01
Full Text Available Objective: To examine the correlation of lactase persistence phenotype with genotype in Omani adults.Methods: Lactase persistence phenotype was tested by hydrogen breath test in 52 Omani Adults using the Micro H2 analyzer. Results were checked against genotyping using direct DNA sequencing.Results: Forty one individuals with C/C-13910 and T/T-13915 genotypes had positive breath tests (≥20 ppm; while eight of nine individuals with T/C-13910 or T/G-13915 genotypes had negative breath tests (<20 ppm and two subjects were non-hydrogen producers. The agreement between phenotype and genotype using Kappa value was very good (0.93.Conclusion: Genotyping both T/C-13910 and T/G-13915 alleles can be used to assist diagnosis and predict lactose intolerance in the Omani population.
-
Li, Feng; Yao, Li; Wu, Hong; Cao, Shihong
2016-09-01
To discuss the manifestations of endocrine and metabolism for polycystic ovary syndrome patients with different phenotype. This study selected 226 cases of Rotterdam Standard diagnosed polycystic ovary syndrome patients in People's Hospital of Zhengzhou from October 2013 to February 2015. The control group was the 100 cases of non hyperandrogen menstrual women as the control group. Polycystic ovary syndrome included 4 phenotype: /or anovulatio (O) combined with hyperandrogenism (H) and polycystic ovary morphology (P), phenotype of O and P, phenotype of H and P, and phenotype of O and P. All patients were detected for the clinical endocrine and metabolism related parameters. The phenotype of O and P occupied 55.8%, it had significant difference on the comparison between control group and the luteinizing hormone (LH) and luteinizing hormone/follicle stimulating hormone (LH/FSH) of phenotype of O, H and P, phenotype of O and H and phenotype of O and P; the testosterone (T) of phenotype of O,H and P and phenotype of O and H was apparently higher than phenotype of O and P and control group; The total cholesterol (TC) and triglyceride (TG) in phenotype of O, H and P was greatly higher than phenotype of O and P and control group. The phenotype of O and P was the most common phenotype in PCOS patients. It was same for the clinical endocrine and metabolism of two classic characteristics in PCOS. Compared to other PCOS phenotype, the metabolism in phenotype of O and P was lower. The phenotype classification of PCOS patients could better guide clinical individualized treatment in patients with PCOS.
-
Vulval lichen planus-lichen sclerosus overlap.
Howard, Matthew; Hall, Anthony
2018-01-01
Vulval lichen planus-lichen sclerosus overlap is an emerging observation. Few clinical reports exist with no reviews of literature. We present a focused update of this phenomenon and discuss a clinical case. We report a 63-year-old woman with a 20-year history of ulcerative vulvo-vaginitis, initially diagnosed as benign mucous membrane (cicatricial) pemphigoid. This led to prolonged treatment with oral corticosteroids with minimal improvement in symptoms. Subsequent complications of long-term use of systemic corticosteroid ensued. A clinico-pathological diagnosis of severe erosive lichen planus was made on clinical findings and on non-specific biopsy changes of ulceration and inflammation. Treatment with topical clobetasol propionate 0.05% ointment twice daily led to dramatic improvement of ulceration, easing of discomfort and marked improvement in quality of life. Clinical examination revealed Wickham's striae on the labia majora supporting the diagnosis. Six years after commencement of topical clobetasol, white plaques were noticed on the labia majora, perineum and peri-anal region consistent with lichen sclerosus, confirmed by repeat vulval skin biopsy and on vulvectomy. This case highlights the challenge of diagnosis of extensive vulvo-vaginal ulceration and the necessity to re-examine a previous diagnosis if there is poor response to treatment.
-
Generalized morphea/eosinophilic fasciitis overlap after epoxy exposure
Directory of Open Access Journals (Sweden)
Warren H. Chan, MS
2018-03-01
Full Text Available Generalized morphea is associated with epoxy resin vapors and is characterized by the development of lesions shortly after exposure. Morphea presenting along with eosinophilic fasciitis (EF, or morphea/EF overlap, is rare and an indicator of poor prognosis and resistance to treatment. Here we present a case of generalized morphea/EF overlap linked to epoxy exposure. Our patient received multiple therapies—ultraviolet A1 phototherapy, prednisone, methotrexate, azathioprine, mycophenolate mofetil, cyclophosphamide, cyclosporine, and rituximab—none of which led to a significant response. The refractory nature of this disease warrants vigilance in its association with epoxy exposure.
-
Walkable self-overlapping virtual reality maze and map visualization demo
DEFF Research Database (Denmark)
Serubugo, Sule; Skantarova, Denisa; Evers, Nicolaj
2017-01-01
This paper describes our demonstration of a walkable self-overlapping maze and its corresponding map to facilitate asymmetric collaboration for room-scale virtual reality setups in public places.......This paper describes our demonstration of a walkable self-overlapping maze and its corresponding map to facilitate asymmetric collaboration for room-scale virtual reality setups in public places....
-
[The automatic iris map overlap technology in computer-aided iridiagnosis].
He, Jia-feng; Ye, Hu-nian; Ye, Miao-yuan
2002-11-01
In the paper, iridology and computer-aided iridiagnosis technologies are briefly introduced and the extraction method of the collarette contour is then investigated. The iris map can be overlapped on the original iris image based on collarette contour extraction. The research on collarette contour extraction and iris map overlap is of great importance to computer-aided iridiagnosis technologies.
-
International Nuclear Information System (INIS)
Kaasinen, Valtteri; Kinos, Maija; Joutsa, Juho; Seppaenen, Marko; Noponen, Tommi
2014-01-01
Parkinson's disease (PD) can manifest with a tremor-dominant or a non-tremor (akinetic-rigid) phenotype. Although the tremor-dominant subtype may show a better prognosis, there is limited information on the phenotypic differences regarding the level of striatal dopamine transmission. The present study investigated striatal dopamine transporter (DAT) binding characteristics in a large sample of patients with and without tremor. [ 123 I]FP-CIT SPECT scans of 231 patients with a clinical diagnosis of PD and abnormal FP-CIT binding (157 with tremor, 74 without tremor) and 230 control patients with normal FP-CIT binding (148 with tremor, 82 without tremor) were analysed using an automated region-of-interest analysis of the scans (BRASS). Specific striatal binding ratios were compared between phenotypes and groups using age, sex, and symptom duration, predominant side of symptoms, dopaminergic medications and scanner as covariates. Patients with PD had 28.1 - 65.0 % lower binding in all striatal regions compared to controls (p < 0.001). The mean FP-CIT caudate nucleus uptake and the left caudate nucleus uptake were higher in PD patients with tremor than in PD patients without tremor (mean 9.0 % higher, left 10.5 % higher; p < 0.05), whereas there were no differences between tremor and non-tremor control patients. No significant effects of tremor on DAT binding were observed in the anterior or posterior putamen. The motor phenotype is associated with the extent of caudate dopamine terminal loss in PD, as dopamine function is relatively more preserved in tremor patients. Symptom type is related to caudate dopamine function only in association with Parkinsonian dopaminergic degeneration, not in intact dopamine systems in patients with non-PD tremor. (orig.)
-
An empirical analysis of overlap publication in Chinese language and English research manuscripts.
Directory of Open Access Journals (Sweden)
Joseph D Tucker
Full Text Available BACKGROUND: There are a number of sound justifications for publishing nearly identical information in Chinese and English medical journals, assuming several conditions are met. Although overlap publication is perceived as undesirable and ethically questionable in Europe and North America, it may serve an important function in some regions where English is not the native tongue. There is no empirical data on the nature and degree of overlap publication in English and Chinese language journals. METHODS/PRINCIPAL FINDINGS: A random sample of 100 English manuscripts from Chinese institutions was selected from PubMed. Key words and institutions were searched in the China National Knowledge Infrastructure, a comprehensive Chinese language research database. Unacknowledged overlap was a priori defined according to International Committee of Medical Journal Editor (ICMJE guidelines following examination by two individuals. 19% (95% CI 11-27 of English manuscripts from Chinese institutions were found to have substantial overlap with Chinese published work based on full text examination. None of the manuscripts met all of the criteria established by the ICMJE for an acknowledged overlap publication. Individual-level, journal-level, and institutional factors seem to influence overlap publication. Manuscripts associated with an institution outside of China and with more than one institution were significantly less likely to have substantial overlap (p<0.05. CONCLUSIONS/SIGNIFICANCE: Overlap publication was common in this context, but instances of standard ICMJE notations to acknowledge this practice were rare. This research did not cite the identified overlap manuscripts with the hope that these empirical data will inform journal policy changes and structural initiatives to promote clearer policies and manuscripts.
-
Non-Hodgkin's Lymphoma of the Tongue Presenting as an Ulcerative Lesion
Directory of Open Access Journals (Sweden)
Bijan Khademi
2011-10-01
Full Text Available Malignant lymphoma may occur in the oral cavity and oropharynx, but is most commonly located in Waldeyer's ring, particularly in the palatine and lingual tonsil. The occurrence of malignant lymphoma in the tongue is very rare. Clinical features are nonspecific ulcerative lesions that do not heal. In the literature, the majority of casesare non-Hodgkin’s lymphoma, diffuse large B cell type; however T-cell phenotype also may occur. We describe a 60-year-old man who presented with an ulcerative mass in the left lateral aspect of his tongue, unresponsive to medical therapy. After tissue biopsy, histopathological and immunohistochemical analyses confirmed a diagnosis of non-Hodgkin’s lymphoma, diffuse large B cell type.
-
An Autoimmune Myositis-Overlap Syndrome Associated With Autoantibodies to Nuclear Pore Complexes
Senécal, Jean-Luc; Isabelle, Catherine; Fritzler, Marvin J.; Targoff, Ira N.; Goldstein, Rose; Gagné, Michel; Raynauld, Jean-Pierre; Joyal, France; Troyanov, Yves; Dabauvalle, Marie-Christine
2014-01-01
Abstract Autoimmune myositis encompasses various myositis-overlap syndromes, each being identified by the presence of serum marker autoantibodies. We describe a novel myositis-overlap syndrome in 4 patients characterized by the presence of a unique immunologic marker, autoantibodies to nuclear pore complexes. The clinical phenotype was characterized by prominent myositis in association with erosive, anti-CCP, and rheumatoid factor-positive arthritis, trigeminal neuralgia, mild interstitial lung disease, Raynaud phenomenon, and weight loss. The myositis was typically chronic, relapsing, and refractory to corticosteroids alone, but remitted with the addition of a second immunomodulating drug. There was no clinical or laboratory evidence for liver disease. The prognosis was good with 100% long-term survival (mean follow-up 19.5 yr). By indirect immunofluorescence on HEp-2 cells, sera from all 4 patients displayed a high titer of antinuclear autoantibodies (ANA) with a distinct punctate peripheral (rim) fluorescent pattern of the nuclear envelope characteristic of nuclear pore complexes. Reactivity with nuclear pore complexes was confirmed by immunoelectron microscopy. In a cohort of 100 French Canadian patients with autoimmune myositis, the nuclear pore complex fluorescent ANA pattern was restricted to these 4 patients (4%). It was not observed in sera from 393 adult patients with systemic sclerosis (n = 112), mixed connective tissue disease (n = 35), systemic lupus (n = 94), rheumatoid arthritis (n = 45), or other rheumatic diseases (n = 107), nor was it observed in 62 normal adults. Autoantibodies to nuclear pore complexes were predominantly of IgG isotype. No other IgG autoantibody markers for defined connective tissue diseases or overlap syndromes were present, indicating a selective and highly focused immune response. In 3 patients, anti-nuclear pore complex autoantibody titers varied in parallel with myositis activity, suggesting a pathogenic
-
Continuum-limit scaling of overlap fermions as valence quarks
International Nuclear Information System (INIS)
Cichy, Krzysztof; Herdoiza, Gregorio; Jansen, Karl
2009-10-01
We present the results of a mixed action approach, employing dynamical twisted mass fermions in the sea sector and overlap valence fermions, with the aim of testing the continuum limit scaling behaviour of physical quantities, taking the pion decay constant as an example. To render the computations practical, we impose for this purpose a fixed finite volume with lattice size L∼1.3 fm. We also briefly review the techniques we have used to deal with overlap fermions. (orig.)
-
Solving radiative transfer with line overlaps using Gauss-Seidel algorithms
Daniel, F.; Cernicharo, J.
2008-09-01
Context: The improvement in observational facilities requires refining the modelling of the geometrical structures of astrophysical objects. Nevertheless, for complex problems such as line overlap in molecules showing hyperfine structure, a detailed analysis still requires a large amount of computing time and thus, misinterpretation cannot be dismissed due to an undersampling of the whole space of parameters. Aims: We extend the discussion of the implementation of the Gauss-Seidel algorithm in spherical geometry and include the case of hyperfine line overlap. Methods: We first review the basics of the short characteristics method that is used to solve the radiative transfer equations. Details are given on the determination of the Lambda operator in spherical geometry. The Gauss-Seidel algorithm is then described and, by analogy to the plan-parallel case, we see how to introduce it in spherical geometry. Doing so requires some approximations in order to keep the algorithm competitive. Finally, line overlap effects are included. Results: The convergence speed of the algorithm is compared to the usual Jacobi iterative schemes. The gain in the number of iterations is typically factors of 2 and 4 for the two implementations made of the Gauss-Seidel algorithm. This is obtained despite the introduction of approximations in the algorithm. A comparison of results obtained with and without line overlaps for N2H^+, HCN, and HNC shows that the J=3-2 line intensities are significantly underestimated in models where line overlap is neglected.
-
Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms.
Taillon-Miller, P; Gu, Z; Li, Q; Hillier, L; Kwok, P Y
1998-07-01
An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21-7q22, and 13q12-13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations.
-
Directory of Open Access Journals (Sweden)
V. D. Pasechnikov
2017-01-01
Full Text Available Rationale: The phenomenon of overlap of two disorders, non-erosive gastroesophageal reflux disease (NERD and functional dyspepsia (FD is an important clinical problem, while the symptoms in such patients are more severe and prevalent than in those with non-overlapping NERD or FD. This phenomenon may lead to treatment failure, if therapy does not take into account the specific pathophysiological mechanisms of the NERD and FD overlap.Aim: To study motility of the proximal and distal parts of the stomach in patients with the overlap syndrome of NERD with FD.Materials and methods: The study enrolled 56 patients (34 women and 22 men, aged from 18 to 45 years, who met the diagnostic criteria for NERD and FD (the Rome criteria III, esophageal endoscopy, 24-hour pH measurement or 24-hour impedance pH measurement, and had both NERD and FD symptoms simultaneously (overlap; 46 healthy volunteers. The accommodation of the proximal (fundal part of the stomach and motility of the distal gastric part was assessed by ultrasonography (Aixplorer, SuperSonic Imagine, France, with convex probe 1–6 MHz before and after the intake of the liquid test food. The patients filled in questionnaires to assess the symptoms and their severity (scored from 0 to 3. The difference between their mean ± standard deviation (SD values was assessed by Students t-test and was considered significant at p < 0.05.Results: After intake of the liquid test food, the patients with the FD and NERD overlap syndrome demonstrated an advanced and statistically significant gastric motility abnormality both in its proximal and distal parts, compared to healthy control: accommodation disturbances and its reduction, decreased amplitude (61.4 ± 7.5 vs 90.2 ± 6.9%, p < 0.05, frequency of contractions of the antrum during 3-minute interval (4.3 ± 1.5 vs 9.7 ± 1
-
Measuring the extent of overlaps in protected area designations.
Deguignet, Marine; Arnell, Andy; Juffe-Bignoli, Diego; Shi, Yichuan; Bingham, Heather; MacSharry, Brian; Kingston, Naomi
2017-01-01
Over the past decades, a number of national policies and international conventions have been implemented to promote the expansion of the world's protected area network, leading to a diversification of protected area strategies, types and designations. As a result, many areas are protected by more than one convention, legal instrument, or other effective means which may result in a lack of clarity around the governance and management regimes of particular locations. We assess the degree to which different designations overlap at global, regional and national levels to understand the extent of this phenomenon at different scales. We then compare the distribution and coverage of these multi-designated areas in the terrestrial and marine realms at the global level and among different regions, and we present the percentage of each county's protected area extent that is under more than one designation. Our findings show that almost a quarter of the world's protected area network is protected through more than one designation. In fact, we have documented up to eight overlapping designations. These overlaps in protected area designations occur in every region of the world, both in the terrestrial and marine realms, but are more common in the terrestrial realm and in some regions, notably Europe. In the terrestrial realm, the most common overlap is between one national and one international designation. In the marine realm, the most common overlap is between any two national designations. Multi-designations are therefore a widespread phenomenon but its implications are not well understood. This analysis identifies, for the first time, multi-designated areas across all designation types. This is a key step to understand how these areas are managed and governed to then move towards integrated and collaborative approaches that consider the different management and conservation objectives of each designation.
-
Analyses of Environmental Impacts of Non Hazardous Regional Landfills in Macedonia
Directory of Open Access Journals (Sweden)
Katerina Donevska
2013-12-01
Full Text Available This paper presents an assessment of potential environmental impacts for eight planned non-hazardous regional landfills in Macedonia. Waste quantities for each waste management region and landfill capacities are estimated. Expected leachate quantities are calculated using Water Balance Method. Analyses and comparison of the likely landfill leachate per capita are presented, demonstrating that higher rates of leachate are generated per capita in waste management regions with higher annual sums of rainfall. An assessment of the potential landfill impacts on the water environment taking into consideration local geology and hydrogeology conditions is presented. Some general measures for leachate treatment that are in compliance with the modern EU standards are indicated. The goal of the study is to facilitate a better understanding about the sustainable waste management practices in cases of landfilling of municipal solid waste.
-
Afzali, Mohammad H; Sunderland, Matthew; Teesson, Maree; Carragher, Natacha; Mills, Katherine; Slade, Tim
2017-01-15
The role of symptom overlap between major depressive disorder and posttraumatic stress disorder in comorbidity between two disorders is unclear. The current study applied network analysis to map the structure of symptom associations between these disorders. Data comes from a sample of 909 Australian adults with a lifetime history of trauma and depressive symptoms. Data analysis consisted of the construction of two comorbidity networks of PTSD/MDD with and without overlapping symptoms, identification of the bridging symptoms, and computation of the centrality measures. The prominent bridging role of four overlapping symptoms (i.e., sleep problems, irritability, concentration problems, and loss of interest) and five non-overlapping symptoms (i.e., feeling sad, feelings of guilt, psychomotor retardation, foreshortened future, and experiencing flashbacks) is highlighted. The current study uses DSM-IV criteria for PTSD and does not take into consideration significant changes made to PTSD criteria in DSM-5. Moreover, due to cross-sectional nature of the data, network estimates do not provide information on whether a symptom actively triggers other symptoms or whether a symptom mostly is triggered by other symptoms. The results support the role of dysphoria-related symptoms in PTSD/MDD comorbidity. Moreover, Identification of central symptoms and bridge symptoms will provide useful targets for interventions that seek to intervene early in the development of comorbidity. Copyright © 2016 Elsevier B.V. All rights reserved.
-
Mukhopadhyay, Partha; Farrell, Tracy; Sharma, Gayatri; McGuire, Timothy R; O'Kane, Barbara; Sharp, J Graham
2013-01-01
Breast cancer grows, metastasizes and relapses from rare, therapy resistant cells with a stem cell phenotype (cancer stem cells/CSCs). However, there is a lack of studies comparing the functions of CSCs isolated using different phenotypes in order to determine if CSCs are homogeneous or heterogeneous. Cells with various stem cell phenotypes were isolated by sorting from Clone 66 murine breast cancer cells that grow orthotopically in immune intact syngeneic mice. These populations were compared by in vitro functional assays for proliferation, growth, sphere and colony formation; and in vivo limiting dilution analysis of tumorigenesis. The proportion of cells expressing CD44(high)CD24(low/neg), side population (SP) cells, ALDH1(+), CD49f(high), CD133(high), and CD34(high) differed, suggesting heterogeneity. Differences in frequency and size of tumor spheres from these populations were observed. Higher rates of proliferation of non-SP, ALDH1(+), CD34(low), and CD49f(high) suggested properties of transit amplifying cells. Colony formation was higher from ALDH1(-) and non-SP cells than ALDH1(+) and SP cells suggesting a progenitor phenotype. The frequency of clonal colonies that grew in agar varied and was differentially altered by the presence of Matrigel™. In vivo, fewer cells with a stem cell phenotype were needed for tumor formation than "non-stem" cells. Fewer SP cells were needed to form tumors than ALDH1(+) cells suggesting further heterogeneities of cells with stem phenotypes. Different levels of cytokines/chemokines were produced by Clone 66 with RANTES being the highest. Whether the heterogeneity reflects soluble factor production remains to be determined. These data demonstrate that Clone 66 murine breast cancer cells that express stem cell phenotypes are heterogeneous and exhibit different functional properties, and this may also be the case for human breast cancer stem cells.
-
A review of multivariate analyses in imaging genetics
Directory of Open Access Journals (Sweden)
Jingyu eLiu
2014-03-01
Full Text Available Recent advances in neuroimaging technology and molecular genetics provide the unique opportunity to investigate genetic influence on the variation of brain attributes. Since the year 2000, when the initial publication on brain imaging and genetics was released, imaging genetics has been a rapidly growing research approach with increasing publications every year. Several reviews have been offered to the research community focusing on various study designs. In addition to study design, analytic tools and their proper implementation are also critical to the success of a study. In this review, we survey recent publications using data from neuroimaging and genetics, focusing on methods capturing multivariate effects accommodating the large number of variables from both imaging data and genetic data. We group the analyses of genetic or genomic data into either a prior driven or data driven approach, including gene-set enrichment analysis, multifactor dimensionality reduction, principal component analysis, independent component analysis (ICA, and clustering. For the analyses of imaging data, ICA and extensions of ICA are the most widely used multivariate methods. Given detailed reviews of multivariate analyses of imaging data available elsewhere, we provide a brief summary here that includes a recently proposed method known as independent vector analysis. Finally, we review methods focused on bridging the imaging and genetic data by establishing multivariate and multiple genotype-phenotype associations, including sparse partial least squares, sparse canonical correlation analysis, sparse reduced rank regression and parallel ICA. These methods are designed to extract latent variables from both genetic and imaging data, which become new genotypes and phenotypes, and the links between the new genotype-phenotype pairs are maximized using different cost functions. The relationship between these methods along with their assumptions, advantages, and
-
Tobler, Michael; Dewitt, Thomas J; Schlupp, Ingo; García de León, Francisco J; Herrmann, Roger; Feulner, Philine G D; Tiedemann, Ralph; Plath, Martin
2008-10-01
Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.
-
A Heuristic Parameterization for the Integrated Vertical Overlap of Cumulus and Stratus
Park, Sungsu
2017-10-01
The author developed a heuristic parameterization to handle the contrasting vertical overlap structures of cumulus and stratus in an integrated way. The parameterization assumes that cumulus is maximum-randomly overlapped with adjacent cumulus; stratus is maximum-randomly overlapped with adjacent stratus; and radiation and precipitation areas at each model interface are grouped into four categories, that is, convective, stratiform, mixed, and clear areas. For simplicity, thermodynamic scalars within individual portions of cloud, radiation, and precipitation areas are assumed to be internally homogeneous. The parameterization was implemented into the Seoul National University Atmosphere Model version 0 (SAM0) in an offline mode and tested over the globe. The offline control simulation reasonably reproduces the online surface precipitation flux and longwave cloud radiative forcing (LWCF). Although the cumulus fraction is much smaller than the stratus fraction, cumulus dominantly contributes to precipitation production in the tropics. For radiation, however, stratus is dominant. Compared with the maximum overlap, the random overlap of stratus produces stronger LWCF and, surprisingly, more precipitation flux due to less evaporation of convective precipitation. Compared with the maximum overlap, the random overlap of cumulus simulates stronger LWCF and weaker precipitation flux. Compared with the control simulation with separate cumulus and stratus, the simulation with a single-merged cloud substantially enhances the LWCF in the tropical deep convection and midlatitude storm track regions. The process-splitting treatment of convective and stratiform precipitation with an independent precipitation approximation (IPA) simulates weaker surface precipitation flux than the control simulation in the tropical region.
-
Microbial community analysis of field-grown soybeans with different nodulation phenotypes.
Ikeda, Seishi; Rallos, Lynn Esther E; Okubo, Takashi; Eda, Shima; Inaba, Shoko; Mitsui, Hisayuki; Minamisawa, Kiwamu
2008-09-01
Microorganisms associated with the stems and roots of nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans [Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod(+) soybean roots. Fusarium solani was stably associated with nodulated (Nod(+) and Nod(++)) roots and less abundant in Nod(-) soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod(-), Nod(+), or Nod(++)). The analysis of root samples indicated that the microbial community in Nod(-) soybeans was more similar to that in Nod(++) soybeans than to that in Nod(+) soybeans.