WorldWideScience

Sample records for comparative molecular similarity

  1. Molecular similarity measures.

    Science.gov (United States)

    Maggiora, Gerald M; Shanmugasundaram, Veerabahu

    2011-01-01

    Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

  2. Molecular and Cellular Profiling of Scalp Psoriasis Reveals Differences and Similarities Compared to Skin Psoriasis

    Science.gov (United States)

    Ruano, Juan; Suárez-Fariñas, Mayte; Shemer, Avner; Oliva, Margeaux

    2016-01-01

    Scalp psoriasis shows a variable clinical spectrum and in many cases poses a great therapeutic challenge. However, it remains unknown whether the immune response of scalp psoriasis differs from understood pathomechanisms of psoriasis in other skin areas. We sought to determine the cellular and molecular phenotype of scalp psoriasis by performing a comparative analysis of scalp and skin using lesional and nonlesional samples from 20 Caucasian subjects with untreated moderate to severe psoriasis and significant scalp involvement and 10 control subjects without psoriasis. Our results suggest that even in the scalp, psoriasis is a disease of the inter-follicular skin. The immune mechanisms that mediate scalp psoriasis were found to be similar to those involved in skin psoriasis. However, the magnitude of dysregulation, number of differentially expressed genes, and enrichment of the psoriatic genomic fingerprint were more prominent in skin lesions. Furthermore, the scalp transcriptome showed increased modulation of several gene-sets, particularly those induced by interferon-gamma, compared with that of skin psoriasis, which was mainly associated with activation of TNFα/L-17/IL-22-induced keratinocyte response genes. We also detected differences in expression of gene-sets involving negative regulation, epigenetic regulation, epidermal differentiation, and dendritic cell or Th1/Th17/Th22-related T-cell processes. PMID:26849645

  3. Low molecular weight dextran provides similar optical coherence tomography coronary imaging compared to radiographic contrast media.

    Science.gov (United States)

    Frick, Kyle; Michael, Tesfaldet T; Alomar, Mohammed; Mohammed, Atif; Rangan, Bavana V; Abdullah, Shuaib; Grodin, Jerrold; Hastings, Jeffrey L; Banerjee, Subhash; Brilakis, Emmanouil S

    2014-11-01

    Optical coherence tomography (OCT) coronary imaging requires displacement of red blood cells from the vessel lumen. This is usually accomplished using radiographic contrast. Low molecular weight dextran has low cost and is safe in low volumes. In the present study, we compared dextran with contrast for coronary OCT imaging. Fifty-one vessels in 26 patients were sequentially imaged using manual injection of radiographic contrast (iodixanol) and dextran. OCT images were analyzed at 1 mm intervals to determine the image clarity (defined as a visible lumen border > 270°) and to measure the lumen area and lumen diameter. To correct for the refractive index of dextran, the dextran area measurements were multiplied by 1.117 and the dextran length measurements were multiplied by 1.057. A total of 3,418 cross-sections (1,709 with contrast and 1,709 with dextran) were analyzed. There were no complications related to OCT imaging or to contrast or dextran administration. Clear image segments were observed in 97.0% vs. 96.7% of the cross-sections obtained with contrast and dextran, respectively (P = 0.45). The mean lumen areas were also similar: 6.69 ± 1.95 mm(2) with iodixanol vs. 7.06 ± 2.06 mm(2) with dextran (correlation coefficient 0.984). The image quality and measurements during OCT image acquisition are similar for dextran and contrast. Dextran could be used instead of contrast for OCT imaging, especially in patients in whom contrast load minimization is desired. © 2013 Wiley Periodicals, Inc.

  4. Comparing Harmonic Similarity Measures

    NARCIS (Netherlands)

    de Haas, W.B.; Robine, M.; Hanna, P.; Veltkamp, R.C.; Wiering, F.

    2010-01-01

    We present an overview of the most recent developments in polyphonic music retrieval and an experiment in which we compare two harmonic similarity measures. In contrast to earlier work, in this paper we specifically focus on the symbolic chord description as the primary musical representation and

  5. A Similarity Search Using Molecular Topological Graphs

    Directory of Open Access Journals (Sweden)

    Yoshifumi Fukunishi

    2009-01-01

    Full Text Available A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.

  6. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    Science.gov (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  7. QSAR models based on quantum topological molecular similarity.

    Science.gov (United States)

    Popelier, P L A; Smith, P J

    2006-07-01

    A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

  8. When high similarity copycats lose and moderate similarity copycats gain: The impact of comparative evaluation

    NARCIS (Netherlands)

    Van Horen, F.; Pieters, R.

    2012-01-01

    Copycats imitate features of leading brands to free ride on their equity. The prevailing belief is that the more similar copycats are to the leader brand, the more positive their evaluation is, and thus the more they free ride. Three studies demonstrate when the reverse holds true:

  9. When high similarity copycats lose and moderate similarity copycats gain : The impact of comparative evaluation

    NARCIS (Netherlands)

    van Horen, F.; Pieters, R.

    2012-01-01

    Copycats imitate features of leading brands to free ride on their equity. The prevailing belief is that the more similar copycats are to the leader brand, the more positive their evaluation is, and thus the more they free ride. Three studies demonstrate when the reverse holds true:

  10. Comparative mapping reveals similar linkage of functional genes to ...

    Indian Academy of Sciences (India)

    genes between O. sativa and B. napus may have consistent function and control similar traits, which may be ..... acea chromosomes reveals islands of conserved organization. ... 1998 Conserved structure and function of the Arabidopsis flow-.

  11. Molecular basis sets - a general similarity-based approach for representing chemical spaces.

    Science.gov (United States)

    Raghavendra, Akshay S; Maggiora, Gerald M

    2007-01-01

    A new method, based on generalized Fourier analysis, is described that utilizes the concept of "molecular basis sets" to represent chemical space within an abstract vector space. The basis vectors in this space are abstract molecular vectors. Inner products among the basis vectors are determined using an ansatz that associates molecular similarities between pairs of molecules with their corresponding inner products. Moreover, the fact that similarities between pairs of molecules are, in essentially all cases, nonzero implies that the abstract molecular basis vectors are nonorthogonal, but since the similarity of a molecule with itself is unity, the molecular vectors are normalized to unity. A symmetric orthogonalization procedure, which optimally preserves the character of the original set of molecular basis vectors, is used to construct appropriate orthonormal basis sets. Molecules can then be represented, in general, by sets of orthonormal "molecule-like" basis vectors within a proper Euclidean vector space. However, the dimension of the space can become quite large. Thus, the work presented here assesses the effect of basis set size on a number of properties including the average squared error and average norm of molecular vectors represented in the space-the results clearly show the expected reduction in average squared error and increase in average norm as the basis set size is increased. Several distance-based statistics are also considered. These include the distribution of distances and their differences with respect to basis sets of differing size and several comparative distance measures such as Spearman rank correlation and Kruscal stress. All of the measures show that, even though the dimension can be high, the chemical spaces they represent, nonetheless, behave in a well-controlled and reasonable manner. Other abstract vector spaces analogous to that described here can also be constructed providing that the appropriate inner products can be directly

  12. Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

    Directory of Open Access Journals (Sweden)

    Jenny Farmer

    2017-11-01

    Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

  13. Molecular diversity of Clostridium botulinum and phenotypically similar strains.

    Science.gov (United States)

    Grenda, T; Kukier, E; Sieradzki, Z; Goldsztejn, M; Kwiatek, K

    2016-12-01

    This study was undertaken to examine phenotypic and genetic features of strains preliminary classified as Clostridium botulinum species. The phenotypic characteristics were assessed with different culture media and biochemical tests. The genetic characterization included detection of botulinum toxin genes by PCR and macrorestriction analysis with SmaI, XhoI and SacII by PFGE (Pulsed-field Gel Electrophoresis). Despite similar biochemical properties of all analysed strains, only 47% of them contained genes determining toxicity specific to C. botulinum species. The most valuable differentiation of C. botulinum and C. botulinum-like strains was obtained after SmaI digestion. The highest affinity was observed among C. botulinum type B profiles which was even up to 100%. It was found 100% of affinity between C. botulinum and C. botulinum-like strains, however, the similarity among C. botulinum and C. botulinum-like was generally lower than 80%.

  14. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

    Science.gov (United States)

    Skinnider, Michael A; Dejong, Chris A; Franczak, Brian C; McNicholas, Paul D; Magarvey, Nathan A

    2017-08-16

    Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosynthesis and alignment, and find that when rule-based retrobiosynthesis can be applied, this approach outperforms conventional two-dimensional fingerprints, suggesting it may represent a valuable approach for the targeted exploration of natural product chemical space and microbial genome mining. Our open-source algorithm is an extensible method of enumerating hypothetical natural product structures with diverse potential applications in bioinformatics.

  15. On the measurements of molecular similarity: a connection between quantum chemistry and artificial intelligence

    International Nuclear Information System (INIS)

    Carbo, R.; Calabuig, B.

    1988-01-01

    Molecular similarity measures within the quantum concept of density functions are described and analyzed. It is intended to show how artificial intelligence techniques can be used within the framework of quantum theory, in order to study and classify the molecular structures and their properties. (A.C.A.S) [pt

  16. SpolSimilaritySearch - A web tool to compare and search similarities between spoligotypes of Mycobacterium tuberculosis complex.

    Science.gov (United States)

    Couvin, David; Zozio, Thierry; Rastogi, Nalin

    2017-07-01

    Spoligotyping is one of the most commonly used polymerase chain reaction (PCR)-based methods for identification and study of genetic diversity of Mycobacterium tuberculosis complex (MTBC). Despite its known limitations if used alone, the methodology is particularly useful when used in combination with other methods such as mycobacterial interspersed repetitive units - variable number of tandem DNA repeats (MIRU-VNTRs). At a worldwide scale, spoligotyping has allowed identification of information on 103,856 MTBC isolates (corresponding to 98049 clustered strains plus 5807 unique isolates from 169 countries of patient origin) contained within the SITVIT2 proprietary database of the Institut Pasteur de la Guadeloupe. The SpolSimilaritySearch web-tool described herein (available at: http://www.pasteur-guadeloupe.fr:8081/SpolSimilaritySearch) incorporates a similarity search algorithm allowing users to get a complete overview of similar spoligotype patterns (with information on presence or absence of 43 spacers) in the aforementioned worldwide database. This tool allows one to analyze spread and evolutionary patterns of MTBC by comparing similar spoligotype patterns, to distinguish between widespread, specific and/or confined patterns, as well as to pinpoint patterns with large deleted blocks, which play an intriguing role in the genetic epidemiology of M. tuberculosis. Finally, the SpolSimilaritySearch tool also provides with the country distribution patterns for each queried spoligotype. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Molecular moment similarity between several nucleoside analogs of thymidine and thymidine. sil@watson.ibm.com.

    Science.gov (United States)

    Silverman, B D; Pitman, M C; Platt, D E

    1999-06-01

    Molecular moment descriptors of the shape and charge distributions of twenty five nucleoside structures have been examined. The structures include thymidine as well as the difluorotoluene nucleoside analog which has been found to pair efficiently with adenine by polymerase catalysis. The remaining twenty three structures have been chosen to be as structurally similar to thymidine and to the difluorotoluene nucleoside analog as possible. The moment descriptors which include a description of the relationship of molecular charge to shape show the difluorotoluene nucleoside to be one of the most proximate molecules to thymidine in the space of the molecular moments. The calculations, therefore, suggest that polymerase specificity might be not only a consequence of molecular steric features alone but also of the molecular electrostatic environment and its registration with molecular shape.

  18. Molecular techniques to distinguish morphologically similar Hydrilla verticillata, Egeria densa, Elodea nuttallii, and Elodea canadensis

    Science.gov (United States)

    Rybicki, Nancy B.; Kirshtein, Julie D.; Voytek, Mary A.

    2013-01-01

    The four submerged aquatic species, hydrilla (Hydrilla verticillata [monoecious and dioecious]), Brazilian waterweed (Egeria densa), Canadian waterweed (Elodea canadensis), and western waterweed (Elodea nuttallii), are difficult to positively identify because of their morphological similarity to each other, resulting in possible misidentification. This limits our ability to understand their past and present distribution, which is important in aquatic plant management. We investigated a molecular technique to identify these species, which are problematic because of their invasive nature on multiple continents. Approximately 100 samples of these species, ranging in age from 40-yr-old herbarium samples to recently collected plants, were collected from regions across the United States. The distribution and range of the samples collected in this research were compared to those reported in the literature. We confirmed information on the current wide distribution of both hydrilla biotypes in the United States and discovered that hydrilla had actually invaded the waterways near Washington, DC 6 yr earlier than originally reported. In addition, we found evidence of the confusion, dating back to the 1980s, between Canadian waterweed and western waterweed in the mid-Atlantic region of the United States. Canadian waterweed was previously reported as common and western waterweed as rare; however, our samples indicate the opposite is true. This information indicates there is a need for investigators to anticipate the spread of hydrilla populations to northern U.S. waterways, where it will compete with existing plant species, including Canadian and western waterweeds. Our ability to confirm distribution and pace of spread of invasive and noninvasive species will improve with increased application of molecular techniques.

  19. Characteristic Variations and Similarities in Biochemical, Molecular, and Functional Properties of Glyoxalases across Prokaryotes and Eukaryotes.

    Science.gov (United States)

    Kaur, Charanpreet; Sharma, Shweta; Hasan, Mohammad Rokebul; Pareek, Ashwani; Singla-Pareek, Sneh L; Sopory, Sudhir K

    2017-03-30

    The glyoxalase system is the ubiquitous pathway for the detoxification of methylglyoxal (MG) in the biological systems. It comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), which act sequentially to convert MG into d-lactate, thereby helping living systems get rid of this otherwise cytotoxic byproduct of metabolism. In addition, a glutathione-independent GLYIII enzyme activity also exists in the biological systems that can directly convert MG to d-lactate. Humans and Escherichia coli possess a single copy of GLYI (encoding either the Ni- or Zn-dependent form) and GLYII genes, which through MG detoxification provide protection against various pathological and disease conditions. By contrast, the plant genome possesses multiple GLYI and GLYII genes with a role in abiotic stress tolerance. Plants possess both Ni 2+ - and Zn 2+ -dependent forms of GLYI, and studies on plant glyoxalases reveal the various unique features of these enzymes distinguishing them from prokaryotic and other eukaryotic glyoxalases. Through this review, we provide an overview of the plant glyoxalase family along with a comparative analysis of glyoxalases across various species, highlighting similarities as well as differences in the biochemical, molecular, and physiological properties of these enzymes. We believe that the evolution of multiple glyoxalases isoforms in plants is an important component of their robust defense strategies.

  20. A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

    Science.gov (United States)

    Simon, Sílvia; Duran, Miquel

    1997-08-01

    Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.

  1. Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

    Science.gov (United States)

    Huang, Bing; von Lilienfeld, O. Anatole

    2016-10-01

    The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Inspired by the postulates of quantum mechanics, we introduce a hierarchy of representations which meet uniqueness and target similarity criteria. To systematically control target similarity, we simply rely on interatomic many body expansions, as implemented in universal force-fields, including Bonding, Angular (BA), and higher order terms. Addition of higher order contributions systematically increases similarity to the true potential energy and predictive accuracy of the resulting ML models. We report numerical evidence for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heat capacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After training, BAML predicts energies or electronic properties of out-of-sample molecules with unprecedented accuracy and speed.

  2. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

    NARCIS (Netherlands)

    Liu, Yang; Sethi, Nilay S; Hinoue, Toshinori; Schneider, Barbara G; Cherniack, Andrew D; Sanchez-Vega, Francisco; Seoane, Jose A; Farshidfar, Farshad; Bowlby, Reanne; Islam, Mirazul; Kim, Jaegil; Chatila, Walid; Akbani, Rehan; Kanchi, Rupa S; Rabkin, Charles S; Willis, Joseph E; Wang, Kenneth K; McCall, Shannon J; Mishra, Lopa; Ojesina, Akinyemi I; Bullman, Susan; Pedamallu, Chandra Sekhar; Lazar, Alexander J; Sakai, Ryo; Thorsson, Vésteinn; Bass, Adam J; Laird, Peter W; de Krijger, RR

    2018-01-01

    We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and comprised those enriched for

  3. Total and high molecular weight adiponectin have similar utility for the identification of insulin resistance

    Directory of Open Access Journals (Sweden)

    Aguilar-Salinas Carlos A

    2010-06-01

    Full Text Available Abstract Background Insulin resistance (IR and related metabolic disturbances are characterized by low levels of adiponectin. High molecular weight adiponectin (HMWA is considered the active form of adiponectin and a better marker of IR than total adiponectin. The objective of this study is to compare the utility of total adiponectin, HMWA and the HMWA/total adiponectin index (SA index for the identification of IR and related metabolic conditions. Methods A cross-sectional analysis was performed in a group of ambulatory subjects, aged 20 to 70 years, in Mexico City. Areas under the receiver operator characteristic (ROC curve for total, HMWA and the SA index were plotted for the identification of metabolic disturbances. Sensitivity and specificity, positive and negative predictive values, and accuracy for the identification of IR were calculated. Results The study included 101 men and 168 women. The areas under the ROC curve for total and HMWA for the identification of IR (0.664 vs. 0.669, P = 0.74, obesity (0.592 vs. 0.610, P = 0.32, hypertriglyceridemia (0.661 vs. 0.671, P = 0.50 and hypoalphalipoproteinemia (0.624 vs. 0.633, P = 0.58 were similar. A total adiponectin level of 8.03 μg/ml was associated with a sensitivity of 57.6%, a specificity of 65.9%, a positive predictive value of 50.0%, a negative predictive value of 72.4%, and an accuracy of 62.7% for the diagnosis of IR. The corresponding figures for a HMWA value of 4.25 μg/dl were 59.6%, 67.1%, 51.8%, 73.7% and 64.2%. The area under the ROC curve of the SA index for the identification of IR was 0.622 [95% CI 0.554-0.691], obesity 0.613 [95% CI 0.536-0.689], hypertriglyceridemia 0.616 [95% CI 0.549-0.683], and hypoalphalipoproteinemia 0.606 [95% CI 0.535-0.677]. Conclusions Total adiponectin, HMWA and the SA index had similar utility for the identification of IR and metabolic disturbances.

  4. A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects.

    Directory of Open Access Journals (Sweden)

    Jeanette Prinz

    2016-09-01

    Full Text Available The molecular mechanisms that translate drug treatment into beneficial and unwanted effects are largely unknown. We present here a novel approach to detect gene-drug and gene-side effect associations based on the phenotypic similarity of drugs and single gene perturbations in mice that account for the polypharmacological property of drugs. We scored the phenotypic similarity of human side effect profiles of 1,667 small molecules and biologicals to profiles of phenotypic traits of 5,384 mouse genes. The benchmarking with known relationships revealed a strong enrichment of physical and indirect drug-target connections, causative drug target-side effect links as well as gene-drug links involved in pharmacogenetic associations among phenotypically similar gene-drug pairs. The validation by in vitro assays and the experimental verification of an unknown connection between oxandrolone and prokineticin receptor 2 reinforces the ability of this method to provide new molecular insights underlying drug treatment. Thus, this approach may aid in the proposal of novel and personalized treatments.

  5. Comparative studies on different molecular methods for ...

    African Journals Online (AJOL)

    The present study aims to evaluate two molecular methods for epidemiological typing of multi drug resistant Klebsiella pneumoniae isolated from Mansoura Hospitals. In this study, a total of 300 clinical isolates were collected from different patients distributed among Mansoura Hospitals, Dakahlia governorate, Egypt.

  6. Testicular cells exhibit similar molecular responses to cigarette smoke condensate ex vivo and in vivo.

    Science.gov (United States)

    Esakky, Prabagaran; Hansen, Deborah A; Drury, Andrea M; Felder, Paul; Cusumano, Andrew; Moley, Kelle H

    2018-01-01

    Male exposure to cigarette smoke is associated with seminal defects and with congenital anomalies and childhood cancers in offspring. In mice, paternal exposure to cigarette smoke condensate (CSC) causes molecular defects in germ cells and phenotypic effects in their offspring. Here we used an ex vivo testicular explant model and in vivo exposure to determine the concentration at which CSC impairs spermatogenesis and offspring development. We explanted testis tissue at postnatal day (P)5.5 and cultured it until P11.5. Assessment of growth parameters by analyzing expression of cell-specific markers revealed that the explant system maintained structural and functional integrity. We exposed the P5.5 to -11.5 explants to various concentrations (40-160 µg/ml) of CSC and confirmed that nicotine in the CSC was metabolized to cotinine. We assessed various growth and differentiation parameters, as well as testosterone production, and observed that many spermatogenesis features were impaired at 160 µg/ml CSC. The same parameters were impaired by a similar CSC concentration in vivo Finally, females mated to males that were exposed to 160 µg/ml CSC neonatally had increased rates of pup resorption. We conclude that male exposure to CSC impairs offspring development and that the concentration at which CSC impairs spermatogenesis is similar in vivo and ex vivo. Given that the concentrations of CSC we used contained similar doses of nicotine as human smokers are exposed to, we argue that our model mimics human male reproductive effects of smoking.-Esakky, P., Hansen, D. A., Drury, A. M., Felder, P., Cusumano, A., Moley, K. H. Testicular cells exhibit similar molecular responses to cigarette smoke condensate ex vivo and in vivo . © FASEB.

  7. Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis

    Science.gov (United States)

    Vilar, Santiago; Harpaz, Rave; Chase, Herbert S; Costanzi, Stefano; Rabadan, Raul

    2011-01-01

    Background Adverse drug events (ADE) cause considerable harm to patients, and consequently their detection is critical for patient safety. The US Food and Drug Administration maintains an adverse event reporting system (AERS) to facilitate the detection of ADE in drugs. Various data mining approaches have been developed that use AERS to detect signals identifying associations between drugs and ADE. The signals must then be monitored further by domain experts, which is a time-consuming task. Objective To develop a new methodology that combines existing data mining algorithms with chemical information by analysis of molecular fingerprints to enhance initial ADE signals generated from AERS, and to provide a decision support mechanism to facilitate the identification of novel adverse events. Results The method achieved a significant improvement in precision in identifying known ADE, and a more than twofold signal enhancement when applied to the ADE rhabdomyolysis. The simplicity of the method assists in highlighting the etiology of the ADE by identifying structurally similar drugs. A set of drugs with strong evidence from both AERS and molecular fingerprint-based modeling is constructed for further analysis. Conclusion The results demonstrate that the proposed methodology could be used as a pharmacovigilance decision support tool to facilitate ADE detection. PMID:21946238

  8. Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes.

    Science.gov (United States)

    Bonachéra, Fanny; Parent, Benjamin; Barbosa, Frédérique; Froloff, Nicolas; Horvath, Dragos

    2006-01-01

    This paper introduces a novel molecular description--topological (2D) fuzzy pharmacophore triplets, 2D-FPT--using the number of interposed bonds as the measure of separation between the atoms representing pharmacophore types (hydrophobic, aromatic, hydrogen-bond donor and acceptor, cation, and anion). 2D-FPT features three key improvements with respect to the state-of-the-art pharmacophore fingerprints: (1) The first key novelty is fuzzy mapping of molecular triplets onto the basis set of pharmacophore triplets: unlike in the binary scheme where an atom triplet is set to highlight the bit of a single, best-matching basis triplet, the herein-defined fuzzy approach allows for gradual mapping of each atom triplet onto several related basis triplets, thus minimizing binary classification artifacts. (2) The second innovation is proteolytic equilibrium dependence, by explicitly considering all of the conjugated acids and bases (microspecies). 2D-FPTs are concentration-weighted (as predicted at pH=7.4) averages of microspecies fingerprints. Therefore, small structural modifications, not affecting the overall pharmacophore pattern (in the sense of classical rule-based assignment), but nevertheless triggering a pKa shift, will have a major impact on 2D-FPT. Pairs of almost identical compounds with significantly differing activities ("activity cliffs" in classical descriptor spaces) were in many cases predictable by 2D-FPT. (3) The third innovation is a new similarity scoring formula, acknowledging that the simultaneous absence of a triplet in two molecules is a less-constraining indicator of similarity than its simultaneous presence. It displays excellent neighborhood behavior, outperforming 2D or 3D two-point pharmacophore descriptors or chemical fingerprints. The 2D-FPT calculator was developed using the chemoinformatics toolkit of ChemAxon (www.chemaxon.com).

  9. Comparative Analysis of Networks of Phonologically Similar Words in English and Spanish

    Directory of Open Access Journals (Sweden)

    Michael S. Vitevitch

    2010-03-01

    Full Text Available Previous network analyses of several languages revealed a unique set of structural characteristics. One of these characteristics—the presence of many smaller components (referred to as islands—was further examined with a comparative analysis of the island constituents. The results showed that Spanish words in the islands tended to be phonologically and semantically similar to each other, but English words in the islands tended only to be phonologically similar to each other. The results of this analysis yielded hypotheses about language processing that can be tested with psycholinguistic experiments, and offer insight into cross-language differences in processing that have been previously observed.

  10. Tableau Calculus for the Logic of Comparative Similarity over Arbitrary Distance Spaces

    Science.gov (United States)

    Alenda, Régis; Olivetti, Nicola

    The logic CSL (first introduced by Sheremet, Tishkovsky, Wolter and Zakharyaschev in 2005) allows one to reason about distance comparison and similarity comparison within a modal language. The logic can express assertions of the kind "A is closer/more similar to B than to C" and has a natural application to spatial reasoning, as well as to reasoning about concept similarity in ontologies. The semantics of CSL is defined in terms of models based on different classes of distance spaces and it generalizes the logic S4 u of topological spaces. In this paper we consider CSL defined over arbitrary distance spaces. The logic comprises a binary modality to represent comparative similarity and a unary modality to express the existence of the minimum of a set of distances. We first show that the semantics of CSL can be equivalently defined in terms of preferential models. As a consequence we obtain the finite model property of the logic with respect to its preferential semantic, a property that does not hold with respect to the original distance-space semantics. Next we present an analytic tableau calculus based on its preferential semantics. The calculus provides a decision procedure for the logic, its termination is obtained by imposing suitable blocking restrictions.

  11. Bioengineered human IAS reconstructs with functional and molecular properties similar to intact IAS

    Science.gov (United States)

    Singh, Jagmohan

    2012-01-01

    Because of its critical importance in rectoanal incontinence, we determined the feasibility to reconstruct internal anal sphincter (IAS) from human IAS smooth muscle cells (SMCs) with functional and molecular attributes similar to the intact sphincter. The reconstructs were developed using SMCs from the circular smooth muscle layer of the human IAS, grown in smooth muscle differentiation media under sterile conditions in Sylgard-coated tissue culture plates with central Sylgard posts. The basal tone in the reconstructs and its changes were recorded following 0 Ca2+, KCl, bethanechol, isoproterenol, protein kinase C (PKC) activator phorbol 12,13-dibutyrate, and Rho kinase (ROCK) and PKC inhibitors Y-27632 and Gö-6850, respectively. Western blot (WB), immunofluorescence (IF), and immunocytochemical (IC) analyses were also performed. The reconstructs developed spontaneous tone (0.68 ± 0.26 mN). Bethanechol (a muscarinic agonist) and K+ depolarization produced contraction, whereas isoproterenol (β-adrenoceptor agonist) and Y-27632 produced a concentration-dependent decrease in the tone. Maximal decrease in basal tone with Y-27632 and Gö-6850 (each 10−5 M) was 80.45 ± 3.29 and 17.76 ± 3.50%, respectively. WB data with the IAS constructs′ SMCs revealed higher levels of RhoA/ROCK, protein kinase C-potentiated inhibitor or inhibitory phosphoprotein for myosin phosphatase (CPI-17), phospho-CPI-17, MYPT1, and 20-kDa myosin light chain vs. rectal smooth muscle. WB, IF, and IC studies of original SMCs and redispersed from the reconstructs for the relative distribution of different signal transduction proteins confirmed the feasibility of reconstruction of IAS with functional properties similar to intact IAS and demonstrated the development of myogenic tone with critical dependence on RhoA/ROCK. We conclude that it is feasible to bioengineer IAS constructs using human IAS SMCs that behave like intact IAS. PMID:22790596

  12. Defining the molecular pathologies in cloaca malformation: similarities between mouse and human

    Directory of Open Access Journals (Sweden)

    Laura A. Runck

    2014-04-01

    Full Text Available Anorectal malformations are congenital anomalies that form a spectrum of disorders, from the most benign type with excellent functional prognosis, to very complex, such as cloaca malformation in females in which the rectum, vagina and urethra fail to develop separately and instead drain via a single common channel into the perineum. The severity of this phenotype suggests that the defect occurs in the early stages of embryonic development of the organs derived from the cloaca. Owing to the inability to directly investigate human embryonic cloaca development, current research has relied on the use of mouse models of anorectal malformations. However, even studies of mouse embryos lack analysis of the earliest stages of cloaca patterning and morphogenesis. Here we compared human and mouse cloaca development and retrospectively identified that early mis-patterning of the embryonic cloaca might underlie the most severe forms of anorectal malformation in humans. In mouse, we identified that defective sonic hedgehog (Shh signaling results in early dorsal-ventral epithelial abnormalities prior to the reported defects in septation. This is manifested by the absence of Sox2 and aberrant expression of keratins in the embryonic cloaca of Shh knockout mice. Shh knockout embryos additionally develop a hypervascular stroma, which is defective in BMP signaling. These epithelial and stromal defects persist later, creating an indeterminate epithelium with molecular alterations in the common channel. We then used these animals to perform a broad comparison with patients with mild-to-severe forms of anorectal malformations including cloaca malformation. We found striking parallels with the Shh mouse model, including nearly identical defective molecular identity of the epithelium and surrounding stroma. Our work strongly suggests that early embryonic cloacal epithelial differentiation defects might be the underlying cause of severe forms of anorectal malformations

  13. Peroral endoscopic myotomy achieves similar clinical response but incurs lesser charges compared to robotic heller myotomy.

    Science.gov (United States)

    Khashab, Mouen A; Kumbhari, Vivek; Tieu, Alan H; El Zein, Mohamad H; Ismail, Amr; Ngamruengphong, Saowanee; Singh, Vikesh K; Kalloo, Anthony N; Clarke, John O; Stein, Ellen M

    2017-01-01

    Several uncontrolled studies comparing peroral endoscopic myotomy (POEM) and Heller myotomy have demonstrated equivalent short-term efficacy and safety. However, no data exists rergarding the cost of POEM and how it compares to that of robotic Heller myotomy (RHM). The primary aim of this study was to compare the inpatient charges incurred in patients who underwent POEM or RHM for the treatment of achalasia. A retrospective single center review was conducted among 52 consecutive POEM patients (2012-2014) and 52 consecutive RHM patients (2009-2014). All RHM procedures included a Toupet fundoplication and were performed via a transabdominal approach. All POEM procedures were performed by a gastroenterologist in the endoscopy unit. Clinical response was defined by improvement of symptoms and decrease in Eckardt stage to ≤I. All procedural and facility charges were obtained from review of the hospital finance records. There was no difference between POEM and RHM with regards to age, gender, symptom duration, achalasia subtype, manometry findings, or Eckardt symptom stage. There was no significant difference in the rate of adverse events (19.2% vs 9.6%, P = 0.26) or the length of stay (1.9 vs. 2.3, P = 0.18) between both groups. Clinical response rate of patients in the POEM groups was similar to that in the RHM group (94.3% vs. 88.5%, P = 0.48). POEM incurred significantly less total charges compared to LHM ($14481 vs. $17782, P = 0.02). POEM when performed in an endoscopy unit was similar in efficacy and safety to RHM. However, POEM was associated with significant cost savings ($3301/procedure).

  14. Similar early migration when comparing CR and PS in Triathlon™ TKA: A prospective randomised RSA trial.

    Science.gov (United States)

    Molt, Mats; Toksvig-Larsen, Sören

    2014-10-01

    The objective of this study was to compare the early migration of the cruciate retaining and posterior stabilising versions of the recently introduced Triathlon™ total knee system, with a view to predicting long term fixation performance. Sixty patients were prospectively randomised to receive either Triathlon™ posterior stabilised cemented knee prosthesis or Triathlon™ cruciate retaining cemented knee prosthesis. Tibial component migration was measured by radiostereometric analysis postoperatively and at three months, one year and two years. Clinical outcome was measured by the American Knee Society Score and Knee Osteoarthritis and Injury Outcome Score. There were no differences in rotation around the three coordinal axes or in the maximum total point motion (MTPM) during the two year follow-up. The posterior stabilised prosthesis had more posterior-anterior translation at three months and one year and more caudal-cranial translation at one year and two years. There were no differences in functional outcome between the groups. The tibial tray of the Triathlon™ cemented knee prosthesis showed similar early stability. Level I. Article focus: This was a prospective randomised trial aiming to compare the single radius posterior stabilised (PS) Triathlon™ total knee arthroplasty (TKA) to the cruciate retaining Triathlon™ TKA system with regard to fixation. Strengths and limitations of this study: Strength of this study was that it is a randomised prospective trial using an objective measuring tool. The sample size of 25-30 patients was reportedly sufficient for the screening of implants using RSA [1]. ClinicalTrials.gov Identifier: NCT00436982. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Compassion Fatigue is Similar in Emergency Medicine Residents Compared to other Medical and Surgical Specialties

    Directory of Open Access Journals (Sweden)

    M. Fernanda Bellolio

    2014-09-01

    Full Text Available Introduction: Compassion fatigue (CF is the emotional and physical burden felt by those helping others in distress, leading to a reduced capacity and interest in being empathetic towards future suffering. Emergency care providers are at an increased risk of CF secondary to their first responder roles and exposure to traumatic events. We aimed to investigate the current state of compassion fatigue among emergency medicine (EM resident physicians, including an assessment of contributing factors. Methods: We distributed a validated electronic questionnaire consisting of the Professional Quality of Life Scale with subscales for the three components of CF (compassion satisfaction, burnout and secondary traumatic stress, with each category scored independently. We collected data pertaining to day- versus night-shift distribution, hourly workload and child dependents. We included residents in EM, neurology, orthopedics, family medicine, pediatrics, obstetrics, and general surgery. Results: We surveyed 255 residents, with a response rate of 75%. Of the 188 resident respondents, 18% worked a majority of their clinical shifts overnight, and 32% had child dependents. Burnout scores for residents who worked greater than 80 hours per week, or primarily worked overnight shifts, were higher than residents who worked less than 80 hours (mean score 25.0 vs 21.5; p=0.013, or did not work overnight (mean score 23.5 vs 21.3; p=0.022. EM residents had similar scores in all three components of CF when compared to other specialties. Secondary traumatic stress scores for residents who worked greater than 80 hours were higher than residents who worked less than 80 hours (mean score 22.2 vs 19.5; p=0.048, and those with child dependents had higher secondary traumatic stress than those without children (mean score 21.0 vs 19.1; p=0.012. Conclusion: CF scores in EM residents are similar to residents in other surgical and medical specialties. Residents working primarily

  16. Comparative molecular analysis of old olive ( Olea europaea L ...

    African Journals Online (AJOL)

    We compared the genetic profiles of six old olive cultivars from an Eastern Mediterranean Region of Turkey to 15 modern Turkish olive cultivars from different geographical origins. The RAPD profiles successfully clarified the molecular relationships among the genotypes tested. Seventeen RAPD primers generated 153 ...

  17. A Model for Comparative Analysis of the Similarity between Android and iOS Operating Systems

    Directory of Open Access Journals (Sweden)

    Lixandroiu R.

    2014-12-01

    Full Text Available Due to recent expansion of mobile devices, in this article we try to do an analysis of two of the most used mobile OSS. This analysis is made on the method of calculating Jaccard's similarity coefficient. To complete the analysis, we developed a hierarchy of factors in evaluating OSS. Analysis has shown that the two OSS are similar in terms of functionality, but there are a number of factors that weighted make a difference.

  18. A comparative cellular and molecular biology of longevity database.

    Science.gov (United States)

    Stuart, Jeffrey A; Liang, Ping; Luo, Xuemei; Page, Melissa M; Gallagher, Emily J; Christoff, Casey A; Robb, Ellen L

    2013-10-01

    Discovering key cellular and molecular traits that promote longevity is a major goal of aging and longevity research. One experimental strategy is to determine which traits have been selected during the evolution of longevity in naturally long-lived animal species. This comparative approach has been applied to lifespan research for nearly four decades, yielding hundreds of datasets describing aspects of cell and molecular biology hypothesized to relate to animal longevity. Here, we introduce a Comparative Cellular and Molecular Biology of Longevity Database, available at ( http://genomics.brocku.ca/ccmbl/ ), as a compendium of comparative cell and molecular data presented in the context of longevity. This open access database will facilitate the meta-analysis of amalgamated datasets using standardized maximum lifespan (MLSP) data (from AnAge). The first edition contains over 800 data records describing experimental measurements of cellular stress resistance, reactive oxygen species metabolism, membrane composition, protein homeostasis, and genome homeostasis as they relate to vertebrate species MLSP. The purpose of this review is to introduce the database and briefly demonstrate its use in the meta-analysis of combined datasets.

  19. Molecular Quantum Similarity Measures from Fermi hole Densities: Modeling Hammett Sigma Constants

    Czech Academy of Sciences Publication Activity Database

    Girónes, X.; Ponec, Robert

    2006-01-01

    Roč. 46, č. 3 (2006), s. 1388-1393 ISSN 1549-9596 Grant - others:SMCT(ES) SAF2000/0223/C03/01 Institutional research plan: CEZ:AV0Z40720504 Keywords : molecula quantum similarity measures * fermi hole densities * substituent effect Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.423, year: 2006

  20. The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets

    Science.gov (United States)

    Trepalin, Sergey; Osadchiy, Nikolay

    2005-09-01

    Chemical structure provides exhaustive description of a compound, but it is often proprietary and thus an impediment in the exchange of information. For example, structure disclosure is often needed for the selection of most similar or dissimilar compounds. Authors propose a centroidal algorithm based on structural fragments (screens) that can be efficiently used for the similarity and diversity selections without disclosing structures from the reference set. For an increased security purposes, authors recommend that such set contains at least some tens of structures. Analysis of reverse engineering feasibility showed that the problem difficulty grows with decrease of the screen's radius. The algorithm is illustrated with concrete calculations on known steroidal, quinoline, and quinazoline drugs. We also investigate a problem of scaffold identification in combinatorial library dataset. The results show that relatively small screens of radius equal to 2 bond lengths perform well in the similarity sorting, while radius 4 screens yield better results in diversity sorting. The software implementation of the algorithm taking SDF file with a reference set generates screens of various radii which are subsequently used for the similarity and diversity sorting of external SDFs. Since the reverse engineering of the reference set molecules from their screens has the same difficulty as the RSA asymmetric encryption algorithm, generated screens can be stored openly without further encryption. This approach ensures an end user transfers only a set of structural fragments and no other data. Like other algorithms of encryption, the centroid algorithm cannot give 100% guarantee of protecting a chemical structure from dataset, but probability of initial structure identification is very small-order of 10-40 in typical cases.

  1. Comparative Analysis of Diversity and Similarity Indices with Special Relevance to Vegetations around Sewage Drains

    OpenAIRE

    Ekta Singh

    2012-01-01

    Indices summarizing community structure are used to evaluate fundamental community ecology, species interaction, biogeographical factors, and environmental stress. Some of these indices are insensitive to gross community changes induced by contaminants of pollution. Diversity indices and similarity indices are reviewed considering their ecological application, both theoretical and practical. For some useful indices, empirical equations are given to calculate the expected ...

  2. Emotion recognition impairment in traumatic brain injury compared with schizophrenia spectrum: similar deficits with different origins.

    Science.gov (United States)

    Mancuso, Mauro; Magnani, Nadia; Cantagallo, Anna; Rossi, Giulia; Capitani, Donatella; Galletti, Vania; Cardamone, Giuseppe; Robertson, Ian Hamilton

    2015-02-01

    The aim of our study was to identify the common and separate mechanisms that might underpin emotion recognition impairment in patients with traumatic brain injury (TBI) and schizophrenia (Sz) compared with healthy controls (HCs). We recruited 21 Sz outpatients, 24 severe TBI outpatients, and 38 HCs, and we used eye-tracking to compare facial emotion processing performance. Both Sz and TBI patients were significantly poorer at recognizing facial emotions compared with HC. Sz patients showed a different way of exploring the Pictures of Facial Affects stimuli and were significantly worse in recognition of neutral expressions. Selective or sustained attention deficits in TBI may reduce efficient emotion recognition, whereas in Sz, there is a more strategic deficit underlying the observed problem. There would seem to be scope for adjustment of effective rehabilitative training focused on emotion recognition.

  3. Similar problems, different solutions: Comparing refuse collection in the Netherlands and Spain

    NARCIS (Netherlands)

    Gradus, R.H.J.M.; Bel, G.; Dijkgraaf, E.; Fageda, X.

    2010-01-01

    Because of differences in institutional arrangements, public service markets, and national traditions regarding government intervention, local public service provision can vary greatly. In this paper we compare the procedures adopted by the local governments of The Netherlands and Spain in arranging

  4. Similar problems, different solutions: comparing refuse collection in the Netherlands and Spain.

    Science.gov (United States)

    Bel, Germà; Fageda, Xavier; Dijkgraaf, Elbert; Gradus, Raymond

    2010-01-01

    Because of differences in institutional arrangements, public service markets, and national traditions regarding government intervention, local public service provision can vary greatly. In this paper we compare the procedures adopted by the local governments of The Netherlands and Spain in arranging for the provision of solid waste collection. We find that Spain faces a problem of consolidation, opting more frequently to implement policies of privatization and cooperation, at the expense of competition. By contrast, The Netherlands, which has larger municipalities on average, resorts somewhat less to privatization and cooperation, and more to competition. Both options-cooperation and competition-have their merits when striving to strike a balance between transaction costs and scale economies. The choices made in organizational reform seem to be related to several factors, among which the nature of the political system and the size of municipalities appear to be relevant.

  5. Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability.

    Directory of Open Access Journals (Sweden)

    Catarina Barbosa

    Full Text Available Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23, under low (67 mg/L and high nitrogen (670 mg/L regimes, at three time points during fermentation (12 h, 24 h and 96 h. Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this

  6. Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

    Science.gov (United States)

    Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

    2015-01-01

    Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape

  7. Musicians' and nonmusicians' short-term memory for verbal and musical sequences: comparing phonological similarity and pitch proximity.

    Science.gov (United States)

    Williamson, Victoria J; Baddeley, Alan D; Hitch, Graham J

    2010-03-01

    Language-music comparative studies have highlighted the potential for shared resources or neural overlap in auditory short-term memory. However, there is a lack of behavioral methodologies for comparing verbal and musical serial recall. We developed a visual grid response that allowed both musicians and nonmusicians to perform serial recall of letter and tone sequences. The new method was used to compare the phonological similarity effect with the impact of an operationalized musical equivalent-pitch proximity. Over the course of three experiments, we found that short-term memory for tones had several similarities to verbal memory, including limited capacity and a significant effect of pitch proximity in nonmusicians. Despite being vulnerable to phonological similarity when recalling letters, however, musicians showed no effect of pitch proximity, a result that we suggest might reflect strategy differences. Overall, the findings support a limited degree of correspondence in the way that verbal and musical sounds are processed in auditory short-term memory.

  8. How to compare movement? A review of physical movement similarity measures in geographic information science and beyond.

    Science.gov (United States)

    Ranacher, Peter; Tzavella, Katerina

    2014-05-27

    In geographic information science, a plethora of different approaches and methods is used to assess the similarity of movement. Some of these approaches term two moving objects similar if they share akin paths. Others require objects to move at similar speed and yet others consider movement similar if it occurs at the same time. We believe that a structured and comprehensive classification of movement comparison measures is missing. We argue that such a classification not only depicts the status quo of qualitative and quantitative movement analysis, but also allows for identifying those aspects of movement for which similarity measures are scarce or entirely missing. In this review paper we, first, decompose movement into its spatial, temporal, and spatiotemporal movement parameters. A movement parameter is a physical quantity of movement, such as speed, spatial path, or temporal duration. For each of these parameters we then review qualitative and quantitative methods of how to compare movement. Thus, we provide a systematic and comprehensive classification of different movement similarity measures used in geographic information science. This classification is a valuable first step toward a GIS toolbox comprising all relevant movement comparison methods.

  9. Bench press and push-up at comparable levels of muscle activity results in similar strength gains.

    Science.gov (United States)

    Calatayud, Joaquin; Borreani, Sebastien; Colado, Juan C; Martin, Fernando; Tella, Victor; Andersen, Lars L

    2015-01-01

    Electromyography (EMG) exercise evaluation is commonly used to measure the intensity of muscle contraction. Although researchers assume that biomechanically comparable resistance exercises with similar high EMG levels will produce similar strength gains over the long term, no studies have actually corroborated this hypothesis. This study evaluated EMG levels during 6 repetition maximum (6RM) bench press and push-up, and subsequently performed a 5-week training period where subjects were randomly divided into 3 groups (i.e., 6RM bench press group, 6RM elastic band push-up group, or control group) to evaluate muscle strength gains. Thirty university students with advanced resistance training experience participated in the 2-part study. During the training period, exercises were performed using the same loads and variables that were used during the EMG data collection. At baseline, EMG amplitude showed no significant difference between 6RM bench press and band push-up. Significant differences among the groups were found for percent change (Δ) between pretest and posttest for 6RM (p = 0.017) and for 1 repetition maximum (1RM) (p bench press group and 6RM elastic band push-up group improved their 1RM and 6RM (Δ ranging from 13.65 to 22.21) tests significantly with similar gains, whereas control group remains unchanged. Thus, when the EMG values are comparable and the same conditions are reproduced, the aforementioned exercises can provide similar muscle strength gains.

  10. Intrinsic atopic dermatitis (AD) shows similar Th2 and higher Th17 immune activation compared to extrinsic AD

    Science.gov (United States)

    Suárez-Fariñas, M; Dhingra, N; Gittler, J; Shemer, A; Cardinale, I; de Guzman Strong, C; Krueger, JG; Guttman-Yassky, E

    2013-01-01

    Background Atopic dermatitis (AD) is classified as extrinsic (ADe) and intrinsic (ADi), representing approximately 80% and 20% of patients, respectively. While sharing a similar clinical phenotype, only ADe is characterized by high serum IgE. Since most AD patients exhibit high IgE, an “allergic”/IgE-mediated disease pathogenesis was hypothesized. However, current models associate AD with T-cell activation, particularly Th2/Th22 polarization, and epidermal barrier defects. Objective To define if both variants share a common pathogenesis. Methods We stratified 51 severe AD patients as ADe (42) and ADi (9) (with similar mean disease activity/SCORAD), and analyzed the molecular and cellular skin pathology of lesional and non-lesional ADi and ADe using gene-expression (RT-PCR) and immunohistochemistry. Results A significant correlation between IgE levels and SCORAD (r=0.76, pextrinsic and intrinsic AD variants might be treated with T-cell targeted therapeutics or agents that modify keratinocyte responses. PMID:23777851

  11. A comparative analysis of Painleve, Lax pair, and similarity transformation methods in obtaining the integrability conditions of nonlinear Schroedinger equations

    International Nuclear Information System (INIS)

    Al Khawaja, U.

    2010-01-01

    We derive the integrability conditions of nonautonomous nonlinear Schroedinger equations using the Lax pair and similarity transformation methods. We present a comparative analysis of these integrability conditions with those of the Painleve method. We show that while the Painleve integrability conditions restrict the dispersion, nonlinearity, and dissipation/gain coefficients to be space independent and the external potential to be only a quadratic function of position, the Lax Pair and the similarity transformation methods allow for space-dependent coefficients and an external potential that is not restricted to the quadratic form. The integrability conditions of the Painleve method are retrieved as a special case of our general integrability conditions. We also derive the integrability conditions of nonautonomous nonlinear Schroedinger equations for two- and three-spacial dimensions.

  12. Assessing intrinsic and specific vulnerability models ability to indicate groundwater vulnerability to groups of similar pesticides: A comparative study

    Science.gov (United States)

    Douglas, Steven; Dixon, Barnali; Griffin, Dale W.

    2018-01-01

    With continued population growth and increasing use of fresh groundwater resources, protection of this valuable resource is critical. A cost effective means to assess risk of groundwater contamination potential will provide a useful tool to protect these resources. Integrating geospatial methods offers a means to quantify the risk of contaminant potential in cost effective and spatially explicit ways. This research was designed to compare the ability of intrinsic (DRASTIC) and specific (Attenuation Factor; AF) vulnerability models to indicate groundwater vulnerability areas by comparing model results to the presence of pesticides from groundwater sample datasets. A logistic regression was used to assess the relationship between the environmental variables and the presence or absence of pesticides within regions of varying vulnerability. According to the DRASTIC model, more than 20% of the study area is very highly vulnerable. Approximately 30% is very highly vulnerable according to the AF model. When groundwater concentrations of individual pesticides were compared to model predictions, the results were mixed. Model predictability improved when concentrations of the group of similar pesticides were compared to model results. Compared to the DRASTIC model, the AF model more accurately predicts the distribution of the number of contaminated wells within each vulnerability class.

  13. Intrinsic atopic dermatitis shows similar TH2 and higher TH17 immune activation compared with extrinsic atopic dermatitis.

    Science.gov (United States)

    Suárez-Fariñas, Mayte; Dhingra, Nikhil; Gittler, Julia; Shemer, Avner; Cardinale, Irma; de Guzman Strong, Cristina; Krueger, James G; Guttman-Yassky, Emma

    2013-08-01

    Atopic dermatitis (AD) is classified as extrinsic and intrinsic, representing approximately 80% and 20% of patients with the disease, respectively. Although sharing a similar clinical phenotype, only extrinsic AD is characterized by high serum IgE levels. Because most patients with AD exhibit high IgE levels, an "allergic"/IgE-mediated disease pathogenesis was hypothesized. However, current models associate AD with T-cell activation, particularly TH2/TH22 polarization, and epidermal barrier defects. We sought to define whether both variants share a common pathogenesis. We stratified 51 patients with severe AD into extrinsic AD (n = 42) and intrinsic AD (n = 9) groups (with similar mean disease activity/SCORAD scores) and analyzed the molecular and cellular skin pathology of lesional and nonlesional intrinsic AD and extrinsic AD by using gene expression (real-time PCR) and immunohistochemistry. A significant correlation between IgE levels and SCORAD scores (r = 0.76, P extrinsic AD. Marked infiltrates of T cells and dendritic cells and corresponding epidermal alterations (keratin 16, Mki67, and S100A7/A8/A9) defined lesional skin of patients with both variants. However, higher activation of all inflammatory axes (including TH2) was detected in patients with intrinsic AD, particularly TH17 and TH22 cytokines. Positive correlations between TH17-related molecules and SCORAD scores were only found in patients with intrinsic AD, whereas only patients with extrinsic AD showed positive correlations between SCORAD scores and TH2 cytokine (IL-4 and IL-5) levels and negative correlations with differentiation products (loricrin and periplakin). Although differences in TH17 and TH22 activation exist between patients with intrinsic AD and those with extrinsic AD, we identified common disease-defining features of T-cell activation, production of polarized cytokines, and keratinocyte responses to immune products. Our data indicate that a TH2 bias is not the sole cause of high Ig

  14. Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease.

    Science.gov (United States)

    Ellingford, Jamie M; Barton, Stephanie; Bhaskar, Sanjeev; Williams, Simon G; Sergouniotis, Panagiotis I; O'Sullivan, James; Lamb, Janine A; Perveen, Rahat; Hall, Georgina; Newman, William G; Bishop, Paul N; Roberts, Stephen A; Leach, Rick; Tearle, Rick; Bayliss, Stuart; Ramsden, Simon C; Nemeth, Andrea H; Black, Graeme C M

    2016-05-01

    To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD). Case series. A total of 562 patients diagnosed with IRD. We performed a direct comparative analysis of current molecular diagnostics with WGS. We retrospectively reviewed the findings from a diagnostic NGS DNA test for 562 patients with IRD. A subset of 46 of 562 patients (encompassing potential clinical outcomes of diagnostic analysis) also underwent WGS, and we compared mutation detection rates and molecular diagnostic yields. In addition, we compared the sensitivity and specificity of the 2 techniques to identify known single nucleotide variants (SNVs) using 6 control samples with publically available genotype data. Diagnostic yield of genomic testing. Across known disease-causing genes, targeted NGS and WGS achieved similar levels of sensitivity and specificity for SNV detection. However, WGS also identified 14 clinically relevant genetic variants through WGS that had not been identified by NGS diagnostic testing for the 46 individuals with IRD. These variants included large deletions and variants in noncoding regions of the genome. Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing. Weighted estimates, accounting for population structure, suggest that WGS methods could result in an overall 29% (95% confidence interval, 15-45) uplift in diagnostic yield. We show that WGS methods can detect disease-causing genetic variants missed by current NGS diagnostic methodologies for IRD and thereby demonstrate the clinical utility and additional value of WGS. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  15. Obturator externus was larger, while obturator internus size was similar in ballet dancers compared to nondancing athletes.

    Science.gov (United States)

    Mayes, Susan; Ferris, April-Rose; Smith, Peter; Cook, Jill

    2018-06-02

    To compare the cross-sectional area (CSA) of hip external rotators, obturator externus (OE) and obturator internus (OI), in ballet dancers and nondancing athletes, and evaluate the relationship between obturator muscle size and hip pain. Case-control study. Elite ballet and sport. 33 male and female professional ballet dancers and 33 age and sex-matched athletes. CSA's of OE and OI measured on magnetic resonance imaging (MRI) of one hip. Hip pain was scored with the Copenhagen Hip and Groin Outcome Score (HAGOS): HAGOS pain score of 100 was defined as no pain and a score less than 100 was defined as pain. Participants weight and height. Estimated marginal mean CSA of OE was 14% larger in dancers than athletes (p = 0.01, ηp2 = 0.1); the size of OI was similar (p > 0.05). Men and women in both groups had similar sized OI and OE. There was no interaction between the estimated marginal mean CSA of either obturator and hip pain. It appears that ballet selectively increases muscle size of OE, but not OI. Obturator size was not related to mild hip pain, as OE and OI size was similar in dancers and athletes with and without pain. Copyright © 2018. Published by Elsevier Ltd.

  16. Poor prognosis with in vitro fertilization in Indian women compared to Caucasian women despite similar embryo quality.

    Directory of Open Access Journals (Sweden)

    Lora K Shahine

    Full Text Available BACKGROUND: Disease prevalence and response to medical therapy may differ among patients of diverse ethnicities. Poor outcomes with in vitro fertilization (IVF treatment have been previously shown in Indian women compared to Caucasian women, and some evidence suggests that poor embryo quality may be a cause for the discrepancy. In our center, only patients with the highest quality cleavage stage embryos are considered eligible for extending embryo culture to the blastocyst stage. We compared live birth rates (LBR between Indian and Caucasian women after blastocyst transfer to investigate whether differences in IVF outcomes between these ethnicities would persist in patients who transferred similar quality embryos. METHODOLOGY/PRINCIPAL FINDINGS: In this retrospective cohort analysis, we compared IVF outcome between 145 Caucasians and 80 Indians who had a blastocyst transfer between January 1, 2005 and June 31, 2007 in our university center. Indians were younger than Caucasians by 2.7 years (34.03 vs. 36.71, P = 0.03, were more likely to have an agonist down regulation protocol (68% vs. 43%, P<0.01, and were more likely to have polycystic ovarian syndrome (PCOS, although not significant, (24% vs. 14%, P = 0.06. Sixty eight percent of Indian patients had the highest quality embryos (4AB blastocyst or better transferred compared to 71% of the Caucasians (P = 0.2. LBR was significantly lower in the Indians compared to the Caucasians (24% vs. 41%, P<0.01 with an odds ratio of 0.63, (95%CI 0.46-0.86. Controlling for age, stimulation protocol and PCOS showed persistently lower LBR with an adjusted odds ratio of 0.56, (95%CI 0.40-0.79 in the multivariate analysis. CONCLUSIONS/SIGNIFICANCE: Despite younger age and similar embryo quality, Indians had a significantly lower LBR than Caucasians. In this preliminary study, poor prognosis after IVF for Indian ethnicity persisted despite limiting analysis to patients with high quality embryos transferred

  17. Saccharin and aspartame, compared with sucrose, induce greater weight gain in adult Wistar rats, at similar total caloric intake levels.

    Science.gov (United States)

    Feijó, Fernanda de Matos; Ballard, Cíntia Reis; Foletto, Kelly Carraro; Batista, Bruna Aparecida Melo; Neves, Alice Magagnin; Ribeiro, Maria Flávia Marques; Bertoluci, Marcello Casaccia

    2013-01-01

    It has been suggested that the use of nonnutritive sweeteners (NNSs) can lead to weight gain, but evidence regarding their real effect in body weight and satiety is still inconclusive. Using a rat model, the present study compares the effect of saccharin and aspartame to sucrose in body weight gain and in caloric intake. Twenty-nine male Wistar rats received plain yogurt sweetened with 20% sucrose, 0.3% sodium saccharin or 0.4% aspartame, in addition to chow and water ad libitum, while physical activity was restrained. Measurements of cumulative body weight gain, total caloric intake, caloric intake of chow and caloric intake of sweetened yogurt were performed weekly for 12 weeks. Results showed that addition of either saccharin or aspartame to yogurt resulted in increased weight gain compared to addition of sucrose, however total caloric intake was similar among groups. In conclusion, greater weight gain was promoted by the use of saccharin or aspartame, compared with sucrose, and this weight gain was unrelated to caloric intake. We speculate that a decrease in energy expenditure or increase in fluid retention might be involved. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Similar Mediterranean diet adherence but greater central adiposity is observed among Greek diaspora adolescents living in Istanbul, compared to Athens.

    Science.gov (United States)

    Grammatikopoulou, Maria G; Maraki, Maria I; Giannopoulou, Despoina; Poulimeneas, Dimitrios; Sidossis, Labros S; Tsigga, Maria

    2018-02-01

    The aim of this case-control study was to compare Mediterranean diet (MD) adherence and anthropometry between Greek diaspora adolescents living in Istanbul and Greek adolescents, inhabitants of Athens. A total of 206 adolescents (103 from each site), aged 10.0-19.0 years old, all of Greek origin, were recruited from schools in Athens and minority schools in Istanbul, for the present case-control study. Participants at each site were age and sex-matched. Anthropometric measurements were performed, and diet adherence was assessed with the KIDMED score. Breakfast skipping, decreased dairy and increased commercially baked good/pastries consumption for breakfast, fast-food intake and consumption of several sweets each day was more prevalent in Istanbul, but, on the other hand, students from Athens reported eating fewer fruit, vegetables and nuts. The adoption of unhealthy eating habits in each site was counterbalanced by a more 'healthy' dietary element, resulting in an overall similar MD adherence between both sites. Additionally, although weight status was indifferent between the two cities, higher rates of abdominal obesity were recorded in Istanbul, when the weight-to-height ratio was used for diagnosis. Differences in several domains of the KIDMED score were recorded among cities, possibly as results of food availability and prices. However, MD adherence and weight status appeared similar, indicating that the dietary transition and acculturation experienced by the remnants is actually very slow and minimal during the 93 years since population exchange.

  19. Nocturnal blood pressure dipping is similar in rheumatoid arthritis patients as compared to a normal population.

    Science.gov (United States)

    Turgay Yildirim, O; Gonullu, E; Aydin, F; Aksit, E; Huseyinoglu Aydin, A; Dagtekin, E

    2018-04-12

    Rheumatoid arthritis (RA) is a systemic autoimmune inflammatory disorder which further doubles the risk of developing cardiovascular disease. Some studies suggest that in RA patients, the prevalence of hypertension increases due to prednisolone use, clinical status, genetic factors, and physical inactivity. On the other hand, dipper and non-dipper status in RA patients compared to non-RA subjects has not been investigated to our knowledge. Purpose of the study is to investigate whether non-dipper status is more deteriorated in RA patients. Sixty-five RA patients and 61 age-sex-matched control patients were evaluated in this cross-sectional study. Patients were classified according to 24-h ambulatory blood pressure monitoring results. Patients with previous hypertension diagnosis, coronary artery disease, and abnormal kidney function were excluded. Mean age of the study sample was 53.7 ± 12.3 years and 40.5% were male. There was no significant difference between groups in terms of basic demographic characteristics. Leukocyte counts (p = 0.001), neutrophil counts (p = 0.001), and red cell distribution width (p = 0.000) were significantly higher in the RA group. ABPM results indicate no significant difference between RA patients and the control group in terms of daytime systolic and diastolic blood pressure, nighttime systolic and diastolic blood pressure, and average systolic and diastolic blood pressure results (p > 0.05). There was no statistical difference regarding the non-dipper status of patient groups (p = 0.412). Nocturnal blood pressure dipping was significantly similar between groups (p = 0.980). In conclusion, RA patients have similar values in terms of nocturnal blood pressure dipping and hypertension diagnosis as compared to normal population.

  20. Similar healthy osteoclast and osteoblast activity on nanocrystalline hydroxyapatite and nanoparticles of tri-calcium phosphate compared to natural bone

    Directory of Open Access Journals (Sweden)

    MacMillan AK

    2014-12-01

    Full Text Available Adam K MacMillan,1 Francis V Lamberti,1 Julia N Moulton,2 Benjamin M Geilich,2 Thomas J Webster2,3 1RTI Surgical, Alachua, FL, USA; 2Department of Chemical Engineering, Northeastern University, Boston, MA, USA; 3Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, Saudi Arabia Abstract: While there have been numerous studies to determine osteoblast (bone forming cell functions on nanocrystalline compared to micron crystalline ceramics, there have been few studies which have examined osteoclast activity (including tartrate-resistant acid phosphatase, formation of resorption pits, size of resorption pits, and receptor activator of nuclear factor κB [RANK]. This is despite the fact that osteoclasts are an important part of maintaining healthy bone since they resorb bone during the bone remodeling process. Moreover, while it is now well documented that bone formation is enhanced on nanoceramics compared to micron ceramics, some have pondered whether osteoblast functions (such as osteoprotegerin and RANK ligand [RANKL] are normal (ie, non-diseased on such materials compared to natural bone. For these reasons, the objective of the present in vitro study was to determine various functions of osteoclasts and osteoblasts on nanocrystalline and micron crystalline hydroxyapatite as well as tri-calcium phosphate materials and compare such results to cortical and cancellous bone. Results showed for the first time similar osteoclast activity (including tartrate-resistant acid phosphatase, formation of resorption pits, size of resorption pits, and RANK and osteoblast activity (osteoprotegerin and RANKL on nanocrystalline hydroxyapatite compared to natural bone, whereas osteoclast and osteoblast functions on micron crystalline versions of these ceramics were much different than natural bone. In this manner, this study provides additional evidence that nanocrystalline calcium phosphates can serve as suitable synthetic

  1. Duplicate Abalone Egg Coat Proteins Bind Sperm Lysin Similarly, but Evolve Oppositely, Consistent with Molecular Mimicry at Fertilization

    Science.gov (United States)

    Aagaard, Jan E.; Springer, Stevan A.; Soelberg, Scott D.; Swanson, Willie J.

    2013-01-01

    Sperm and egg proteins constitute a remarkable paradigm in evolutionary biology: despite their fundamental role in mediating fertilization (suggesting stasis), some of these molecules are among the most rapidly evolving ones known, and their divergence can lead to reproductive isolation. Because of strong selection to maintain function among interbreeding individuals, interacting fertilization proteins should also exhibit a strong signal of correlated divergence among closely related species. We use evidence of such molecular co-evolution to target biochemical studies of fertilization in North Pacific abalone (Haliotis spp.), a model system of reproductive protein evolution. We test the evolutionary rates (d N/d S) of abalone sperm lysin and two duplicated egg coat proteins (VERL and VEZP14), and find a signal of co-evolution specific to ZP-N, a putative sperm binding motif previously identified by homology modeling. Positively selected residues in VERL and VEZP14 occur on the same face of the structural model, suggesting a common mode of interaction with sperm lysin. We test this computational prediction biochemically, confirming that the ZP-N motif is sufficient to bind lysin and that the affinities of VERL and VEZP14 are comparable. However, we also find that on phylogenetic lineages where lysin and VERL evolve rapidly, VEZP14 evolves slowly, and vice versa. We describe a model of sexual conflict that can recreate this pattern of anti-correlated evolution by assuming that VEZP14 acts as a VERL mimic, reducing the intensity of sexual conflict and slowing the co-evolution of lysin and VERL. PMID:23408913

  2. Duplicate abalone egg coat proteins bind sperm lysin similarly, but evolve oppositely, consistent with molecular mimicry at fertilization.

    Directory of Open Access Journals (Sweden)

    Jan E Aagaard

    Full Text Available Sperm and egg proteins constitute a remarkable paradigm in evolutionary biology: despite their fundamental role in mediating fertilization (suggesting stasis, some of these molecules are among the most rapidly evolving ones known, and their divergence can lead to reproductive isolation. Because of strong selection to maintain function among interbreeding individuals, interacting fertilization proteins should also exhibit a strong signal of correlated divergence among closely related species. We use evidence of such molecular co-evolution to target biochemical studies of fertilization in North Pacific abalone (Haliotis spp., a model system of reproductive protein evolution. We test the evolutionary rates (d(N/d(S of abalone sperm lysin and two duplicated egg coat proteins (VERL and VEZP14, and find a signal of co-evolution specific to ZP-N, a putative sperm binding motif previously identified by homology modeling. Positively selected residues in VERL and VEZP14 occur on the same face of the structural model, suggesting a common mode of interaction with sperm lysin. We test this computational prediction biochemically, confirming that the ZP-N motif is sufficient to bind lysin and that the affinities of VERL and VEZP14 are comparable. However, we also find that on phylogenetic lineages where lysin and VERL evolve rapidly, VEZP14 evolves slowly, and vice versa. We describe a model of sexual conflict that can recreate this pattern of anti-correlated evolution by assuming that VEZP14 acts as a VERL mimic, reducing the intensity of sexual conflict and slowing the co-evolution of lysin and VERL.

  3. A blended design in acute care training: similar learning results, less training costs compared with a traditional format.

    Science.gov (United States)

    Dankbaar, Mary E W; Storm, Diana J; Teeuwen, Irene C; Schuit, Stephanie C E

    2014-09-01

    Introduction There is a demand for more attractive and efficient training programmes in postgraduate health care training. This retrospective study aims to show the effectiveness of a blended versus traditional face-to-face training design. For nurses in postgraduate Acute and Intensive Care training, the effectiveness of a blended course design was compared with a traditional design. Methods In a first pilot study 57 students took a traditional course (2-h lecture and 2-h workshop) and 46 students took a blended course (2-h lecture and 2-h online self-study material). Test results were compared for both groups. After positive results in the pilot study, the design was replicated for the complete programme in Acute and Intensive Care. Now 16 students followed the traditional programme (11 days face-to-face education) and 31 students did the blended programme (7 days face-to-face and 40 h online self-study). An evaluation was done after the pilot and course costs were calculated. Results Results show that the traditional and blended groups were similar regarding the main characteristics and did not differ in learning results for both the pilot and the complete programme. Student evaluations of both designs were positive; however, the blended group were more confident that they had achieved the learning objectives. Training costs were reduced substantially. Conclusion The blended training design offers an effective and attractive training solution, leading to a significant reduction in costs.

  4. Similarities and differences between excessive exercising anorexia nervosa patients compared with DSM-IV defined anorexia nervosa subtypes.

    Science.gov (United States)

    Kiezebrink, K; Campbell, D; Mann, E; Blundell, J

    2009-12-01

    This study describes anorexia nervosa (AN) patients who use excessive exercise for weight management and how this behaviour relates to the classical Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition (DSM-IV) sub-grouping of AN. The study compared 428 clinical AN patients with 119 age and gender-matched controls. The AN cases were initially dichotomised according to DSM-IV subtype criteria into restricting (RAN; N=198) and binge-purge (BPAN; N=230) anorexia. The psychometric instruments were chosen to reflect key features concerning the diagnosis of eating disorders and characteristics of eating and food behaviour and included the 26-item Eating Attitude Test (EAT-26), Three Factor Eating Questionnaire (TFEQ), Dutch Eating Behaviour Questionnaire (DEBQ), Eysenck Personality Inventory (EPI) and Rosenberg Self-Esteem scale (RSE). Structured clinical interviews (1) were carried out in order to identify the subgroup of patients who use excessive exercise in order to facilitate weight control (EAN). The three groups (RAN, BPAN, EAN) did not differ in measures of current age, current body mass index, age of onset of AN and measures of restrained eating. However, significant differences were observed on EAT-26, DEBQ emotional and external factors, TFEQ disinhibition and hunger factors, EPI extraversion and neuroticism, and self-esteem. The EAN were similar to the RAN on the majority of variables but showed significant differences on extraversion, neuroticism, self-esteem and disease pathology (EAT-26). Compared with BPAN, EAN had lower disease pathology (EAT-26 scores), scored higher on the EPI extraversion scale, lower on the neuroticism scale and had greater self-esteem. The EAN also displayed significantly lower emotional and external eating (DEBQ) than BPAN and significantly lower disinhibition and hunger scores (TFEQ). These data suggest that EAN group display a mixed profile of characteristics resembling both BPAN and RAN. When EAN are defined as

  5. Investigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations.

    Science.gov (United States)

    Song, Wei; Guo, Jun-Tao

    2015-01-01

    Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) simulations. Protein flexibility has been considered as a key factor in molecular recognition, which is intrinsically a dynamic process involving fine structural fitting between binding components. In this study, we performed comparative MD simulations on wild-type and F10V mutant P22 Arc repressor in both free and complex conformations. The F10V mutant has lower DNA-binding specificity though both the bound and unbound main-chain structures between the wild-type and F10V mutant Arc are highly similar. We found that the DNA-binding motif of wild-type Arc is structurally more flexible than the F10V mutant in the unbound state, especially for the six DNA base-contacting residues in each dimer. We demonstrated that the flexible side chains of wild-type Arc lead to a higher DNA-binding specificity through forming more hydrogen bonds with DNA bases upon binding. Our simulations also showed a possible conformational selection mechanism for Arc-DNA binding. These results indicate the important roles of protein flexibility and dynamic properties in protein-DNA-binding specificity.

  6. Kinetic and Thermodynamic Rationale for SAHA Being a Preferential Human HDAC8 Inhibitor as Compared to the Structurally Similar Ligand, TSA

    Science.gov (United States)

    Singh, Raushan K.; Lall, Naveena; Leedahl, Travis S.; McGillivray, Abigail; Mandal, Tanmay; Haldar, Manas; Mallik, Sanku; Cook, Gregory; Srivastava, D.K.

    2013-01-01

    Of the different hydroxamate-based histone deacetylase (HDAC) inhibitors, Suberoylanilide hydroxamic acid (SAHA) has been approved by the FDA for treatment of T-cell lymphoma. Interestingly, a structurally similar inhibitor, Trichostatin A (TSA), which has a higher in vitro inhibitory-potency against HDAC8, reportedly shows a poor efficacy in clinical settings. In order to gain the molecular insight into the above discriminatory feature, we performed transient kinetic and isothermal titration calorimetric studies for the interaction of SAHA and TSA to the recombinant form of human HDAC8. The transient kinetic data revealed that the binding of both the inhibitors to the enzyme showed the biphasic profiles, which represented an initial encounter of enzyme with the inhibitor followed by the isomerization of the transient enzyme-inhibitor complexes. The temperature-dependent transient kinetic studies with the above inhibitors revealed that the bimolecular process is primarily dominated by favorable enthalpic changes, as opposed to the isomerization step; which is solely contributed by entropic changes. The standard binding-enthalpy (ΔH0) of SAHA, deduced from the transient kinetic as well as the isothermal titration calorimetric experiments, was 2–3 kcal/mol higher as compared to TSA. The experimental data presented herein suggests that SAHA serves as a preferential (target-specific/selective) HDAC8 inhibitor as compared to TSA. Arguments are presented that the detailed kinetic and thermodynamic studies may guide in the rational design of HDAC inhibitors as therapeutic agents. PMID:24079912

  7. Molecular tweezers with varying anions: a comparative study.

    Science.gov (United States)

    Dutt, Som; Wilch, Constanze; Gersthagen, Thomas; Talbiersky, Peter; Bravo-Rodriguez, Kenny; Hanni, Matti; Sánchez-García, Elsa; Ochsenfeld, Christian; Klärner, Frank-Gerrit; Schrader, Thomas

    2013-07-05

    Selective binding of the phosphate-substituted molecular tweezer 1a to protein lysine residues was suggested to explain the inhibition of certain enzymes and the aberrant aggregation of amyloid petide Aβ42 or α-synuclein, which are assumed to be responsible for Alzheimer's and Parkinson's disease, respectively. In this work we systematically investigated the binding of four water-soluble tweezers 1a-d (substituted by phosphate, methanephosphonate, sulfate, or O-methylenecarboxylate groups) to amino acids and peptides containing lysine or arginine residues by using fluorescence spectroscopy, NMR spectroscopy, and isothermal titration calorimetry (ITC). The comparison of the experimental results with theoretical data obtained by a combination of QM/MM and ab initio(1)H NMR shift calculations provides clear evidence that the tweezers 1a-c bind the amino acid or peptide guest molecules by threading the lysine or arginine side chain through the tweezers' cavity, whereas in the case of 1d the guest molecule is preferentially positioned outside the tweezer's cavity. Attractive ionic, CH-π, and hydrophobic interactions are here the major binding forces. The combination of experiment and theory provides deep insight into the host-guest binding modes, a prerequisite to understanding the exciting influence of these tweezers on the aggregation of proteins and the activity of enzymes.

  8. [Is the rate of medical publication from Israel similar to other countries? A comparative study of three medical specialties].

    Science.gov (United States)

    Zer, Matan; Lindner, Arie; Greenstein, Alexander; Leibovici, Dan

    2011-07-01

    Academic careers of individual doctors are commonly evaluated by examining the number and quality of authored publications. Similarly, the extent and quality of medical research may be assessed nationwide by measuring the number of publications originating from the country of interest over time. This in turn, may indicate on the quality of medicine practiced. To evaluate the extent and quality of IsraeLi publications we measured the rate and quality of medical publications originating from Israel for two decades in the fields of urology, cardiology and orthopedics, and compared the data to those of other countries. Leading journals in urology, cardiology, and orthopedics were selected. A Medline search (http://www.ncbi.ntm.nih.gov/sites/entrez] was conducted for all the publications originating in Israel between the years 1990-2009 in the selected journals. Data from Israel was compared to those from Italy, France, Germany, Egypt and Turkey. The change in rate of publications was tested using Linear regression. The quality of publications was calculated by multiplying the number of publications by the relevant impact factor. While the urology publications rate in Israel increased by 32.7% in the second study decade as compared with the first, the urology publication rates during the same time period from Italy, France, Germany, Egypt and Turkey were 199%, 115%, 184%, 180% and 227% respectively. The regression coefficient for the urology publication rate was 0.51 for Israel, and 0.78, 0.95, 0.78, 0.87 and 0.97 for the other countries, respectively. The regression coefficient for the change in the quality of publications from Israel was 0.31 and 0.81, 0.75, 0.92, 0.73, and 0.92 for the other countries, respectively. In cardiology, the Israeli publication rate increased by 26% during the second study decade, whereas in the other countries the increments were 46%, 35%, 76%, 80% and 309% respectively. The regression coefficient for Israeli pubLication rate was 0.45, and

  9. Comparative Analysis of Mass Spectral Similarity Measures on Peak Alignment for Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry

    Science.gov (United States)

    2013-01-01

    Peak alignment is a critical procedure in mass spectrometry-based biomarker discovery in metabolomics. One of peak alignment approaches to comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data is peak matching-based alignment. A key to the peak matching-based alignment is the calculation of mass spectral similarity scores. Various mass spectral similarity measures have been developed mainly for compound identification, but the effect of these spectral similarity measures on the performance of peak matching-based alignment still remains unknown. Therefore, we selected five mass spectral similarity measures, cosine correlation, Pearson's correlation, Spearman's correlation, partial correlation, and part correlation, and examined their effects on peak alignment using two sets of experimental GC×GC-MS data. The results show that the spectral similarity measure does not affect the alignment accuracy significantly in analysis of data from less complex samples, while the partial correlation performs much better than other spectral similarity measures when analyzing experimental data acquired from complex biological samples. PMID:24151524

  10. Novel applications of array comparative genomic hybridization in molecular diagnostics.

    Science.gov (United States)

    Cheung, Sau W; Bi, Weimin

    2018-05-31

    In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

  11. Comparative classical and 'ab initio' molecular dynamics study of molten and glassy germanium dioxide

    International Nuclear Information System (INIS)

    Hawlitzky, M; Horbach, J; Binder, K; Ispas, S; Krack, M

    2008-01-01

    A molecular dynamics (MD) study of the static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modeled by the classical pair potential proposed by Oeffner and Elliott (OE) (1998 Phys. Rev. B 58 14791). We compare our results to experiments and previous simulations. In addition, an 'ab initio' method, the so-called Car-Parrinello molecular dynamics (CPMD), is applied to check the accuracy of the structural properties, as obtained by the classical MD simulations with the OE potential. As in a similar study for SiO 2 , the structure predicted by CPMD is only slightly softer than that resulting from the classical MD. In contrast to earlier simulations, both the static structure and dynamic properties are in very good agreement with pertinent experimental data. MD simulations with the OE potential are also used to study the relaxation dynamics. As previously found for SiO 2 , for high temperatures the dynamics of molten GeO 2 is compatible with a description in terms of mode coupling theory

  12. Molecular biology of the blood-brain and the blood-cerebrospinal fluid barriers: similarities and differences

    Directory of Open Access Journals (Sweden)

    Redzic Zoran

    2011-01-01

    Full Text Available Abstract Efficient processing of information by the central nervous system (CNS represents an important evolutionary advantage. Thus, homeostatic mechanisms have developed that provide appropriate circumstances for neuronal signaling, including a highly controlled and stable microenvironment. To provide such a milieu for neurons, extracellular fluids of the CNS are separated from the changeable environment of blood at three major interfaces: at the brain capillaries by the blood-brain barrier (BBB, which is localized at the level of the endothelial cells and separates brain interstitial fluid (ISF from blood; at the epithelial layer of four choroid plexuses, the blood-cerebrospinal fluid (CSF barrier (BCSFB, which separates CSF from the CP ISF, and at the arachnoid barrier. The two barriers that represent the largest interface between blood and brain extracellular fluids, the BBB and the BCSFB, prevent the free paracellular diffusion of polar molecules by complex morphological features, including tight junctions (TJs that interconnect the endothelial and epithelial cells, respectively. The first part of this review focuses on the molecular biology of TJs and adherens junctions in the brain capillary endothelial cells and in the CP epithelial cells. However, normal function of the CNS depends on a constant supply of essential molecules, like glucose and amino acids from the blood, exchange of electrolytes between brain extracellular fluids and blood, as well as on efficient removal of metabolic waste products and excess neurotransmitters from the brain ISF. Therefore, a number of specific transport proteins are expressed in brain capillary endothelial cells and CP epithelial cells that provide transport of nutrients and ions into the CNS and removal of waste products and ions from the CSF. The second part of this review concentrates on the molecular biology of various solute carrier (SLC transport proteins at those two barriers and underlines

  13. Atrazine Molecular Imprinted Polymers: Comparative Analysis by Far-Infrared and Ultraviolet Induced Polymerization

    Directory of Open Access Journals (Sweden)

    Jun Chen

    2014-01-01

    Full Text Available Atrazine molecular imprinted polymers (MIPs were comparatively synthesized using identical polymer formulation by far-infrared (FIR radiation and ultraviolet (UV-induced polymerization, respectively. Equilibrium binding experiments were carried out with the prepared MIPs; the results showed that MIPuv possessed specific binding to atrazine compared with their MIPFIR radiation counterparts. Scatchard plot’s of both MIPs indicated that the affinities of the binding sites in MIPs are heterogeneous and can be approximated by two dissociation-constants corresponding to the high- and low-affinity binding sites. Moreover, several common pesticides including atrazine, cyromazine, metamitron, simazine, ametryn, terbutryn were tested to determine their specificity, similar imprinting factor (IF and different selectivity index (SI for both MIPs. Physical characterization of the polymers revealed that the different polymerization methods led to slight differences in polymer structures and performance by scanning electron microscope (SEM, Fourier transform infrared absorption (FT-IR, and mercury analyzer (MA. Finally, both MIPs were used as selective sorbents for solid phase extraction (SPE of atrazine from lake water, followed by high performance liquid chromatography (HPLC analysis. Compared with commercial C18 SPE sorbent (86.4%–94.8%, higher recoveries of atrazine in spiked lake water were obtained in the range of 90.1%–97.1% and 94.4%–101.9%, for both MIPs, respectively.

  14. Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation

    Science.gov (United States)

    Wood, Irene; Martini, M. Florencia; Pickholz, Mónica

    2013-08-01

    In this work, we report a molecular dynamics (MD) simulations study of relevant biological molecules as serotonin (neutral and protonated) and its precursors, tryptophan and 5-hydroxy-tryptophan, in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC). The simulations were carried out at the fluid lamellar phase of POPC at constant pressure and temperature conditions. Two guest molecules of each type were initially placed at the water phase. We have analyzed, the main localization, preferential orientation and specific interactions of the guest molecules within the bilayer. During the simulation run, the four molecules were preferentially found at the water-lipid interphase. We found that the interactions that stabilized the systems are essentially hydrogen bonds, salt bridges and cation-π. None of the guest molecules have access to the hydrophobic region of the bilayer. Besides, zwitterionic molecules have access to the water phase, while protonated serotonin is anchored in the interphase. Even taking into account that these simulations were done using a model membrane, our results suggest that the studied molecules could not cross the blood brain barrier by diffusion. These results are in good agreement with works that show that serotonin and Trp do not cross the BBB by simple diffusion.

  15. Comparing the similarity of responses received from studies in Amazon's Mechanical Turk to studies conducted online and with direct recruitment.

    Directory of Open Access Journals (Sweden)

    Christoph Bartneck

    Full Text Available Computer and internet based questionnaires have become a standard tool in Human-Computer Interaction research and other related fields, such as psychology and sociology. Amazon's Mechanical Turk (AMT service is a new method of recruiting participants and conducting certain types of experiments. This study compares whether participants recruited through AMT give different responses than participants recruited through an online forum or recruited directly on a university campus. Moreover, we compare whether a study conducted within AMT results in different responses compared to a study for which participants are recruited through AMT but which is conducted using an external online questionnaire service. The results of this study show that there is a statistical difference between results obtained from participants recruited through AMT compared to the results from the participant recruited on campus or through online forums. We do, however, argue that this difference is so small that it has no practical consequence. There was no significant difference between running the study within AMT compared to running it with an online questionnaire service. There was no significant difference between results obtained directly from within AMT compared to results obtained in the campus and online forum condition. This may suggest that AMT is a viable and economical option for recruiting participants and for conducting studies as setting up and running a study with AMT generally requires less effort and time compared to other frequently used methods. We discuss our findings as well as limitations of using AMT for empirical studies.

  16. Comparing the similarity of responses received from studies in Amazon's Mechanical Turk to studies conducted online and with direct recruitment.

    Science.gov (United States)

    Bartneck, Christoph; Duenser, Andreas; Moltchanova, Elena; Zawieska, Karolina

    2015-01-01

    Computer and internet based questionnaires have become a standard tool in Human-Computer Interaction research and other related fields, such as psychology and sociology. Amazon's Mechanical Turk (AMT) service is a new method of recruiting participants and conducting certain types of experiments. This study compares whether participants recruited through AMT give different responses than participants recruited through an online forum or recruited directly on a university campus. Moreover, we compare whether a study conducted within AMT results in different responses compared to a study for which participants are recruited through AMT but which is conducted using an external online questionnaire service. The results of this study show that there is a statistical difference between results obtained from participants recruited through AMT compared to the results from the participant recruited on campus or through online forums. We do, however, argue that this difference is so small that it has no practical consequence. There was no significant difference between running the study within AMT compared to running it with an online questionnaire service. There was no significant difference between results obtained directly from within AMT compared to results obtained in the campus and online forum condition. This may suggest that AMT is a viable and economical option for recruiting participants and for conducting studies as setting up and running a study with AMT generally requires less effort and time compared to other frequently used methods. We discuss our findings as well as limitations of using AMT for empirical studies.

  17. More Similar but Less Satisfying: Comparing Preferences for and the Efficacy of Within- and Cross-Category Substitutes for Food.

    Science.gov (United States)

    Huh, Young Eun; Vosgerau, Joachim; Morewedge, Carey K

    2016-06-01

    When people cannot get what they want, they often satisfy their desire by consuming a substitute. Substitutes can originate from within the taxonomic category of the desired stimulus (i.e., within-category substitutes) or from a different taxonomic category that serves the same basic goal (i.e., cross-category substitutes). Both a store-brand chocolate (within-category substitute) and a granola bar (cross-category substitute), for example, can serve as substitutes for gourmet chocolate. Here, we found that people believe that within-category substitutes, which are more similar to desired stimuli, will more effectively satisfy their cravings than will cross-category substitutes (Experiments 1, 2a, and 2b). However, because within-category substitutes are more similar than cross-category substitutes to desired stimuli, they are more likely to evoke an unanticipated negative contrast effect. As a result, unless substitutes are equivalent in quality to the desired stimulus, cross-category substitutes more effectively satisfy cravings for the desired stimulus (Experiments 3 and 4). © The Author(s) 2016.

  18. Similarity Digest Search: A Survey and Comparative Analysis of Strategies to Perform Known File Filtering Using Approximate Matching

    Directory of Open Access Journals (Sweden)

    Vitor Hugo Galhardo Moia

    2017-01-01

    Full Text Available Digital forensics is a branch of Computer Science aiming at investigating and analyzing electronic devices in the search for crime evidence. There are several ways to perform this search. Known File Filter (KFF is one of them, where a list of interest objects is used to reduce/separate data for analysis. Holding a database of hashes of such objects, the examiner performs lookups for matches against the target device. However, due to limitations over hash functions (inability to detect similar objects, new methods have been designed, called approximate matching. This sort of function has interesting characteristics for KFF investigations but suffers mainly from high costs when dealing with huge data sets, as the search is usually done by brute force. To mitigate this problem, strategies have been developed to better perform lookups. In this paper, we present the state of the art of similarity digest search strategies, along with a detailed comparison involving several aspects, as time complexity, memory requirement, and search precision. Our results show that none of the approaches address at least these main aspects. Finally, we discuss future directions and present requirements for a new strategy aiming to fulfill current limitations.

  19. Comparative study of adipose-derived stem cells and bone marrow-derived stem cells in similar microenvironmental conditions

    Energy Technology Data Exchange (ETDEWEB)

    Guneta, Vipra [Division of Materials Technology, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); Tan, Nguan Soon [School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); KK Research Centre, KK Women' s and Children Hospital, 100 Bukit Timah Road, Singapore 229899 (Singapore); Institute of Molecular and Cell Biology, Agency for Science Technology & Research - A*STAR, 61 Biopolis Drive, Proteos, Singapore 138673 (Singapore); Chan, Soon Kiat Jeremy [School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); Tanavde, Vivek [Bioinformatics Institute, Agency for Science Technology & Research - A*STAR, 30 Biopolis Street, Matrix, Singapore 138671 (Singapore); Lim, Thiam Chye [Division of Plastic, Reconstructive and Aesthetic Surgery, Department of Surgery, National University Hospital (NUH) and National University of Singapore (NUS), Kent Ridge Wing, Singapore 119074 (Singapore); Wong, Thien Chong Marcus [Plastic, Reconstructive and Aesthetic Surgery Section, Tan Tock Seng Hospital (TTSH), 11, Jalan Tan Tock Seng, Singapore 308433 (Singapore); Choong, Cleo, E-mail: cleochoong@ntu.edu.sg [Division of Materials Technology, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); KK Research Centre, KK Women' s and Children Hospital, 100 Bukit Timah Road, Singapore 229899 (Singapore)

    2016-11-01

    Mesenchymal stem cells (MSCs), which were first isolated from the bone marrow, are now being extracted from various other tissues in the body, including the adipose tissue. The current study presents systematic evidence of how the adipose tissue-derived stem cells (ASCs) and bone marrow-derived mesenchymal stem cells (Bm-MSCs) behave when cultured in specific pro-adipogenic microenvironments. The cells were first characterized and identified as MSCs in terms of their morphology, phenotypic expression, self-renewal capabilities and multi-lineage potential. Subsequently, the proliferation and gene expression profiles of the cell populations cultured on two-dimensional (2D) adipose tissue extracellular matrix (ECM)-coated tissue culture plastic (TCP) and in three-dimensional (3D) AlgiMatrix® microenvironments were analyzed. Overall, it was found that adipogenesis was triggered in both cell populations due to the presence of adipose tissue ECM. However, in 3D microenvironments, ASCs and Bm-MSCs were predisposed to the adipogenic and osteogenic lineages respectively. Overall, findings from this study will contribute to ongoing efforts in adipose tissue engineering as well as provide new insights into the role of the ECM and cues provided by the immediate microenvironment for stem cell differentiation. - Highlights: • Native adipose tissue ECM coated on 2D TCP triggers adipogenesis in both ASCs and Bm-MSCs. • A 3D microenvironment with similar stiffness to adipose tissue induces adipogenic differentiation of ASCs. • ASCs cultured in 3D alginate scaffolds exhibit predisposition to adipogenesis. • Bm-MSCs cultured in 3D alginate scaffolds exhibit predisposition to osteogenesis. • The native microenvironment of the cells affects their differentiation behaviour in vitro.

  20. Injury-related hospital admissions of military dependents compared with similarly aged nonmilitary insured infants, children, and adolescents.

    Science.gov (United States)

    Pressley, Joyce C; Dawson, Patrick; Carpenter, Dustin J

    2012-10-01

    Military deployment of one or both parents is associated with declines in school performance, behavioral difficulties, and increases in reported mental health conditions, but less is known regarding injury risks in pediatric military dependents. Kid Health Care Cost and Utilization Project 2006 (KID) was used to identify military dependents aged 0.1 year to 17 years through expected insurance payer being CHAMPUS, Tricare, or CHAMPVA (n = 12,310) and similarly aged privately insured nonmilitary in CHAMPUS, Tricare, or CHAMPVA states (n = 730,065). Mental health diagnoses per 1,000 hospitalizations and mechanisms of injury per 1,000 injury-related hospitalizations are reported. Unweighted univariate analyses used Fisher's exact, χ(2), and analysis of variance tests for significance. Odds ratios are age and sex adjusted with 95% confidence intervals. Injury-related admissions were higher in military than in nonmilitary dependents (15.5% vs. 13.2%, p sex-adjusted motor vehicle occupant and pedestrian injuries were significantly lower in all-age military dependents but not in age-stratified categories. Very young military dependents had higher all-cause injury admissions (p < 0.0001), drowning/near drowning (p < 0.0001), and intracranial injury (p < 0.0001) and showed a tendency toward higher suffocation (p = 0.055) and crushing injury (p = 0.065). Military adolescents and teenagers had higher suicide/suicide attempts (p = 0.0001) and poisonings from medicinal substances (p = 0.0001). Mental health diagnoses were significantly higher in every age category of military dependents. All-cause in-hospital mortality tended to be greater in military than in nonmilitary dependents (p = 0.052). This study suggests that military dependents are a vulnerable population with special needs and provides clues to areas where injury prevention professionals might begin to address their needs. Prognostic/epidemiologic study, level II.

  1. Comparative study of adipose-derived stem cells and bone marrow-derived stem cells in similar microenvironmental conditions

    International Nuclear Information System (INIS)

    Guneta, Vipra; Tan, Nguan Soon; Chan, Soon Kiat Jeremy; Tanavde, Vivek; Lim, Thiam Chye; Wong, Thien Chong Marcus; Choong, Cleo

    2016-01-01

    Mesenchymal stem cells (MSCs), which were first isolated from the bone marrow, are now being extracted from various other tissues in the body, including the adipose tissue. The current study presents systematic evidence of how the adipose tissue-derived stem cells (ASCs) and bone marrow-derived mesenchymal stem cells (Bm-MSCs) behave when cultured in specific pro-adipogenic microenvironments. The cells were first characterized and identified as MSCs in terms of their morphology, phenotypic expression, self-renewal capabilities and multi-lineage potential. Subsequently, the proliferation and gene expression profiles of the cell populations cultured on two-dimensional (2D) adipose tissue extracellular matrix (ECM)-coated tissue culture plastic (TCP) and in three-dimensional (3D) AlgiMatrix® microenvironments were analyzed. Overall, it was found that adipogenesis was triggered in both cell populations due to the presence of adipose tissue ECM. However, in 3D microenvironments, ASCs and Bm-MSCs were predisposed to the adipogenic and osteogenic lineages respectively. Overall, findings from this study will contribute to ongoing efforts in adipose tissue engineering as well as provide new insights into the role of the ECM and cues provided by the immediate microenvironment for stem cell differentiation. - Highlights: • Native adipose tissue ECM coated on 2D TCP triggers adipogenesis in both ASCs and Bm-MSCs. • A 3D microenvironment with similar stiffness to adipose tissue induces adipogenic differentiation of ASCs. • ASCs cultured in 3D alginate scaffolds exhibit predisposition to adipogenesis. • Bm-MSCs cultured in 3D alginate scaffolds exhibit predisposition to osteogenesis. • The native microenvironment of the cells affects their differentiation behaviour in vitro.

  2. Characterization of ceramic electrical insulators discarded by the electricity distribution networks and compared with similar products without use

    International Nuclear Information System (INIS)

    Franco, C.S.; Mantovani, V.A.; Favero, M.; Morales, J.; Hasegawa, H.L.

    2010-01-01

    The maintenance of distribution networks for electricity generates a large amount of waste. Among these, one of the most representative weights is from porcelain, found in para-rays, braces, insulators. The aim of this study was to evaluate the recycling potential of two models of ceramic insulators, new and used. It had been subjected to comparative tests of scanning electron microscopy, coupled with Energy Dispersive Spectroscopy, x-ray diffraction, contact angle, volatile content and density. In general, samples of new and used ceramic showed no differences that might be associated of material degradation by using. This indicates that the materials discarded and new ones are very close, which may encourage the reuse and recycling. (author)

  3. Recombinant deamidated mutants of Erwinia chrysanthemi L-asparaginase have similar or increased activity compared to wild-type enzyme.

    Science.gov (United States)

    Gervais, David; Foote, Nicholas

    2014-10-01

    The enzyme Erwinia chrysanthemi L-asparaginase (ErA) is an important biopharmaceutical product used in the treatment of acute lymphoblastic leukaemia. Like all proteins, certain asparagine (Asn) residues of ErA are susceptible to deamidation to aspartic acid (Asp), which may be a concern with respect to enzyme activity and potentially to pharmaceutical efficacy. Recombinant ErA mutants containing Asn to Asp changes were expressed, purified and characterised. Two mutants with single deamidation sites (N41D and N281D) were found to have approximately the same specific activity (1,062 and 924 U/mg, respectively) as the wild-type (908 U/mg). However, a double mutant (N41D N281D) had an increased specific activity (1261 U/mg). The N41D mutation conferred a slight increase in the catalytic constant (k cat 657 s(-1)) when compared to the WT (k cat 565 s(-1)), which was further increased in the double mutant, with a k cat of 798 s(-1). Structural analyses showed that the slight changes caused by point mutation of Asn41 to Asp may have reduced the number of hydrogen bonds in this α-helical part of the protein structure, resulting in subtle changes in enzyme turnover, both structurally and catalytically. The increased α-helical content observed with the N41D mutation by circular dichroism spectroscopy correlates with the difference in k cat, but not K m. The N281D mutation resulted in a lower glutaminase activity compared with WT and the N41D mutant, however the N281D mutation also imparted less stability to the enzyme at elevated temperatures. Taken as a whole, these data suggest that ErA deamidation at the Asn41 and Asn281 sites does not affect enzyme activity and should not be a concern during processing, storage or clinical use. The production of recombinant deamidated variants has proven an effective and powerful means of studying the effect of these changes and may be a useful strategy for other biopharmaceutical products.

  4. Detection of molecular markers by comparative sequence analysis of enzymes from mycobacteria species

    International Nuclear Information System (INIS)

    Asad, S.; Hussain, M.; Siddiqua, A.; Ain, Q.U.

    2014-01-01

    Mycobacterial species are one of the most important pathogens and among these members of non-tuberculous mycobacteria (NTM) and mycobacterial tuberculousis complex (MTC) are the causative agent of a relatively milder form of Tuberculosis. Traditional methods for identification of these groups of pathogens are time consuming, lack specificity and sensitivity and furthermore lead to the misidentification due to high similarity index. Therefore, more rapid, specific and cost-effective methods are required for the accurate identification of Mycobacterium species in routine diagnostics. In our study, we identified molecular markers in order to differentiate closely related cousin species of genus Mycobacterium including M. bovis, M. avium, M. leprae and M. tuberculosis. The nucleotide sequences of selected unique markers, i.e., enzymes (used previously in various biochemical tests for the identification of M. species) were selected and their ORFs were retrieved and selected functional proteins of respective biosynthetic pathways were compared in-silico. Result suggested that the variations in nucleotide sequences of the selected enzymes can be directly used for M. species discrimination in one step PCR test. We believe that the in-silico identification and storage of these distinctive characteristics of individual M. species will help in more precise recognition of pathogenic strains and hence specie specific targeted therapy. (author)

  5. Comparative study of the second antibody for radioimmunoassay totally produced in the country to a similar imported one (sheep serum anti-rabbit IgG)

    International Nuclear Information System (INIS)

    Silva, S.R. da; Borghi, V.C.; Wajchenberg, B.L.

    1992-01-01

    This work compares a second antibody for radioimmunoassay (RIA) produced at IPEN-CNEN/SP with a commercial one of known quality, produced by Radioassay Systems Laboratories, U.S.A.. This antiserum, sheep serum anti-rabbit IgG produced in its totality in the country, presented title and precipitation characteristics similar to those exhibited by the commercial product, being as suitable for the RIA separation as its imported similar. (author)

  6. Molecular profiling--a tool for addressing emerging gaps in the comparative risk assessment of GMOs.

    Science.gov (United States)

    Heinemann, Jack A; Kurenbach, Brigitta; Quist, David

    2011-10-01

    Assessing the risks of genetically modified organisms (GMOs) is required by both international agreement and domestic legislation. Many view the use of the "omics" tools for profiling classes of molecules as useful in risk assessment, but no consensus has formed on the need or value of these techniques for assessing the risks of all GMOs. In this and many other cases, experts support case-by-case use of molecular profiling techniques for risk assessment. We review the latest research on the applicability and usefulness of molecular profiling techniques for GMO risk assessment. As more and more kinds of GMOs and traits are developed, broader use of molecular profiling in a risk assessment may be required to supplement the comparative approach to risk assessment. The literature-based discussions on the use of profiling appear to have settled on two findings: 1. profiling techniques are reliable and relevant, at least no less so than other techniques used in risk assessment; and 2. although not required routinely, regulators should be aware of when they are needed. The dismissal of routine molecular profiling may be confusing to regulators who then lack guidance on when molecular profiling might be worthwhile. Molecular profiling is an important way to increase confidence in risk assessments if the profiles are properly designed to address relevant risks and are applied at the correct stage of the assessment. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space.

    Science.gov (United States)

    Koutsoukas, Alexios; Paricharak, Shardul; Galloway, Warren R J D; Spring, David R; Ijzerman, Adriaan P; Glen, Robert C; Marcus, David; Bender, Andreas

    2014-01-27

    Chemical diversity is a widely applied approach to select structurally diverse subsets of molecules, often with the objective of maximizing the number of hits in biological screening. While many methods exist in the area, few systematic comparisons using current descriptors in particular with the objective of assessing diversity in bioactivity space have been published, and this shortage is what the current study is aiming to address. In this work, 13 widely used molecular descriptors were compared, including fingerprint-based descriptors (ECFP4, FCFP4, MACCS keys), pharmacophore-based descriptors (TAT, TAD, TGT, TGD, GpiDAPH3), shape-based descriptors (rapid overlay of chemical structures (ROCS) and principal moments of inertia (PMI)), a connectivity-matrix-based descriptor (BCUT), physicochemical-property-based descriptors (prop2D), and a more recently introduced molecular descriptor type (namely, "Bayes Affinity Fingerprints"). We assessed both the similar behavior of the descriptors in assessing the diversity of chemical libraries, and their ability to select compounds from libraries that are diverse in bioactivity space, which is a property of much practical relevance in screening library design. This is particularly evident, given that many future targets to be screened are not known in advance, but that the library should still maximize the likelihood of containing bioactive matter also for future screening campaigns. Overall, our results showed that descriptors based on atom topology (i.e., fingerprint-based descriptors and pharmacophore-based descriptors) correlate well in rank-ordering compounds, both within and between descriptor types. On the other hand, shape-based descriptors such as ROCS and PMI showed weak correlation with the other descriptors utilized in this study, demonstrating significantly different behavior. We then applied eight of the molecular descriptors compared in this study to sample a diverse subset of sample compounds (4%) from an

  8. Intergenerational Perceptions, Similarities and Differences: A Comparative Analysis of Lesbian, Gay, and Bisexual Millennial Youth with Generation X and Baby Boomers

    Science.gov (United States)

    Vaccaro, Annemarie

    2009-01-01

    This article shares the findings from a qualitative study of 49 lesbian, gay, and bisexual people from three generations: Baby Boomer, Generation X, and Millennial. Baby Boomer and Generation X perceptions of Millennials are compared to the lived experiences as told by the youth themselves. While there were more intergenerational similarities than…

  9. Molecular structural differences between low methoxy pectins induced by pectin methyl esterase II: effects on texture, release and perception of aroma in gels of similar modulus of elasticity.

    Science.gov (United States)

    Kim, Yang; Kim, Young-Suk; Yoo, Sang-Ho; Kim, Kwang-Ok

    2014-02-15

    Six low-methoxy pectins with different degrees of methylesterification and amidation, and molecular weights were used to prepare gels with similar moduli of elasticity by varying the concentrations of pectin and calcium phosphate. Five aroma compounds were added to the gels and their sensory textural properties, release and perception of aromas were investigated. Sensory firmness, springiness, adhesiveness, chewiness and cohesiveness differed according to the gel type, even though the moduli of elasticity were not significantly different (ppectin exhibited the lowest release and perception for all the aroma compounds, while pectin-methylesterase-treated pectin gels exhibited relatively higher aroma release and perception. These results showed that the structural properties of pectins and gelling factors that increase the non-polar character of the gel matrices could decrease the release and perception of aromas in pectin gel systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach

    Science.gov (United States)

    Scott, Milcah C.; Sarver, Aaron L.; Gavin, Katherine J.; Thayanithy, Venugopal; Getzy, David M.; Newman, Robert A.; Cutter, Gary R.; Lindblad-Toh, Kerstin; Kisseberth, William C.; Hunter, Lawrence E.; Subramanian, Subbaya; Breen, Matthew; Modiano, Jaime F.

    2011-01-01

    The heterogeneous and chaotic nature of osteosarcoma has confounded accurate molecular classification, prognosis, and prediction for this tumor. The occurrence of spontaneous osteosarcoma is largely confined to humans and dogs. While the clinical features are remarkably similar in both species, the organization of dogs into defined breeds provides a more homogeneous genetic background that may increase the likelihood to uncover molecular subtypes for this complex disease. We thus hypothesized that molecular profiles derived from canine osteosarcoma would aid in molecular subclassification of this disease when applied to humans. To test the hypothesis, we performed genome wide gene expression profiling in a cohort of dogs with osteosarcoma, primarily from high-risk breeds. To further reduce inter-sample heterogeneity, we assessed tumor-intrinsic properties through use of an extensive panel of osteosarcoma-derived cell lines. We observed strong differential gene expression that segregated samples into two groups with differential survival probabilities. Groupings were characterized by the inversely correlated expression of genes associated with G2/M transition and DNA damage checkpoint and microenvironment-interaction categories. This signature was preserved in data from whole tumor samples of three independent dog osteosarcoma cohorts, with stratification into the two expected groups. Significantly, this restricted signature partially overlapped a previously defined, predictive signature for soft tissue sarcomas, and it unmasked orthologous molecular subtypes and their corresponding natural histories in five independent data sets from human patients with osteosarcoma. Our results indicate that the narrower genetic diversity of dogs can be utilized to group complex human osteosarcoma into biologically and clinically relevant molecular subtypes. This in turn may enhance prognosis and prediction, and identify relevant therapeutic targets. PMID:21621658

  11. Another cat and mouse game: Deciphering the evolution of the SCGB superfamily and exploring the molecular similarity of major cat allergen Fel d 1 and mouse ABP using computational approaches

    Science.gov (United States)

    Pageat, Patrick; Bienboire-Frosini, Cécile

    2018-01-01

    The mammalian secretoglobin (SCGB) superfamily contains functionally diverse members, among which the major cat allergen Fel d 1 and mouse salivary androgen-binding protein (ABP) display similar subunits. We searched for molecular similarities between Fel d 1 and ABP to examine the possibility that they play similar roles. We aimed to i) cluster the evolutionary relationships of the SCGB superfamily; ii) identify divergence patterns, structural overlap, and protein-protein docking between Fel d 1 and ABP dimers; and iii) explore the residual interaction between ABP dimers and steroid binding in chemical communication using computational approaches. We also report that the evolutionary tree of the SCGB superfamily comprises seven unique palm-like clusters, showing the evolutionary pattern and divergence time tree of Fel d 1 with 28 ABP paralogs. Three ABP subunits (A27, BG27, and BG26) share phylogenetic relationships with Fel d 1 chains. The Fel d 1 and ABP subunits show similarities in terms of sequence conservation, identical motifs and binding site clefts. Topologically equivalent positions were visualized through superimposition of ABP A27:BG27 (AB) and ABP A27:BG26 (AG) dimers on a heterodimeric Fel d 1 model. In docking, Fel d 1-ABP dimers exhibit the maximum surface binding ability of AG compared with that of AB dimers and the several polar interactions between ABP dimers with steroids. Hence, cat Fel d 1 is an ABP-like molecule in which monomeric chains 1 and 2 are the equivalent of the ABPA and ABPBG monomers, respectively. These findings suggest that the biological and molecular function of Fel d 1 is similar to that of ABP in chemical communication, possibly via pheromone and/or steroid binding. PMID:29771985

  12. Another cat and mouse game: Deciphering the evolution of the SCGB superfamily and exploring the molecular similarity of major cat allergen Fel d 1 and mouse ABP using computational approaches.

    Science.gov (United States)

    Durairaj, Rajesh; Pageat, Patrick; Bienboire-Frosini, Cécile

    2018-01-01

    The mammalian secretoglobin (SCGB) superfamily contains functionally diverse members, among which the major cat allergen Fel d 1 and mouse salivary androgen-binding protein (ABP) display similar subunits. We searched for molecular similarities between Fel d 1 and ABP to examine the possibility that they play similar roles. We aimed to i) cluster the evolutionary relationships of the SCGB superfamily; ii) identify divergence patterns, structural overlap, and protein-protein docking between Fel d 1 and ABP dimers; and iii) explore the residual interaction between ABP dimers and steroid binding in chemical communication using computational approaches. We also report that the evolutionary tree of the SCGB superfamily comprises seven unique palm-like clusters, showing the evolutionary pattern and divergence time tree of Fel d 1 with 28 ABP paralogs. Three ABP subunits (A27, BG27, and BG26) share phylogenetic relationships with Fel d 1 chains. The Fel d 1 and ABP subunits show similarities in terms of sequence conservation, identical motifs and binding site clefts. Topologically equivalent positions were visualized through superimposition of ABP A27:BG27 (AB) and ABP A27:BG26 (AG) dimers on a heterodimeric Fel d 1 model. In docking, Fel d 1-ABP dimers exhibit the maximum surface binding ability of AG compared with that of AB dimers and the several polar interactions between ABP dimers with steroids. Hence, cat Fel d 1 is an ABP-like molecule in which monomeric chains 1 and 2 are the equivalent of the ABPA and ABPBG monomers, respectively. These findings suggest that the biological and molecular function of Fel d 1 is similar to that of ABP in chemical communication, possibly via pheromone and/or steroid binding.

  13. Molecular identification of similar species of the genus Biomphalaria (Mollusca: Planorbidae determined by a polymerase chain reaction-restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta Lima

    1998-01-01

    Full Text Available The freshwater snails Biomphalaria straminea, B. intermedia, B. kuhniana and B. peregrina, are morphologically similar; based on this similarity the first three species were therefore grouped in the complex B. straminea. The morphological identification of these species is based on characters such as vaginal wrinkling, relation between prepuce: penial sheath:deferens vas and number of muscle layers in the penis wall. In this study the polymerase chain reaction restriction fragment length polymorphism technique was used for molecular identification of these molluscs. This technique is based on the amplification of the internal transcribed spacer regions ITS1 e ITS2 of the ribosomal RNA gene and subsequent digestion of these fragments by restriction enzymes. Six enzymes were tested: Dde I, Mnl I, Hae III, Rsa I, Hpa II e Alu I. The restriction patterns obtained with DdeI presented the best profile for separation of the four species of Biomphalaria. The profiles obtained with all the enzymes were used to estimate the genetic distances among the species through analysis of common banding patterns.

  14. Treatment outcome in patients with triple negative early stage breast cancers compared with other molecular subtypes

    International Nuclear Information System (INIS)

    Kim, Ja Young; Chang, Sei Kyung; Lee, Bo Mi; Shin, Hyun Soo; Park, Heily

    2012-01-01

    To determine whether triple negative (TN) early stage breast cancers have poorer survival rates compared with other molecular types. Between August 2000 and July 2006, patients diagnosed with stage I, II early stage breast cancers, in whom all three markers (estrogen receptor, progesterone receptor, and human epidermal growth factor receptor [HER]-2) were available and treated with modified radical mastectomy or breast conserving surgery followed by radiotherapy, were retrospectively reviewed. Of 446 patients, 94 (21.1%) were classified as TN, 57 (12.8%) as HER-2 type, and 295 (66.1%) as luminal. TN was more frequently associated with young patients younger than 35 years old (p = 0.002), higher histologic grade (p 0.05). We found that patients with TN early stage breast cancers had no difference in survival rates compared with other molecular subtypes. Prospective study in homogeneous treatment group will need for a prognosis of TN early stage breast cancer.

  15. Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

    Science.gov (United States)

    Amalanathan, M.; Jasmine, G. Femina; Roy, S. Dawn Dharma

    2017-08-01

    The molecular structure, vibrational spectra and polarizabilities of Ethyl 4-Dimethylaminobenzoate (EDAB) was investigated by density functional theory employing Becke's three parameter hybrid exchange functional with Lee-Yang-Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set and compared with some other levels. A detailed interpretation of the IR and Raman spectra of EDBA have been reported and analyzed. Complete vibrational assignments of the vibrational modes have been done on the basis of the potential energy distribution (TED) using VEDA software. The molecular electrostatic potential mapped onto total density surface has been obtained. A study on the electronic properties, such as absorption wavelength, and frontier molecular orbitals energy, was performed using DFT approach. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The natural and Mulliken charge also calculated and compared with different level of calculation. The dipole moment, polarizability and first, second order hyperpolarizabilities of the title molecule were calculated and compared with the experimental values. The energy gap between frontier orbitals has been used along with electric moments and first order hyperpolarizability, to understand the non linear optical (NLO) activity of the molecule. The NLO activity of molecule was confirmed by SHG analysis.

  16. A comparative molecular dynamics study on thermostability of human and chicken prion proteins

    International Nuclear Information System (INIS)

    Ji, Hong-Fang; Zhang, Hong-Yu

    2007-01-01

    To compare the thermostabilities of human and chicken normal cellular prion proteins (HuPrP C and CkPrP C ), molecular dynamics (MD) simulations were performed for both proteins at an ensemble level (10 parallel simulations at 400 K and 5 parallel simulations at 300 K as a control). It is found that the thermostability of HuPrP C is comparable with that of CkPrP C , which implicates that the non-occurrence of prion diseases in non-mammals cannot be completely attributed to the thermodynamic properties of non-mammalian PrP C

  17. Tianeptine, olanzapine and fluoxetine show similar restoring effects on stress induced molecular changes in mice brain: An FT-IR study

    Science.gov (United States)

    Türker-Kaya, Sevgi; Mutlu, Oğuz; Çelikyurt, İpek K.; Akar, Furuzan; Ulak, Güner

    2016-05-01

    Chronic stress which can cause a variety of disorders and illness ranging from metabolic and cardiovascular to mental leads to alterations in content, structure and dynamics of biomolecules in brain. The determination of stress-induced changes along with the effects of antidepressant treatment on these parameters might bring about more effective therapeutic strategies. In the present study, we investigated unpredictable chronic mild stress (UCMS)-induced changes in biomolecules in mouse brain and the restoring effects of tianeptine (TIA), olanzapine (OLZ) and fluoxetine (FLX) on these variations, by Fourier transform infrared (FT-IR) spectroscopy. The results revealed that chronic stress causes different membrane packing and an increase in lipid peroxidation, membrane fluidity. A significant increment for lipid/protein, Cdbnd O/lipid, CH3/lipid, CH2/lipid, PO-2/lipid, COO-/lipid and RNA/protein ratios but a significant decrease for lipid/protein ratios were also obtained. Additionally, altered protein secondary structure components were estimated, such as increment in random coils and beta structures. The administration of TIA, OLZ and FLX drugs restored these stress-induced variations except for alterations in protein structure and RNA/protein ratio. This may suggest that these drugs have similar restoring effects on the consequences of stress activity in brain, in spite of the differences in their action mechanisms. All findings might have importance in understanding molecular mechanisms underlying chronic stress and contribute to studies aimed for drug development.

  18. Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

    Science.gov (United States)

    Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

    2011-11-01

    The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.

  19. Molecular epidemiology of mastitis pathogens of dairy cattle and comparative relevance to humans.

    Science.gov (United States)

    Zadoks, Ruth N; Middleton, John R; McDougall, Scott; Katholm, Jorgen; Schukken, Ynte H

    2011-12-01

    Mastitis, inflammation of the mammary gland, can be caused by a wide range of organisms, including gram-negative and gram-positive bacteria, mycoplasmas and algae. Many microbial species that are common causes of bovine mastitis, such as Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae and Staphylococcus aureus also occur as commensals or pathogens of humans whereas other causative species, such as Streptococcus uberis, Streptococcus dysgalactiae subsp. dysgalactiae or Staphylococcus chromogenes, are almost exclusively found in animals. A wide range of molecular typing methods have been used in the past two decades to investigate the epidemiology of bovine mastitis at the subspecies level. These include comparative typing methods that are based on electrophoretic banding patterns, library typing methods that are based on the sequence of selected genes, virulence gene arrays and whole genome sequencing projects. The strain distribution of mastitis pathogens has been investigated within individual animals and across animals, herds, countries and host species, with consideration of the mammary gland, other animal or human body sites, and environmental sources. Molecular epidemiological studies have contributed considerably to our understanding of sources, transmission routes, and prognosis for many bovine mastitis pathogens and to our understanding of mechanisms of host-adaptation and disease causation. In this review, we summarize knowledge gleaned from two decades of molecular epidemiological studies of mastitis pathogens in dairy cattle and discuss aspects of comparative relevance to human medicine.

  20. Molecular modeling studies of structural properties of polyvinyl alcohol: a comparative study using INTERFACE force field.

    Science.gov (United States)

    Radosinski, Lukasz; Labus, Karolina

    2017-10-05

    Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. Graphical abstract Molecular Dynamics and Monte Carlo studies indicate that it is possible to predict properties of the PVA in narrow temperature range by using the INTERFACE force field.

  1. Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae.

    Science.gov (United States)

    Mameaux, Sabine; Cockram, James; Thiel, Thomas; Steuernagel, Burkhard; Stein, Nils; Taudien, Stefan; Jack, Peter; Werner, Peter; Gray, John C; Greenland, Andy J; Powell, Wayne

    2012-01-01

    The genomes of cereals such as wheat (Triticum aestivum) and barley (Hordeum vulgare) are large and therefore problematic for the map-based cloning of agronomicaly important traits. However, comparative approaches within the Poaceae permit transfer of molecular knowledge between species, despite their divergence from a common ancestor sixty million years ago. The finding that null variants of the rice gene cytokinin oxidase/dehydrogenase 2 (OsCKX2) result in large yield increases provides an opportunity to explore whether similar gains could be achieved in other Poaceae members. Here, phylogenetic, molecular and comparative analyses of CKX families in the sequenced grass species rice, brachypodium, sorghum, maize and foxtail millet, as well as members identified from the transcriptomes/genomes of wheat and barley, are presented. Phylogenetic analyses define four Poaceae CKX clades. Comparative analyses showed that CKX phylogenetic groupings can largely be explained by a combination of local gene duplication, and the whole-genome duplication event that predates their speciation. Full-length OsCKX2 homologues in barley (HvCKX2.1, HvCKX2.2) and wheat (TaCKX2.3, TaCKX2.4, TaCKX2.5) are characterized, with comparative analysis at the DNA, protein and genetic/physical map levels suggesting that true CKX2 orthologs have been identified. Furthermore, our analysis shows CKX2 genes in barley and wheat have undergone a Triticeae-specific gene-duplication event. Finally, by identifying ten of the eleven CKX genes predicted to be present in barley by comparative analyses, we show that next-generation sequencing approaches can efficiently determine the gene space of large-genome crops. Together, this work provides the foundation for future functional investigation of CKX family members within the Poaceae. © 2011 National Institute of Agricultural Botany (NIAB). Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell

  2. Dissociation: adjustment or distress? Dissociative phenomena, absorption and quality of life among Israeli women who practice channeling compared to women with similar traumatic history.

    Science.gov (United States)

    Stolovy, Tali; Lev-Wiesel, Rachel; Witztum, Eliezer

    2015-06-01

    This study aimed to explore the relationship between traumatic history, dissociative phenomena, absorption and quality of life among a population of channelers, in comparison with a population of non-channelers with similar traumatic history. The study sample included 150 women. The measures included Traumatic Experiences Scale, Dissociative Experience Scale, Absorption Scale, Brief Symptom Inventory and Quality of Life (QOL) Assessment. Channelers presented significantly higher levels of dissociation, absorption and psychological health compared to the other group. Dissociation and absorption were trauma-related only among the comparison group. Hence, dissociation has different qualities among different people, and spiritual practice contributes to QOL.

  3. The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

    Science.gov (United States)

    Moreno, Inmaculada; Cicinelli, Ettore; Garcia-Grau, Iolanda; Gonzalez-Monfort, Marta; Bau, Davide; Vilella, Felipe; De Ziegler, Dominique; Resta, Leonardo; Valbuena, Diana; Simon, Carlos

    2018-06-01

    Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture

  4. Comparative investigation of third- and fifth-harmonic generation in atomic and molecular gases driven by midinfrared ultrafast laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Ni Jielei; Yao Jinping; Zeng Bin; Chu Wei; Li Guihua; Zhang Haisu; Jing Chenrui [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 800-211, Shanghai 201800 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100039 (China); Chin, S. L. [Department of Physics, Engineering Physics and Optics, and Center for Optics, Photonics and Laser (COPL), Laval University, Laval, Quebec, G1K 7P4 (Canada); Cheng, Y.; Xu, Z. [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 800-211, Shanghai 201800 (China)

    2011-12-15

    We report on the comparative experimental investigation on third- and fifth-harmonic generation (THG and FHG) in atomic and molecular gases driven by midinfrared ultrafast laser pulses at a wavelength of {approx}1500 nm. We observe that the conversion efficiencies of both the THG and FHG processes saturate at similar peak intensities close to {approx}1.5 x 10{sup 14} W/cm{sup 2} for argon, nitrogen, and air, whose ionization potentials are close to each other. Near the saturation intensity, the ratio of yields of the FHG and THG reaches {approx}10{sup -1} for all the gases. Our results show that high-order Kerr effect seems to exist; however, contribution from the fourth-order Kerr refractive index coefficient alone is insufficient to balance the Kerr self-focusing without the assistance of plasma generation.

  5. Driving clinical study efficiency by using a productivity breakdown model: comparative evaluation of a global clinical study and a similar Japanese study.

    Science.gov (United States)

    Takahashi, K; Sengoku, S; Kimura, H

    2011-02-01

    A fundamental management imperative of pharmaceutical companies is to contain surging costs of developing and launching drugs globally. Clinical studies are a research and development (R&D) cost driver. The objective of this study was to develop a productivity breakdown model, or a key performance indicator (KPI) tree, for an entire clinical study and to use it to compare a global clinical study with a similar Japanese study. We, thereby, hope to identify means of improving study productivity. We developed the new clinical study productivity breakdown model, covering operational aspects and cost factors. Elements for improving clinical study productivity were assessed from a management viewpoint by comparing empirical tracking data from a global clinical study with a Japanese study with similar protocols. The following unique and material differences, beyond simple international difference in cost of living, that could affect the efficiency of future clinical trials were identified: (i) more frequent site visits in the Japanese study, (ii) head counts at the Japanese study sites more than double those of the global study and (iii) a shorter enrollment time window of about a third that of the global study at the Japanese study sites. We identified major differences in the performance of the two studies. These findings demonstrate the potential of the KPI tree for improving clinical study productivity. Trade-offs, such as those between reduction in head count at study sites and expansion of the enrollment time window, must be considered carefully. © 2010 Blackwell Publishing Ltd.

  6. An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids.

    Science.gov (United States)

    Li, Yushuang; Song, Tian; Yang, Jiasheng; Zhang, Yi; Yang, Jialiang

    2016-01-01

    In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences. We then apply this method into the ND5 dataset consisting of the ND5 protein sequences of 9 species, and the F10 and G11 datasets representing two of the xylanases containing glycoside hydrolase families, i.e., families 10 and 11. As a result, our method achieves a correlation coefficient of 0.962 with the canonical protein sequence aligner ClustalW in the ND5 dataset, much higher than those of other 5 popular alignment-free methods. In addition, we successfully separate the xylanases sequences in the F10 family and the G11 family and illustrate that the F10 family is more heat stable than the G11 family, consistent with a few previous studies. Moreover, we prove mathematically an identity equation involving the Pseudo-Markov transition probability vector and the amino acids content ratio vector.

  7. Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung.

    Directory of Open Access Journals (Sweden)

    Weiling Zheng

    Full Text Available The fish swimbladder is a unique organ in vertebrate evolution and it functions for regulating buoyancy in most teleost species. It has long been postulated as a homolog of the tetrapod lung, but the molecular evidence is scarce. In order to understand the molecular function of swimbladder as well as its relationship with lungs in tetrapods, transcriptomic analyses of zebrafish swimbladder were carried out by RNA-seq. Gene ontology classification showed that genes in cytoskeleton and endoplasmic reticulum were enriched in the swimbladder. Further analyses depicted gene sets and pathways closely related to cytoskeleton constitution and regulation, cell adhesion, and extracellular matrix. Several prominent transcription factor genes in the swimbladder including hoxc4a, hoxc6a, hoxc8a and foxf1 were identified and their expressions in developing swimbladder during embryogenesis were confirmed. By comparison of enriched transcripts in the swimbladder with those in human and mouse lungs, we established the resemblance of transcriptome of the zebrafish swimbladder and mammalian lungs. Based on the transcriptomic data of zebrafish swimbladder, the predominant functions of swimbladder are in its epithelial and muscular tissues. Our comparative analyses also provide molecular evidence of the relatedness of the fish swimbladder and mammalian lung.

  8. Comparing hair-morphology and molecular methods to identify fecal samples from Neotropical felids.

    Directory of Open Access Journals (Sweden)

    Carlos C Alberts

    Full Text Available To avoid certain problems encountered with more-traditional and invasive methods in behavioral-ecology studies of mammalian predators, such as felids, molecular approaches have been employed to identify feces found in the field. However, this method requires a complete molecular biology laboratory, and usually also requires very fresh fecal samples to avoid DNA degradation. Both conditions are normally absent in the field. To address these difficulties, identification based on morphological characters (length, color, banding, scales and medullar patterns of hairs found in feces could be employed as an alternative. In this study we constructed a morphological identification key for guard hairs of eight Neotropical felids (jaguar, oncilla, Geoffroy's cat, margay, ocelot, Pampas cat, puma and jaguarundi and compared its efficiency to that of a molecular identification method, using the ATP6 region as a marker. For this molecular approach, we simulated some field conditions by postponing sample-conservation procedures. A blind test of the identification key obtained a nearly 70% overall success rate, which we considered equivalent to or better than the results of some molecular methods (probably due to DNA degradation found in other studies. The jaguar, puma and jaguarundi could be unequivocally discriminated from any other Neotropical felid. On a scale ranging from inadequate to excellent, the key proved poor only for the margay, with only 30% of its hairs successfully identified using this key; and have intermediate success rates for the remaining species, the oncilla, Geoffroy's cat, ocelot and Pampas cat, were intermediate. Complementary information about the known distributions of felid populations may be necessary to substantially improve the results obtained with the key. Our own molecular results were even better, since all blind-tested samples were correctly identified. Part of these identifications were made from samples kept in suboptimal

  9. The Effect of Comparatively-Framed versus Similarity-Framed E-Cigarette and Snus Print Ads on Young Adults’ Ad and Product Perceptions

    Science.gov (United States)

    Banerjee, Smita C.; Greene, Kathryn; Li, Yuelin; Ostroff, Jamie S.

    2016-01-01

    Objectives This study examined the effects of comparative-framing [C-F; ads highlighting differences between the advertised product and conventional cigarettes and/or smokeless tobacco products] versus similarity-framing (S-F; ads highlighting congruence with conventional cigarettes and/or smokeless tobacco products) in e-cigarette and snus ads on young adult smokers’ and non-smokers’ ad- and product-related perceptions. Methods One thousand fifty one (1,051) young adults (18–24 years; 76% women; 50% smokers) from existing consumer panels were recruited in a within-subjects quasi-experiment. Each participant viewed 4 online advertisements, varied by tobacco product type (e-cigarette or snus) and ad framing (C-F or S-F). The dependent measures for this study were ad-related (ad perceptions, ad credibility) and product-related perceptions (absolute and comparative risk perceptions, product appeal, and product use intentions). Results Former and current smokers rated C-F ads as more persuasive than S-F ads, as evidenced by favorable ad perceptions and high product use intentions. Former and current smokers also rated e-cigarette ads with more favorable ad perceptions, low absolute and comparative risk perceptions, high product appeal, and high product use intentions as compared to snus ads. However, the effect sizes of the significant differences are less than.2, indicating small magnitude of difference between the study variables. Conclusions Unless FDA regulates e-cig and snus advertising, there is a potential of decreasing risk perceptions and increasing use of e-cigs among young adults. Further research on implicit/explicit comparative claims in e-cigarettes and snus advertisements that encourage risk misperceptions is recommended. PMID:28042597

  10. The Effect of Comparatively-Framed versus Similarity-Framed E-Cigarette and Snus Print Ads on Young Adults' Ad and Product Perceptions.

    Science.gov (United States)

    Banerjee, Smita C; Greene, Kathryn; Li, Yuelin; Ostroff, Jamie S

    2016-07-01

    This study examined the effects of comparative-framing [C-F; ads highlighting differences between the advertised product and conventional cigarettes and/or smokeless tobacco products] versus similarity-framing (S-F; ads highlighting congruence with conventional cigarettes and/or smokeless tobacco products) in e-cigarette and snus ads on young adult smokers' and non-smokers' ad- and product-related perceptions. One thousand fifty one (1,051) young adults (18-24 years; 76% women; 50% smokers) from existing consumer panels were recruited in a within-subjects quasi-experiment. Each participant viewed 4 online advertisements, varied by tobacco product type (e-cigarette or snus) and ad framing (C-F or S-F). The dependent measures for this study were ad-related (ad perceptions, ad credibility) and product-related perceptions (absolute and comparative risk perceptions, product appeal, and product use intentions). Former and current smokers rated C-F ads as more persuasive than S-F ads, as evidenced by favorable ad perceptions and high product use intentions. Former and current smokers also rated e-cigarette ads with more favorable ad perceptions, low absolute and comparative risk perceptions, high product appeal, and high product use intentions as compared to snus ads. However, the effect sizes of the significant differences are less than.2, indicating small magnitude of difference between the study variables. Unless FDA regulates e-cig and snus advertising, there is a potential of decreasing risk perceptions and increasing use of e-cigs among young adults. Further research on implicit/explicit comparative claims in e-cigarettes and snus advertisements that encourage risk misperceptions is recommended.

  11. Comparative 25-OH-vitamin D level in institutionalized women older than 65 years from two cities in Spain and Argentina having a similar solar radiation index.

    Science.gov (United States)

    Portela, María Luz Pita Martin; Mónico, Amália; Barahona, Antonieta; Dupraz, Hernan; Sol Gonzales-Chaves, Macarena Maria; Zeni, Susana Noemi

    2010-03-01

    The present study evaluated and compared vitamin D nutritional status and calcium-phosphorus metabolism in institutionalized women >65 y from two cities that have a similar sun irradiation index (heliophany). The study was carried out in women living in similar social-status institutions from geographic cities having a similar solar radiation index (Lleida, Spain, n=49, and suburban Buenos Aires, Argentina [BA], n=48) at the end of summer. Fish consumption was higher in the Lleida group, as was red-meat consumption in the BA group. In both groups mean calcium intake was 800 mg/d. The daily intake of vitamin D was higher in the BA group (P100 pg/mL were found in 24% and 20% of women in Lleida and BA, respectively. There was a marked increase in carboxy-terminal telopeptide cross-links of type I collagen levels and a decrease in 25OHD with an increase in PTH levels (Pbone alkaline phosphatase increased significantly only when the PTH concentration duplicated the reference range. Even at the end of summer, vitamin D deficiency/insufficiency was prevalent in the two studied institutionalized elderly women. In the narrow range of the dietary calcium intake (close to 800 mg/d) of both studied groups, secondary hyperparathyroidism was absent when 25OHD levels were >17 ng/dL, indicating changes in the regulation control of serum PTH and consequently the changes in this threshold. As a result, vitamin D deficiency must be reversed to avoid the increment in bone turnover and to ensure the endocrine and paracrine functions of vitamin D for overall health and well-being. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  12. Comparative molecular dynamics study of neuromyelitis optica-immunoglobulin G binding to aquaporin-4 extracellular domains.

    Science.gov (United States)

    Alberga, Domenico; Trisciuzzi, Daniela; Lattanzi, Gianluca; Bennett, Jeffrey L; Verkman, Alan S; Mangiatordi, Giuseppe Felice; Nicolotti, Orazio

    2017-08-01

    Neuromyelitis optica (NMO) is an inflammatory demyelinating disease of the central nervous system in which most patients have serum autoantibodies (called NMO-IgG) that bind to astrocyte water channel aquaporin-4 (AQP4). A potential therapeutic strategy in NMO is to block the interaction of NMO-IgG with AQP4. Building on recent observation that some single-point and compound mutations of the AQP4 extracellular loop C prevent NMO-IgG binding, we carried out comparative Molecular Dynamics (MD) investigations on three AQP4 mutants, TP 137-138 AA, N 153 Q and V 150 G, whose 295-ns long trajectories were compared to that of wild type human AQP4. A robust conclusion of our modeling is that loop C mutations affect the conformation of neighboring extracellular loop A, thereby interfering with NMO-IgG binding. Analysis of individual mutations suggested specific hydrogen bonding and other molecular interactions involved in AQP4-IgG binding to AQP4. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Energy Cost and Gait Efficiency of Below-Knee Amputee and Normal Subject with Similar Physical Parameters & Quality of Life: A Comparative Case Study

    Directory of Open Access Journals (Sweden)

    Durbadal Biswas

    2010-10-01

    Full Text Available The study focused on the comparative analysis of energy cost and gait efficiency between a below knee (BK amputee and a reference subject (without amputation. It also attempted to indicate the specific feature responsible for a controlled gait with optimum energy cost for BK amputees. Selection criteria of the subjects were similar physical parameters and quality of life studied with WHOQOL-100 quality of life assessment. A Cosmed® k4 b2 Respiratory Analyzer system was used for the measurement of Oxygen Uptake (VO2, Energy Expenditure per minute (EE and Heart Rate (HR. Gait efficiency (p < 0.0002 was found higher for BK amputee than normal subject. The therapeutic activities and mainly walking rhythm contributed to improve the mobility & balance. This ensures the optimum time & co-ordination of movements and hence improves the gait efficiency for the BK amputee. Comparison with control group was performed to validate the data.

  14. Comparative assessment of groundwater quality in the Tangshan region of the People's Republic of China and similar areas in the U.S.

    Science.gov (United States)

    Domagalski, Joseph L.; Chao, L.; Xinquan, Z.

    2001-01-01

    Groundwater quality with respect to nitrate, major inorganic constituents, stable isotopes, and tritium was assessed in the agricultural Tangshan region in the Hai He River Basin of the People's Republic of China and compared with three regions in the U.S.: the Delmarva Peninsula of Delaware, Maryland, and Virginia; the San Joaquin Valley of California; and the Sacramento Valley of California. The China and U.S. regions are similar in size and land use, but have different climatic conditions and patterns of water use for irrigation. The Tangshan region has been in agricultural production for a much longer time, probably several centuries, than the three U.S. regions; however, the widespread use of synthetic fertilizers and other soil amendments probably started at a similar time in all four regions. In all four regions, median nitrate concentrations were generally below the U.S. drinking water standard of 10 mg/l of nitrate as nitrogen. However, higher concentrations and a greater range were evident for the Tangshan region. In the water samples collected from a shallow aquifer in the Tangshan region (over 25% of all samples), nitrate concentrations exceeded the Chinese standard of 20 mg/l, whereas few comparative samples (2.6%) collected in the U.S. exceeded 20 mg/l. In Tangshan, relatively low nitrate, which is indicative of uncontaminated background concentrations, was measured in older water of deeper wells. Recently recharged water was detected in wells drilled as deep as 150 m. Nitrate concentrations above background levels were also measured in water samples from these wells. In addition to nitrate, the agricultural area of the Tangshan region has been affected by elevated total dissolved solids and iron, the latter attributed to widespread application of animal wastes and sewage deposited on the land surface, which lead to oxygen depletion in the subsurface environment and dissolution of iron. The elevated total dissolved solids of the Tangshan study area

  15. Cytoreductive surgery and HIPEC offers similar outcomes in patients with rectal peritoneal metastases compared to colon cancer patients: a matched case control study.

    Science.gov (United States)

    Simkens, Geert A; van Oudheusden, Thijs R; Braam, Hidde J; Wiezer, Marinus J; Nienhuijs, Simon W; Rutten, Harm J; van Ramshorst, Bert; de Hingh, Ignace H

    2016-04-01

    The effect of cytoreduction and hyperthermic intraperitoneal chemotherapy (HIPEC) in patients with rectal peritoneal metastases (PM) is unclear. This case-control study aims to assess the results of cytoreduction and HIPEC in patients with rectal PM compared to colon PM patients. Colorectal PM patients treated with complete macroscopic cytoreduction and HIPEC were included. Two colon cancer patients were case-matched for each rectal cancer patient, based on prognostic factors (T stage, N stage, histology type, and extent of PM). Short- and long-term outcomes were compared between both groups. From 317 patients treated with complete macroscopic cytoreduction and HIPEC, 29 patients (9.1%) had rectal PM. Fifty-eight colon cases were selected as control patients. Baseline characteristics were similar between groups. Major morbidity was 27.6% and 34.5% in the rectal and colon group, respectively (P = 0.516). Median disease-free survival was 13.5 months in the rectal group and 13.6 months in the colon group (P = 0.621). Two- and five-year overall survival rates were 54%/32% in rectal cancer patients, and 61%/24% in colon cancer patients (P = 0.987). Cytoreduction and HIPEC in selected patients with rectal PM is feasible and provides similar outcomes as in colon cancer patients. Rectal PM should not be regarded a contra-indication for cytoreduction and HIPEC in selected patients. J. Surg. Oncol. 2016;113:548-553. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  16. Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Balaji Petety V

    2006-04-01

    Full Text Available Abstract Background The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%. Results Unlike the sequence similarity servers, fold-recognition servers identified CstII, a α2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15–20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs. Conclusion The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate

  17. Thermodynamic Molecular Switch in Sequence-Specific Hydrophobic Interaction: Two Computational Models Compared

    Directory of Open Access Journals (Sweden)

    Paul Chun

    2003-01-01

    Full Text Available We have shown in our published work the existence of a thermodynamic switch in biological systems wherein a change of sign in ΔCp°(Treaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence, a maximum in the related Keq. We have examined 35 pair-wise, sequence-specific hydrophobic interactions over the temperature range of 273–333 K, based on data reported by Nemethy and Scheraga in 1962. A closer look at a single example, the pair-wise hydrophobic interaction of leucine-isoleucine, will demonstrate the significant differences when the data are analyzed using the Nemethy-Scheraga model or treated by the Planck-Benzinger methodology which we have developed. The change in inherent chemical bond energy at 0 K, ΔH°(T0 is 7.53 kcal mol-1 compared with 2.4 kcal mol-1, while ‹ts› is 365 K as compared with 355 K, for the Nemethy-Scheraga and Planck-Benzinger model, respectively. At ‹tm›, the thermal agitation energy is about five times greater than ΔH°(T0 in the Planck-Benzinger model, that is 465 K compared to 497 K in the Nemethy-Scheraga model. The results imply that the negative Gibbs free energy minimum at a well-defined ‹ts›, where TΔS° = 0 at about 355 K, has its origin in the sequence-specific hydrophobic interactions, which are highly dependent on details of molecular structure. The Nemethy-Scheraga model shows no evidence of the thermodynamic molecular switch that we have found to be a universal feature of biological interactions. The Planck-Benzinger method is the best known for evaluating the innate temperature-invariant enthalpy, ΔH°(T0, and provides for better understanding of the heat of reaction for biological molecules.

  18. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars

    KAUST Repository

    Thind, Anupriya Kaur

    2018-02-08

    Background: Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale. Results: Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes, the old landrace Chinese Spring and the elite Swiss spring wheat line CH Campala Lr22a. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of >100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of 8 Mb, 9 Mb and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Conclusions: This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.

  19. Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae with comparative transcriptomics

    Directory of Open Access Journals (Sweden)

    Dingxuan He

    2018-02-01

    Full Text Available Many plant species exhibit different leaf morphologies within a single plant, or heterophylly. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, at different stages of development, were sequenced using high-throughput sequencing (RNA-Seq, in order to aid gene discovery and functional studies of genes involved in heterophylly. A total of 81,103 unigenes were identified in submerged and floating leaves and 6,822 differentially expressed genes (DEGs were identified by comparing samples at differing time points of development. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways. A total of 24,025 differentially expressed genes were involved in carbon metabolic pathways, biosynthesis of amino acids, ribosomal processes, and plant-pathogen interactions. In particular, KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. The high-throughput transcriptomic results presented here highlight the potential for understanding the molecular mechanisms underlying heterophylly, which is still poorly understood. Further, these data provide a framework to better understand heterophyllous leaf development in P. octandrus via targeted studies utilizing gene cloning and functional analyses.

  20. Cerebrospinal Fluid Aβ43 Is Reduced in Early-Onset Compared to Late-Onset Alzheimer’s Disease, But Has Similar Diagnostic Accuracy to Aβ42

    Directory of Open Access Journals (Sweden)

    Camilla Lauridsen

    2017-06-01

    Full Text Available Background: Amyloid beta 1–43 (Aβ43 may be a useful additional biomarker for diagnosing Alzheimer’s disease (AD. We have investigated cerebrospinal fluid (CSF levels of Aβ43 in patients with early-onset AD in contrast to levels in late-onset AD. For comparison, in addition to the ‘core’ biomarkers, several other analytes were also determined [YKL-40, neurofilament light (NF-L, glial fibrillary acidic protein (GFAP, and progranulin].Material and Methods: Cerebrospinal fluid samples were obtained from patients with early-onset AD (age ≤ 62, n = 66, late-onset AD (age ≥ 68, n = 25, and groups of cognitively intact individuals (age ≤ 62, n = 41, age ≥ 68, n = 39. Core CSF AD biomarkers [amyloid beta 1–42 (Aβ42, total tau, phosphorylated tau] were analyzed, as well as levels of Aβ43 and other analytes, using commercially available enzyme-linked immunosorbent assays.Results: Cerebrospinal fluid Aβ43 was significantly reduced in early-onset AD compared to late-onset AD (14.8 ± 7.3 vs. 21.8 ± 9.4 pg/ml, respectively, whereas the levels of Aβ42 in the two AD groups were not significantly different (474.9 ± 142.0 vs. 539.6 ± 159.9 pg/ml, respectively. Aβ43 and all core biomarkers were significantly altered in patients with AD compared to corresponding controls. NF-L was significantly increased in early-onset AD compared to younger controls, an effect not found between the older groups. Relationships between the Aβ peptides and tau proteins, YKL-40, NF-L, GFAP and progranulin were also investigated without finding marked associations. However, age-associated increases in levels of tau proteins, YKL-40, NF-L and GFAP were found with respect to age in healthy controls. Results for these other analytes were similar to previously published data. Aβ43 did not improve diagnostic accuracy in either AD group compared to Aβ42. Discussion: Cerebrospinal fluid Aβ43, but not Aβ42 levels, varied significantly with age in patients with

  1. Density functional theory, comparative vibrational spectroscopic studies, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis of Linezolid

    Science.gov (United States)

    Rajalakshmi, K.; Gunasekaran, S.; Kumaresan, S.

    2015-06-01

    The Fourier transform infrared spectra and Fourier transform Raman spectra of Linezolid have been recorded in the regions 4,000-400 and 4,000-100 cm-1, respectively. Utilizing the observed Fourier transform infrared spectra and Fourier transform Raman spectra data, a complete vibrational assignment and analysis of the fundamental modes of the compound have been carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, have been calculated by density functional theory with 6-31G(d,p), 6-311G(d,p) and M06-2X/6-31G(d,p) levels. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of Linezolid is reported. Mulliken's net charges have also been calculated. Ultraviolet-visible spectrum of the title molecule has also been calculated using time-dependent density functional method. Besides, molecular electrostatic potential, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis and several thermodynamic properties have been performed by the density functional theoretical method.

  2. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina

    2016-01-01

    spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets....... Our results show that the proposed functions work better than other methods proposed in the literature....

  3. Gender identification of Grasshopper Sparrows comparing behavioral, morphological, and molecular techniques

    Science.gov (United States)

    Ammer, F.K.; Wood, P.B.; McPherson, R.J.

    2008-01-01

    Correct gender identification in monomorphic species is often difficult especially if males and females do not display obvious behavioral and breeding differences. We compared gender specific morphology and behavior with recently developed DNA techniques for gender identification in the monomorphic Grasshopper Sparrow (Ammodramus savannarum). Gender was ascertained with DNA in 213 individuals using the 2550F/2718R primer set and 3% agarose gel electrophoresis. Field observations using behavior and breeding characteristics to identify gender matched DNA analyses with 100% accuracy for adult males and females. Gender was identified with DNA for all captured juveniles that did not display gender specific traits or behaviors in the field. The molecular techniques used offered a high level of accuracy and may be useful in studies of dispersal mechanisms and winter assemblage composition in monomorphic species.

  4. Comparative Assessment of Groundwater Quality in the Tangshan Region of the People�s Republic of China and Similar Areas in the U.S.

    Directory of Open Access Journals (Sweden)

    Joseph L. Domagalski

    2001-01-01

    Full Text Available Groundwater quality with respect to nitrate, major inorganic constituents, stable isotopes, and tritium was assessed in the agricultural Tangshan region in the Hai He River Basin of the People’s Republic of China and compared with three regions in the U.S.: the Delmarva Peninsula of Delaware, Maryland, and Virginia; the San Joaquin Valley of California; and the Sacramento Valley of California. The China and U.S. regions are similar in size and land use, but have different climatic conditions and patterns of water use for irrigation. The Tangshan region has been in agricultural production for a much longer time, probably several centuries, than the three U.S. regions; however, the widespread use of synthetic fertilizers and other soil amendments probably started at a similar time in all four regions. In all four regions, median nitrate concentrations were generally below the U.S. drinking water standard of 10 mg/l of nitrate as nitrogen. However, higher concentrations and a greater range were evident for the Tangshan region. In the water samples collected from a shallow aquifer in the Tangshan region (over 25% of all samples, nitrate concentrations exceeded the Chinese standard of 20 mg/l, whereas few comparative samples (2.6% collected in the U.S. exceeded 20 mg/l. In Tangshan, relatively low nitrate, which is indicative of uncontaminated background concentrations, was measured in older water of deeper wells. Recently recharged water was detected in wells drilled as deep as 150 m. Nitrate concentrations above background levels were also measured in water samples from these wells. In addition to nitrate, the agricultural area of the Tangshan region has been affected by elevated total dissolved solids and iron, the latter attributed to widespread application of animal wastes and sewage deposited on the land surface, which lead to oxygen depletion in the subsurface environment and dissolution of iron. The elevated total dissolved solids of the

  5. 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.

  6. Ultrasound-guided transversus abdominis plane block in patients undergoing open inguinal hernia repair: 0.125% bupivacaine provides similar analgesic effect compared to 0.25% bupivacaine.

    Science.gov (United States)

    Erdoğan Arı, Dilek; Yıldırım Ar, Arzu; Karadoğan, Firdevs; Özcabı, Yetkin; Koçoğlu, Ayşegül; Kılıç, Fatih; Akgün, Fatma Nur

    2016-02-01

    To evaluate the effectiveness of 0.125% bupivacaine compared to 0.25% bupivacaine for ultrasound-guided transversus abdominis plane (TAP) block in patients undergoing open inguinal hernia repair. Randomized, double-blind study. Educational and research hospital. Forty adult patients of American Society of Anesthesiologists physical status I-III undergoing elective primary unilateral open inguinal hernia repair under spinal anesthesia. Patients in group I received 20 mL of 0.25% bupivacaine, whereas patients in group II received 20 mL of 0.125% bupivacaine for TAP block at the end of the surgery. Pain intensity was assessed at rest and during coughing using 10-cm visual analog scale score at 5, 15, 30, and 45 minutes and 1, 2, 4, 6, 12, and 24 hours after TAP block. Morphine consumption and time to first morphine requirement were recorded. Visual analog scale scores at rest and during coughing were not significantly different between groups at all time points measured. Twenty-four hours of morphine consumption (7.72±7.33 mg in group I and 6.06±5.20 mg in group II; P=.437) and time to first morphine requirement (182.35±125.16 minutes in group I and 143.21±87.28 minutes in group II; P=.332) were not different between groups. 0.125% Bupivacaine provides similar analgesic effect compared to 0.25% bupivacaine for ultrasound-guided TAP block in patients undergoing open inguinal hernia repair. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Professional ballet dancers have a similar prevalence of articular cartilage defects compared to age- and sex-matched non-dancing athletes.

    Science.gov (United States)

    Mayes, Susan; Ferris, April-Rose; Smith, Peter; Garnham, Andrew; Cook, Jill

    2016-12-01

    Ballet exposes the hip joint to repetitive loading in extreme ranges of movement and may predispose a dancer to pain and osteoarthritis (OA). The aims of this study were to compare the prevalence of cartilage defects in professional ballet dancers and athletes and to determine the relationship of clinical signs and symptoms. Forty-nine male and female, current and retired professional ballet dancers and 49 age- and sex-matched non-dancing athletes completed hip pain questionnaires, including the Copenhagen Hip and Groin Outcome Score (HAGOS), and underwent hip range of movement (ROM) testing and 3-Tesla magnetic resonance imaging to score cartilage defects (no defect, grade 1: focal partial defect and grade 2: diffuse or full thickness defect). Thirty (61 %) dancers and 27 (55 %) athletes had cartilage defects (p = 0.54). The frequency of grade 1 and 2 cartilage defects did not differ between dancers and athletes (p = 0.83). The frequency of cartilage defects was similar in male and female dancers (p = 0.34), and male and female athletes (p = 0.24). Cartilage defects were not related to history of hip pain (p = 0.34), HAGOS pain (p = 0.14), sports/rec (p = 0.15) scores or hip internal rotation ≤20° (p > 0.01). Cartilage defects were related to age in male dancers (p = 0.002). Ballet dancers do not appear to be at a greater risk of cartilage injury compared to non-dancing athletes. Male dancers develop cartilage defects at an earlier age than athletes and female dancers. Cartilage defects were not related to clinical signs and symptoms; thus, prospective studies are required to determine which cartilage defects progress to symptomatic hip OA.

  8. A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes.

    Science.gov (United States)

    Mazola, Yuliet; Guirola, Osmany; Palomares, Sucel; Chinea, Glay; Menéndez, Carmen; Hernández, Lázaro; Musacchio, Alexis

    2015-09-01

    Arabidopsis thaliana cell wall invertase 1 (AtcwINV1) and Thermotoga maritima β-fructosidase (BfrA) are among the best structurally studied members of the glycoside hydrolase family 32. Both enzymes hydrolyze sucrose as the main substrate but differ strongly in their thermal stability. Mesophilic AtcwINV1 and thermophilic BfrA have divergent sequence similarities in the N-terminal five bladed β-propeller catalytic domain (31 %) and the C-terminal β-sandwich domain (15 %) of unknown function. The two enzymes were subjected to 200 ns molecular dynamics simulations at 300 K (27 °C) and 353 K (80 °C). Regular secondary structure regions, but not loops, in AtcwINV1 and BfrA showed no significant fluctuation differences at both temperatures. BfrA was more rigid than AtcwINV1 at 300 K. The simulation at 353 K did not alter the structural stability of BfrA, but did increase the overall flexibility of AtcwINV1 exhibiting the most fluctuating regions in the β-propeller domain. The simulated heat treatment also increased the gyration radius and hydrophobic solvent accessible surface area of the plant enzyme, consistent with the initial steps of an unfolding process. The preservation of the conformational rigidity of BfrA at 353 K is linked to the shorter size of the protein loops. Shortening of BfrA loops appears to be a key mechanism for thermostability.

  9. Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.

    Science.gov (United States)

    Leroy, G; Verrier, E; Meriaux, J C; Rognon, X

    2009-06-01

    The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.

  10. Improved end-stage high-intensity performance but similar glycemic responses after waxy barley starch ingestion compared to dextrose in type 1 diabetes.

    Science.gov (United States)

    Gray, Benjamin J; Page, Rhydian; Turner, Daniel; West, Daniel J; Campbell, Matthew D; Kilduff, Liam P; Stephens, Jeffrey W; Bain, Stephen C; Bracken, Richard M

    2016-11-01

    Pre-exercise carbohydrate (CHO) ingestion is an effective strategy for reducing the occurrence of hypoglycemia during or after exercise in individuals with type 1 diabetes (T1DM). The metabolic effects of ingestion of different CHOs for glycemic or performance gains have been under-researched. This study compared metabolic responses and fuel use during sub-maximal and high-intensity performance running following pre-exercise ingestion of waxy barley starch (WBS) or dextrose (DEX) in T1DM. Seven participants attended the laboratory on two separate occasions following preliminary testing. On each visit participants consumed either 0.6 g/kg body mass of DEX or WBS 2 hours before a 26-minute discontinuous incremental treadmill protocol (4-minute running: 1.5-min rest) finishing at 80±4% V̇O2peak followed by a 10-min performance run on a non-motorized treadmill. Capillary blood samples were taken at rest, during and following exercise and analyzed for glucose (BG) and acid-base variables. Data (mean ± SEM) were analyzed using repeated measures ANOVA (P0.05). In the final quartile of the performance run, a greater distance was completed under WBS (WBS 323±21 vs. DEX 301±20 m, P=0.02). Consumption of WBS demonstrated similar hyperglycemic responses to dextrose ingestion but a greater rate of CHO use at rest. Interestingly, T1DM individuals displayed an improved performance at the latter stages of a high-intensity run test.

  11. Concurrent validity and clinical utility of the HCR-20V3 compared with the HCR-20 in forensic mental health nursing: similar tools but improved method.

    Science.gov (United States)

    Bjørkly, Stål; Eidhammer, Gunnar; Selmer, Lars Erik

    2014-01-01

    The main scope of this small-scale investigation was to compare clinical application of the HCR-20V3 with its predecessor, the HCR-20. To explore concurrent validity, two experienced nurses assessed 20 forensic mental health service patients with the tools. Estimates of internal consistency for the HCR-20 and the HCR-20V3 were calculated by Cronbach's alpha for two levels of measurement: the H-, C-, and R-scales and the total sum scores. We found moderate (C-scale) to good (H- and R- scales and aggregate scores) estimates of internal consistency and significant differences for the two versions of the HCR. This finding indicates that the two versions reflect common underlying dimensions and that there still appears to be differences between V2 and V3 ratings for the same patients. A case from forensic mental health was used to illustrate similarities and differences in assessment results between the two HCR-20 versions. The case illustration depicts clinical use of the HCR-20V3 and application of two structured nursing interventions pertaining to the risk management part of the tool. According to our experience, Version 3 is superior to Version 2 concerning: (a) item clarity; (b) the distinction between presence and relevance of risk factors; (c) the integration of risk formulation and risk scenario; and (d) the explicit demand to construct a risk management plan as part of the standard assessment procedure.

  12. A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis.

    Science.gov (United States)

    Fakhar, Zeynab; Naiker, Suhashni; Alves, Claudio N; Govender, Thavendran; Maguire, Glenn E M; Lameira, Jeronimo; Lamichhane, Gyanu; Kruger, Hendrik G; Honarparvar, Bahareh

    2016-11-01

    An alarming rise of multidrug-resistant Mycobacterium tuberculosis strains and the continuous high global morbidity of tuberculosis have reinvigorated the need to identify novel targets to combat the disease. The enzymes that catalyze the biosynthesis of peptidoglycan in M. tuberculosis are essential and noteworthy therapeutic targets. In this study, the biochemical function and homology modeling of MurI, MurG, MraY, DapE, DapA, Alr, and Ddl enzymes of the CDC1551 M. tuberculosis strain involved in the biosynthesis of peptidoglycan cell wall are reported. Generation of the 3D structures was achieved with Modeller 9.13. To assess the structural quality of the obtained homology modeled targets, the models were validated using PROCHECK, PDBsum, QMEAN, and ERRAT scores. Molecular dynamics simulations were performed to calculate root mean square deviation (RMSD) and radius of gyration (Rg) of MurI and MurG target proteins and their corresponding templates. For further model validation, RMSD and Rg for selected targets/templates were investigated to compare the close proximity of their dynamic behavior in terms of protein stability and average distances. To identify the potential binding mode required for molecular docking, binding site information of all modeled targets was obtained using two prediction algorithms. A docking study was performed for MurI to determine the potential mode of interaction between the inhibitor and the active site residues. This study presents the first accounts of the 3D structural information for the selected M. tuberculosis targets involved in peptidoglycan biosynthesis.

  13. Comparative molecular species delimitation in the charismatic Nawab butterflies (Nymphalidae, Charaxinae, Polyura).

    Science.gov (United States)

    Toussaint, Emmanuel F A; Morinière, Jérôme; Müller, Chris J; Kunte, Krushnamegh; Turlin, Bernard; Hausmann, Axel; Balke, Michael

    2015-10-01

    The charismatic tropical Polyura Nawab butterflies are distributed across twelve biodiversity hotspots in the Indomalayan/Australasian archipelago. In this study, we tested an array of species delimitation methods and compared the results to existing morphology-based taxonomy. We sequenced two mitochondrial and two nuclear gene fragments to reconstruct phylogenetic relationships within Polyura using both Bayesian inference and maximum likelihood. Based on this phylogenetic framework, we used the recently introduced bGMYC, BPP and PTP methods to investigate species boundaries. Based on our results, we describe two new species Polyura paulettae Toussaint sp. n. and Polyura smilesi Toussaint sp. n., propose one synonym, and five populations are raised to species status. Most of the newly recognized species are single-island endemics likely resulting from the recent highly complex geological history of the Indomalayan-Australasian archipelago. Surprisingly, we also find two newly recognized species in the Indomalayan region where additional biotic or abiotic factors have fostered speciation. Species delimitation methods were largely congruent and succeeded to cross-validate most extant morphological species. PTP and BPP seem to yield more consistent and robust estimations of species boundaries with respect to morphological characters while bGMYC delivered contrasting results depending on the different gene trees considered. Our findings demonstrate the efficiency of comparative approaches using molecular species delimitation methods on empirical data. They also pave the way for the investigation of less well-known groups to unveil patterns of species richness and catalogue Earth's concealed, therefore unappreciated diversity. Published by Elsevier Inc.

  14. Comparative organochlorine accumulation in two ecologically similar shark species (Carcharodon carcharias and Carcharhinus obscurus) with divergent uptake based on different life history.

    Science.gov (United States)

    Beaudry, Marina C; Hussey, Nigel E; McMeans, Bailey C; McLeod, Anne M; Wintner, Sabine P; Cliff, Geremy; Dudley, Sheldon F J; Fisk, Aaron T

    2015-09-01

    Trophic position and body mass are traits commonly used to predict organochlorine burdens. Sharks, however, have a variety of feeding and life history strategies and metabolize lipid uniquely. Because of this diversity, and the lipid-association of organochlorines, the dynamics of organochlorine accumulation in sharks may be predicted ineffectively by stable isotope-derived trophic position and body mass, as is typical for other taxa. The present study compared ontogenetic organochlorine profiles in the dusky shark (Carcharhinus obscurus) and white shark (Carcharodon carcharias), which differ in metabolic thermoregulation and trophic position throughout their ontogeny. Although greater organochlorine concentrations were observed in the larger bodied and higher trophic position white shark (e.g., p,p'-dichlorodiphenyldichloroethylene: 20.2 ± 2.7 ng/g vs 9.3 ± 2.2 ng/g in the dusky shark), slopes of growth-dilution corrected concentrations with age were equal to those of the dusky shark. Similar ontogenetic trophic position increases in both species, less frequent white shark seal predation than previously assumed, or inaccurate species-specific growth parameters are possible explanations. Inshore habitat use (indicated by δ(13)C values) and mass were important predictors in white and dusky sharks, respectively, of both overall compound profiles and select organochlorine concentrations. The present study clarified understanding of trophic position and body mass as reliable predictors of interspecific organochlorine accumulation in sharks, whereas regional endothermy and diet shifting were shown to have less impact on overall rates of accumulation. © 2015 SETAC.

  15. Comparative characterization of humic substances extracted from freshwater and peat of different apparent molecular sizes

    Directory of Open Access Journals (Sweden)

    Eliane Sloboda Rigobello

    2017-09-01

    Full Text Available This paper compares the structural characteristics of aquatic humic substances (AHS with humic substances from peat (HSP through different analytical techniques, including elemental analysis, solid state 13C cross polarization/magic-angle-spinning nuclear magnetic resonance spectroscopy (13C CP-MAS NMR, ultraviolet/visible (UV/Vis spectroscopy and Fourier transform infrared (FTIR spectroscopy and total organic carbon (TOC. The AHS were extracted from water collected in a tributary of the Itapanhaú River (Bertioga/SP using XAD 8 resin, and the HSP were extracted from peat collected in the Mogi Guaçu River bank (Luis Antonio/SP with a KOH solution. After dialysis, both AHS and HSP extracts were filtered in membrane of 0.45 µm pore size (Fraction F1: < 0.45 µm and fractioned by ultrafiltration in different apparent molecular sizes (AMS (F2: 100 kDa-0.45 μm; F3: 30 kDa-100 kDa and F4: < 30 kDa. The extracts with the lowest AMS (F3 and F4 showed a higher number of aliphatic carbons than aromatic carbons, a higher concentration of groups containing oxygen and a higher percentage of fulvic acids (FA than humic acids (HA for both AHS and HSP. However, the AHS presented higher FA than HA content in relation to the HSP and distinct structural properties.

  16. Comparative molecular analysis of evolutionarily distant glyceraldehyde-3-phosphate dehydrogenase from Sardina pilchardus and Octopus vulgaris.

    Science.gov (United States)

    Baibai, Tarik; Oukhattar, Laila; Mountassif, Driss; Assobhei, Omar; Serrano, Aurelio; Soukri, Abdelaziz

    2010-12-01

    The NAD(+)-dependent cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12), which is recognized as a key to central carbon metabolism in glycolysis and gluconeogenesis and as an important allozymic polymorphic biomarker, was purified from muscles of two marine species: the skeletal muscle of Sardina pilchardus Walbaum (Teleost, Clupeida) and the incompressible arm muscle of Octopus vulgaris (Mollusca, Cephalopoda). Comparative biochemical studies have revealed that they differ in their subunit molecular masses and in pI values. Partial cDNA sequences corresponding to an internal region of the GapC genes from Sardina and Octopus were obtained by polymerase chain reaction using degenerate primers designed from highly conserved protein motifs. Alignments of the deduced amino acid sequences were used to establish the 3D structures of the active site of two enzymes as well as the phylogenetic relationships of the sardine and octopus enzymes. These two enzymes are the first two GAPDHs characterized so far from teleost fish and cephalopod, respectively. Interestingly, phylogenetic analyses indicated that the sardina GAPDH is in a cluster with the archetypical enzymes from other vertebrates, while the octopus GAPDH comes together with other molluscan sequences in a distant basal assembly closer to bacterial and fungal orthologs, thus suggesting their different evolutionary scenarios.

  17. Molecular Characterization and Comparative Phylogenetic Analysis of Phytases from Fungi with Their Prospective Applications

    Directory of Open Access Journals (Sweden)

    Sharad Tiwari

    2013-01-01

    Full Text Available Plant seeds that have high phytate content are used as animal feed. Phytases, enzymes that catalyze the breakdown of phytate into inorganic phosphorus and myoinositol phosphate derivatives, have been intensively studied in recent years and gained immense attention because of their application in reducing phytate content in animal feed and food for human consumption, thus indirectly lowering environmental pollution caused by undigested phytate. This review is focused on summarising the current knowledge on recent developments of fungal and yeast phytases. Comparative account on diverse sources and physiological roles, molecular characteristics and regulation mechanisms of phytases are discussed. Phylogenetic relationship of phytases from different classes of fungi is studied in details. It is inferred on the basis of phylogeny that phytases from Ascomycetes and Basidiomycetes differ in the amino acid sequences, therefore they fall in separate clade in the tree. The prospective biotechnological applications of microbial phytases such as animal feed additives, probiotics, pharmaceuticals, as well as in aquaculture, food industry, paper manufacturing, development of transgenic plants and animals with special reference to its use as biofertilizers are also emphasised in this review.

  18. Comparative Analytical Utility of DNA Derived from Alternative Human Specimens for Molecular Autopsy and Diagnostics

    Science.gov (United States)

    Klassen, Tara L.; von Rüden, Eva-Lotta; Drabek, Janice; Noebels, Jeffrey L.; Goldman, Alica M.

    2013-01-01

    Genetic testing and research have increased the demand for high-quality DNA that has traditionally been obtained by venipuncture. However, venous blood collection may prove difficult in special populations and when large-scale specimen collection or exchange is prerequisite for international collaborative investigations. Guthrie/FTA card–based blood spots, buccal scrapes, and finger nail clippings are DNA-containing specimens that are uniquely accessible and thus attractive as alternative tissue sources (ATS). The literature details a variety of protocols for extraction of nucleic acids from a singular ATS type, but their utility has not been systematically analyzed in comparison with conventional sources such as venous blood. Additionally, the efficacy of each protocol is often equated with the overall nucleic acid yield but not with the analytical performance of the DNA during mutation detection. Together with a critical in-depth literature review of published extraction methods, we developed and evaluated an all-inclusive approach for serial, systematic, and direct comparison of DNA utility from multiple biological samples. Our results point to the often underappreciated value of these alternative tissue sources and highlight ways to maximize the ATS-derived DNA for optimal quantity, quality, and utility as a function of extraction method. Our comparative analysis clarifies the value of ATS in genomic analysis projects for population-based screening, diagnostics, molecular autopsy, medico-legal investigations, or multi-organ surveys of suspected mosaicisms. PMID:22796560

  19. Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes.

    Science.gov (United States)

    Carlson, David E; Hedin, Marshal

    2017-01-01

    Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.

  20. Effect O6-Guanine Alkylation on DNA Flexibility Studied by Comparative Molecular Dynamics Simulations

    Czech Academy of Sciences Publication Activity Database

    Kara, M.; Dršata, Tomáš; Lankaš, Filip; Zacharias, M.

    2015-01-01

    Roč. 103, č. 1 (2015), s. 23-32 ISSN 0006-3525 R&D Projects: GA ČR(CZ) GA14-21893S Institutional support: RVO:61388963 Keywords : DNA damage * DNA alkylation * DNA repair * molecular simulation * molecular dynamics simulation Subject RIV: BO - Biophysics Impact factor: 2.248, year: 2015

  1. A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

    Science.gov (United States)

    Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

    2011-01-01

    Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

  2. Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability.

    Science.gov (United States)

    Marchetti, Adrian; Schruth, David M; Durkin, Colleen A; Parker, Micaela S; Kodner, Robin B; Berthiaume, Chris T; Morales, Rhonda; Allen, Andrew E; Armbrust, E Virginia

    2012-02-07

    In vast expanses of the oceans, growth of large phytoplankton such as diatoms is limited by iron availability. Diatoms respond almost immediately to the delivery of iron and rapidly compose the majority of phytoplankton biomass. The molecular bases underlying the subsistence of diatoms in iron-poor waters and the plankton community dynamics that follow iron resupply remain largely unknown. Here we use comparative metatranscriptomics to identify changes in gene expression associated with iron-stimulated growth of diatoms and other eukaryotic plankton. A microcosm iron-enrichment experiment using mixed-layer waters from the northeastern Pacific Ocean resulted in increased proportions of diatom transcripts and reduced proportions of transcripts from most other taxa within 98 h after iron addition. Hundreds of diatom genes were differentially expressed in the iron-enriched community compared with the iron-limited community; transcripts of diatom genes required for synthesis of photosynthesis and chlorophyll components, nitrate assimilation and the urea cycle, and synthesis of carbohydrate storage compounds were significantly overrepresented. Transcripts of genes encoding rhodopsins in eukaryotic phytoplankton were significantly underrepresented following iron enrichment, suggesting rhodopsins help cells cope with low-iron conditions. Oceanic diatoms appear to display a distinctive transcriptional response to iron enrichment that allows chemical reduction of available nitrogen and carbon sources along with a continued dependence on iron-free photosynthetic proteins rather than substituting for iron-containing functional equivalents present within their gene repertoire. This ability of diatoms to divert their newly acquired iron toward nitrate assimilation may underlie why diatoms consistently dominate iron enrichments in high-nitrate, low-chlorophyll regions.

  3. Effect O6-guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations.

    Science.gov (United States)

    Kara, Mahmut; Drsata, Tomas; Lankas, Filip; Zacharias, Martin

    2015-01-01

    Alkylation of guanine at the O6 atom is a highly mutagenic DNA lesion because it alters the coding specificity of the base causing G:C to A:T transversion mutations. Specific DNA repair enzymes, e.g. O(6)-alkylguanin-DNA-Transferases (AGT), recognize and repair such damage after looping out the damaged base to transfer it into the enzyme active site. The exact mechanism how the repair enzyme identifies a damaged site within a large surplus of undamaged DNA is not fully understood. The O(6)-alkylation of guanine may change the deformability of DNA which may facilitate the initial binding of a repair enzyme at the damaged site. In order to characterize the effect of O(6)-methyl-guanine (O(6)-MeG) containing base pairs on the DNA deformability extensive comparative molecular dynamics (MD) simulations on duplex DNA with central G:C, O(6)-MeG:C or O(6)-MeG:T base pairs were performed. The simulations indicate significant differences in the helical deformability due to the presence of O(6)-MeG compared to regular undamaged DNA. This includes enhanced base pair opening, shear and stagger motions and alterations in the backbone fine structure caused in part by transient rupture of the base pairing at the damaged site and transient insertion of water molecules. It is likely that the increased opening motions of O(6)-MeG:C or O(6)-MeG:T base pairs play a decisive role for the induced fit recognition or for the looping out of the damaged base by repair enzymes. © 2014 Wiley Periodicals, Inc.

  4. Comparative characterization of molecular varieties of thyroxine-binding human globulin

    International Nuclear Information System (INIS)

    Ermolenko, M.N.; Sviridov, O.V.; Strel'chenok, O.A.

    1986-01-01

    Two molecular varieties of thyroxine-binding globulin (TBG) of human retroplacental blood, obtained as a result of fractionation of pure TBG on concanavalin A-Sepharose, were studied. It was shown that these varieties (TBG-1 and TBG-2) are immunologically identical; they have the same molecular weight and amino acid composition, exhibit the same affinity for thyroid hormones, and are indistinguishable in spectral characteristics. And yet, TBG-1 and TBG-2 have differences in charge, detectable in isoelectrofocusing, and a different monosaccharide composition. The existence of molecular varieties of TBG during pregnancy is apparently due to the peculiarities of the glycosylation of the polypeptide chain during TBG biosynthesis

  5. High level of molecular and phenotypic biodiversity in Jatropha curcas from Central America compared to Africa, Asia and South America

    Science.gov (United States)

    2014-01-01

    Background The main bottleneck to elevate jatropha (Jatropha curcas L.) from a wild species to a profitable biodiesel crop is the low genetic and phenotypic variation found in different regions of the world, hampering efficient plant breeding for productivity traits. In this study, 182 accessions from Asia (91), Africa (35), South America (9) and Central America (47) were evaluated at genetic and phenotypic level to find genetic variation and important traits for oilseed production. Results Genetic variation was assessed with SSR (Simple Sequence Repeat), TRAP (Target Region Amplification Polymorphism) and AFLP (Amplified fragment length polymorphism) techniques. Phenotypic variation included seed morphological characteristics, seed oil content and fatty acid composition and early growth traits. Jaccard’s similarity and cluster analysis by UPGM (Unweighted Paired Group Method) with arithmetic mean and PCA (Principle Component Analysis) indicated higher variability in Central American accessions compared to Asian, African and South American accessions. Polymorphism Information Content (PIC) values ranged from 0 to 0.65. In the set of Central American accessions. PIC values were higher than in other regions. Accessions from the Central American population contain alleles that were not found in the accessions from other populations. Analysis of Molecular Variance (AMOVA; P jatropha oil significantly differed (P < 0.05) between regions. Conclusions The pool of Central American accessions showed very large genetic variation as assessed by DNA-marker variation compared to accessions from other regions. Central American accessions also showed the highest phenotypic variation and should be considered as the most important source for plant breeding. Some variation in early growth traits was found within a group of accessions from Asia and Africa, while these accessions did not differ in a single DNA-marker, possibly indicating epigenetic variation. PMID:24666927

  6. Molecular composition of the W chromatin in some moth species studied by comparative genomic hybridization (CGH)

    Czech Academy of Sciences Publication Activity Database

    Sahara, K.; Marec, František; Eickhoff, U.; Traut, E.

    09, č. 1 (2001), s. 78 ISSN 0967-3849. [International Chromosome Conference /14./. 04.09.2001-08.09.2001, Wurzburg] Institutional research plan: CEZ:Av0Z5007907 Keywords : W chromatin Subject RIV: EB - Genetics ; Molecular Biology

  7. Molecular Detection of Streptococcus pneumoniae on Dried Blood Spots from Febrile Nigerian Children Compared to Culture.

    Directory of Open Access Journals (Sweden)

    Pui-Ying Iroh Tam

    Full Text Available Nigeria has one of the highest burdens of pneumococcal disease in the world, but accurate surveillance is lacking. Molecular detection of infectious pathogens in dried blood spots (DBS is an ideal method for surveillance of infections in resource-limited settings because of its low cost, minimal blood volumes involved, and ease of storage at ambient temperature. Our study aim was to evaluate a Streptococcus pneumoniae real-time polymerase chain reaction (rt-PCR assay on DBS from febrile Nigerian children on Whatman 903 and FTA filter papers, compared to the gold standard of culture.Between September 2011 to May 2015, blood was collected from children 5 years of age or under who presented to six hospital study sites throughout northern and central Nigeria with febrile illness, and inoculated into blood culture bottles or spotted onto Whatman 903 or FTA filter paper. Culture and rt-PCR were performed on all samples.A total of 537 DBS specimens from 535 children were included in the study, of which 15 were culture-positive for S. pneumoniae. The rt-PCR assay detected S. pneumoniae in 12 DBS specimens (2.2%. One positive rt-PCR result was identified in a culture-negative specimen from a high-risk subject, and two positive rt-PCR results were negative on repeat testing. Six culture-confirmed cases of S. pneumoniae bacteremia were missed. Compared to culture, the overall sensitivities of Whatman 903 and FTA DBS for detection of S. pneumoniae were 57.1% (95% CI 18.4-90.1% and 62.5% (95% CI 24.5-91.5%, respectively. Nonspecific amplification was noted in an additional 22 DBS (4.1%. Among these, six were positive for a non-S. pneumoniae pathogen on culture.Rt-PCR was able to detect S. pneumoniae from clinical DBS specimens, including from a culture-negative specimen. Our findings show promise of this approach as a surveillance diagnostic, but also raise important cautionary questions. Several DBS specimens were detected as S. pneumoniae by rt-PCR despite

  8. Molecular Detection of Streptococcus pneumoniae on Dried Blood Spots from Febrile Nigerian Children Compared to Culture.

    Science.gov (United States)

    Iroh Tam, Pui-Ying; Hernandez-Alvarado, Nelmary; Schleiss, Mark R; Hassan-Hanga, Fatimah; Onuchukwu, Chuma; Umoru, Dominic; Obaro, Stephen K

    2016-01-01

    Nigeria has one of the highest burdens of pneumococcal disease in the world, but accurate surveillance is lacking. Molecular detection of infectious pathogens in dried blood spots (DBS) is an ideal method for surveillance of infections in resource-limited settings because of its low cost, minimal blood volumes involved, and ease of storage at ambient temperature. Our study aim was to evaluate a Streptococcus pneumoniae real-time polymerase chain reaction (rt-PCR) assay on DBS from febrile Nigerian children on Whatman 903 and FTA filter papers, compared to the gold standard of culture. Between September 2011 to May 2015, blood was collected from children 5 years of age or under who presented to six hospital study sites throughout northern and central Nigeria with febrile illness, and inoculated into blood culture bottles or spotted onto Whatman 903 or FTA filter paper. Culture and rt-PCR were performed on all samples. A total of 537 DBS specimens from 535 children were included in the study, of which 15 were culture-positive for S. pneumoniae. The rt-PCR assay detected S. pneumoniae in 12 DBS specimens (2.2%). One positive rt-PCR result was identified in a culture-negative specimen from a high-risk subject, and two positive rt-PCR results were negative on repeat testing. Six culture-confirmed cases of S. pneumoniae bacteremia were missed. Compared to culture, the overall sensitivities of Whatman 903 and FTA DBS for detection of S. pneumoniae were 57.1% (95% CI 18.4-90.1%) and 62.5% (95% CI 24.5-91.5%), respectively. Nonspecific amplification was noted in an additional 22 DBS (4.1%). Among these, six were positive for a non-S. pneumoniae pathogen on culture. Rt-PCR was able to detect S. pneumoniae from clinical DBS specimens, including from a culture-negative specimen. Our findings show promise of this approach as a surveillance diagnostic, but also raise important cautionary questions. Several DBS specimens were detected as S. pneumoniae by rt-PCR despite growth of

  9. Clinical features of patients with nodal marginal zone lymphoma compared to follicular lymphoma: similar presentation, but differences in prognostic factors and rate of transformation.

    Science.gov (United States)

    van den Brand, Michiel; van der Velden, Walter J F M; Diets, Illja J; Ector, Geneviève I C G; de Haan, Anton F J; Stevens, Wendy B C; Hebeda, Konnie M; Groenen, Patricia J T A; van Krieken, Han J M

    2016-07-01

    Nodal marginal zone lymphoma (NMZL) is a rare type of B-cell non-Hodgkin lymphoma. This study assessed the clinical features of 56 patients with NMZL in comparison to 46 patients with follicular lymphoma (FL). Patients with NMZL and FL had a largely similar clinical presentation, but patients with FL had a higher disease stage at presentation, more frequent abdominal lymphadenopathy and bone marrow involvement, and showed more common transformation into diffuse large B-cell lymphoma (DLBCL) during the course of disease. Overall survival and event-free survival were similar for patients with NMZL and FL, but factors associated with worse prognosis differed between the two groups. Transformation into DLBCL was associated with a significantly poorer outcome in both groups, but the phenotypes were different: DLBCL arising in FL was mainly of germinal center B-cell phenotype, whereas DLBCL arising in NMZL was mainly of non-germinal center B-cell phenotype.

  10. Patients cured from craniopharyngioma or nonfunctioning pituitary macroadenoma (NFMA) suffer similarly from increased daytime somnolence despite normal sleep patterns compared to healthy controls

    NARCIS (Netherlands)

    van der Klaauw, Agatha A.; Biermasz, Nienke R.; Pereira, Alberto M.; van Kralingen, Klaas W.; Dekkers, Olaf M.; Rabe, Klaus F.; Smit, Johannes W. A.; Romijn, Johannes A.

    2008-01-01

    Adults patients previously treated for craniopharyngioma have increased general and physical fatigue compared to healthy controls. This could be related to disturbed sleep patterns. The aim of this study was to compare sleepiness and sleep patterns in those patients to healthy controls and to

  11. Molecular characterization of a Leishmania donovani cDNA clone with similarity to human 20S proteasome a-type subunit

    DEFF Research Database (Denmark)

    Christensen, C B; Jørgensen, L; Jensen, A T

    2000-01-01

    Using plasma from patients infected or previously infected with Leishmania donovanii, we isolated a L. donovanii cDNA clone with similarity to the proteasome a-type subunit from humans and other eukaryotes. The cDNA clone, designated LePa, was DNA sequenced and Northern blot analysis of L....... donovanii poly(A(+))mRNA indicated the isolation of a full length cDNA clone with a transcript size of 1.9 kb. The expressed recombinant LePa fusion protein induced proliferation of peripheral blood mononuclear cells in one out of seven patients who had suffered from visceral leishmaniasis. Plasma from 16...

  12. Comparative molecular neuroanatomy of mammalian neocortex: what can gene expression tell us about areas and layers?

    Science.gov (United States)

    Watakabe, Akiya

    2009-04-01

    It is over 100 years since Brodmann proposed the homology of layer and area structure of the cerebral cortex across species. His proposal was based on the extensive comparative analyses of various mammalian brains. Although such homology is now well accepted, the recent data in our laboratory showed striking variations of gene expression patterns across areas and species. Are cortical layers and areas really homologous? If they are, to what extent and how are they similar or different? We are trying to answer these questions by identifying the homologous neuronal types common to various areas and species. Toward this goal, we started to classify the cortical pyramidal neurons by expression of particular sets of genes. By using fluorescent double in situ hybridization combined with retrograde tracers, we are characterizing the gene expression phenotypes and projection specificity of cortical excitatory neuron types. In this review, I discuss the recent findings in our laboratory in light of the past and present knowledge about cortical cell types, which provides insight to the homology (and lack thereof) of the mammalian neocortical organization.

  13. A single midcycle dose of levonorgestrel similar to emergency contraceptive does not alter the expression of the L-selectin ligand or molecular markers of endometrial receptivity.

    Science.gov (United States)

    Palomino, Wilder Alberto; Kohen, Paulina; Devoto, Luigi

    2010-10-01

    To examine the effects of a single-dose of 1.5 mg of levonorgestrel (commonly used as emergency contraceptive) on endometrial receptivity biomarkers through the oral or vaginal route. Prospective randomized single-blinded trial. Affiliated Hospital and University Research Center. Fertile normal women previously sterilized by tubal ligation. Levonorgestrel (1.5 mg) was administered on the day of LH surge either orally (n = 14) or vaginally (n = 13). Molecular assessment of endometrial progesterone receptors, L-selectin ligand, glicodelin-A and αvβ3 integrin by Immunohistochemistry and reverse transcriptase-polymerase chain reaction. Plasma progesterone concentration and endometrial dating were not different. The pattern of progesterone receptors and glycodelin-A expression was not affected during the early and midsecretory phase. Some endometrial biopsies from the group in which levonorgetrel was orally administered showed areas of glandular atrophy and stromal decidualization. However, the expression of the progesterone receptor, L-selectin ligand, αvβ3 integrin, and glycodelin-A were not different between the groups. Levonorgestrel, given as emergency contraceptive on the day of LH surge, does not disrupt either ovulation or progesterone production by the corpus luteum. The contraceptive mechanism of levonorgestrel at the time of LH surge does not include changes in the progesterone receptors or the endometrial receptivity biomarkers. Copyright © 2010 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  14. Comparative anatomy of the frontal sinuses in the primitive sabre-toothed felid Promegantereon ogygia (Felidae, Machairodontinae and similarly sized extant felines

    Directory of Open Access Journals (Sweden)

    Morales, J.

    2011-12-01

    Full Text Available In the present work, the frontal sinuses of the sabre-toothed felid Promegantereon ogygia are analysed, in comparison to those of the extant felines Acinonyx jubatus, Puma conocolor and Panthera pardus, of similar body weight. The study was carried out using 3D virtual models obtained from CT Scan images, a non-destructive technique that has revealed as a powerful tool for accessing to all kind of intracranial information. Our study shows that the frontal sinuses of P. ogygia were more similar to those of P. concolor, both in the presence of several struts reinforcing the dorsal part, and in the development of a remarkable caudal expansion. This caudal expansion would act as a thermal insulator of the brain, and would indicate a more open environment than previously supposed for this species, whereas the struts would be related to biomechanical stresses produced during the “canine shear-bite”, the killing method of the machairodontines.En el presente trabajo, se analizan los senos frontales del félido dientes de sable Promegantereon ogygia, en comparación con los de los felinos actuales Acinonyx jubatus, Puma conocolor y Panthera pardus, de similar peso corporal. El estudio se llevó a cabo utilizando modelos virtuales 3D obtenidos por tomografía axial computerizada, una técnica no destructiva que se ha revelado como una poderosa herramienta para acceder a todo tipo de información intracraneal. Nuestro estudio muestra que los senos frontales de P. ogygia eran más similares a los de P. concolor, tanto en la presencia de varios puntales óseos de refuerzo de la parte dorsal, y en el desarrollo de una notable expansión caudal. Esta expansión caudal actuaría como un aislante térmico del cerebro, y podría indicar un entorno más abierto de lo que se supone para esta especie, mientras que los puntales óseos se relacionarían con tensiones biomecánicas producidas durante el mordisco típico de los macairodontinos, el método de ataque

  15. A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties

    NARCIS (Netherlands)

    Roldán-Ruiz, I.; Eeuwijk, van F.A.; Gilliland, T.J.; Dubreuil, P.; Dillmann, C.; Lallemand, J.; Loose, De M.; Baril, C.P.

    2001-01-01

    A sample set of registered perennial ryegrass varieties was used to compare how morphological characterisation and AFLP® (AFLP® is a registered trademark of Keygene N.V.) and STS molecular markers described variety relationships. All the varieties were confirmed as morphologically distinct, and both

  16. Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections

    DEFF Research Database (Denmark)

    Rudkjøbing, Vibeke Børsholt; Thomsen, Trine Rolighed; Xu, Yijuan

    2016-01-01

    BACKGROUND: Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold...... to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods. Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also...... that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially...

  17. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    International Nuclear Information System (INIS)

    Asafi, M S; Tekpinar, M; Yildirim, A

    2016-01-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated. (paper)

  18. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji

    2017-07-01

    Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and  offers a contribution to solving the problem mentioned above.

  19. Ebolavirus diagnosis made simple, comparable and faster than molecular detection methods: preparing for the future.

    Science.gov (United States)

    James, Ameh S; Todd, Shawn; Pollak, Nina M; Marsh, Glenn A; Macdonald, Joanne

    2018-04-23

    The 2014/2015 Ebolavirus outbreak resulted in more than 28,000 cases and 11,323 reported deaths, as of March 2016. Domestic transmission of the Guinea strain associated with the outbreak occurred mainly in six African countries, and international transmission was reported in four countries. Outbreak management was limited by the inability to rapidly diagnose infected cases. A further fifteen countries in Africa are predicted to be at risk of Ebolavirus outbreaks in the future as a consequence of climate change and urbanization. Early detection of cases and reduction of transmission rates is critical to prevent and manage future severe outbreaks. We designed a rapid assay for detection of Ebolavirus using recombinase polymerase amplification, a rapid isothermal amplification technology that can be combined with portable lateral flow detection technology. The developed rapid assay operates in 30 min and was comparable with real-time TaqMan™ PCR. Designed, screened, selected and optimized oligonucleotides using the NP coding region from Ebola Zaire virus (Guinea strain). We determined the analytical sensitivity of our Ebola rapid molecular test by testing selected primers and probe with tenfold serial dilutions (1.34 × 10 10-  1.34 × 10 1 copies/μL) of cloned NP gene from Mayinga strain of Zaire ebolavirus in pCAGGS vector, and serially diluted cultured Ebolavirus as established by real-time TaqMan™ PCR that was performed using ABI7500 in Fast Mode. We tested extracted and reverse transcribed RNA from cultured Zaire ebolavirus strains - Mayinga, Gueckedou C05, Gueckedou C07, Makona, Kissidougou and Kiwit. We determined the analytical specificity of our assay with related viruses: Marburg, Ebola Reston and Ebola Sudan. We further tested for Dengue virus 1-4, Plasmodium falciparum and West Nile Virus (Kunjin strain). The assay had a detection limit of 134 copies per μL of plasmid containing the NP gene of Ebolavirus Mayinga, and cultured Ebolavirus

  20. Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh

    Science.gov (United States)

    Begum, Rabeya; Alam, Sheikh Shamimul; Menzel, Gerhard; Schmidt, Thomas

    2009-01-01

    Background and Aims Dendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera. Methods In order to isolate highly repetitive sequences, a c0t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH). Key Results Characterization of the c0t-1 library resulted in the detection of repetitive sequences including the (GA)n dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S–5·8S–25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species. Conclusions The repeated sequences isolated from D. moschatum c0t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal

  1. Comparative Transcriptome Analysis of Latex Reveals Molecular Mechanisms Underlying Increased Rubber Yield in Hevea brasiliensis Self-Rooting Juvenile Clones

    OpenAIRE

    Li, Hui-Liang; Guo, Dong; Zhu, Jia-Hong; Wang, Ying; Chen, Xiong-Ting; Peng, Shi-Qing

    2016-01-01

    Rubber tree (Hevea brasiliensis) self-rooting juvenile clones (JCs) are promising planting materials for rubber production. In a comparative trial between self-rooting JCs and donor clones (DCs), self-rooting JCs exhibited better performance in rubber yield. To study the molecular mechanism associated with higher rubber yield in self-rooting JCs, we sequenced and comparatively analyzed the latex of rubber tree self-rooting JCs and DCs at the transcriptome level. Total raw reads of 34,632,012 ...

  2. Inflammatory Adipokines Decrease Expression of Two High Molecular Weight Isoforms of Tropomyosin Similar to the Change in Type 2 Diabetic Patients.

    Directory of Open Access Journals (Sweden)

    Stuart A Savill

    Full Text Available Cardiovascular disease and cancer are increased in Type 2 diabetes. TPM1 and TPM4 genes encode proteins associated with cardiovascular and neoplastic disease. High (HMW and low (LMW molecular weight isoforms from TPM1 and TPM4 are altered in several cancer cells and the 3'UTR of TPM1 mRNA is tumour suppressive. Leukocytes influence cardiovascular and neoplastic disease by immunosurveillance for cancer and by chronic inflammation in Type 2 diabetes and cardiovascular disease. The aim was to determine changes in expression of isoforms from TPM1 and TPM4 genes in leukocytes from Type 2 diabetic patients and to use the leukocyte cell line THP1 to identify possible mediators of changes in the patients. Gene expression was determined by RT-qPCR. In diabetes, expression of HMW isoforms from TPM1 were markedly decreased (0.55 v 1.00; p = 0.019 but HMW isoforms from TPM4 were not significantly different (0.76 v 1.00; p = 0.205. Within individual variance in expression of HMW isoforms was very high. The change in expression in HMW isoforms from TPM1 and TPM4 was replicated in THP1 cells treated with 1 ng/ml TNFα (0.10 and 0.12 v 1.00 respectively or 10 ng/ml IL-1α (0.17 and 0.14 v 1.00 respectively. Increased insulin or glucose concentrations had no substantial effects on TPM1 or TPM4 expression. Decreased TPM1 mRNA resulted in decreases in HMW protein levels. Expression of HMW isoforms from TPM1 is decreased in Type 2 diabetes. This is probably due to increased levels of inflammatory cytokines TNFα and IL-1α in Type 2 diabetes. Lower levels of TPM1 mRNA reduce tumour suppression and could contribute to increased cancer risk in Type 2 diabetes. Decreased HMW tropomyosin isoforms are associated with cancer. Decreased HMW isoforms give rise to cells that are more plastic, motile, invasive and prone to dedifferentiation resulting in leukocytes that are more invasive but less functionally effective.

  3. Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

    Czech Academy of Sciences Publication Activity Database

    Akpinar, B.A.; Yuce, M.; Lucas, S.; Vrána, Jan; Burešová, Veronika; Doležel, Jaroslav; Budak, H.

    2015-01-01

    Roč. 5, JUN 18 (2015) ISSN 2045-2322 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : TURGIDUM VAR. DICOCCOIDES * MARKER DEVELOPMENT * GENOME SEQUENCE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.228, year: 2015

  4. A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities

    NARCIS (Netherlands)

    De Tender, C.; Schlundt, C.; Devriese, L.; Mincer, T.J.; Zettler, E.R.; Amaral-Zettler, L.A.

    2017-01-01

    Plastic is currently the most abundant form of debris in the ocean. Since the early 70's, investigators have recognized the presence of life such as pennate diatoms, bryozoans and bacteria on plastic debris, sometimes referred to as the “Plastisphere”. This review provides an overview of molecular

  5. INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH

    Science.gov (United States)

    Genome sequencing efforts in the past decade were aimed at generating draft sequences of many prokaryotic and eukaryotic model organisms. Successful completion of unicellular eukaryotes, worm, fly and human genome have opened up the new field of molecular biology and function...

  6. The Effect That Comparing Molecular Animations of Varying Accuracy Has on Students' Submicroscopic Explanations

    Science.gov (United States)

    Kelly, Resa M.; Akaygun, Sevil; Hansen, Sarah J. R.; Villalta-Cerdas, Adrian

    2017-01-01

    In this qualitative study, we examined how a group of seventeen first semester General Chemistry students responded when they were shown contrasting molecular animations of a reduction-oxidation (redox) reaction between solid copper and aqueous silver nitrate for which they first viewed a video of the actual experiment. The animations contrasted…

  7. Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

    Science.gov (United States)

    Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

    2018-01-01

    A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…

  8. A comparative molecular dynamics study of diffusion of n-decane ...

    Indian Academy of Sciences (India)

    Administrator

    Abstract. Molecular dynamics simulations are reported on the structure and dynamics of n-decane and. 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We.

  9. A comparative study of ibuprofen and ketoprofen glass-forming liquids by molecular dynamics simulations

    Science.gov (United States)

    Ottou Abe, M. T.; Correia, N. T.; Ndjaka, J. M. B.; Affouard, F.

    2015-10-01

    In this paper, structural and dynamical properties of ibuprofen and ketoprofen glass-forming liquids have been investigated by means of molecular dynamics simulations. Molecular mobility of both materials is analyzed with respect to the different inter-molecular linear/cyclic hydrogen bonding associations. For ibuprofen, the dominant organization is found to be composed of small hydrogen bonding aggregates corresponding to cyclic dimers through the carboxyl group. For ketoprofen, the propensity of cyclic dimers is significantly reduced by the formation of hydrogen bonds with the ketone oxygen of the molecule altering the hydrogen bond (HB) associating structures that can be formed and thus molecular dynamics. The issue of the presence/absence of the peculiar low frequency Debye-type process in dielectric relaxation spectroscopy (DRS) data in these materials is addressed. Results obtained from simulations confirm that the Debye process originates from the internal cis-trans conversion of the —COOH carboxyl group. It is shown that the specific intermolecular HB structures associated to a given profen control the main dynamical features of this conversion, in particular its separation from the α-process, which make it detectable or not from DRS. For ibuprofen, the possible role of the —CCCO torsion motion, more "local" than the —COOH motion since it is less influenced by the intermolecular HBs, is suggested in the microscopic origin of the quite intense secondary γ-relaxation process detected from DRS.

  10. Similar or Different?: A Comparative Analysis of Higher Education Research in Political Science and International Relations between the United States of America and the United Kingdom

    Science.gov (United States)

    Blair, Alasdair

    2015-01-01

    This article focuses on the nature of the writing in 73 articles published in six U.S. and U.K. political science and international relations journals that focus on teaching and learning. A comparative analysis is made of the articles through a review of the characteristics of the authors, the themes researched, the analytical focus, the research…

  11. Molecular phylogeny and species separation of five morphologically similar Holosticha-complex ciliates (Protozoa, Ciliophora) using ARDRA riboprinting and multigene sequence data

    Science.gov (United States)

    Gao, Feng; Yi, Zhenzhen; Gong, Jun; Al-Rasheid Khaled, A. S.; Song, Weibo

    2010-05-01

    To separate and redefine the ambiguous Holosticha-complex, a confusing group of hypotrichous ciliates, six strains belonging to five morphospecies of three genera, Holosticha heterofoissneri, Anteholosticha sp. pop1, Anteholosticha sp. pop2, A. manca, A. gracilis and Nothoholosticha fasciola, were analyzed using 12 restriction enzymes on the basis of amplified ribosomal DNA restriction analysis. Nine of the 12 enzymes could digest the DNA products, four ( Hinf I, Hind III, Msp I, Taq I) yielded species-specific restriction patterns, and Hind III and Taq I produced different patterns for two Anteholosticha sp. populations. Distinctly different restriction digestion haplotypes and similarity indices can be used to separate the species. The secondary structures of the five species were predicted based on the ITS2 transcripts and there were several minor differences among species, while two Anteholosticha sp. populations were identical. In addition, phylogenies based on the SSrRNA gene sequences were reconstructed using multiple algorithms, which grouped them generally into four clades, and exhibited that the genus Anteholosticha should be a convergent assemblage. The fact that Holosticha species clustered with the oligotrichs and choreotrichs, though with very low support values, indicated that the topology may be very divergent and unreliable when the number of sequence data used in the analyses is too low.

  12. 3D-QSAR comparative molecular field analysis on opioid receptor antagonists: pooling data from different studies.

    Science.gov (United States)

    Peng, Youyi; Keenan, Susan M; Zhang, Qiang; Kholodovych, Vladyslav; Welsh, William J

    2005-03-10

    Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) on a series of opioid receptor antagonists. To obtain statistically significant and robust CoMFA models, a sizable data set of naltrindole and naltrexone analogues was assembled by pooling biological and structural data from independent studies. A process of "leave one data set out", similar to the traditional "leave one out" cross-validation procedure employed in partial least squares (PLS) analysis, was utilized to study the feasibility of pooling data in the present case. These studies indicate that our approach yields statistically significant and highly predictive CoMFA models from the pooled data set of delta, mu, and kappa opioid receptor antagonists. All models showed excellent internal predictability and self-consistency: q(2) = 0.69/r(2) = 0.91 (delta), q(2) = 0.67/r(2) = 0.92 (mu), and q(2) = 0.60/r(2) = 0.96 (kappa). The CoMFA models were further validated using two separate test sets: one test set was selected randomly from the pooled data set, while the other test set was retrieved from other published sources. The overall excellent agreement between CoMFA-predicted and experimental binding affinities for a structurally diverse array of ligands across all three opioid receptor subtypes gives testimony to the superb predictive power of these models. CoMFA field analysis demonstrated that the variations in binding affinity of opioid antagonists are dominated by steric rather than electrostatic interactions with the three opioid receptor binding sites. The CoMFA steric-electrostatic contour maps corresponding to the delta, mu, and kappa opioid receptor subtypes reflected the characteristic similarities and differences in the familiar "message-address" concept of opioid receptor ligands. Structural modifications to increase selectivity for the delta over mu and kappa opioid receptors have been predicted on the

  13. Comparative molecular study of Mycobacterium tuberculosis strains, in times of antimicrobial drug resistance

    Directory of Open Access Journals (Sweden)

    G. Varela

    2005-03-01

    Full Text Available Strains of Mycobacterium tuberculosis were compared using two DNA fingerprinting techniques: Restriction Fragment Length Polymorphism (RFLP and Double-Repetitive-Element-PCR (DRE-PCR. Two of these strains: IH1 (susceptible to isoniazid and IH2 (resistant to isoniazid were recovered from cases of pulmonary tuberculosis which occurred in two brothers who lived together. The first one was recognized on July 1999, and the second was diagnosed one year later. IH1 and IH2 showed the same pattern of bands with both molecular tests. These results suggest that single drug chemoprophylaxis may occasionally select resistant strains for that drug, which can eventually cause disease and be recognized through these tests. Strains IH3, IH4 and IH5 were obtained from sputum samples of 3 different patients, and intra-laboratory cross-contamination was suspected when it was realized that the 3 positive materials had been consecutively processed the same day by the same worker in the same biological safety cabinet. Again, the 3 strains revealed identical band patterns with RFLP and DRE-PCR, confirming the posed suspicion. The results with DRE-PCR were obtained after only 8 hours of work, without the need for subcultures. This procedure allows quick correction of treatment conducts, avoiding unnecessary exposure of people and bacteria to antimicrobial drugs.Se compararon cepas de Mycobacterium tuberculosis utilizando 2 procedimientos de ADN fingerprinting: polimorfismo de los fragmentos de restricción (RFLP y Double-Repetitive-Element-PCR (DRE-PCR. Dos de las cepas: IH1 (susceptible a isoniazida e IH2 (resistente a isoniazida se recuperaron a partir de casos de tuberculosis pulmonar que ocurrieron en dos hermanos convivientes. La primera fue aislada en julio de 1999 y la segunda un año después. IH1 e IH2 mostraron el mismo patrón de bandas por ambos procedimientos. Estos resultados sugieren que la quimioprofilaxis con una sola droga puede ocasionalmente

  14. Comparative molecular analyses of invasive fall armyworm in Togo reveal strong similarities to populations from the eastern United States and the Greater Antilles

    Science.gov (United States)

    The fall armyworm (Spodoptera frugiperda, J.E. Smith) is a major and ubiquitous noctuid pest of agricultural in the Western Hemisphere. Infestations have recently been identified in several locations in Africa, indicating its establishment in the Eastern Hemisphere where it poses an immediate and si...

  15. Toxoplasmosis: The value of molecular methods in diagnosis compared to conventional methods

    Directory of Open Access Journals (Sweden)

    Zineb Tlamçani

    2013-06-01

    Full Text Available Toxoplasmosis is a parasitic infection due to Toxoplasma gondii an obligate intracellular protozoan parasite. It is considerateone of the most common parasite worldwide. The contamination of the parasite is generally occurred via consumptionof infected food or water or, undercooked contaminated meat. Toxoplasma gondii infection may lead to seriousillness when the organism is contracted while pregnancy or when it is reactivated in immune-suppressed persons.Diagnosis of toxoplasmosis in humans is elaborated using various techniques such as detection of anti-Toxoplasmaantibodies, mouse inoculation, histological revelation of tachyzoites in tissue sections or smears of body fluid, but thedetection of Toxoplasma gondii DNA by molecular methods has revolutionized prenatal diagnosis of congenital toxoplasmosisand in immunocompromised patients. In this paper we will discuss the parasite and different methods ofdiagnosis including the usefulness of molecular methods. J Microbiol Infect Dis 2013; 3(2: 93-99Key words: Toxoplamosis, Toxoplasma gondii, diagnosis

  16. Comparative analysis of the molecular mechanisms of recombination in hepatitis C virus

    DEFF Research Database (Denmark)

    Galli, Andrea; Bukh, Jens

    2014-01-01

    Genetic recombination is an important evolutionary mechanism for RNA viruses. The significance of this phenomenon for hepatitis C virus (HCV) has recently become evident, with the identification of circulating recombinant forms in HCV-infected individuals and by novel data from studies permitted...... by advances in HCV cell culture systems and genotyping protocols. HCV is readily able to produce viable recombinants, using replicative and non-replicative molecular mechanisms. However, our knowledge of the required molecular mechanisms remains limited. Understanding how HCV recombines might be instrumental...... for a better monitoring of global epidemiology, to clarify the virus evolution, and evaluate the impact of recombinant forms on the efficacy of oncoming combination drug therapies. For the latter, frequency and location of recombination events could affect the efficacy of multidrug regimens. This review...

  17. Using Patient Health Questionnaire-9 item parameters of a common metric resulted in similar depression scores compared to independent item response theory model reestimation.

    Science.gov (United States)

    Liegl, Gregor; Wahl, Inka; Berghöfer, Anne; Nolte, Sandra; Pieh, Christoph; Rose, Matthias; Fischer, Felix

    2016-03-01

    To investigate the validity of a common depression metric in independent samples. We applied a common metrics approach based on item-response theory for measuring depression to four German-speaking samples that completed the Patient Health Questionnaire (PHQ-9). We compared the PHQ item parameters reported for this common metric to reestimated item parameters that derived from fitting a generalized partial credit model solely to the PHQ-9 items. We calibrated the new model on the same scale as the common metric using two approaches (estimation with shifted prior and Stocking-Lord linking). By fitting a mixed-effects model and using Bland-Altman plots, we investigated the agreement between latent depression scores resulting from the different estimation models. We found different item parameters across samples and estimation methods. Although differences in latent depression scores between different estimation methods were statistically significant, these were clinically irrelevant. Our findings provide evidence that it is possible to estimate latent depression scores by using the item parameters from a common metric instead of reestimating and linking a model. The use of common metric parameters is simple, for example, using a Web application (http://www.common-metrics.org) and offers a long-term perspective to improve the comparability of patient-reported outcome measures. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Molecular mechanisms in the selective basal activation of pyrabactin receptor 1: Comparative analysis of mutants.

    Science.gov (United States)

    Dorosh, Lyudmyla; Rajagopalan, Nandhakishore; Loewen, Michele C; Stepanova, Maria

    2014-01-01

    Pyrabactin receptors (PYR) play a central role in abscisic acid (ABA) signal transduction; they are ABA receptors that inhibit type 2C protein phosphatases (PP2C). Molecular aspects contributing to increased basal activity of PYR against PP2C are studied by molecular dynamics (MD) simulations. An extensive series of MD simulations of the apo-form of mutagenized PYR1 as a homodimer and in complex with homology to ABA-insensitive 1 (HAB1) phosphatase are reported. In order to investigate the detailed molecular mechanisms mediating PYR1 activity, the MD data was analyzed by essential collective dynamics (ECD), a novel approach that allows the identification, with atomic resolution, of persistent dynamic correlations based on relatively short MD trajectories. Employing the ECD method, the effects of select mutations on the structure and dynamics of the PYR1 complexes were investigated and considered in the context of experimentally determined constitutive activities against HAB1. Approaches to rationally design constitutively active PYR1 constructs to increase PP2C inhibition are discussed.

  19. Aberrant cell divisions in root meristeme of maize following exposure to X-rays low doses compared to similar effects of 50 Hz electromagnetic exposure

    Directory of Open Access Journals (Sweden)

    Luchian T.

    2012-04-01

    Full Text Available The response of maize to radiation exposure was investigated by two cytogenetic methods considering the importance of the geno-toxic effect for environmental and agricultural purposes. Uniform genophond seeds, freshly germinated, were exposed to relatively low radiation doses using a radiotherapy X-ray applicator from a hospital irradiation device and to a 50 Hz electromagnetic field with about 10 mT magnetic induction (generated within laboratory assembled electromagnetic coils. Radicular meristeme tissue aliquots were prevailed for cytogenetic investigation based on microscopic observations and cell counting. Microscope slides were prepared following a specific procedure (squash technique and Feulgen method based on modified Carr reactive coloration. Mitotic index as well as chromosomal aberration percentage were calculated for more than 30,000 cells taken into account. From a qualitative viewpoint, chromosomal aberrations such as interchromatidian bridges, lagging and expelled chromosomes and multipolar divisions were evidenced - no distinct situation for either ionizing radiation or electromagnetic field being identified. The main quantitative difference consisted in the increased mitotic index for electromagnetic exposure increased times compared with the diminished mitotic index in the case of low X-ray doses.

  20. Use of molecular markers to compare Escherichia coli transport to traditional groundwater tracers in epikarst

    Science.gov (United States)

    Bacterial contamination of karst aquifers is a concern as water quality across the globe deteriorates in the face of decreasing water security. Traditional groundwater tracers (dye and microspheres) do not exhibit surface properties similar to bacteria and pathogens and therefore are not good proxie...

  1. Aggregation work at polydisperse micellization: ideal solution and "dressed micelle" models comparing to molecular dynamics simulations.

    Science.gov (United States)

    Burov, S V; Shchekin, A K

    2010-12-28

    General thermodynamic relations for the work of polydisperse micelle formation in the model of ideal solution of molecular aggregates in nonionic surfactant solution and the model of "dressed micelles" in ionic solution have been considered. In particular, the dependence of the aggregation work on the total concentration of nonionic surfactant has been analyzed. The analogous dependence for the work of formation of ionic aggregates has been examined with regard to existence of two variables of a state of an ionic aggregate, the aggregation numbers of surface active ions and counterions. To verify the thermodynamic models, the molecular dynamics simulations of micellization in nonionic and ionic surfactant solutions at two total surfactant concentrations have been performed. It was shown that for nonionic surfactants, even at relatively high total surfactant concentrations, the shape and behavior of the work of polydisperse micelle formation found within the model of the ideal solution at different total surfactant concentrations agrees fairly well with the numerical experiment. For ionic surfactant solutions, the numerical results indicate a strong screening of ionic aggregates by the bound counterions. This fact as well as independence of the coefficient in the law of mass action for ionic aggregates on total surfactant concentration and predictable behavior of the "waterfall" lines of surfaces of the aggregation work upholds the model of "dressed" ionic aggregates.

  2. Comparative molecular simulation study of low and high density polymer glasses: A competition between attractive and repulsive interactions

    Science.gov (United States)

    Singh, Jalim; Jose, Prasanth

    Results of molecular dynamics simulations of a system of Kremer and Grest linear polymer melts are presented at moderate and high number density. A detailed study of molecular pair distribution function shows that potential of mean force between the molecules has form of Gaussian with an attractive tail at number density ρ = 0.85 (in Lennard-Jones units), which is due to the dominating attractive interactions from temperature T = 0.7. This system shows gelation assisted glass transition, which is interpreted from peaks of molecular structure factor at small wave-numbers. At low temperature, this system phase separate to form dense domains whose local density is high; these domains show many dynamical features of glass transition in monomer and molecular level of relaxation indicating glass transition is assisted by gelation in this system. In the same system, at ρ = 1.0, repulsive interactions dominate, structure does not change even at low temperatures; the system exhibits dynamic heterogeneity and known to undergo glass transition. In this work, we compare and contrast the structure and dynamics of the system near its glass transition. Also, we computed correlation length of systems from the peak value of four-point structural dynamic susceptibility. HPC facility at IIT Mandi.

  3. The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity.

    Directory of Open Access Journals (Sweden)

    Matthias Stein

    Full Text Available Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood.Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics.We have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity.

  4. Molecular characterization and similarity relationships among ...

    African Journals Online (AJOL)

    However, some genotypes have the same specific characters that influence their clustering, and as a result, the results of the principal coordinate analysis (PCoA) largely corresponded to those obtained through cluster analysis. Key words: Cluster analysis, genetic diversity, principal coordinate analysis, sunflower, simple ...

  5. Toward an understanding of the molecular mechanisms of barnacle larval settlement: A comparative transcriptomic approach

    KAUST Repository

    Chen, Zhang-Fan

    2011-07-29

    Background: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Methodology and Principal Findings: Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Conclusions: Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species. © 2011 Chen et al.

  6. Molecular evolution of a-kinase anchoring protein (AKAP-7: implications in comparative PKA compartmentalization

    Directory of Open Access Journals (Sweden)

    Johnson Keven R

    2012-07-01

    Full Text Available Abstract Background A-Kinase Anchoring Proteins (AKAPs are molecular scaffolding proteins mediating the assembly of multi-protein complexes containing cAMP-dependent protein kinase A (PKA, directing the kinase in discrete subcellular locations. Splice variants from the AKAP7 gene (AKAP15/18 are vital components of neuronal and cardiac phosphatase complexes, ion channels, cardiac Ca2+ handling and renal water transport. Results Shown in evolutionary analyses, the formation of the AKAP7-RI/RII binding domain (required for AKAP/PKA-R interaction corresponds to vertebrate-specific gene duplication events in the PKA-RI/RII subunits. Species analyses of AKAP7 splice variants shows the ancestral AKAP7 splice variant is AKAP7α, while the ancestral long form AKAP7 splice variant is AKAP7γ. Multi-species AKAP7 gene alignments, show the recent formation of AKAP7δ occurs with the loss of native AKAP7γ in rats and basal primates. AKAP7 gene alignments and two dimensional Western analyses indicate that AKAP7γ is produced from an internal translation-start site that is present in the AKAP7δ cDNA of mice and humans but absent in rats. Immunofluorescence analysis of AKAP7 protein localization in both rat and mouse heart suggests AKAP7γ replaces AKAP7δ at the cardiac sarcoplasmic reticulum in species other than rat. DNA sequencing identified Human AKAP7δ insertion-deletions (indels that promote the production of AKAP7γ instead of AKAP7δ. Conclusions This AKAP7 molecular evolution study shows that these vital scaffolding proteins developed in ancestral vertebrates and that independent mutations in the AKAP7 genes of rodents and early primates has resulted in the recent formation of AKAP7δ, a splice variant of likely lesser importance in humans than currently described.

  7. Comparable investigation of the molecular size distribution and the amount of humic substances isolated from ONKALO, Olkiluoto, 2010

    International Nuclear Information System (INIS)

    Vilhunen, S.; Manninen, P.

    2010-11-01

    The humic substances at groundwater from Onkalo, Olkiluoto were studied in order to determine the molecular size distribution and the amount of humic substances. Humic substances were isolated from the water sample using DAX-8 resin and eluted with 0.1 M NaOH. The molecular size distribution was defined using high performance size exclusion chromatography (HPSEC) and ultraviolet (UV) or reflactive index (RI) detector. Two calibration standard sets (poly(styrene sulfonate) sodium salt (PSS) or polyethylene glycol (PEG) standards) with distinct structures as well as two eluents (0.05 M NaNO3 or 0.01 M Na-acetate) were studied and the results were compared with the previous ones. The calibration standards and eluents were found to have major effect on the measured parameters. The amount of humic substances was determined using total organic carbon (TOC) measurements. (orig.)

  8. Comparing molecular composition of dissolved organic matter in soil and stream water: Influence of land use and chemical characteristics.

    Science.gov (United States)

    Seifert, Anne-Gret; Roth, Vanessa-Nina; Dittmar, Thorsten; Gleixner, Gerd; Breuer, Lutz; Houska, Tobias; Marxsen, Jürgen

    2016-11-15

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) was used to examine the molecular composition of dissolved organic matter (DOM) from soils under different land use regimes and how the DOM composition in the catchment is reflected in adjacent streams. The study was carried out in a small area of the Schwingbach catchment, an anthropogenic-influenced landscape in central Germany. We investigated 30 different soil water samples from 4 sites and different depths (managed meadow (0-5cm, 40-50cm), deciduous forest (0-5cm), mixed-coniferous forest (0-5cm) and agricultural land (0-5cm, 40-50cm)) and 8 stream samples. 6194 molecular formulae and their magnitude-weighted parameters ((O/C)w, (H/C)w, (N/C)w, (AI-mod)w, (DBE/C)w, (DBE/O)w, (DBE-O)w, (C#)w, (MW)w) were used to describe the molecular composition of the samples. The samples can be roughly divided in three groups. Group 1 contains samples from managed meadow 40-50cm and stream water, which are characterized by high saturation compared to samples from group 2 including agricultural samples and samples from the surface meadow (0-5cm), which held more nitrogen containing and aromatic compounds. Samples from both forested sites (group 3) are characterized by higher molecular weight and O/C ratio. Environmental parameters vary between sites and among these parameters pH and nitrate significantly affect chemical composition of DOM. Results indicate that most DOM in streams is of terrestrial origin. However, 120 molecular formulae were detected only in streams and not in any of the soil samples. These compounds share molecular formulae with peptides, unsaturated aliphatics and saturated FA-CHO/FA-CHOX. Compounds only found in soil samples are much more aromatic, have more double bonds and a much lower H/C ratio but higher oxygen content, which indicates the availability of fresh plant material and less microbial processed material compared to stream samples. Copyright

  9. [Comparative characterization of cultured methane-oxidizing bacteria by serological and molecular methods].

    Science.gov (United States)

    Slobodova, N V; Kolganova, T V; Bulygina, E S; Kuznetsov, B B; Turova, T P; Kravchenko, I K

    2006-01-01

    Three stable methane-oxidizing enrichment cultures, SB26, SB31, and SB31A were analyzed by transmission electron microscopy and by serological and molecular techniques. Electron microscopy revealed the presence of both type I and type II methanotrophs in SB31 and SB31A enrichments; only type II methanotrophs were found in SB26 enrichment. Methylosinus trichosporium was detected in all three enrichments by the application of species-specific antibodies. Additionally, Methylocystis echinoides was found in SB26 culture; Methylococcus capsulatus, in SB31 and SB31A; and Methylomonas methanica, in SB31. The analysis with pmoA and nifH gene sequences as phylogenetic markers revealed the presence of Methylosinus/Methylocystis group in all communities. Moreover, the analysis of pmoA sequences revealed the presence of Methylomonas in SB31. Methylocella was detected in SB31 and SB31A enrichments only by nifH analysis. It was concluded that the simultaneous application of different approaches reveals more reliable information on the diversity of methanotrophs.

  10. Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

    Directory of Open Access Journals (Sweden)

    Jianguo Zhou

    2018-02-01

    Full Text Available Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three Papaver species. These differences include the ycf1 gene and intergenic regions, such as rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, and ccsA-ndhD. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of Papaver species and will benefit further investigations of these species.

  11. Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5

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    Inger Lindin

    2014-03-01

    Full Text Available The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD simulations of: (1 MK5 alone; (2 MK5 in complex with an inhibitor; and (3 MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.

  12. A comparative analysis of electronic and molecular quantum dot cellular automata

    International Nuclear Information System (INIS)

    Umamahesvari, H.; Ajitha, D.

    2015-01-01

    This paper presents a comparative analysis of electronic quantum-dot cellular automata (EQCA) and Magnetic quantum dot Cellular Automata (MQCA). QCA is a computing paradigm that encodes and processes information by the position of individual electrons. To enhance the high dense and ultra-low power devices, various researches have been actively carried out to find an alternative way to continue and follow Moore’s law, so called “beyond CMOS technology”. There have been several proposals for physically implementing QCA, EQCA and MQCA are the two important QCAs reported so far. This paper provides a comparative study on these two QCAs

  13. Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host.

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    Roman Leontovyč

    2016-02-01

    Full Text Available To date, most molecular investigations of schistosomatids have focused principally on blood flukes (schistosomes of humans. Despite the clinical importance of cercarial dermatitis in humans caused by Trichobilharzia regenti and the serious neuropathologic disease that this parasite causes in its permissive avian hosts and accidental mammalian hosts, almost nothing is known about the molecular aspects of how this fluke invades its hosts, migrates in host tissues and how it interacts with its hosts' immune system. Here, we explored selected aspects using a transcriptomic-bioinformatic approach. To do this, we sequenced, assembled and annotated the transcriptome representing two consecutive life stages (cercariae and schistosomula of T. regenti involved in the first phases of infection of the avian host. We identified key biological and metabolic pathways specific to each of these two developmental stages and also undertook comparative analyses using data available for taxonomically related blood flukes of the genus Schistosoma. Detailed comparative analyses revealed the unique involvement of carbohydrate metabolism, translation and amino acid metabolism, and calcium in T. regenti cercariae during their invasion and in growth and development, as well as the roles of cell adhesion molecules, microaerobic metabolism (citrate cycle and oxidative phosphorylation, peptidases (cathepsins and other histolytic and lysozomal proteins in schistosomula during their particular migration in neural tissues of the avian host. In conclusion, the present transcriptomic exploration provides new and significant insights into the molecular biology of T. regenti, which should underpin future genomic and proteomic investigations of T. regenti and, importantly, provides a useful starting point for a range of comparative studies of schistosomatids and other trematodes.

  14. Comparative Transcriptome Analysis of Latex Reveals Molecular Mechanisms Underlying Increased Rubber Yield in Hevea brasiliensis Self-Rooting Juvenile Clones.

    Science.gov (United States)

    Li, Hui-Liang; Guo, Dong; Zhu, Jia-Hong; Wang, Ying; Chen, Xiong-Ting; Peng, Shi-Qing

    2016-01-01

    Rubber tree (Hevea brasiliensis) self-rooting juvenile clones (JCs) are promising planting materials for rubber production. In a comparative trial between self-rooting JCs and donor clones (DCs), self-rooting JCs exhibited better performance in rubber yield. To study the molecular mechanism associated with higher rubber yield in self-rooting JCs, we sequenced and comparatively analyzed the latex of rubber tree self-rooting JCs and DCs at the transcriptome level. Total raw reads of 34,632,012 and 35,913,020 bp were obtained from the library of self-rooting JCs and DCs, respectively, by using Illumina HiSeq 2000 sequencing technology. De novo assemblies yielded 54689 unigenes from the library of self-rooting JCs and DCs. Among 54689 genes, 1716 genes were identified as differentially expressed between self-rooting JCs and DCs via comparative transcript profiling. Functional analysis showed that the genes related to the mass of categories were differentially enriched between the two clones. Several genes involved in carbohydrate metabolism, hormone metabolism and reactive oxygen species scavenging were up-regulated in self-rooting JCs, suggesting that the self-rooting JCs provide sufficient molecular basis for the increased rubber yielding, especially in the aspects of improved latex metabolisms and latex flow. Some genes encoding epigenetic modification enzymes were also differentially expressed between self-rooting JCs and DCs. Epigenetic modifications may lead to gene differential expression between self-rooting JCs and DCs. These data will provide new cues to understand the molecular mechanism underlying the improved rubber yield of H. brasiliensis self-rooting clones.

  15. Comparable investigation of the molecular size distribution and the amount of humic substances isolated from ONKALO, Olkiluoto, 2011

    International Nuclear Information System (INIS)

    Luste, S.; Maekelae, J.; Manninen, P.

    2012-06-01

    The humic substances (HS) at groundwater from ONKALO, Olkiluoto were studied in order to determine the apparent molecular size distribution and the amount of humic substances. Humic substances were isolated from the water sample using DAX-8 resin and eluted with 0.1 M NaOH. The molecular size distribution was defined using high performance size exclusion chromatography (HPSEC) and ultraviolet (UV) and refractive index (RI) detector. In the SEC calibration (polystyrene sulfonate) sodium salts (PSS) were employed. Different eluents (NaNO 3 , Na-acetate and asetonitrile) with phosphate buffer and distinct ionic strengths were studied in order to optimize the determination method. The amount of humic substances was determined using total organic carbon (TOC) measurements. The results were compared with the previous ones in order to find out the variation of different methods (HPSEC) and to follow up the HS quantity (TOC). The method developed during the study is considered to be suitable for the HS molecular size distribution follow up, although the method development is suggested to be continued. (orig.)

  16. Comparable investigation of the molecular size distribution and the amount of humic substances isolated from ONKALO, Olkiluoto, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Luste, S.; Maekelae, J.; Manninen, P. [Ramboll Finland Oy, Espoo (Finland)

    2012-06-15

    The humic substances (HS) at groundwater from ONKALO, Olkiluoto were studied in order to determine the apparent molecular size distribution and the amount of humic substances. Humic substances were isolated from the water sample using DAX-8 resin and eluted with 0.1 M NaOH. The molecular size distribution was defined using high performance size exclusion chromatography (HPSEC) and ultraviolet (UV) and refractive index (RI) detector. In the SEC calibration (polystyrene sulfonate) sodium salts (PSS) were employed. Different eluents (NaNO{sub 3}, Na-acetate and asetonitrile) with phosphate buffer and distinct ionic strengths were studied in order to optimize the determination method. The amount of humic substances was determined using total organic carbon (TOC) measurements. The results were compared with the previous ones in order to find out the variation of different methods (HPSEC) and to follow up the HS quantity (TOC). The method developed during the study is considered to be suitable for the HS molecular size distribution follow up, although the method development is suggested to be continued. (orig.)

  17. Comparative molecular modeling study of Arabidopsis NADPH-dependent thioredoxin reductase and its hybrid protein.

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    Yuno Lee

    Full Text Available 2-Cys peroxiredoxins (Prxs play important roles in the protection of chloroplast proteins from oxidative damage. Arabidopsis NADPH-dependent thioredoxin reductase isotype C (AtNTRC was identified as efficient electron donor for chloroplastic 2-Cys Prx-A. There are three isotypes (A, B, and C of thioredoxin reductase (TrxR in Arabidopsis. AtNTRA contains only TrxR domain, but AtNTRC consists of N-terminal TrxR and C-terminal thioredoxin (Trx domains. AtNTRC has various oligomer structures, and Trx domain is important for chaperone activity. Our previous experimental study has reported that the hybrid protein (AtNTRA-(Trx-D, which was a fusion of AtNTRA and Trx domain from AtNTRC, has formed variety of structures and shown strong chaperone activity. But, electron transfer mechanism was not detected at all. To find out the reason of this problem with structural basis, we performed two different molecular dynamics (MD simulations on AtNTRC and AtNTRA-(Trx-D proteins with same cofactors such as NADPH and flavin adenine dinucleotide (FAD for 50 ns. Structural difference has found from superimposition of two structures that were taken relatively close to average structure. The main reason that AtNTRA-(Trx-D cannot transfer the electron from TrxR domain to Trx domain is due to the difference of key catalytic residues in active site. The long distance between TrxR C153 and disulfide bond of Trx C387-C390 has been observed in AtNTRA-(Trx-D because of following reasons: i unstable and unfavorable interaction of the linker region, ii shifted Trx domain, and iii different or weak interface interaction of Trx domains. This study is one of the good examples for understanding the relationship between structure formation and reaction activity in hybrid protein. In addition, this study would be helpful for further study on the mechanism of electron transfer reaction in NADPH-dependent thioredoxin reductase proteins.

  18. Tissue Molecular Anatomy Project (TMAP): an expression database for comparative cancer proteomics.

    Science.gov (United States)

    Medjahed, Djamel; Luke, Brian T; Tontesh, Tawady S; Smythers, Gary W; Munroe, David J; Lemkin, Peter F

    2003-08-01

    By mining publicly accessible databases, we have developed a collection of tissue-specific predictive protein expression maps as a function of cancer histological state. Data analysis is applied to the differential expression of gene products in pooled libraries from the normal to the altered state(s). We wish to report the initial results of our survey across different tissues and explore the extent to which this comparative approach may help uncover panels of potential biomarkers of tumorigenesis which would warrant further examination in the laboratory.

  19. Molecular characterisation and similarity relationships among iranian basil (Ocimum basilicum L. accessions using inter simple sequence repeat markers Caracterização molecular de acessos de Ocimum basilicum L. por meio de marcadores ISSR

    Directory of Open Access Journals (Sweden)

    Mohammad Aghaei

    2012-06-01

    Full Text Available The study of genetic relationships is a prerequisite for plant breeding activities as well as for conservation of genetic resources. In the present study, genetic diversity among 50 Iranian basil (Ocimum basilicum L. accessions was determined using inter simple sequence repeat (ISSR markers. Thirty-eight alleles were generated at 12 ISSR loci. The number of alleles per locus ranged from 1 to 5 with an average of 3.17. The maximum number of alleles was observed at the A7, 818, 825 and 849 loci, and their size ranged from 300 to 2500 bp. A similarity matrix based on Jaccard's coefficient for all 50 basil accessions gave values from 1.00-0.60. The maximum similarity (1.00 was observed between the "Urmia" and "Shahr-e-Rey II" accessions as well as between the "Urmia" and "Qazvin II" accessions. The lowest similarity (0.60 was observed between the "Tuyserkan I" and "Gom II" accessions. The unweighted pair- group method using arithmetique average UPGMA clustering algorithm classified the studied accessions into three distinct groups. All of the basil accessions, with the exception of "Babol III", "Ahvaz II", "Yazd II" and "Ardebil I", were placed in groups I and II. Leaf colour was a specific characteristic that influenced the clustering of Iranian basil accessions. Because of this relationship, the results of the principal coordinate analysis (PCoA approximately corresponded to those obtained through cluster analysis. Our results revealed that the geographical distribution of genotypes could not be used as a basis for crossing parents to obtain high heterosis, and therefore, it must be carried out by genetic studies.O estudo das relações genéticas é um pré-requisito para atividades em reprodução de plantas assim como para conservação de recursos genéticos. Neste trabalho a diversidade genética entre 50 acessos de Manejericão Iraniano (Ocimum basilicum L. foram determinadas usando marcadores de Seqüência Simples Repetida Interna (ISSR

  20. Comparative molecular pathology of cadmium- and all-trans-retinoic acid-induced postaxial forelimb ectrodactyly

    International Nuclear Information System (INIS)

    Liao Xiaoyan; Lee, Grace S.; Shimizu, Hirohito; Collins, Michael D.

    2007-01-01

    Cadmium chloride (CdCl 2 ) and all-trans-retinoic acid (RA) induce postaxial forelimb ectrodactyly in C57BL/6N mice when administered during early limb development, and co-administration yields a synergistic response suggesting a common final pathway to the defect. In the current study, forelimb buds from embryos given high maternal teratogenic doses of CdCl 2 or RA, or the combination of both agents at low doses were collected at various time points after treatment on GD 9.5 and examined for cellular apoptosis, proliferation, and patterning genes. Some cellular perturbations detected in the developing limb bud were similar for both teratogens, whereas other alterations were unique to each agent. For example, at 12 and 18 h, CdCl 2 treatment increased apoptotic cells in the mesenchyme underneath the apical ectodermal ridge (AER), whereas RA caused apoptosis in the AER and proximal mesenchyme. Further, the combined low-dose treatment increased cell death synergistically in all three regions. CdCl 2 and the low-dose combined treatment inhibited mesenchymal proliferation at 12 h, which was associated with induction of p21 cip1 and inhibition of phospho-c-Jun. In contrast, RA did not inhibit mesenchymal proliferation and did not induce p21 cip1 expression or change c-Jun phosphorylation. All three treatment groups showed a delay in the patterning of distal chondrogenesis centers as indicated by Sox9 expression. There was also common inhibition in the expression of AER markers, Fgf8 and Fgf4, and the mesenchymal marker Msx1 involved in the maintenance of epithelial-mesenchymal interactions. Collectively, a model is hypothesized where limb patterning can be perturbed by insults to both ectoderm and mesoderm

  1. First comparative study of primate morphological and molecular evolutionary rates including muscle data: implications for the tempo and mode of primate and human evolution

    Science.gov (United States)

    Diogo, Rui; Peng, Zuogang; Wood, Bernard

    2013-01-01

    Here we provide the first report about the rates of muscle evolution derived from Bayesian and parsimony cladistic analyses of primate higher-level phylogeny, and compare these rates with published rates of molecular evolution. It is commonly accepted that there is a ‘general molecular slow-down of hominoids’, but interestingly the rates of muscle evolution in the nodes leading and within the hominoid clade are higher than those in the vast majority of other primate clades. The rate of muscle evolution at the node leading to Homo (1.77) is higher than that at the nodes leading to Pan (0.89) and particularly to Gorilla (0.28). Notably, the rates of muscle evolution at the major euarchontan and primate nodes are different, but within each major primate clade (Strepsirrhini, Platyrrhini, Cercopithecidae and Hominoidea) the rates at the various nodes, and particularly at the nodes leading to the higher groups (i.e. including more than one genera), are strikingly similar. We explore the implications of these new data for the tempo and mode of primate and human evolution. PMID:23320764

  2. COMPAR

    International Nuclear Information System (INIS)

    Kuefner, K.

    1976-01-01

    COMPAR works on FORTRAN arrays with four indices: A = A(i,j,k,l) where, for each fixed k 0 ,l 0 , only the 'plane' [A(i,j,k 0 ,l 0 ), i = 1, isub(max), j = 1, jsub(max)] is held in fast memory. Given two arrays A, B of this type COMPAR has the capability to 1) re-norm A and B ind different ways; 2) calculate the deviations epsilon defined as epsilon(i,j,k,l): =[A(i,j,k,l) - B(i,j,k,l)] / GEW(i,j,k,l) where GEW (i,j,k,l) may be chosen in three different ways; 3) calculate mean, standard deviation and maximum in the array epsilon (by several intermediate stages); 4) determine traverses in the array epsilon; 5) plot these traverses by a printer; 6) simplify plots of these traverses by the PLOTEASY-system by creating input data blocks for this system. The main application of COMPAR is given (so far) by the comparison of two- and three-dimensional multigroup neutron flux-fields. (orig.) [de

  3. Prospective molecular profiling of canine cancers provides a clinically relevant comparative model for evaluating personalized medicine (PMed trials.

    Directory of Open Access Journals (Sweden)

    Melissa Paoloni

    Full Text Available Molecularly-guided trials (i.e. PMed now seek to aid clinical decision-making by matching cancer targets with therapeutic options. Progress has been hampered by the lack of cancer models that account for individual-to-individual heterogeneity within and across cancer types. Naturally occurring cancers in pet animals are heterogeneous and thus provide an opportunity to answer questions about these PMed strategies and optimize translation to human patients. In order to realize this opportunity, it is now necessary to demonstrate the feasibility of conducting molecularly-guided analysis of tumors from dogs with naturally occurring cancer in a clinically relevant setting.A proof-of-concept study was conducted by the Comparative Oncology Trials Consortium (COTC to determine if tumor collection, prospective molecular profiling, and PMed report generation within 1 week was feasible in dogs. Thirty-one dogs with cancers of varying histologies were enrolled. Twenty-four of 31 samples (77% successfully met all predefined QA/QC criteria and were analyzed via Affymetrix gene expression profiling. A subsequent bioinformatics workflow transformed genomic data into a personalized drug report. Average turnaround from biopsy to report generation was 116 hours (4.8 days. Unsupervised clustering of canine tumor expression data clustered by cancer type, but supervised clustering of tumors based on the personalized drug report clustered by drug class rather than cancer type.Collection and turnaround of high quality canine tumor samples, centralized pathology, analyte generation, array hybridization, and bioinformatic analyses matching gene expression to therapeutic options is achievable in a practical clinical window (<1 week. Clustering data show robust signatures by cancer type but also showed patient-to-patient heterogeneity in drug predictions. This lends further support to the inclusion of a heterogeneous population of dogs with cancer into the preclinical

  4. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Directory of Open Access Journals (Sweden)

    Catherine L Worth

    Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

  5. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Science.gov (United States)

    Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

    2009-09-16

    Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

  6. Comparative studies of high-frequency and direct current molecular gas discharges

    International Nuclear Information System (INIS)

    Goichman, V.H.; Goldfarb, V.M.; Tendler, M.B.

    1975-01-01

    Electron gas parameters, gas temperatures, ionization and thermal instability are found to be markedly different in direct current glow discharges from capactive electrodless high frequency discharge even when equal net power input is provided. It is reasonable to expect that the combined discharge containing both types of discharges mentioned above may be expected to improve significantly both the steady-state and transient characteristics of the plasma. The characteristics of different discharges in air, nitrogen air-CO 2 -He mixture have been compared. Because of the lack of the direct electrical methods for measurements of the hf plasma, exphasis in this investigation has been laid on both theoretical) based on the analytical expression for electron energy distribution function received previously and experimental spectroscopic evaluations of the plasma parameters. (Auth.)

  7. Comparative molecular analysis of early and late cancer cachexia-induced muscle wasting in mouse models.

    Science.gov (United States)

    Sun, Rulin; Zhang, Santao; Lu, Xing; Hu, Wenjun; Lou, Ning; Zhao, Yan; Zhou, Jia; Zhang, Xiaoping; Yang, Hongmei

    2016-12-01

    Cancer-induced muscle wasting, which commonly occurs in cancer cachexia, is characterized by impaired quality of life and poor patient survival. To identify an appropriate treatment, research on the mechanism underlying muscle wasting is essential. Thus far, studies on muscle wasting using cancer cachectic models have generally focused on early cancer cachexia (ECC), before severe body weight loss occurs. In the present study, we established models of ECC and late cancer cachexia (LCC) and compared different stages of cancer cachexia using two cancer cachectic mouse models induced by colon-26 (C26) adenocarcinoma or Lewis lung carcinoma (LLC). In each model, tumor-bearing (TB) and control (CN) mice were injected with cancer cells and PBS, respectively. The TB and CN mice, which were euthanized on the 24th day or the 36th day after injection, were defined as the ECC and ECC-CN mice or the LCC and LCC-CN mice. In addition, the tissues were harvested and analyzed. We found that both the ECC and LCC mice developed cancer cachexia. The amounts of muscle loss differed between the ECC and LCC mice. Moreover, the expression of some molecules was altered in the muscles from the LCC mice but not in those from the ECC mice compared with their CN mice. In conclusion, the molecules with altered expression in the muscles from the ECC and LCC mice were not exactly the same. These findings may provide some clues for therapy which could prevent the muscle wasting in cancer cachexia from progression to the late stage.

  8. Comparative modelling and molecular docking of nitrate reductase from Bacillus weihenstephanensis (DS45

    Directory of Open Access Journals (Sweden)

    R. Seenivasagan

    2016-07-01

    Full Text Available Nitrate reductase catalyses the oxidation of NAD(PH and the reduction of nitrate to nitrite. NR serves as a central point for the integration of metabolic pathways by governing the flux of reduced nitrogen through several regulatory mechanisms in plants, algae and fungi. Bacteria express nitrate reductases that convert nitrate to nitrite, but mammals lack these specific enzymes. The microbial nitrate reductase reduces toxic compounds to nontoxic compounds with the help of NAD(PH. In the present study, our results revealed that Bacillus weihenstephanensis expresses a nitrate reductase enzyme, which was made to generate the 3D structure of the enzyme. Six different modelling servers, namely Phyre2, RaptorX, M4T Server, HHpred, SWISS MODEL and Mod Web, were used for comparative modelling of the structure. The model was validated with standard parameters (PROCHECK and Verify 3D. This study will be useful in the functional characterization of the nitrate reductase enzyme and its docking with nitrate molecules, as well as for use with autodocking.

  9. Comparative transcriptional analysis provides new insights into the molecular basis of adventitious rooting recalcitrance in Eucalyptus.

    Science.gov (United States)

    de Almeida, Márcia Rodrigues; de Bastiani, Daniela; Gaeta, Marcos Letaif; de Araújo Mariath, Jorge Ernesto; de Costa, Fernanda; Retallick, Jeffrey; Nolan, Lana; Tai, Helen H; Strömvik, Martina V; Fett-Neto, Arthur Germano

    2015-10-01

    Adventitious rooting (AR) is essential in clonal propagation. Eucalyptus globulus is relevant for the cellulose industry due to its low lignin content. However, several useful clones are recalcitrant to AR, often requiring exogenous auxin, adding cost to clonal garden operations. In contrast, E. grandis is an easy-to-root species widely used in clonal forestry. Aiming at contributing to the elucidation of recalcitrance causes in E. globulus, we conducted a comparative analysis with these two species differing in rooting competence, combining gene expression and anatomical techniques. Recalcitrance in E. globulus is reversed by exposure to exogenous indole-3-acetic acid (IAA), which promotes important gene expression modifications in both species. The endogenous content of IAA was significantly higher in E. grandis than in E. globulus. The cambium zone was identified as an active area during AR, concentrating the first cell divisions. Immunolocalization assay showed auxin accumulation in cambium cells, further indicating the importance of this region for rooting. We then performed a cambium zone-specific gene expression analysis during AR using laser microdissection. The results indicated that the auxin-related genes TOPLESS and IAA12/BODENLOS and the cytokinin-related gene ARR1may act as negative regulators of AR, possibly contributing to the hard-to-root phenotype of E. globulus. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  10. Nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in Alphaproteobacteria

    Directory of Open Access Journals (Sweden)

    Olga V Tsoy

    2016-08-01

    Full Text Available Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of Bacteria and Archaea. Being a complex and sensitive process, nitrogen fixation requires a complicated regulatory system, also, on the level of transcription. The transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class Alphaproteobacteria. This regulatory network includes the activator of nitrogen fixation NifA, working in tandem with the alternative sigma-factor RpoN as well as oxygen-responsive regulatory systems, one-component regulators FnrN/FixK and two-component system FixLJ. Here we used a comparative genomics analysis for in silico study of the transcriptional regulatory network in 50 genomes of Alphaproteobacteria. We extended the known regulons and proposed the scenario for the evolution of the nitrogen fixation transcriptional network. The reconstructed network substantially expands the existing knowledge of transcriptional regulation in nitrogen-fixing microorganisms and can be used for genetic experiments, metabolic reconstruction, and evolutionary analysis.

  11. Multiplex molecular testing for management of infectious gastroenteritis in a hospital setting: a comparative diagnostic and clinical utility study.

    Science.gov (United States)

    Halligan, E; Edgeworth, J; Bisnauthsing, K; Bible, J; Cliff, P; Aarons, E; Klein, J; Patel, A; Goldenberg, S

    2014-08-01

    Laboratory diagnosis and clinical management of inpatients with diarrhoea is complex and time consuming. Tests are often requested sequentially and undertaken in different laboratories. This causes prolonged unnecessary presumptive isolation of patients, because most cases are non-infectious. A molecular multiplex test (Luminex(®) Gastrointestinal Pathogen Panel (GPP)) was compared with conventional testing over 8 months to determine diagnostic accuracy, turnaround times, laboratory costs, use of isolation facilities and user acceptability. A total of 262 (12%) patients had a pathogen detected by conventional methods compared with 483 (22.1%) by GPP. Most additional cases were detected in patients developing symptoms in the first 4 days of admission. Additional cases were detected because of presumed improved diagnostic sensitivity but also because clinicians had not requested the correct pathogen. Turnaround time (41.8 h) was faster than bacterial culture (66.5 h) and parasite investigation (66.5 h) but slower than conventional testing for Clostridium difficile (17.3 h) and viruses (27 h). The test could allow simplified requesting by clinicians and a consolidated laboratory workflow, reducing the overall number of specimens received by the laboratory. A total of 154 isolation days were saved at an estimated cost of £30 800. Consumables and labour were estimated at £150 641 compared with £63 431 for conventional testing. Multiplex molecular testing using a panel of targets allowed enhanced detection and a consolidated laboratory workflow. This is likely to be of greater benefit to cases that present within the first 4 days of hospital admission. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

  12. Prospective molecular profiling of canine cancers provides a clinically relevant comparative model for evaluating personalized medicine (PMed) trials.

    Science.gov (United States)

    Paoloni, Melissa; Webb, Craig; Mazcko, Christina; Cherba, David; Hendricks, William; Lana, Susan; Ehrhart, E J; Charles, Brad; Fehling, Heather; Kumar, Leena; Vail, David; Henson, Michael; Childress, Michael; Kitchell, Barbara; Kingsley, Christopher; Kim, Seungchan; Neff, Mark; Davis, Barbara; Khanna, Chand; Trent, Jeffrey

    2014-01-01

    Molecularly-guided trials (i.e. PMed) now seek to aid clinical decision-making by matching cancer targets with therapeutic options. Progress has been hampered by the lack of cancer models that account for individual-to-individual heterogeneity within and across cancer types. Naturally occurring cancers in pet animals are heterogeneous and thus provide an opportunity to answer questions about these PMed strategies and optimize translation to human patients. In order to realize this opportunity, it is now necessary to demonstrate the feasibility of conducting molecularly-guided analysis of tumors from dogs with naturally occurring cancer in a clinically relevant setting. A proof-of-concept study was conducted by the Comparative Oncology Trials Consortium (COTC) to determine if tumor collection, prospective molecular profiling, and PMed report generation within 1 week was feasible in dogs. Thirty-one dogs with cancers of varying histologies were enrolled. Twenty-four of 31 samples (77%) successfully met all predefined QA/QC criteria and were analyzed via Affymetrix gene expression profiling. A subsequent bioinformatics workflow transformed genomic data into a personalized drug report. Average turnaround from biopsy to report generation was 116 hours (4.8 days). Unsupervised clustering of canine tumor expression data clustered by cancer type, but supervised clustering of tumors based on the personalized drug report clustered by drug class rather than cancer type. Collection and turnaround of high quality canine tumor samples, centralized pathology, analyte generation, array hybridization, and bioinformatic analyses matching gene expression to therapeutic options is achievable in a practical clinical window (strategies may aid cancer drug development.

  13. A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Davide Michetti

    Full Text Available The psychrophilic and mesophilic endonucleases A (EndA from Aliivibrio salmonicida (VsEndA and Vibrio cholera (VcEndA have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.

  14. Molecular phylogeny and comparative morphology indicate that odontostomatids (Alveolata, Ciliophora) form a distinct class-level taxon related to Armophorea.

    Science.gov (United States)

    Fernandes, Noemi M; Vizzoni, Vinicius F; Borges, Bárbara do N; A G Soares, Carlos; Silva-Neto, Inácio D da; S Paiva, Thiago da

    2018-04-18

    The odontostomatids are among the least studied ciliates, possibly due to their small sizes, restriction to anaerobic environments and difficulty in culturing. Consequently, their phylogenetic affinities to other ciliate taxa are still poorly understood. In the present study, we analyzed newly obtained ribosomal gene sequences of the odontostomatids Discomorphella pedroeneasi and Saprodinium dentatum, together with sequences from the literature, including Epalxella antiquorum and a large assemblage of ciliate sequences representing the major recognized classes. The results show that D. pedroeneasi and S. dentatum form a deep-diverging branch related to metopid and clevelandellid armophoreans, corroborating the old literature. However E. antiquorum clustered with the morphologically discrepant plagiopylids, indicating that either the complex odontostomatid body architecture evolved convergently, or the positioning of E. antiquorum as a plagiopylid is artifactual. A new ciliate class, Odontostomatea n. cl., is proposed based on molecular analyses and comparative morphology of odontostomatids with related taxa. Copyright © 2018. Published by Elsevier Inc.

  15. Epigenetic: A missing paradigm in cellular and molecular pathways of sulfur mustard lung: a prospective and comparative study

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    Saber Imani

    2015-08-01

    Full Text Available Sulfur mustard (SM, bis- (2-chloroethyl sulphide is a chemical warfare agent that causes DNA alkylation, protein modification and membrane damage. SM can trigger several molecular pathways involved in inflammation and oxidative stress, which cause cell necrosis and apoptosis, and loss of cells integrity and function. Epigenetic regulation of gene expression is a growing research topic and is addressed by DNA methylation, histone modification, chromatin remodeling, and noncoding RNAs expression. It seems SM can induce the epigenetic modifications that are translated into change in gene expression. Classification of epigenetic modifications long after exposure to SM would clarify its mechanism and paves a better strategy for the treatment of SM-affected patients. In this study, we review the key aberrant epigenetic modifications that have important roles in chronic obstructive pulmonary disease (COPD and compared with mustard lung.

  16. Altitudinal distribution and advertisement call of Colostethus latinasus (Amphibia: Dendrobatidae), endemic species from eastern Panama and type species of Colostethus , with a molecular assessment of similar sympatric species.

    Science.gov (United States)

    Ibáñez, Roberto D; Griffith, Edgardo J; Lips, Karen R; Crawford, Andrew J

    2017-04-12

    We conducted a molecular assessment of Colostethus-like frogs along an elevational gradient in the Serranía de Pirre, above Santa Cruz de Cana, eastern Panama, aiming to establish their species identity and to determine the altitudinal distribution of C. latinasus. Our findings confirm the view of C. latinasus as an endemic species restricted to the highlands of this mountain range, i.e., 1350-1475 m.a.s.l., considered to be type locality of this species. We described the advertisement call of C. latinasus that consists of a series of 4-18 single, short and relatively loud "peep"-like notes given in rapid succession, and its spectral and temporal features were compared with calls of congeneric species. For the first time, DNA sequences from C. latinasus were obtained, since previously reported sequences were based on misidentified specimens. This is particularly important because C. latinasus is the type species of Colostethus, a genus considered paraphyletic according to recent phylogenetic analyses based on molecular data.

  17. Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

    Directory of Open Access Journals (Sweden)

    Steven R. Ahrendt

    2017-04-01

    Full Text Available Background Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins are a subfamily of G-protein coupled receptors (GPCRs, a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if the sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion This represents the first test of structure/function relationship of a type 2 rhodopsin

  18. Equilibrium Molecular Dynamics (MD Simulation Study of Thermal Conductivity of Graphene Nanoribbon: A Comparative Study on MD Potentials

    Directory of Open Access Journals (Sweden)

    Asir Intisar Khan

    2015-12-01

    Full Text Available The thermal conductivity of graphene nanoribbons (GNRs has been investigated using equilibrium molecular dynamics (EMD simulation based on Green-Kubo (GK method to compare two interatomic potentials namely optimized Tersoff and 2nd generation Reactive Empirical Bond Order (REBO. Our comparative study includes the estimation of thermal conductivity as a function of temperature, length and width of GNR for both the potentials. The thermal conductivity of graphene nanoribbon decreases with the increase of temperature. Quantum correction has been introduced for thermal conductivity as a function of temperature to include quantum effect below Debye temperature. Our results show that for temperatures up to Debye temperature, thermal conductivity increases, attains its peak and then falls off monotonically. Thermal conductivity is found to decrease with the increasing length for optimized Tersoff potential. However, thermal conductivity has been reported to increase with length using 2nd generation REBO potential for the GNRs of same size. Thermal conductivity, for the specified range of width, demonstrates an increasing trend with the increase of width for both the concerned potentials. In comparison with 2nd generation REBO potential, optimized Tersoff potential demonstrates a better modeling of thermal conductivity as well as provides a more appropriate description of phonon thermal transport in graphene nanoribbon. Such comparative study would provide a good insight for the optimization of the thermal conductivity of graphene nanoribbons under diverse conditions.

  19. Comparative proteomic analysis of fluoride treated rat bone provides new insights into the molecular mechanisms of fluoride toxicity.

    Science.gov (United States)

    Wei, Yan; Zeng, Beibei; Zhang, Hua; Chen, Cheng; Wu, Yanli; Wang, Nanlan; Wu, Yanqiu; Zhao, Danqing; Zhao, Yuxi; Iqbal, Javed; Shen, Liming

    2018-07-01

    Long-term excessive intake of fluoride (F) could lead to chronic fluorosis. To explore the underlying molecular mechanisms, present study is designed to elucidate the effect of fluoride on proteome expression of bone in sodium fluoride (NaF)-treated SD rats. Hematoxylin and eosin (H&E) staining was used to determine the severity of osteofluorosis, and bone samples were submitted for iTRAQ analysis. The results showed that the cortical thickness and trabecular area of femur bone in medium- and high-dose groups were higher than in control group. Contrary to this, trabecular area was reduced in the low-dose group, indicating that the bone mass was increased in medium- and high-dose groups, and decreased in the low-dose group. Thirteen (13), 35, and 34 differentially expressed proteins were identified in low-, medium-, and high-dose group, respectively. The medium- and high-dose groups shared a more similar protein expression pattern. These proteins were mainly associated with collagen metabolism, proteoglycans (PGs), matrix metalloproteinases (MMPs), etc. The results suggested that the effect of NaF on SD rats is in a dose-dependent manner. Some key proteins found here may be involved in affecting the bone tissues and bone marrow or muscle, and account for the complex pathology and clinical symptoms of fluorosis. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Increased expression of damage-associated molecular patterns (DAMPs) in osteoarthritis of human knee joint compared to hip joint.

    Science.gov (United States)

    Rosenberg, John H; Rai, Vikrant; Dilisio, Matthew F; Sekundiak, Todd D; Agrawal, Devendra K

    2017-12-01

    Osteoarthritis (OA) is a degenerative disease characterized by the destruction of cartilage. The greatest risk factors for the development of OA include age and obesity. Recent studies suggest the role of inflammation in the pathogenesis of OA. The two most common locations for OA to occur are in the knee and hip joints. The knee joint experiences more mechanical stress, cartilage degeneration, and inflammation than the hip joint. This could contribute to the increased incidence of OA in the knee joint. Damage-associated molecular patterns (DAMPs), including high-mobility group box-1, receptor for advanced glycation end products, and alarmins (S100A8 and S100A9), are released in the joint in response to stress-mediated chondrocyte and cartilage damage. This facilitates increased cartilage degradation and inflammation in the joint. Studies have documented the role of DAMPs in the pathogenesis of OA; however, the comparison of DAMPs and its influence on OA has not been discussed. In this study, we compared the DAMPs between OA knee and hip joints and found a significant difference in the levels of DAMPs expressed in the knee joint compared to the hip joint. The increased levels of DAMPs suggest a difference in the underlying pathogenesis of OA in the knee and the hip and highlights DAMPs as potential therapeutic targets for OA in the future.

  1. Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events.

    Directory of Open Access Journals (Sweden)

    Xianxin Li

    Full Text Available Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. Further comparative analyses at the systems level revealed that significant aberrations of the cell adhesion process, p53 signaling, calcium signaling, the ECM-receptor and cell cycle pathways, the DNA repair and replication processes and the immune and inflammatory response processes were the common hallmarks of human cancers. Gene sets showing testicular cancer-specific deregulation patterns were mainly implicated in processes related to male reproductive function, and general disruptions of multiple metabolic pathways and processes related to cell migration were the characteristic molecular events for renal and bladder cancer, respectively. Furthermore, we also demonstrated that tumors with the same histological origins and genes with similar functions tended to group together in a clustering analysis. By assessing the correlation between the expression of each miRNA and its targets, we determined that deregulation of 'key' miRNAs may result in the global aberration of one or more pathways or processes as a whole.This systematic analysis deciphered the molecular phenotypes of three genitourinary cancers and investigated their variations at the miRNA level simultaneously. Our results provided a valuable source for future studies and highlighted some promising genes, miRNAs, pathways and processes that may be useful for diagnostic or

  2. The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

    Directory of Open Access Journals (Sweden)

    Pawlowski Marcin

    2012-11-01

    Full Text Available Abstract Background Computational models of protein structures were proved to be useful as search models in Molecular Replacement (MR, a common method to solve the phase problem faced by macromolecular crystallography. The success of MR depends on the accuracy of a search model. Unfortunately, this parameter remains unknown until the final structure of the target protein is determined. During the last few years, several Model Quality Assessment Programs (MQAPs that predict the local accuracy of theoretical models have been developed. In this article, we analyze whether the application of MQAPs improves the utility of theoretical models in MR. Results For our dataset of 615 search models, the real local accuracy of a model increases the MR success ratio by 101% compared to corresponding polyalanine templates. On the contrary, when local model quality is not utilized in MR, the computational models solved only 4.5% more MR searches than polyalanine templates. For the same dataset of the 615 models, a workflow combining MR with predicted local accuracy of a model found 45% more correct solution than polyalanine templates. To predict such accuracy MetaMQAPclust, a “clustering MQAP” was used. Conclusions Using comparative models only marginally increases the MR success ratio in comparison to polyalanine structures of templates. However, the situation changes dramatically once comparative models are used together with their predicted local accuracy. A new functionality was added to the GeneSilico Fold Prediction Metaserver in order to build models that are more useful for MR searches. Additionally, we have developed a simple method, AmIgoMR (Am I good for MR?, to predict if an MR search with a template-based model for a given template is likely to find the correct solution.

  3. Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes.

    Directory of Open Access Journals (Sweden)

    Yunsheng Wang

    Full Text Available In this study, we identified and compared nucleotide-binding site (NBS domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China. Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR domain and two different Non-TIR groups in which most of proteins contain the Coiled Coil (CC domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three Citrus genomes. This suggests that three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that sequence variation amongst Citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different Citrus genomes. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention.

  4. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis.

    Directory of Open Access Journals (Sweden)

    Emmanuel Dias-Neto

    2009-12-01

    Full Text Available Combinatorial phage display has been used in the last 20 years in the identification of protein-ligands and protein-protein interactions, uncovering relevant molecular recognition events. Rate-limiting steps of combinatorial phage display library selection are (i the counting of transducing units and (ii the sequencing of the encoded displayed ligands. Here, we adapted emerging genomic technologies to minimize such challenges.We gained efficiency by applying in tandem real-time PCR for rapid quantification to enable bacteria-free phage display library screening, and added phage DNA next-generation sequencing for large-scale ligand analysis, reporting a fully integrated set of high-throughput quantitative and analytical tools. The approach is far less labor-intensive and allows rigorous quantification; for medical applications, including selections in patients, it also represents an advance for quantitative distribution analysis and ligand identification of hundreds of thousands of targeted particles from patient-derived biopsy or autopsy in a longer timeframe post library administration. Additional advantages over current methods include increased sensitivity, less variability, enhanced linearity, scalability, and accuracy at much lower cost. Sequences obtained by qPhage plus pyrosequencing were similar to a dataset produced from conventional Sanger-sequenced transducing-units (TU, with no biases due to GC content, codon usage, and amino acid or peptide frequency. These tools allow phage display selection and ligand analysis at >1,000-fold faster rate, and reduce costs approximately 250-fold for generating 10(6 ligand sequences.Our analyses demonstrates that whereas this approach correlates with the traditional colony-counting, it is also capable of a much larger sampling, allowing a faster, less expensive, more accurate and consistent analysis of phage enrichment. Overall, qPhage plus pyrosequencing is superior to TU-counting plus Sanger

  5. Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

    International Nuclear Information System (INIS)

    Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp; Behler, Jörg

    2016-01-01

    Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy is constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.

  6. Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

    Energy Technology Data Exchange (ETDEWEB)

    Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at [Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna (Austria); Behler, Jörg [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150, Bochum (Germany)

    2016-05-21

    Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy is constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.

  7. [Molecular organization of glutamate-sensitive chemoexcitatory membranes of nerve cells. Comparative analysis of glutamate-binding membrane proteins from the cerebral cortex of rats and humans].

    Science.gov (United States)

    Dambinova, S A; Gorodinskiĭ, A I; Lekomtseva, T M; Koreshonkov, O N

    1987-10-01

    The kinetics of 3H-L-glutamate binding to human brain synaptic membranes revealed the existence of one type of binding sites with Kd and Vmax comparable with those for freshly isolated rat brain membranes. The fraction of glutamate-binding proteins (GBP) was shown to contain three components with Mr of 14, 60 and 280 kD whose stoichiometry is specific for human and rat brain. All fractions were found to bind the radiolabeled neurotransmitter and to dissociate into subunits with Mr of 14 kD after treatment with-potent detergents (with the exception of the 56-60 kD component). Study of association-dissociation of GBP protein subunits by high performance liquid chromatography confirmed the hypothesis on the oligomeric structure of glutamate receptors which are made up of low molecular weight glycoprotein-lipid subunits and which form ionic channels by way of repeated association. Despite the similarity of antigen determinants in the active center of glutamate receptors from human and rat brain, it was assumed that the stoichiometry of structural organization of receptor subunits isolated from different sources is different. The functional role of structural complexity of human brain glutamate receptors is discussed.

  8. Phoneme Similarity and Confusability

    Science.gov (United States)

    Bailey, T.M.; Hahn, U.

    2005-01-01

    Similarity between component speech sounds influences language processing in numerous ways. Explanation and detailed prediction of linguistic performance consequently requires an understanding of these basic similarities. The research reported in this paper contrasts two broad classes of approach to the issue of phoneme similarity-theoretically…

  9. The role of pyrimidine and water as underlying molecular constituents for describing radiation damage in living tissue: A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Fuss, M. C.; Ellis-Gibbings, L. [Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid (Spain); Jones, D. B. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Brunger, M. J. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur (Malaysia); Blanco, F. [Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Avenida Complutense, 28040 Madrid (Spain); Muñoz, A. [Centro de Investigaciones Energéticas Medioambientales y Tecnológicas, Avenida Complutense 22, 28040 Madrid (Spain); Limão-Vieira, P. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); García, G., E-mail: g.garcia@csic.es [Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid (Spain); Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW 2522 (Australia)

    2015-06-07

    Water is often used as the medium for characterizing the effects of radiation on living tissue. However, in this study, charged-particle track simulations are employed to quantify the induced physicochemical and potential biological implications when a primary ionising particle with energy 10 keV strikes a medium made up entirely of water or pyrimidine. Note that pyrimidine was chosen as the DNA/RNA bases cytosine, thymine, and uracil can be considered pyrimidine derivatives. This study aims to assess the influence of the choice of medium on the charged-particle transport, and identify how appropriate it is to use water as the default medium to describe the effects of ionising radiation on living tissue. Based on the respective electron interaction cross sections, we provide a model, which allows the study of radiation effects not only in terms of energy deposition (absorbed dose and stopping power) but also in terms of the number of induced molecular processes. Results of these parameters for water and pyrimidine are presented and compared.

  10. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Pabit, Suzette A.; Katz, Andrea M.; Pollack, Lois [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States); Tolokh, Igor S. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States); Drozdetski, Aleksander [Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States); Baker, Nathan [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Onufriev, Alexey V. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States); Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States)

    2016-05-28

    Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

  11. Molecular binding of toxic phenothiazinium derivatives, azures to bovine serum albumin: A comparative spectroscopic, calorimetric, and in silico study.

    Science.gov (United States)

    Das, Somnath; Islam, Md Maidul; Jana, Gopal Chandra; Patra, Anirudha; Jha, Pradeep K; Hossain, Maidul

    2017-07-01

    In this paper, the comparative binding behavior of antimalarial drug azure A, azure B and azure C with bovine serum albumin (BSA) has been studied. The interaction has been confirmed by multispectroscopic (UV, fluorescence, Fourier transform infrared (FT-IR), and circular dichroism) and molecular docking techniques. The experimental results show that azure B has the highest BSA binding affinity followed by azure A and azure C. The experimental evidence of binding showed a static quenching mechanism in the interaction azures with BSA. The isothermal titration calorimetry result reveals that the binding was exothermic with positive entropy contribution in each case. The thermodynamic parameters ΔH, ΔG, and ΔS at 25°C were calculated, which indicates that the weak van der Waals forces and hydrogen bonding rather than the hydrophobic effect played an important role in the interaction. According to the theory of Förster nonradiative energy transfer, the distance (r) between the donor (BSA) and acceptor azures found to be albumins. We hope, the outcome of this work will be most helpful for synthesizing a new type of phenothiazinium derivatives of the better therapeutic application. Copyright © 2017 John Wiley & Sons, Ltd.

  12. Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae.

    Science.gov (United States)

    Mao, Yunrui; Zhang, Yonghua; Xu, Chuan; Qiu, Yingxiong

    2016-01-01

    Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa. © 2015 John Wiley & Sons Ltd.

  13. Global genomic analysis of intraductal papillary mucinous neoplasms of the pancreas reveals significant molecular differences compared to ductal adenocarcinoma.

    Science.gov (United States)

    Fritz, Stefan; Fernandez-del Castillo, Carlos; Mino-Kenudson, Mari; Crippa, Stefano; Deshpande, Vikram; Lauwers, Gregory Y; Warshaw, Andrew L; Thayer, Sarah P; Iafrate, A John

    2009-03-01

    To determine whether intraductal papillary mucinous neoplasms of the pancreas (IPMNs) have a different genetic background compared with ductal adenocarcinoma (PDAC). The biologic and clinical behavior of IPMNs and IPMN-associated adenocarcinomas is different from PDAC in having a less aggressive tumor growth and significantly improved survival. Up to date, the molecular mechanisms underlying the clinical behavior of IPMNs are incompletely understood. 128 cystic pancreatic lesions were prospectively identified during the course of 2 years. From the corresponding surgical specimens, 57 IPMNs were separated and subdivided by histologic criteria into those with low-grade dysplasia, moderate dysplasia, high-grade dysplasia, and invasive cancer. Twenty specimens were suitable for DNA isolation and subsequent performance of array CGH. While none of the IPMNs with low-grade dysplasia displayed detectable chromosomal aberrations, IPMNs with moderate and high-grade dysplasia showed frequent copy number alterations. Commonly lost regions were located on chromosome 5q, 6q, 10q, 11q, 13q, 18q, and 22q. The incidence of loss of chromosome 5q, 6q, and 11q was significantly higher in IPMNs with high-grade dysplasia or invasion compared with PDAC. Ten of 13 IPMNs with moderate dysplasia or malignancy had loss of part or all of chromosome 6q, with a minimal deleted region between linear positions 78.0 and 130.0. This study is the first to use array CGH to characterize IPMNs. Recurrent cytogenetic alterations were identified and were different than those described in PDAC. Array CGH may help distinguish between these 2 entities and give insight into the differences in their biology and prognosis.

  14. Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis

    Science.gov (United States)

    Woolfrey, John R.; Avery, Mitchell A.; Doweyko, Arthur M.

    1998-03-01

    Two three-dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL), were compared with respect to the analysis of a training set of 154 artemisinin analogues. Five models were created, including a complete HASL and two trimmed versions, as well as two CoMFA models (leave-one-out standard CoMFA and the guided-region selection protocol). Similar r2 and q2 values were obtained by each method, although some striking differences existed between CoMFA contour maps and the HASL output. Each of the four predictive models exhibited a similar ability to predict the activity of a test set of 23 artemisinin analogues, although some differences were noted as to which compounds were described well by either model.

  15. Avoiding pitfalls in molecular genetic testing: case studies of high-resolution array comparative genomic hybridization testing in the definitive diagnosis of Mowat-Wilson syndrome.

    Science.gov (United States)

    Kluk, Michael Joseph; An, Yu; James, Philip; Coulter, David; Harris, David; Wu, Bai-Lin; Shen, Yiping

    2011-05-01

    The molecular testing options available for the diagnosis of genetic disorders are numerous and include a variety of different assay platforms. The consultative input of molecular pathologists and cytogeneticists, working closely with the ordering clinicians, is often important for definitive diagnosis. Herein, we describe two patients who had long histories of unexplained signs and symptoms with a high clinical suspicion of an underlying genetic etiology. Initial molecular testing in both cases was negative, but the application of high-resolution array comparative genomic hybridization technology lead to definitive diagnosis in both cases. We summarize the clinical findings and molecular testing in each case, discuss the differential diagnoses, and review the clinical and pathological findings of Mowat-Wilson syndrome. This report highlights the importance for those involved in molecular testing to know the nature of the underlying genetic abnormalities associated with the suspected diagnosis, to recognize the limitations of each testing platform, and to persistently pursue repeat testing using high-resolution technologies when indicated. This concept is applicable to both germline and somatic molecular genetic testing. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  16. A COMPARISON OF SEMANTIC SIMILARITY MODELS IN EVALUATING CONCEPT SIMILARITY

    Directory of Open Access Journals (Sweden)

    Q. X. Xu

    2012-08-01

    Full Text Available The semantic similarities are important in concept definition, recognition, categorization, interpretation, and integration. Many semantic similarity models have been established to evaluate semantic similarities of objects or/and concepts. To find out the suitability and performance of different models in evaluating concept similarities, we make a comparison of four main types of models in this paper: the geometric model, the feature model, the network model, and the transformational model. Fundamental principles and main characteristics of these models are introduced and compared firstly. Land use and land cover concepts of NLCD92 are employed as examples in the case study. The results demonstrate that correlations between these models are very high for a possible reason that all these models are designed to simulate the similarity judgement of human mind.

  17. Molecular and Phenotypic Characterization of Staphylococcus epidermidis Isolates from Healthy Conjunctiva and a Comparative Analysis with Isolates from Ocular Infection.

    Directory of Open Access Journals (Sweden)

    Luis A Flores-Páez

    Full Text Available Staphylococcus epidermidis is a common commensal of healthy conjunctiva and it can cause endophthalmitis, however its presence in conjunctivitis, keratitis and blepharitis is unknown. Molecular genotyping of S. epidermidis from healthy conjunctiva could provide information about the origin of the strains that infect the eye. In this paper two collections of S. epidermidis were used: one from ocular infection (n = 62, and another from healthy conjunctiva (n = 45. All isolates were genotyped by pulsed field gel electrophoresis (PFGE, multilocus sequence typing (MLST, staphylococcal cassette chromosome mec (SCCmec, detection of the genes icaA, icaD, IS256 and polymorphism type of agr locus. The phenotypic data included biofilm production and antibiotic resistance. The results displayed 61 PFGE types from 107 isolates and they were highly discriminatory. MLST analysis generated a total of 25 STs, of which 11 STs were distributed among the ocular infection isolates and lineage ST2 was the most frequent (48.4%, while 14 STs were present in the healthy conjunctiva isolates and lineage ST5 was the most abundant (24.4%. By means of a principal coordinates analysis (PCoA and a discriminant analysis (DA it was found that ocular infection isolates had as discriminant markers agr III or agr II, SCCmec V or SCCmec I, mecA gene, resistance to tobramycin, positive biofilm, and IS256+. In contrast to the healthy conjunctiva isolates, the discriminating markers were agr I, and resistance to chloramphenicol, ciprofloxacin, gatifloxacin and oxacillin. The discriminant biomarkers of ocular infection were examined in healthy conjunctiva isolates, and it was found that 3 healthy conjunctiva isolates [two with ST2 and another with ST9] (3/45, 6.66% had similar genotypic and phenotypic characteristics to ocular infection isolates, therefore a small population from healthy conjunctiva could cause an ocular infection. These data suggest that the healthy conjunctiva

  18. Kefir drink causes a significant yet similar improvement in serum lipid profile, compared with low-fat milk, in a dairy-rich diet in overweight or obese premenopausal women: A randomized controlled trial.

    Science.gov (United States)

    Fathi, Yasamin; Ghodrati, Naeimeh; Zibaeenezhad, Mohammad-Javad; Faghih, Shiva

    Controversy exists as to whether the lipid-lowering properties of kefir drink (a fermented probiotic dairy product) in animal models could be replicated in humans. To assess and compare the potential lipid-lowering effects of kefir drink with low-fat milk in a dairy-rich diet in overweight or obese premenopausal women. In this 8-week, single-center, multiarm, parallel-group, outpatient, randomized controlled trial, 75 eligible Iranian women aged 25 to 45 years were randomly allocated to kefir, milk, or control groups. Women in the control group received a weight-maintenance diet containing 2 servings/d of low-fat dairy products, whereas subjects in the milk and kefir groups received a similar diet containing 2 additional servings/d (a total of 4 servings/d) of dairy products from low-fat milk or kefir drink, respectively. At baseline and study end point, serum levels/ratios of total cholesterol (TC), low- and high-density lipoprotein cholesterol (LDLC and HDLC), triglyceride, Non-HDLC, TC/HDLC, LDLC/HDLC, and triglyceride/LDLC were measured as outcome measures. After 8 weeks, subjects in the kefir group had significantly lower serum levels/ratios of lipoproteins than those in the control group (mean between-group differences were -10.4 mg/dL, -9.7 mg/dL, -11.5 mg/dL, -0.4, and -0.3 for TC, LDLC, non-HDLC, TC/HDLC, and LDLC/HDLC, respectively; all P < .05). Similar results were observed in the milk group. However, no such significant differences were found between the kefir and milk groups. Kefir drink causes a significant yet similar improvement in serum lipid profile, compared with low-fat milk, in a dairy-rich diet in overweight or obese premenopausal women. Copyright © 2016 National Lipid Association. Published by Elsevier Inc. All rights reserved.

  19. Processes of Similarity Judgment

    Science.gov (United States)

    Larkey, Levi B.; Markman, Arthur B.

    2005-01-01

    Similarity underlies fundamental cognitive capabilities such as memory, categorization, decision making, problem solving, and reasoning. Although recent approaches to similarity appreciate the structure of mental representations, they differ in the processes posited to operate over these representations. We present an experiment that…

  20. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the

  1. Kefir drink leads to a similar weight loss, compared with milk, in a dairy-rich non-energy-restricted diet in overweight or obese premenopausal women: a randomized controlled trial.

    Science.gov (United States)

    Fathi, Yasamin; Faghih, Shiva; Zibaeenezhad, Mohammad Javad; Tabatabaei, Sayed Hamid Reza

    2016-02-01

    Controversy exists regarding whether increasing dairy intake without energy restriction would lead to weight loss. We aimed to compare the potential weight-reducing effects of kefir drink (a probiotic dairy product) and milk in a dairy-rich non-energy-restricted diet in overweight or obese premenopausal women. One hundred and forty-four subjects were assessed for eligibility in this single-center, multi-arm, parallel-group, randomized controlled trial. Of these, seventy-five eligible women aged 25-45 years were randomly assigned to three groups, labeled as control, milk, and kefir, to receive an outpatient dietary regimen for 8 weeks. Subjects in the control group received a diet providing a maintenance level of energy intake, containing 2 servings/day of low-fat dairy products, while those in the milk and kefir groups received a weight maintenance diet, containing 2 additional servings/day (a total of 4 servings/day) of dairy products from low-fat milk or commercial kefir drink, respectively. Anthropometric outcomes including weight, body mass index (BMI), and waist circumference (WC) were measured every 2 weeks. Fifty-eight subjects completed the study. Using analysis of covariance models in the intention-to-treat population (n = 75), we found that at 8 weeks, subjects in the kefir and milk groups had significantly greater reductions in weight, BMI, and WC compared to those in the control group (all p < 0.01). However, no such significant differences were found between the kefir and milk groups. Kefir drink leads to a similar weight loss, compared with milk, in a dairy-rich non-energy-restricted diet in overweight or obese premenopausal women. However, further studies are warranted.

  2. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2013-12-01

    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  3. Comparative proteomic analysis reveals molecular mechanism of seedling roots of different salt tolerant soybean genotypes in responses to salinity stress

    Directory of Open Access Journals (Sweden)

    Hongyu Ma

    2014-09-01

    Full Text Available Salinity stress is one of the major abiotic stresses that limit agricultural yield. To understand salt-responsive protein networks in soybean seedling, the extracted proteins from seedling roots of two different genotypes (Lee 68 and Jackson were analyzed under salt stress by two-dimensional polyacrylamide gel electrophoresis. Sixty-eight differentially expressed proteins were detected and identified. The identified proteins were involved in 13 metabolic pathways and cellular processes. Proteins correlated to brassinosteroid and gilbberellin signalings were significantly increased only in the genotype Lee 68 under salt stress; abscisic acid content was positively correlated with this genotype; proteins that can be correlated to Ca2+ signaling were more strongly enhanced by salt stress in the seedling roots of genotype Lee 68 than in those of genotype Jackson; moreover, genotype Lee 68 had stronger capability of reactive oxygen species scavenging and cell K+/Na+ homeostasis maintaining in seedling roots than genotype Jackson under salt stress. Since the genotype Lee 68 has been described in literature as being tolerant and Jackson as sensitive, we hypothesize that these major differences in the genotype Lee 68 might contribute to salt tolerance. Combined with our previous comparative proteomics analysis on seedling leaves, the similarities and differences between the salt-responsive protein networks found in the seedling leaves and roots of both the genotypes were discussed. Such a result will be helpful in breeding of salt-tolerant soybean cultivars.

  4. Comparing men who have sex with men and transgender women who use Grindr, other similar social and sexual networking apps, or no social and sexual networking apps: Implications for recruitment and health promotion.

    Science.gov (United States)

    Sun, Christina J; Sutfin, Erin; Bachmann, Laura H; Stowers, Jason; Rhodes, Scott D

    2018-01-01

    Researchers and public health professionals have increased their attention to GPS-based social and sexual networking applications (apps) tailored to gay, bisexual, other men who have sex with men (MSM) and transgender women. These populations continue to be disproportionately affected by HIV in the United States, therefore these apps, in particular Grindr, have become an important sampling venue for the recruitment of HIV-related research participants. As such, it is essential to identify differences among app users to avoid potential sampling bias. This paper seeks to identify differences in MSM and transgender women who use Grindr and those who use other similar apps. A community-based participatory research (CBPR) approach was used to recruit participants online who then completed a 25-item anonymous survey. Five domains were assessed: sociodemographics, HIV testing, sexual risk, substance abuse, and use of GPS-based social and sexual networking apps. 457 participants completed surveys. There were significant differences in the sociodemographic characteristics by app use, including age, race/ethnicity, sexual orientation, and outness. After adjusting for the sociodemographic characteristics associated with app use, there were significant differences in HIV risk and substance use between the groups. This paper is the first to report on findings that compare MSM and transgender women who report using Grindr to MSM and transgender women who report using other similar apps. GPS-based social and sexual networking apps may offer a valuable recruitment tool for future HIV research seeking to recruit populations at increased risk for HIV or those living with HIV for therapeutic trials. Because of the differences identified across users of different apps, these findings suggest that if researchers recruited participants from just one app, they could end up with a sample quite different than if they had recruited MSM and transgender women from other apps.

  5. Whole-Body High-Intensity Interval Training Induce Similar Cardiorespiratory Adaptations Compared With Traditional High-Intensity Interval Training and Moderate-Intensity Continuous Training in Healthy Men.

    Science.gov (United States)

    Schaun, Gustavo Z; Pinto, Stephanie S; Silva, Mariana R; Dolinski, Davi B; Alberton, Cristine L

    2018-05-07

    Schaun, GZ, Pinto, SS, Silva, MR, Dolinski, DB, and Alberton, CL. Sixteen weeks of whole-body high-intensity interval training induce similar cardiorespiratory responses compared with traditional high-intensity interval training and moderate-intensity continuous training in healthy men. J Strength Cond Res XX(X): 000-000, 2018-Low-volume high-intensity interval training (HIIT) protocols that use the body weight as resistance could be an interesting and inexpensive alternative to traditional ergometer-based high-intensity interval training (HIIT-T) and moderate-intensity continuous training (MICT). Therefore, our aim was to compare the effects of 16 weeks of whole-body HIIT (HIIT-WB), HIIT-T, and MICT on maximal oxygen uptake (V[Combining Dot Above]O2max), second ventilatory threshold (VT2), and running economy (RE) outcomes. Fifty-five healthy men (23.7 ± 0.7 years, 1.79 ± 0.01 m, 78.5 ± 1.7 kg) were randomized into 3 training groups (HIIT-T = 17; HIIT-WB = 19; MICT = 19) for 16 weeks (3× per week). The HIIT-T group performed eight 20-second bouts at 130% of the velocity associated to V[Combining Dot Above]O2max (vV[Combining Dot Above]O2max) interspersed by 10-second passive recovery on a treadmill, whereas HIIT-WB group performed the same protocol but used calisthenics exercises at an all-out intensity instead of treadmill running. Finally, MICT group exercised for 30 minutes at 90-95% of the heart rate (HR) associated to VT2. After the intervention, all groups improved V[Combining Dot Above]O2max, vV[Combining Dot Above]O2max, time to exhaustion (Tmax), VT2, velocity associated with VT2 (vVT2), and time to reach VT2 (tVT2) significantly (p HIIT-T compared with HIIT-WB (p HIIT-WB can be as effective as traditional HIIT while also being time-efficient compared with MICT to improve health-related outcomes after 16 weeks of training. However, HIIT-T and MICT seem preferable to enhance performance-related outcomes compared with HIIT-WB.

  6. Gender similarities and differences.

    Science.gov (United States)

    Hyde, Janet Shibley

    2014-01-01

    Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research.

  7. Evaluating enzootic bovine leukemia virus infection by means of molecular probe compared with the results of serological tests

    International Nuclear Information System (INIS)

    Reichert, M.; Grundbock, J.; Rulka, J.; Kozaczynska, B.; Stec, J.

    1994-01-01

    The present studies were aimed at determining the relation between the finding obtained by means of serological tests and the specific molecular probe. Serological tests were performed according to the methods recommended by the Polish Ministry of Agriculture; ELISA was run with ''Bioveta'' and ''Rhone Merieux'' kits and the AGID test was performed with EBL antigen made in our laboratory. The molecular probe was prepared from the previously cloned provirus DNA of EBL virus. The EBL provirus was detected in 28 samples taken from 44 randomly selected cows in three herds on which a leukemia eradication programme was in process. Three sera out of 28 positive reacting animals were negative in AGID test and only one serum in ELISA. The results indicate that the use of a specific molecular probe has some advantages in the diagnosis of latent virus infections. Besides, it can be applied in the studies on the pathogenesis of enzootic bovine leukemia. (author). 13 refs, 1 fig., 1 tab

  8. IDENTIFICATION OF PARAMECIUM BURSARIA SYNGENS THROUGH MOLECULAR MARKERS – COMPARATIVE ANALYSIS OF MITOCHONDRIAL CYTOCHROME C OXIDASE SUBUNIT I (COI

    Directory of Open Access Journals (Sweden)

    Patrycja Zagata

    2014-08-01

    Full Text Available The aim of this study is an identification of Paramecium bursaria syngens originating from different geographical locations and proving the correlation between distributions and belonging to any of five syngens. Ten strains of Paramecium bursaria belonging to five different syngens and strain of Paramecium multimicronucleatum were investigated using molecular marker — mitochondrial cytochrome c oxidase subunit I (COI. According to results, obtained in this study, using phylogenetic methods like Neighbor Joining (NJ and Maximum Likelihood (ML, relationship between analyzing strains through their clustering in clusters and correlation between strains belonging to any syngen and syngen’s distribution was confirmed. Phylograms constructed using NJ and ML methods revealed strains’ grouping in five clusters. Results which were obtained revealed usefulness of COI as a biomarker, which is important in identification of Paramecium bursaria syngens. This reports to a great potential of COI as a molecular marker and obtaining dependable results through combination of molecular methods with classical ones.

  9. Unsupervised Analysis of Array Comparative Genomic Hybridization Data from Early-Onset Colorectal Cancer Reveals Equivalence with Molecular Classification and Phenotypes

    Directory of Open Access Journals (Sweden)

    María Arriba

    2017-01-01

    Full Text Available AIM: To investigate whether chromosomal instability (CIN is associated with tumor phenotypes and/or with global genomic status based on MSI (microsatellite instability and CIMP (CpG island methylator phenotype in early-onset colorectal cancer (EOCRC. METHODS: Taking as a starting point our previous work in which tumors from 60 EOCRC cases (≤45 years at the time of diagnosis were analyzed by array comparative genomic hybridization (aCGH, in the present study we performed an unsupervised hierarchical clustering analysis of those aCGH data in order to unveil possible associations between the CIN profile and the clinical features of the tumors. In addition, we evaluated the MSI and the CIMP statuses of the samples with the aim of investigating a possible relationship between copy number alterations (CNAs and the MSI/CIMP condition in EOCRC. RESULTS: Based on the similarity of the CNAs detected, the unsupervised analysis stratified samples into two main clusters (A, B and four secondary clusters (A1, A2, B3, B4. The different subgroups showed a certain correspondence with the molecular classification of colorectal cancer (CRC, which enabled us to outline an algorithm to categorize tumors according to their CIMP status. Interestingly, each subcluster showed some distinctive clinicopathological features. But more interestingly, the CIN of each subcluster mainly affected particular chromosomes, allowing us to define chromosomal regions more specifically affected depending on the CIMP/MSI status of the samples. CONCLUSIONS: Our findings may provide a basis for a new form of classifying EOCRC according to the genomic status of the tumors.

  10. Comparative analysis of molecular signatures suggests the use of gabapentin for the management of endometriosis-associated pain

    Directory of Open Access Journals (Sweden)

    Bellessort B

    2018-04-01

    Full Text Available Brice Bellessort,1 Anne Bachelot,1,2 Virginie Grouthier,2 Camille De Lombares,1 Nicolas Narboux-Neme,1 Paolo Garagnani,3,4 Chiara Pirazzini,3,4 Simonetta Astigiano,5 Luca Mastracci,6,7 Anastasia Fontaine,1 Gladys Alfama,1 Evelyne Duvernois-Berthet,1 Giovanni Levi1 1Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France; 2AP-HP, Department of Endocrinology and Reproductive Medicine, Reference Center for Rare Endocrine Diseases, Pitié-Salpêtrière Hospital, UPMC, Paris, France; 3Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy; 4Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy; 5Department of Integrated Oncological Therapies, San Martino Hospital, Genova, Italy; 6Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genoa, Genova, Italy; 7Division of Anatomic Pathology, Department of Surgical Science and Integrated Diagnostics, University of Genoa, Genova, Italy Background: It has been repetitively shown that the transcription factors DLX5 and DLX6 are drastically downregulated in endometriotic lesions when compared with eutopic endometrium. These findings suggest that regulatory cascades involving DLX5/6 might be at the origin of endometriosis symptoms such as chronic pelvic pain (CPP. We have shown that inactivation of Dlx5 and Dlx5/6 in the mouse uterus results in an endometrial phenotype reminiscent of endometriosis. Methods: We focused on genes that present a similar deregulation in endometriosis and in Dlx5/6-null mice in search of new endometriosis targets. Results: We confirmed a strong reduction of DLX5 expression in endometriosis implants. We identified a signature of 30 genes similarly deregulated in human endometriosis implants and in Dlx5/6-null mouse uteri, reinforcing the notion that the downregulation of Dlx5/6 is an early event in

  11. Cytomorphology of six halotolerant coccoid cyanobacteria using DAPI fluorescent and transmission electron microscopy, compared with molecular data

    Czech Academy of Sciences Publication Activity Database

    Cepák, Vladislav; Komárek, Jiří

    2010-01-01

    Roč. 10, č. 2 (2010), s. 229-234 ISSN 1802-5439 R&D Projects: GA AV ČR IAA600050704 Institutional research plan: CEZ:AV0Z60050516 Keywords : halophilic cyanobacteria * cytomorphology * molecular evaluation Subject RIV: EF - Botanics Impact factor: 0.978, year: 2010

  12. Infertile women below the age of 40 have similar anti-Müllerian hormone levels and antral follicle count compared with women of the same age with no history of infertility.

    Science.gov (United States)

    Hvidman, H W; Bentzen, J G; Thuesen, L L; Lauritsen, M P; Forman, J L; Loft, A; Pinborg, A; Nyboe Andersen, A

    2016-05-01

    Do infertile patients below the age of 40 years have a lower ovarian reserve, estimated by anti-Müllerian hormone (AMH) and total antral follicle count (AFC), than women of the same age with no history of infertility? Serum AMH and AFC were not lower in infertile patients aged 20-39 years compared with a control group of the same age with no history of infertility. WHAT IS KNOWN ALREADY?: The management of patients with a low ovarian reserve and a poor response to controlled ovarian stimulation (COS) remains a challenge in assisted reproductive technologies (ART). Both AMH levels and AFC reflect the ovarian reserve and are valuable predictors of the ovarian response to exogenous gonadotrophins. However, there is a large inter-individual variation in the age-related depletion of the ovarian reserve and a broad variability in the levels of AMH and AFC compatible with conception. Women with an early depletion of the ovarian reserve may experience infertility as a consequence of postponement of childbearing. Thus, low ovarian reserve is considered to be overrepresented among infertile patients. A prospective cohort study including 382 women with a male partner referred to fertility treatment at Rigshospitalet, Copenhagen, Denmark during 2011-2013 compared with a control group of 350 non-users of hormonal contraception with no history of infertility recruited during 2008-2010. Included patients and controls were aged 20-39 years. Women with polycystic ovary syndrome were excluded. On Cycle Days 2-5, AFC and ovarian volume were measured by transvaginal sonography, and serum levels of AMH, FSH and LH were assessed. Infertile patients had similar AMH levels (11%, 95% confidence interval (CI): -1;24%) and AFC (1%, 95% CI: -7;8%) compared with controls with no history of infertility in an age-adjusted linear regression analysis. The prevalence of very low AMH levels (<5 pmol/l) was similar in the two cohorts (age-adjusted odds ratio: 0.9, 95% CI: 0.5;1.7). The findings

  13. Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study.

    Directory of Open Access Journals (Sweden)

    Musa Ozboyaci

    Full Text Available BACKGROUND: Histone demethylase, JMJD2A, specifically recognizes and binds to methylated lysine residues at histone H3 and H4 tails (especially trimethylated H3K4 (H3K4me3, trimethylated H3K9 (H3K9me3 and di,trimethylated H4K20 (H4K20me2, H4K20me3 via its tandem tudor domains. Crystal structures of JMJD2A-tudor binding to H3K4me3 and H4K20me3 peptides are available whereas the others are not. Complete picture of the recognition of the four histone peptides by the tandem tudor domains yet remains to be clarified. METHODOLOGY/PRINCIPAL FINDINGS: We report a detailed molecular dynamics simulation and binding energy analysis of the recognition of JMJD2A-tudor with four different histone tails. 25 ns fully unrestrained molecular dynamics simulations are carried out for each of the bound and free structures. We investigate the important hydrogen bonds and electrostatic interactions between the tudor domains and the peptide molecules and identify the critical residues that stabilize the complexes. Our binding free energy calculations show that H4K20me2 and H3K9me3 peptides have the highest and lowest affinity to JMJD2A-tudor, respectively. We also show that H4K20me2 peptide adopts the same binding mode with H4K20me3 peptide, and H3K9me3 peptide adopts the same binding mode with H3K4me3 peptide. Decomposition of the enthalpic and the entropic contributions to the binding free energies indicate that the recognition of the histone peptides is mainly driven by favourable van der Waals interactions. Residue decomposition of the binding free energies with backbone and side chain contributions as well as their energetic constituents identify the hotspots in the binding interface of the structures. CONCLUSION: Energetic investigations of the four complexes suggest that many of the residues involved in the interactions are common. However, we found two receptor residues that were related to selective binding of the H3 and H4 ligands. Modifications or mutations

  14. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom

    2013-01-01

    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field......-shaped relation exists between expenditure strategy isomorphism and structure isomorphism in a longitudinal quantitative study of Danish municipalities....

  15. Fast business process similarity search

    NARCIS (Netherlands)

    Yan, Z.; Dijkman, R.M.; Grefen, P.W.P.J.

    2012-01-01

    Nowadays, it is common for organizations to maintain collections of hundreds or even thousands of business processes. Techniques exist to search through such a collection, for business process models that are similar to a given query model. However, those techniques compare the query model to each

  16. Randomization to a low-carbohydrate diet advice improves health related quality of life compared with a low-fat diet at similar weight-loss in Type 2 diabetes mellitus.

    Science.gov (United States)

    Guldbrand, H; Lindström, T; Dizdar, B; Bunjaku, B; Östgren, C J; Nystrom, F H; Bachrach-Lindström, M

    2014-11-01

    To compare the effects on health-related quality of life (HRQoL) of a 2-year intervention with a low-fat diet (LFD) or a low-carbohydrate diet (LCD) based on four group-meetings to achieve compliance. To describe different aspects of taking part in the intervention following the LFD or LCD. Prospective, randomized trial of 61 adults with Type 2 diabetes mellitus. The SF-36 questionnaire was used at baseline, 6, 12 and 24 months. Patients on LFD aimed for 55-60 energy percent (E%) and those on LCD for 20 E% from carbohydrates. The patients were interviewed about their experiences of the intervention. Mean body-mass-index was 32.7 ± 5.4 kg/m(2) at baseline. Weight-loss did not differ between groups and was maximal at 6 months, LFD: -3.99 ± 4.1 kg, LCD: -4.31 ± 3.6 kg (p<0.001 within groups). There was an increase in the physical component score of SF-36 from 44.1 (10.0) to 46.7 (10.5) at 12 months in the LCD group (p < 0.009) while no change occurred in the LFD group (p < 0.03 between groups). At 12 months the physical function, bodily pain and general health scores improved within the LCD group (p values 0.042-0.009) while there was no change within the LFD group. Weight-changes did not differ between the diet groups while improvements in HRQoL only occurred after one year during treatment with LCD. No changes of HRQoL occurred in the LFD group in spite of a similar reduction in body weight. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  17. More symptoms but similar blood glucose curve after oral carbohydrate provocation in patients with a history of hypoglycemia-like symptoms compared to asymptomatic patients after Roux-en-Y gastric bypass.

    Science.gov (United States)

    Laurenius, Anna; Werling, Malin; Le Roux, Carel W; Fändriks, Lars; Olbers, Torsten

    2014-01-01

    Laparoscopic Roux-en-Y gastric bypass (LRYGB) is an effective treatment for obesity through altering several physiologic mechanisms. Some patients experience symptoms suggestive of hypglycemia after LRYGB, but whether these symptoms always are associated with low blood glucose are unclear. The objective of this study was to investigate the correlation between symptoms suggestive of hypglycemia, plasma glucose levels and gut hormones involved in glycemic control. Eight LRYGB patients with hypglycemia-like symptoms (SY) and 8 patients with no hypglycemia-like symptoms (ASY) ingested a liquid carbohydrate meal. Insulin, plasma-glucose, glucagon-like peptide 1 (GLP-1) and glucagon were measured intermittently 180 minutes postprandially. In addition, pulse rate, blood pressure and symptoms were assessed. Plasma glucose at 120 min was lower in the ASY mean (95% CI) 2.4 (1.6,3.3) mmol/L (43.2 mg/dL) compared to the SY group 3.0 (3.1,4.6) mmol/L (54.6 mg/dL), (P = .050). The ASY group had larger reduction in plasma glucose than the SY group from pre- to 120 min postmeal -2.2 (-2.8,-1.7) mmol/L (-39.6 mg/dL) versus -1.1 (-1.7,-0.4) mmol/L (-19.8 mg/dL), (P = .011). The concentrations of insulin, GLP-1 and glucagon did not differ significantly between groups. Blood pressure was similar between groups, but the AUC for pulse rate was higher in the SY than ASY group 13009 (11148,14870) versus 11569 (10837,12300) beats/180 minutes, (P = .038). The SY group reported more symptoms than the ASY group, AUC for Sigstad scale 60 to 180 minutes was 970 (-274,1667) for SY versus 170 for ASY (-39,379), (P = .028). Patients with a history of symptoms suggestive of hypglycemia after LRYGB neither demonstrated lower plasma glucose nor greater insulin response compared to asymptomatic patients in response to a liquid carbohydrate meal, but perceived more symptoms. Copyright © 2014 American Society for Bariatric Surgery. Published by Elsevier Inc. All rights reserved.

  18. Comparative genomic analysis of Campylobacter jejuni associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity

    Directory of Open Access Journals (Sweden)

    Endtz Hubert P

    2007-10-01

    Full Text Available Abstract Background Campylobacter jejuni infection represents the most frequent antecedent infection triggering the onset of the neuropathic disorders Guillain-Barré syndrome (GBS and Miller Fisher syndrome (MFS. Although sialylated ganglioside-mimicking lipo-oligosaccharide (LOS structures are the strongest neuropathogenic determinants in C. jejuni, they do not appear to be the only requirement for a neuropathic outcome since strains capable of their production have been isolated from patients with uncomplicated cases of enteritis. Consequently, other pathogen and/or host-related factors contribute to the onset of neurological complications. We have used comparative genomic hybridization to perform a detailed genomic comparison of strains isolated from GBS/MFS and enteritis-only patients. Our dataset, in which the gene conservation profile for 1712 genes was assayed in 102 strains, including 56 neuropathogenic isolates, represents the largest systematic search for C. jejuni factors associated with GBS/MFS to date and has allowed us to analyze the genetic background of neuropathogenic C. jejuni strains with an unprecedented level of resolution. Results The majority of GBS/MFS strains can be assigned to one of six major lineages, suggesting that several genetic backgrounds can result in a neuropathogenic phenotype. A statistical analysis of gene conservation rates revealed that although genes involved in the sialylation of LOS structures were significantly associated with neuropathogenic strains, still many enteritis-control strains both bear these genes and share remarkable levels of genomic similarity with their neuropathogenic counterparts. Two capsule biosynthesis genes (Cj1421c and Cj1428c showed higher conservation rates among neuropathogenic strains compared to enteritis-control strains. Any potential involvement of these genes in neuropathogenesis must be assessed. A single gene (HS:3 Cj1135 had a higher conservation rate among enteritis

  19. Identification of Paramecium bursaria syngens through molecular markers--comparative analysis of three loci in the nuclear and mitochondrial DNA.

    Science.gov (United States)

    Greczek-Stachura, Magdalena; Potekhin, Alexey; Przyboś, Ewa; Rautian, Maria; Skoblo, Inna; Tarcz, Sebastian

    2012-09-01

    This is the first attempt to resolve the phylogenetic relationship between different syngens of Paramecium bursaria and to investigate at a molecular level the intraspecific differentiation of strains originating from very distant geographical locations. Herein we introduce a new collection of five P. bursaria syngens maintained at St Petersburg State University, as the international collection of syngens was lost in the 1960s. To analyze the degree of speciation within Paramecium bursaria, we examined 26 strains belonging to five different syngens from distant and geographically isolated localities using rDNA (ITS1-5.8S-ITS2-5'LSU) fragments, mitochondrial cytochrome c oxidase subunit I (COI), and H4 gene fragments. It was shown that P. bursaria strains of the same syngens cluster together in all three inferred molecular phylogenies. The genetic diversity among the studied P. bursaria strains based on rDNA sequences was rather low. The COI divergence of Paramecium bursaria was also definitely lower than that observed in the Paramecium aurelia complex. The nucleotide sequences of the H4 gene analyzed in the present study indicate the extent of genetic differences between the syngens of Paramecium bursaria. Our study demonstrates the diagnostic value of molecular markers, which are important tools in the identification of Paramecium bursaria syngens. Copyright © 2011 Elsevier GmbH. All rights reserved.

  20. Identification of light absorbing oligomers from glyoxal and methylglyoxal aqueous processing: a comparative study at the molecular level

    Science.gov (United States)

    Finessi, Emanuela; Hamilton, Jacqueline; Rickard, Andrew; Baeza-Romero, Maria; Healy, Robert; Peppe, Salvatore; Adams, Tom; Daniels, Mark; Ball, Stephen; Goodall, Iain; Monks, Paul; Borras, Esther; Munoz, Amalia

    2014-05-01

    Numerous studies point to the reactive uptake of gaseous low molecular weight carbonyls onto atmospheric waters (clouds/fog droplets and wet aerosols) as an important SOA formation route not yet included in current models. However, the evaluation of these processes is challenging because water provides a medium for a complex array of reactions to take place such as self-oligomerization, aldol condensation and Maillard-type browning reactions in the presence of ammonium salts. In addition to adding to SOA mass, aqueous chemistry products have been shown to include light absorbing, surface-active and high molecular weight oligomeric species, and can therefore affect climatically relevant aerosol properties such as light absorption and hygroscopicity. Glyoxal (GLY) and methylglyoxal (MGLY) are the gaseous carbonyls that have perhaps received the most attention to date owing to their ubiquity, abundance and reactivity in water, with the majority of studies focussing on bulk physical properties. However, very little is known at the molecular level, in particular for MGLY, and the relative potential of these species as aqueous SOA precursors in ambient air is still unclear. We have conducted experiments with both laboratory solutions and chamber-generated particles to simulate the aqueous processing of GLY and MGLY with ammonium sulphate (AS) under typical atmospheric conditions and investigated their respective aging products. Both high performance liquid chromatography coupled with UV-Vis detection and ion trap mass spectrometry (HPLC-DAD-MSn) and high resolution mass spectrometry (FTICRMS) have been used for molecular identification purposes. Comprehensive gas chromatography with nitrogen chemiluminescence detection (GCxGC-NCD) has been applied for the first time to these systems, revealing a surprisingly high number of nitrogen-containing organics (ONs), with a large extent of polarities. GCxGC-NCD proved to be a valuable tool to determine overall amount and rates of

  1. Domain similarity based orthology detection.

    Science.gov (United States)

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

    2015-05-13

    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

  2. Comparative study of LaNiO$_3$/LaAlO$_3$ heterostructures grown by pulsed laser deposition and oxide molecular beam epitaxy

    OpenAIRE

    Wrobel, F.; Mark, A. F.; Christiani, G.; Sigle, W.; Habermeier, H. -U.; van Aken, P. A.; Logvenov, G.; Keimer, B.; Benckiser, E.

    2017-01-01

    Variations in growth conditions associated with different deposition techniques can greatly affect the phase stability and defect structure of complex oxide heterostructures. We synthesized superlattices of the paramagnetic metal LaNiO3 and the large band gap insulator LaAlO3 by atomic layer-by-layer molecular beam epitaxy (MBE) and pulsed laser deposition (PLD) and compared their crystallinity, microstructure as revealed by high-resolution transmission electron microscopy images and resistiv...

  3. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico

    2015-01-01

    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  4. Comparative Molecular and Morphological Variation Analysis of Siderastrea (Anthozoa, Scleractinia) Reveals the Presence of Siderastrea stellata in the Gulf of Mexico.

    Science.gov (United States)

    García, Norberto A Colín; Campos, Jorge E; Musi, José L Tello; Forsman, Zac H; Muñoz, Jorge L Montero; Reyes, Alejandro Monsalvo; González, Jesús E Arias

    2017-02-01

    The genus Siderastrea exhibits high levels of morphological variability. Some of its species share similar morphological characteristics with congeners, making their identification difficult. Siderastrea stellata has been reported as an intermediary of S. siderea and S. radians in the Brazilian reef ecosystem. In an earlier study conducted in Mexico, we detected Siderastrea colonies with morphological features that were not consistent with some siderastreid species previously reported in the Gulf of Mexico. Thus, we performed a combined morphological and molecular analysis to identify Siderastrea species boundaries from the Gulf of Mexico. Some colonies presented high morphologic variability, with characteristics that corresponded to Siderastrea stellata. Molecular analysis, using the nuclear ITS and ITS2 region, corroborated the morphological results, revealing low genetic variability between S. radians and S. stellata. Since the ITS sequences did not distinguish between Siderastrea species, we used the ITS2 region to differentiate S. stellata from S. radians. This is the first report of Siderastrea stellata and its variability in the Gulf of Mexico that is supported by morphological and molecular analyses.

  5. Modeling of similar economies

    Directory of Open Access Journals (Sweden)

    Sergey B. Kuznetsov

    2017-06-01

    Full Text Available Objective to obtain dimensionless criteria ndash economic indices characterizing the national economy and not depending on its size. Methods mathematical modeling theory of dimensions processing statistical data. Results basing on differential equations describing the national economy with the account of economical environment resistance two dimensionless criteria are obtained which allow to compare economies regardless of their sizes. With the theory of dimensions we show that the obtained indices are not accidental. We demonstrate the implementation of the obtained dimensionless criteria for the analysis of behavior of certain countriesrsquo economies. Scientific novelty the dimensionless criteria are obtained ndash economic indices which allow to compare economies regardless of their sizes and to analyze the dynamic changes in the economies with time. nbsp Practical significance the obtained results can be used for dynamic and comparative analysis of different countriesrsquo economies regardless of their sizes.

  6. Clinical similarity of the biosimilar ABP 501 compared with adalimumab after single transition: long-term results from a randomized controlled, double-blind, 52-week, phase III trial in patients with moderate-to-severe plaque psoriasis.

    Science.gov (United States)

    Papp, K; Bachelez, H; Costanzo, A; Foley, P; Gooderham, M; Kaur, P; Philipp, S; Spelman, L; Zhang, N; Strober, B

    2017-12-01

    ABP 501, a U.S.A. Food and Drug Administration- and European Medicines Agency-approved biosimilar, is highly similar to adalimumab in structure, function and pharmacokinetics. To demonstrate similarity in efficacy, safety and immunogenicity of ABP 501 vs. adalimumab for moderate-to-severe plaque psoriasis (clinical trial: NCT01970488). Patients were randomized (1 : 1) to receive ABP 501 or adalimumab 40 mg every 2 weeks for 16 weeks. At week 16, patients with ≥ 50% improvement from baseline in Psoriasis Area and Severity Index (PASI) score were eligible to continue to week 52. Patients receiving ABP 501 continued; adalimumab patients were rerandomized (1 : 1) to continue adalimumab or undergo a single transition to ABP 501. Key efficacy assessments included percentage PASI improvement from baseline, PASI responders and mean change in affected body surface area from baseline to weeks 16, 32 and 50. Safety was monitored via adverse events (AEs) and antidrug antibodies (ADAs) were assessed. A total of 308 patients were rerandomized at week 16 (ABP 501/ABP 501, n = 152; adalimumab/adalimumab, n = 79; adalimumab/ABP 501, n = 77). PASI percentage improvements from baseline were similar across groups for weeks 16, 32 and 50 (range: 85·8-88·2%), with no significant differences detected across groups in percentages of PASI 50, 75, 90 and 100 responders. Changes from baseline in percentage body surface area affected were similar across groups and time points. No new safety signals were detected. AEs were balanced between groups. Percentages of patients with binding and neutralizing ADAs were similar across treatments. ABP 501 and adalimumab have similar clinical efficacy, safety and immunogenicity profiles over 52 weeks, including after single transition, in this patient population. © 2017 British Association of Dermatologists.

  7. Molecular cloning and expression of a novel keratinocyte protein (psoriasis-associated fatty acid-binding protein [PA-FABP]) that is highly up-regulated in psoriatic skin and that shares similarity to fatty acid-binding proteins

    DEFF Research Database (Denmark)

    Madsen, Peder; Rasmussen, H H; Leffers, H

    1992-01-01

    termed PA-FABP (psoriasis-associated fatty acid-binding protein). The deduced sequence predicted a protein with molecular weight of 15,164 daltons and a calculated pI of 6.96, values that are close to those recorded in the keratinocyte 2D gel protein database. The protein comigrated with PA-FABP...... as determined by 2D gel analysis of [35S]-methionine-labeled proteins expressed by transformed human amnion (AMA) cells transfected with clone 1592 using the vaccinia virus expression system and reacted with a rabbit polyclonal antibody raised against 2D gel purified PA-FABP. Structural analysis of the amino...... acid sequence revealed 48%, 52%, and 56% identity to known low-molecular-weight fatty acid-binding proteins belonging to the FABP family. Northern blot analysis showed that PA-FABP mRNA is indeed highly up-regulated in psoriatic keratinocytes. The transcript is present in human cell lines of epithelial...

  8. Similarity-based Fisherfaces

    DEFF Research Database (Denmark)

    Delgado-Gomez, David; Fagertun, Jens; Ersbøll, Bjarne Kjær

    2009-01-01

    databases (XM2VTS, AR and Equinox) show consistently good results. The proposed algorithm achieves Equal Error Rate (EER) and Half-Total Error Rate (HTER) values in the ranges of 0.41-1.67% and 0.1-1.95%, respectively. Our approach yields results comparable to the top two winners in recent contests reported...

  9. Selective separation of uranium from nuclear waste solution by bis (2,4,4-trimethylpentyl phosphinic) acid in ionic liquid and molecular diluents: a comparative study

    International Nuclear Information System (INIS)

    Singh, Manpreet; Sengupta, Arijit; Murali, M.S.; Adya, V.C.; Kadam, R.M.

    2016-01-01

    Room temperature ionic liquid has been world-wide considered as the potential 'green' alternatives to the molecular diluents. A comparative study was carried out for studying selective separation of uranium from radioactive waste solution using Bis(2,4,4-trimethylpentyl phosphinic) acid in molecular diluent (xylene) and ionic liquid (C 8 mimNTf 2 ). For ionic liquid based system, the extraction kinetics was found to be slower compared to the molecular diluents. This was attributed to the higher viscosity of ionic liquid. In ionic liquid the extraction occurs with the predominance of 'ion exchange' mechanism through (UO 2 (NO 3 ). 2L) + species, while for xylene based system 'solvation' mechanism predominates at higher feed acidity. The extraction process in ionic liquid was found to be thermodynamically more favoured than in xylene. The nature of the extracted species was found to be different in ionic liquid and xylene as obtained from difference in luminescence emission profiles and lifetime of the extracted complex. Ionic liquid based system was found to be radiolytically more stable than the molecular diluents based solvent system. Na 2 CO 3 solution was found to back extract the uranyl ion almost quantitatively (99.9 %) from the loaded organic phase but overall stripping from ionic liquid phase is comparatively poorer than that of xylene phase. The processing of Simulated High Level Waste (SHLW) of Pressurized Heavy Water Reactor (PHWR) or Research Reactor (RR) origin revealed that bis(2,4,4-trimethylpentyl phosphinic) acid can effectively be used for the preferential extraction of U with better selectivity for ionic liquid phase. But the ion exchange mechanism is one of the disadvantages for its plant scale application. (author)

  10. A comparative study of the biologic and molecular basis of murine mammary carcinoma: a model for human breast cancer

    International Nuclear Information System (INIS)

    Schlom, J.; Kufe, D.; Hehlman, R.; Spiegelman, S.; Bentvelzen, P.; Michalides, R.; Hageman, P.

    1976-01-01

    Tritiated-DNA complementary to mouse mammary tumor virus (MMTV) RNA was synthesized in an endogeneous reaction with MMTV particles. This DNA was used as a probe via molecular hybridization to detect MMTV-specific RNA in 'spontaneous' mammary tumors of several strains of mice, including the 'nonproducer' BALB/c mammary tumors. MMTV-specific RNA was also found in certain normal tissues (spleen, kidney, and epididymis) of a high-mammary-cancer strain (GR). Aging or treatment with nonviral carcinogens also induced the appearance of MMTV-specific RNA in certain normal tissues of the low-mammary-cancer strains, C57BL and BALB/c. The relationship of the presence of MMTV-specific RNA to the etiology and pathogenesis of murine mammary neoplasia and its potential application to human breast cancer are discussed

  11. Molecular and comparative analysis of Salmonella enterica Senftenberg from humans and animals using PFGE, MLST and NARMS

    Directory of Open Access Journals (Sweden)

    Petermann Shana R

    2011-06-01

    Full Text Available Abstract Background Salmonella species are recognized worldwide as a significant cause of human and animal disease. In this study the molecular profiles and characteristics of Salmonella enterica Senftenberg isolated from human cases of illness and those recovered from healthy or diagnostic cases in animals were assessed. Included in the study was a comparison with our own sequenced strain of S. Senfteberg recovered from production turkeys in North Dakota. Isolates examined in this study were subjected to antimicrobial susceptibility profiling using the National Antimicrobial Resistance Monitoring System (NARMS panel which tested susceptibility to 15 different antimicrobial agents. The molecular profiles of all isolates were determined using Pulsed Field Gel Electrophoresis (PFGE and the sequence types of the strains were obtained using Multi-Locus Sequence Type (MLST analysis based on amplification and sequence interrogation of seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thrA. PFGE data was input into BioNumerics analysis software to generate a dendrogram of relatedness among the strains. Results The study found 93 profiles among 98 S. Senftenberg isolates tested and there were primarily two sequence types associated with humans and animals (ST185 and ST14 with overlap observed in all host types suggesting that the distribution of S. Senftenberg sequence types is not host dependent. Antimicrobial resistance was observed among the animal strains, however no resistance was detected in human isolates suggesting that animal husbandry has a significant influence on the selection and promotion of antimicrobial resistance. Conclusion The data demonstrates the circulation of at least two strain types in both animal and human health suggesting that S. Senftenberg is relatively homogeneous in its distribution. The data generated in this study could be used towards defining a pathotype for this serovar.

  12. Devices used by automated milking systems are similarly accurate in estimating milk yield and in collecting a representative milk sample compared with devices used by farms with conventional milk recording

    NARCIS (Netherlands)

    Kamphuis, Claudia; Dela Rue, B.; Turner, S.A.; Petch, S.

    2015-01-01

    Information on accuracy of milk-sampling devices used on farms with automated milking systems (AMS) is essential for development of milk recording protocols. The hypotheses of this study were (1) devices used by AMS units are similarly accurate in estimating milk yield and in collecting

  13. Similar or different?

    DEFF Research Database (Denmark)

    Cornér, Solveig; Pyhältö, Kirsi; Peltonen, Jouni

    2018-01-01

    Previous research has identified researcher community and supervisory support as key determinants of the doctoral journey contributing to students’ persistence and robustness. However, we still know little about cross-cultural variation in the researcher community and supervisory support experien...... counter partners, whereas the Finnish students perceived lower levels of instrumental support than the Danish students. The findings imply that seemingly similar contexts hold valid differences in experienced social support and educational strategies at the PhD level....... experienced by PhD students within the same discipline. This study explores the support experiences of 381 PhD students within the humanities and social sciences from three research-intensive universities in Denmark (n=145) and Finland (n=236). The mixed methods design was utilized. The data were collected...... counter partners. The results also indicated that the only form of support in which the students expressed more matched support than mismatched support was informational support. Further investigation showed that the Danish students reported a high level of mismatch in emotional support than their Finnish...

  14. Molecular insights on analogs of HIV PR inhibitors toward HTLV-1 PR through QM/MM interactions and molecular dynamics studies: comparative structure analysis of wild and mutant HTLV-1 PR.

    Science.gov (United States)

    Selvaraj, Chandrabose; Singh, Poonam; Singh, Sanjeev Kumar

    2014-12-01

    Retroviruses HTLV-1 and HIV-1 are the primary causative agents of fatal adult T-cell leukemia and acquired immune deficiency syndrome (AIDS) disease. Both retroviruses are similar in characteristics mechanism, and it encodes for protease that mainly involved in the viral replication process. On the basis of the therapeutic success of HIV-1 PR inhibitors, the protease of HTLV-1 is mainly considered as a potential target for chemotherapy. At the same time, structural similarities in both enzymes that originate HIV PR inhibitors can also be an HTLV-1 PR inhibitor. But the expectations failed because of rejection of HIV PR inhibitors from the HTLV-1 PR binding pocket. In this present study, the reason for the HIV PR inhibitor rejection from the HTLV-1 binding site was identified through sequence analysis and molecular dynamics simulation method. Functional analysis of M37A mutation in HTLV PR clearly shows that the MET37 specificity and screening of potential inhibitors targeting MET37 is performed by using approved 90% similar HIV PR inhibitor compounds. From this approach, we report few compounds with a tendency to accept/donate electron specifically to an important site residue MET37 in HTLV-1 PR binding pocket. Copyright © 2014 John Wiley & Sons, Ltd.

  15. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)

    2015-12-28

    We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

  16. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    International Nuclear Information System (INIS)

    Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian; Sugii, Taisuke

    2015-01-01

    We investigate the volumetric glass transition temperature T g in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T g increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T g in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T g is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment

  17. A Comparative Study of Molecular Structure, pKa, Lipophilicity, Solubility, Absorption and Polar Surface Area of Some Antiplatelet Drugs

    Directory of Open Access Journals (Sweden)

    Milan Remko

    2016-03-01

    Full Text Available Theoretical chemistry methods have been used to study the molecular properties of antiplatelet agents (ticlopidine, clopidogrel, prasugrel, elinogrel, ticagrelor and cangrelor and several thiol-containing active metabolites. The geometries and energies of most stable conformers of these drugs have been computed at the Becke3LYP/6-311++G(d,p level of density functional theory. Computed dissociation constants show that the active metabolites of prodrugs (ticlopidine, clopidogrel and prasugrel and drugs elinogrel and cangrelor are completely ionized at pH 7.4. Both ticagrelor and its active metabolite are present at pH = 7.4 in neutral undissociated form. The thienopyridine prodrugs ticlopidine, clopidogrel and prasugrel are lipophilic and insoluble in water. Their lipophilicity is very high (about 2.5–3.5 logP values. The polar surface area, with regard to the structurally-heterogeneous character of these antiplatelet drugs, is from very large interval of values of 3–255 Å2. Thienopyridine prodrugs, like ticlopidine, clopidogrel and prasugrel, with the lowest polar surface area (PSA values, exhibit the largest absorption. A high value of polar surface area (PSA of cangrelor (255 Å2 results in substantial worsening of the absorption in comparison with thienopyridine drugs.

  18. The mortality of acutely ill medical patients for up to 60 days after admission to a resource poor hospital in sub-Saharan Africa compared with patients of similar illness severity admitted to a Danish Regional Teaching Hospital

    DEFF Research Database (Denmark)

    Nabayigga, Barbara; Kellett, John; Brabrand, Mikkel

    2016-01-01

    BACKGROUND: The outcomes of patients with the same severity of illness in the developed and developing countries have not been compared. Illness severity can now be measured anywhere by the National Early Warning Score (NEWS). METHODS: An exploratory observational study that compared the 7, 30 an...

  19. Compressional Alfven Eigenmode Similarity Study

    Science.gov (United States)

    Heidbrink, W. W.; Fredrickson, E. D.; Gorelenkov, N. N.; Rhodes, T. L.

    2004-11-01

    NSTX and DIII-D are nearly ideal for Alfven eigenmode (AE) similarity experiments, having similar neutral beams, fast-ion to Alfven speed v_f/v_A, fast-ion pressure, and shape of the plasma, but with a factor of 2 difference in the major radius. Toroidicity-induced AE with ˜100 kHz frequencies were compared in an earlier study [1]; this paper focuses on higher frequency AE with f ˜ 1 MHz. Compressional AE (CAE) on NSTX have a polarization, dependence on the fast-ion distribution function, frequency scaling, and low-frequency limit that are qualitatively consistent with CAE theory [2]. Global AE (GAE) are also observed. On DIII-D, coherent modes in this frequency range are observed during low-field (0.6 T) similarity experiments. Experiments will compare the CAE stability limits on DIII-D with the NSTX stability limits, with the aim of determining if CAE will be excited by alphas in a reactor. Predicted differences in the frequency splitting Δ f between excited modes will also be used. \\vspace0.25em [1] W.W. Heidbrink, et al., Plasmas Phys. Control. Fusion 45, 983 (2003). [2] E.D. Fredrickson, et al., Princeton Plasma Physics Laboratory Report PPPL-3955 (2004).

  20. Clustering biomolecular complexes by residue contacts similarity

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, João; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

    Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions.

  1. Comparative studies of Zr-based MCM-41 and MCM-48 mesoporous molecular sieves: Synthesis and physicochemical properties

    Energy Technology Data Exchange (ETDEWEB)

    Chen, L.F. [Departamento de Ciencias Basicas, Universidad Autonoma Metropolitana-A, Av. San Pablo 180, Col. Reynosa-Tamaulipas, 02200 Mexico D.F. (Mexico)]. E-mail: chenlf2001@yahoo.com; Zhou, X.L. [Petroleum Processing Research Center, East China University of Science and Technology, 200237 Shanghai (China); Norena, L.E. [Departamento de Ciencias Basicas, Universidad Autonoma Metropolitana-A, Av. San Pablo 180, Col. Reynosa-Tamaulipas, 02200 Mexico D.F. (Mexico)]. E-mail: lnf@correo.azc.uam.mx; Wang, J.A. [Laboratorio de Catalisis y Materiales, SEPI-ESIQIE, Instituto Politecnico Nacional, Av. Politecnico S/N, Col. Zacatenco, 07738 Mexico D.F. (Mexico); Navarrete, J. [Grupo de Molecular Ingenieria, Instituto Mexicano del Petroleo, Eje Lazaro Cardenas 152, 07730 Mexico D.F. (Mexico); Salas, P. [Grupo de Molecular Ingenieria, Instituto Mexicano del Petroleo, Eje Lazaro Cardenas 152, 07730 Mexico D.F. (Mexico); Montoya, A. [Grupo de Molecular Ingenieria, Instituto Mexicano del Petroleo, Eje Lazaro Cardenas 152, 07730 Mexico D.F. (Mexico); Del Angel, P. [Grupo de Molecular Ingenieria, Instituto Mexicano del Petroleo, Eje Lazaro Cardenas 152, 07730 Mexico D.F. (Mexico); Llanos, M.E. [Grupo de Molecular Ingenieria, Instituto Mexicano del Petroleo, Eje Lazaro Cardenas 152, 07730 Mexico D.F. (Mexico)

    2006-12-30

    Two surfactant-templated synthetic routes are developed for the preparation of new types of mesoporous molecular sieves, Zr-MCM-41 and Zr-MCM-48, using different Si sources but keeping the same zirconium precursor (zirconium-n-propoxide). When fumed silica was used as Si precursor, a Zr-MCM-48 material of cubic structure was formed with a surface area of 654.8 m{sup 2}/g and an unimodal pore diameter distribution. It shows low stability: after calcination at 600 deg. C, the ordered structure was transformed into a relatively disordered worm-like mesostructure with many defects and silanol groups. The use of tetraethyl orthosilicate as Si source led to the formation of a Zr-MCM-41 mesoporous solid, which had good thermal stability and a highly ordered hexagonal arrangement, with a surface area 677.9 m{sup 2}/g and an uniform pore diameter distribution. Fourier transform infrared (FT-IR) characterization and {sup 29}Si NMR analysis confirm that zirconium ions indeed incorporated into the framework of the solid. The in situ FT-IR spectroscopy of pyridine adsorption reveals that both, Lewis and Broensted acid sites, were formed on the surface of these mesoporous materials. The strength and number of the Broensted acid sites of the Zr-MCM-48 solid were greater than those of the Zr-MCM-41, due to a lower degree of condensation reaction during the synthesis that led to more structural defects in the framework and more silanol groups stretching from the solid surface.

  2. Comparative evaluation of molecular diagnostic tests for Nucleospora salmonis and prevalence in migrating juvenile salmonids from the Snake River, USA

    Science.gov (United States)

    Badil, Samantha; Elliott, Diane G.; Kurobe, Tomofumi; Hedrick, Ronald P.; Clemens, Kathy; Blair, Marilyn; Purcell, Maureen K.

    2011-01-01

    Nucleospora salmonis is an intranuclear microsporidian that primarily infects lymphoblast cells and contributes to chronic lymphoblastosis and a leukemia-like condition in a range of salmonid species. The primary goal of this study was to evaluate the prevalence of N. salmonis in out-migrating juvenile hatchery and wild Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss from the Snake River in the U.S. Pacific Northwest. To achieve this goal, we first addressed the following concerns about current molecular diagnostic tests for N. salmonis: (1) nonspecific amplification patterns by the published nested polymerase chain reaction (nPCR) test, (2) incomplete validation of the published quantitative PCR (qPCR) test, and (3) whether N. salmonis can be detected reliably from nonlethal samples. Here, we present an optimized nPCR protocol that eliminates nonspecific amplification. During validation of the published qPCR test, our laboratory developed a second qPCR test that targeted a different gene sequence and used different probe chemistry for comparison purposes. We simultaneously evaluated the two different qPCR tests for N. salmonis and found that both assays were highly specific, sensitive, and repeatable. The nPCR and qPCR tests had good overall concordance when DNA samples derived from both apparently healthy and clinically diseased hatchery rainbow trout were tested. Finally, we demonstrated that gill snips were a suitable tissue for nonlethal detection of N. salmonis DNA in juvenile salmonids. Monitoring of juvenile salmonid fish in the Snake River over a 3-year period revealed low prevalence of N. salmonis in hatchery and wild Chinook salmon and wild steelhead but significantly higher prevalence in hatchery-derived steelhead. Routine monitoring of N. salmonis is not performed for all hatchery steelhead populations. At present, the possible contribution of this pathogen to delayed mortality of steelhead has not been determined.

  3. Comparative studies of Zr-based MCM-41 and MCM-48 mesoporous molecular sieves: Synthesis and physicochemical properties

    International Nuclear Information System (INIS)

    Chen, L.F.; Zhou, X.L.; Norena, L.E.; Wang, J.A.; Navarrete, J.; Salas, P.; Montoya, A.; Del Angel, P.; Llanos, M.E.

    2006-01-01

    Two surfactant-templated synthetic routes are developed for the preparation of new types of mesoporous molecular sieves, Zr-MCM-41 and Zr-MCM-48, using different Si sources but keeping the same zirconium precursor (zirconium-n-propoxide). When fumed silica was used as Si precursor, a Zr-MCM-48 material of cubic structure was formed with a surface area of 654.8 m 2 /g and an unimodal pore diameter distribution. It shows low stability: after calcination at 600 deg. C, the ordered structure was transformed into a relatively disordered worm-like mesostructure with many defects and silanol groups. The use of tetraethyl orthosilicate as Si source led to the formation of a Zr-MCM-41 mesoporous solid, which had good thermal stability and a highly ordered hexagonal arrangement, with a surface area 677.9 m 2 /g and an uniform pore diameter distribution. Fourier transform infrared (FT-IR) characterization and 29 Si NMR analysis confirm that zirconium ions indeed incorporated into the framework of the solid. The in situ FT-IR spectroscopy of pyridine adsorption reveals that both, Lewis and Broensted acid sites, were formed on the surface of these mesoporous materials. The strength and number of the Broensted acid sites of the Zr-MCM-48 solid were greater than those of the Zr-MCM-41, due to a lower degree of condensation reaction during the synthesis that led to more structural defects in the framework and more silanol groups stretching from the solid surface

  4. Molecular cloning and expression of a novel keratinocyte protein (psoriasis-associated fatty acid-binding protein [PA-FABP]) that is highly up-regulated in psoriatic skin and that shares similarity to fatty acid-binding proteins

    DEFF Research Database (Denmark)

    Madsen, Peder; Rasmussen, H H; Leffers, H

    1992-01-01

    termed PA-FABP (psoriasis-associated fatty acid-binding protein). The deduced sequence predicted a protein with molecular weight of 15,164 daltons and a calculated pI of 6.96, values that are close to those recorded in the keratinocyte 2D gel protein database. The protein comigrated with PA......-FABP as determined by 2D gel analysis of [35S]-methionine-labeled proteins expressed by transformed human amnion (AMA) cells transfected with clone 1592 using the vaccinia virus expression system and reacted with a rabbit polyclonal antibody raised against 2D gel purified PA-FABP. Structural analysis of the amino...... with epidermal growth factor (EGF), pituitary extract, and 10% fetal calf serum] revealed a strong up-regulation of PA-FABP, psoriasin, calgranulins A and B, and a few other proteins that are highly expressed in psoriatic skin. The levels of these proteins exceeded by far those observed in non-cultured normal...

  5. [Levels and molecular heterogeneity of serotonin transporter protein in platelets of patients with different mental diseases: a comparative analysis with the use of monoclonal and polyclonal antibodies].

    Science.gov (United States)

    Brusov, O S; Faktor, M I; Zlobina, G P; Bologov, P V; Kaleda, V G; Oleĭchik, I V; Korenev, A N; Piatnitskiĭ, A N; Dupin, A M; Katasonov, A B; Morozova, M A; Beniashvili, A G; Lozier, R Kh; Pavlova, E V; Segal, O L; Massino, Iu S; Dmitriev, A D

    2001-01-01

    Polyclonal (PAb) and monoclonal (MAb) antibodies to CT2-epitope of the C-terminal fragment of serotonin transporter (SERT) protein were used to study the levels and molecular heterogeneity of platelet SERT in healthy donors and patients with affective (AD) and somatoform (SD) disorders, schizoaffective disorder (SAD) and schizophrenia. SERT was found to exist as high molecular wight (HMW) and low molecular weight (LMW) forms separated after electrophoresis. The levels of HMW and LMW forms of SERT were significantly, decreased in mentally ill patients as compared to healthy individuals. Unlike PAb, horse radish peroxidase (HRP)-conjugated MAbs were more sensitive and specific to SERT and could detect the LMW form of SERT as a duplet protein form with MW about 40 and 43 kDa. The MAb to CT2 C-terminal fragment of SERT conjugated with HRP is considered to be a new valuable tool for further investigation of SERT expression, properties, and posttranslation modification in the controls and in patients with different psychopathology.

  6. Raman spectroscopy in comparative investigations of mechanisms of binding of three molecular probes - fluorescein, eosin, and erythrosin - to human serum albumin

    Science.gov (United States)

    Vlasova, I. M.; Saletsky, A. M.

    2008-11-01

    The comparative analysis of binding of three molecular fluorescent probes (fluorescein, eosin, and erythrosin), belonging to one homologous family, to human serum albumin (HSA) is made by Raman spectroscopy method. The binding of all three probes to binding Center I of HSA is registered. The character of binding of initial probe of the given homologous family - fluorescein - to protein differs from character of binding of its halogen-derivatives (eosin and erythrosin) to protein. The differences in binding of these three probes to HSA are determined by value of electronegativity of atoms of lateral radicals in structural formulas of probes and, therefore, by value of pK of their ionized groups.

  7. Comparative evaluation of low-molecular-mass proteins from Mycobacterium tuberculosis identifies members of the ESAT-6 family as immunodominant T-cell antigens

    DEFF Research Database (Denmark)

    Skjøt, Rikke L. V.; Oettinger, Thomas; Rosenkrands, Ida

    2000-01-01

    . The molecules were characterized, mapped in a two-dimensional electrophoresis reference map of short-term culture filtrate, and compared with another recently identified low-mass protein, CFP10 (F. X. Berthet, P, B. Rasmussen, I. Rosenkrands, P. Andersen, and B. Gicquel. Microbiology 144:3195-3203, 1998......), and the well-described ESAT-6 antigen. Genetic analyses demonstrated that TB10.4 as well as CFP10 belongs to the ESAT-6 family of low-mass proteins, whereas TB7.3 is a low-molecular-mass protein outside this family. The proteins were expressed in Escherichia coli, and their immunogenicity was tested...

  8. Molecular nature of X-ray-induced mutations compared with that of spontaneous ones in human c-hprt gene integrated into mammalian chromosomal DNA

    International Nuclear Information System (INIS)

    Kimura, Hiroshi; Kato, Takesi.

    1992-01-01

    X-ray-induced mutations were analysed at molecular levels in comparison with spontaneous mutations. Altered sequences were determined tentatively of 30 independent X-ray-induced mutations in a cDNA of the human hprt gene which was integrated into mammalian chromosome as a part of a shuttle vector. Mutations consisted of base substitutions (37 %), frameshifts (27 %), deletions (27 %) and others (10 %). All these mutational events were distributed randomly over the gene without there being hot spots. The spectrum and distribution of X-ray-induced mutations resembled those of spontaneous mutations. Among base substitutions, transversions were predominant and base substitution mutations occurred more at A:T sites than at G:C sites, which is also the case in spontaneous mutations. Most of the frameshift and deletion mutations induced by X-rays, as well as those spontaneously arising, were characterized by the existence of short direct repeats of several identical bases in a row at the sites of the mutations. A slippage misalignment mechanism in replication well accounts for the generation of these classes of mutations. Judging from the data accumulated so far, it can be concluded that X-ray-induced mutations at molecular levels are similar to those spontaneously occurring. (author)

  9. Comparing the Spectroscopic and Molecular Characteristics of Different Dissolved Organic Matter Fractions Isolated by Hydrophobic and Anionic Exchange Resins Using Fluorescence Spectroscopy and FT-ICR-MS

    Directory of Open Access Journals (Sweden)

    Morgane Derrien

    2017-07-01

    Full Text Available Despite the environmental significance of dissolved organic matter (DOM, characterizing DOM is still challenging due to its structural complexity and heterogeneity. In this study, three different chemical fractions, including hydrophobic acid (HPOA, transphilic acid (TPIA, and hydrophilic neutral and base (HPIN/B fractions, were separated from bulk aquatic DOM samples, and their spectral features and the chemical composition at the molecular level were compared using both fluorescence excitation emission matrix-parallel factor analysis (EEM-PARAFAC and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS. The HPIN/B fraction was distinguished from the two acidic fractions (i.e., HPOA and TPIA by the EEM-PARAFAC, while the TPIA fraction was discriminated by using the molecular parameters derived from the FT-ICR MS analyses. Statistical comparison suggests that the spectral dissimilarity among the three chemical fractions might result from the acido-basic properties of DOM samples, while the differences in molecular composition were more likely to be affected by the hydrophobicity of the DOM fractions. The non-metric multidimensional scaling map further revealed that the HPOA was the most heterogeneous among the three fractions. The number of overlapping formulas among the three chemical fractions constituted only <5% of all identified formulas, and those between two different fractions ranged from 2.0% to 24.1%, implying relatively homogeneous properties of the individual chemical fractions with respect to molecular composition. Although employing chemical fractionation achieved a lowering of the DOM heterogeneity, prevalent signatures of either acido-basic property or the hydrophobic nature of DOM on the characteristics of three chemical isolated fractions were not found for this study.

  10. Comparative Physiological and Molecular Analyses of Two Contrasting Flue-Cured Tobacco Genotypes under Progressive Drought Stress

    Directory of Open Access Journals (Sweden)

    Xinhong Su

    2017-05-01

    Full Text Available Drought is a major environmental factor that limits crop growth and productivity. Flue-cured tobacco (Nicotiana tabacum is one of the most important commercial crops worldwide and its productivity is vulnerable to drought. However, comparative analyses of physiological, biochemical and gene expression changes in flue-cured tobacco varieties differing in drought tolerance under long-term drought stress are scarce. In this study, drought stress responses of two flue-cured tobacco varieties, LJ851 and JX6007, were comparatively studied at the physiological and transcriptional levels. After exposing to progressive drought stress, the drought-tolerant LJ851 showed less growth inhibition and chlorophyll reduction than the drought-sensitive JX6007. Moreover, higher antioxidant enzyme activities and lower levels of H2O2, Malondialdehyde (MDA, and electrolyte leakage after drought stress were found in LJ851 when compared with JX6007. Further analysis showed that LJ851 plants had much less reductions than the JX6007 in the net photosynthesis rate and stomatal conductance during drought stress; indicating that LJ851 had better photosynthetic performance than JX6007 during drought. In addition, transcriptional expression analysis revealed that LJ851 exhibited significantly increased transcripts of several categories of drought-responsive genes in leaves and roots under drought conditions. Together, these results indicated that LJ851 was more drought-tolerant than JX6007 as evidenced by better photosynthetic performance, more powerful antioxidant system, and higher expression of stress defense genes during drought stress. This study will be valuable for the development of novel flue-cured tobacco varieties with improved drought tolerance by exploitation of natural genetic variations in the future.

  11. Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes

    Science.gov (United States)

    In this study, we identified and compared nucleotide-binding site (NBS) domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China). Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approxima...

  12. Lower glucose-dependent insulinotropic polypeptide (GIP) response but similar glucagon-like peptide 1 (GLP-1), glycaemic, and insulinaemic response to ancient wheat compared to modern wheat depends on processing

    DEFF Research Database (Denmark)

    Bakhøj, S; Flint, A.; Holst, Jens Juul

    2003-01-01

    with honey-salt added, leavening crushed whole grain, and conventional leavening with yeast added. Bread made from modern wheat was prepared by conventional leavening with yeast added. SUBJECTS: A total of 11 healthy young men. RESULTS: The postprandial GIP response was significantly (P... by the Einkorn breads processed with honey-salt leavening and by using crushed whole grain bread compared to the yeast leavened bread made from modern wheat or from Einkorn. No significant differences were found in the responses of GLP-1, insulin or glucose. CONCLUSION: Einkorn honey-salt leavened and Einkorn...... whole grain bread elicit a reduced gastrointestinal response of GIP compared to conventional yeast bread. No differences were found in the glycaemic, insulinaemic and GLP-1 responses. Processing of starchy foods such as wheat may be a powerful tool to modify the postprandial GIP response....

  13. Whole-body low-dose computed tomography in multiple myeloma staging: Superior diagnostic performance in the detection of bone lesions, vertebral compression fractures, rib fractures and extraskeletal findings compared to radiography with similar radiation exposure.

    Science.gov (United States)

    Lambert, Lukas; Ourednicek, Petr; Meckova, Zuzana; Gavelli, Giampaolo; Straub, Jan; Spicka, Ivan

    2017-04-01

    The primary objective of the present prospective study was to compare the diagnostic performance of conventional radiography (CR) and whole-body low-dose computed tomography (WBLDCT) with a comparable radiation dose reconstructed using hybrid iterative reconstruction technique, in terms of the detection of bone lesions, skeletal fractures, vertebral compressions and extraskeletal findings. The secondary objective was to evaluate lesion attenuation in relation to its size. A total of 74 patients underwent same-day skeletal survey by CR and WBLDCT. In CR and WBLDCT, two readers assessed the number of osteolytic lesions at each region and stage according to the International Myeloma Working Group (IMWG) criteria. A single reader additionally assessed extraskeletal findings and their significance, the number of vertebral compressions and bone fractures. The radiation exposure was 2.7±0.9 mSv for WBLDCT and 2.5±0.9 mSv for CR (P=0.054). CR detected bone involvement in 127 out of 486 regions (26%; Prib fractures compared with CR (188 vs. 47; Pfractures, vertebral compressions and extraskeletal findings, which results in up- or downstaging in 24% patients according to the IMWG criteria. The attenuation of osteolytic lesions can be measured with the avoidance of the partial volume effect.

  14. A comparative analysis of preservation techniques for the optimal molecular detection of hookworm DNA in a human fecal specimen

    Science.gov (United States)

    Pilotte, Nils; Baumer, Ben; Grant, Jessica; Asbjornsdottir, Kristjana; Schaer, Fabian; Hu, Yan; Aroian, Raffi; Walson, Judd; Williams, Steven A.

    2018-01-01

    Background Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time. Methodology Quantitative real-time PCR was used in this study as a measure of the effectiveness of seven commercially available products to preserve hookworm DNA over time and at different temperatures. Results were compared against “no preservative” controls and the “gold standard” of rapidly freezing samples at -20°C. The preservation methods were compared at both 4°C and at simulated tropical ambient temperature (32°C) over a period of 60 days. Evaluation of the effectiveness of each preservative was based on quantitative real-time PCR detection of target hookworm DNA. Conclusions At 4°C there were no significant differences in DNA amplification efficiency (as measured by Cq values) regardless of the preservation method utilized over the 60-day period. At 32°C, preservation with FTA cards, potassium dichromate, and a silica bead two-step desiccation process proved most advantageous for minimizing Cq value increases, while RNA later, 95% ethanol and Paxgene also demonstrate some protective effect. These results suggest that fecal samples spiked with known concentrations of hookworm-derived egg material can remain at 4°C for 60 days in the absence of preservative, without significant degradation of the DNA target. Likewise, a variety of preservation methods can provide a measure of protection in the absence of a cold chain. As a result, other factors, such as preservative toxicity

  15. [Molecular phylogeny of Turbellaria, based on data from comparing the nucleotide sequences of 18S ribosomal RNA genes].

    Science.gov (United States)

    Kuznedelov, K D; Timoshkin, O A

    1995-01-01

    Polymerase chain reaction and direct sequencing of the 5'-end region of the 18S ribosomal RNA gene were used to infer phylogenetic relationship among turbellarian flatworms from Lake Baikal. Representatives of 5 orders (Tricladida--10 spp., Lecithoepitheliata--5 spp., Prolecithophora--3 spp., Proseriata and Kalyptorhynchia one for each) were studied; nucleotide sequence of more than 340 nucleotides was determined for each species. Consensus sequence for each order having more than one representative species was determined. Distance matrix and maximum parsimony approaches were applied to infer phylogenies. Bootstrap procedure was used to estimate confidence limits, at the 100% level by bootstrapping, the group of three orders: Kalyptorhynchia, Proseriata and Lecithoepitheliata was found to be monophyletic. However, subsets inside the group had no significant support to be preferred or rejected. Our data do not support traditional systematics which joins two suborders Tricladida and Proseriata into the single order Seriata, and also do not support comparative anatomical data which show close relationship of Lecithoepitheliata and lower Prolecithophora.

  16. A Comparative Histopathology, Serology and Molecular Study, on Experimental Ocular Toxocariasis by Toxocara cati in Mongolian Gerbils and Wistar Rats

    Directory of Open Access Journals (Sweden)

    Mohammad Zibaei

    2013-01-01

    Full Text Available The aim of this study was to compare the performance of three in-house diagnostic tests, that is, histopathology, enzyme-linked immunosorbent assay (ELISA, and polymerase chain reaction (PCR, for the diagnosis after experimental infection with Toxocara cati. Twenty Mongolian gerbils and Wistar rats were divided into ten groups (n=2/group. Toxocara cati infections were established in Mongolian gerbils and Wistar rats by administering doses of 240 and 2500 embryonated Toxocara cati eggs by gavage, respectively. Tissue sections were stained with Haematoxylin and Eosin and observed under the light microscope. Sera and vitreous fluid collected from separate infected groups were tested against Toxocara cati antigens, for 92 days postinfection. Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE blocks, and aqueous fluids belong to the animals. The histopathology test gave negative results among the groups of animals examined between 5 and 92 days postinfection. The ELISA results showed that anti-Toxocara antibodies have risen between 7 and 61 days postinfection in sera and vitreous fluid in the animals infected, respectively. Analysis of PCR products revealed positive band (660 bp in the orbital tissue infected Mongolian gerbils at 5 days postinfection. Of the three evaluated methods, the PCR could be recommended for scientific and laboratory diagnoses of toxocariasis in experimentally infected animals.

  17. How to use and integrate bioinformatics tools to compare proteomic data from distinct conditions? A tutorial using the pathological similarities between Aortic Valve Stenosis and Coronary Artery Disease as a case-study.

    Science.gov (United States)

    Trindade, Fábio; Ferreira, Rita; Magalhães, Beatriz; Leite-Moreira, Adelino; Falcão-Pires, Inês; Vitorino, Rui

    2018-01-16

    Nowadays we are surrounded by a plethora of bioinformatics tools, powerful enough to deal with the large amounts of data arising from proteomic studies, but whose application is sometimes hard to find. Therefore, we used a specific clinical problem - to discriminate pathophysiology and potential biomarkers between two similar cardiovascular diseases, aortic valve stenosis (AVS) and coronary artery disease (CAD) - to make a step-by-step guide through four bioinformatics tools: STRING, DisGeNET, Cytoscape and ClueGO. Proteome data was collected from articles available on PubMed centered on proteomic studies enrolling subjects with AVS or CAD. Through the analysis of gene ontology provided by STRING and ClueGO we could find specific biological phenomena associated with AVS, such as down-regulation of elastic fiber assembly, and with CAD, such as up-regulation of plasminogen activation. Moreover, through Cytoscape and DisGeNET we could pinpoint surrogate markers either for AVS (e.g. popeye domain containing protein 2 and 28S ribosomal protein S36, mitochondrial) or for CAD (e.g. ankyrin repeat and SOCS box protein 7) which deserve future validation. Data recycling and integration as well as research orientation are among the main advantages of resorting to bioinformatics analysis, hence these tutorials can be of great convenience for proteomics investigators. As we saw for aortic valve stenosis and coronary artery disease, it can be of great relevance to perform preliminary bioinformatics analysis with already published proteomics data. It not only saves us time in the lab (avoiding work duplication) as it points out new hypothesis to explain the phenotypical presentation of the diseases as well as new surrogate markers with clinical relevance, deserving future scrutiny. These essential steps can be easily overcome if one follows the steps proposed in our tutorial for STRING, DisGeNET, Cytoscape and ClueGO utilization. Copyright © 2017 Elsevier B.V. All rights

  18. Characterization of methane oxidation in a simulated landfill cover system by comparing molecular and stable isotope mass balances.

    Science.gov (United States)

    Schulte, Marcel; Jochmann, Maik A; Gehrke, Tobias; Thom, Andrea; Ricken, Tim; Denecke, Martin; Schmidt, Torsten C

    2017-11-01

    Biological methane oxidation may be regarded as a method of aftercare treatment for landfills to reduce climate relevant methane emissions. It is of social and economic interest to estimate the behavior of bacterial methane oxidation in aged landfill covers due to an adequate long-term treatment of the gas emissions. Different approaches assessing methane oxidation in laboratory column studies have been investigated by other authors recently. However, this work represents the first study in which three independent approaches, ((i) mass balance, (ii) stable isotope analysis, and (iii) stoichiometric balance of product (CO 2 ) and reactant (CH 4 ) by CO 2 /CH 4 -ratio) have been compared for the estimation of the biodegradation by a robust statistical validation on a rectangular, wide soil column. Additionally, an evaluation by thermal imaging as a potential technique for the localization of the active zone of bacterial methane oxidation has been addressed in connection with stable isotope analysis and CO 2 /CH 4 -ratios. Although landfills can be considered as open systems the results for stable isotope analysis based on a closed system correlated better with the mass balance than calculations based on an open system. CO 2 /CH 4 -ratios were also in good agreement with mass balance. In general, highest values for biodegradation were determined from mass balance, followed by CO 2 /CH 4 -ratio, and stable isotope analysis. The investigated topsoil proved to be very suitable as a potential cover layer by removing up to 99% of methane for CH 4 loads of 35-65gm -2 d -1 that are typical in the aftercare phase of landfills. Finally, data from stable isotope analysis and the CO 2 /CH 4 -ratios were used to trace microbial activity within the reactor system. It was shown that methane consumption and temperature increase, as a cause of high microbial activity, correlated very well. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods

    Directory of Open Access Journals (Sweden)

    Pérez-Martínez Gaspar

    2010-09-01

    Full Text Available Abstract Background Comparative genomic hybridization (CGH constitutes a powerful tool for identification and characterization of bacterial strains. In this study we have applied this technique for the characterization of a number of Lactobacillus strains isolated from the intestinal content of rats fed with a diet supplemented with sorbitol. Results Phylogenetic analysis based on 16S rRNA gene, recA, pheS, pyrG and tuf sequences identified five bacterial strains isolated from the intestinal content of rats as belonging to the recently described Lactobacillus taiwanensis species. DNA-DNA hybridization experiments confirmed that these five strains are distinct but closely related to Lactobacillus johnsonii and Lactobacillus gasseri. A whole genome DNA microarray designed for the probiotic L. johnsonii strain NCC533 was used for CGH analysis of L. johnsonii ATCC 33200T, L. johnsonii BL261, L. gasseri ATCC 33323T and L. taiwanensis BL263. In these experiments, the fluorescence ratio distributions obtained with L. taiwanensis and L. gasseri showed characteristic inter-species profiles. The percentage of conserved L. johnsonii NCC533 genes was about 83% in the L. johnsonii strains comparisons and decreased to 51% and 47% for L. taiwanensis and L. gasseri, respectively. These results confirmed the separate status of L. taiwanensis from L. johnsonii at the level of species, and also that L. taiwanensis is closer to L. johnsonii than L. gasseri is to L. johnsonii. Conclusion Conventional taxonomic analyses and microarray-based CGH analysis have been used for the identification and characterization of the newly species L. taiwanensis. The microarray-based CGH technology has been shown as a remarkable tool for the identification and fine discrimination between phylogenetically close species, and additionally provided insight into the adaptation of the strain L. taiwanensis BL263 to its ecological niche.

  20. A Comparative Genomic Survey Provides Novel Insights into Molecular Evolution of l-Aromatic Amino Acid Decarboxylase in Vertebrates

    Directory of Open Access Journals (Sweden)

    Yanping Li

    2018-04-01

    Full Text Available Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 aaad nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one aaad gene and a new aaad-like gene, which formed a novel AAAD family. However, in tetraploid teleosts, there were two copies of the aaad gene due to whole genome duplication. A subsequent synteny analysis investigated 81 aaad sequences and revealed their collinearity and systematic evolution. Interestingly, we discovered that platypus (Ornithorhynchus anatinus, Atlantic cod (Guadus morhua, Mexican tetra (Astyanax mexicanus, and a Sinocyclocheilus cavefish (S. anshuiensis have long evolutionary branches in the phylogenetic topology. We also performed pseudogene identification and selection pressure analysis; however, the results revealed a deletion of 37 amino acids in Atlantic cod and premature stop codons in the cave-restricted S. anshuiensis and A. mexicanus, suggesting weakening or disappearing rhythms in these cavefishes. Selective pressure analysis of aaad between platypus and other tetrapods showed that rates of nonsynonymous (Ka and synonymous (Ks substitutions were higher when comparing the platypus to other representative tetrapods, indicating that, in this semiaquatic mammal, the aaad gene experienced selection during the process of evolution. In summary, our current work provides novel insights into aaad genes in vertebrates from a genome-wide view.

  1. In type 2 diabetes, randomisation to advice to follow a low-carbohydrate diet transiently improves glycaemic control compared with advice to follow a low-fat diet producing a similar weight loss.

    Science.gov (United States)

    Guldbrand, H; Dizdar, B; Bunjaku, B; Lindström, T; Bachrach-Lindström, M; Fredrikson, M; Ostgren, C J; Nystrom, F H

    2012-08-01

    The study aimed to compare the effects of a 2 year intervention with a low-fat diet (LFD) or a low-carbohydrate diet (LCD), based on four group meetings to achieve compliance. This was a prospective randomised parallel trial involving 61 adults with type 2 diabetes consecutively recruited in primary care and randomised by drawing ballots. Patients that did not speak Swedish could not be recruited. The primary outcomes in this non-blinded study were weight and HbA(1c). Patients on the LFD aimed for 55-60 energy per cent (E%) and those on LCD for 20 E% from carbohydrate. The mean BMI and HbA(1c) of the participants were 32.7 ± 5.4 kg/m(2) and 57.0 ± 9.2 mmol/mol, respectively. No patients were lost to follow-up. Weight loss did not differ between groups and was maximal at 6 months: LFD -3.99 ± 4.1 kg (n=31); LCD -4.31 ± 3.6 kg (n=30); p carbohydrates is safe with respect to cardiovascular risk compared with the traditional LFD and this approach could constitute a treatment alternative. ClinicalTrials.gov NCT01005498 University Hospital of Linköping Research Funds, Linköping University, the County Council of Östergötland, and the Diabetes Research Centre of Linköping University.

  2. Molecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS

    Science.gov (United States)

    Hertkorn, Norbert; Harir, Mourad; Cawley, Kaelin M.; Schmitt-Kopplin, Philippe; Jaffé, Rudolf

    2016-04-01

    Wetlands provide quintessential ecosystem services such as maintenance of water quality, water supply and biodiversity, among others; however, wetlands are also among the most threatened ecosystems worldwide. Natural dissolved organic matter (DOM) is an abundant and critical component in wetland biogeochemistry. This study describes the first detailed, comparative, molecular characterization of DOM in subtropical, pulsed, wetlands, namely the Everglades (USA), the Pantanal (Brazil) and the Okavango Delta (Botswana), using optical properties, high-field nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (FT-ICRMS), and compares compositional features to variations in organic matter sources and flooding characteristics (i.e., differences in hydroperiod). While optical properties showed a high degree of variability within and between the three wetlands, analogies in DOM fluorescence properties were such that an established excitation emission matrix fluorescence parallel factor analysis (EEM-PARAFAC) model for the Everglades was perfectly applicable to the other two wetlands. Area-normalized 1H NMR spectra of selected samples revealed clear distinctions of samples while a pronounced congruence within the three pairs of wetland DOM readily suggested the presence of an individual wetland-specific molecular signature. Within sample pairs (long- vs. short-hydroperiod sites), internal differences mainly referred to intensity variations (denoting variable abundance) rather than to alterations of NMR resonances positioning (denoting diversity of molecules). The relative disparity was largest between the Everglades long- and short-hydroperiod samples, whereas Pantanal and Okavango samples were more alike among themselves. Otherwise, molecular divergence was most obvious in the case of unsaturated protons (δH > 5 ppm). 2-D NMR spectroscopy for a particular sample revealed a large richness of aliphatic and unsaturated substructures, likely derived from

  3. Antitumor evaluation and 3D-QSAR studies of a new series of the spiropyrroloquinoline isoindolinone/aza-isoindolinone derivatives by comparative molecular field analysis (CoMFA).

    Science.gov (United States)

    Sadeghzadeh, Masoud; Salahinejad, Maryam; Zarezadeh, Nahid; Ghandi, Mehdi; Baghery, Maryam Keshavarz

    2017-11-01

    In current study, antitumor activity of two series of the newly synthesized spiropyrroloquinoline isoindolinone and spiropyrroloquinoline aza-isoindolinone scaffolds was evaluated against three human breast normal and cancer cell lines (MCF-10A, MCF-7 and SK-BR-3) and compared with cytotoxicity values of doxorubicin and colchicine as the standard drugs. It was found that several compounds were endowed with cytotoxicity in the low micromolar range. Among these two series, compounds 6i, 6j, 6k and 7l, 7m, 7n, 7o containing 3-ethyl-1H-indole moiety were found to be highly effective against both cancer cell lines ranging from [Formula: see text] to [Formula: see text] in comparison with the corresponding analogs. Compared with human cancer cells, the most potent compounds did not show high cytotoxicity against human breast normal MCF-10A cells. Generally, most of the evaluated compounds 6a-l and 7a-o series showed more antitumor activity against SK-BR-3 than MCF-7 cells. Moreover, comparative molecular field analysis (CoMFA) as a popular tools of three-dimensional quantitative structure-activity relationship (3D-QSAR) studies was carried out on 27 spiropyrroloquinolineisoindolinone and spiropyrroloquinolineaza-isoindolinone derivatives with antitumor activity against on SK-BR-3 cells. The obtained CoMFA models showed statistically excellent performance, which also possessed good predictive ability for an external test set. The results confirm the important effect of molecular steric and electrostatic interactions of these compounds on in vitro cytotoxicity against SK-BR-3.

  4. Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii

    Directory of Open Access Journals (Sweden)

    Muhammad Y. Ali

    2017-08-01

    Full Text Available Systemic acid-base balance and osmotic/ionic regulation in decapod crustaceans are in part maintained by a set of transport-related enzymes such as carbonic anhydrase (CA, Na+/K+-ATPase (NKA, H+-ATPase (HAT, Na+/K+/2Cl− cotransporter (NKCC, Na+/Cl−/HCO ${}_{3}^{-}$ 3 − cotransporter (NBC, Na+/H+ exchanger (NHE, Arginine kinase (AK, Sarcoplasmic Ca+2-ATPase (SERCA and Calreticulin (CRT. We carried out a comparative molecular analysis of these genes in three commercially important yet eco-physiologically distinct freshwater crayfish, Cherax quadricarinatus, C. destructor and C. cainii, with the aim to identify mutations in these genes and determine if observed patterns of mutations were consistent with the action of natural selection. We also conducted a tissue-specific expression analysis of these genes across seven different organs, including gills, hepatopancreas, heart, kidney, liver, nerve and testes using NGS transcriptome data. The molecular analysis of the candidate genes revealed a high level of sequence conservation across the three Cherax sp. Hyphy analysis revealed that all candidate genes showed patterns of molecular variation consistent with neutral evolution. The tissue-specific expression analysis showed that 46% of candidate genes were expressed in all tissue types examined, while approximately 10% of candidate genes were only expressed in a single tissue type. The largest number of genes was observed in nerve (84% and gills (78% and the lowest in testes (66%. The tissue-specific expression analysis also revealed that most of the master genes regulating pH and osmoregulation (CA, NKA, HAT, NKCC, NBC, NHE were expressed in all tissue types indicating an important physiological role for these genes outside of osmoregulation in other tissue types. The high level of sequence conservation observed in the candidate genes may be explained by the important role of these genes as well as potentially having a number of other basic

  5. Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii.

    Science.gov (United States)

    Ali, Muhammad Y; Pavasovic, Ana; Dammannagoda, Lalith K; Mather, Peter B; Prentis, Peter J

    2017-01-01

    Systemic acid-base balance and osmotic/ionic regulation in decapod crustaceans are in part maintained by a set of transport-related enzymes such as carbonic anhydrase (CA), Na + /K + -ATPase (NKA), H + -ATPase (HAT), Na + /K + /2Cl - cotransporter (NKCC), Na + /Cl - /HCO[Formula: see text] cotransporter (NBC), Na + /H + exchanger (NHE), Arginine kinase (AK), Sarcoplasmic Ca +2 -ATPase (SERCA) and Calreticulin (CRT). We carried out a comparative molecular analysis of these genes in three commercially important yet eco-physiologically distinct freshwater crayfish , Cherax quadricarinatus, C. destructor and C. cainii , with the aim to identify mutations in these genes and determine if observed patterns of mutations were consistent with the action of natural selection. We also conducted a tissue-specific expression analysis of these genes across seven different organs, including gills, hepatopancreas, heart, kidney, liver, nerve and testes using NGS transcriptome data. The molecular analysis of the candidate genes revealed a high level of sequence conservation across the three Cherax sp. Hyphy analysis revealed that all candidate genes showed patterns of molecular variation consistent with neutral evolution. The tissue-specific expression analysis showed that 46% of candidate genes were expressed in all tissue types examined, while approximately 10% of candidate genes were only expressed in a single tissue type. The largest number of genes was observed in nerve (84%) and gills (78%) and the lowest in testes (66%). The tissue-specific expression analysis also revealed that most of the master genes regulating pH and osmoregulation (CA, NKA, HAT, NKCC, NBC, NHE) were expressed in all tissue types indicating an important physiological role for these genes outside of osmoregulation in other tissue types. The high level of sequence conservation observed in the candidate genes may be explained by the important role of these genes as well as potentially having a number of

  6. A molecular dynamics calculation of solid phase of malonic acid ...

    Indian Academy of Sciences (India)

    Sathya S R R Perumal

    Keywords. Hydrogen bond chain; elastic constants; molecular dynamics. 1. Introduction ... theory - a probabilistic model to determine the hydro- gen bonds within the .... compares poorly with the experimental value of 108.5. Similarly β and γ ...

  7. Exploring pyrazolo[3,4-d]pyrimidine phosphodiesterase 1 (PDE1) inhibitors: a predictive approach combining comparative validated multiple molecular modelling techniques.

    Science.gov (United States)

    Amin, Sk Abdul; Bhargava, Sonam; Adhikari, Nilanjan; Gayen, Shovanlal; Jha, Tarun

    2018-02-01

    Phosphodiesterase 1 (PDE1) is a potential target for a number of neurodegenerative disorders such as Schizophrenia, Parkinson's and Alzheimer's diseases. A number of pyrazolo[3,4-d]pyrimidine PDE1 inhibitors were subjected to different molecular modelling techniques [such as regression-based quantitative structure-activity relationship (QSAR): multiple linear regression, support vector machine and artificial neural network; classification-based QSAR: Bayesian modelling and Recursive partitioning; Monte Carlo based QSAR; Open3DQSAR; pharmacophore mapping and molecular docking analyses] to get a detailed knowledge about the physicochemical and structural requirements for higher inhibitory activity. The planarity of the pyrimidinone ring plays an important role for PDE1 inhibition. The N-methylated function at the 5th position of the pyrazolo[3,4-d]pyrimidine core is required for interacting with the PDE1 enzyme. The cyclopentyl ring fused with the parent scaffold is necessary for PDE1 binding potency. The phenylamino substitution at 3rd position is crucial for PDE1 inhibition. The N2-substitution at the pyrazole moiety is important for PDE1 inhibition compared to the N1-substituted analogues. Moreover, the p-substituted benzyl side chain at N2-position helps to enhance the PDE1 inhibitory profile. Depending on these observations, some new molecules are predicted that may possess better PDE1 inhibition.

  8. A new measure for functional similarity of gene products based on Gene Ontology

    Directory of Open Access Journals (Sweden)

    Lengauer Thomas

    2006-06-01

    Full Text Available Abstract Background Gene Ontology (GO is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. Results We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; simRel and funSim. One measure (simRel is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. Conclusion The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

  9. Utility and diagnostic performance of Mycobacterium tuberculosis complex by two immunochromatographic assays as compared with the molecular Genotype assay in Nigeria

    Directory of Open Access Journals (Sweden)

    Benjamin Thumamo Pokam

    2013-01-01

    Full Text Available Among the disadvantages of smear microscopy for detection of tuberculosis cases is its inability to differentiate between Mycobacterium tuberculosis (MTB and non-tuberculous mycobacteria (NTM. This study evaluated two, new immunochromatographic assays – Capilia TB-Neo and SD Bioline – on unheated and heated cultures at 80 °C for 30 min respectively for their ability to discriminate between MTB complex and NTM as compared with the molecular Genotype assay. Mycobacteria used in the study were obtained from smear-positive specimens collected from patients at four major hospitals in Cross River State, Nigeria. Capilia TB-Neo and SD Bioline showed sensitivities of 98.8% and 93.8% respectively and 100% specificity for both assays. Heating the isolates did not significantly impact the test performance. Both tests are recommended for use in rapid differentiation of strains isolated in Nigeria.

  10. Comparative evaluation of low-molecular-mass proteins from Mycobacterium tuberculosis identifies members of the ESAT-6 family as immunodominant T-cell antigens

    DEFF Research Database (Denmark)

    Skjøt, R L; Oettinger, T; Rosenkrands, I

    2000-01-01

    Culture filtrate from Mycobacterium tuberculosis contains protective antigens of relevance for the generation of a new antituberculosis vaccine. We have identified two previously uncharacterized M. tuberculosis proteins (TB7.3 and TB10.4) from the highly active low-mass fraction of culture filtrate....... The molecules were characterized, mapped in a two-dimensional electrophoresis reference map of short-term culture filtrate, and compared with another recently identified low-mass protein, CFP10 (F. X. Berthet, P. B. Rasmussen, I. Rosenkrands, P. Andersen, and B. Gicquel. Microbiology 144:3195-3203, 1998......), and the well-described ESAT-6 antigen. Genetic analyses demonstrated that TB10.4 as well as CFP10 belongs to the ESAT-6 family of low-mass proteins, whereas TB7.3 is a low-molecular-mass protein outside this family. The proteins were expressed in Escherichia coli, and their immunogenicity was tested...

  11. Quantitative Characterization of Molecular Similarity Spaces: Tools for Computational Toxicology

    Science.gov (United States)

    2000-01-20

    acid n 1.7 catechol o 1.8 clofibrate 0 o 1.9 di(2-ethylhexyl)phthalate (DEHP) 1.10 hydroquinone n 1.11 p-methoxyphenol o 1.12 sesamol n 1.13...Juric. A.. 1995b. A novel QSPR approach to physicochemical prop- erties of the ct-amino acids . Croat. Chem. Acta 68, 435- 450. Lucic, B...density at 20° C. 2. a A measure of the hydrogen bond donor acidity of a compound in forming a hydrogen bond. 3 ß A scale of the hydrogen bond

  12. Comparative mapping reveals similar linkage of functional genes to ...

    Indian Academy of Sciences (India)

    related traits between Brassica napus and Oryza sativa. Fupeng Li, Chaozhi Ma, Qingfang Chen, Touming Liu, Jinxiong Shen, Jinxing Tu, Yongzhong Xing and Tingdong Fu. J. Genet. 91, 163–170. Length of. Position of. Position of. Expect.

  13. Nested-PCR real time as alternative molecular tool for detection of Borrelia burgdorferi compared to the classical serological diagnosis of the blood.

    Science.gov (United States)

    Sroka-Oleksiak, Agnieszka; Ufir, Krzysztof; Salamon, Dominika; Bulanda, Malgorzata; Gosiewski, Tomasz

    Lyme disease, caused by Borrelia burgdorferi, is a multisystem disease that often makes difficulties to recognize caused by their genetic heterogenity. Currently, the gold standard for the detection of Lyme disease (LD) is serologic diagnostics based mainly on tests: ELISA and Western blot (WB). These methods, however, are subject to consider- able defect, especially in the initial phase of infection due to the occurrence of so-called serological window period and low specificity. For this reason, they might be replaced by molecular methods, for example polymerase chain reaction (PCR), which should be more sensitivity and specificity. In the present study we attempt to optimize the PCR reaction conditions and enhance existing test sensitivity by applying the equivalent of real time PCR - nested PCR for detection B. burgdorferi DNA in the patient's blood. The study involved 94 blood samples of patients with suspected LD. From each sample, 1.5 ml of blood was used for the isolation of bacterial DNA and PCR real time am- plification and its equivalent, in nested version. The remaining part earmarked for serologi- cal testing. Optimization of the reaction conditions made experimentally, using gradient of the temperature and gradient of the magnesium ions concentration for reaction real time in nested-PCR and PCR version. The results show that the nested-PCR real time, has a much higher sensitivity 45 (47.8%) of positive results for the detection of B. burgdorferi compared to the single- variety, without a preceding pre-amplification 2 (2.1%). Serological methods allowed the detection of infection in 41 (43.6%) samples. These results support of the nested PCR method as a better molecular tool for the detection of B. burgdorferi infection than classical PCR real time reaction. The nested-PCR real time method may be considered as a complement to ELISA and WB mainly in the early stages of infection, when in the blood circulating B. burgdorferi cells. By contrast, the

  14. Establishment of a new human pleomorphic malignant fibrous histiocytoma cell line, FU-MFH-2: molecular cytogenetic characterization by multicolor fluorescence in situ hybridization and comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Isayama Teruto

    2010-11-01

    Full Text Available Abstract Background Pleomorphic malignant fibrous histiocytoma (MFH is one of the most frequent malignant soft tissue tumors in adults. Despite the considerable amount of research on MFH cell lines, their characterization at a molecular cytogenetic level has not been extensively analyzed. Methods and results We established a new permanent human cell line, FU-MFH-2, from a metastatic pleomorphic MFH of a 72-year-old Japanese man, and applied multicolor fluorescence in situ hybridization (M-FISH, Urovysion™ FISH, and comparative genomic hybridization (CGH for the characterization of chromosomal aberrations. FU-MFH-2 cells were spindle or polygonal in shape with oval nuclei, and were successfully maintained in vitro for over 80 passages. The histological features of heterotransplanted tumors in severe combined immunodeficiency mice were essentially the same as those of the original tumor. Cytogenetic and M-FISH analyses displayed a hypotriploid karyotype with numerous structural aberrations. Urovysion™ FISH revealed a homozygous deletion of the p16INK4A locus on chromosome band 9p21. CGH analysis showed a high-level amplification of 9q31-q34, gains of 1p12-p34.3, 2p21, 2q11.2-q21, 3p, 4p, 6q22-qter, 8p11.2, 8q11.2-q21.1, 9q21-qter, 11q13, 12q24, 15q21-qter, 16p13, 17, 20, and X, and losses of 1q43-qter, 4q32-qter, 5q14-q23, 7q32-qter, 8p21-pter, 8q23, 9p21-pter, 10p11.2-p13, and 10q11.2-q22. Conclusion The FU-MFH-2 cell line will be a particularly useful model for studying molecular pathogenesis of human pleomorphic MFH.

  15. [Long-term treatment with a low-molecular-weight heparin administered subcutaneously compared with a vitamin K antagonist: subanalysis of patients with cancer].

    Science.gov (United States)

    Romera-Villegas, Antonio; Martí Mestre, Xavier; Vila Coll, Ramón; Colomé Nafría, Esteve

    2015-01-01

    We performed a subanalysis of cancer patients enrolled in a clinical trial that compared long-term (6 months) treatment with a low-molecular-weight heparin (LMWH) administered subcutaneously or with acenocoumarol. The subanalysis assessed whether the characteristics of the tumor had an influence on the clinical response. A randomized open trial included 69 patients with cancer and symptomatic proximal deep vein thrombosis of the lower limbs. The tumor characteristics and treatment type were recorded. The main assessment criterion was the 12-month incidence of recurrent symptomatic venous thromboembolism (VTE). Sixty-one patients (88.4%) were analyzed. At the time of inclusion, the cancer characteristics and treatment were comparable between the 2 groups. Over the course of 12 months, the recurrent VTE was significantly greater in the elderly patients (71.5 ± 6.4 vs. 62.0 ± 15.1; p=.006). The logistic regression analysis showed no association between VTE recurrence and the location or extent of the tumor. However, the use of thrombogenic chemotherapy (p=.045) was independently associated with VTE recurrence, and longterm treatment with tinzaparin was almost a protective factor (p=.15). In this small sample, we observed an association between thrombogenic chemotherapy and recurrent VTE. The tendency towards a reduction in VTE recurrence at 12 months in patients with cancer in the LMWH group could be attributed to the effect of the full LMWH dosage. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  16. Molecular pathways of early CD105-positive erythroid cells as compared with CD34-positive common precursor cells by flow cytometric cell-sorting and gene expression profiling

    International Nuclear Information System (INIS)

    Machherndl-Spandl, S; Suessner, S; Danzer, M; Proell, J; Gabriel, C; Lauf, J; Sylie, R; Klein, H-U; Béné, M C; Weltermann, A; Bettelheim, P

    2013-01-01

    Special attention has recently been drawn to the molecular network of different genes that are responsible for the development of erythroid cells. The aim of the present study was to establish in detail the immunophenotype of early erythroid cells and to compare the gene expression profile of freshly isolated early erythroid precursors with that of the CD34-positive (CD34 + ) compartment. Multiparameter flow cytometric analyses of human bone marrow mononuclear cell fractions (n=20) defined three distinct early erythroid stages. The gene expression profile of sorted early erythroid cells was analyzed by Affymetrix array technology. For 4524 genes, a differential regulation was found in CD105-positive erythroid cells as compared with the CD34 + progenitor compartment (2362 upregulated genes). A highly significant difference was observed in the expression level of genes involved in transcription, heme synthesis, iron and mitochondrial metabolism and transforming growth factor-β signaling. A comparison with recently published data showed over 1000 genes that as yet have not been reported to be upregulated in the early erythroid lineage. The gene expression level within distinct pathways could be illustrated directly by applying the Ingenuity software program. The results of gene expression analyses can be seen at the Gene Expression Omnibus repository

  17. Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune

    2010-04-01

    Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

  18. New Genome Similarity Measures based on Conserved Gene Adjacencies.

    Science.gov (United States)

    Doerr, Daniel; Kowada, Luis Antonio B; Araujo, Eloi; Deshpande, Shachi; Dantas, Simone; Moret, Bernard M E; Stoye, Jens

    2017-06-01

    Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, for example, to elucidate the phylogenetic relationships between species. The power of different genome comparison methods varies with the underlying formal model of a genome. The simplest models impose the strong restriction that each genome under study must contain the same genes, each in exactly one copy. More realistic models allow several copies of a gene in a genome. One speaks of gene families, and comparative genomic methods that allow this kind of input are called gene family-based. The most powerful-but also most complex-models avoid this preprocessing of the input data and instead integrate the family assignment within the comparative analysis. Such methods are called gene family-free. In this article, we study an intermediate approach between family-based and family-free genomic similarity measures. Introducing this simpler model, called gene connections, we focus on the combinatorial aspects of gene family-free genome comparison. While in most cases, the computational costs to the general family-free case are the same, we also find an instance where the gene connections model has lower complexity. Within the gene connections model, we define three variants of genomic similarity measures that have different expression powers. We give polynomial-time algorithms for two of them, while we show NP-hardness for the third, most powerful one. We also generalize the measures and algorithms to make them more robust against recent local disruptions in gene order. Our theoretical findings are supported by experimental results, proving the applicability and performance of our newly defined similarity measures.

  19. SIMILARITIES OF ELDERLY AND THERAPY-RELATED AML

    Directory of Open Access Journals (Sweden)

    Francesco D'Alò

    2011-11-01

    Full Text Available Acute myeloid leukemia (AML is a clonal disorder of the hematopoietic stem cell, typical of the elderly, with a median age of over 60 years at diagnosis. In AML, older age is one of the strongest independent adverse prognostic factor, associated with decreased complete response rate, worse disease-free and overall survival, with highest rates of treatment related mortality, resistant disease and relapse, compared to younger patients. While clinical risk factors do not significantly differ between older and younger patients, outcomes are compromised in elderly patients not only by increased comorbidities and susceptibility to toxicity from therapy, but it is now recognized that elderly AML represents a biologically distinct disease, that is itself more aggressive and less responsive to therapy. In elderly individuals prolonged exposure to environmental carcinogens may be the basis for the aggressive biology of the disease. This may also be the basis for similarities between elderly AML and therapy-related myeloid malignancies, mimicking toxic effects of previous cytotoxic treatments on hematopoietic stem cells. Age is itself a risk factor for t-MN, which are more frequent in elderly patients, where also a shorter latency between treatment of primary tumor and t-MN has been reported. Similarities between therapy-related malignancies and elderly AML include morphological aspects, as the presence of multilineage dysplasia preceding and/or concomitant to the development of leukemia, and adverse cytogenetics, including poor karyotype and chromosome 5 and/or 7 abnormalities. Looking at molecular prognosticators in elderly AML, similar to t-MN,  reduced frequency of favorable factors, as reduced number of NPM1 and CEBPA mutated cases has been observed, together with increased incidence of negative factors, as increased MDR1 expression, accelerated telomere shortening  and frequency of methylation changes. Given the unfavorable prognosis of elderly and

  20. Quantity and quality of black carbon molecular markers as obtained by two chromatographic methods (GC-FID and HPLC-DAD) - How do results compare?

    Science.gov (United States)

    Schneider, M. P. W.; Smittenberg, R. H.; Dittmar, T.; Schmidt, M. W. I.

    2009-04-01

    Chars produced by wildfires are an important source of black carbon (BC) in the environment. After their deposition on the soil surface they can be distributed into rivers, marine waters and sediments. The analysis of benzenepolycarboxylic acids (BPCAs) as a quantitative measure for black carbon (BC) in soil and sediment samples is a well-established method (Glaser et al., 1998; Brodowski et al., 2005). Briefly, the nitric acid oxidation of fused aromatic ring systems in BC forms eight molecular markers (BPCAs), which can be assigned to BC, and which subsequently can be quantified by GC-FID (gas chromatography with flame ionization detector). Recently, this method was modified for the quantification of BC in seawater samples using HPLC-DAD (High performance liquid chromatography with diode array detector) for the determination of individual BPCAs (Dittmar, 2008). A direct comparison of both analytical techniques is lacking but would be important for future data comparison aimed at the calculation of global BC budgets. Here we present a systematic comparison of the two BPCA quantification methods. We prepared chars under well-defined laboratory conditions. In order to cover a broad spectrum of char properties we used two sources of biomass and a wide range of pyrolysis temperatures. Chestnut hardwood chips (Castanea sativa) and rice straw (Oryza sativa) were pyrolysed at temperatures between 200 and 1000°C under a constant N2 stream. The maximum temperatures were held constant for 5 hours (Hammes et al., 2006). The BC contents of the chars have been analysed using the BPCA extraction method followed by either GC-FID or HPLC-DAD quantification. Preliminary results suggest that both methods yield similar total quantities of BPCA, and also the proportions of the individual markers are similar. Ongoing experiments will allow for a more detailed comparison of the two methods. The BPCA composition of chars formed at different temperatures and from different precursor

  1. Avoiding Pitfalls in Molecular Genetic Testing: Case Studies of High-Resolution Array Comparative Genomic Hybridization Testing in the Definitive Diagnosis of Mowat-Wilson Syndrome

    OpenAIRE

    Kluk, Michael Joseph; An, Yu; James, Philip; Coulter, David; Harris, David; Wu, Bai-Lin; Shen, Yiping

    2011-01-01

    The molecular testing options available for the diagnosis of genetic disorders are numerous and include a variety of different assay platforms. The consultative input of molecular pathologists and cytogeneticists, working closely with the ordering clinicians, is often important for definitive diagnosis. Herein, we describe two patients who had long histories of unexplained signs and symptoms with a high clinical suspicion of an underlying genetic etiology. Initial molecular testing in both ca...

  2. Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study.

    Science.gov (United States)

    Dong, Minghui; Liu, Haiyan

    2008-08-21

    The Escherichia coli peptide deformylase (PDF) and Bacillus thermoproteolyticus thermolysin (TLN) are two representative metal-requiring peptidases having remarkably similar active centers but distinctively different metal preferences. Zinc is a competent catalytic cofactor for TLN but not for PDF. Reaction pathways and the associated energetics for both enzymes were determined using combined semiempirical and ab initio quantum mechanical/molecular mechanical modeling, without presuming reaction coordinates. The results confirmed that both enzymes catalyze via the same chemical steps, and reproduced their different preferences for zinc or iron as competent cofactors. Further analyses indicated that different feasibility of the nucleophilic attack step leads to different metal preferences of the two enzymes. In TLN, the substrate is strongly activated and can serve as the fifth coordination ligand of zinc prior to the chemical steps. In PDF, the substrate carbonyl is activated by the chemical step itself, and becomes the fifth coordination partner of zinc only in a later stage of the nucleophilic attack. These leads to a much more difficult nucleophilic attack in PDF than in TLN. Different from some earlier suggestions, zinc has no difficulty in accepting an activated substrate as the fifth ligand to switch from tetra- to penta-coordination in either PDF or TLN. When iron replaces zinc, its stronger interaction with the hydroxide ligand may lead to higher activation barrier in TLN. In PDF, the stronger interactions of iron with ligands allow iron-substrate coordination to take place either before or at a very early stage of the chemical step, leading to effective catalysis. Our calculations also show combined semiempirical and ab initio quantum mechanical modeling can be efficient approaches to explore complicated reaction pathways in enzyme systems.

  3. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

    Full Text Available In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemmingfrom its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problemat hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, bysurveying established results and new developments in the theory and methods of similarity-preservingassociative lookup and dimensionality reduction — critical components of many cognitive functions, aswell as of intelligent data management in computer vision. We focus in particular on the growing familyof algorithms that support associative memory by performing hashing that respects local similarity, andon the uses of similarity in representing structured objects and scenes. Insofar as these similarity-basedideas and methods are useful in cognitive modeling and in AI applications, they should be included inthe core conceptual toolkit of computational neuroscience.

  4. Evaluation of molecular brain changes associated with environmental stress in rodent models compared to human major depressive disorder: A proteomic systems approach.

    Science.gov (United States)

    Cox, David Alan; Gottschalk, Michael Gerd; Stelzhammer, Viktoria; Wesseling, Hendrik; Cooper, Jason David; Bahn, Sabine

    2016-11-25

    Rodent models of major depressive disorder (MDD) are indispensable when screening for novel treatments, but assessing their translational relevance with human brain pathology has proved difficult. Using a novel systems approach, proteomics data obtained from post-mortem MDD anterior prefrontal cortex tissue (n = 12) and matched controls (n = 23) were compared with equivalent data from three commonly used preclinical models exposed to environmental stressors (chronic mild stress, prenatal stress and social defeat). Functional pathophysiological features associated with depression-like behaviour were identified in these models through enrichment of protein-protein interaction networks. A cross-species comparison evaluated which model(s) represent human MDD pathology most closely. Seven functional domains associated with MDD and represented across at least two models such as "carbohydrate metabolism and cellular respiration" were identified. Through statistical evaluation using kernel-based machine learning techniques, the social defeat model was found to represent MDD brain changes most closely for four of the seven domains. This is the first study to apply a method for directly evaluating the relevance of the molecular pathology of multiple animal models to human MDD on the functional level. The methodology and findings outlined here could help to overcome translational obstacles of preclinical psychiatric research.

  5. Self-similar cosmological models

    Energy Technology Data Exchange (ETDEWEB)

    Chao, W Z [Cambridge Univ. (UK). Dept. of Applied Mathematics and Theoretical Physics

    1981-07-01

    The kinematics and dynamics of self-similar cosmological models are discussed. The degrees of freedom of the solutions of Einstein's equations for different types of models are listed. The relation between kinematic quantities and the classifications of the self-similarity group is examined. All dust local rotational symmetry models have been found.

  6. Self-similar factor approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.; Sornette, D.

    2003-01-01

    The problem of reconstructing functions from their asymptotic expansions in powers of a small variable is addressed by deriving an improved type of approximants. The derivation is based on the self-similar approximation theory, which presents the passage from one approximant to another as the motion realized by a dynamical system with the property of group self-similarity. The derived approximants, because of their form, are called self-similar factor approximants. These complement the obtained earlier self-similar exponential approximants and self-similar root approximants. The specific feature of self-similar factor approximants is that their control functions, providing convergence of the computational algorithm, are completely defined from the accuracy-through-order conditions. These approximants contain the Pade approximants as a particular case, and in some limit they can be reduced to the self-similar exponential approximants previously introduced by two of us. It is proved that the self-similar factor approximants are able to reproduce exactly a wide class of functions, which include a variety of nonalgebraic functions. For other functions, not pertaining to this exactly reproducible class, the factor approximants provide very accurate approximations, whose accuracy surpasses significantly that of the most accurate Pade approximants. This is illustrated by a number of examples showing the generality and accuracy of the factor approximants even when conventional techniques meet serious difficulties

  7. Dynamic similarity in erosional processes

    Science.gov (United States)

    Scheidegger, A.E.

    1963-01-01

    A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

  8. Personalized recommendation with corrected similarity

    International Nuclear Information System (INIS)

    Zhu, Xuzhen; Tian, Hui; Cai, Shimin

    2014-01-01

    Personalized recommendation has attracted a surge of interdisciplinary research. Especially, similarity-based methods in applications of real recommendation systems have achieved great success. However, the computations of similarities are overestimated or underestimated, in particular because of the defective strategy of unidirectional similarity estimation. In this paper, we solve this drawback by leveraging mutual correction of forward and backward similarity estimations, and propose a new personalized recommendation index, i.e., corrected similarity based inference (CSI). Through extensive experiments on four benchmark datasets, the results show a greater improvement of CSI in comparison with these mainstream baselines. And a detailed analysis is presented to unveil and understand the origin of such difference between CSI and mainstream indices. (paper)

  9. Towards Personalized Medicine: Leveraging Patient Similarity and Drug Similarity Analytics

    Science.gov (United States)

    Zhang, Ping; Wang, Fei; Hu, Jianying; Sorrentino, Robert

    2014-01-01

    The rapid adoption of electronic health records (EHR) provides a comprehensive source for exploratory and predictive analytic to support clinical decision-making. In this paper, we investigate how to utilize EHR to tailor treatments to individual patients based on their likelihood to respond to a therapy. We construct a heterogeneous graph which includes two domains (patients and drugs) and encodes three relationships (patient similarity, drug similarity, and patient-drug prior associations). We describe a novel approach for performing a label propagation procedure to spread the label information representing the effectiveness of different drugs for different patients over this heterogeneous graph. The proposed method has been applied on a real-world EHR dataset to help identify personalized treatments for hypercholesterolemia. The experimental results demonstrate the effectiveness of the approach and suggest that the combination of appropriate patient similarity and drug similarity analytics could lead to actionable insights for personalized medicine. Particularly, by leveraging drug similarity in combination with patient similarity, our method could perform well even on new or rarely used drugs for which there are few records of known past performance. PMID:25717413

  10. Similarity search processing. Paralelization and indexing technologies.

    Directory of Open Access Journals (Sweden)

    Eder Dos Santos

    2015-08-01

    The next Scientific-Technical Report addresses the similarity search and the implementation of metric structures on parallel environments. It also presents the state of the art related to similarity search on metric structures and parallelism technologies. Comparative analysis are also proposed, seeking to identify the behavior of a set of metric spaces and metric structures over processing platforms multicore-based and GPU-based.

  11. Similarity indices I: what do they measure

    International Nuclear Information System (INIS)

    Johnston, J.W.

    1976-11-01

    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities

  12. Measuring transferring similarity via local information

    Science.gov (United States)

    Yin, Likang; Deng, Yong

    2018-05-01

    Recommender systems have developed along with the web science, and how to measure the similarity between users is crucial for processing collaborative filtering recommendation. Many efficient models have been proposed (i.g., the Pearson coefficient) to measure the direct correlation. However, the direct correlation measures are greatly affected by the sparsity of dataset. In other words, the direct correlation measures would present an inauthentic similarity if two users have a very few commonly selected objects. Transferring similarity overcomes this drawback by considering their common neighbors (i.e., the intermediates). Yet, the transferring similarity also has its drawback since it can only provide the interval of similarity. To break the limitations, we propose the Belief Transferring Similarity (BTS) model. The contributions of BTS model are: (1) BTS model addresses the issue of the sparsity of dataset by considering the high-order similarity. (2) BTS model transforms uncertain interval to a certain state based on fuzzy systems theory. (3) BTS model is able to combine the transferring similarity of different intermediates using information fusion method. Finally, we compare BTS models with nine different link prediction methods in nine different networks, and we also illustrate the convergence property and efficiency of the BTS model.

  13. Similarity indices I: what do they measure.

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, J.W.

    1976-11-01

    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities.

  14. Molecular diagnosis of canine visceral leishmaniasis: a comparative study of three methods using skin and spleen from dogs with natural Leishmania infantum infection.

    Science.gov (United States)

    Reis, Levi Eduardo Soares; Coura-Vital, Wendel; Roatt, Bruno Mendes; Bouillet, Leoneide Érica Maduro; Ker, Henrique Gama; Fortes de Brito, Rory Cristiane; Resende, Daniela de Melo; Carneiro, Mariângela; Giunchetti, Rodolfo Cordeiro; Marques, Marcos José; Carneiro, Cláudia Martins; Reis, Alexandre Barbosa

    2013-11-08

    Polymerase chain reaction (PCR) and its variations represent highly sensitive and specific methods for Leishmania DNA detection and subsequent canine visceral leishmaniasis (CVL) diagnosis. The aim of this work was to compare three different molecular diagnosis techniques (conventional PCR [cPCR], seminested PCR [snPCR], and quantitative PCR [qPCR]) in samples of skin and spleen from 60 seropositive dogs by immunofluorescence antibody test and enzyme-linked immunosorbent assay. Parasitological analysis was conducted by culture of bone marrow aspirate and optical microscopic assessment of ear skin and spleen samples stained with Giemsa, the standard tests for CVL diagnosis. The primers L150/L152 and LINR4/LIN17/LIN19 were used to amplify the conserved region of the Leishmania kDNA minicircle in the cPCR, and snPCR and qPCR were performed using the DNA polymerase gene (DNA pol α) primers from Leishmania infantum. The parasitological analysis revealed parasites in 61.7% of the samples. Sensitivities were 89.2%, 86.5%, and 97.3% in the skin and 81.1%, 94.6%, and 100.0% in spleen samples used for cPCR, snPCR, and qPCR, respectively. We demonstrated that the qPCR method was the best technique to detect L. infantum in both skin and spleen samples. However, we recommend the use of skin due to the high sensitivity and sampling being less invasive. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Comparative transcriptome analysis reveals different molecular mechanisms of Bacillus coagulans 2-6 response to sodium lactate and calcium lactate during lactic acid production.

    Directory of Open Access Journals (Sweden)

    Jiayang Qin

    Full Text Available Lactate production is enhanced by adding calcium carbonate or sodium hydroxide during fermentation. However, Bacillus coagulans 2-6 can produce more than 180 g/L L-lactic acid when calcium lactate is accumulated, but less than 120 g/L L-lactic acid when sodium lactate is formed. The molecular mechanisms by which B. coagulans responds to calcium lactate and sodium lactate remain unclear. In this study, comparative transcriptomic methods based on high-throughput RNA sequencing were applied to study gene expression changes in B. coagulans 2-6 cultured in non-stress, sodium lactate stress and calcium lactate stress conditions. Gene expression profiling identified 712 and 1213 significantly regulated genes in response to calcium lactate stress and sodium lactate stress, respectively. Gene ontology assignments of the differentially expressed genes were performed. KEGG pathway enrichment analysis revealed that 'ATP-binding cassette transporters' were significantly affected by calcium lactate stress, and 'amino sugar and nucleotide sugar metabolism' was significantly affected by sodium lactate stress. It was also found that lactate fermentation was less affected by calcium lactate stress than by sodium lactate stress. Sodium lactate stress had negative effect on the expression of 'glycolysis/gluconeogenesis' genes but positive effect on the expression of 'citrate cycle (TCA cycle' genes. However, calcium lactate stress had positive influence on the expression of 'glycolysis/gluconeogenesis' genes and had minor influence on 'citrate cycle (TCA cycle' genes. Thus, our findings offer new insights into the responses of B. coagulans to different lactate stresses. Notably, our RNA-seq dataset constitute a robust database for investigating the functions of genes induced by lactate stress in the future and identify potential targets for genetic engineering to further improve L-lactic acid production by B. coagulans.

  16. Comparative transcriptome analysis reveals different molecular mechanisms of Bacillus coagulans 2-6 response to sodium lactate and calcium lactate during lactic acid production.

    Science.gov (United States)

    Qin, Jiayang; Wang, Xiuwen; Wang, Landong; Zhu, Beibei; Zhang, Xiaohua; Yao, Qingshou; Xu, Ping

    2015-01-01

    Lactate production is enhanced by adding calcium carbonate or sodium hydroxide during fermentation. However, Bacillus coagulans 2-6 can produce more than 180 g/L L-lactic acid when calcium lactate is accumulated, but less than 120 g/L L-lactic acid when sodium lactate is formed. The molecular mechanisms by which B. coagulans responds to calcium lactate and sodium lactate remain unclear. In this study, comparative transcriptomic methods based on high-throughput RNA sequencing were applied to study gene expression changes in B. coagulans 2-6 cultured in non-stress, sodium lactate stress and calcium lactate stress conditions. Gene expression profiling identified 712 and 1213 significantly regulated genes in response to calcium lactate stress and sodium lactate stress, respectively. Gene ontology assignments of the differentially expressed genes were performed. KEGG pathway enrichment analysis revealed that 'ATP-binding cassette transporters' were significantly affected by calcium lactate stress, and 'amino sugar and nucleotide sugar metabolism' was significantly affected by sodium lactate stress. It was also found that lactate fermentation was less affected by calcium lactate stress than by sodium lactate stress. Sodium lactate stress had negative effect on the expression of 'glycolysis/gluconeogenesis' genes but positive effect on the expression of 'citrate cycle (TCA cycle)' genes. However, calcium lactate stress had positive influence on the expression of 'glycolysis/gluconeogenesis' genes and had minor influence on 'citrate cycle (TCA cycle)' genes. Thus, our findings offer new insights into the responses of B. coagulans to different lactate stresses. Notably, our RNA-seq dataset constitute a robust database for investigating the functions of genes induced by lactate stress in the future and identify potential targets for genetic engineering to further improve L-lactic acid production by B. coagulans.

  17. Comparative Study of Molecular Basket Sorbents Consisting of Polyallylamine and Polyethylenimine Functionalized SBA-15 for CO2 Capture from Flue Gas.

    Science.gov (United States)

    Wang, Dongxiang; Wang, Xiaoxing; Song, Chunshan

    2017-11-17

    Polyallylamine (PAA)-based molecular basket sorbents (MBS) have been studied for CO 2 capture in comparison with polyethylenimine (PEI)-based MBS. The characterizations including N 2 physisorption, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and thermogravimetric analysis (TGA) showed that PAA (M n =15 000) is more rigid and has more steric hindrance inside SBA-15 pores than PEI owing mainly to its different polymer structure. The effects of temperature and PAA loading on the CO 2 sorption capacity of PAA-based MBS have been examined by TGA by using 100 % CO 2 gas stream and compared with PEI/SBA-15. It was found that the capacity of the PAA/SBA-15 sorbent increased with increasing temperature. The optimum capacity of 88 mg CO2  g sorb -1 was obtained at 140 °C for PAA(50)/SBA-15 whereas the optimum sorption temperature was 75 and 90 °C for PEI-I(50)/SBA-15 (PEI-I, M n =423) and PEI-II(50)/SBA-15 (PEI-II, M n =25 000), respectively. The capacity initially increased with the increase of PAA loading and then dropped at high amine contents, owing to the increased diffusion barrier. The highest CO 2 capacity of 109 mg CO2  g sorb -1 was obtained at a PAA loading of 65 wt %, whereas the PAA(50)/SBA-15 sorbent gave the best amine efficiency of 0.23 mol CO2  mol N -1 . The effect of moisture was examined in a fixed-bed flow system with simulated flue gas containing 15 % CO 2 and 4.5 % O 2 in N 2 . It was found that the presence of moisture significantly enhanced CO 2 sorption over PAA(50)/SBA-15 and greatly improved its cyclic stability and regenerability. Compared with PEI/SBA-15, PAA/SBA-15 possesses a better thermal stability and higher resistance to oxidative degradation. However, the CO 2 sorption rate over the PAA(50)/SBA-15 sorbent was much slower. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Spectroscopic investigation on structure (monomer and dimer), molecular characteristics and comparative study on vibrational analysis of picolinic and isonicotinic acids using experimental and theoretical (DFT & IVP) methods

    Science.gov (United States)

    Ramesh, Gaddam; Reddy, Byru Venkatram

    2018-05-01

    In this investigation, the monomeric structure is determined for picolinic and isonicotinic acids based on geometry optimization for one of the four possible conformers and intramolecular hydrogen bond of Osbnd H⋯O using density functional theory (DFT) employing B3LYP functional supplemented with 6-311++G(d,p) basis set. Using this optimized monomeric form, the dimer structure is determined based on minimum energy and length of hydrogen bonds obtained for two possible dimeric forms yielded due to head-to-tail intermolecular Osbnd H⋯N hydrogen bond (dimer 1) linkage and tail-to -tail intermolecular Osbnd H⋯O hydrogen bond (dimer 2) linkage between pyridine ring and carboxyl group. The structure parameters obtained for monomer and dimer forms are in good agreement with the experimental literature values. The vibrational assignments have been made unambiguously for all the vibrations from FTIR and FT-Raman spectra based on the potential energy distribution (PED) and eigen vectors obtained in DFT and inverse vibrational problem (IVP) computations. The rms error between the observed and scaled frequencies is 7.7 and 9.4 cm-1 for PIA and INA, respectively. A 74-element modified valence force field is derived by Wilson's GF matrix method using 58 experimental frequencies of the two molecules in overlay least-squares technique. The average error between observed and computed frequencies by this method is calculated to be 10.39 cm-1. The results of both DFT and IVP computations yielded good agreement between observed and calculated frequencies. The NLO behaviour using hyperpolarizability values; and HOMO and LUMO energies; of the two molecules are investigated by DFT. Charge density distribution and site of chemical reactivity of the molecules are studied by molecular electrostatic surface potential (MESP). Stability of the molecules arising from hyper conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO

  19. Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations.

    Science.gov (United States)

    Ikram, Najmul; Qadir, Muhammad Abdul; Afzal, Muhammad Tanvir

    2018-01-01

    Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic similarity methods, and in protein function prediction. In this research, we investigate the relationship between the two similarity methods. The results suggest absence of a strong correlation between sequence and semantic similarities. There is a large number of proteins with low sequence similarity and high semantic similarity. We observe that Pearson's correlation coefficient is not sufficient to explain the nature of this relationship. Interestingly, the term semantic similarity values above 0 and below 1 do not seem to play a role in improving the correlation. That is, the correlation coefficient depends only on the number of common GO terms in proteins under comparison, and the semantic similarity measurement method does not influence it. Semantic similarity and sequence similarity have a distinct behavior. These findings are of significant effect for future works on protein comparison, and will help understand the semantic similarity between proteins in a better way.

  20. Comparative evaluation of positive tests to Mycobacterium avium subsp. paratuberculosis in clinically healthy sheep and goats in south-west Greece using molecular techniques, serology, and culture.

    Science.gov (United States)

    Ikonomopoulos, John; Balaskas, Christos; Kantzoura, Bagia; Fragiadaki, Eirini; Pavlik, Ivo; Bartos, Milan; Lukas, John C; Gazouli, Maria

    2007-09-01

    Mycobacterium avium subsp. paratuberculosis (MAP) is the cause of paratuberculosis, which affects mainly ruminants although there is a growing concern about its possible implication in Crohn's disease in humans especially in connection with environmental spread and risks to the food chain. Retail cheese may represent a significant source of human exposure to MAP and the aim of this study was to assess MAP status in clinically healthy sheep and goats in Greece, comparing techniques routinely used in the positive diagnosis of the disease. From a total of 30 flocks, 632 sheep and goats had faecal, serum, and whole-blood samples examined by culture, complement fixation test (CFT), and polymerase chain reaction (PCR) targeted at IS900, IS1245, and IS6110. PCR produced positive results in 21% of the animals tested, with 5.6%, 3.9%, and 11.5% being identified as MAP, Mycobacterium avium subsp. avium, and Mycobacterium tuberculosis complex, respectively. CFT produced positive and suspicious results in 4.4% and 14.4% of the cases. Faecal cultures were negative in all but a single case that was identified as restriction fragment length polymorphism (RFLP)-type BC1. Agreement between results obtained by PCR and CFT was poor with isolated cases although an assessment of the MAP positive tests produced similar results for both methods. The findings indicate the need for additional measures of control, although the costs may be substantial if public health protection justifies elimination of MAP from livestock.

  1. Diagnostic molecular microbiology: a 2013 snapshot.

    Science.gov (United States)

    Fairfax, Marilynn Ransom; Salimnia, Hossein

    2013-12-01

    Molecular testing has a large and increasing role in the diagnosis of infectious diseases. It has evolved significantly since the first probe tests were FDA approved in the early 1990s. This article highlights the uses of molecular techniques in diagnostic microbiology, including "older," as well as innovative, probe techniques, qualitative and quantitative RT-PCR, highly multiplexed PCR panels, some of which use sealed microfluidic test cartridges, MALDI TOF, and nuclear magnetic resonance. Tests are grouped together by technique and target. Tests with similar roles for similar analytes are compared with respect to benefits, drawbacks, and possible problems. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Similarity search of business process models

    NARCIS (Netherlands)

    Dumas, M.; García-Bañuelos, L.; Dijkman, R.M.

    2009-01-01

    Similarity search is a general class of problems in which a given object, called a query object, is compared against a collection of objects in order to retrieve those that most closely resemble the query object. This paper reviews recent work on an instance of this class of problems, where the

  3. Music Retrieval based on Melodic Similarity

    NARCIS (Netherlands)

    Typke, R.

    2007-01-01

    This thesis introduces a method for measuring melodic similarity for notated music such as MIDI files. This music search algorithm views music as sets of notes that are represented as weighted points in the two-dimensional space of time and pitch. Two point sets can be compared by calculating how

  4. Revisiting Inter-Genre Similarity

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Gouyon, Fabien

    2013-01-01

    We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...... not perform well, even for data that satisfies all its assumptions....

  5. Glove boxes and similar containments

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    According to the present invention a glove box or similar containment is provided with an exhaust system including a vortex amplifier venting into the system, the vortex amplifier also having its main inlet in fluid flow connection with the containment and a control inlet in fluid flow connection with the atmosphere outside the containment. (U.S.)

  6. Meningiomas: A Comparative Study of 68Ga-DOTATOC, 68Ga-DOTANOC and 68Ga-DOTATATE for Molecular Imaging in Mice

    Science.gov (United States)

    Soto-Montenegro, María Luisa; Peña-Zalbidea, Santiago; Mateos-Pérez, Jose María; Oteo, Marta; Romero, Eduardo; Morcillo, Miguel Ángel; Desco, Manuel

    2014-01-01

    Purpose The goal of this study was to compare the tumor uptake kinetics and diagnostic value of three 68Ga-DOTA-labeled somatostatin analogues (68Ga-DOTATOC, 68Ga-DOTANOC, and 68Ga-DOTATATE) using PET/CT in a murine model with subcutaneous meningioma xenografts. Methods The experiment was performed with 16 male NUDE NU/NU mice bearing xenografts of a human meningioma cell line (CH-157MN). 68Ga-DOTATOC, 68Ga-DOTANOC, and 68Ga-DOTATATE were produced in a FASTLab automated platform. Imaging was performed on an Argus small-animal PET/CT scanner. The SUVmax of the liver and muscle, and the tumor-to-liver (T/L) and tumor-to-muscle (T/M) SUV ratios were computed. Kinetic analysis was performed using Logan graphical analysis for a two-tissue reversible compartmental model, and the volume of distribution (Vt) was determined. Results Hepatic SUVmax and Vt were significantly higher with 68Ga-DOTANOC than with 68Ga-DOTATOC and 68Ga-DOTATATE. No significant differences between tracers were found for SUVmax in tumor or muscle. No differences were found in the T/L SUV ratio between 68Ga-DOTATATE and 68Ga-DOTATOC, both of which had a higher fraction than 68Ga-DOTANOC. The T/M SUV ratio was significantly higher with 68Ga-DOTATATE than with 68Ga-DOTATOC and 68Ga-DOTANOC. The Vt for tumor was higher with 68Ga-DOTATATE than with 68Ga-DOTANOC and relatively similar to that of 68Ga-DOTATOC. Conclusions This study demonstrates, for the first time, the ability of the three radiolabeled somatostatin analogues tested to image a human meningioma cell line. Although Vt was relatively similar with 68Ga-DOTATATE and 68Ga-DOTATOC, uptake was higher with 68Ga-DOTATATE in the tumor than with 68Ga-DOTANOC and 68Ga-DOTATOC, suggesting a higher diagnostic value of 68Ga-DOTATATE for detecting meningiomas. PMID:25369268

  7. Meningiomas: a comparative study of 68Ga-DOTATOC, 68Ga-DOTANOC and 68Ga-DOTATATE for molecular imaging in mice.

    Directory of Open Access Journals (Sweden)

    María Luisa Soto-Montenegro

    Full Text Available The goal of this study was to compare the tumor uptake kinetics and diagnostic value of three (68Ga-DOTA-labeled somatostatin analogues ((68Ga-DOTATOC, (68Ga-DOTANOC, and (68Ga-DOTATATE using PET/CT in a murine model with subcutaneous meningioma xenografts.The experiment was performed with 16 male NUDE NU/NU mice bearing xenografts of a human meningioma cell line (CH-157MN. (68Ga-DOTATOC, (68Ga-DOTANOC, and (68Ga-DOTATATE were produced in a FASTLab automated platform. Imaging was performed on an Argus small-animal PET/CT scanner. The SUVmax of the liver and muscle, and the tumor-to-liver (T/L and tumor-to-muscle (T/M SUV ratios were computed. Kinetic analysis was performed using Logan graphical analysis for a two-tissue reversible compartmental model, and the volume of distribution (Vt was determined.Hepatic SUVmax and Vt were significantly higher with (68Ga-DOTANOC than with (68Ga-DOTATOC and (68Ga-DOTATATE. No significant differences between tracers were found for SUVmax in tumor or muscle. No differences were found in the T/L SUV ratio between (68Ga-DOTATATE and (68Ga-DOTATOC, both of which had a higher fraction than (68Ga-DOTANOC. The T/M SUV ratio was significantly higher with (68Ga-DOTATATE than with (68Ga-DOTATOC and (68Ga-DOTANOC. The Vt for tumor was higher with (68Ga-DOTATATE than with (68Ga-DOTANOC and relatively similar to that of (68Ga-DOTATOC.This study demonstrates, for the first time, the ability of the three radiolabeled somatostatin analogues tested to image a human meningioma cell line. Although Vt was relatively similar with (68Ga-DOTATATE and (68Ga-DOTATOC, uptake was higher with (68Ga-DOTATATE in the tumor than with (68Ga-DOTANOC and (68Ga-DOTATOC, suggesting a higher diagnostic value of (68Ga-DOTATATE for detecting meningiomas.

  8. How reliably can northeast Atlantic sand lances of the genera Ammodytes and Hyperoplus be distinguished? A comparative application of morphological and molecular methods

    Directory of Open Access Journals (Sweden)

    Ralf Thiel

    2016-09-01

    Full Text Available Accurate stock assessments for each of the dominant species of sand lances in the northeast Atlantic Ocean and adjacent areas are not available due to the lack of a reliable identification procedure; therefore, appropriate measures of fisheries management or conservation of sand lances cannot be implemented. In this study, detailed morphological and molecular features are assessed to discriminate between four species of sand lances belonging to the genera Ammodytes and Hyperoplus. Morphological characters described by earlier authors as useful for identification of the genera are confirmed, and two additional distinguishing characters are added. A combination of the following morphological characters is recommended to distinguish between the genera Hyperoplus and Ammodytes: the protrusibility of the premaxillae, the presence of hooked ends of the prevomer, the number of dermal plicae, and the pectoral-fin length as a percentage of the standard length. The discriminant function analysis revealed that morphometric data are not very useful to distinguish the species of each of the two genera. The following meristic characters improve the separation of H. lanceolatus from H. immaculatus: the number of lower arch gill rakers, total number of gill rakers, numbers of caudal vertebrae and total vertebrae, and numbers of dorsal-fin and anal-fin rays. It is confirmed that A. tobianus differs from A. marinus by its belly scales that are organised in tight chevrons, scales which are present over the musculature at the base of the caudal fin, as well as by the lower numbers of dermal plicae, dorsal-fin rays, and total vertebrae. In contrast to the morphological data, mitochondrial COI sequences (DNA barcodes failed to separate unambiguously the four investigated species. Ammodytes tobianus and H. lanceolatus showed an overlap between intraspecific and interspecific K2P genetic distances and cannot be reliably distinguished using the common DNA barcoding

  9. Guar gum and scleroglucan interactions with borax: experimental and theoretical studies of an unexpected similarity.

    Science.gov (United States)

    Bocchinfuso, Gianfranco; Mazzuca, Claudia; Sandolo, Chiara; Margheritelli, Silvia; Alhaique, Franco; Coviello, Tommasina; Palleschi, Antonio

    2010-10-21

    Guar gum is a galactomannan that assumes a very flexible conformation in solution, while Scleroglucan is a very rigid polysaccharide that dissolves in water as triple helices. Both polymers can form gels in the presence of borax. Despite their structural differences, the freeze-dried gel systems of both polymers, when compressed to form tablets, show a peculiar anisotropic swelling in water that reflects an amazing similarity in terms of their molecular properies. In this paper the behavior of the Guar/borax gel is compared with that of Scleroglucan/borax. The macroscopic properties of the two systems were characterized in terms of rheological measurements. Atomic force microscopy images and molecular dynamics simulation allowed to evaluate, at molecular level, the effect of borax addition to the Guar polymer. Both experiments show that an increasing of the polymer rigidity is produced by borax. The role played by galactose in the side chain was also discussed.

  10. [Similarity system theory to evaluate similarity of chromatographic fingerprints of traditional Chinese medicine].

    Science.gov (United States)

    Liu, Yongsuo; Meng, Qinghua; Jiang, Shumin; Hu, Yuzhu

    2005-03-01

    The similarity evaluation of the fingerprints is one of the most important problems in the quality control of the traditional Chinese medicine (TCM). Similarity measures used to evaluate the similarity of the common peaks in the chromatogram of TCM have been discussed. Comparative studies were carried out among correlation coefficient, cosine of the angle and an improved extent similarity method using simulated data and experimental data. Correlation coefficient and cosine of the angle are not sensitive to the differences of the data set. They are still not sensitive to the differences of the data even after normalization. According to the similarity system theory, an improved extent similarity method was proposed. The improved extent similarity is more sensitive to the differences of the data sets than correlation coefficient and cosine of the angle. And the character of the data sets needs not to be changed compared with log-transformation. The improved extent similarity can be used to evaluate the similarity of the chromatographic fingerprints of TCM.

  11. An Alfven eigenmode similarity experiment

    International Nuclear Information System (INIS)

    Heidbrink, W W; Fredrickson, E; Gorelenkov, N N; Hyatt, A W; Kramer, G; Luo, Y

    2003-01-01

    The major radius dependence of Alfven mode stability is studied by creating plasmas with similar minor radius, shape, magnetic field (0.5 T), density (n e ≅3x10 19 m -3 ), electron temperature (1.0 keV) and beam ion population (near-tangential 80 keV deuterium injection) on both NSTX and DIII-D. The major radius of NSTX is half the major radius of DIII-D. The super-Alfvenic beam ions that drive the modes have overlapping values of v f /v A in the two devices. Observed beam-driven instabilities include toroidicity-induced Alfven eigenmodes (TAE). The stability threshold for the TAE is similar in the two devices. As expected theoretically, the most unstable toroidal mode number n is larger in DIII-D

  12. Similarity joins in relational database systems

    CERN Document Server

    Augsten, Nikolaus

    2013-01-01

    State-of-the-art database systems manage and process a variety of complex objects, including strings and trees. For such objects equality comparisons are often not meaningful and must be replaced by similarity comparisons. This book describes the concepts and techniques to incorporate similarity into database systems. We start out by discussing the properties of strings and trees, and identify the edit distance as the de facto standard for comparing complex objects. Since the edit distance is computationally expensive, token-based distances have been introduced to speed up edit distance comput

  13. Serological & molecular diagnostic surveys combined with examining hematological profiles suggest increased levels of infection & hematological response of cattle to babesiosis infections compared to native buffaloes in Egypt

    Science.gov (United States)

    Background: Babesiosis threatens the development of the cattle and buffaloes industries in Egypt and improved control is needed. The main objectives of this study are surveying the presence of bovine babesiosis in distinct selected bovine and buffalo populations in Egypt using novel molecular and pr...

  14. Molecular dynamics simulations of lipid bilayers : major artifacts due to truncating electrostatic interactions

    NARCIS (Netherlands)

    Patra, M.; Karttunen, M.E.J.; Hyvönen, M.T.; Falck, E.; Lindqvist, P.; Vattulainen, I.

    2003-01-01

    We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using

  15. Similarity analysis between quantum images

    Science.gov (United States)

    Zhou, Ri-Gui; Liu, XingAo; Zhu, Changming; Wei, Lai; Zhang, Xiafen; Ian, Hou

    2018-06-01

    Similarity analyses between quantum images are so essential in quantum image processing that it provides fundamental research for the other fields, such as quantum image matching, quantum pattern recognition. In this paper, a quantum scheme based on a novel quantum image representation and quantum amplitude amplification algorithm is proposed. At the end of the paper, three examples and simulation experiments show that the measurement result must be 0 when two images are same, and the measurement result has high probability of being 1 when two images are different.

  16. Similarity flows in relativistic hydrodynamics

    International Nuclear Information System (INIS)

    Blaizot, J.P.; Ollitrault, J.Y.

    1986-01-01

    In ultra-relativistic heavy ion collisions, one expects in particular to observe a deconfinement transition leading to a formation of quark gluon plasma. In the framework of the hydrodynamic model, experimental signatures of such a plasma may be looked for as observable consequences of a first order transition on the evolution of the system. In most of the possible scenario, the phase transition is accompanied with discontinuities in the hydrodynamic flow, such as shock waves. The method presented in this paper has been developed to treat without too much numerical effort such discontinuous flow. It relies heavily on the use of similarity solutions of the hydrodynamic equations

  17. Comparing and correlating solubility parameters governing the self-assembly of molecular gels using 1,3:2,4-dibenzylidene sorbitol as the gelator.

    Science.gov (United States)

    Lan, Yaqi; Corradini, Maria G; Liu, Xia; May, Tim E; Borondics, Ferenc; Weiss, Richard G; Rogers, Michael A

    2014-12-02

    Solvent properties play a central role in mediating the aggregation and self-assembly of molecular gelators and their growth into fibers. Numerous attempts have been made to correlate the solubility parameters of solvents and gelation abilities of molecular gelators, but a comprehensive comparison of the most important parameters has yet to appear. Here, the degree to which partition coefficients (log P), Henry's law constants (HLC), dipole moments, static relative permittivities (ε(r)), solvatochromic E(T)(30) parameters, Kamlet-Taft parameters (β, α, and π), Catalan's solvatochromic parameters (SPP, SB, and SA), Hildebrand solubility parameters (δ(i)), and Hansen solubility parameters (δ(p), δ(d), δ(h)) and the associated Hansen distance (R(ij)) of 62 solvents (covering a wide range of properties) can be correlated with the self-assembly and gelation of 1,3:2,4-dibenzylidene sorbitol (DBS) gelation, a classic molecular gelator, is assessed systematically. The approach presented describes the basis for each of the parameters and how it can be applied. As such, it is an instructional blueprint for how to assess the appropriate type of solvent parameter for use with other molecular gelators as well as with molecules forming other types of self-assembled materials. The results also reveal several important insights into the factors favoring the gelation of solvents by DBS. The ability of a solvent to accept or donate a hydrogen bond is much more important than solvent polarity in determining whether mixtures with DBS become solutions, clear gels, or opaque gels. Thermodynamically derived parameters could not be correlated to the physical properties of the molecular gels unless they were dissected into their individual HSPs. The DBS solvent phases tend to cluster in regions of Hansen space and are highly influenced by the hydrogen-bonding HSP, δ(h). It is also found that the fate of this molecular gelator, unlike that of polymers, is influenced not only by

  18. A single center retrospective cohort study comparing low-molecular-weight heparins to direct oral anticoagulants for the treatment of venous thromboembolism in patients with cancer - A real world experience.

    Science.gov (United States)

    Phelps, Megan K; Wiczer, Tracy E; Erdeljac, H Paige; Van Deusen, Kelsey R; Porter, Kyle; Philips, Gary; Wang, Tzu-Fei

    2018-01-01

    Introduction Low-molecular-weight heparins are the standard treatment for cancer-associated thrombosis. Recently, direct oral anticoagulants are a new option for thrombosis treatment; however, data supporting the use of direct oral anticoagulants for cancer-associated thrombosis are limited. Objectives The primary objective of this study was to determine the rate of recurrent cancer-associated thrombosis and major bleeding within 6 months of starting either low-molecular-weight heparin or direct oral anticoagulant for treatment of cancer-associated thrombosis. Secondary objectives were to determine the rates of clinically relevant-non-major bleeding and all-cause mortality. Patients/methods This is a retrospective cohort study including adults with cancer-associated thrombosis treated with low-molecular-weight heparin or direct oral anticoagulant between 2010 and 2016 at the Ohio State University. Medical records were reviewed for 6 months after initiation of anticoagulation or until the occurrence of recurrent cancer-associated thrombosis, major bleeding, cessation of anticoagulation of interest, or death, whichever occurred first. Results Four hundred and eighty patients were included (290 low-molecular-weight heparin and 190 direct oral anticoagulant). Patients treated with direct oral anticoagulant were found to carry "lower risk" features including cancer with lower VTE risk and lower rate of metastatic disease. After adjustment for baseline differences, there was no significant difference in the rate of recurrent cancer-associated thrombosis (7.2% low-molecular-weight heparin vs 6.3% direct oral anticoagulant, p = 0.71) or major bleeding (7.6% low-molecular-weight heparin vs 2.6% direct oral anticoagulant, p = 0.08). Conclusions Our study demonstrates that in a select population of cancer patients with VTE, direct oral anticoagulant use can be as effective and safe compared to the standard therapy with low-molecular-weight heparin.

  19. Self-similar gravitational clustering

    International Nuclear Information System (INIS)

    Efstathiou, G.; Fall, S.M.; Hogan, C.

    1979-01-01

    The evolution of gravitational clustering is considered and several new scaling relations are derived for the multiplicity function. These include generalizations of the Press-Schechter theory to different densities and cosmological parameters. The theory is then tested against multiplicity function and correlation function estimates for a series of 1000-body experiments. The results are consistent with the theory and show some dependence on initial conditions and cosmological density parameter. The statistical significance of the results, however, is fairly low because of several small number effects in the experiments. There is no evidence for a non-linear bootstrap effect or a dependence of the multiplicity function on the internal dynamics of condensed groups. Empirical estimates of the multiplicity function by Gott and Turner have a feature near the characteristic luminosity predicted by the theory. The scaling relations allow the inference from estimates of the galaxy luminosity function that galaxies must have suffered considerable dissipation if they originally formed from a self-similar hierarchy. A method is also developed for relating the multiplicity function to similar measures of clustering, such as those of Bhavsar, for the distribution of galaxies on the sky. These are shown to depend on the luminosity function in a complicated way. (author)

  20. Comparative study of the interactions between bisphenol-A and its endocrine disrupting analogues with bovine serum albumin using multi-spectroscopic and molecular docking studies.

    Science.gov (United States)

    Ikhlas, Shoeb; Usman, Afia; Ahmad, Masood

    2018-04-24

    Interaction studies of bisphenol analogues; biphenol-A (BPA), bisphenol-B (BPB), and bisphenol-F (BPF) with bovine serum albumin (BSA) were performed using multi-spectroscopic and molecular docking studies at the protein level. The mechanism of binding of bisphenols with BSA was dynamic in nature. SDS refolding experiments demonstrated no stabilization of BSA structure denatured by BPB, however, BSA denatured by BPA and BPF was found to get stabilized. Also, CD spectra and molecular docking studies revealed that BPB bound more strongly and induced more conformational changes in BSA in comparison to BPA. Hence, this study throws light on the replacement of BPA by its analogues and whether the replacement is associated with a possible risk, raising a doubt that perhaps BPB is not a good substitute of BPA.

  1. Identifying mechanistic similarities in drug responses

    KAUST Repository

    Zhao, C.

    2012-05-15

    Motivation: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.Results: We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge. © The Author 2012. Published by Oxford University Press. All rights reserved.

  2. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

    In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

  3. Seniority bosons from similarity transformations

    International Nuclear Information System (INIS)

    Geyer, H.B.

    1986-01-01

    The requirement of associating in the boson space seniority with twice the number of non-s bosons defines a similarity transformation which re-expresses the Dyson pair boson images in terms of seniority bosons. In particular the fermion S-pair creation operator is mapped onto an operator which, unlike the pair boson image, does not change the number of non-s bosons. The original results of Otsuka, Arima and Iachello are recovered by this procedure while at the same time they are generalized to include g-bosons or even bosons with J>4 as well as any higher order boson terms. Furthermore the seniority boson images are valid for an arbitrary number of d- or g-bosons - a result which is not readily obtainable within the framework of the usual Marumori- or OAI-method

  4. Multidimensional Scaling Visualization using Parametric Similarity Indices

    OpenAIRE

    Machado, J. A. Tenreiro; Lopes, António M.; Galhano, A.M.

    2015-01-01

    In this paper, we apply multidimensional scaling (MDS) and parametric similarity indices (PSI) in the analysis of complex systems (CS). Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, an...

  5. Predicting the performance of fingerprint similarity searching.

    Science.gov (United States)

    Vogt, Martin; Bajorath, Jürgen

    2011-01-01

    Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

  6. Comparative molecular-orbital and atomic-orbital study of electron transfer and excitation in He++Na(3s) collisions at energies of 0.05 to 20 keV/amu

    International Nuclear Information System (INIS)

    Fritsch, W.; Kimura, M.; Lane, N.F.

    1990-01-01

    Electron transfer and excitation in 0.05- to 20-keV/amu He + +Na(3s) collisions is studied theoretically within the close-coupling method with two-electron molecular- and atomic-orbital expansion basis sets. Results agree with the trend of other information on this system. Remaining discrepancies that are larger than those in similar contemporary studies of one-electron systems are discussed with reference to the convergence of this two-electron study. Results for the integral alignment parameter A 20 are also presented as a guideline for future experimental study

  7. Alaska, Gulf spills share similarities

    International Nuclear Information System (INIS)

    Usher, D.

    1991-01-01

    The accidental Exxon Valdez oil spill in Alaska and the deliberate dumping of crude oil into the Persian Gulf as a tactic of war contain both glaring differences and surprising similarities. Public reaction and public response was much greater to the Exxon Valdez spill in pristine Prince William Sound than to the war-related tragedy in the Persian Gulf. More than 12,000 workers helped in the Alaskan cleanup; only 350 have been involved in Kuwait. But in both instances, environmental damages appear to be less than anticipated. Natures highly effective self-cleansing action is primarily responsible for minimizing the damages. One positive action growing out of the two incidents is increased international cooperation and participation in oil-spill clean-up efforts. In 1990, in the aftermath of the Exxon Valdez spill, 94 nations signed an international accord on cooperation in future spills. The spills can be historic environmental landmarks leading to creation of more sophisticated response systems worldwide

  8. IntelliGO: a new vector-based semantic similarity measure including annotation origin

    Directory of Open Access Journals (Sweden)

    Devignes Marie-Dominique

    2010-12-01

    Full Text Available Abstract Background The Gene Ontology (GO is a well known controlled vocabulary describing the biological process, molecular function and cellular component aspects of gene annotation. It has become a widely used knowledge source in bioinformatics for annotating genes and measuring their semantic similarity. These measures generally involve the GO graph structure, the information content of GO aspects, or a combination of both. However, only a few of the semantic similarity measures described so far can handle GO annotations differently according to their origin (i.e. their evidence codes. Results We present here a new semantic similarity measure called IntelliGO which integrates several complementary properties in a novel vector space model. The coefficients associated with each GO term that annotates a given gene or protein include its information content as well as a customized value for each type of GO evidence code. The generalized cosine similarity measure, used for calculating the dot product between two vectors, has been rigorously adapted to the context of the GO graph. The IntelliGO similarity measure is tested on two benchmark datasets consisting of KEGG pathways and Pfam domains grouped as clans, considering the GO biological process and molecular function terms, respectively, for a total of 683 yeast and human genes and involving more than 67,900 pair-wise comparisons. The ability of the IntelliGO similarity measure to express the biological cohesion of sets of genes compares favourably to four existing similarity measures. For inter-set comparison, it consistently discriminates between distinct sets of genes. Furthermore, the IntelliGO similarity measure allows the influence of weights assigned to evidence codes to be checked. Finally, the results obtained with a complementary reference technique give intermediate but correct correlation values with the sequence similarity, Pfam, and Enzyme classifications when compared to

  9. The efficiency of similarity-focused comparisons in person perception.

    Science.gov (United States)

    Corcoran, Katja

    2013-01-01

    Comparison processes are ubiquitous in person perception. Comparative thinking can follow two routes: People either search for similarities or for dissimilarities while comparing. Which of these two routes is more efficient? Previous research indicates that people could compare two geometrical figures faster if they focused on similarities rather than dissimilarities. I examine comparisons of people and measure the consumption of cognitive resources as indicator for efficiency. The results confirm an efficiency-advantage of similarity-focused comparisons for social stimuli.

  10. Molecular scale

    Directory of Open Access Journals (Sweden)

    Christopher H. Childers

    2016-03-01

    Full Text Available This manuscript demonstrates the molecular scale cure rate dependence of di-functional epoxide based thermoset polymers cured with amines. A series of cure heating ramp rates were used to determine the influence of ramp rate on the glass transition temperature (Tg and sub-Tg transitions and the average free volume hole size in these systems. The networks were comprised of 3,3′-diaminodiphenyl sulfone (33DDS and diglycidyl ether of bisphenol F (DGEBF and were cured at ramp rates ranging from 0.5 to 20 °C/min. Differential scanning calorimetry (DSC and NIR spectroscopy were used to explore the cure ramp rate dependence of the polymer network growth, whereas broadband dielectric spectroscopy (BDS and free volume hole size measurements were used to interrogate networks’ molecular level structural variations upon curing at variable heating ramp rates. It was found that although the Tg of the polymer matrices was similar, the NIR and DSC measurements revealed a strong correlation for how these networks grow in relation to the cure heating ramp rate. The free volume analysis and BDS results for the cured samples suggest differences in the molecular architecture of the matrix polymers due to cure heating rate dependence.

  11. Comparing Laser Desorption Ionization and Atmospheric Pressure Photoionization Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry To Characterize Shale Oils at the Molecular Level

    Science.gov (United States)

    Cho, Yunjo; Jin, Jang Mi; Witt, Matthias; Birdwell, Justin E.; Na, Jeong-Geol; Roh, Nam-Sun; Kim, Sunghwan

    2013-01-01

    Laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to analyze shale oils. Previous work showed that LDI is a sensitive ionization technique for assessing aromatic nitrogen compounds, and oils generated from Green River Formation oil shales are well-documented as being rich in nitrogen. The data presented here demonstrate that LDI is effective in ionizing high-double-bond-equivalent (DBE) compounds and, therefore, is a suitable method for characterizing compounds with condensed structures. Additionally, LDI generates radical cations and protonated ions concurrently, the distribution of which depends upon the molecular structures and elemental compositions, and the basicity of compounds is closely related to the generation of protonated ions. This study demonstrates that LDI FT-ICR MS is an effective ionization technique for use in the study of shale oils at the molecular level. To the best of our knowledge, this is the first time that LDI FT-ICR MS has been applied to shale oils.

  12. Measuring structural similarity in large online networks.

    Science.gov (United States)

    Shi, Yongren; Macy, Michael

    2016-09-01

    Structural similarity based on bipartite graphs can be used to detect meaningful communities, but the networks have been tiny compared to massive online networks. Scalability is important in applications involving tens of millions of individuals with highly skewed degree distributions. Simulation analysis holding underlying similarity constant shows that two widely used measures - Jaccard index and cosine similarity - are biased by the distribution of out-degree in web-scale networks. However, an alternative measure, the Standardized Co-incident Ratio (SCR), is unbiased. We apply SCR to members of Congress, musical artists, and professional sports teams to show how massive co-following on Twitter can be used to map meaningful affiliations among cultural entities, even in the absence of direct connections to one another. Our results show how structural similarity can be used to map cultural alignments and demonstrate the potential usefulness of social media data in the study of culture, politics, and organizations across the social and behavioral sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Retrospective group fusion similarity search based on eROCE evaluation metric.

    Science.gov (United States)

    Avram, Sorin I; Crisan, Luminita; Bora, Alina; Pacureanu, Liliana M; Avram, Stefana; Kurunczi, Ludovic

    2013-03-01

    In this study, a simple evaluation metric, denoted as eROCE was proposed to measure the early enrichment of predictive methods. We demonstrated the superior robustness of eROCE compared to other known metrics throughout several active to inactive ratios ranging from 1:10 to 1:1000. Group fusion similarity search was investigated by varying 16 similarity coefficients, five molecular representations (binary and non-binary) and two group fusion rules using two reference structure set sizes. We used a dataset of 3478 actives and 43,938 inactive molecules and the enrichment was analyzed by means of eROCE. This retrospective study provides optimal similarity search parameters in the case of ALDH1A1 inhibitors. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-06-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  15. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-03-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  16. Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures.

    Science.gov (United States)

    Zhang, Bijun; Vogt, Martin; Maggiora, Gerald M; Bajorath, Jürgen

    2015-10-01

    Chemical space networks (CSNs) have recently been introduced as an alternative to other coordinate-free and coordinate-based chemical space representations. In CSNs, nodes represent compounds and edges pairwise similarity relationships. In addition, nodes are annotated with compound property information such as biological activity. CSNs have been applied to view biologically relevant chemical space in comparison to random chemical space samples and found to display well-resolved topologies at low edge density levels. The way in which molecular similarity relationships are assessed is an important determinant of CSN topology. Previous CSN versions were based on numerical similarity functions or the assessment of substructure-based similarity. Herein, we report a new CSN design that is based upon combined numerical and substructure similarity evaluation. This has been facilitated by calculating numerical similarity values on the basis of maximum common substructures (MCSs) of compounds, leading to the introduction of MCS-based CSNs (MCS-CSNs). This CSN design combines advantages of continuous numerical similarity functions with a robust and chemically intuitive substructure-based assessment. Compared to earlier version of CSNs, MCS-CSNs are characterized by a further improved organization of local compound communities as exemplified by the delineation of drug-like subspaces in regions of biologically relevant chemical space.

  17. The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

    Directory of Open Access Journals (Sweden)

    Ané Jean-Michel

    2002-01-01

    Full Text Available Abstract Background The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315 on the basis of their molecular and phenotypic polymorphism. Results An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16. Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa, implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7. Conclusions These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant.

  18. Comparative MiRNA Expressional Profiles and Molecular Networks in Human Small Bowel Tissues of Necrotizing Enterocolitis and Spontaneous Intestinal Perforation.

    Directory of Open Access Journals (Sweden)

    Pak Cheung Ng

    Full Text Available Necrotizing enterocolitis (NEC and spontaneous intestinal perforation (SIP are acute intestinal conditions which could result in mortality and severe morbidity in preterm infants. Our objective was to identify dysregulated micro-RNAs (miRNAs in small bowel tissues of NEC and SIP, and their possible roles in disease pathophysiology.We performed differential miRNA arrays on tissues of NEC (n = 4, SIP (n = 4 and surgical-control (Surg-CTL; n = 4, and validated target miRNAs by qPCR (n = 10 each group. The association of target miRNAs with 52 dysregulated mRNAs was investigated by bioinformatics on functional and base-pair sequence algorithms, and correlation in same tissue samples.We presented the first miRNA profiles of NEC, SIP and Surg-CTL intestinal tissues in preterm infants. Of 28 validated miRNAs, 21 were significantly different between NEC or SIP and Surg-CTL. Limited overlapping in the aberrant expression of miRNAs between NEC and SIP indicated their distinct molecular mechanisms. A proposed network of dysregulated miRNA/mRNA pairs in NEC suggested interaction at bacterial receptor TLR4 (miR-31, miR-451, miR-203, miR-4793-3p, mediated via key transcription factors NFKB2 (miR-203, AP-1/FOSL1 (miR-194-3p, FOXA1 (miR-21-3p, miR-431 and miR-1290 and HIF1A (miR-31, and extended downstream to pathways of angiogenesis, arginine metabolism, cell adhesion and chemotaxis, extracellular matrix remodeling, hypoxia/oxidative stress, inflammation and muscle contraction. In contrast, upregulation of miR-451 and miR-223 in SIP suggested modulation of G-protein-mediated muscle contraction.The robust response of miRNA dysregulation in NEC and SIP, and concerted involvement of specific miRNAs in the molecular networks indicated their crucial roles in mucosa integrity and disease pathophysiology.

  19. Comparative study by infrared spectrometry of the behaviour of Y-H and Y-D groups. Valencies frequency and molecular association constants

    International Nuclear Information System (INIS)

    Leicknam, J.P.

    1966-02-01

    In the first part of the report a comparison is made of the relative lowering of the frequencies determined using homologous hydrogenated and deuterated vibrators dissolved in various solvents, with the gaseous state as reference. It is confirmed that one always has (Δν/ν g ) YH ≥ (Δν/ν g ) YD . Certain results suggest the existence of interactions between vibrational and electronic states, but the different behaviours of OH and OD molecules and of NH and deuterated-N compounds show that the phenomenon is complex. In the second part of the report a quantitative examination is made of about a hundred molecular associations which are formed in solution in an inert solvent by means of hydrogen or deuterium bridges. The proton and deuton donor auto-associations are studied first of all, the association constants K H are then determined for the proton donors with various acceptors, as are the K D /K H ratios obtained after partial substitution in these donors of the hydrogen by deuterium. The results show that it is necessary to distinguish thermo-dynamic effects (which can be calculated when all frequencies of the free dynamic and complexed molecules, are known) and chemical effects connected with the nature of the donors and acceptors; among these latter, the possible formation of 'ionic pairs' has without doubt a great influence on the direction of the isotopic effect. (author) [fr

  20. Comparative Infection Progress Analysis of Lettuce big-vein virus and Mirafiori lettuce virus in Lettuce Crops by Developed Molecular Diagnosis Techniques.

    Science.gov (United States)

    Navarro, Jose A; Botella, Francisco; Maruhenda, Antonio; Sastre, Pedro; Sánchez-Pina, M Amelia; Pallas, Vicente

    2004-05-01

    ABSTRACT Nonisotopic molecular dot blot hybridization technique and multiplex reverse transcription-polymerase chain reaction assay for the specific detection of Lettuce big-vein virus (LBVV) and Mirafiori lettuce virus (MiLV) in lettuce tissue were developed. Both procedures were suitable for the specific detection of both viruses in a range of naturally infected lettuce plants from various Spanish production areas and seven different cultivars. The study of the distribution of both viruses in the plant revealed that the highest concentration of LBVV and MiLV occurred in roots and old leaves, respectively. LBVV infection progress in a lettuce production area was faster than that observed for MiLV. In spite of different rates of virus infection progress, most lettuce plants became infected with both viruses about 100 days posttransplant. The appearance of both viruses in lettuce crops was preceded by a peak in the concentration of resting spores and zoosporangia of the fungus vector Olpidium brassicae in lettuce roots.

  1. A comparative study of the enhancement of molecular emission in a spatially confined plume through optical emission spectroscopy and probe beam deflection measurements

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Dayu; Liang, Peipei; Wu, Jiada; Xu, Ning; Ying, Zhifeng; Sun, Jian, E-mail: jsun@fudan.edu.cn

    2013-01-01

    The spatial confinement effects of shock wave on the expansion of a carbon plume induced by pulsed laser ablation of graphite in air and the enhancement of the plume emission were studied by optical emission spectroscopy and probe beam deflection measurements. A metal disk was set in the way of the ablation-generated shock wave to block and reflect the supersonically propagating shock wave. The reflected shock wave propagated backwards and confined the expanding plume. The optical emission of CN molecules was enhanced in contrast to the case without the block disk and the emission enhancement was dependent on the position of the disk. Based on the results of time-integrated and -resolved optical emission spectroscopy, and the time- and space-resolved probe beam deflection measurements, the processes occurring in the plume were discussed and the mechanisms responsible for the enhancement of molecular emission in the spatially confined plume were investigated. - Highlights: ► Spatial confinement and optical emission enhancement of carbon plume were studied. ► Ablation-generated shockwave propagating in air was reflected by a block disk. ► The effects of reflected shockwave on the emission enhancement were confirmed. ► The reflect shockwave confined the carbon plume and enhanced the plume emission.

  2. A comparative study of the enhancement of molecular emission in a spatially confined plume through optical emission spectroscopy and probe beam deflection measurements

    International Nuclear Information System (INIS)

    Ding, Dayu; Liang, Peipei; Wu, Jiada; Xu, Ning; Ying, Zhifeng; Sun, Jian

    2013-01-01

    The spatial confinement effects of shock wave on the expansion of a carbon plume induced by pulsed laser ablation of graphite in air and the enhancement of the plume emission were studied by optical emission spectroscopy and probe beam deflection measurements. A metal disk was set in the way of the ablation-generated shock wave to block and reflect the supersonically propagating shock wave. The reflected shock wave propagated backwards and confined the expanding plume. The optical emission of CN molecules was enhanced in contrast to the case without the block disk and the emission enhancement was dependent on the position of the disk. Based on the results of time-integrated and -resolved optical emission spectroscopy, and the time- and space-resolved probe beam deflection measurements, the processes occurring in the plume were discussed and the mechanisms responsible for the enhancement of molecular emission in the spatially confined plume were investigated. - Highlights: ► Spatial confinement and optical emission enhancement of carbon plume were studied. ► Ablation-generated shockwave propagating in air was reflected by a block disk. ► The effects of reflected shockwave on the emission enhancement were confirmed. ► The reflect shockwave confined the carbon plume and enhanced the plume emission

  3. A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics.

    Science.gov (United States)

    Tirler, Andreas O; Hofer, Thomas S

    2015-07-09

    Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.

  4. Molecular Vibration-Activity Relationship in the Agonism of Adenosine Receptors

    OpenAIRE

    Chee, Hyun Keun; Oh, S. June

    2013-01-01

    The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated by structure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. The resulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram result produced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study of adenosine ...

  5. Venous thromboembolism prophylaxis in meningioma surgery - a population based comparative effectiveness study of routine mechanical prophylaxis with or without preoperative low molecular weight heparin

    DEFF Research Database (Denmark)

    Sjåvik, Kristin; Bartek, Jiri; Solheim, Ole

    2015-01-01

    neurosurgical centers with population-based referral. We compared two different treatment strategies analyzing frequencies of VTE and proportions of postoperative intracranial hematomas requiring surgery or intensified subsequent observation or care (ICU or other intensified observation and/or treatment). One......: In the LMWH routine group, VTE was diagnosed after 24/626 operations (3.9%), while VTE was diagnosed after 11/353 (3.1%) operations in the LMWH as needed group (p=0.56). Clinically relevant postoperative hematomas occurred after 57/626 operations (9.1%) in the LMWH routine group compared to 23/353 (6.......5%) in the LMWH as needed group (p=0.16). Surgically evacuated postoperative hematomas occurred after 19/626 operations (3.0%) in the LMWH routine group compared to 8/353 operations (2.3%) in the LMWH as needed group (p=0.26). CONCLUSION: There is no benefit of routine preoperative LMWH starting before...

  6. Effect of Side Chains on Molecular Conformation of Anthracene-Ethynylene-Phenylene-Vinylene Oligomers: A Comparative Density Functional Study With and Without Dispersion Interaction.

    Science.gov (United States)

    Dong, Chuanding; Hoppe, Harald; Beenken, Wichard J D

    2016-06-02

    Using density functional calculations with and without dispersion interaction, we studied the effects of linear octyl and branched 2-ethylhexyl side chains on the oligomer conformation of the conjugated copolymer poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene). With dispersion included, the branched side chains can cause significant bending of the oligomer backbone, while without dispersion they induce mainly torsional disorder. The oligomers with mainly linear side chains keep good planarity when optimized with and without dispersion. Despite their dramatically different conformations, the calculated absorption spectra of the oligomers with various side chain combinations are very similar, indicating that the conformation of the copolymer is not the main reason for the experimentally observed different spectra of ordered and disordered phases.

  7. Development of similarity theory for control systems

    Science.gov (United States)

    Myshlyaev, L. P.; Evtushenko, V. F.; Ivushkin, K. A.; Makarov, G. V.

    2018-05-01

    The area of effective application of the traditional similarity theory and the need necessity of its development for systems are discussed. The main statements underlying the similarity theory of control systems are given. The conditions for the similarity of control systems and the need for similarity control control are formulated. Methods and algorithms for estimating and similarity control of control systems and the results of research of control systems based on their similarity are presented. The similarity control of systems includes the current evaluation of the degree of similarity of control systems and the development of actions controlling similarity, and the corresponding targeted change in the state of any element of control systems.

  8. Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study.

    Directory of Open Access Journals (Sweden)

    Dimitrios Spiliotopoulos

    Full Text Available PHD fingers represent one of the largest families of epigenetic readers capable of decoding post-translationally modified or unmodified histone H3 tails. Because of their direct involvement in human pathologies they are increasingly considered as a potential therapeutic target. Several PHD/histone-peptide structures have been determined, however relatively little information is available on their dynamics. Studies aiming to characterize the dynamic and energetic determinants driving histone peptide recognition by epigenetic readers would strongly benefit from computational studies. Herein we focus on the dynamic and energetic characterization of the PHD finger subclass specialized in the recognition of histone H3 peptides unmodified in position K4 (H3K4me0. As a case study we focused on the first PHD finger of autoimmune regulator protein (AIRE-PHD1 in complex with H3K4me0. PCA analysis of the covariance matrix of free AIRE-PHD1 highlights the presence of a "flapping" movement, which is blocked in an open conformation upon binding to H3K4me0. Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes. MM/PBSA calculations have also been applied to the energetic analysis of other PHD fingers recognizing H3K4me0. In this case we observe excellent correlation between computed and experimental binding free energies. Overall calculations show that H3K4me0 recognition by PHD fingers relies on compensation of the electrostatic and polar solvation energy terms and is stabilized by non-polar interactions.

  9. Determination of subjective similarity for pairs of masses and pairs of clustered microcalcifications on mammograms: Comparison of similarity ranking scores and absolute similarity ratings

    International Nuclear Information System (INIS)

    Muramatsu, Chisako; Li Qiang; Schmidt, Robert A.; Shiraishi, Junji; Suzuki, Kenji; Newstead, Gillian M.; Doi, Kunio

    2007-01-01

    The presentation of images that are similar to that of an unknown lesion seen on a mammogram may be helpful for radiologists to correctly diagnose that lesion. For similar images to be useful, they must be quite similar from the radiologists' point of view. We have been trying to quantify the radiologists' impression of similarity for pairs of lesions and to establish a ''gold standard'' for development and evaluation of a computerized scheme for selecting such similar images. However, it is considered difficult to reliably and accurately determine similarity ratings, because they are subjective. In this study, we compared the subjective similarities obtained by two different methods, an absolute rating method and a 2-alternative forced-choice (2AFC) method, to demonstrate that reliable similarity ratings can be determined by the responses of a group of radiologists. The absolute similarity ratings were previously obtained for pairs of masses and pairs of microcalcifications from five and nine radiologists, respectively. In this study, similarity ranking scores for eight pairs of masses and eight pairs of microcalcifications were determined by use of the 2AFC method. In the first session, the eight pairs of masses and eight pairs of microcalcifications were grouped and compared separately for determining the similarity ranking scores. In the second session, another similarity ranking score was determined by use of mixed pairs, i.e., by comparison of the similarity of a mass pair with that of a calcification pair. Four pairs of masses and four pairs of microcalcifications were grouped together to create two sets of eight pairs. The average absolute similarity ratings and the average similarity ranking scores showed very good correlations in the first study (Pearson's correlation coefficients: 0.94 and 0.98 for masses and microcalcifications, respectively). Moreover, in the second study, the correlations between the absolute ratings and the ranking scores were also

  10. Molecular beam epitaxy of GaAs nanowires and their sustainability for optoelectronic applications. Comparing Au- and self-assisted growth methods

    Energy Technology Data Exchange (ETDEWEB)

    Breuer, Steffen

    2011-09-28

    In this work the synthesis of GaAs nanowires by molecular beam epitaxy (MBE) using the vapour-liquid-solid (VLS) mechanism is investigated. A comparison between Au- and self-assisted VLS growth is at the centre of this thesis. While the Au-assisted method is established as a versatile tool for nanowire growth, the recently developed self-assisted variation results from the exchange of Au by Ga droplets and thus eliminates any possibility of Au incorporation. By both methods, we achieve nanowires with epitaxial alignment to the Si(111) substrates. Caused by differences during nanowire nucleation, a parasitic planar layer grows between the nanowires by the Au-assisted method, but can be avoided by the self-assisted method. Au-assisted nanowires grow predominantly in the metastable wurtzite crystal structure, while their self-assisted counterparts have the zincblende structure. All GaAs nanowires are fully relaxed and the strain arising from the lattice mismatch between GaAs and Si of 4.1 % is accommodated by misfit dislocations at the interface. Self-assisted GaAs nanowires are generally found to have vertical and non-polar side facets, while tilted and polar nanofacets were described for Au-assisted GaAs nanowires. We employ VLS nucleation theory to understand the effect of the droplet material on the lateral facets. Optoelectronic applications require long minority carrier lifetimes at room temperature. We fabricate GaAs/(Al,Ga)As core-shell nanowires and analyse them by transient photoluminescence (PL) spectroscopy. The results are 2.5 ns for the self-assisted nanowires as well as 9 ps for the Au-assisted nanowires. By temperature-dependent PL measurements we find a characteristic activation energy of 77 meV that is present only in the Au-assisted nanowires. We conclude that most likely Au is incorporated from the droplets into the GaAs nanowires and acts as a deep, non-radiative recombination centre.

  11. Molecular characterization of UGT94F2 and UGT86C4, two glycosyltransferases from Picrorhiza kurrooa: comparative structural insight and evaluation of substrate recognition.

    Directory of Open Access Journals (Sweden)

    Wajid Waheed Bhat

    Full Text Available Uridine diphosphate glycosyltransferases (UGTs are pivotal in the process of glycosylation for decorating natural products with sugars. It is one of the versatile mechanisms in determining chemical complexity and diversity for the production of suite of pharmacologically active plant natural products. Picrorhiza kurrooa is a highly reputed medicinal herb known for its hepato-protective properties which are attributed to a novel group of iridoid glycosides known as picrosides. Although the plant is well studied in terms of its pharmacological properties, very little is known about the biosynthesis of these important secondary metabolites. In this study, we identified two family-1 glucosyltransferases from P. kurrooa. The full length cDNAs of UGT94F4 and UGT86C4 contained open reading frames of 1455 and 1422 nucleotides, encoding polypeptides of 484 and 473 amino acids respectively. UGT94F2 and UGT86C4 showed differential expression pattern in leaves, rhizomes and inflorescence. To elucidate whether the differential expression pattern of the two Picrorhiza UGTs correlate with transcriptional regulation via their promoters and to identify elements that could be recognized by known iridoid-specific transcription factors, upstream regions of each gene were isolated and scanned for putative cis-regulatory elements. Interestingly, the presence of cis-regulatory elements within the promoter regions of each gene correlated positively with their expression profiles in response to different phytohormones. HPLC analysis of picrosides extracted from different tissues and elicitor-treated samples showed a significant increase in picroside levels, corroborating well with the expression profile of UGT94F2 possibly indicating its implication in picroside biosynthesis. Using homology modeling and molecular docking studies, we provide an insight into the donor and acceptor specificities of both UGTs identified in this study. UGT94F2 was predicted to be an iridoid

  12. Marriage Matters: Spousal Similarity in Life Satisfaction

    OpenAIRE

    Ulrich Schimmack; Richard Lucas

    2006-01-01

    Examined the concurrent and cross-lagged spousal similarity in life satisfaction over a 21-year period. Analyses were based on married couples (N = 847) in the German Socio-Economic Panel (SOEP). Concurrent spousal similarity was considerably higher than one-year retest similarity, revealing spousal similarity in the variable component of life satisfac-tion. Spousal similarity systematically decreased with length of retest interval, revealing simi-larity in the changing component of life sati...

  13. Assessment of Clinically Suspected Tubercular Lymphadenopathy by Real-Time PCR Compared to Non-Molecular Methods on Lymph Node Aspirates.

    Science.gov (United States)

    Gupta, Vivek; Bhake, Arvind

    2018-01-01

    The diagnosis of tubercular lymphadenitis (TBLN) is challenging. This study assesses the role of diagnostic intervention with real-time PCR in clinically suspected tubercular lymphadenopathy in relation to cytology and microbiological methods. The cross-sectional study involved 214 patients, and PCR, cytology, and Ziehl-Neelsen (ZN) staining was performed on aspirates. The findings were compared with culture on Lowenstein-Jensen medium. The overall concordance of cytology and PCR, both individually and combined, was calculated. χ2 and Phi values were assessed between cytology, PCR, and culture. A cytological diagnosis of tuberculosis (TB), reactive lymphoid hyperplasia, and suppurative lymphadenitis was made in 71, 112, and 6 patients, respectively. PCR and culture were positive in 40% of the cases. Among the TBLN patients, PCR showed higher positivity in necrosis and culture showed higher positivity in necrotizing granuloma. Positive ZN staining was observed in 29.6% of the TBLN cases, with an overall positivity of 11%. PCR could additionally detect 82 cases missed by ZN staining. The overall concordance rate for either diagnostic modality, i.e., PCR or cytology, was highest (75%), and for PCR alone was 74%. Phi values were observed to be 0.47 between PCR and culture. Real-time PCR for Mycobacterium tuberculosis complex on aspirates offers a definitive and comparable diagnosis of TBLN. Including this approach as the primary investigation in the work-up of TBLN could reduce the burden of TB. © 2017 S. Karger AG, Basel.

  14. Diversification patterns in cosmopolitan earthworms: similar mode but different tempo.

    Science.gov (United States)

    Fernández, Rosa; Novo, Marta; Marchán, Daniel F; Díaz Cosín, Darío J

    2016-01-01

    Comparative phylogeography of widespread species that span the same geographic areas can elucidate the influence of historical events on current patterns of biodiversity, identify patterns of co-vicariance, and therefore aid the understanding of general evolutionary processes. Soil-dwelling animals present characteristics that make them suitable for testing the effect of the palaeogeographical events on their distribution and diversification, such as their low vagility and population structure. In this study, we shed light on the spatial lineage diversification and cladogenesis of two widely-distributed cosmopolitan and invasive earthworms (Aporrectodea rosea and A. trapezoides) in their putative ancestral area of origin, the Western Palearctic, and a few populations in North America. Molecular analyses were conducted on mitochondrial and nuclear markers from 220 (A. rosea) and 198 (A. trapezoides) individuals collected in 56 and 57 localities, respectively. We compared the lineage diversification pattern, genetic variability and cladogenesis in both species. Our findings showed that both species underwent a similar diversification from the Western Mediterranean plates to (i) Northern Europe and (ii) the Iberian Peninsula, establishing their two main lineages. Their diversification was in concordance with the main palaeogeographical events in the Iberian Peninsula and Western Mediterranean, followed by a later colonization of North America from individuals derived exclusively from the Eurosiberian lineage. Their diversification occurred at different times, with the diversification of A. rosea being potentially more ancient. Cladogenesis in both species seems to have been modelled only by the Mediterranean plate shifts, ignoring historical climatic oscillations such as the Messinian salinity crisis. Their high genetic variability, strong population structure, lack of gene flow and stepping-stone-like cladogenesis suggest the existence of different cryptic lineages

  15. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  16. Drug target identification using side-effect similarity

    DEFF Research Database (Denmark)

    Campillos, Monica; Kuhn, Michael; Gavin, Anne-Claude

    2008-01-01

    Targets for drugs have so far been predicted on the basis of molecular or cellular features, for example, by exploiting similarity in chemical structure or in activity across cell lines. We used phenotypic side-effect similarities to infer whether two drugs share a target. Applied to 746 marketed...... drugs, a network of 1018 side effect-driven drug-drug relations became apparent, 261 of which are formed by chemically dissimilar drugs from different therapeutic indications. We experimentally tested 20 of these unexpected drug-drug relations and validated 13 implied drug-target relations by in vitro...... binding assays, of which 11 reveal inhibition constants equal to less than 10 micromolar. Nine of these were tested and confirmed in cell assays, documenting the feasibility of using phenotypic information to infer molecular interactions and hinting at new uses of marketed drugs....

  17. Textual and chemical information processing: different domains but similar algorithms

    Directory of Open Access Journals (Sweden)

    Peter Willett

    2000-01-01

    Full Text Available This paper discusses the extent to which algorithms developed for the processing of textual databases are also applicable to the processing of chemical structure databases, and vice versa. Applications discussed include: an algorithm for distribution sorting that has been applied to the design of screening systems for rapid chemical substructure searching; the use of measures of inter-molecular structural similarity for the analysis of hypertext graphs; a genetic algorithm for calculating term weights for relevance feedback searching for determining whether a molecule is likely to exhibit biological activity; and the use of data fusion to combine the results of different chemical similarity searches.

  18. Soldier motivation – different or similar?

    DEFF Research Database (Denmark)

    Brænder, Morten; Andersen, Lotte Bøgh

    Recent research in military sociology has shown that in addition to their strong peer motivation modern soldiers are oriented toward contributing to society. It has not, however, been tested how soldier motivation differs from the motivation of other citizens in this respect. In this paper......, by means of public service motivation, a concept developed within the public administration literature, we compare soldier and civilian motivation. The contribution of this paper is an analysis of whether and how Danish combat soldiers differs from other Danes in regard to public service motivation? Using...... surveys with similar questions, we find that soldiers are more normatively motivated to contribute to society than other citizens (higher commitment to the public interest), while their affectively based motivation is lower (lower compassion). This points towards a potential problem in regard...

  19. Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: Comparing the early molecular response using time-series transcriptomic and metabolomic analyses

    Directory of Open Access Journals (Sweden)

    Dutta Bhaskar

    2010-12-01

    Full Text Available Abstract Background In this study, we investigated the individual and combinatorial effect of elevated CO2 conditions and salinity stress on the dynamics of both the transcriptional and metabolic physiology of Arabidopsis thaliana liquid hydroponic cultures over the first 30 hours of continuous treatment. Both perturbations are of particular interest in plant and agro-biotechnological applications. Moreover, within the timeframe of this experiment, they are expected to affect plant growth to opposite directions. Thus, a major objective was to investigate whether this expected "divergence" was valid for the individual perturbations and to study how it is manifested under the combined stress at two molecular levels of cellular function, using high-throughput analyses. Results We observed that a high salinity has stronger effect than elevated CO2 at both the transcriptional and metabolic levels, b the transcriptional responses to the salinity and combined stresses exhibit strong similarity, implying a robust transcriptional machinery acting to the salinity stress independent of the co-occurrence of elevated CO2, c the combinatorial effect of the two perturbations on the metabolic physiology is milder than of the salinity stress alone. Metabolomic analysis suggested that the beneficial role of elevated CO2 on salt-stressed plants within the timeframe of this study should be attributed to the provided additional resources; these allow the plants to respond to high salinity without having to forfeit other major metabolic functions, and d 9 h-12 h and 24 h of treatment coincide with significant changes in the metabolic physiology under any of the investigated stresses. Significant differences between the acute and longer term responses were observed at both molecular levels. Conclusions This study contributes large-scale dynamic omic data from two levels of cellular function for a plant system under various stresses. It provides an additional example

  20. Optical signature of nerve tissue-Exploratory ex vivo study comparing optical, histological, and molecular characteristics of different adipose and nerve tissues.

    Science.gov (United States)

    Balthasar, Andrea J R; Bydlon, Torre M; Ippel, Hans; van der Voort, Marjolein; Hendriks, Benno H W; Lucassen, Gerald W; van Geffen, Geert-Jan; van Kleef, Maarten; van Dijk, Paul; Lataster, Arno

    2018-05-14

    During several anesthesiological procedures, needles are inserted through the skin of a patient to target nerves. In most cases, the needle traverses several tissues-skin, subcutaneous adipose tissue, muscles, nerves, and blood vessels-to reach the target nerve. A clear identification of the target nerve can improve the success of the nerve block and reduce the rate of complications. This may be accomplished with diffuse reflectance spectroscopy (DRS) which can provide a quantitative measure of the tissue composition. The goal of the current study was to further explore the morphological, biological, chemical, and optical characteristics of the tissues encountered during needle insertion to improve future DRS classification algorithms. To compare characteristics of nerve tissue (sciatic nerve) and adipose tissues, the following techniques were used: histology, DRS, absorption spectrophotometry, high-resolution magic-angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy, and solution 2D 13 C- 1 H heteronuclear single-quantum coherence spectroscopy. Tissues from five human freshly frozen cadavers were examined. Histology clearly highlights a higher density of cellular nuclei, collagen, and cytoplasm in fascicular nerve tissue (IFAS). IFAS showed lower absorption of light around 1200 nm and 1750 nm, higher absorption around 1500 nm and 2000 nm, and a shift in the peak observed around 1000 nm. DRS measurements showed a higher water percentage and collagen concentration in IFAS and a lower fat percentage compared to all other tissues. The scattering parameter (b) was highest in IFAS. The HR-MAS NMR data showed three extra chemical peak shifts in IFAS tissue. Collagen, water, and cellular nuclei concentration are clearly different between nerve fascicular tissue and other adipose tissue and explain some of the differences observed in the optical absorption, DRS, and HR-NMR spectra of these tissues. Some differences observed between fascicular

  1. Molecular Structure of Human-Liver Glycogen.

    Directory of Open Access Journals (Sweden)

    Bin Deng

    Full Text Available Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.

  2. Molecular systematic of three species of Oithona (Copepoda, Cyclopoida from the Atlantic Ocean: comparative analysis using 28S rDNA.

    Directory of Open Access Journals (Sweden)

    Georgina D Cepeda

    Full Text Available Species of Oithona (Copepoda, Cyclopoida are highly abundant, ecologically important, and widely distributed throughout the world oceans. Although there are valid and detailed descriptions of the species, routine species identifications remain challenging due to their small size, subtle morphological diagnostic traits, and the description of geographic forms or varieties. This study examined three species of Oithona (O. similis, O. atlantica and O. nana occurring in the Argentine sector of the South Atlantic Ocean based on DNA sequence variation of a 575 base-pair region of 28S rDNA, with comparative analysis of these species from other North and South Atlantic regions. DNA sequence variation clearly resolved and discriminated the species, and revealed low levels of intraspecific variation among North and South Atlantic populations of each species. The 28S rDNA region was thus shown to provide an accurate and reliable means of identifying the species throughout the sampled domain. Analysis of 28S rDNA variation for additional species collected throughout the global ocean will be useful to accurately characterize biogeographical distributions of the species and to examine phylogenetic relationships among them.

  3. On different forms of self similarity

    International Nuclear Information System (INIS)

    Aswathy, R.K.; Mathew, Sunil

    2016-01-01

    Fractal geometry is mainly based on the idea of self-similar forms. To be self-similar, a shape must able to be divided into parts that are smaller copies, which are more or less similar to the whole. There are different forms of self similarity in nature and mathematics. In this paper, some of the topological properties of super self similar sets are discussed. It is proved that in a complete metric space with two or more elements, the set of all non super self similar sets are dense in the set of all non-empty compact sub sets. It is also proved that the product of self similar sets are super self similar in product metric spaces and that the super self similarity is preserved under isometry. A characterization of super self similar sets using contracting sub self similarity is also presented. Some relevant counterexamples are provided. The concepts of exact super and sub self similarity are introduced and a necessary and sufficient condition for a set to be exact super self similar in terms of condensation iterated function systems (Condensation IFS’s) is obtained. A method to generate exact sub self similar sets using condensation IFS’s and the denseness of exact super self similar sets are also discussed.

  4. Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology.

    Science.gov (United States)

    Shaik, Sabiha; Kumar, Narender; Lankapalli, Aditya K; Tiwari, Sumeet K; Baddam, Ramani; Ahmed, Niyaz

    2016-01-01

    A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

  5. A New Trajectory Similarity Measure for GPS Data

    KAUST Repository

    Ismail, Anas; Vigneron, Antoine E.

    2016-01-01

    We present a new algorithm for measuring the similarity between trajectories, and in particular between GPS traces. We call this new similarity measure the Merge Distance (MD). Our approach is robust against subsampling and supersampling. We perform experiments to compare this new similarity measure with the two main approaches that have been used so far: Dynamic Time Warping (DTW) and the Euclidean distance. © 2015 ACM.

  6. A New Trajectory Similarity Measure for GPS Data

    KAUST Repository

    Ismail, Anas

    2016-08-08

    We present a new algorithm for measuring the similarity between trajectories, and in particular between GPS traces. We call this new similarity measure the Merge Distance (MD). Our approach is robust against subsampling and supersampling. We perform experiments to compare this new similarity measure with the two main approaches that have been used so far: Dynamic Time Warping (DTW) and the Euclidean distance. © 2015 ACM.

  7. Magnetismo Molecular (Molecular Magentism)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  8. Visual reconciliation of alternative similarity spaces in climate modeling

    Science.gov (United States)

    J Poco; A Dasgupta; Y Wei; William Hargrove; C.R. Schwalm; D.N. Huntzinger; R Cook; E Bertini; C.T. Silva

    2015-01-01

    Visual data analysis often requires grouping of data objects based on their similarity. In many application domains researchers use algorithms and techniques like clustering and multidimensional scaling to extract groupings from data. While extracting these groups using a single similarity criteria is relatively straightforward, comparing alternative criteria poses...

  9. Demonstration of Functional Similarity of Proposed Biosimilar ABP 501 to Adalimumab.

    Science.gov (United States)

    Velayudhan, Jyoti; Chen, Yuh-Feng; Rohrbach, Amanda; Pastula, Christina; Maher, Gwen; Thomas, Heather; Brown, Ryan; Born, Teresa L

    2016-08-01

    Due to the complex molecular structure and proprietary manufacturing processes of monoclonal antibodies (mAbs), differences in structure and function may be expected during development of biosimilar mAbs. Important regulatory requirements for approval of biosimilar products involve comprehensive assessments of any potential differences between proposed biosimilars and reference mAbs, including differences in all known mechanisms of action, using sensitive and relevant methods. Any identified structural differences should not result in differences in biofunctional or clinical activity. A comprehensive assessment comparing the Amgen biosimilar candidate ABP 501 with FDA-licensed adalimumab (adalimumab [US]) and EU-authorized adalimumab (adalimumab [EU]) was conducted to demonstrate similarity in biofunctional activity. The functional similarity assessment included testing of binding kinetics to soluble tumor necrosis factor α (TNFα) and relative binding to transmembrane TNFα. The neutralization of TNFα-induced caspase activation, TNFα- and lymphotoxin-α (LTα)-induced chemokine production, and cytotoxicity was also tested. Binding to Fc-gamma receptors FcγRIa, FcγRIIa (131H), FcγRIIIa (158V and 158F), and neonatal Fc receptor (FcRn) was compared with the reference mAbs, as was antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. The data demonstrate that ABP 501 is similar to both adalimumab (US) and adalimumab (EU) with respect to evaluated biofunctional activities. Similarity in biofunctional activity is a critical component of the totality of evidence required for demonstration of biosimilarity. The functional similarity demonstrated for ABP 501 comprehensively assesses the known mechanisms of action of adalimumab, supporting the conclusion that ABP 501, adalimumab (US), and adalimumab (EU) are likely to be clinically similar.

  10. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim; Cisse, Moustapha; Gao, Xin; Zhang, Xiangliang

    2016-01-01

    Classification with indefinite similarities has attracted attention in the machine learning community. This is partly due to the fact that many similarity functions that arise in practice are not symmetric positive semidefinite, i.e. the Mercer

  11. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji; Genton, Marc G.; Jun, Mikyoung

    2016-01-01

    extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi

  12. Optimal neighborhood indexing for protein similarity search.

    Science.gov (United States)

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

    2008-12-16

    Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  13. Optimal neighborhood indexing for protein similarity search

    Directory of Open Access Journals (Sweden)

    Nguyen Van

    2008-12-01

    Full Text Available Abstract Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. Results The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. Conclusion We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  14. Personality similarity and life satisfaction in couples

    OpenAIRE

    Furler Katrin; Gomez Veronica; Grob Alexander

    2013-01-01

    The present study examined the association between personality similarity and life satisfaction in a large nationally representative sample of 1608 romantic couples. Similarity effects were computed for the Big Five personality traits as well as for personality profiles with global and differentiated indices of similarity. Results showed substantial actor and partner effects indicating that both partners' personality traits were related to both partners' life satisfaction. Personality similar...

  15. Molecular hematology

    National Research Council Canada - National Science Library

    Provan, Drew; Gribben, John

    2010-01-01

    ... The molecular basis of hemophilia, 219 Paul LF Giangrande 4 The genetics of acute myeloid leukemias, 42 Carolyn J Owen & Jude Fitzgibbon 19 The molecular basis of von Willebrand disease, 233 Luciano Baronc...

  16. Molecular vibration-activity relationship in the agonism of adenosine receptors.

    Science.gov (United States)

    Chee, Hyun Keun; Oh, S June

    2013-12-01

    The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated by structure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. The resulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram result produced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study of adenosine receptor agonism and antagonism. The tree that was produced by clustering analysis of molecular vibration patterns showed its potential for the functional classification of adenosine receptor ligands.

  17. Molecular Vibration-Activity Relationship in the Agonism of Adenosine Receptors

    Directory of Open Access Journals (Sweden)

    Hyun Keun Chee

    2013-12-01

    Full Text Available The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated by structure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. The resulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram result produced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study of adenosine receptor agonism and antagonism. The tree that was produced by clustering analysis of molecular vibration patterns showed its potential for the functional classification of adenosine receptor ligands.

  18. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  19. Comparable results of autologous and allogeneic haematopoietic stem cell transplantation for adults with Philadelphia-positive acute lymphoblastic leukaemia in first complete molecular remission: An analysis by the Acute Leukemia Working Party of the EBMT.

    Science.gov (United States)

    Giebel, Sebastian; Labopin, Myriam; Potter, Michael; Poiré, Xavier; Sengeloev, Henrik; Socié, Gerard; Huynh, Anne; Afanasyev, Boris V; Schanz, Urs; Ringden, Olle; Kalhs, Peter; Beelen, Dietrich W; Campos, Antonio M; Masszi, Tamás; Canaani, Jonathan; Mohty, Mohamad; Nagler, Arnon

    2018-06-01

    Allogeneic haematopoietic stem cell transplantation (alloHSCT) is considered a standard treatment for patients with Philadelphia chromosome-positive acute lymphoblastic leukaemia (Ph+ ALL) achieving complete remission after induction containing tyrosine kinase inhibitors (TKIs). We retrospectively compared results of myeloablative alloHSCT from either matched sibling donor (MSD) or unrelated donor (URD) with autologous (auto) HSCT for adults with Ph+ ALL in molecular remission, treated between 2007 and 2014. In univariate analysis, the incidence of relapse at 2 years was 47% after autoHSCT, 28% after MSD-HSCT and 19% after URD-HSCT (P = 0.0002). Respective rates of non-relapse mortality were 2%, 18%, and 22% (P = 0.001). The probabilities of leukaemia-free survival were 52%, 55% and 60% (P = 0.69), while overall survival rates were 70%, 70% and 69% (P = 0.58), respectively. In multivariate analysis, there was a trend towards increased risk of overall mortality after MSD-HSCT (hazard ratio [HR], 1.5, P = 0.12) and URD-HSCT (HR, 1.6, P = 0.08) when referred to autoHSCT. The use of total body irradiation (TBI)-based regimens was associated with reduced risk of relapse (HR, 0.65, P = 0.02) and overall mortality (HR, 0.67, P = 0.01). In the era of TKIs, outcomes of myeloablative autoHSCT and alloHSCT for patients with Ph+ ALL in first molecular remission are comparable. Therefore, autoHSCT appears to be an attractive treatment option potentially allowing for circumvention of alloHSCT sequelae. Irrespective of the type of donor, TBI-based regimens should be considered the preferable type of conditioning for Ph+ ALL. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. Application of 3D Zernike descriptors to shape-based ligand similarity searching

    Directory of Open Access Journals (Sweden)

    Venkatraman Vishwesh

    2009-12-01

    Full Text Available Abstract Background The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. Results In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. Conclusion The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD.

  1. Application of 3D Zernike descriptors to shape-based ligand similarity searching.

    Science.gov (United States)

    Venkatraman, Vishwesh; Chakravarthy, Padmasini Ramji; Kihara, Daisuke

    2009-12-17

    The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD.

  2. Multidimensional Scaling Visualization Using Parametric Similarity Indices

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2015-03-01

    Full Text Available In this paper, we apply multidimensional scaling (MDS and parametric similarity indices (PSI in the analysis of complex systems (CS. Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, and we generate the corresponding MDS maps of ‘points’. Third, we use Procrustes analysis to linearly transform the MDS charts for maximum superposition and to build a globalMDS map of “shapes”. This final plot captures the time evolution of the phenomena and is sensitive to the PSI adopted. The generalized correlation, theMinkowski distance and four entropy-based indices are tested. The proposed approach is applied to the Dow Jones Industrial Average stock market index and the Europe Brent Spot Price FOB time-series.

  3. A Similarity Analysis of Audio Signal to Develop a Human Activity Recognition Using Similarity Networks

    Directory of Open Access Journals (Sweden)

    Alejandra García-Hernández

    2017-11-01

    Full Text Available Human Activity Recognition (HAR is one of the main subjects of study in the areas of computer vision and machine learning due to the great benefits that can be achieved. Examples of the study areas are: health prevention, security and surveillance, automotive research, and many others. The proposed approaches are carried out using machine learning techniques and present good results. However, it is difficult to observe how the descriptors of human activities are grouped. In order to obtain a better understanding of the the behavior of descriptors, it is important to improve the abilities to recognize the human activities. This paper proposes a novel approach for the HAR based on acoustic data and similarity networks. In this approach, we were able to characterize the sound of the activities and identify those activities looking for similarity in the sound pattern. We evaluated the similarity of the sounds considering mainly two features: the sound location and the materials that were used. As a result, the materials are a good reference classifying the human activities compared with the location.

  4. [-25]A Similarity Analysis of Audio Signal to Develop a Human Activity Recognition Using Similarity Networks.

    Science.gov (United States)

    García-Hernández, Alejandra; Galván-Tejada, Carlos E; Galván-Tejada, Jorge I; Celaya-Padilla, José M; Gamboa-Rosales, Hamurabi; Velasco-Elizondo, Perla; Cárdenas-Vargas, Rogelio

    2017-11-21

    Human Activity Recognition (HAR) is one of the main subjects of study in the areas of computer vision and machine learning due to the great benefits that can be achieved. Examples of the study areas are: health prevention, security and surveillance, automotive research, and many others. The proposed approaches are carried out using machine learning techniques and present good results. However, it is difficult to observe how the descriptors of human activities are grouped. In order to obtain a better understanding of the the behavior of descriptors, it is important to improve the abilities to recognize the human activities. This paper proposes a novel approach for the HAR based on acoustic data and similarity networks. In this approach, we were able to characterize the sound of the activities and identify those activities looking for similarity in the sound pattern. We evaluated the similarity of the sounds considering mainly two features: the sound location and the materials that were used. As a result, the materials are a good reference classifying the human activities compared with the location.

  5. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji

    2016-07-14

    Self-similar processes have been widely used in modeling real-world phenomena occurring in environmetrics, network traffic, image processing, and stock pricing, to name but a few. The estimation of the degree of self-similarity has been studied extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi-self-similarity for a random field indexed in higher dimensions. If self-similarity is not rejected, our test provides a set of estimated self-similarity indexes. The key is to test stationarity of the inverse Lamperti transformations of the process. The inverse Lamperti transformation of a self-similar process is a strongly stationary process, revealing a theoretical connection between the two processes. To demonstrate the capability of our test, we test self-similarity of fractional Brownian motions and sheets, their time deformations and mixtures with Gaussian white noise, and the generalized Cauchy family. We also apply the self-similarity test to real data: annual minimum water levels of the Nile River, network traffic records, and surface heights of food wrappings. © 2016, International Biometric Society.

  6. Similarity increases altruistic punishment in humans.

    Science.gov (United States)

    Mussweiler, Thomas; Ockenfels, Axel

    2013-11-26

    Humans are attracted to similar others. As a consequence, social networks are homogeneous in sociodemographic, intrapersonal, and other characteristics--a principle called homophily. Despite abundant evidence showing the importance of interpersonal similarity and homophily for human relationships, their behavioral correlates and cognitive foundations are poorly understood. Here, we show that perceived similarity substantially increases altruistic punishment, a key mechanism underlying human cooperation. We induced (dis)similarity perception by manipulating basic cognitive mechanisms in an economic cooperation game that included a punishment phase. We found that similarity-focused participants were more willing to punish others' uncooperative behavior. This influence of similarity is not explained by group identity, which has the opposite effect on altruistic punishment. Our findings demonstrate that pure similarity promotes reciprocity in ways known to encourage cooperation. At the same time, the increased willingness to punish norm violations among similarity-focused participants provides a rationale for why similar people are more likely to build stable social relationships. Finally, our findings show that altruistic punishment is differentially involved in encouraging cooperation under pure similarity vs. in-group conditions.

  7. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  8. Notions of similarity for systems biology models.

    Science.gov (United States)

    Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

    2018-01-01

    Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

  9. Similar speaker recognition using nonlinear analysis

    International Nuclear Information System (INIS)

    Seo, J.P.; Kim, M.S.; Baek, I.C.; Kwon, Y.H.; Lee, K.S.; Chang, S.W.; Yang, S.I.

    2004-01-01

    Speech features of the conventional speaker identification system, are usually obtained by linear methods in spectral space. However, these methods have the drawback that speakers with similar voices cannot be distinguished, because the characteristics of their voices are also similar in spectral space. To overcome the difficulty in linear methods, we propose to use the correlation exponent in the nonlinear space as a new feature vector for speaker identification among persons with similar voices. We show that our proposed method surprisingly reduces the error rate of speaker identification system to speakers with similar voices

  10. Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP

    Directory of Open Access Journals (Sweden)

    Kihara Daisuke

    2010-05-01

    Full Text Available Abstract Background A new paradigm of biological investigation takes advantage of technologies that produce large high throughput datasets, including genome sequences, interactions of proteins, and gene expression. The ability of biologists to analyze and interpret such data relies on functional annotation of the included proteins, but even in highly characterized organisms many proteins can lack the functional evidence necessary to infer their biological relevance. Results Here we have applied high confidence function predictions from our automated prediction system, PFP, to three genome sequences, Escherichia coli, Saccharomyces cerevisiae, and Plasmodium falciparum (malaria. The number of annotated genes is increased by PFP to over 90% for all of the genomes. Using the large coverage of the function annotation, we introduced the functional similarity networks which represent the functional space of the proteomes. Four different functional similarity networks are constructed for each proteome, one each by considering similarity in a single Gene Ontology (GO category, i.e. Biological Process, Cellular Component, and Molecular Function, and another one by considering overall similarity with the funSim score. The functional similarity networks are shown to have higher modularity than the protein-protein interaction network. Moreover, the funSim score network is distinct from the single GO-score networks by showing a higher clustering degree exponent value and thus has a higher tendency to be hierarchical. In addition, examining function assignments to the protein-protein interaction network and local regions of genomes has identified numerous cases where subnetworks or local regions have functionally coherent proteins. These results will help interpreting interactions of proteins and gene orders in a genome. Several examples of both analyses are highlighted. Conclusion The analyses demonstrate that applying high confidence predictions from PFP

  11. On self-similar Tolman models

    International Nuclear Information System (INIS)

    Maharaj, S.D.

    1988-01-01

    The self-similar spherically symmetric solutions of the Einstein field equation for the case of dust are identified. These form a subclass of the Tolman models. These self-similar models contain the solution recently presented by Chi [J. Math. Phys. 28, 1539 (1987)], thereby refuting the claim of having found a new solution to the Einstein field equations

  12. Mining Diagnostic Assessment Data for Concept Similarity

    Science.gov (United States)

    Madhyastha, Tara; Hunt, Earl

    2009-01-01

    This paper introduces a method for mining multiple-choice assessment data for similarity of the concepts represented by the multiple choice responses. The resulting similarity matrix can be used to visualize the distance between concepts in a lower-dimensional space. This gives an instructor a visualization of the relative difficulty of concepts…

  13. On distributional assumptions and whitened cosine similarities

    DEFF Research Database (Denmark)

    Loog, Marco

    2008-01-01

    Recently, an interpretation of the whitened cosine similarity measure as a Bayes decision rule was proposed (C. Liu, "The Bayes Decision Rule Induced Similarity Measures,'' IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 29, no. 6, pp. 1086-1090, June 2007. This communication makes th...

  14. Self-Similar Traffic In Wireless Networks

    OpenAIRE

    Jerjomins, R.; Petersons, E.

    2005-01-01

    Many studies have shown that traffic in Ethernet and other wired networks is self-similar. This paper reveals that wireless network traffic is also self-similar and long-range dependant by analyzing big amount of data captured from the wireless router.

  15. Similarity Structure of Wave-Collapse

    DEFF Research Database (Denmark)

    Rypdal, Kristoffer; Juul Rasmussen, Jens; Thomsen, Kenneth

    1985-01-01

    Similarity transformations of the cubic Schrödinger equation (CSE) are investigated. The transformations are used to remove the explicit time variation in the CSE and reduce it to differential equations in the spatial variables only. Two different methods for similarity reduction are employed and...

  16. Low-molecular-weight heparinoid compared with warfarin for prophylaxis of deep-vein thrombosis in patients who are operated on for fracture of the hip. A prospective, randomized trial

    International Nuclear Information System (INIS)

    Gerhart, T.N.; Yett, H.S.; Robertson, L.K.; Lee, M.A.; Smith, M.; Salzman, E.W.

    1991-01-01

    In a randomized, prospective trial, a low-molecular-weight heparinoid (Org 10172 [Lomoparan]) was compared with warfarin for efficacy and safety in preventing deep-vein thrombosis in 263 patients who had an operatively treated fracture of the hip. One group of patients received Org 10172 in a dose of 750 units subcutaneously every twelve hours until the ninth postoperative day; on the seventh postoperative day, warfarin was added to the regimen. The other group received only warfarin. Both drugs were begun preoperatively, immediately after the admission evaluation. In the patients who received warfarin, the desired prothrombin time was one and one-half times the control level. Deep-vein thrombosis was detected by 125 I-fibrinogen scanning and impedance plethysmography and was confirmed by phlebography and compression ultrasonography. Deep-vein thrombosis was found in nine (7 per cent) of the 132 patients who received Org 10172 and in twenty-eight (21 per cent) of the 131 patients who received warfarin (p less than 0.001). Adverse reactions were not significantly different in the two groups. Major bleeding complications occurred in eight patients in the Org-10172 group, only four of whom were receiving the drug at the time of bleeding, and in five patients who were receiving warfarin (not significant). There was no difference in intraoperative loss of blood or in requirements for transfusion. We concluded that the low-molecular-weight heparinoid Org 10172 is a safe, convenient, effective antithrombotic agent for the prevention of venous thrombosis after an operation for fracture of the hip

  17. Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    Rafael Gustavo Ferreira Morales

    2011-12-01

    Full Text Available Most strawberry (Fragaria × ananassa Duchesne cultivars used in Brazil are developed in other countries, it became clear the need to start the strawberry breeding program in the country. To start a breeding program is necessary the genetic characterization of the germplasm available. Molecular markers are important tools that can be used for this purpose. The objectives of the present study were to assess the genetic similarity among 11 strawberry cultivars using RAPD and ISSR molecular markers and to indicate the possible promising crosses. The DNA of the eleven strawberry cultivars was extracted and amplified by PCR with RAPD and ISSR primers. The DNA fragments were separated in agarose gel for the RAPD markers and in polyacrylamide gel for the ISSR markers. The genetic similarity matrix was estimated by the Jaccard coefficient. Based on this matrix, the cultivars were grouped using the UPGMA method. The dendogram generated by the RAPD markers distributed the cultivars in three groups while the ISSR markers generated two groups. There was no direct relationship between the marker groups when the two types of markers were compared. The grouping proposed by the ISSR markers was more coherent with the origin and the genealogy of the cultivars than that proposed by the RAPD markers, and it can be considered the most efficient method for the study of genetic divergence in strawberry. The most promising crosses, based on the genetic divergence estimated from the RAPD and ISSR molecular data were between the Tudla and Ventana and the Oso Grande and Ventana cultivars, respectively.

  18. Expanding the boundaries of local similarity analysis.

    Science.gov (United States)

    Durno, W Evan; Hanson, Niels W; Konwar, Kishori M; Hallam, Steven J

    2013-01-01

    Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence of local and lagged relationships, but determining significance through a p-value has been algorithmically cumbersome due to an intensive permutation test, shuffling rows and columns and repeatedly calculating the statistic. Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets. To improve the performance of LSA on big datasets, an asymptotic upper bound on the p-value calculation was derived without the assumption of normality. This change in the bound calculation markedly improved computational speed from O(pm²n) to O(m²n), where p is the number of permutations in a permutation test, m is the number of time series, and n is the length of each time series. The bounding process is implemented as a computationally efficient software package, FASTLSA, written in C and optimized for threading on multi-core computers, improving its practical computation time. We computationally compare our approach to previous implementations of LSA, demonstrate broad applicability by analyzing time series data from public health, microbial ecology, and social media, and visualize resulting networks using the Cytoscape software. The FASTLSA software package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FASTLSA allows investigators to view correlated cliques and explore previously unrecognized network relationships. The software is freely available for download at: http://www.cmde.science.ubc.ca/hallam/fastLSA/.

  19. UNSOLVED AND LATENT CRIME: DIFFERENCES AND SIMILARITIES

    Directory of Open Access Journals (Sweden)

    Mikhail Kleymenov

    2017-01-01

    Full Text Available УДК 343Purpose of the article is to study the specific legal and informational nature of the unsolved crime in comparison with the phenomenon of delinquency, special study and analysis to improve the efficiency of law enforcement.Methods of research are abstract-logical, systematic, statistical, study of documents. The main results of research. Unsolved crime has specific legal, statistical and informational na-ture as the crime phenomenon, which is expressed in cumulative statistical population of unsolved crimes. An array of unsolved crimes is the sum of the number of acts, things of which is suspended and not terminated. The fault of the perpetrator in these cases is not proven, they are not considered by the court, it is not a conviction. Unsolved crime must be registered. Latent crime has a different informational nature. The main symptom of latent crimes is the uncertainty for the subjects of law enforcement, which delegated functions of identification, registration and accounting. Latent crime is not recorded. At the same time, there is a "border" area between the latent and unsolved crimes, which includes covered from the account of the crime. In modern Russia the majority of crimes covered from accounting by passing the decision about refusal in excitation of criminal case. Unsolved crime on their criminogenic consequences represents a significant danger to the public is higher compared to latent crime.It is conducted in the article a special analysis of the differences and similarities in the unsolved latent crime for the first time in criminological literature.The analysis proves the need for radical changes in the current Russian assessment of the state of crime and law enforcement to solve crimes. The article argues that an unsolved crime is a separate and, in contrast to latent crime, poorly understood phenomenon. However unsolved latent crime and have common features and areas of interaction.

  20. Information filtering based on transferring similarity.

    Science.gov (United States)

    Sun, Duo; Zhou, Tao; Liu, Jian-Guo; Liu, Run-Ran; Jia, Chun-Xiao; Wang, Bing-Hong

    2009-07-01

    In this Brief Report, we propose an index of user similarity, namely, the transferring similarity, which involves all high-order similarities between users. Accordingly, we design a modified collaborative filtering algorithm, which provides remarkably higher accurate predictions than the standard collaborative filtering. More interestingly, we find that the algorithmic performance will approach its optimal value when the parameter, contained in the definition of transferring similarity, gets close to its critical value, before which the series expansion of transferring similarity is convergent and after which it is divergent. Our study is complementary to the one reported in [E. A. Leicht, P. Holme, and M. E. J. Newman, Phys. Rev. E 73, 026120 (2006)], and is relevant to the missing link prediction problem.

  1. Self-similar continued root approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.

    2012-01-01

    A novel method of summing asymptotic series is advanced. Such series repeatedly arise when employing perturbation theory in powers of a small parameter for complicated problems of condensed matter physics, statistical physics, and various applied problems. The method is based on the self-similar approximation theory involving self-similar root approximants. The constructed self-similar continued roots extrapolate asymptotic series to finite values of the expansion parameter. The self-similar continued roots contain, as a particular case, continued fractions and Padé approximants. A theorem on the convergence of the self-similar continued roots is proved. The method is illustrated by several examples from condensed-matter physics.

  2. Correlation between social proximity and mobility similarity.

    Science.gov (United States)

    Fan, Chao; Liu, Yiding; Huang, Junming; Rong, Zhihai; Zhou, Tao

    2017-09-20

    Human behaviors exhibit ubiquitous correlations in many aspects, such as individual and collective levels, temporal and spatial dimensions, content, social and geographical layers. With rich Internet data of online behaviors becoming available, it attracts academic interests to explore human mobility similarity from the perspective of social network proximity. Existent analysis shows a strong correlation between online social proximity and offline mobility similarity, namely, mobile records between friends are significantly more similar than between strangers, and those between friends with common neighbors are even more similar. We argue the importance of the number and diversity of common friends, with a counter intuitive finding that the number of common friends has no positive impact on mobility similarity while the diversity plays a key role, disagreeing with previous studies. Our analysis provides a novel view for better understanding the coupling between human online and offline behaviors, and will help model and predict human behaviors based on social proximity.

  3. Scalar Similarity for Relaxed Eddy Accumulation Methods

    Science.gov (United States)

    Ruppert, Johannes; Thomas, Christoph; Foken, Thomas

    2006-07-01

    The relaxed eddy accumulation (REA) method allows the measurement of trace gas fluxes when no fast sensors are available for eddy covariance measurements. The flux parameterisation used in REA is based on the assumption of scalar similarity, i.e., similarity of the turbulent exchange of two scalar quantities. In this study changes in scalar similarity between carbon dioxide, sonic temperature and water vapour were assessed using scalar correlation coefficients and spectral analysis. The influence on REA measurements was assessed by simulation. The evaluation is based on observations over grassland, irrigated cotton plantation and spruce forest. Scalar similarity between carbon dioxide, sonic temperature and water vapour showed a distinct diurnal pattern and change within the day. Poor scalar similarity was found to be linked to dissimilarities in the energy contained in the low frequency part of the turbulent spectra ( definition.

  4. Surf similarity and solitary wave runup

    DEFF Research Database (Denmark)

    Fuhrman, David R.; Madsen, Per A.

    2008-01-01

    The notion of surf similarity in the runup of solitary waves is revisited. We show that the surf similarity parameter for solitary waves may be effectively reduced to the beach slope divided by the offshore wave height to depth ratio. This clarifies its physical interpretation relative to a previ...... functional dependence on their respective surf similarity parameters. Important equivalencies in the runup of sinusoidal and solitary waves are thus revealed.......The notion of surf similarity in the runup of solitary waves is revisited. We show that the surf similarity parameter for solitary waves may be effectively reduced to the beach slope divided by the offshore wave height to depth ratio. This clarifies its physical interpretation relative...... to a previous parameterization, which was not given in an explicit form. Good coherency with experimental (breaking) runup data is preserved with this simpler parameter. A recasting of analytical (nonbreaking) runup expressions for sinusoidal and solitary waves additionally shows that they contain identical...

  5. SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association.

    Directory of Open Access Journals (Sweden)

    Liang Cheng

    Full Text Available Measuring similarity between diseases plays an important role in disease-related molecular function research. Functional associations between disease-related genes and semantic associations between diseases are often used to identify pairs of similar diseases from different perspectives. Currently, it is still a challenge to exploit both of them to calculate disease similarity. Therefore, a new method (SemFunSim that integrates semantic and functional association is proposed to address the issue.SemFunSim is designed as follows. First of all, FunSim (Functional similarity is proposed to calculate disease similarity using disease-related gene sets in a weighted network of human gene function. Next, SemSim (Semantic Similarity is devised to calculate disease similarity using the relationship between two diseases from Disease Ontology. Finally, FunSim and SemSim are integrated to measure disease similarity.The high average AUC (area under the receiver operating characteristic curve (96.37% shows that SemFunSim achieves a high true positive rate and a low false positive rate. 79 of the top 100 pairs of similar diseases identified by SemFunSim are annotated in the Comparative Toxicogenomics Database (CTD as being targeted by the same therapeutic compounds, while other methods we compared could identify 35 or less such pairs among the top 100. Moreover, when using our method on diseases without annotated compounds in CTD, we could confirm many of our predicted candidate compounds from literature. This indicates that SemFunSim is an effective method for drug repositioning.

  6. Similarity in Bilateral Isolated Internal Orbital Fractures.

    Science.gov (United States)

    Chen, Hung-Chang; Cox, Jacob T; Sanyal, Abanti; Mahoney, Nicholas R

    2018-04-13

    In evaluating patients sustaining bilateral isolated internal orbital fractures, the authors have observed both similar fracture locations and also similar expansion of orbital volumes. In this study, we aim to investigate if there is a propensity for the 2 orbits to fracture in symmetrically similar patterns when sustaining similar trauma. A retrospective chart review was performed studying all cases at our institution of bilateral isolated internal orbital fractures involving the medial wall and/or the floor at the time of presentation. The similarity of the bilateral fracture locations was evaluated using the Fisher's exact test. The bilateral expanded orbital volumes were analyzed using the Wilcoxon signed-rank test to assess for orbital volume similarity. Twenty-four patients with bilateral internal orbital fractures were analyzed for fracture location similarity. Seventeen patients (70.8%) had 100% concordance in the orbital subregion fractured, and the association between the right and the left orbital fracture subregion locations was statistically significant (P < 0.0001). Fifteen patients were analyzed for orbital volume similarity. The average orbital cavity volume was 31.2 ± 3.8 cm on the right and 32.0 ± 3.7 cm on the left. There was a statistically significant difference between right and left orbital cavity volumes (P = 0.0026). The data from this study suggest that an individual who suffers isolated bilateral internal orbital fractures has a statistically significant similarity in the location of their orbital fractures. However, there does not appear to be statistically significant similarity in the expansion of the orbital volumes in these patients.

  7. The study on the cephalometric similarity between parents and offspring

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Woo Ghon; Ahn, Hyung Kyu [Department of Radiology, College of Dentistry, Seoul National University, Seoul (Korea, Republic of)

    1975-11-15

    The study was performed to investigate cephalometric similarity between parents and offspring of the Korean family by lateral cephalometric analysis. The lateral cephalograms consist of the 8 families comprising 16 parents, 5 sons and 7 daughters. In order to make an investigation of the similarity, 12 measuring points were set up, and 22 linear measurements on each depth, height and 5 angular measurements were made. The author drew up the profilograms to compare parents with offspring in each family group. The obtained results were as follows: 1. There was no common similarity on specific region between parents and offspring in each family group. 2. There was partial similarity between single parent and offspring. 3. The partial similarity between single parent and offspring was noted on the upper face in general.

  8. Relativistic quantum similarities in atoms in position and momentum spaces

    International Nuclear Information System (INIS)

    Maldonado, P.; Sarsa, A.; Buendia, E.; Galvez, F.J.

    2011-01-01

    A study of different quantum similarity measures and their corresponding quantum similarity indices is carried out for the atoms from H to Lr (Z=1-103). Relativistic effects in both position and momentum spaces have been studied by comparing the relativistic values to the non-relativistic ones. We have used the atomic electron density in both position and momentum spaces obtained within relativistic and non-relativistic numerical-parameterized optimized effective potential approximations. -- Highlights: → Quantum similarity measures and indices in electronic structure of atoms. → Position and momentum electronic densities. → Similarity of relativistic and non-relativistic densities. → Similarity of core and valence regions of different atoms. → Dependence with Z along the Periodic Table.

  9. Classification of Unknown Thermocouple Types Using Similarity Factor Measurement

    Directory of Open Access Journals (Sweden)

    Seshu K. DAMARLA

    2011-01-01

    Full Text Available In contrast to classification using PCA method, a new methodology is proposed for type identification of unknown thermocouple. The new methodology is based on calculating the degree of similarity between two multivariate datasets using two types of similarity factors. One similarity factor is based on principle component analysis and the angles between the principle component subspaces while the other is based on the Mahalanobis distance between the datasets. Datasets containing thermo-emfs against given temperature ranges are formed for each type of thermocouple (e.g. J, K, S, T, R, E, B and N type by experimentation are considered as reference datasets. Datasets corresponding to unknown type are captured. Similarity factor between the datasets one of which being the unknown type and the other being each known type are compared. When maximum similarity factor occurs, then the class of unknown type is allocated to that of known type.

  10. The study on the cephalometric similarity between parents and offspring

    International Nuclear Information System (INIS)

    Kang, Woo Ghon; Ahn, Hyung Kyu

    1975-01-01

    The study was performed to investigate cephalometric similarity between parents and offspring of the Korean family by lateral cephalometric analysis. The lateral cephalograms consist of the 8 families comprising 16 parents, 5 sons and 7 daughters. In order to make an investigation of the similarity, 12 measuring points were set up, and 22 linear measurements on each depth, height and 5 angular measurements were made. The author drew up the profilograms to compare parents with offspring in each family group. The obtained results were as follows: 1. There was no common similarity on specific region between parents and offspring in each family group. 2. There was partial similarity between single parent and offspring. 3. The partial similarity between single parent and offspring was noted on the upper face in general.

  11. Estimating correlation and covariance matrices by weighting of market similarity

    OpenAIRE

    Michael C. M\\"unnix; Rudi Sch\\"afer; Oliver Grothe

    2010-01-01

    We discuss a weighted estimation of correlation and covariance matrices from historical financial data. To this end, we introduce a weighting scheme that accounts for similarity of previous market conditions to the present one. The resulting estimators are less biased and show lower variance than either unweighted or exponentially weighted estimators. The weighting scheme is based on a similarity measure which compares the current correlation structure of the market to the structures at past ...

  12. Investigation of psychophysical similarity measures for selection of similar images in the diagnosis of clustered microcalcifications on mammograms

    Energy Technology Data Exchange (ETDEWEB)

    Muramatsu, Chisako; Li Qiang; Schmidt, Robert; Shiraishi, Junji; Doi, Kunio [Department of Radiology, University of Chicago, 5841 South Maryland Avenue, Chicago, Illinois 60637 (United States) and Department of Intelligent Image Information, Gifu University, 1-1 Yanagido, Gifu (Japan); Department of Radiology, Duke Advanced Imaging Labs, Duke University, 2424 Erwin Road, Suite 302, Durham, North Carolina 27705 (United States); Department of Radiology, University of Chicago, 5841 South Maryland Avenue, Chicago, Illinois 60637 (United States)

    2008-12-15

    was selected. The correlation coefficient between the gold standard and the psychophysical similarity measure through the use of seven features was relatively high (r=0.71) and was comparable to the correlation coefficients between the ratings by one radiologist and the average ratings by nine radiologists (r=0.69{+-}0.07). The correlation coefficient was improved compared to that of a distance-based method (r=0.58). The result indicated that similar images selected by the psychophysical similarity measure may be useful to radiologists in the diagnosis of clustered microcalcifications on mammograms.

  13. Investigation of psychophysical similarity measures for selection of similar images in the diagnosis of clustered microcalcifications on mammograms

    International Nuclear Information System (INIS)

    Muramatsu, Chisako; Li Qiang; Schmidt, Robert; Shiraishi, Junji; Doi, Kunio

    2008-01-01

    coefficient between the gold standard and the psychophysical similarity measure through the use of seven features was relatively high (r=0.71) and was comparable to the correlation coefficients between the ratings by one radiologist and the average ratings by nine radiologists (r=0.69±0.07). The correlation coefficient was improved compared to that of a distance-based method (r=0.58). The result indicated that similar images selected by the psychophysical similarity measure may be useful to radiologists in the diagnosis of clustered microcalcifications on mammograms.

  14. Measure of Node Similarity in Multilayer Networks.

    Directory of Open Access Journals (Sweden)

    Anders Mollgaard

    Full Text Available The weight of links in a network is often related to the similarity of the nodes. Here, we introduce a simple tunable measure for analysing the similarity of nodes across different link weights. In particular, we use the measure to analyze homophily in a group of 659 freshman students at a large university. Our analysis is based on data obtained using smartphones equipped with custom data collection software, complemented by questionnaire-based data. The network of social contacts is represented as a weighted multilayer network constructed from different channels of telecommunication as well as data on face-to-face contacts. We find that even strongly connected individuals are not more similar with respect to basic personality traits than randomly chosen pairs of individuals. In contrast, several socio-demographics variables have a significant degree of similarity. We further observe that similarity might be present in one layer of the multilayer network and simultaneously be absent in the other layers. For a variable such as gender, our measure reveals a transition from similarity between nodes connected with links of relatively low weight to dis-similarity for the nodes connected by the strongest links. We finally analyze the overlap between layers in the network for different levels of acquaintanceships.

  15. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar

    2016-03-21

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users\\' intuition about model similarity, and to support complex model searches in databases.

  16. Trajectory similarity join in spatial networks

    KAUST Repository

    Shang, Shuo

    2017-09-07

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider the case of trajectory similarity join (TS-Join), where the objects are trajectories of vehicles moving in road networks. Thus, given two sets of trajectories and a threshold θ, the TS-Join returns all pairs of trajectories from the two sets with similarity above θ. This join targets applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm\\'s per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

  17. The baryonic self similarity of dark matter

    International Nuclear Information System (INIS)

    Alard, C.

    2014-01-01

    The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominated regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M 1/4 . These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.

  18. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar; Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knuepfer, Christian; Liebermeister, Wolfram

    2016-01-01

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users' intuition about model similarity, and to support complex model searches in databases.

  19. Multi-Scale Scattering Transform in Music Similarity Measuring

    Science.gov (United States)

    Wang, Ruobai

    Scattering transform is a Mel-frequency spectrum based, time-deformation stable method, which can be used in evaluating music similarity. Compared with Dynamic time warping, it has better performance in detecting similar audio signals under local time-frequency deformation. Multi-scale scattering means to combine scattering transforms of different window lengths. This paper argues that, multi-scale scattering transform is a good alternative of dynamic time warping in music similarity measuring. We tested the performance of multi-scale scattering transform against other popular methods, with data designed to represent different conditions.

  20. Similarity-based pattern analysis and recognition

    CERN Document Server

    Pelillo, Marcello

    2013-01-01

    This accessible text/reference presents a coherent overview of the emerging field of non-Euclidean similarity learning. The book presents a broad range of perspectives on similarity-based pattern analysis and recognition methods, from purely theoretical challenges to practical, real-world applications. The coverage includes both supervised and unsupervised learning paradigms, as well as generative and discriminative models. Topics and features: explores the origination and causes of non-Euclidean (dis)similarity measures, and how they influence the performance of traditional classification alg

  1. Photoionization and molecular structure

    International Nuclear Information System (INIS)

    Palma, A.

    1983-01-01

    A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

  2. Systematic characterizations of text similarity in full text biomedical publications.

    Science.gov (United States)

    Sun, Zhaohui; Errami, Mounir; Long, Tara; Renard, Chris; Choradia, Nishant; Garner, Harold

    2010-09-15

    Computational methods have been used to find duplicate biomedical publications in MEDLINE. Full text articles are becoming increasingly available, yet the similarities among them have not been systematically studied. Here, we quantitatively investigated the full text similarity of biomedical publications in PubMed Central. 72,011 full text articles from PubMed Central (PMC) were parsed to generate three different datasets: full texts, sections, and paragraphs. Text similarity comparisons were performed on these datasets using the text similarity algorithm eTBLAST. We measured the frequency of similar text pairs and compared it among different datasets. We found that high abstract similarity can be used to predict high full text similarity with a specificity of 20.1% (95% CI [17.3%, 23.1%]) and sensitivity of 99.999%. Abstract similarity and full text similarity have a moderate correlation (Pearson correlation coefficient: -0.423) when the similarity ratio is above 0.4. Among pairs of articles in PMC, method sections are found to be the most repetitive (frequency of similar pairs, methods: 0.029, introduction: 0.0076, results: 0.0043). In contrast, among a set of manually verified duplicate articles, results are the most repetitive sections (frequency of similar pairs, results: 0.94, methods: 0.89, introduction: 0.82). Repetition of introduction and methods sections is more likely to be committed by the same authors (odds of a highly similar pair having at least one shared author, introduction: 2.31, methods: 1.83, results: 1.03). There is also significantly more similarity in pairs of review articles than in pairs containing one review and one nonreview paper (frequency of similar pairs: 0.0167 and 0.0023, respectively). While quantifying abstract similarity is an effective approach for finding duplicate citations, a comprehensive full text analysis is necessary to uncover all potential duplicate citations in the scientific literature and is helpful when

  3. HYPOTHESIS TESTING WITH THE SIMILARITY INDEX

    Science.gov (United States)

    Mulltilocus DNA fingerprinting methods have been used extensively to address genetic issues in wildlife populations. Hypotheses concerning population subdivision and differing levels of diversity can be addressed through the use of the similarity index (S), a band-sharing coeffic...

  4. On self-similarity of crack layer

    Science.gov (United States)

    Botsis, J.; Kunin, B.

    1987-01-01

    The crack layer (CL) theory of Chudnovsky (1986), based on principles of thermodynamics of irreversible processes, employs a crucial hypothesis of self-similarity. The self-similarity hypothesis states that the value of the damage density at a point x of the active zone at a time t coincides with that at the corresponding point in the initial (t = 0) configuration of the active zone, the correspondence being given by a time-dependent affine transformation of the space variables. In this paper, the implications of the self-similarity hypothesis for qusi-static CL propagation is investigated using polystyrene as a model material and examining the evolution of damage distribution along the trailing edge which is approximated by a straight segment perpendicular to the crack path. The results support the self-similarity hypothesis adopted by the CL theory.

  5. Bilateral Trade Flows and Income Distribution Similarity

    Science.gov (United States)

    2016-01-01

    Current models of bilateral trade neglect the effects of income distribution. This paper addresses the issue by accounting for non-homothetic consumer preferences and hence investigating the role of income distribution in the context of the gravity model of trade. A theoretically justified gravity model is estimated for disaggregated trade data (Dollar volume is used as dependent variable) using a sample of 104 exporters and 108 importers for 1980–2003 to achieve two main goals. We define and calculate new measures of income distribution similarity and empirically confirm that greater similarity of income distribution between countries implies more trade. Using distribution-based measures as a proxy for demand similarities in gravity models, we find consistent and robust support for the hypothesis that countries with more similar income-distributions trade more with each other. The hypothesis is also confirmed at disaggregated level for differentiated product categories. PMID:27137462

  6. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation.......Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...

  7. Abundance estimation of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-07-01

    Full Text Available This paper evaluates a spectral unmixing method for estimating the partial abundance of spectrally similar minerals in complex mixtures. The method requires formulation of a linear function of individual spectra of individual minerals. The first...

  8. Lagrangian-similarity diffusion-deposition model

    International Nuclear Information System (INIS)

    Horst, T.W.

    1979-01-01

    A Lagrangian-similarity diffusion model has been incorporated into the surface-depletion deposition model. This model predicts vertical concentration profiles far downwind of the source that agree with those of a one-dimensional gradient-transfer model

  9. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Parrado-Hernandez, Emilio; Meng, Anders

    Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...... for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation....

  10. Outsourced similarity search on metric data assets

    KAUST Repository

    Yiu, Man Lung

    2012-02-01

    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying it to the service provider for similarity queries on the transformed data. Our techniques provide interesting trade-offs between query cost and accuracy. They are then further extended to offer an intuitive privacy guarantee. Empirical studies with real data demonstrate that the techniques are capable of offering privacy while enabling efficient and accurate processing of similarity queries.

  11. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  12. Parallel trajectory similarity joins in spatial networks

    KAUST Repository

    Shang, Shuo

    2018-04-04

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

  13. Parallel trajectory similarity joins in spatial networks

    KAUST Repository

    Shang, Shuo; Chen, Lisi; Wei, Zhewei; Jensen, Christian S.; Zheng, Kai; Kalnis, Panos

    2018-01-01

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

  14. Are calanco landforms similar to river basins?

    Science.gov (United States)

    Caraballo-Arias, N A; Ferro, V

    2017-12-15

    In the past badlands have been often considered as ideal field laboratories for studying landscape evolution because of their geometrical similarity to larger fluvial systems. For a given hydrological process, no scientific proof exists that badlands can be considered a model of river basin prototypes. In this paper the measurements carried out on 45 Sicilian calanchi, a type of badlands that appears as a small-scale hydrographic unit, are used to establish their morphological similarity with river systems whose data are available in the literature. At first the geomorphological similarity is studied by identifying the dimensionless groups, which can assume the same value or a scaled one in a fixed ratio, representing drainage basin shape, stream network and relief properties. Then, for each property, the dimensionless groups are calculated for the investigated calanchi and the river basins and their corresponding scale ratio is evaluated. The applicability of Hack's, Horton's and Melton's laws for establishing similarity criteria is also tested. The developed analysis allows to conclude that a quantitative morphological similarity between calanco landforms and river basins can be established using commonly applied dimensionless groups. In particular, the analysis showed that i) calanchi and river basins have a geometrically similar shape respect to the parameters Rf and Re with a scale factor close to 1, ii) calanchi and river basins are similar respect to the bifurcation and length ratios (λ=1), iii) for the investigated calanchi the Melton number assumes values less than that (0.694) corresponding to the river case and a scale ratio ranging from 0.52 and 0.78 can be used, iv) calanchi and river basins have similar mean relief ratio values (λ=1.13) and v) calanchi present active geomorphic processes and therefore fall in a more juvenile stage with respect to river basins. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Molecular Diagnostics

    OpenAIRE

    Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...

  16. Molecular genetics

    International Nuclear Information System (INIS)

    Parkinson, D.R.; Krontiris, T.G.

    1986-01-01

    In this chapter the authors review new findings concerning the molecular genetics of malignant melanoma in the context of other information obtained from clinical, epidemiologic, and cytogenetic studies in this malignancy. These new molecular approaches promise to provide a more complete understanding of the mechanisms involved in the development of melanoma, thereby suggesting new methods for its treatment and prevention

  17. Molecular Modeling

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

  18. Biorthogonal projected energies of a Gutzwiller similarity transformed Hamiltonian.

    Science.gov (United States)

    Wahlen-Strothman, J M; Scuseria, G E

    2016-12-07

    We present a method incorporating biorthogonal orbital-optimization, symmetry projection, and double-occupancy screening with a non-unitary similarity transformation generated by the Gutzwiller factor [Formula: see text], and apply it to the Hubbard model. Energies are calculated with mean-field computational scaling with high-quality results comparable to coupled cluster singles and doubles. This builds on previous work performing similarity transformations with more general, two-body Jastrow-style correlators. The theory is tested on 2D lattices ranging from small systems into the thermodynamic limit and is compared to available reference data.

  19. Overlapping molecular pathological themes link Charcot-Marie-Tooth neuropathies and hereditary spastic paraplegias.

    Science.gov (United States)

    Timmerman, Vincent; Clowes, Virginia E; Reid, Evan

    2013-08-01

    In this review we focus on Charcot-Marie-Tooth (CMT) neuropathies and hereditary spastic paraplegias (HSPs). Although these diseases differ in whether they primarily affect the peripheral or central nervous system, both are genetically determined, progressive, long axonopathies that affect motor and sensory pathways. This commonality suggests that there might be similarities in the molecular pathology underlying these conditions, and here we compare the molecular genetics and cellular pathology of the two groups. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Silane and Germane Molecular Electronics.

    Science.gov (United States)

    Su, Timothy A; Li, Haixing; Klausen, Rebekka S; Kim, Nathaniel T; Neupane, Madhav; Leighton, James L; Steigerwald, Michael L; Venkataraman, Latha; Nuckolls, Colin

    2017-04-18

    This Account provides an overview of our recent efforts to uncover the fundamental charge transport properties of Si-Si and Ge-Ge single bonds and introduce useful functions into group 14 molecular wires. We utilize the tools of chemical synthesis and a scanning tunneling microscopy-based break-junction technique to study the mechanism of charge transport in these molecular systems. We evaluated the fundamental ability of silicon, germanium, and carbon molecular wires to transport charge by comparing conductances within families of well-defined structures, the members of which differ only in the number of Si (or Ge or C) atoms in the wire. For each family, this procedure yielded a length-dependent conductance decay parameter, β. Comparison of the different β values demonstrates that Si-Si and Ge-Ge σ bonds are more conductive than the analogous C-C σ bonds. These molecular trends mirror what is seen in the bulk. The conductance decay of Si and Ge-based wires is similar in magnitude to those from π-based molecular wires such as paraphenylenes However, the chemistry of the linkers that attach the molecular wires to the electrodes has a large influence on the resulting β value. For example, Si- and Ge-based wires of many different lengths connected with a methyl-thiomethyl linker give β values of 0.36-0.39 Å -1 , whereas Si- and Ge-based wires connected with aryl-thiomethyl groups give drastically different β values for short and long wires. This observation inspired us to study molecular wires that are composed of both π- and σ-orbitals. The sequence and composition of group 14 atoms in the σ chain modulates the electronic coupling between the π end-groups and dictates the molecular conductance. The conductance behavior originates from the coupling between the subunits, which can be understood by considering periodic trends such as bond length, polarizability, and bond polarity. We found that the same periodic trends determine the electric field

  1. An open-label randomized controlled trial of low molecular weight heparin compared to heparin and coumadin for the treatment of venous thromboembolic events in children: the REVIVE trial.

    Science.gov (United States)

    Massicotte, Patricia; Julian, Jim A; Gent, Michael; Shields, Karen; Marzinotto, Velma; Szechtman, Barbara; Andrew, Maureen

    2003-01-25

    Venous thromboembolic events (VTE) are serious complications in children and for which the standard of care, unfractionated heparin followed by oral anticoagulation (UFH/OA), is problematic. The objective of REVIVE was to compare the efficacy and safety of a low molecular weight heparin (reviparin-sodium) to UFH/OA for the treatment of VTE in children. This multicenter, open-label study, with blinded central outcome adjudication, randomized patients with objectively confirmed VTE to receive either