Self assertion modeled as a network repertoire of multi-determinant antibodies

NARCIS (Netherlands)

Takumi, K.; Boer, R.J. de

1996-01-01

We study repertoire selection in a network of natural antibodies that is maintained by stimulatory idiotypic interactions. The natural antibody repertoire develops in an environment of self epitopes to which the self-reactive B cell clones are completely tolerant. For the modeling formalism, we

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

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Ilja V. Khavrutskii

2017-08-01

Full Text Available Recent advances in the next-generation sequencing of B-cell receptors (BCRs enable the characterization of humoral responses at a repertoire-wide scale and provide the capability for identifying unique features of immune repertoires in response to disease, vaccination, or infection. Immunosequencing now readily generates 103–105 sequences per sample; however, statistical analysis of these repertoires is challenging because of the high genetic diversity of BCRs and the elaborate clonal relationships among them. To date, most immunosequencing analyses have focused on reporting qualitative trends in immunoglobulin (Ig properties, such as usage or somatic hypermutation (SHM percentage of the Ig heavy chain variable (IGHV gene segment family, and on reducing complex Ig property distributions to simple summary statistics. However, because Ig properties are typically not normally distributed, any approach that fails to assess the distribution as a whole may be inadequate in (1 properly assessing the statistical significance of repertoire differences, (2 identifying how two repertoires differ, and (3 determining appropriate confidence intervals for assessing the size of the differences and their potential biological relevance. To address these issues, we have developed a technique that uses Wilcox’ robust statistics toolbox to identify statistically significant vaccine-specific differences between Ig repertoire properties. The advantage of this technique is that it can determine not only whether but also where the distributions differ, even when the Ig repertoire properties are non-normally distributed. We used this technique to characterize murine germinal center (GC B-cell repertoires in response to a complex Ebola virus-like particle (eVLP vaccine candidate with known protective efficacy. The eVLP-mediated GC B-cell responses were highly diverse, consisting of thousands of clonotypes. Despite this staggering diversity, we identified statistically

Developing Professional “Game Teacher” Repertoires

DEFF Research Database (Denmark)

Lieberoth, Andreas; Hanghøj, Thorkild

2017-01-01

for in their professional careers. We expand and explain these findings using embedded mixed methods analysis, and conclude that games are a good practical case for training various teaching competences, but that building flexible professional repertoires requires more varied experiences than a single course can muster.......The first Danish Game-Based Learning course offered by a teachers college enrolled 42 students with a variety of backgrounds and interests in games. We characterize the students who enrolled in the course in terms of gaming literacies and preferences, and gauge the impact of the course in terms...... of building actionable skill sets. Following Schön (1986) we use these data to frame students’ transition from gamers or game curious teachers to developing professional repertoires.Interviews and statistical comparison to other students indicate that while student’s existing preferences for the “heavier...

Quantitative Analysis of Repertoire Scale Immunoglobulin properties in Vaccine Induced B cell Responses

Science.gov (United States)

Immunosequencing now readily generates 103105 sequences per sample ; however, statistical analysis of these repertoires is challenging because of the high genetic...diversity of BCRs and the elaborate clonal relationships among them. To date, most immunosequencing analyses have focused on reporting qualitative ...repertoire differences, (2) identifying how two repertoires differ, and (3) determining appropriate confidence intervals for assessing the size of the differences and their potential biological relevance.

Strategies for B-cell receptor repertoire analysis in Primary Immunodeficiencies:From severe combined immunodeficiency to common variable immunodeficiency

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Hanna eIJspeert

2015-04-01

Full Text Available The antigen receptor repertoires of B and T cells form the basis of the adaptive immune response. The repertoires should be sufficiently diverse to recognize all possible pathogens. However, careful selection is needed to prevent responses to self or harmless antigens. Limited antigen receptor repertoire diversity leads to immunodeficiency, whereas unselected or misdirected repertoires can result in autoimmunity. The antigen receptor repertoire harbors information about abnormalities in many immunological disorders. Recent developments in next generation sequencing allow the analysis of the antigen receptor repertoire in much greater detail than ever before. Analyzing the antigen receptor repertoire in patients with mutations in genes responsible for the generation of the antigen receptor repertoire will give new insights into repertoire formation and selection. In this perspective we describe strategies and considerations for analysis of the naive and antigen selected B-cell repertoires in primary immunodeficiency (PID patients with a focus on severe combined immunodeficiency (SCID and common variable immunodeficiency (CVID.

Antibody Repertoire Development in Swine

Czech Academy of Sciences Publication Activity Database

Butler, J. E.; Wertz, N.; Šinkora, Marek

2017-01-01

Roč. 5, FEB 17 (2017), s. 255-279 ISSN 2165-8102 R&D Projects: GA ČR GA15-02274S; GA ČR(CZ) GA16-09296S Institutional support: RVO:61388971 Keywords : swine * pre-immune antibody repertoire * ileal Peyer's patches Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 4.708, year: 2016

Regulatory T cells expanded from HIV-1-infected individuals maintain phenotype, TCR repertoire and suppressive capacity.

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Mathieu Angin

Full Text Available While modulation of regulatory T cell (Treg function and adoptive Treg transfer are being explored as therapeutic modalities in the context of autoimmune diseases, transplantation and cancer, their role in HIV-1 pathogenesis remains less well defined. Controversy persists regarding their beneficial or detrimental effects in HIV-1 disease, which warrants further detailed exploration. Our objectives were to investigate if functional CD4(+ Tregs can be isolated and expanded from HIV-1-infected individuals for experimental or potential future therapeutic use and to determine phenotype and suppressive capacity of expanded Tregs from HIV-1 positive blood and tissue. Tregs and conventional T cell controls were isolated from blood and gut-associated lymphoid tissue of individuals with HIV-1 infection and healthy donors using flow-based cell-sorting. The phenotype of expanded Tregs was assessed by flow-cytometry and quantitative PCR. T-cell receptor ß-chain (TCR-β repertoire diversity was investigated by deep sequencing. Flow-based T-cell proliferation and chromium release cytotoxicity assays were used to determine Treg suppressive function. Tregs from HIV-1 positive individuals, including infants, were successfully expanded from PBMC and GALT. Expanded Tregs expressed high levels of FOXP3, CTLA4, CD39 and HELIOS and exhibited a highly demethylated TSDR (Treg-specific demethylated region, characteristic of Treg lineage. The TCRß repertoire was maintained following Treg expansion and expanded Tregs remained highly suppressive in vitro. Our data demonstrate that Tregs can be expanded from blood and tissue compartments of HIV-1+ donors with preservation of Treg phenotype, function and TCR repertoire. These results are highly relevant for the investigation of potential future therapeutic use, as currently investigated for other disease states and hold great promise for detailed studies on the role of Tregs in HIV-1 infection.

Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development

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Victor Greiff

2017-05-01

Full Text Available Antibody repertoire diversity and plasticity is crucial for broad protective immunity. Repertoires change in size and diversity across multiple B cell developmental stages and in response to antigen exposure. However, we still lack fundamental quantitative understanding of the extent to which repertoire diversity is predetermined. Therefore, we implemented a systems immunology framework for quantifying repertoire predetermination on three distinct levels: (1 B cell development (pre-B cell, naive B cell, plasma cell, (2 antigen exposure (three structurally different proteins, and (3 four antibody repertoire components (V-gene usage, clonal expansion, clonal diversity, repertoire size extracted from antibody repertoire sequencing data (400 million reads. Across all three levels, we detected a dynamic balance of high genetic (e.g., >90% for V-gene usage and clonal expansion in naive B cells and antigen-driven (e.g., 40% for clonal diversity in plasma cells predetermination and stochastic variation. Our study has implications for the prediction and manipulation of humoral immunity.

Epidural analgesia in early labour blocks the stress response but uterine contractions remain unchanged.

Science.gov (United States)

Scull, T J; Hemmings, G T; Carli, F; Weeks, S K; Mazza, L; Zingg, H H

1998-07-01

To determine the effect of epidural analgesia on biochemical markers of stress, plasma oxytocin concentrations and frequency of uterine contractions during the first stage of labour. Nine nulliparous women, in spontaneous labour, with a singleton fetus and cervical dilatation < or = 5 cm were enrolled. Epidural bupivacaine 0.25% (range 10-14 ml) was administered and bilateral sensory blockade to ice (T8-L4) achieved. Blood samples were collected before the epidermal block and every 10 min for one hour after the block was achieved for the measurement of plasma beta-endorphin, cortical, glucose, lactate and oxytocin concentrations. No exogenous oxytocin was given. Intensity of pain was assessed at the time of the blood sampling using a 10 cm visual analogue scale (VAS). The frequency of uterine contractions was recorded for 60 min before and after the epidural block. There was a decrease in plasma beta-endorphin and cortisol concentrations after epidural block (P < 0.01). There were no changes in plasma glucose and lactate concentrations. The mean VAS for pain decreased 10 min after epidural block was achieved and remained < 2 throughout the study period (P < 0.001). Mean plasma oxytocin concentrations did not change. The frequency of uterine contractions before and after the epidural block was similar. The metabolic stress response to the pain of labour was attenuated by epidural analgesia. In contrast, plasma oxytocin concentration and frequency of uterine contractions were unaffected by the attenuation of metabolic stress response.

Rule-Governed Behavior: Teaching a Preliminary Repertoire of Rule-Following to Children With Autism

OpenAIRE

Tarbox, Jonathan; Zuckerman, Carrie K; Bishop, Michele R; Olive, Melissa L; O'Hora, Denis P

2011-01-01

Rule-governed behavior is generally considered an integral component of complex verbal repertoires but has rarely been the subject of empirical research. In particular, little or no previous research has attempted to establish rule-governed behavior in individuals who do not already display the repertoire. This study consists of two experiments that evaluated multiple exemplar training procedures for teaching a simple component skill, which may be necessary for developing a repertoire of rule...

Average sperm count remains unchanged despite reduction in maternal smoking

DEFF Research Database (Denmark)

Priskorn, L; Nordkap, L; Bang, A K

2018-01-01

STUDY QUESTION: How are temporal trends in lifestyle factors, including exposure to maternal smoking in utero, associated to semen quality in young men from the general population? SUMMARY ANSWER: Exposure to maternal smoking was associated with lower sperm counts but no overall increase in sperm...... temporal trends. Parental age increased, and exposure in utero to maternal smoking declined from 40% among men investigated in 1996-2000 to 18% among men investigated in 2011-2016. Exposure to maternal smoking was associated with lower sperm counts but no overall increase in sperm counts was observed...... counts was observed during the study period despite a decrease in this exposure. WHAT IS KNOWN ALREADY: Meta-analyses suggest a continuous decline in semen quality but few studies have investigated temporal trends in unselected populations recruited and analysed with the same protocol over a long period...

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.

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Mikhail Shugay

2015-11-01

Full Text Available Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

Severity of Acute Infectious Mononucleosis Correlates with Cross-Reactive Influenza CD8 T-Cell Receptor Repertoires.

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Aslan, Nuray; Watkin, Levi B; Gil, Anna; Mishra, Rabinarayan; Clark, Fransenio G; Welsh, Raymond M; Ghersi, Dario; Luzuriaga, Katherine; Selin, Liisa K

2017-12-05

Fifty years after the discovery of Epstein-Barr virus (EBV), it remains unclear how primary infection with this virus leads to massive CD8 T-cell expansion and acute infectious mononucleosis (AIM) in young adults. AIM can vary greatly in severity, from a mild transient influenza-like illness to a prolonged severe syndrome. We questioned whether expansion of a unique HLA-A2.01-restricted, cross-reactive CD8 T-cell response between influenza virus A-M1 58 (IAV-M1) and EBV BMLF1 280 (EBV-BM) could modulate the immune response to EBV and play a role in determining the severity of AIM in 32 college students. Only ex vivo total IAV-M1 and IAV-M1+EBV-BM cross-reactive tetramer + frequencies directly correlated with AIM severity and were predictive of severe disease. Expansion of specific cross-reactive memory IAV-M1 T-cell receptor (TCR) Vβ repertoires correlated with levels of disease severity. There were unique profiles of qualitatively different functional responses in the cross-reactive and EBV-specific CD8 T-cell responses in each of the three groups studied, severe-AIM patients, mild-AIM patients, and seropositive persistently EBV-infected healthy donors, that may result from differences in TCR repertoire use. IAV-M1 tetramer + cells were functionally cross-reactive in short-term cultures, were associated with the highest disease severity in AIM, and displayed enhanced production of gamma interferon, a cytokine that greatly amplifies immune responses, thus frequently contributing to induction of immunopathology. Altogether, these data link heterologous immunity via CD8 T-cell cross-reactivity to CD8 T-cell repertoire selection, function, and resultant disease severity in a common and important human infection. In particular, it highlights for the first time a direct link between the TCR repertoire with pathogenesis and the diversity of outcomes upon pathogen encounter. IMPORTANCE The pathogenic impact of immune responses that by chance cross-react to unrelated

High diversity of the T-cell receptor repertoire of tumor-infiltrating lymphocytes in basal cell carcinoma

DEFF Research Database (Denmark)

Omland, Silje H; Hamrouni, Abdelbasset; Gniadecki, Robert

2017-01-01

to determine the clonality of TCR and degree of overlap in TCR repertoires between skin resident T-cells and TILs. We found high diversity of the TCR repertoire in BCC and control skin with random V-J gene usage and similar CDR3-length distribution. Lack of TCR repertoire restriction indicates absence of tumor......Whether specific T-cell clones are present in tumor infiltrating lymphocytes (TILs) in BCC is unknown. We employed deep sequencing of mRNA coding for the T-cell receptor (TCR) chains α- and β to characterize the repertoire of TILs in BCC. V and J gene-usage and CDR3 length were computed...

Negotiation over self-control and activity: an analysis of balancing in the repertoires of Finnish healthy lifestyles.

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Pajari, Pia M; Jallinoja, Piia; Absetz, Pilvikki

2006-05-01

This study analyses arguments for and against the notion of healthy lifestyles, and the construction of responsibility for health, in group discussions in Finland. With data from four focus groups, we identified five interpretative repertoires: a strong activity repertoire reflects the dominant cultural value of health and emphasizes self-control. Three other repertoires--illness, external barriers, and weak character--share the underlying values of the activity repertoire, but exemplify situations where the individual lacks control, seeking to justify deviations from the norm of activity. One counter-repertoire, the pleasure repertoire, questions the hegemonic value of health, and discusses other competing values. The discussion of health is an ongoing dialectical process drawing from the different repertoires. In order to avoid stigmatization and to save face in the social situation of a focus group, the subjects strive to balance their accounts of behaviours considered unhealthy by also claiming healthy behaviours. They also strike a balance between extreme rigidity and carelessness, emphasizing the ideal of moderation and harmony. The findings point to a need to consider variations in and underpinnings of a "good life" at the individual level. Encouraging people to specify the meaning and content of moderation in their personal lives could provide a new perspective for health education and health promotion.

Friendship Repertoires and Care Arrangement: A Praxeological Approach.

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Hahmann, Julia

2017-01-01

Friends are important companions and serve as sources for diverse dimensions of social support, including elderly care. Rather than researching populations that have already established care arrangements including friends, the author seeks to understand relationship systems with a focus on the inner logic friendship to consequently describe and understand involved care arrangements, be it with family members or friends. To illustrate the diversity of friendship repertoires, qualitative interviews with older adult Germans are analyzed regarding cognitive concepts of friendships in contrast to familiar ties as well as social practices around relationship systems. While some repertoires successfully include chosen ties in their care arrangements, others not only focus on family, they do not wish to receive care from friends. The article's praxeological approach highlights the need to reflect habitual differences when thinking about elderly informal care arrangements. © The Author(s) 2016.

BRAZILIAN FEMINIST MOVEMENT: REPERTOIRE AND STRATEGIES FOR ACTION

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Carla de Paiva Bezerra

2014-08-01

Full Text Available This article aims at analyzing the development of and changes in, the repertoire and strategies for action of the Brazilian feminist movement, in the period between the democratic “re-opening” set in the 1980s and the first decade of the XXI century. Our interest is centered in two foci of analysis: on the one hand, it focuses on the movement’s positioning in relation to the State, which varied from a situation of opposition, or even of indifference, to direct attempts at influencing public policies and actions in the State sphere, whether through party politics or participative institutions. On the other hand, we are interested in analyzing how, and in which specific moments, agency beyond the national feminist frontiers takes place and in which measure this influences the local repertoires and vice-versa.

Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires

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Pemberton Trevor J

2006-09-01

Full Text Available Abstract Background The peptidyl-prolyl cis/trans isomerase (PPIase class of proteins is present in all known eukaryotes, prokaryotes, and archaea, and it is comprised of three member families that share the ability to catalyze the cis/trans isomerisation of a prolyl bond. Some fungi have been used as model systems to investigate the role of PPIases within the cell, however how representative these repertoires are of other fungi or humans has not been fully investigated. Results PPIase numbers within these fungal repertoires appears associated with genome size and orthology between repertoires was found to be low. Phylogenetic analysis showed the single-domain FKBPs to evolve prior to the multi-domain FKBPs, whereas the multi-domain cyclophilins appear to evolve throughout cyclophilin evolution. A comparison of their known functions has identified, besides a common role within protein folding, multiple roles for the cyclophilins within pre-mRNA splicing and cellular signalling, and within transcription and cell cycle regulation for the parvulins. However, no such commonality was found with the FKBPs. Twelve of the 17 human cyclophilins and both human parvulins, but only one of the 13 human FKBPs, identified orthologues within these fungi. hPar14 orthologues were restricted to the Pezizomycotina fungi, and R. oryzae is unique in the known fungi in possessing an hCyp33 orthologue and a TPR-containing FKBP. The repertoires of Cryptococcus neoformans, Aspergillus fumigatus, and Aspergillus nidulans were found to exhibit the highest orthology to the human repertoire, and Saccharomyces cerevisiae one of the lowest. Conclusion Given this data, we would hypothesize that: (i the evolution of the fungal PPIases is driven, at least in part, by the size of the proteome, (ii evolutionary pressures differ both between the different PPIase families and the different fungi, and (iii whilst the cyclophilins and parvulins have evolved to perform conserved

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires.

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Mikhail V Pogorelyy

2017-07-01

Full Text Available The diversity of T-cell receptors recognizing foreign pathogens is generated through a highly stochastic recombination process, making the independent production of the same sequence rare. Yet unrelated individuals do share receptors, which together constitute a "public" repertoire of abundant clonotypes. The TCR repertoire is initially formed prenatally, when the enzyme inserting random nucleotides is downregulated, producing a limited diversity subset. By statistically analyzing deep sequencing T-cell repertoire data from twins, unrelated individuals of various ages, and cord blood, we show that T-cell clones generated before birth persist and maintain high abundances in adult organisms for decades, slowly decaying with age. Our results suggest that large, low-diversity public clones are created during pre-natal life, and survive over long periods, providing the basis of the public repertoire.

Immune Repertoire Characteristics and Dynamics in Cancer

DEFF Research Database (Denmark)

Liu, Xiao

The diversity of T and B cells in terms of their receptors is huge in the invertebrate’s immune system, to provide broad protection against the vast diversity of pathogens. Immune repertoire is defined as the sum of total subtypes that makes the organism’s immune system, either T cell receptor or...

Antibody repertoire profiling with mimotope arrays

OpenAIRE

Pashova, Shina; Schneider, Christoph; von Gunten, Stephan; Pashov, Anastas

2016-01-01

Large-scale profiling and monitoring of antibody repertoires is possible through next generation sequencing (NGS), phage display libraries and microarrays. These methods can be combined in a pipeline, which ultimately maps the antibody reactivities onto defined arrays of structures - peptides or carbohydrates. The arrays can help analyze the individual specificities or can be used as complex patterns. In any case, the targets recognized should formally be considered mimotopes unless they are ...

Rule-Governed Behavior: Teaching a Preliminary Repertoire of Rule-Following to Children with Autism

Science.gov (United States)

Tarbox, Jonathan; Zuckerman, Carrie K.; Bishop, Michele R.; Olive, Melissa L.; O'Hora, Denis P.

2011-01-01

Rule-governed behavior is generally considered an integral component of complex verbal repertoires but has rarely been the subject of empirical research. In particular, little or no previous research has attempted to establish rule-governed behavior in individuals who do not already display the repertoire. This study consists of two experiments…

Monitoring pharmacologically induced immunosuppression by immune repertoire sequencing to detect acute allograft rejection in heart transplant patients: a proof-of-concept diagnostic accuracy study.

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Christopher Vollmers

2015-10-01

Full Text Available It remains difficult to predict and to measure the efficacy of pharmacological immunosuppression. We hypothesized that measuring the B-cell repertoire would enable assessment of the overall level of immunosuppression after heart transplantation.In this proof-of-concept study, we implemented a molecular-barcode-based immune repertoire sequencing assay that sensitively and accurately measures the isotype and clonal composition of the circulating B cell repertoire. We used this assay to measure the temporal response of the B cell repertoire to immunosuppression after heart transplantation. We selected a subset of 12 participants from a larger prospective cohort study (ClinicalTrials.gov NCT01985412 that is ongoing at Stanford Medical Center and for which enrollment started in March 2010. This subset of 12 participants was selected to represent post-heart-transplant events, with and without acute rejection (six participants with moderate-to-severe rejection and six without. We analyzed 130 samples from these patients, with an average follow-up period of 15 mo. Immune repertoire sequencing enables the measurement of a patient's net state of immunosuppression (correlation with tacrolimus level, r = -0.867, 95% CI -0.968 to -0.523, p = 0.0014, as well as the diagnosis of acute allograft rejection, which is preceded by increased immune activity with a sensitivity of 71.4% (95% CI 30.3% to 94.9% and a specificity of 82.0% (95% CI 72.1% to 89.1% (cell-free donor-derived DNA as noninvasive gold standard. To illustrate the potential of immune repertoire sequencing to monitor atypical post-transplant trajectories, we analyzed two more patients, one with chronic infections and one with amyloidosis. A larger, prospective study will be needed to validate the power of immune repertoire sequencing to predict rejection events, as this proof-of-concept study is limited to a small number of patients who were selected based on several criteria including the

Co-regulation of a large and rapidly evolving repertoire of odorant receptor genes

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Lane Robert P

2007-09-01

Full Text Available Abstract The olfactory system meets niche- and species-specific demands by an accelerated evolution of its odorant receptor repertoires. In this review, we describe evolutionary processes that have shaped olfactory and vomeronasal receptor gene families in vertebrate genomes. We emphasize three important periods in the evolution of the olfactory system evident by comparative genomics: the adaptation to land in amphibian ancestors, the decline of olfaction in primates, and the delineation of putative pheromone receptors concurrent with rodent speciation. The rapid evolution of odorant receptor genes, the sheer size of the repertoire, as well as their wide distribution in the genome, presents a developmental challenge: how are these ever-changing odorant receptor repertoires coordinated within the olfactory system? A central organizing principle in olfaction is the specialization of sensory neurons resulting from each sensory neuron expressing only ~one odorant receptor allele. In this review, we also discuss this mutually exclusive expression of odorant receptor genes. We have considered several models to account for co-regulation of odorant receptor repertoires, as well as discussed a new hypothesis that invokes important epigenetic properties of the system.

Antibodies: From novel repertoires to defining and refining the structure of biologically important targets.

Science.gov (United States)

Conroy, Paul J; Law, Ruby H P; Caradoc-Davies, Tom T; Whisstock, James C

2017-03-01

Antibodies represent a highly successful class of molecules that bind a wide-range of targets in therapeutic-, diagnostic- and research-based applications. The antibody repertoire is composed of the building blocks required to develop an effective adaptive immune response against foreign insults. A number of species have developed novel genetic and structural mechanisms from which they derive these antibody repertoires, however, traditionally antibodies are isolated from human, and rodent sources. Due to their high-value therapeutic, diagnostic, biotechnological and research applications, much innovation has resulted in techniques and approaches to isolate novel antibodies. These approaches are bolstered by advances in our understanding of species immune repertoires, next generation sequencing capacity, combinatorial antibody discovery and high-throughput screening. Structural determination of antibodies and antibody-antigen complexes has proven to be pivotal to our current understanding of the immune repertoire for a range of species leading to advances in man-made libraries and fine tuning approaches to develop antibodies from immune-repertoires. Furthermore, the isolation of antibodies directed against antigens of importance in health, disease and developmental processes, has yielded a plethora of structural and functional insights. This review highlights the significant contribution of antibody-based crystallography to our understanding of adaptive immunity and its application to providing critical information on a range of human-health related indications. Copyright © 2017 Elsevier Inc. All rights reserved.

The porcine antibody repertoire: Variations on the textbook theme

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John eButler

2012-06-01

Full Text Available The genes encoding the heavy and light chains of swine antibodies are organized in the same manner as in other eutherian mammals. There are ~ 30 VH genes, two functional DH genes and one functional JH gene. There are 14-60 V genes and 5 J segments, >22V genes and at least four JC cassettes. The heavy chain constant regions encode the same repertoire of isotypes common to other eutherian mammals. The piglet models offers advantage over rodent models since the fetal repertoire develops without maternal influences and the precocial nature of their multiple offspring allows the experimenter to control the influences of environmental and maternal factors on repertoire development postnatally. B cell lymphogenesis in swine begins in the fetal yolk sac at 20 days of gestation (DG, moves to the fetal liver at 30 DG and eventually to the bone marrow which dominates until birth (114 DG and to at least 5 weeks postpartum. There is no evidence that the ileal Peyers patches are a site of B cell lymphogenesis or are required for B cell maintenance. Unlike rodents and humans, light chain rearrangement begins first in the lambda locus; kappa rearrangements are not seen until late gestation.Dissimilar to lab rodents and more in the direction of the rabbit, swine utilize a small number of VH genes to form >90% of their pre-immune repertoire. Diversification in response to environmental antigen does not alter this pattern and is achieved by somatic hypermutation (SHM of the same small number of VH genes. The situation for light chains is less-well studied, but certain V and J and V and J are dominant in transcripts. The transcribed and secreted pre-immune antibodies of the fetus include mainly IgM, IgA and IgG3; this last isotype may provide a type of first responder mucosal immunity. Development of functional adaptive immunity is dependent on bacterial PAMPs or PAMPs provided by viral infections, indicating the importance of innate

Iterative Design toward Equity: Youth Repertoires of Practice in a High School Maker Space

Science.gov (United States)

Martin, Lee; Dixon, Colin; Betser, Sagit

2018-01-01

Despite their potential, maker activities do not always support equitable engagement. The authors report on a design research study where they worked to support equitable engagement of youth repertoires of practice in a high school makerspace. Their orientation toward equity is grounded in the construct of repertoires of practice, and they focus…

At the end of a two-year follow-up elevated TSH levels normalize or remain unchanged in most the children with subclinical hypothyroidism

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De Luca Filippo

2010-01-01

Full Text Available Abstract Data about the natural evolution of subclinical hypothyroidism (SH in pediatric age are very scanty. Moreover all the available reports in both aged and young patients were based on unselected study populations including also patients with either thyroid disorders or other pathological causes that are well known to be able to affect SH development and evolution. Aim of the study by Wasniewska et al was to prospectively evaluate for the first time the natural course of SH in children and adolescents with no underlying diseases and no risk factors that might interfere with the progression of SH. On the basis of the 2-year follow-up results, the Authors concluded that: a the natural course of TSH values in a pediatric population with idiopathic SH is characterized by a progressive decrease over time; b the majority of patients (88% normalized or maintained unchanged their TSH; and c TSH changes were not associated with changes of either FT4 values or clinical status or auxological parameters. Study design of this study is very accurate and the results are robust, thus supporting the Authors' conclusions.

METHODOLOGICAL PRINCIPLES OF FORMING REPERTOIRE OF STUDENTS’ FOLK INSTRUMENTAL ORCHESTRA

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Mykola Pshenychnykh

2016-11-01

Full Text Available One of the main aspects of forming future music teachers’ professional competence, connected with mastering professional musical and performing skills in the course “Orchestra Class” and realized in the activity of students’ performing group, is revealed. Nowadays the problem of creative personality development is relevant, as creative future music art teachers freely orient themselves and guide pupils students in today's cultural environment, music and media space, have a strong musical taste and aesthetic guidelines. The music genre groups have been characterized in the article. It is thought that these groups are the traditional components of repertoire of folk and orchestra student groups: arrangements of folk tunes; works of Ukrainian and world classics, orchestrated for the folk groups, taking into account each orchestra performing possibilities; works by contemporary authors, written specifically for the orchestra of folk instruments. The main methodological principles of selecting the repertoire for the student orchestra of folk instruments are disclosed, including: technical, artistic and performing capabilities of student groups; involvement of works of different genres into the repertoire; correspondence of orchestra scores to instrumental composition of the student orchestra, and their correction if it is necessary; selecting works, whose performing arouses interest of the student audience; using the experience of the leading professional ensembles of folk instruments; constant updating the orchestra's repertoire. In the conclusion the author emphasizes that taking into account the methodological tips helps solve the main tasks within the course of “Orchestra Class”. These tips are the following: students’ acquaintance with the history of foundation, composition, ways of musicianship, technique of playing the instrument of folk instrument orchestra and acquaintance with specific orchestral music; development of all

Linking experiences with emotions and the development of interpretive repertoires

Science.gov (United States)

McRae, Norah I.

2010-03-01

In this paper I consider the case of one student, Todd Alexander, through analyzing the transcripts of his interviews between him and his teacher (Wolff-Michael Roth). I examine the role that emotions play in the development of the interpretive repertoires that Todd employed as he talked about his scientific and his religious beliefs. I identify how lived experiences support the development of emotions and what educational conditions are necessary to allow for appropriate lived experiences. In so doing we might be able to support educational conditions that result in interpretive repertoires that allow for acceptance of multiple perspectives with a moral grounding, leading to students who are well positioned to be valuable contributors to society.

Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences.

Science.gov (United States)

Galson, Jacob D; Trück, Johannes; Fowler, Anna; Clutterbuck, Elizabeth A; Münz, Márton; Cerundolo, Vincenzo; Reinhard, Claudia; van der Most, Robbert; Pollard, Andrew J; Lunter, Gerton; Kelly, Dominic F

2015-12-01

Generating a diverse B cell immunoglobulin repertoire is essential for protection against infection. The repertoire in humans can now be comprehensively measured by high-throughput sequencing. Using hepatitis B vaccination as a model, we determined how the total immunoglobulin sequence repertoire changes following antigen exposure in humans, and compared this to sequences from vaccine-specific sorted cells. Clonal sequence expansions were seen 7 days after vaccination, which correlated with vaccine-specific plasma cell numbers. These expansions caused an increase in mutation, and a decrease in diversity and complementarity-determining region 3 sequence length in the repertoire. We also saw an increase in sequence convergence between participants 14 and 21 days after vaccination, coinciding with an increase of vaccine-specific memory cells. These features allowed development of a model for in silico enrichment of vaccine-specific sequences from the total repertoire. Identifying antigen-specific sequences from total repertoire data could aid our understanding B cell driven immunity, and be used for disease diagnostics and vaccine evaluation.

Identification of a bitter-taste receptor gene repertoire in different Lagomorphs species

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Ana M. Ferreira

2016-04-01

Full Text Available The repertoires of bitter taste receptor (T2R gene have been described for several animal species, but these data are still scarce for Lagomorphs. The aim of the present work is to identify potential repertoires of T2R in several Lagomorph species, covering a wide geographical distribution. We studied these genes in Lepus timidus, Lepus europaeus, Oryctolagus cuniculus algirus, Romerolagus diazi and Sylvilagus floridanus, using Oryctolagus cuniculus cuniculus as control species for PCR and DNA sequencing. We studied the identities of the DNA sequences and built the corresponding phylogenetic tree. Sequencing was successful for both subspecies of Oryctolagus cuniculus for all T2R genes studied, for five genes in Lepus, and for three genes in Romerolagus diazi and Sylvilagus floridanus. We describe for the first time the partial repertoires of T2R genes for Lagomorphs species, other than the common rabbit. Our phylogenetic analyses indicate that sequence proximity levels follow the established taxonomic classification.

A Comparison of the Basic Song Repertoire of Vocal/Choral and Instrumental Music Education Majors.

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Prickett, Carol A.; Bridges, Madeline S.

2000-01-01

Explores whether the basic song repertoire of vocal/choral music education majors is significantly better than instrumental music education majors. Participants attempted to identify 25 standard songs. Reveals no significant difference between the two groups, indicating that neither had developed a strong repertoire of songs. (CMK)

From everyday communicative figurations to rigorous audience news repertoires

DEFF Research Database (Denmark)

Kobbernagel, Christian; Schrøder, Kim Christian

2016-01-01

In the last couple of decades there has been an unprecedented explosion of news media platforms and formats, as a succession of digital and social media have joined the ranks of legacy media. We live in a ‘hybrid media system’ (Chadwick, 2013), in which people build their cross-media news...... repertoires from the ensemble of old and new media available. This article presents an innovative mixed-method approach with considerable explanatory power to the exploration of patterns of news media consumption. This approach tailors Q-methodology in the direction of a qualitative study of news consumption......, in which a card sorting exercise serves to translate the participants’ news media preferences into a form that enables the researcher to undertake a rigorous factor-analytical construction of their news consumption repertoires. This interpretive, factor-analytical procedure, which results in the building...

High-throughput Sequencing Based Immune Repertoire Study during Infectious Disease

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Dongni Hou

2016-08-01

Full Text Available The selectivity of the adaptive immune response is based on the enormous diversity of T and B cell antigen-specific receptors. The immune repertoire, the collection of T and B cells with functional diversity in the circulatory system at any given time, is dynamic and reflects the essence of immune selectivity. In this article, we review the recent advances in immune repertoire study of infectious diseases that achieved by traditional techniques and high-throughput sequencing techniques. High-throughput sequencing techniques enable the determination of complementary regions of lymphocyte receptors with unprecedented efficiency and scale. This progress in methodology enhances the understanding of immunologic changes during pathogen challenge, and also provides a basis for further development of novel diagnostic markers, immunotherapies and vaccines.

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

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Lorenzo Asti

2016-04-01

Full Text Available The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high-frequency mutation rate in the genome region that codes for the antibody active site. Eventually, cells that produce antibodies with higher affinity for their cognate antigen are selected and clonally expanded. Here, we propose a new statistical approach based on maximum entropy modeling in which a scoring function related to the binding affinity of antibodies against a specific antigen is inferred from a sample of sequences of the immune repertoire of an individual. We use our inference strategy to infer a statistical model on a data set obtained by sequencing a fairly large portion of the immune repertoire of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10-6, outperforming other sequence- and structure-based models.

Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences

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Jacob D. Galson

2015-12-01

Full Text Available Generating a diverse B cell immunoglobulin repertoire is essential for protection against infection. The repertoire in humans can now be comprehensively measured by high-throughput sequencing. Using hepatitis B vaccination as a model, we determined how the total immunoglobulin sequence repertoire changes following antigen exposure in humans, and compared this to sequences from vaccine-specific sorted cells. Clonal sequence expansions were seen 7 days after vaccination, which correlated with vaccine-specific plasma cell numbers. These expansions caused an increase in mutation, and a decrease in diversity and complementarity-determining region 3 sequence length in the repertoire. We also saw an increase in sequence convergence between participants 14 and 21 days after vaccination, coinciding with an increase of vaccine-specific memory cells. These features allowed development of a model for in silico enrichment of vaccine-specific sequences from the total repertoire. Identifying antigen-specific sequences from total repertoire data could aid our understanding B cell driven immunity, and be used for disease diagnostics and vaccine evaluation.

Diversification of the Primary Antibody Repertoire by AID-Mediated Gene Conversion.

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Lanning, Dennis K; Knight, Katherine L

2015-01-01

Gene conversion, mediated by activation-induced cytidine deaminase (AID), has been found to contribute to generation of the primary antibody repertoire in several vertebrate species. Generation of the primary antibody repertoire by gene conversion of immunoglobulin (Ig) genes occurs primarily in gut-associated lymphoid tissues (GALT) and is best described in chicken and rabbit. Here, we discuss current knowledge of the mechanism of gene conversion as well as the contribution of the microbiota in promoting gene conversion of Ig genes. Finally, we propose that the antibody diversification strategy used in GALT species, such as chicken and rabbit, is conserved in a subset of human and mouse B cells.

IgM repertoire biodiversity is reduced in HIV-1 infection and systemic lupus erythematosus

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Li eYin

2013-11-01

Full Text Available Background: HIV-1 infection or systemic lupus erythematosus [SLE] disrupt B cell homeostasis, reduce memory B cells, and impair function of IgG and IgM antibodies. Objective: To determine how disturbances in B cell populations producing polyclonal antibodies relate to the IgM repertoire, the IgM transcriptome in health and disease was explored at the complementarity determining region 3 [CDRH3] sequence population level. Methods: 454-deep pyrosequencing in combination with a novel analysis pipeline was applied to define populations of IGHM CDRH3 sequences based on absence or presence of somatic hypermutations [SHM] in peripheral blood B cells. Results: HIV or SLE subjects have reduced biodiversity within their IGHM transcriptome compared to healthy subjects, mainly due to a significant decrease in the number of unique combinations of alleles, although recombination machinery was intact. While major differences between sequences without or with SHM occurred among all groups, IGHD and IGHJ allele use, CDRH3 length distribution, or generation of SHM were similar among study cohorts. Antiretroviral therapy failed to normalize IGHM biodiversity in HIV-infected individuals. All subjects had a low frequency of allelic combinations within the IGHM repertoire similar to known broadly-neutralizing HIV-1 antibodies. Conclusions: Polyclonal expansion would decrease overall IgM biodiversity independent of other mechanisms for development of the B cell repertoire. Applying deep sequencing as a strategy to follow development of the IgM repertoire in health and disease provides a novel molecular assessment of multiple points along the B cell differentiation pathway that is highly sensitive for detecting perturbations within the repertoire at the population level.

Difficulties when assessing birdsong learning programmes under field conditions: a re-evaluation of song repertoire flexibility in the great tit.

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Rivera-Gutierrez, Hector F; Pinxten, Rianne; Eens, Marcel

2011-01-17

There is a remarkable diversity of song-learning strategies in songbirds. Establishing whether a species is closed- or open-ended is important to be able to interpret functional and evolutionary consequences of variation in repertoire size. Most of our knowledge regarding the timing of vocal learning is based on laboratory studies, despite the fact that these may not always replicate the complex ecological and social interactions experienced by birds in the wild. Given that field studies cannot provide the experimental control of laboratory studies, it may not be surprising that species such as the great tit that were initially assumed to be closed-ended learners have later been suggested to be open-ended learners. By using an established colour-ringed population, by following a standardized recording protocol, and by taking into account the species' song ecology (using only recordings obtained during peak of singing at dawn), we replicated two previous studies to assess song repertoire learning and flexibility in adult wild great tits elicited by social interactions. First, we performed a playback experiment to test repertoire plasticity elicited by novel versus own songs. Additionally, in a longitudinal study, we followed 30 males in two consecutive years and analysed whether new neighbours influenced any change in the repertoire. Contrary to the previous studies, song repertoire size and composition were found to be highly repeatable both between years and after confrontation with a novel song. Our results suggest that great tits are closed-ended learners and that their song repertoire probably does not change during adulthood. Methodological differences that may have led to an underestimation of the repertoires or population differences may explain the discrepancy in results with previous studies. We argue that a rigorous and standardized assessment of the repertoire is essential when studying age- or playback-induced changes in repertoire size and composition

Repertoire of free-living protozoa in contact lens solutions.

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Bouchoucha, Ibtissem; Aziz, Aurore; Hoffart, Louis; Drancourt, Michel

2016-10-29

The repertoire of free-living protozoa in contact lens solutions is poorly known despite the fact that such protozoa may act as direct pathogens and may harbor intra-cellular pathogens. Between 2009 and 2014, the contact lens solutions collected from patients presenting at our Ophthalmology Department for clinically suspected keratitis, were cultured on non-nutrient agar examined by microscope for the presence of free-living protozoa. All protozoa were identified by 18S rRNA gene sequencing. A total of 20 of 233 (8.6 %) contact lens solution specimens collected from 16 patients were cultured. Acanthamoeba amoeba in 16 solutions (80 %) collected from 12 patients and Colpoda steini, Cercozoa sp., Protostelium sp. and a eukaryotic more closely related to Vermamoeba sp., were each isolated in one solution. Cercozoa sp., Colpoda sp., Protostelium sp. and Vermamoeba sp. are reported for the first time as contaminating contact lens solutions. The repertoire of protozoa in contact lens solutions is larger than previously known.

Impact of clonal competition for peptide-MHC complexes on the CD8[superscript +] T-cell repertoire selection in a persistent viral infection

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Wynn, Katherine K.; Fulton, Zara; Cooper, Leanne; Silins, Sharon L.; Gras, Stephanie; Archbold, Julia K.; Tynan, Fleur E.; Miles, John J.; McCluskey, James; Burrows, Scott R.; Rossjohn, Jamie; Khanna, Rajiv (Monash); (Queensland Inst. of Med. Rsrch.); (Melbourne)

2008-04-29

CD8{sup +} T-cell responses to persistent viral infections are characterized by the accumulation of an oligoclonal T-cell repertoire and a reduction in the naive T-cell pool. However, the precise mechanism for this phenomenon remains elusive. Here we show that human cytomegalovirus (HCMV)-specific CD8{sup +} T cells recognizing distinct epitopes from the pp65 protein and restricted through an identical HLA class I allele (HLA B*3508) exhibited either a highly conserved public T-cell repertoire or a private, diverse T-cell response, which was uniquely altered in each donor following in vitro antigen exposure. Selection of a public T-cell receptor (TCR) was coincident with an atypical major histocompatibility complex (MHC)-peptide structure, in that the epitope adopted a helical conformation that bulged from the peptide-binding groove, while a diverse TCR profile was observed in response to the epitope that formed a flatter, more 'featureless' landscape. Clonotypes with biased TCR usage demonstrated more efficient recognition of virus-infected cells, a greater CD8 dependency, and were more terminally differentiated in their phenotype when compared with the T cells expressing diverse TCR. These findings provide new insights into our understanding on how the biology of antigen presentation in addition to the structural features of the pMHC-I might shape the T-cell repertoire and its phenotype.

A depauperate immune repertoire precedes evolution of sociality in bees.

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Barribeau, Seth M; Sadd, Ben M; du Plessis, Louis; Brown, Mark J F; Buechel, Severine D; Cappelle, Kaat; Carolan, James C; Christiaens, Olivier; Colgan, Thomas J; Erler, Silvio; Evans, Jay; Helbing, Sophie; Karaus, Elke; Lattorff, H Michael G; Marxer, Monika; Meeus, Ivan; Näpflin, Kathrin; Niu, Jinzhi; Schmid-Hempel, Regula; Smagghe, Guy; Waterhouse, Robert M; Yu, Na; Zdobnov, Evgeny M; Schmid-Hempel, Paul

2015-04-24

Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees and other sequenced social insects have far fewer canonical immune genes relative to solitary insects. Social protection from infection, including behavioral responses, may explain this depauperate immune repertoire. Here, based on full genome sequences, we describe the immune repertoire of two ecologically and commercially important bumblebee species that diverged approximately 18 million years ago, the North American Bombus impatiens and European Bombus terrestris. We find that the immune systems of these bumblebees, two species of honeybee, and a solitary leafcutting bee, are strikingly similar. Transcriptional assays confirm the expression of many of these genes in an immunological context and more strongly in young queens than males, affirming Bateman's principle of greater investment in female immunity. We find evidence of positive selection in genes encoding antiviral responses, components of the Toll and JAK/STAT pathways, and serine protease inhibitors in both social and solitary bees. Finally, we detect many genes across pathways that differ in selection between bumblebees and honeybees, or between the social and solitary clades. The similarity in immune complement across a gradient of sociality suggests that a reduced immune repertoire predates the evolution of sociality in bees. The differences in selection on immune genes likely reflect divergent pressures exerted by parasites across social contexts.

Next-Generation Sequencing of Antibody Display Repertoires

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Romain Rouet

2018-02-01

Full Text Available In vitro selection technology has transformed the development of therapeutic monoclonal antibodies. Using methods such as phage, ribosome, and yeast display, high affinity binders can be selected from diverse repertoires. Here, we review strategies for the next-generation sequencing (NGS of phage- and other antibody-display libraries, as well as NGS platforms and analysis tools. Moreover, we discuss recent examples relating to the use of NGS to assess library diversity, clonal enrichment, and affinity maturation.

Identity, small stories and interpretative repertoires in research interviews. An account of market researchers’ discursive positioning strategies

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Cosmin Toth

2014-12-01

Full Text Available My main purpose in this paper is to illustrate how participants in a research interview occasioned conversation make use of two important discursive devices, namely: small stories and interpretative repertoires for positioning during interaction in order to foster certain situated identity claims. The premises I work with in this paper are that identity is a practiced situated accomplishment, that small stories are devices employed frequently for identity work that are no less important than extended autobiographical expositions, and that interpretative repertoires are practiced ways of speaking that allow participants to manage their positions in certain ways. Moreover, I will try to show that positioning by means of small stories and interpretative repertoires should be understood in direct relation with the identities and other membership categories made relevant by the interviewer. When participants’ positions are conflicting or miss-aligned, a more pronounced identity work is employed on the part of the interviewee, sustained by certain repertoires’ management strategies: alternation, nuancing, or rejecting certain repertoires.

Leisure repertoire among persons with a spinal cord injury: Interests, performance, and well-being

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Lundström, Ulrica; Lilja, Margareta; Petersson, Ingela; Lexell, Jan; Isaksson, Gunilla

2014-01-01

Objective To explore and describe the leisure repertoire of persons with traumatic spinal cord injury (SCI) and how the repertoire is related to interest, performance, and well-being. Design Cross-sectional study. Setting A total of 97 persons with traumatic SCI were recruited from the non-profit national organization, RG Active Rehabilitation in Sweden. Outcome measure Data were collected through a two-part postal survey. The first comprised of questions investigating socio-demographic variables and injury characteristics; the second part included an interest checklist with 20 areas of leisure activities. Results The participants were mostly interested in, performed, and experienced well-being from social and culture activities and TV/DVD/movies. The areas of leisure activities in which they had most likely experienced changes after the SCI were outdoor activities, exercise, and gardening. Sex, age, and to some extent, time since injury were related to interest, performance, well-being, and changed performance. Conclusions The results provided an explanation and limited description of a changed leisure repertoire among persons after a traumatic SCI. The study showed that sex, age, and time since injury were more closely related to the choice of leisure activities to include in the leisure repertoire than the level of injury. This knowledge can be of importance when professionals in the field of rehabilitation are planning and implementing interventions concerning leisure activities for persons with SCI. PMID:24090284

Effects of spaceflight on the immunoglobulin repertoire of unimmunized C57BL/6 mice

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Ward, Claire; Rettig, Trisha A.; Hlavacek, Savannah; Bye, Bailey A.; Pecaut, Michael J.; Chapes, Stephen K.

2018-02-01

Spaceflight has been shown to suppress the adaptive immune response, altering the distribution and function of lymphocyte populations. B lymphocytes express highly specific and highly diversified receptors, known as immunoglobulins (Ig), that directly bind and neutralize pathogens. Ig diversity is achieved through the enzymatic splicing of gene segments within the genomic DNA of each B cell in a host. The collection of Ig specificities within a host, or Ig repertoire, has been increasingly characterized in both basic research and clinical settings using high-throughput sequencing technology (HTS). We utilized HTS to test the hypothesis that spaceflight affects the B-cell repertoire. To test this hypothesis, we characterized the impact of spaceflight on the unimmunized Ig repertoire of C57BL/6 mice that were flown aboard the International Space Station (ISS) during the Rodent Research One validation flight in comparison to ground controls. Individual gene segment usage was similar between ground control and flight animals, however, gene segment combinations and the junctions in which gene segments combine was varied among animals within and between treatment groups. We also found that spontaneous somatic mutations in the IgH and Igκ gene loci were not increased. These data suggest that space flight did not affect the B cell repertoire of mice flown and housed on the ISS over a short period of time.

Sustained multiplicity in everyday cholesterol reduction: repertoires and practices in talk about 'healthy living'.

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Will, Catherine M; Weiner, Kate

2014-02-01

This article is concerned with talk about and the practices of healthy living in relation to cholesterol reduction. It draws on qualitative interviews with 89 people who are current or former users of either cholesterol-lowering functional foods or statins for cardiovascular risk reduction. Focusing on data about everyday activities including food preparation, shopping and exercise, we illustrate four repertoires that feature in talk about cholesterol reduction (health, pleasure, sociality and pragmatism). Using Gilbert and Mulkay's notion of a 'reconciliation device', we suggest ways in which apparently contradictory repertoires are combined (for example, through talk about moderation) or kept apart. We suggest that, in contrast to the interactiveness of the repertoires of health and pleasure, a pragmatic repertoire concerning food provisioning, storage and cooking as well as the realities of exercise, appears distinct from talk about health and is relatively inert. Finally we consider the implications of these discursive patterns for daily practices. Our data suggest there is little emphasis on coherence in people's practices and illustrate the significance of temporal, spatial and social distribution in allowing people to pursue different priorities in their everyday lives. Rather than the calculated trade-offs of earlier medical sociology we draw on Mol to foreground the possibility of sustained multiplicity in daily practices. © 2014 The Authors. Sociology of Health & Illness © 2014 Foundation for the Sociology of Health & Illness/John Wiley & Sons Ltd.

Leisure repertoire among persons with a spinal cord injury: interests, performance, and well-being.

Science.gov (United States)

Lundström, Ulrica; Lilja, Margareta; Petersson, Ingela; Lexell, Jan; Isaksson, Gunilla

2014-03-01

To explore and describe the leisure repertoire of persons with traumatic spinal cord injury (SCI) and how the repertoire is related to interest, performance, and well-being. Cross-sectional study. A total of 97 persons with traumatic SCI were recruited from the non-profit national organization, RG Active Rehabilitation in Sweden. Data were collected through a two-part postal survey. The first comprised of questions investigating socio-demographic variables and injury characteristics; the second part included an interest checklist with 20 areas of leisure activities. The participants were mostly interested in, performed, and experienced well-being from social and culture activities and TV/DVD/movies. The areas of leisure activities in which they had most likely experienced changes after the SCI were outdoor activities, exercise, and gardening. Sex, age, and to some extent, time since injury were related to interest, performance, well-being, and changed performance. The results provided an explanation and limited description of a changed leisure repertoire among persons after a traumatic SCI. The study showed that sex, age, and time since injury were more closely related to the choice of leisure activities to include in the leisure repertoire than the level of injury. This knowledge can be of importance when professionals in the field of rehabilitation are planning and implementing interventions concerning leisure activities for persons with SCI.

Frequency and genetic characterization of V(DD)J recombinants in the human peripheral blood antibody repertoire.

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Briney, Bryan S; Willis, Jordan R; Hicar, Mark D; Thomas, James W; Crowe, James E

2012-09-01

Antibody heavy-chain recombination that results in the incorporation of multiple diversity (D) genes, although uncommon, contributes substantially to the diversity of the human antibody repertoire. Such recombination allows the generation of heavy chain complementarity determining region 3 (HCDR3) regions of extreme length and enables junctional regions that, because of the nucleotide bias of N-addition regions, are difficult to produce through normal V(D)J recombination. Although this non-classical recombination process has been observed infrequently, comprehensive analysis of the frequency and genetic characteristics of such events in the human peripheral blood antibody repertoire has not been possible because of the rarity of such recombinants and the limitations of traditional sequencing technologies. Here, through the use of high-throughput sequencing of the normal human peripheral blood antibody repertoire, we analysed the frequency and genetic characteristics of V(DD)J recombinants. We found that these recombinations were present in approximately 1 in 800 circulating B cells, and that the frequency was severely reduced in memory cell subsets. We also found that V(DD)J recombination can occur across the spectrum of diversity genes, indicating that virtually all recombination signal sequences that flank diversity genes are amenable to V(DD)J recombination. Finally, we observed a repertoire bias in the diversity gene repertoire at the upstream (5') position, and discovered that this bias was primarily attributable to the order of diversity genes in the genomic locus. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.

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Teresa Nogueira

Full Text Available Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.

Mother-Newborn Pairs in Malawi Have Similar Antibody Repertoires to Diverse Malaria Antigens.

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Boudová, Sarah; Walldorf, Jenny A; Bailey, Jason A; Divala, Titus; Mungwira, Randy; Mawindo, Patricia; Pablo, Jozelyn; Jasinskas, Algis; Nakajima, Rie; Ouattara, Amed; Adams, Matthew; Felgner, Philip L; Plowe, Christopher V; Travassos, Mark A; Laufer, Miriam K

2017-10-01

Maternal antibodies may play a role in protecting newborns against malaria disease. Plasmodium falciparum parasite surface antigens are diverse, and protection from infection requires allele-specific immunity. Although malaria-specific antibodies have been shown to cross the placenta, the extent to which antibodies that respond to the full repertoire of diverse antigens are transferred from the mother to the infant has not been explored. Understanding the breadth of maternal antibody responses and to what extent these antibodies are transferred to the child can inform vaccine design and evaluation. We probed plasma from cord blood and serum from mothers at delivery using a customized protein microarray that included variants of malaria vaccine target antigens to assess the intensity and breadth of seroreactivity to three malaria vaccine candidate antigens in mother-newborn pairs in Malawi. Among the 33 paired specimens that were assessed, mothers and newborns had similar intensity and repertoire of seroreactivity. Maternal antibody levels against vaccine candidate antigens were the strongest predictors of infant antibody levels. Placental malaria did not significantly impair transplacental antibody transfer. However, mothers with placental malaria had significantly higher antibody levels against these blood-stage antigens than mothers without placental malaria. The repertoire and levels of infant antibodies against a wide range of malaria vaccine candidate antigen variants closely mirror maternal levels in breadth and magnitude regardless of evidence of placental malaria. Vaccinating mothers with an effective malaria vaccine during pregnancy may induce high and potentially protective antibody repertoires in newborns. Copyright © 2017 American Society for Microbiology.

Precarious Voices? Types of “Political Citizens” and Repertoires of Action among European Youth

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Lara Monticelli

2017-01-01

Full Text Available This article’s goal is to explore the existence of ‘political citizens’ profiles across three European cities (Turin, Cologne and Lyon and to ascertain the role of an unstable occupational status on the repertoires of action deployed. For this purpose, a technique called latent class cluster analysis (LCCA is applied to a large sample, including young precarious and regular workers (deployed as a reference group. This technique allowed us to derive five descriptive probabilistic profiles of ‘political citizens’ and their repertoires of action in each city. The empirical findings underline the emergence of hybrid repertoires of action together with ‘single-issue’ or ‘cause-oriented’ forms of political participation. This study represents an attempt to encourage the dialogue between two strands of research in social sciences, namely sociology of work and political participation and to foster the formation of an innovative research agenda crossing these two fields.

Flexible knowledge repertoires: communication by leaders in trauma teams

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Jacobsson Maritha

2012-07-01

Full Text Available Abstract Background In emergency situations, it is important for the trauma team to efficiently communicate their observations and assessments. One common communication strategy is “closed-loop communication”, which can be described as a transmission model in which feedback is of great importance. The role of the leader is to create a shared goal in order to achieve consensus in the work for the safety of the patient. The purpose of this study was to analyze how formal leaders communicate knowledge, create consensus, and position themselves in relation to others in the team. Methods Sixteen trauma teams were audio- and video-recorded during high fidelity training in an emergency department. Each team consisted of six members: one surgeon or emergency physician (the designated team leader, one anaesthesiologist, one nurse anaesthetist, one enrolled nurse from the theatre ward, one registered nurse and one enrolled nurse from the emergency department (ED. The communication was transcribed and analyzed, inspired by discourse psychology and Strauss’ concept of “negotiated order”. The data were organized and coded in NVivo 9. Results The findings suggest that leaders use coercive, educational, discussing and negotiating strategies to work things through. The leaders in this study used different repertoires to convey their knowledge to the team, in order to create a common goal of the priorities of the work. Changes in repertoires were dependent on the urgency of the situation and the interaction between team members. When using these repertoires, the leaders positioned themselves in different ways, either on an authoritarian or a more egalitarian level. Conclusion This study indicates that communication in trauma teams is complex and consists of more than just transferring messages quickly. It also concerns what the leaders express, and even more importantly, how they speak to and involve other team members.

Flexible knowledge repertoires: communication by leaders in trauma teams

Science.gov (United States)

2012-01-01

Background In emergency situations, it is important for the trauma team to efficiently communicate their observations and assessments. One common communication strategy is “closed-loop communication”, which can be described as a transmission model in which feedback is of great importance. The role of the leader is to create a shared goal in order to achieve consensus in the work for the safety of the patient. The purpose of this study was to analyze how formal leaders communicate knowledge, create consensus, and position themselves in relation to others in the team. Methods Sixteen trauma teams were audio- and video-recorded during high fidelity training in an emergency department. Each team consisted of six members: one surgeon or emergency physician (the designated team leader), one anaesthesiologist, one nurse anaesthetist, one enrolled nurse from the theatre ward, one registered nurse and one enrolled nurse from the emergency department (ED). The communication was transcribed and analyzed, inspired by discourse psychology and Strauss’ concept of “negotiated order”. The data were organized and coded in NVivo 9. Results The findings suggest that leaders use coercive, educational, discussing and negotiating strategies to work things through. The leaders in this study used different repertoires to convey their knowledge to the team, in order to create a common goal of the priorities of the work. Changes in repertoires were dependent on the urgency of the situation and the interaction between team members. When using these repertoires, the leaders positioned themselves in different ways, either on an authoritarian or a more egalitarian level. Conclusion This study indicates that communication in trauma teams is complex and consists of more than just transferring messages quickly. It also concerns what the leaders express, and even more importantly, how they speak to and involve other team members. PMID:22747848

Flexible knowledge repertoires: communication by leaders in trauma teams.

Science.gov (United States)

Jacobsson, Maritha; Hargestam, Maria; Hultin, Magnus; Brulin, Christine

2012-07-02

In emergency situations, it is important for the trauma team to efficiently communicate their observations and assessments. One common communication strategy is "closed-loop communication", which can be described as a transmission model in which feedback is of great importance. The role of the leader is to create a shared goal in order to achieve consensus in the work for the safety of the patient. The purpose of this study was to analyze how formal leaders communicate knowledge, create consensus, and position themselves in relation to others in the team. Sixteen trauma teams were audio- and video-recorded during high fidelity training in an emergency department. Each team consisted of six members: one surgeon or emergency physician (the designated team leader), one anaesthesiologist, one nurse anaesthetist, one enrolled nurse from the theatre ward, one registered nurse and one enrolled nurse from the emergency department (ED). The communication was transcribed and analyzed, inspired by discourse psychology and Strauss' concept of "negotiated order". The data were organized and coded in NVivo 9. The findings suggest that leaders use coercive, educational, discussing and negotiating strategies to work things through. The leaders in this study used different repertoires to convey their knowledge to the team, in order to create a common goal of the priorities of the work. Changes in repertoires were dependent on the urgency of the situation and the interaction between team members. When using these repertoires, the leaders positioned themselves in different ways, either on an authoritarian or a more egalitarian level. This study indicates that communication in trauma teams is complex and consists of more than just transferring messages quickly. It also concerns what the leaders express, and even more importantly, how they speak to and involve other team members.

The mimetic repertoire of the spotted bowerbird Ptilonorhynchus maculatus

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Kelley, Laura A.; Healy, Susan D.

2011-06-01

Although vocal mimicry in songbirds is well documented, little is known about the function of such mimicry. One possibility is that the mimic produces the vocalisations of predatory or aggressive species to deter potential predators or competitors. Alternatively, these sounds may be learned in error as a result of their acoustic properties such as structural simplicity. We determined the mimetic repertoires of a population of male spotted bowerbirds Ptilonorhynchus maculatus, a species that mimics predatory and aggressive species. Although male mimetic repertoires contained an overabundance of vocalisations produced by species that were generally aggressive, there was also a marked prevalence of mimicry of sounds that are associated with alarm such as predator calls, alarm calls and mobbing calls, irrespective of whether the species being mimicked was aggressive or not. We propose that it may be the alarming context in which these sounds are first heard that may lead both to their acquisition and to their later reproduction. We suggest that enhanced learning capability during acute stress may explain vocal mimicry in many species that mimic sounds associated with alarm.

Functional immunomics: microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes.

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Quintana, Francisco J; Hagedorn, Peter H; Elizur, Gad; Merbl, Yifat; Domany, Eytan; Cohen, Irun R

2004-10-05

One's present repertoire of antibodies encodes the history of one's past immunological experience. Can the present autoantibody repertoire be consulted to predict resistance or susceptibility to the future development of an autoimmune disease? Here, we developed an antigen microarray chip and used bioinformatic analysis to study a model of type 1 diabetes developing in nonobese diabetic male mice in which the disease was accelerated and synchronized by exposing the mice to cyclophosphamide at 4 weeks of age. We obtained sera from 19 individual mice, treated the mice to induce cyclophosphamide-accelerated diabetes (CAD), and found, as expected, that 9 mice became severely diabetic, whereas 10 mice permanently resisted diabetes. We again obtained serum from each mouse after CAD induction. We then analyzed, by using rank-order and superparamagnetic clustering, the patterns of antibodies in individual mice to 266 different antigens spotted on the chip. A selected panel of 27 different antigens (10% of the array) revealed a pattern of IgG antibody reactivity in the pre-CAD sera that discriminated between the mice resistant or susceptible to CAD with 100% sensitivity and 82% specificity (P = 0.017). Surprisingly, the set of IgG antibodies that was informative before CAD induction did not separate the resistant and susceptible groups after the onset of CAD; new antigens became critical for post-CAD repertoire discrimination. Thus, at least for a model disease, present antibody repertoires can predict future disease, predictive and diagnostic repertoires can differ, and decisive information about immune system behavior can be mined by bioinformatic technology. Repertoires matter.

Dance choreography is coordinated with song repertoire in a complex avian display.

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Dalziell, Anastasia H; Peters, Richard A; Cockburn, Andrew; Dorland, Alexandra D; Maisey, Alex C; Magrath, Robert D

2013-06-17

All human cultures have music and dance, and the two activities are so closely integrated that many languages use just one word to describe both. Recent research points to a deep cognitive connection between music and dance-like movements in humans, fueling speculation that music and dance have coevolved and prompting the need for studies of audiovisual displays in other animals. However, little is known about how nonhuman animals integrate acoustic and movement display components. One striking property of human displays is that performers coordinate dance with music by matching types of dance movements with types of music, as when dancers waltz to waltz music. Here, we show that a bird also temporally coordinates a repertoire of song types with a repertoire of dance-like movements. During displays, male superb lyrebirds (Menura novaehollandiae) sing four different song types, matching each with a unique set of movements and delivering song and dance types in a predictable sequence. Crucially, display movements are both unnecessary for the production of sound and voluntary, because males sometimes sing without dancing. Thus, the coordination of independently produced repertoires of acoustic and movement signals is not a uniquely human trait. Copyright © 2013 Elsevier Ltd. All rights reserved.

Strategies for B-cell receptor repertoire analysis in primary immunodeficiencies: From severe combined immunodeficiency to common variable immunodeficiency

NARCIS (Netherlands)

H. IJspeert (Hanna); M. Wentink (Marjolein); D. van Zessen (David); G.J.A. Driessen (Gertjan); V.A.S.H. Dalm (Virgil); M.P. van Hagen (Martin); I. Pico-Knijnenburg (Ingrid); E.J. Simons (Erik J.); J.J.M. van Dongen (Jacques); A. Stubbs (Andrew); M. van der Burg (Mirjam)

2015-01-01

textabstractThe antigen receptor repertoires of B- and T-cells form the basis of the adaptive immune response. The repertoires should be sufficiently diverse to recognize all possible pathogens. However, careful selection is needed to prevent responses to self or harmless antigens. Limited antigen

A comparative review of estimates of the proportion unchanged genes and the false discovery rate

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Broberg Per

2005-08-01

Full Text Available Abstract Background In the analysis of microarray data one generally produces a vector of p-values that for each gene give the likelihood of obtaining equally strong evidence of change by pure chance. The distribution of these p-values is a mixture of two components corresponding to the changed genes and the unchanged ones. The focus of this article is how to estimate the proportion unchanged and the false discovery rate (FDR and how to make inferences based on these concepts. Six published methods for estimating the proportion unchanged genes are reviewed, two alternatives are presented, and all are tested on both simulated and real data. All estimates but one make do without any parametric assumptions concerning the distributions of the p-values. Furthermore, the estimation and use of the FDR and the closely related q-value is illustrated with examples. Five published estimates of the FDR and one new are presented and tested. Implementations in R code are available. Results A simulation model based on the distribution of real microarray data plus two real data sets were used to assess the methods. The proposed alternative methods for estimating the proportion unchanged fared very well, and gave evidence of low bias and very low variance. Different methods perform well depending upon whether there are few or many regulated genes. Furthermore, the methods for estimating FDR showed a varying performance, and were sometimes misleading. The new method had a very low error. Conclusion The concept of the q-value or false discovery rate is useful in practical research, despite some theoretical and practical shortcomings. However, it seems possible to challenge the performance of the published methods, and there is likely scope for further developing the estimates of the FDR. The new methods provide the scientist with more options to choose a suitable method for any particular experiment. The article advocates the use of the conjoint information

Expressed var gene repertoire and variant surface antigen diversity in a shrinking Plasmodium falciparum population.

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Carlos, Bianca C; Fotoran, Wesley L; Menezes, Maria J; Cabral, Fernanda J; Bastos, Marcele F; Costa, Fabio T M; Sousa-Neto, Jayme A; Ribolla, Paulo E M; Wunderlich, Gerhard; Ferreira, Marcelo U

2016-11-01

The var gene-encoded erythrocyte membrane protein-1 of Plasmodium falciparum (PfEMP-1) is the main variant surface antigen (VSA) expressed on infected erythrocytes. The rate at which antibody responses to VSA expressed by circulating parasites are acquired depends on the size of the local VSA repertoire and the frequency of exposure to new VSA. Because parasites from areas with declining malaria endemicity, such as the Amazon, typically express a restricted PfEMP-1 repertoire, we hypothesized that Amazonians would rapidly acquire antibodies to most locally circulating VSA. Consistent with our expectations, the analysis of 5878 sequence tags expressed by 10 local P. falciparum samples revealed little PfEMP-1 DBL1α domain diversity. Among the most commonly expressed DBL1α types, 45% were shared by two or more independent parasite lines. Nevertheless, Amazonians displayed major gaps in their repertoire of anti-VSA antibodies, although the breadth of anti-VSA antibody responses correlated positively with their cumulative exposure to malaria. We found little antibody cross-reactivity even when testing VSA from related parasites expressing the same dominant DBL1α types. We conclude that variant-specific immunity to P. falciparum VSAs develops slowly despite the relatively restricted PfEMP-1 repertoire found in low-endemicity settings. Copyright © 2016 Elsevier Inc. All rights reserved.

'They don't understand…you cut yourself in order to live.' Interpretative repertoires jointly constructing interactions between adult women who self-harm and professional caregivers.

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Lindgren, Britt-Marie; Oster, Inger; Aström, Sture; Hällgren Graneheim, Ulla

2011-01-01

The aim of the study was to illuminate interpretative repertoires that jointly construct the interaction between adult women who self-harm and professional caregivers in psychiatric inpatient care. Participant observations and informal interviews were conducted among six women who self-harm and their professional caregivers in two psychiatric inpatient wards, and analysed using the concept of interpretative repertoires from the discipline of discursive psychology. The analysis revealed four interpretative repertoires that jointly constructed the interaction. The professional caregivers used a "fostering repertoire" and a "supportive repertoire" and the women who self-harmed used a "victim repertoire" and an "expert repertoire." The women and the caregivers were positioned and positioned themselves and people around them within and among these interpretative repertoires to make sense of their experiences of the interaction. It was necessary to consider each woman's own life chances and knowledge about herself and her needs. The participants made it clear that it was essential for them to be met with respect as individuals. Professional caregivers need to work in partnership with individuals who self-harm-experts by profession collaborating with experts by experience. Caregivers need to look beyond behavioural symptoms and recognise each individual's possibilities for agency.

Rules of song development and their use in vocal interactions by birds with large repertoires

OpenAIRE

Geberzahn Nicole; Hultsch Henrike

2004-01-01

Songbirds are well known for settling their disputes by vocal signals, and their singing plays a dominant role. Most studies on this issue have concentrated on bird species that develop and use small vocal repertoires. In this article we will go farther and focus on examples of how species with large song repertoires make use of their vocal competence. In particular, we will outline the study of interaction rules which have been elucidated by examining time- and pattern-specific relationships...

Beyond Languages, beyond Modalities: Transforming the Study of Semiotic Repertoires

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Kusters, Annelies; Spotti, Massimiliano; Swanwick, Ruth; Tapio, Elina

2017-01-01

This paper presents a critical examination of key concepts in the study of (signed and spoken) language and multimodality. It shows how shifts in conceptual understandings of language use, moving from bilingualism to multilingualism and (trans)languaging, have resulted in the revitalisation of the concept of language repertoires. We discuss key…

Repertoires, Characters and Scenes: Sociolinguistic Difference in Turkish-German Comedy

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Androutsopoulos, Jannis

2012-01-01

This paper examines representations of sociolinguistic difference in a German "ethnic comedy" as a means to contribute to a framework for the sociolinguistic study of film. Three levels of analysis of sociolinguistic difference in film are distinguished: repertoire analysis reconstructs the entirety of codes used in a film and their…

Rules of song development and their use in vocal interactions by birds with large repertoires.

Science.gov (United States)

Geberzahn, Nicole; Hultsch, Henrike

2004-06-01

Songbirds are well known for settling their disputes by vocal signals, and their singing plays a dominant role. Most studies on this issue have concentrated on bird species that develop and use small vocal repertoires. In this article we will go farther and focus on examples of how species with large song repertoires make use of their vocal competence. In particular, we will outline the study of interaction rules which have been elucidated by examining time- and pattern-specific relationships between signals exchanged by territorial neighbors. First we present an inquiry into the rules of song learning and development. In birds with large song repertoires, the ontogeny of such rules proceeds along a number of trajectories which help in understanding the often remarkable accomplishments of adult birds. In both approaches, our model species will be the Common Nightingale Luscinia megarhynchos that has been investigated intensively in the field and in the laboratory.

Practical compassions: repertoires of practice and compassion talk in acute mental healthcare.

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Brown, Brian; Crawford, Paul; Gilbert, Paul; Gilbert, Jean; Gale, Corinne

2014-03-01

This article reports an exploratory study of the concept of compassion in the work of 20 mental health practitioners in a UK Midlands facility. Using notions of practice derived from phenomenology and Bourdieusian sociology and notions of emotional labour we identify two contrasting interpretive repertoires in discussions of compassion. The first, the practical compassion repertoire, evokes the practical, physical and bodily aspects of compassion. It involves organising being with patients, playing games, anticipating disruption and taking them outside for cigarettes. Practitioners described being aware that these practical, bodily activities could lead to patients 'opening up', disclosing their interior concerns and enabling practical, compassionate mental health work to take place. In contrast, the second, organisational repertoire, concerns organisational constraints on compassionate practice. The shortage of staff, the record-keeping and internal processes of quality control were seen as time-greedy and apt to detract from contact with patients. The findings are discussed in relation to Bourdieu and Merleau-Ponty's phenomenological accounts of practice and habit and set in context in the growing interest in placing compassion centrally in healthcare. We also explore how the exercise of compassion in the way our participants describe it can afford the more effective exercise of medical power. © 2013 The Author. Sociology of Health & Illness © 2013 Foundation for the Sociology of Health & Illness/John Wiley & Sons Ltd.

The self-nonself discrimination and the nature and acquisition of the antibody repertoire.

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Coutinho, A

1980-01-01

Network ideas are confronted with current hypotheses for the origin of antibody diversity and self-nonself discrimination. The difficulties of reconciling the promethean evolution of the antibody system with "germ line" theories are discussed, as well as the problems of "somatic" hypotheses to explain the completeness of the antibody repertoire. The formal incompatibility of the network theory with ideas basing self-nonself discrimination on the elimination of self-reactive cells is demonstrated, as well as the difficulties of these and other environment-dependent hypotheses for lymphocyte activation, to encompass the internal activity in the immune system. It is argued, on the other hand, that the limitations of the network theory in providing a functional basis for the idiotypic network and in accounting for self-nonself discrimination, can be solved by finding in a complete repertoire of antibody-combining sites the complementary structures to growth receptors on B lymphocytes, and by using these as internal mitogens in the expansion of the precursor cell pools and in the maintenance of the mature steady states. Letting self-nonself discrimination be accounted for by such growth receptors, both the integrity of the antibody repertoire and the internal activity in the system can also be ensured. Moreover, by postulating a germ line origin for the antireceptor antibodies and by accepting idiotypic cross-reactivity between growth receptors and other germ line antibodies, the possibilities are set for a phylogenetically and ontogenically autonomous immune system embodied with the capabilities for self-expansion, diversification and selection of available repertoires. Its promethean characteristics are explained by its completeness, and this is achieved by idiotypic interactions between growth receptors and a limited number of complementary or cross-reactive germ line antibodies, naturally selected on the basis of their structural relationships with growth receptors.

Sexual repertoires of heterosexuals: implications for HIV/sexually transmitted disease risk and prevention. The ACSF Group, Analyse des Comportements Sexuels en France.

Science.gov (United States)

Messiah, A; Blin, P; Fiche, V

1995-12-01

To provide a quantitative and population-based analysis of sexual repertoires among heterosexuals. The French National Survey of Sexual Behaviour (ACSF), conducted between September 1991 and February 1992 on a representative sample of the population aged 18-69 years. Sexual practices of the last heterosexual encounter were investigated among 4261 individuals; we measured the combinations of different practices and their correlations with age, and calculated frequencies for the main repertoires and their correlations with the interpartner relationship. Vaginal penetration and caressing were almost systematic, self-masturbation and anal penetration were rare, while mutual masturbation and orogenital practices had intermediate levels of occurrence. Examination of the correlations revealed (1) a very high correlation between practices which are reciprocal or symmetrical, (2) a strong association between genito-manual and genito-oral practices, (3) an association between anal penetration and fellatio, and (4) no clear correlation between any set of practices and vaginal sex or condom use. A small number of repertoires accounted for the vast majority of encounters. Younger people tended to have a more diversified repertoire. Repertoire types and diversity were strongly correlated to the pattern of interpartner relationship, independently of age. Reciprocity seems a standard feature of the heterosexual repertoire. The absence of a negative correlation between vaginal or anal penetration and other practices argues against promotion of the latter as substitute for the former. By contrast, the independence between condom use and any specific repertoire argues for its promotion as a universal means of protection.

Fundamental characteristics of the expressed immunoglobulin VH and VL repertoire in different canine breeds in comparison with those of humans and mice.

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Steiniger, Sebastian C J; Dunkle, William E; Bammert, Gary F; Wilson, Thomas L; Krishnan, Abhiram; Dunham, Steven A; Ippolito, Gregory C; Bainbridge, Graeme

2014-05-01

Complementarity determining regions (CDR) are responsible for binding antigen and provide substantial diversity to the antibody repertoire, with VH CDR3 of the immunoglobulin variable heavy (VH) domain playing a dominant role. In this study, we examined 1200 unique canine VH and 500 unique variable light (VL) sequences of large and small canine breeds derived from peripheral B cells. Unlike the human and murine repertoire, the canine repertoire is heavily dominated by the Canis lupus familiaris IGHV1 subgroup, evolutionarily closest to the human IGHV3 subgroup. Our studies clearly show that the productive canine repertoire of all analyzed breeds shows similarities to both human and mouse; however, there are distinct differences in terms of VH CDR3 length and amino acid paratope composition. In comparison with the human and murine antibody repertoire, canine VH CDR3 regions are shorter in length than the human counterparts, but longer than the murine VH CDR3. Similar to corresponding human and mouse VH CDR3, the amino acids at the base of the VH CDR3 loop are strictly conserved. For identical CDR positions, there were significant changes in chemical paratope composition. Similar to human and mouse repertoires, the neutral amino acids tyrosine, glycine and serine dominate the canine VH CDR3 interval (comprising 35%) although the interval is nonetheless relatively depleted of tyrosine when compared to human and mouse. Furthermore, canine VH CDR3 displays an overrepresentation of the neutral amino acid threonine and the negatively charged aspartic acid while proline content is similar to that in the human repertoire. In general, the canine repertoire shows a bias towards small, negatively charged amino acids. Overall, this analysis suggests that functional canine therapeutic antibodies can be obtained from human and mouse sequences by methods of speciation and affinity maturation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Immune Antibody Libraries: Manipulating The Diverse Immune Repertoire for Antibody Discovery.

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Lim, Theam Soon; Chan, Soo Khim

2016-01-01

Antibody phage display is highly dependent on the availability of antibody libraries. There are several forms of libraries depending mainly on the origin of the source materials. There are three major classes of libraries, mainly the naïve, immune and synthetic libraries. Immune antibody libraries are designed to isolate specific and high affinity antibodies against disease antigens. The pre-exposure of the host to an infection results in the production of a skewed population of antibodies against the particular infection. This characteristic takes advantage of the in vivo editing machinery to generate bias and specific immune repertoire. The skewed but diverse repertoire of immune libraries has been adapted successfully in the generation of antibodies against a wide range of diseases. We envisage immune antibody libraries to play a greater role in the discovery of antibodies for diseases in the near future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Uncovering the Legionella genus effector repertoire - strength in diversity and numbers

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Burstein, David; Amaro, Francisco; Zusman, Tal; Lifshitz, Ziv; Cohen, Ofir; Gilbert, Jack A; Pupko, Tal; Shuman, Howard A; Segal, Gil

2016-01-01

Infection by the human pathogen Legionella pneumophila relies on the translocation of ~300 virulence proteins, termed effectors, which manipulate host-cell processes. However, almost no information exists regarding effectors in other Legionella pathogens. Here we sequenced, assembled and characterized the genomes of 38 Legionella species, and predicted their effector repertoire using a previously validated machine-learning approach. This analysis revealed a treasure trove of 5,885 predicted effectors. The effector repertoire of different Legionella species was found to be largely non-overlapping, and only seven core-effectors were shared among all species studied. Species-specific effectors had atypically low GC content, suggesting exogenous acquisition, possibly from their natural protozoan hosts. Furthermore, we detected numerous novel conserved effector domains, and discovered new domain combinations, which allowed inferring yet undescribed effector functions. The effector collection and network of domain architectures described here can serve as a roadmap for future studies of effector function and evolution. PMID:26752266

Immunoglobulin gene repertoire diversification and selection in the stomach – from gastritis to gastric lymphomas

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Miri eMichaeli

2014-06-01

Full Text Available Chronic gastritis is characterized by gastric mucosal inflammation due to autoimmune responses or infection, frequently with Helicobacter pylori. Gastritis with H. pylori background can cause gastric mucosa-associated lymphoid tissue lymphoma (MALT-L, which sometimes further transforms into diffuse large B cell lymphoma (DLBCL. However, gastric DLBCL can also be initiated de novo. The mechanisms underlying transformation into DLBCL are not completely understood. We analyzed immunoglobulin repertoires and clonal trees to investigate whether and how immunoglobulin gene repertoires, clonal diversification and selection in gastritis, gastric MALT-L and DLBCL differ from each other and from normal responses. The two gastritis types (positive or negative for H. pylori had similarly diverse repertoires. MALT-L dominant clones presented higher diversification and longer mutational histories compared with all other conditions. DLBCL dominant clones displayed lower clonal diversification, suggesting the transforming events are triggered by similar responses in different patients. These results are surprising, as we expected to find similarities between the dominant clones of gastritis and MALT-L and between those of MALT-L and DLBCL.

A REPERTOIRE OF INSTRUMENTS EMPLOYED IN PSYCHOLOGICAL COUNSELING

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Dorina Maria PASCA

2014-10-01

Full Text Available According to Carl Rogers and Albert Ellis [1] [2], a new approach to psychological counseling is needed. Consequently, new and practical means to solve problems that ensue as part of the counseling process are required. From this point of view, this article aims at offering a range of alternatives to approach and involve the client (student in order to achieve the envisaged results of counseling. As such, it offers a concise repertoire of instruments that can be employed in psychological counseling.

Next generation sequencing reveals skewing of the T and B cell receptor repertoires in patients with Wiskott Aldrich syndrome

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Amy E O'Connell

2014-07-01

Full Text Available The Wiskott Aldrich syndrome (WAS is due to mutations of the WAS gene encoding for the cytoskeletal WAS protein (WASp, leading to abnormal downstream signaling from the T cell and B cell antigen receptors (TCR, BCR. We hypothesized that the impaired signaling through the TCR and BCR in WAS would subsequently lead to aberrations in the immune repertoire of WAS patients. Using next generation sequencing, the T cell receptor beta (TRB and B cell immunoglobulin heavy chain (IGH repertoires of 8 patients with WAS and 6 controls were sequenced. Clonal expansions were identified within memory CD4+ cells, as well as in total, naïve and memory CD8+ cells from WAS patients. In the B cell compartment, WAS patient IGH repertoires were also clonally expanded and showed skewed usage of IGHV and IGHJ genes, and increased usage of IGHG constant genes, compared with controls. To our knowledge, this is the first study that demonstrates significant abnormalities of the immune repertoire in WAS patients using next generation sequencing.

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.

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Fähnrich, Anke; Krebbel, Moritz; Decker, Normann; Leucker, Martin; Lange, Felix D; Kalies, Kathrin; Möller, Steffen

2017-03-11

Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background. To facilitate the analysis of T and B cell repertoires by less experienced users, software is needed that combines the most common tools for repertoire analysis. We introduce a graphical user interface (GUI) providing a complete analysis pipeline for processing raw NGS data for human and animal TCR and BCR clonotype determination and advanced differential repertoire studies. It provides two applications. ClonoCalc prepares the raw data for downstream analyses. It combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal TCR/BCR sequences. ClonoPlot wraps the R package tcR and further contributes self-developed plots for the descriptive comparative investigation of immune repertoires. This workflow reduces the amount of programming required to perform the respective analyses and supports both communication and training between scientists and technicians, and across scientific disciplines. The Open Source development in Java and R is modular and invites advanced users to extend its functionality. Software and documentation are freely available at https://bitbucket.org/ClonoSuite/clonocalc-plot .

Ibrutinib Therapy Increases T Cell Repertoire Diversity in Patients with Chronic Lymphocytic Leukemia.

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Yin, Qingsong; Sivina, Mariela; Robins, Harlan; Yusko, Erik; Vignali, Marissa; O'Brien, Susan; Keating, Michael J; Ferrajoli, Alessandra; Estrov, Zeev; Jain, Nitin; Wierda, William G; Burger, Jan A

2017-02-15

The Bruton's tyrosine kinase inhibitor ibrutinib is a highly effective, new targeted therapy for chronic lymphocytic leukemia (CLL) that thwarts leukemia cell survival, growth, and tissue homing. The effects of ibrutinib treatment on the T cell compartment, which is clonally expanded and thought to support the growth of malignant B cells in CLL, are not fully characterized. Using next-generation sequencing technology, we characterized the diversity of TCRβ-chains in peripheral blood T cells from 15 CLL patients before and after 1 y of ibrutinib therapy. We noted elevated CD4 + and CD8 + T cell numbers and a restricted TCRβ repertoire in all pretreatment samples. After 1 y of ibrutinib therapy, elevated peripheral blood T cell numbers and T cell-related cytokine levels had normalized, and T cell repertoire diversity increased significantly. Dominant TCRβ clones in pretreatment samples declined or became undetectable, and the number of productive unique clones increased significantly during ibrutinib therapy, with the emergence of large numbers of low-frequency TCRβ clones. Importantly, broader TCR repertoire diversity was associated with clinical efficacy and lower rates of infections during ibrutinib therapy. These data demonstrate that ibrutinib therapy increases diversification of the T cell compartment in CLL patients, which contributes to cellular immune reconstitution. Copyright © 2017 by The American Association of Immunologists, Inc.

T Cell Phenotype and T Cell Receptor Repertoire in Patients with Major Depressive Disorder

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Kostas Patas

2018-02-01

Full Text Available While a link between inflammation and the development of neuropsychiatric disorders, including major depressive disorder (MDD is supported by a growing body of evidence, little is known about the contribution of aberrant adaptive immunity in this context. Here, we conducted in-depth characterization of T cell phenotype and T cell receptor (TCR repertoire in MDD. For this cross-sectional case–control study, we recruited antidepressant-free patients with MDD without any somatic or psychiatric comorbidities (n = 20, who were individually matched for sex, age, body mass index, and smoking status to a non-depressed control subject (n = 20. T cell phenotype and repertoire were interrogated using a combination of flow cytometry, gene expression analysis, and next generation sequencing. T cells from MDD patients showed significantly lower surface expression of the chemokine receptors CXCR3 and CCR6, which are known to be central to T cell differentiation and trafficking. In addition, we observed a shift within the CD4+ T cell compartment characterized by a higher frequency of CD4+CD25highCD127low/− cells and higher FOXP3 mRNA expression in purified CD4+ T cells obtained from patients with MDD. Finally, flow cytometry-based TCR Vβ repertoire analysis indicated a less diverse CD4+ T cell repertoire in MDD, which was corroborated by next generation sequencing of the TCR β chain CDR3 region. Overall, these results suggest that T cell phenotype and TCR utilization are skewed on several levels in patients with MDD. Our study identifies putative cellular and molecular signatures of dysregulated adaptive immunity and reinforces the notion that T cells are a pathophysiologically relevant cell population in this disorder.

Comprehensive assessment of peripheral blood TCRβ repertoire in infectious mononucleosis and chronic active EBV infection patients.

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Liu, Shenglin; Zhang, Qian; Huang, Dongli; Zhang, Wenli; Zhong, Fengluan; Feng, Jia; Chen, Xueru; Meng, Qingxiang; Chen, Xiaofan; Zhang, Wei; Zhang, Hongyu

2017-04-01

Epstein-Barr virus (EBV) primary infection is usually asymptomatic, but it sometimes progresses to infectious mononucleosis (IM). Occasionally, some people develop chronic active EBV infection (CAEBV) with underlying immunodeficiency, which belongs to a continuous spectrum of EBV-associated lymphoproliferative disorders (EBV + LPD) with heterogeneous clinical presentations and high mortality. It has been well established that T cell-mediated immune response plays a critical role in the disease evolution of EBV infection. Recently, high-throughput sequencing of the hypervariable complementarity-determining region 3 (CDR3) segments of the T cell receptor (T cell receptor β (TCRβ)) has emerged as a sensitive approach to assess the T cell repertoire. In this study, we fully characterized the diversity of peripheral blood TCRβ repertoire in IM (n = 6) and CAEBV patients (n = 5) and EBV-seropositive controls (n = 5). Compared with the healthy EBV-seropositive controls, both IM and CAEBV patients demonstrate a significant decrease in peripheral blood TCRβ repertoire diversity, basically, including narrowed repertoire breadth, highly expanded clones, and skewed CDR3 length distribution. However, there is no significant difference between IM and CAEBV patients. Furthermore, we observed some disease-related preferences in TRBV/TRBJ usage and combinations, as well as lots of T cell clones shared by different groups (unique or overlapped) involved in public T cell responses, which provide more detailed insights into the divergent disease evolution.

Finding meaning in first episode psychosis: experience, agency, and the cultural repertoire.

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Larsen, John Aggergaard

2004-12-01

The article examines individuals' attempts to generate meaning following their experiences with psychosis. The inquiry is based on a person-centered ethnographic study of a Danish mental health community program for early intervention in schizophrenia and involves longitudinal interviews with 15 of its participants. The article takes an existential anthropological perspective emphasizing agency and cultural phenomenology to investigate how individuals draw on resources from the cultural repertoire to make sense of personally disturbing experiences during their psychosis. It is suggested that the concept of "system of explanation" has advantages over, for example, "illness narrative" and "explanatory model" when demonstrating how some individuals engage in the creative analytic and theory-building work of bricolage, selecting, adding, and combining various systems of explanation. Delusions are equally derived from the cultural repertoire but are constructed as dogmatic explanations that are idiosyncratic to the individual who holds them.

Pervasive and stochastic changes in the TCR repertoire of regulatory T-cell-deficient mice.

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Zheng, Lingjie; Sharma, Rahul; Kung, John T; Deshmukh, Umesh S; Jarjour, Wael N; Fu, Shu Man; Ju, Shyr-Te

2008-04-01

We hypothesize that regulatory T-cell (Treg)-deficient strains have an altered TCR repertoire in part due to the expansion of autoimmune repertoire by self-antigen. We compared the Vbeta family expression profile between B6 and Treg-lacking B6.Cg-Foxp3(sf)(/Y) (B6.sf) mice using fluorescent anti-Vbeta mAbs and observed no changes. However, while the spectratypes of 20 Vbeta families among B6 mice were highly similar, the Vbeta family spectratypes of B6.sf mice were remarkably different from B6 mice and from each other. Significant spectratype changes in many Vbeta families were also observed in Treg-deficient IL-2 knockout (KO) and IL-2Ralpha KO mice. Such changes were not observed with anti-CD3 mAb-treated B6 mice or B6 CD4+CD25- T cells. TCR transgenic (OT-II.sf) mice displayed dramatic reduction of clonotypic TCR with concomitant increase in T cells bearing non-transgenic Vbeta and Valpha families, including T cells with dual receptors expressing reduced levels of transgenic Valpha and endogenous Valpha. Collectively, the data demonstrate that Treg deficiency allows polyclonal expansion of T cells in a stochastic manner, resulting in widespread changes in the TCR repertoire.

Understanding the Broad Substrate Repertoire of Nitroreductase Based on Its Kinetic Mechanism*

Science.gov (United States)

Pitsawong, Warintra; Hoben, John P.; Miller, Anne-Frances

2014-01-01

The oxygen-insensitive nitroreductase from Enterobacter cloacae (NR) catalyzes two-electron reduction of nitroaromatics to the corresponding nitroso compounds and, subsequently, to hydroxylamine products. NR has an unusually broad substrate repertoire, which may be related to protein dynamics (flexibility) and/or a simple non-selective kinetic mechanism. To investigate the possible role of mechanism in the broad substrate repertoire of NR, the kinetics of oxidation of NR by para-nitrobenzoic acid (p-NBA) were investigated using stopped-flow techniques at 4 °C. The results revealed a hyperbolic dependence on the p-NBA concentration with a limiting rate of 1.90 ± 0.09 s−1, indicating one-step binding before the flavin oxidation step. There is no evidence for a distinct binding step in which specificity might be enforced. The reduction of p-NBA is rate-limiting in steady-state turnover (1.7 ± 0.3 s−1). The pre-steady-state reduction kinetics of NR by NADH indicate that NADH reduces the enzyme with a rate constant of 700 ± 20 s−1 and a dissociation constant of 0.51 ± 0.04 mm. Thus, we demonstrate simple transient kinetics in both the reductive and oxidative half-reactions that help to explain the broad substrate repertoire of NR. Finally, we tested the ability of NR to reduce para-hydroxylaminobenzoic acid, demonstrating that the corresponding amine does not accumulate to significant levels even under anaerobic conditions. Thus E. cloacae NR is not a good candidate for enzymatic production of aromatic amines. PMID:24706760

[11C]-Flumazenil metabolites: Measurements of unchanged ligand in plasma using thin layer chromatography and rapid liquid chromatography

International Nuclear Information System (INIS)

Loc'h, C.; Hantraye, Ph.; Khalili-Varasteh, M.; Maziere, B.; Delforge, J.; Brouillet, E.; Syrota, A.; Maziere, M.

1990-01-01

To study in vivo benzodiazepine (BZ) receptors using PET, Flumazenil, an imidazobenzodiazepine with selective antagonistic actions, has been labeled with 11 C on its methyl group. The accurate determination of in vivo binding parameters using biomathematical models requires the knowledge of radioligand metabolism and the measurement of the plasmatic concentration of unchanged radioligand is mandatory. The present report describes and compares rapid and simple analytical procedures to measure unchanged [ 11 C]-Flumazenil in plasma

Repertoires of emotion regulation: A person-centered approach to assessing emotion regulation strategies and links to psychopathology.

Science.gov (United States)

Dixon-Gordon, Katherine L; Aldao, Amelia; De Los Reyes, Andres

2015-01-01

Despite growing research on emotion regulation (ER) strategies and psychopathology, research has primarily focused on identifying one-to-one associations between ER strategies and symptoms. Thus, little is known about how patterns in the repertoires of ER strategies are associated with different mental disorders. We utilised latent class analysis to identify distinct repertoires of ER strategies, and their links with various psychopathology domains (i.e., anxiety, depression, disordered eating, borderline personality). Participants (N = 531) reported on their use of seven ER strategies in six recalled stressful contexts, as well as on their symptoms of psychopathology. We identified five classes of ER strategies: Low Regulators (n = 168), High Regulators (n = 140), Adaptive Regulators (n = 99), Worriers/Ruminators (n = 96) and Avoiders (n = 28). Generally, High Regulators and Worriers/Ruminators endorsed greater levels of psychopathology, relative to Low and Adaptive Regulators. Our findings underscore the importance of characterising the dynamics of ER repertoires when seeking to understand links between ER strategies and psychopathology.

Personal receptor repertoires: olfaction as a model

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Olender Tsviya

2012-08-01

Full Text Available Abstract Background Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individuals. To this end, we focused on the complete inventory of human olfactory receptor coding regions as a model for personal receptor repertoires. Results By performing data-mining from public and private sources we scored genetic variations in 413 intact OR loci, for which one or more individuals had an intact open reading frame. Using 1000 Genomes Project haplotypes, we identified a total of 4069 full-length polypeptide variants encoded by these OR loci, average of ~10 per locus, constituting a lower limit for the effective human OR repertoire. Each individual is found to harbor as many as 600 OR allelic variants, ~50% higher than the locus count. Because OR neuronal expression is allelically excluded, this has direct effect on smell perception diversity of the species. We further identified 244 OR segregating pseudogenes (SPGs, loci showing both intact and pseudogene forms in the population, twenty-six of which are annotatively “resurrected” from a pseudogene status in the reference genome. Using a custom SNP microarray we validated 150 SPGs in a cohort of 468 individuals, with every individual genome averaging 36 disrupted sequence variations, 15 in homozygote form. Finally, we generated a multi-source compendium of 63 OR loci harboring deletion Copy Number Variations (CNVs. Our combined data suggest that 271 of the 413 intact OR loci (66% are affected by nonfunctional SNPs/indels and/or CNVs. Conclusions These results portray a case of unusually high genetic diversity, and suggest that individual humans have a highly personalized inventory of functional olfactory receptors, a conclusion that might apply to other receptor multigene families.

Unchanged Levels of Soluble CD14 and IL-6 Over Time Predict Serious Non-AIDS Events in HIV-1-Infected People

Science.gov (United States)

Sunil, Meena; Nigalye, Maitreyee; Somasunderam, Anoma; Martinez, Maria Laura; Yu, Xiaoying; Arduino, Roberto C.; Bell, Tanvir K.

2016-01-01

Abstract HIV-1-infected persons have increased risk of serious non-AIDS events (SNAEs) despite suppressive antiretroviral therapy. Increased circulating levels of soluble CD14 (sCD14), soluble CD163 (sCD163), and interleukin-6 (IL-6) at a single time point have been associated with SNAEs. However, whether changes in these biomarker levels predict SNAEs in HIV-1-infected persons is unknown. We hypothesized that greater decreases in inflammatory biomarkers would be associated with fewer SNAEs. We identified 39 patients with SNAEs, including major cardiovascular events, end stage renal disease, decompensated cirrhosis, non-AIDS-defining malignancies, and death of unknown cause, and age- and sex-matched HIV-1-infected controls. sCD14, sCD163, and IL-6 were measured at study enrollment (T1) and proximal to the event (T2) or equivalent duration in matched controls. Over ∼34 months, unchanged rather than decreasing levels of sCD14 and IL-6 predicted SNAEs. Older age and current illicit substance abuse, but not HCV coinfection, were associated with SNAEs. In a multivariate analysis, older age, illicit substance use, and unchanged IL-6 levels remained significantly associated with SNAEs. Thus, the trajectories of sCD14 and IL-6 levels predict SNAEs. Interventions to decrease illicit substance use may decrease the risk of SNAEs in HIV-1-infected persons. PMID:27344921

First insights into the vocal repertoire of infant and juvenile Southern white rhinoceros.

Science.gov (United States)

Linn, Sabrina N; Boeer, Michael; Scheumann, Marina

2018-01-01

Describing vocal repertoires represents an essential step towards gaining an overview about the complexity of acoustic communication in a given species. The analysis of infant vocalisations is essential for understanding the development and usage of species-specific vocalisations, but is often underrepresented, especially in species with long inter-birth intervals such as the white rhinoceros. Thus, this study aimed for the first time to characterise the infant and juvenile vocal repertoire of the Southern white rhinoceros and to relate these findings to the adult vocal repertoire. The behaviour of seven mother-reared white rhinoceros calves (two males, five females) and one hand-reared calf (male), ranging from one month to four years, was simultaneously audio and video-taped at three zoos. Normally reared infants and juveniles uttered four discriminable call types (Whine, Snort, Threat, and Pant) that were produced in different behavioural contexts. All call types were also uttered by the hand-reared calf. Call rates of Whines, but not of the other call types, decreased with age. These findings provide the first evidence that infant and juvenile rhinoceros utter specific call types in distinct contexts, even if they grow up with limited social interaction with conspecifics. By comparing our findings with the current literature on vocalisations of adult white rhinoceros and other solitary rhinoceros species, we discuss to which extent differences in the social lifestyle across species affect acoustic communication in mammals.

First insights into the vocal repertoire of infant and juvenile Southern white rhinoceros

Science.gov (United States)

Boeer, Michael; Scheumann, Marina

2018-01-01

Describing vocal repertoires represents an essential step towards gaining an overview about the complexity of acoustic communication in a given species. The analysis of infant vocalisations is essential for understanding the development and usage of species-specific vocalisations, but is often underrepresented, especially in species with long inter-birth intervals such as the white rhinoceros. Thus, this study aimed for the first time to characterise the infant and juvenile vocal repertoire of the Southern white rhinoceros and to relate these findings to the adult vocal repertoire. The behaviour of seven mother-reared white rhinoceros calves (two males, five females) and one hand-reared calf (male), ranging from one month to four years, was simultaneously audio and video-taped at three zoos. Normally reared infants and juveniles uttered four discriminable call types (Whine, Snort, Threat, and Pant) that were produced in different behavioural contexts. All call types were also uttered by the hand-reared calf. Call rates of Whines, but not of the other call types, decreased with age. These findings provide the first evidence that infant and juvenile rhinoceros utter specific call types in distinct contexts, even if they grow up with limited social interaction with conspecifics. By comparing our findings with the current literature on vocalisations of adult white rhinoceros and other solitary rhinoceros species, we discuss to which extent differences in the social lifestyle across species affect acoustic communication in mammals. PMID:29513670

The host transcriptome remains unaltered during the establishment of coral-algal symbioses.

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Voolstra, Christian R; Schwarz, Jodi A; Schnetzer, Julia; Sunagawa, Shinichi; Desalvo, Michael K; Szmant, Alina M; Coffroth, Mary Alice; Medina, Mónica

2009-05-01

Coral reefs are based on the symbiotic relationship between corals and photosynthetic dinoflagellates of the genus Symbiodinium. We followed gene expression of coral larvae of Acropora palmata and Montastraea faveolata after exposure to Symbiodinium strains that differed in their ability to establish symbioses. We show that the coral host transcriptome remains almost unchanged during infection by competent symbionts, but is massively altered by symbionts that fail to establish symbioses. Our data suggest that successful coral-algal symbioses depend mainly on the symbionts' ability to enter the host in a stealth manner rather than a more active response from the coral host.

When are nursing students on clinical placements ready to expand their learning repertoire?

DEFF Research Database (Denmark)

Holmberg, Marlene; Stisen, Bente Kjærgaard; Grau, Sarah M.

2018-01-01

Learning styles indicate an individual’s preferred way of learning. Research suggests that it is important for students on clinical placements to begin the learning process with the preferred learning style and subsequently develop their ability to use other styles and become more balanced learners....... What is unknown is when baccalaureate nursing students are ready to develop the other learning styles, and what facilitates such an expansion in their learning style repertoire? This is important, because students need to develop the abilities to learn both by acting and by deepen their knowledge...... of theory to meet the requirements of the nursing profession. An American study found that operating room students felt confident to adopt new learning styles by the third week of clinical placements. No studies to date have retrieved a similar pattern of readiness to expand learning style repertoire among...

Multivariate analysis using high definition flow cytometry reveals distinct T cell repertoires between the foetal-maternal interface and the peripheral blood

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Michelle eNeller

2014-02-01

Full Text Available The human T-cell compartment is a complex system and while some information is known on repertoire composition and dynamics in the peripheral blood, little is known on repertoire composition at different anatomical sites. Here, we determine the T-cell receptor β-variable (TRBV repertoire at the decidua and compare it with the peripheral blood during normal pregnancy and preclampsia. We found total T-cell subset disparity of up to 58% between sites, including large signature TRBV expansions unique to the foetal-maternal interface. Defining the functional nature and specificity of compartment-specific T-cells will be necessary if we are to understand localised immunity, tolerance and pathogenesis.

Long-Lasting Production of New T and B Cells and T-Cell Repertoire Diversity in Patients with Primary Immunodeficiency Who Had Undergone Stem Cell Transplantation: A Single-Centre Experience

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Monica Valotti

2014-01-01

Full Text Available Levels of Kappa-deleting recombination excision circles (KRECs, T-cell receptor excision circles (TRECs, and T-cell repertoire diversity were evaluated in 1038 samples of 124 children with primary immunodeficiency, of whom 102 (54 with severe combined immunodeficiency and 48 with other types of immunodeficiency underwent hematopoietic stem cell transplantation. Twenty-two not transplanted patients with primary immunodeficiency were used as controls. Only data of patients from whom at least five samples were sent to the clinical laboratory for routine monitoring of lymphocyte reconstitutions were included in the analysis. The mean time of the follow-up was 8 years. The long-lasting posttransplantation kinetics of KREC and TREC production occurred similarly in patients with severe combined immunodeficiency and with other types of immunodeficiency and, in both groups, the T-cell reconstitution was more efficient than in nontransplanted children. Although thymic output decreased in older transplanted patients, the degree of T-cell repertoire diversity, after an initial increase, remained stable during the observation period. However, the presence of graft-versus-host disease and ablative conditioning seemed to play a role in the time-related shaping of T-cell repertoire. Overall, our data suggest that long-term B- and T-cell reconstitution was equally achieved in children with severe combined immunodeficiency and with other types of primary immunodeficiency.

The peripheral NK cell repertoire after kidney transplantation is modulated by different immunosuppressive drugs

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Christine eNeudoerfl

2013-02-01

Full Text Available In the context of kidney transplantation, little is known about the involvement of NK cells in the immune reaction leading to either rejection or immunological tolerance under immunosuppression. Therefore, the peripheral NK cell repertoire of patients after kidney transplantation was investigated in order to identify NK cell subsets that may be associated with the individual immune status at the time of their protocol biopsies for histopathological evaluation of the graft. Alterations in the peripheral NK cell repertoire could be correlated to the type of immunosuppression, i.e. calcineurin-inhibitors like CyclosporinA vs. Tacrolimus with or without addition of mTOR inhibitors. Here, we could demonstrate that the NK cell repertoire in peripheral blood of kidney transplant patients differs significantly from healthy individuals. The presence of donor-specific antibodies was associated with reduced numbers of CD56dim NK cells. Moreover, in patients, down-modulation of CD16 and CD6 on CD56dim NK cells was observed with significant differences between CyclosporinA- and Tac-treated patients. Tac-treatment was associated with decreased CD69, HLA-DR and increased CD94/NKG2A expression in CD56dim NK cells indicating that the quality of the immunosuppressive treatment impinges on the peripheral NK cell repertoire. In vitro studies with PBMC of healthy donors showed that this modulation of CD16, CD6, CD69, and HLA-DR could also be induced experimentally. The presence of calcineurin or mTOR inhibitors had also functional consequences regarding degranulation and IFN--production against K562 target cells, respectively. In summary, we postulate that the NK cell composition in peripheral blood of kidney transplanted patients represents an important hallmark of the efficacy of immunosuppression and may be even informative for the immune status after transplantation in terms of rejection vs. drug-induced allograft tolerance. Thus,NK cells can serve as sensors

Broad T-cell receptor repertoire in T-lymphocytes derived from human induced pluripotent stem cells.

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Chia-Wei Chang

Full Text Available Human induced pluripotent stem cells (hiPSCs have enormous potential for the treatment of inherited and acquired disorders. Recently, antigen-specific T lymphocytes derived from hiPSCs have been reported. However, T lymphocyte populations with broad T cell receptor (TCR diversity have not been generated. We report that hiPSCs derived from skin biopsy are capable of producing T lymphocyte populations with a broad TCR repertoire. In vitro T cell differentiation follows a similar developmental program as observed in vivo, indicated by sequential expression of CD7, intracellular CD3 and surface CD3. The γδ TCR locus is rearranged first and is followed by rearrangement of the αβ locus. Both γδ and αβ T cells display a diverse TCR repertoire. Upon activation, the cells express CD25, CD69, cytokines (TNF-α, IFN-γ, IL-2 and cytolytic proteins (Perforin and Granzyme-B. These results suggest that most, if not all, mechanisms required to generate functional T cells with a broad TCR repertoire are intact in our in vitro differentiation protocol. These data provide a foundation for production of patient-specific T cells for the treatment of acquired or inherited immune disorders and for cancer immunotherapy.

Kaarel Irdi repertuaaripoliitilised vaated Vanemuise teatri juhina. Kaarel Ird’s Repertoire Policy as Manager of the Vanemuine Theatre

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Jaak Viller

2012-04-01

Full Text Available This article focuses on the meaning of ’repertoire policy’, which in a broader sense usually means the conformity of someone’s creative activities with their main target groups and the interests and expectations of these target groups. Usually, factors inside the theatre also influence repertoire policy (such as contemporary and classical texts, the relationship between local and foreign material, as well as the consideration of the artistic interests and abilities of the directors and actors involved. When analysing the Vanemuine Theatre and its long-standing manager Kaarel Ird (at Vanemuine during the years 1940–1986, a certain aspect stemming from the ideological doctrine of the totalitarian state should be taken into account: the mandatory quota of Soviet drama works (of the Russian and other Soviet nations written after the revolution of 1917, which had to be no less than two-thirds of the plays staged. One of Ird’s more distinguishable accomplishments in the formation of repertoire policy is the rehabilitation of classical Estonian drama and its legacy, which had been ostracised from the stage during the years following the war (1944–1955. Ird justified this with numerous performances and articles as well as in the choice of repertoire at the Vanemuine Theatre, which was very well received by the growing audience. Ird’s own best directed works were based on the legacy of classic Estonian drama (Lydia Koidula, Oskar Luts and others. The other tendency in Ird’s repertoire policy is the attention paid to the Estonian contemporary drama. His role in enthusing writers to create contributions for the drama genre was remarkable, as well as the care taken in order to make their plays reach the stage at Vanemuine Theatre. Something that should be pointed out in Ird’s favour is his explanation – which at the time was not at all self-evident – of the repertoire to the supervisory organs: that contemporary Estonian dramas ought

Primer sets for cloning the human repertoire of T cell Receptor Variable regions.

Science.gov (United States)

Boria, Ilenia; Cotella, Diego; Dianzani, Irma; Santoro, Claudio; Sblattero, Daniele

2008-08-29

Amplification and cloning of naïve T cell Receptor (TR) repertoires or antigen-specific TR is crucial to shape immune response and to develop immuno-based therapies. TR variable (V) regions are encoded by several genes that recombine during T cell development. The cloning of expressed genes as large diverse libraries from natural sources relies upon the availability of primers able to amplify as many V genes as possible. Here, we present a list of primers computationally designed on all functional TR V and J genes listed in the IMGT, the ImMunoGeneTics information system. The list consists of unambiguous or degenerate primers suitable to theoretically amplify and clone the entire TR repertoire. We show that it is possible to selectively amplify and clone expressed TR V genes in one single RT-PCR step and from as little as 1000 cells. This new primer set will facilitate the creation of more diverse TR libraries than has been possible using currently available primer sets.

VAP rates unchanged

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Robbins RA

2016-12-01

Full Text Available No abstract available. Article truncated at 150 words. In a research letter to JAMA Metersky and colleagues (1 report that ventilator-associated pneumonia (VAP rates have remained near 10% since 2005. The authors reviewed Medicare Patient Safety Monitoring System (MPSMS data on a representative sample of more than 86,000 critically ill patients treated at 1330 US hospitals between 2005 and 2013. To meet a diagnosis of VAP patients were required to have at least 2 days' ventilation in intensive care units; a chest radiograph with a new finding suggesting pneumonia; a physician diagnosis of pneumonia; and an order for antibiotics. VAP incidence was 10.8% (95% confidence interval, 7.4% - 14.4% during 2005 to 2006 and 9.7% (95% confidence interval, 5.1% - 14.9% during 2012 to 2013. In contrast, data from the CDC's National Healthcare Safety Network (NHSN have shown declines in VAP rates of 71% and 62% in medical and surgical intensive care units, respectively, between 2006 and 2012 …

Acute Hepatopancreatic Necrosis Disease-Causing Vibrio parahaemolyticus Strains Maintain an Antibacterial Type VI Secretion System with Versatile Effector Repertoires.

Science.gov (United States)

Li, Peng; Kinch, Lisa N; Ray, Ann; Dalia, Ankur B; Cong, Qian; Nunan, Linda M; Camilli, Andrew; Grishin, Nick V; Salomon, Dor; Orth, Kim

2017-07-01

Acute hepatopancreatic necrosis disease (AHPND) is a newly emerging shrimp disease that has severely damaged the global shrimp industry. AHPND is caused by toxic strains of Vibrio parahaemolyticus that have acquired a "selfish plasmid" encoding the deadly binary toxins PirA vp /PirB vp To better understand the repertoire of virulence factors in AHPND-causing V. parahaemolyticus , we conducted a comparative analysis using the genome sequences of the clinical strain RIMD2210633 and of environmental non-AHPND and toxic AHPND isolates of V. parahaemolyticus Interestingly, we found that all of the AHPND strains, but none of the non-AHPND strains, harbor the antibacterial type VI secretion system 1 (T6SS1), which we previously identified and characterized in the clinical isolate RIMD2210633. This finding suggests that the acquisition of this T6SS might confer to AHPND-causing V. parahaemolyticus a fitness advantage over competing bacteria and facilitate shrimp infection. Additionally, we found highly dynamic effector loci in the T6SS1 of AHPND-causing strains, leading to diverse effector repertoires. Our discovery provides novel insights into AHPND-causing pathogens and reveals a potential target for disease control. IMPORTANCE Acute hepatopancreatic necrosis disease (AHPND) is a serious disease that has caused severe damage and significant financial losses to the global shrimp industry. To better understand and prevent this shrimp disease, it is essential to thoroughly characterize its causative agent, Vibrio parahaemolyticus Although the plasmid-encoded binary toxins PirA vp /PirB vp have been shown to be the primary cause of AHPND, it remains unknown whether other virulent factors are commonly present in V. parahaemolyticus and might play important roles during shrimp infection. Here, we analyzed the genome sequences of clinical, non-AHPND, and AHPND strains to characterize their repertoires of key virulence determinants. Our studies reveal that an antibacterial type

From everyday communicative figurations to rigorous audience news repertoires: A mixed method approach to cross-media news consumption

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Christian Kobbernagel

2016-06-01

Full Text Available In the last couple of decades there has been an unprecedented explosion of news media platforms and formats, as a succession of digital and social media have joined the ranks of legacy media. We live in a ‘hybrid media system’ (Chadwick, 2013, in which people build their cross-media news repertoires from the ensemble of old and new media available. This article presents an innovative mixed-method approach with considerable explanatory power to the exploration of patterns of news media consumption. This approach tailors Q-methodology in the direction of a qualitative study of news consumption, in which a card sorting exercise serves to translate the participants’ news media preferences into a form that enables the researcher to undertake a rigorous factor-analytical construction of their news consumption repertoires. This interpretive, factor-analytical procedure, which results in the building of six audience news repertoires in Denmark, also preserves the qualitative thickness of the participants’ verbal accounts of the communicative figurations of their day-in-the-life with the news media.

Connectome-harmonic decomposition of human brain activity reveals dynamical repertoire re-organization under LSD.

Science.gov (United States)

Atasoy, Selen; Roseman, Leor; Kaelen, Mendel; Kringelbach, Morten L; Deco, Gustavo; Carhart-Harris, Robin L

2017-12-15

Recent studies have started to elucidate the effects of lysergic acid diethylamide (LSD) on the human brain but the underlying dynamics are not yet fully understood. Here we used 'connectome-harmonic decomposition', a novel method to investigate the dynamical changes in brain states. We found that LSD alters the energy and the power of individual harmonic brain states in a frequency-selective manner. Remarkably, this leads to an expansion of the repertoire of active brain states, suggestive of a general re-organization of brain dynamics given the non-random increase in co-activation across frequencies. Interestingly, the frequency distribution of the active repertoire of brain states under LSD closely follows power-laws indicating a re-organization of the dynamics at the edge of criticality. Beyond the present findings, these methods open up for a better understanding of the complex brain dynamics in health and disease.

Discrete Emotion Regulation Strategy Repertoires and Parasympathetic Physiology Characterize Psychopathology Symptoms in Childhood

Science.gov (United States)

Quiñones-Camacho, Laura E.; Davis, Elizabeth L.

2018-01-01

Certain psychopathologies are often linked to dysregulation of specific emotions (e.g., anxiety is associated with dysregulation of fear), but few studies have examined how regulatory repertoires for specific emotions (e.g., the strategies a person uses to regulate fear) relate to psychopathology, and fewer still have examined this in childhood. A…

B cell and antibody repertoire development in rabbits: the requirement of gut-associated lymphoid tissues.

Science.gov (United States)

Mage, Rose G; Lanning, Dennis; Knight, Katherine L

2006-01-01

The antibody repertoire of rabbits has interested immunologists for decades, in part because of the ease with which large quantities of high affinity antibodies can be obtained in serum, and in part because of the presence of genetic variants, allotypes, within V(H), C(H) and C(L) regions. Studies of these allotypes led to the initial descriptions of allelic exclusion, and neonatal suppression of serum Ig production (allotype suppression), and were instrumental in demonstrating that V and C regions are encoded by separate genes and are usually expressed in cis. The immune system of rabbit continues to be of interest primarily because of the use of both gene conversion and somatic hypermutation to diversify rearranged heavy and light chain genes and the role that gut-associated lymphoid tissues (GALT) and intestinal flora play in developing the primary (preimmune) antibody repertoire.

Primer sets for cloning the human repertoire of T cell Receptor Variable regions

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Santoro Claudio

2008-08-01

Full Text Available Abstract Background Amplification and cloning of naïve T cell Receptor (TR repertoires or antigen-specific TR is crucial to shape immune response and to develop immuno-based therapies. TR variable (V regions are encoded by several genes that recombine during T cell development. The cloning of expressed genes as large diverse libraries from natural sources relies upon the availability of primers able to amplify as many V genes as possible. Results Here, we present a list of primers computationally designed on all functional TR V and J genes listed in the IMGT®, the ImMunoGeneTics information system®. The list consists of unambiguous or degenerate primers suitable to theoretically amplify and clone the entire TR repertoire. We show that it is possible to selectively amplify and clone expressed TR V genes in one single RT-PCR step and from as little as 1000 cells. Conclusion This new primer set will facilitate the creation of more diverse TR libraries than has been possible using currently available primer sets.

Distribution and development of the postnatal murine V delta 1 T-cell receptor repertoire

Czech Academy of Sciences Publication Activity Database

Holtmeier, W.; Gille, J.; Zeuzem, S.; Šinkora, Marek

2010-01-01

Roč. 131, č. 2 (2010), s. 192-201 ISSN 0019-2805 R&D Projects: GA ČR GA524/07/0087 Institutional research plan: CEZ:AV0Z50200510 Keywords : gene rearrangement * repertoire development * rodent Subject RIV: EE - Microbiology, Virology Impact factor: 3.302, year: 2010

The natural antibody repertoire of sharks and humans recognizes the potential universe of antigens.

Science.gov (United States)

Adelman, Miranda K; Schluter, Samuel F; Marchalonis, John J

2004-02-01

In ancestral sharks, a rapid emergence in the evolution of the immune system occurred, giving jawed-vertebrates the necessary components for the combinatorial immune response (CIR). To compare the natural antibody (NAb) repertoires of the most divergent vertebrates with the capacity to produce antibodies, we isolated NAbs to the same set of antigens by affinity chromatography from two species of Carcharhine sharks and from human polyclonal IgG and IgM antibody preparations. The activities of the affinity-purified anti-T-cell receptor (anti-TCR) NAbs were compared with those of monoclonal anti-TCR NAbs that were generated from a systemic lupus erythematosus patient. We report that sharks and humans, representing the evolutionary extremes of vertebrate species sharing the CIR, have NAbs to human TCRs, Igs, the human senescent cell antigen, and to numerous retroviral antigens, indicating that essential features of the combinatorial repertoire and the capacity to recognize the potential universe of antigens is shared among all jawed-vertebrates.

The Change of Perinatal Mortality Over Three Decades in a Reference Centre in the Aegean Region: Neonatal Mortality has decreased but Foetal Mortality Remains Unchanged

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Nilgün Kültürsay

2017-12-01

Full Text Available Background: Perinatal, foetal and neonatal mortality statistics are important to show the development of a health care system in a country. However, in our country there are very few national and regional data about the changing pattern of perinatal neonatal mortality along with the development of new technologies in this area. Aims: Evaluation of the changes in mortality rates and the causes of perinatal and neonatal deaths within years in a perinatal reference centre which serves a high-risk population. Study Design: Cross-sectional retrospective study. Methods: The perinatal, neonatal and foetal mortality rates in the years 1979-1980 (1st time point and 1988-1989 (2nd time point were compared with the year 2008 (3rd time point. The causes of mortality were assessed by Wigglesworth classification and death reports. The neonatal mortality in the neonatal intensive care unit was also calculated. Results: Foetal mortality rates were 44/1000, 31.4/1000 and 41.75/1000 births, perinatal mortality rates were 35.6/1000, 18.8/1000 and 9/1000 births, and neonatal mortality rates were 35.6/1000, 18.8/1000 and 9/1000 live births for the three study time points, respectively. The mortality rate in neonatal intensive care unit decreased consistently from 33%, to 22.6% and 10%, respectively, together with decreasing neonatal mortality rates. The causes of perinatal deaths were foetal death 85%, immaturity 4%, and lethal congenital malformations 8% according to Wigglesworth classification in 2008, showing the high impact of foetal deaths on this high perinatal mortality rate. Infectious causes of neonatal deaths decreased but congenital anomalies increased in the last decades. Conclusion: Although neonatal mortality rate decreased significantly; foetal mortality rate has stayed unchanged since the late eighties. In order to decrease foetal and perinatal mortality rates more efficiently, reducing consanguineous marriages and providing better antenatal care for

Behavioural repertoire of free-range laying hens indoors and outdoors, and in relation to distance from the shed.

Science.gov (United States)

Thuy Diep, A; Larsen, H; Rault, J-L

2018-04-01

Access to an outdoor area is believed to allow free-range hens to express a greater behavioural repertoire. However, very little research has been done in this area. We hypothesised that the type and frequency of behaviours would differ between areas that vary in their characteristics and distance from the shed. This preliminary study investigated the behaviour of free-range laying hens in indoor and outdoor areas on one commercial free-range farm, through video recordings and scan sampling of focal hens, with the aim of determining their behavioural repertoire and time budget. While ranging, hens spent most of their time foraging. Indoors, hens preened and rested. Behaviour in the wintergarden showed similarities to both the indoor and outdoor areas, with preening, resting and foraging behaviours. Differences were not in the main behavioural repertoire, but rather in terms of time budget, with access to the range and wintergarden encouraging exploration. There was no difference in the types of behaviours that hens performed in the outdoor range compared with inside the shed, but access to a wintergarden and the outdoor range were favoured by the hens for foraging. © 2018 Australian Veterinary Association.

Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.

Directory of Open Access Journals (Sweden)

Fan Gao

Full Text Available In human immune system, V(DJ recombination produces an enormously large repertoire of immunoglobulins (Ig so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of immunoglobulins. However, these techniques typically require separation of B cell population from whole blood and require a few weeks for running the sequencers, so it may not be practical to implement them in clinical settings. Recently, the Ion Torrent personal genome sequencer has emerged as a tabletop personal genome sequencer that can be operated in a time-efficient and cost-effective manner. In this study, we explored the technical feasibility to use multiplex PCR for amplifying V(DJ recombination for IgH, directly from whole blood, then sequence the amplicons by the Ion Torrent sequencer. The whole process including data generation and analysis can be completed in one day. We tested the method in a pilot study on patients with benign, atypical and malignant meningiomas. Despite the noisy data, we were able to compare the samples by their usage frequencies of the V segment, as well as their somatic hypermutation rates. In summary, our study suggested that it is technically feasible to perform clinical monitoring of V(DJ recombination within a day by personal genome sequencers.

Nuclear and energy policy in Korea. Unchanging illusion of nuclear energy and citizens' challenge

International Nuclear Information System (INIS)

Leem, S.J.

2006-01-01

Korea is the tenth largest energy consumer in the world; the country ranks sixth in oil consumption, seventh in electricity consumption, and ninth in total CO2 emission. Korea now has 20 reactors in operation, nuclear power producing about 40% of its electricity. Its generating capacity from nuclear power plants is the sixth largest in the world; Korea currently exports nuclear technology. The rapid growth of this industry is attributed to extensive subsidy and protection from the Korean government; supported by government-initiated programs a powerful interest group, which consists of nuclear industries, technocrats, and governmental organizations concerned with nuclear policy, now exerts a major influence upon Korea's energy policy for nuclear expansion. Korea's nuclear power policymakers have, however, met opposition since End of the 1980s. The government's attempt to build a nuclear waste repository has provoked strong resistance from environmental movements and local citizens. Even if the government recently succeeded in designating Kyoungju as the nuclear waste site, the nuclear waste issue has awakened public interest in nuclear problems and strengthening public denunciation of Korea's expansive nuclear power policy. In addition, the activation of the Kyoto Protocol in February 2005 has impelled the government to redirect its energy policy towards a sustainable direction. This article focuses on the status and perspectives of Korea's nuclear power policy, enabling a discussion of the degree to which Korea's nuclear and energy policy has changed yet in many ways remains unchanged. (orig.)

Low arousing positive affect broadens visual attention and alters the thought-action repertoire while broadened visual attention does not

Directory of Open Access Journals (Sweden)

Daniel Thomas Jäger

2016-10-01

Full Text Available The Broaden-and-Build Theory states that positive emotions broaden cognition and therefore build personal resources. However, missing theoretical precision regarding the interaction of the cognitive processes involved offers a variety of possible explanations for the mechanisms of broadening and building. In Experiment 1 we tested the causality assumption which states that positive emotions first broaden visual attention which in turn leads to broadened cognition. We examined the effects of a broadened, narrowed or neutral attentional scope of 72 subjects (30 men on their momentary thought-action repertoire. Results showed that there were no significant differences between groups regarding the breadth or the content of the thought-action repertoire. In Experiment 2 we studied the non-causality hypothesis which assumes a non-causal relationship between cognitive processes. We did so by investigating the effects of negative, neutral, and positive affect on the visual attentional scope of 85 subjects (41 men in Experiment 2a, as well as on the thought-action repertoire of 85 participants (42 men in Experiment 2b. Results revealed an attentional broadening effect in Experiment 2a but no differences between groups concerning the breadth of the thought-action repertoire in Experiment 2b. However, a theory driven content analysis showed that positive affect promoted social actions whereas negative affect endorsed resource protecting actions. Thus, our results favor the non-causality assumption. Moreover, results indicate that positive emotions do not target personal resources in general but rather resources associated with social behavior. In conclusion, we argue that the Broaden-and-Build Theory should be refined.

Sequence-Based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen-Specific Antibodies

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Katherine E. Harris

2018-04-01

Full Text Available We created a novel transgenic rat that expresses human antibodies comprising a diverse repertoire of heavy chains with a single common rearranged kappa light chain (IgKV3-15-JK1. This fixed light chain animal, called OmniFlic, presents a unique system for human therapeutic antibody discovery and a model to study heavy chain repertoire diversity in the context of a constant light chain. The purpose of this study was to analyze heavy chain variable gene usage, clonotype diversity, and to describe the sequence characteristics of antigen-specific monoclonal antibodies (mAbs isolated from immunized OmniFlic animals. Using next-generation sequencing antibody repertoire analysis, we measured heavy chain variable gene usage and the diversity of clonotypes present in the lymph node germinal centers of 75 OmniFlic rats immunized with 9 different protein antigens. Furthermore, we expressed 2,560 unique heavy chain sequences sampled from a diverse set of clonotypes as fixed light chain antibody proteins and measured their binding to antigen by ELISA. Finally, we measured patterns and overall levels of somatic hypermutation in the full B-cell repertoire and in the 2,560 mAbs tested for binding. The results demonstrate that OmniFlic animals produce an abundance of antigen-specific antibodies with heavy chain clonotype diversity that is similar to what has been described with unrestricted light chain use in mammals. In addition, we show that sequence-based discovery is a highly effective and efficient way to identify a large number of diverse monoclonal antibodies to a protein target of interest.

The Effects of Multiple Exemplar Instruction on the Relation between Listener and Intraverbal Categorization Repertoires

Science.gov (United States)

Lechago, Sarah A.; Carr, James E.; Kisamore, April N.; Grow, Laura L.

2015-01-01

We evaluated the effects of multiple exemplar instruction (MEI) on the relation between listener and intraverbal categorization repertoires of six typically developing preschool-age children using a nonconcurrent multiple-probe design across participants. After failing to emit intraverbal categorization responses following listener categorization…

Contribution of V(H replacement products in mouse antibody repertoire.

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Lin Huang

Full Text Available VH replacement occurs through RAG-mediated recombination between the cryptic recombination signal sequence (cRSS near the 3' end of a rearranged VH gene and the 23-bp RSS from an upstream unrearranged VH gene. Due to the location of the cRSS, VH replacement leaves a short stretch of nucleotides from the previously rearranged VH gene at the newly formed V-D junction, which can be used as a marker to identify VH replacement products. To determine the contribution of VH replacement products to mouse antibody repertoire, we developed a Java-based VH Replacement Footprint Analyzer (VHRFA program and analyzed 17,179 mouse IgH gene sequences from the NCBI database to identify VH replacement products. The overall frequency of VH replacement products in these IgH genes is 5.29% based on the identification of pentameric VH replacement footprints at their V-D junctions. The identified VH replacement products are distributed similarly in IgH genes using most families of VH genes, although different families of VH genes are used differentially. The frequencies of VH replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies. Moreover, the identified VH replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids. These results revealed a significant contribution of VH replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.

The determination of unchanged [11C]diprenorphine, [11C]L-deprenyl and [11C]raclopride in plasma by HPLC

International Nuclear Information System (INIS)

Luthra, S.K.; Turton, D.R.; Price, G.; Ahier, R.; Martin, F.; Hume, S.; Cremer, J.

1990-01-01

In PET studies a knowledge of the fraction of radioactivity in plasma representing unchanged 11 C-labelled ligand/tracer is essential for correction of the arterial plasma input curve. A number of different approaches (e.g. HPLC and TLC/OPTLC) to the determination of unchanged radio-ligand/tracer have been reported for 11 C-labelled carfentanil, raclopride and L-deprenyl and for 76 Br-labelled bromolisuride. The authors report here how they have applied the simple work-up and analytical procedure, originally reported for [ 11 C]carfentanil, to establish the percentage of unmchanged 11 C-labelled diprenorphine, L-deprenyl and raclopride in human and animal plasma as a function of time

Fundamental characteristics of the immunoglobulin VH repertoire of chickens in comparison with those of humans, mice, and camelids.

Science.gov (United States)

Wu, Leeying; Oficjalska, Katarzyna; Lambert, Matthew; Fennell, Brian J; Darmanin-Sheehan, Alfredo; Ní Shúilleabháin, Deirdre; Autin, Bénédicte; Cummins, Emma; Tchistiakova, Lioudmila; Bloom, Laird; Paulsen, Janet; Gill, Davinder; Cunningham, Orla; Finlay, William J J

2012-01-01

Examination of 1269 unique naive chicken V(H) sequences showed that the majority of positions in the framework (FW) regions were maintained as germline, with high mutation rates observed in the CDRs. Many FW mutations could be clearly related to the modulation of CDR structure or the V(H)-V(L) interface. CDRs 1 and 2 of the V(H) exhibited frequent mutation in solvent-exposed positions, but conservation of common structural residues also found in human CDRs at the same positions. In comparison with humans and mice, the chicken CDR3 repertoire was skewed toward longer sequences, was dominated by small amino acids (G/S/A/C/T), and had higher cysteine (chicken, 9.4%; human, 1.6%; and mouse, 0.25%) but lower tyrosine content (chicken, 9.2%; human, 16.8%; and mouse 26.4%). A strong correlation (R(2) = 0.97) was observed between increasing CDR3 length and higher cysteine content. This suggests that noncanonical disulfides are strongly favored in chickens, potentially increasing CDR stability and complexity in the topology of the combining site. The probable formation of disulfide bonds between CDR3 and CDR1, FW2, or CDR2 was also observed, as described in camelids. All features of the naive repertoire were fully replicated in the target-selected, phage-displayed repertoire. The isolation of a chicken Fab with four noncanonical cysteines in the V(H) that exhibits 64 nM (K(D)) binding affinity for its target proved these constituents to be part of the humoral response, not artifacts. This study supports the hypothesis that disulfide bond-constrained CDR3s are a structural diversification strategy in the restricted germline v-gene repertoire of chickens.

Human Non-linguistic Vocal Repertoire: Call Types and Their Meaning.

Science.gov (United States)

Anikin, Andrey; Bååth, Rasmus; Persson, Tomas

2018-01-01

Recent research on human nonverbal vocalizations has led to considerable progress in our understanding of vocal communication of emotion. However, in contrast to studies of animal vocalizations, this research has focused mainly on the emotional interpretation of such signals. The repertoire of human nonverbal vocalizations as acoustic types, and the mapping between acoustic and emotional categories, thus remain underexplored. In a cross-linguistic naming task (Experiment 1), verbal categorization of 132 authentic (non-acted) human vocalizations by English-, Swedish- and Russian-speaking participants revealed the same major acoustic types: laugh, cry, scream, moan, and possibly roar and sigh. The association between call type and perceived emotion was systematic but non-redundant: listeners associated every call type with a limited, but in some cases relatively wide, range of emotions. The speed and consistency of naming the call type predicted the speed and consistency of inferring the caller's emotion, suggesting that acoustic and emotional categorizations are closely related. However, participants preferred to name the call type before naming the emotion. Furthermore, nonverbal categorization of the same stimuli in a triad classification task (Experiment 2) was more compatible with classification by call type than by emotion, indicating the former's greater perceptual salience. These results suggest that acoustic categorization may precede attribution of emotion, highlighting the need to distinguish between the overt form of nonverbal signals and their interpretation by the perceiver. Both within- and between-call acoustic variation can then be modeled explicitly, bringing research on human nonverbal vocalizations more in line with the work on animal communication.

Human IgG repertoire of malaria antigen-immunized human immune system (HIS) mice.

Science.gov (United States)

Nogueira, Raquel Tayar; Sahi, Vincent; Huang, Jing; Tsuji, Moriya

2017-08-01

Humanized mouse models present an important tool for preclinical evaluation of new vaccines and therapeutics. Here we show the human variable repertoire of antibody sequences cloned from a previously described human immune system (HIS) mouse model that possesses functional human CD4+ T cells and B cells, namely HIS-CD4/B mice. We sequenced variable IgG genes from single memory B-cell and plasma-cell sorted from splenocytes or whole blood lymphocytes of HIS-CD4/B mice that were vaccinated with a human plasmodial antigen, a recombinant Plasmodium falciparum circumsporozoite protein (rPfCSP). We demonstrate that rPfCSP immunization triggers a diverse B-cell IgG repertoire composed of various human VH family genes and distinct V(D)J recombinations that constitute diverse CDR3 sequences similar to humans, although low hypermutated sequences were generated. These results demonstrate the substantial genetic diversity of responding human B cells of HIS-CD4/B mice and their capacity to mount human IgG class-switched antibody response upon vaccination. Copyright © 2017 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Impaired recovery of syllable repertoires after unilateral lesions of the HVC of male domesticated canaries.

NARCIS (Netherlands)

Halle, F; Gahr, M.; Kreutzer, M.

2003-01-01

Particular features of the song of adult male canaries such as a large syllable repertoire resulting in a great diversity of song phrases and special so-called 'complex' syllables enhance various features of female reproductive behaviour. These features are produced in a species or strain dependent

Immunoproteomic analysis of the protein repertoire of unsporulated Eimeria tenella oocysts

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Zhang Zhenchao

2017-01-01

Full Text Available The apicomplexan protozoans Eimeria spp. cause coccidioses, the most common intestinal diseases in chickens. Coccidiosis is associated with significant animal welfare issues and has a high economic impact on the poultry industry. Lack of a full understanding of immunogenic molecules and their precise functions involved in the Eimeria life cycles may limit development of effective vaccines and drug therapies. In this study, immunoproteomic approaches were used to define the antigenic protein repertoire from the total proteins of unsporulated Eimeria tenella oocysts. Approximately 101 protein spots were recognized in sera from chickens infected experimentally with E. tenella. Forty-six spots of unsporulated oocysts were excised from preparative gels and identified by matrix-assisted laser desorption ionization time-of-flight MS (MALDI-TOF-MS and MALDI-TOF/TOF-MS. For unsporulated oocysts, 13 known proteins of E. tenella and 17 homologous proteins to other apicomplexan or protozoan parasites were identified using the ‘Mascot’ server. The remaining proteins were searched against the E. tenella protein sequence database using the ‘Mascot in-house’ search engine (version 2.1 in automated mode, and 12 unknown proteins were identified. The amino acid sequences of the unknown proteins were searched using BLAST against non-redundant sequence databases (NCBI, and 9 homologous proteins in unsporulated oocyst were found homologous to proteins of other apicomplexan parasites. These findings may provide useful evidence for understanding parasite biology, pathogenesis, immunogenicity and immune evasion mechanisms of E. tenella.

The acoustic repertoire of bottlenose dolphins (Tursiops truncatus) from the southern Gulf of Mexico

Science.gov (United States)

Bazua-Duran, Carmen

2005-04-01

Bottlenose dolphins live in a variety of habitats of the world's oceans using their acoustic repertoire to communicate and inspect their environment. This work investigates the acoustic repertoire of bottlenose dolphins that inhabit a coastal lagoon of the southern Gulf of Mexico, the Laguna de Terminos and how it may relate to the dolphins' general behavioral state and herd size, and to the general characteristics of the habitat, such as visibility, depth, and sea state. Preliminary results show that bottlenose dolphins produce by far more clicks than whistles in all behavioral states (feeding, resting, social, and travel) and herd sizes, which may correlate with the decreased visibility and shallow depth of the Laguna de Terminos. Additionally, silence was found during all behavioral states, but very seldom in herds of large size. These preliminary results suggest that bottlenose dolphins are choosing when and where to produce their phonations. Therefore, more detailed studies are needed to understand how these animals are using their acoustic sense to communicate and inspect their environment. [Work supported by CONACyT-Gobierno Edo. de Campeche and PAPIIT, UNAM.

Structural repertoire of immunoglobulin λ light chains

KAUST Repository

Chailyan, Anna

2011-03-01

The immunoglobulin λ isotype is present in nearly all vertebrates and plays an important role in the human immune system. Despite its importance, few systematic studies have been performed to analyze the structural conformation of its variable regions, contrary to what is the case for κ and heavy chains. We show here that an analysis of the structures of λ chains allows the definition of a discrete set of recurring conformations (canonical structures) of their hypervariable loops and, most importantly, the identification of sequence constraints that can be used to predict their structure. We also show that the structural repertoire of λ chains is different and more varied than that of the κ chains, consistently with the current view of the involvement of the two major light-chain families in complementary strategies of the immune system to ensure a fine tuning between diversity and stability in antigen recognition. © 2011 Wiley-Liss, Inc.

Structural repertoire of immunoglobulin λ light chains

KAUST Repository

Chailyan, Anna; Marcatili, Paolo; Cirillo, Davide; Tramontano, Anna

2011-01-01

The immunoglobulin λ isotype is present in nearly all vertebrates and plays an important role in the human immune system. Despite its importance, few systematic studies have been performed to analyze the structural conformation of its variable regions, contrary to what is the case for κ and heavy chains. We show here that an analysis of the structures of λ chains allows the definition of a discrete set of recurring conformations (canonical structures) of their hypervariable loops and, most importantly, the identification of sequence constraints that can be used to predict their structure. We also show that the structural repertoire of λ chains is different and more varied than that of the κ chains, consistently with the current view of the involvement of the two major light-chain families in complementary strategies of the immune system to ensure a fine tuning between diversity and stability in antigen recognition. © 2011 Wiley-Liss, Inc.

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity

DEFF Research Database (Denmark)

Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo

2016-01-01

The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high...... of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10-6), outperforming other sequence- and structure-based models....

Emotional Intelligence and the Conflict Resolution Repertoire of Couples in Tertiary Institutions in Imo State

Science.gov (United States)

Nnodum, B. I.; Ugwuegbulam, C. N.; Agbaenyi, I. G.

2016-01-01

This study is a descriptive survey that investigated the relationship between emotional intelligence and conflict resolution repertoire of couples in tertiary institutions. A sample of 250 married people were drawn from the population of couples in tertiary institutions in Imo State. Two researcher made and validated instruments were used in…

Spectratyping analysis of the islet-reactive T cell repertoire in diabetic NOD Igμnull mice after polyclonal B cell reconstitution

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Sercarz Eli E

2011-07-01

Full Text Available Abstract Background Non Obese Diabetic mice lacking B cells (NOD.Igμnull mice do not develop diabetes despite their susceptible background. Upon reconstitution of B cells using a chimera approach, animals start developing diabetes at 20 weeks of age. Methods We have used the spectratyping technique to follow the T cell receptor (TCR V beta repertoire of NOD.Igμnull mice following B cell reconstitution. This technique provides an unbiased approach to understand the kinetics of TCR expansion. We have also analyzed the TCR repertoire of reconstituted animals receiving cyclophosphamide treatment and following tissue transplants to identify common aggressive clonotypes. Results We found that B cell reconstitution of NOD.Igμnull mice induces a polyclonal TCR repertoire in the pancreas 10 weeks later, gradually diversifying to encompass most BV families. Interestingly, these clonotypic BV expansions are mainly confined to the pancreas and are absent from pancreatic lymph nodes or spleens. Cyclophosphamide-induced diabetes at 10 weeks post-B cell reconstitution reorganized the predominant TCR repertoires by removing potential regulatory clonotypes (BV1, BV8 and BV11 and increasing the frequency of others (BV4, BV5S2, BV9, BV16-20. These same clonotypes are more frequently present in neonatal pancreatic transplants under the kidney capsule of B-cell reconstituted diabetic NOD.Igμnull mice, suggesting their higher invasiveness. Phenotypic analysis of the pancreas-infiltrating lymphocytes during diabetes onset in B cell reconstituted animals show a predominance of CD19+ B cells with a B:T lymphocyte ratio of 4:1. In contrast, in other lymphoid organs (pancreatic lymph nodes and spleens analyzed by FACS, the B:T ratio was 1:1. Lymphocytes infiltrating the pancreas secrete large amounts of IL-6 and are of Th1 phenotype after CD3-CD28 stimulation in vitro. Conclusions Diabetes in NOD.Igμnull mice appears to be caused by a polyclonal repertoire of T cell

WORKS FOR CLARINET AND ACCOMPANIMENT IN OLEG NEGRUŢA’S COMPOSITION REPERTOIRE

OpenAIRE

MUŞAT SERGHEI; CHICIUC NATALIA

2015-01-01

Oleg Negruţa’s composition repertoire for solo instruments with accompaniment, of which clarinet opuses are highlighted, is important for indigenous musical art. In a vast genre complex, it confirms the composer’s constant commitment to the idea of the Bessarabian professional school. In this sense, as relevant works can be considered the three pieces for clarinet and piano: Improvisation, Fantasy on a Theme by Paganini and Elegy. However, this article is meant to offer details in an analytic...

Phenotypic integration and the evolution of signal repertoires: A case study of treefrog acoustic communication.

Science.gov (United States)

Reichert, Michael S; Höbel, Gerlinde

2018-03-01

Animal signals are inherently complex phenotypes with many interacting parts combining to elicit responses from receivers. The pattern of interrelationships between signal components reflects the extent to which each component is expressed, and responds to selection, either in concert with or independently of others. Furthermore, many species have complex repertoires consisting of multiple signal types used in different contexts, and common morphological and physiological constraints may result in interrelationships extending across the multiple signals in species' repertoires. The evolutionary significance of interrelationships between signal traits can be explored within the framework of phenotypic integration, which offers a suite of quantitative techniques to characterize complex phenotypes. In particular, these techniques allow for the assessment of modularity and integration, which describe, respectively, the extent to which sets of traits covary either independently or jointly. Although signal and repertoire complexity are thought to be major drivers of diversification and social evolution, few studies have explicitly measured the phenotypic integration of signals to investigate the evolution of diverse communication systems. We applied methods from phenotypic integration studies to quantify integration in the two primary vocalization types (advertisement and aggressive calls) in the treefrogs Hyla versicolor , Hyla cinerea, and Dendropsophus ebraccatus . We recorded male calls and calculated standardized phenotypic variance-covariance ( P ) matrices for characteristics within and across call types. We found significant integration across call types, but the strength of integration varied by species and corresponded with the acoustic similarity of the call types within each species. H. versicolor had the most modular advertisement and aggressive calls and the least acoustically similar call types. Additionally, P was robust to changing social competition

A role for gut-associated lymphoid tissue in shaping the human B cell repertoire.

Science.gov (United States)

Vossenkämper, Anna; Blair, Paul A; Safinia, Niloufar; Fraser, Louise D; Das, Lisa; Sanders, Theodore J; Stagg, Andrew J; Sanderson, Jeremy D; Taylor, Kirstin; Chang, Fuju; Choong, Lee M; D'Cruz, David P; Macdonald, Thomas T; Lombardi, Giovanna; Spencer, Jo

2013-08-26

We have tracked the fate of immature human B cells at a critical stage in their development when the mature B cell repertoire is shaped. We show that a major subset of bone marrow emigrant immature human B cells, the transitional 2 (T2) B cells, homes to gut-associated lymphoid tissue (GALT) and that most T2 B cells isolated from human GALT are activated. Activation in GALT is a previously unknown potential fate for immature human B cells. The process of maturation from immature transitional B cell through to mature naive B cell includes the removal of autoreactive cells from the developing repertoire, a process which is known to fail in systemic lupus erythematosus (SLE). We observe that immature B cells in SLE are poorly equipped to access the gut and that gut immune compartments are depleted in SLE. Thus, activation of immature B cells in GALT may function as a checkpoint that protects against autoimmunity. In healthy individuals, this pathway may be involved in generating the vast population of IgA plasma cells and also the enigmatic marginal zone B cell subset that is poorly understood in humans.

Antibody repertoires in humanized NOD-scid-IL2Rγ(null mice and human B cells reveals human-like diversification and tolerance checkpoints in the mouse.

Directory of Open Access Journals (Sweden)

Gregory C Ippolito

Full Text Available Immunodeficient mice reconstituted with human hematopoietic stem cells enable the in vivo study of human hematopoiesis. In particular, NOD-scid-IL2Rγ(null engrafted mice have been shown to have reasonable levels of T and B cell repopulation and can mount T-cell dependent responses; however, antigen-specific B-cell responses in this model are generally poor. We explored whether developmental defects in the immunoglobulin gene repertoire might be partly responsible for the low level of antibody responses in this model. Roche 454 sequencing was used to obtain over 685,000 reads from cDNA encoding immunoglobulin heavy (IGH and light (IGK and IGL genes isolated from immature, naïve, or total splenic B cells in engrafted NOD-scid-IL2Rγ(null mice, and compared with over 940,000 reads from peripheral B cells of two healthy volunteers. We find that while naïve B-cell repertoires in humanized mice are chiefly indistinguishable from those in human blood B cells, and display highly correlated patterns of immunoglobulin gene segment use, the complementarity-determining region H3 (CDR-H3 repertoires are nevertheless extremely diverse and are specific for each individual. Despite this diversity, preferential D(H-J(H pairings repeatedly occur within the CDR-H3 interval that are strikingly similar across all repertoires examined, implying a genetic constraint imposed on repertoire generation. Moreover, CDR-H3 length, charged amino-acid content, and hydropathy are indistinguishable between humans and humanized mice, with no evidence of global autoimmune signatures. Importantly, however, a statistically greater usage of the inherently autoreactive IGHV4-34 and IGKV4-1 genes was observed in the newly formed immature B cells relative to naïve B or total splenic B cells in the humanized mice, a finding consistent with the deletion of autoreactive B cells in humans. Overall, our results provide evidence that key features of the primary repertoire are shaped by

Repertoire Development and the Control of Cytotoxic/Effector Function in Human γδ T Cells

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Elizabeth M. Urban

2010-01-01

Full Text Available T cells develop into two major populations distinguished by their T cell receptor (TCR chains. Cells with the αβ TCR generally express CD4 or CD8 lineage markers and mostly fall into helper or cytotoxic/effector subsets. Cells expressing the alternate γδ TCR in humans generally do not express lineage markers, do not require MHC for antigen presentation, and recognize nonpeptidic antigens. We are interested in the dominant Vγ2Vδ2+ T cell subset in human peripheral blood and the control of effector function in this population. We review the literature on γδ T cell generation and repertoire selection, along with recent work on CD56 expression and defining a cytotoxic/effector lineage within the phosphoantigen-reactive Vγ2Vδ2 cells. A unique mechanism for MHC-independent repertoire selection is linked to the control of effector function that is vital to the role for γδ T cells in tumor surveillance. Better understanding of these mechanisms will improve our ability to exploit this population for tumor immunotherapy.

Behavioral Cusps: A Person-Centered Concept for Establishing Pivotal Individual, Family, and Community Behaviors and Repertoires

Science.gov (United States)

Smith, Garnett J.; McDougall, Dennis; Edelen-Smith, Patricia

2006-01-01

Cumulative-hierarchical learning (CHL) and behavior, a premise first introduced by Staats in 1975, describes how higher-level behavioral patterns and structures can emerge from interactions among a set of lower-level actions. Proponents of CHL emphasize the importance of pivotal response interventions, behavior repertoires, generative learning,…

Changes in the repertoire of natural antibodies caused by immunization with bacterial antigens

DEFF Research Database (Denmark)

Shilova, N V; Navakouski, M J; Huflejt, M

2011-01-01

The repertoire of natural anti-glycan antibodies in naïve chickens and in chickens immunized with bacteria Burkholderia mallei, Burkholderia pseudomallei, and Francisella tularensis as well as with peptides from an outer membrane protein of B. pseudomallei was studied. A relatively restricted pat...... pattern of natural antibodies (first of all IgY against bacterial cell wall peptidoglycan fragments, L-Rha, and core N-acetyllactosamine) shrank and, moreover, the level of detectable antibodies decreased as a result of immunization....

Effect of the herbal formulation Jianpijiedu on the TCRVβCDR3 repertoire in rats with hepatocellular carcinoma and subjected to food restriction combined with laxative.

Science.gov (United States)

Sun, Baoguo; Meng, Jun; Xiang, Ting; Zhang, Lei; Deng, Liuxiang; Chen, Yan; Luo, Haoxuan; Yang, Zhangbin; Chen, Zexiong; Zhang, Shijun

2016-03-01

The aim of this study was to investigate the effects of the Chinese herbal formulation Jianpijiedu (JPJD) in a rat model of orthotopic hepatocellular carcinoma (OHC). The tumor-bearing rats underwent food restriction combined with laxative (FRL) treatment in order to model the nutritional and digestive symptoms of patients with hepatocellular carcinoma. In addition, the study aimed to elucidate the effect of JPJD on the T cell receptor Vβ-chain complementarity-determining region 3 (TCRVβCDR3) repertoire and the underlying mechanism. The FRL rat model was established by alternate-day food restriction and the oral administration of Glauber's salt (sodium sulfate), based on which the OHC model was then established. Subsequently, the FRL-OHC induced animals received JPJD or thymopentin-5 (TP5) for 17 days. Differences in the TCRVβCDR3 repertoire in the rat thymus, liver and hepatocellular carcinoma tissues were analyzed by polymerase chain reaction. Compared with the FRL-OHC model animals without any treatment, those treated with JPJD exhibited significantly inhibited hepatocellular carcinoma growth (PSimpsons diversity index (Ds) values and the quasi-Gaussian distribution rate of the TCRVβCDR3 repertoire in the thymus, liver and hepatocellular carcinoma tissues. However, no anti-hepatoma effects were evident in the rats treated with TP5. In addition, TP5 increased the Ds values and the quasi-Gaussian distribution rate of the TCRVβCDR3 repertoire in hepatocellular carcinoma tissues compared with those in the JPJD-treated group. The anti-hepatoma effects of JPJD in FRL-OHC-induced animals may be due to the promotion of the Ds values of the TCRVβCDR3 repertoire.

Cloning of the immunological repertoire in Escherichia coli for generation of monoclonal catalytic antibodies: construction of a heavy chain variable region-specific cDNA library.

OpenAIRE

Sastry, L; Alting-Mees, M; Huse, W D; Short, J M; Sorge, J A; Hay, B N; Janda, K D; Benkovic, S J; Lerner, R A

1989-01-01

Efficient generation of catalytic antibodies is uniquely dependent on the exact nature of the binding interactions in the antigen-antibody complex. Current methods for generation of monoclonal antibodies do not efficiently survey the immunological repertoire and, therefore, they limit the number of catalysts that can be obtained. We are exploring methods to clone and express the immunological repertoire in Escherichia coli. As the essential first step, we present here a method for the establi...

The MicroRNA Repertoire of Symbiodinium, the Dinoflagellate Symbiont of Reef-Building Corals

KAUST Repository

Baumgarten, Sebastian

2013-07-01

Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3’UTRs of 12,858 mRNAs and 53 plantlike target sites in 51,917 genes. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

REFLECTIONS ON THE ORNAMENTAL PHENOMENON WITHIN THE REPERTOIRE OF TRADITIONAL VIOLONISTS IN THE HISTORICAL MOLDOVAN FOLK SPACE

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GRIB VITALIE

2016-12-01

Full Text Available The eclectic style in the interpretative manner of the younger generation of traditional violinists, which oft en distorts the aesthetic essence of folklore creations, has determined the need for research, scientifi c reasoning and elaboration of some methods of learning the traditional ornamental instrumental style, which can be general or individual, yet specifi c to the historical Moldovan folk space. To achieve this, we consider important to identify the types of ornaments in traditional instrumental music; to delimit the interpretative particularities of ornaments in literate and folk music; to analyse the ornamentation styles of songs within the repertoire of diff erent traditional violinists, that belong to the folk space investigated in terms of the type of creation. As a model for analysing the particularities of interpreting these ornaments, we select violinists from older generations, whose repertoire and style of execution has not been aff ected by the media and technological progress.

The vocal repertoire of the African Penguin (Spheniscus demersus): structure and function of calls.

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Favaro, Livio; Ozella, Laura; Pessani, Daniela

2014-01-01

The African Penguin (Spheniscus demersus) is a highly social and vocal seabird. However, currently available descriptions of the vocal repertoire of African Penguin are mostly limited to basic descriptions of calls. Here we provide, for the first time, a detailed description of the vocal behaviour of this species by collecting audio and video recordings from a large captive colony. We combine visual examinations of spectrograms with spectral and temporal acoustic analyses to determine vocal categories. Moreover, we used a principal component analysis, followed by signal classification with a discriminant function analysis, for statistical validation of the vocalisation types. In addition, we identified the behavioural contexts in which calls were uttered. The results show that four basic vocalisations can be found in the vocal repertoire of adult African Penguin, namely a contact call emitted by isolated birds, an agonistic call used in aggressive interactions, an ecstatic display song uttered by single birds, and a mutual display song vocalised by pairs, at their nests. Moreover, we identified two distinct vocalisations interpreted as begging calls by nesting chicks (begging peep) and unweaned juveniles (begging moan). Finally, we discussed the importance of specific acoustic parameters in classifying calls and the possible use of the source-filter theory of vocal production to study penguin vocalisations.

Behavioral Repertoire Influences the Rate and Nature of Learning in Climbing: Implications for Individualized Learning Design in Preparation for Extreme Sports Participation

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Dominic Orth

2018-06-01

Full Text Available Extreme climbing where participants perform while knowing that a simple mistake could result in death requires a skill set normally acquired in non-extreme environments. In the ecological dynamics approach to perception and action, skill acquisition involves a process where the existing repertoire of behavioral capabilities (or coordination repertoire of a learner are destabilized and re-organized through practice—this process can expand the individuals affordance boundaries allowing the individual to explore new environments. Change in coordination repertoire has been observed in bi-manual coordination and postural regulation tasks, where individuals begin practice using one mode of coordination before transitioning to another, more effective, coordination mode during practice. However, individuals may also improve through practice without qualitatively reorganizing movement system components—they do not find a new mode of coordination. To explain these individual differences during learning (i.e., whether or not a new action is discovered, a key candidate is the existing coordination repertoire present prior to practice. In this study, the learning dynamics of body configuration patterns organized with respect to an indoor climbing surface were observed and the existing repertoire of coordination evaluated prior to and after practice. Specifically, performance outcomes and movement patterns of eight beginners were observed across 42 trials of practice over a 7-week period. A pre- and post-test scanning procedure was used to determine existing patterns of movement coordination and the emergence of new movement patterns after the practice period. Data suggested the presence of different learning dynamics by examining trial-to-trial performance in terms of jerk (an indicator of climbing fluency, at the individual level of analysis. The different learning dynamics (identified qualitatively included: continuous improvement, sudden improvement

Rules of song development and their use in vocal interactions by birds with large repertoires

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Nicole Geberzahn

2004-06-01

Full Text Available Songbirds are well known for settling their disputes by vocal signals, and their singing plays a dominant role. Most studies on this issue have concentrated on bird species that develop and use small vocal repertoires. In this article we will go farther and focus on examples of how species with large song repertoires make use of their vocal competence. In particular, we will outline the study of interaction rules which have been elucidated by examining time- and pattern-specific relationships between signals exchanged by territorial neighbors. First we present an inquiry into the rules of song learning and development. In birds with large song repertoires, the ontogeny of such rules proceeds along a number of trajectories which help in understanding the often remarkable accomplishments of adult birds. In both approaches, our model species will be the Common Nightingale Luscinia megarhynchos that has been investigated intensively in the field and in the laboratory.Pássaros canoros são bem conhecidos por resolver suas brigas através de sinais vocais e seu canto tem um papel dominante. A maioria dos estudos sobre este assunto focalizou espécies de aves que desenvolvem e usam repertórios vocais pequenos. Neste artigo iremos mais longe, examinando como espécies com grandes repertórios fazem uso de suas capacidades. Descreveremos particularmente o estudo das regras de interação que foram desvendadas pelo exame das relações temporais e estruturais entre os sinais trocados por vizinhos. Inicialmente, investigamos as regras de aprendizagem e desenvolvimento do canto. Nas aves com grande repertório vocal, a ontogênese dessas regras segue certas trajetórias que ajudam a entender o desempenho dos adultos, geralmente notável. Em ambas abordagens, nossa espécie-modelo será o Rouxinol-comum Luscinia megarhynchos, que foi pesquisado intensamente no campo e no laboratório.

A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4+ T cell receptor repertoire clonality.

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Zhu, Wei; Germain, Claire; Liu, Zheng; Sebastian, Yinong; Devi, Priyanka; Knockaert, Samantha; Brohawn, Philip; Lehmann, Kim; Damotte, Diane; Validire, Pierre; Yao, Yihong; Valge-Archer, Viia; Hammond, Scott A; Dieu-Nosjean, Marie-Caroline; Higgs, Brandon W

2015-12-01

T and B cell receptor (TCR and BCR, respectively) Vβ or immunoglobulin heavy chain complementarity-determining region 3 sequencing allows monitoring of repertoire changes through recognition, clonal expansion, affinity maturation, and T or B cell activation in response to antigen. TCR and BCR repertoire analysis can advance understanding of antitumor immune responses in the tumor microenvironment. TCR and BCR repertoires of sorted CD4 + , CD8 + or CD19 + cells in tumor, non-tumoral distant tissue (NT), and peripheral compartments (blood/draining lymph node [P]) from 47 non-small cell lung cancer (NSCLC) patients (age median = 68 y) were sequenced. The clonotype spectra were assessed among different tissues and correlated with clinical and immunological parameters. In all tissues, CD4 + and CD8 + TCR repertoires had greater clonality relative to CD19 + BCR. CD4 + T cells exhibited greater clonality in NT compared to tumor ( p = 0.002) and P ( p 68). Younger patients exhibited greater CD4 + T cell diversity in P compared to older patients ( p = 0.05), and greater CD4 + T cell clonality in tumor relative to P ( p cell clonality in tumor and P, respectively (both p = 0.05), correlated with high density of tumor-associated tertiary lymphoid structure (TLS) B cells, a biomarker of higher overall survival in NSCLC. Results indicate distinct adaptive immune responses in NSCLC, where peripheral T cell diversity is modulated by age, and tumor T cell clonal expansion is favored by the presence of TLSs in the tumor microenvironment.

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

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Ostrov, David A; Grant, Barry J; Pompeu, Yuri A

2012-01-01

cells, thus causing the equivalent of an alloreactive T-cell response. Indeed, we identified specific self-peptides that are presented only in the presence of abacavir and that were recognized by T cells of hypersensitive patients. The assays that we have established can be applied to test additional...... unclear. Here we show that abacavir can bind within the F pocket of the peptide-binding groove of HLA-B*57:01, thereby altering its specificity. This provides an explanation for HLA-linked idiosyncratic adverse drug reactions, namely that drugs can alter the repertoire of self-peptides presented to T...

Dopamine receptor repertoire of human granulosa cells

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Kunz Lars

2007-10-01

Full Text Available Abstract Background High levels of dopamine (DA were described in human ovary and recently evidence for DA receptors in granulosa and luteal cells has been provided, as well. However, neither the full repertoire of ovarian receptors for DA, nor their specific role, is established. Human granulosa cells (GCs derived from women undergoing in vitro fertilization (IVF are an adequate model for endocrine cells of the follicle and the corpus luteum and were therefore employed in an attempt to decipher their DA receptor repertoire and functionality. Methods Cells were obtained from patients undergoing IVF and examined using cDNA-array, RT-PCR, Western blotting and immunocytochemistry. In addition, calcium measurements (with FLUO-4 were employed. Expression of two DA receptors was also examined by in-situ hybridization in rat ovary. Effects of DA on cell viability and cell volume were studied by using an ATP assay and an electronic cell counter system. Results We found members of the two DA receptor families (D1- and D2 -like associated with different signaling pathways in human GCs, namely D1 (as expected and D5 (both are Gs coupled and linked to cAMP increase and D2, D4 (Gi/Gq coupled and linked to IP3/DAG. D3 was not found. The presence of the trophic hormone hCG (10 IU/ml in the culture medium for several days did not alter mRNA (semiquantitative RT-PCR or protein levels (immunocytochemistry/Western blotting of D1,2,4,5 DA receptors. Expression of prototype receptors for the two families, D1 and D2, was furthermore shown in rat granulosa and luteal cells by in situ hybridization. Among the DA receptors found in human GCs, D2 expression was marked both at mRNA and protein levels and it was therefore further studied. Results of additional RT-PCR and Western blots showed two splice variants (D2L, D2S. Irrespective of these variants, D2 proved to be functional, as DA raised intracellular calcium levels. This calcium mobilizing effect of DA was observed

The limiting conditional probability distribution in a stochastic model of T cell repertoire maintenance.

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Stirk, Emily R; Lythe, Grant; van den Berg, Hugo A; Hurst, Gareth A D; Molina-París, Carmen

2010-04-01

The limiting conditional probability distribution (LCD) has been much studied in the field of mathematical biology, particularly in the context of epidemiology and the persistence of epidemics. However, it has not yet been applied to the immune system. One of the characteristic features of the T cell repertoire is its diversity. This diversity declines in old age, whence the concepts of extinction and persistence are also relevant to the immune system. In this paper we model T cell repertoire maintenance by means of a continuous-time birth and death process on the positive integers, where the origin is an absorbing state. We show that eventual extinction is guaranteed. The late-time behaviour of the process before extinction takes place is modelled by the LCD, which we prove always exists for the process studied here. In most cases, analytic expressions for the LCD cannot be computed but the probability distribution may be approximated by means of the stationary probability distributions of two related processes. We show how these approximations are related to the LCD of the original process and use them to study the LCD in two special cases. We also make use of the large N expansion to derive a further approximation to the LCD. The accuracy of the various approximations is then analysed. (c) 2009 Elsevier Inc. All rights reserved.

Understanding B-cell activation and autoantibody repertoire selection in systemic lupus erythematosus: A B-cell immunomics approach.

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Tipton, Christopher M; Hom, Jennifer R; Fucile, Christopher F; Rosenberg, Alexander F; Sanz, Inaki

2018-07-01

Understanding antibody repertoires and in particular, the properties and fates of B cells expressing potentially pathogenic antibodies is critical to define the mechanisms underlying multiple immunological diseases including autoimmune and allergic conditions as well as transplant rejection. Moreover, an integrated knowledge of the antibody repertoires expressed by B cells and plasma cells (PC) of different functional properties and longevity is essential to develop new therapeutic strategies, better biomarkers for disease segmentation, and new assays to measure restoration of B-cell tolerance or, at least, of normal B-cell homeostasis. Reaching these goals, however, will require a more precise phenotypic, functional and molecular definition of B-cell and PC populations, and a comprehensive analysis of the antigenic reactivity of the antibodies they express. While traditionally hampered by technical and ethical limitations in human experimentation, new technological advances currently enable investigators to address these questions in a comprehensive fashion. In this review, we shall discuss these concepts as they apply to the study of Systemic Lupus Erythematosus. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Acquisition of repertoires of suppressor T cells under the influence of macrophages

International Nuclear Information System (INIS)

Soejima, T.; Nagayama, A.; Sado, T.; Taniguchi, M.

1988-01-01

Acquisition of repertoires and genetic restriction specificities of suppressor T cells (Ts) and their factors were studied by using full allogeneic radiation bone marrow chimera and H-2 congenic pairs, B10.A(3R) and B10.A(5R), which received conventional or cloned macrophages by cell transfer. Suppressor T-cell factor (TsF) from C3H----C57BL/6 or C57BL/6----C3H chimera suppressed only donor but not host-type responses of either C3H or C57BL/6, in an antigen-specific fashion. However, if chimera mice were given conventional or cloned macrophages of the host type, the chimera TsF in turn suppressed both the responses of C3H and C57BL/6 mice but not those of the third party, BALB/c, indicating that macrophages are responsible for the acquisition of host restriction specificity. Similarly, B10.A(5R) mice developed I-Jb restricted Ts or TsF when the B10.A(3R) macrophage cell line was injected at the time of antigen priming. The reverse was also true. B10.A(3R) mice did generate I-Jk restricted Ts when they received the B10.A(5R) macrophage cell line. Thus, the results clearly demonstrated that B10.A(3R) or B10.A(5R) mice potentially possessed their ability to express both I-Jk and I-Jb determinants and that repertoires and genetic restriction specificity of Ts and their TsF were acquired at a macrophage level at the time of antigen-priming

Experimental warming in a dryland community reduced plant photosynthesis and soil CO2 efflux although the relationship between the fluxes remained unchanged

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Wertin, Timothy M.; Belnap, Jayne; Reed, Sasha C.

2016-01-01

1. Drylands represent our planet's largest terrestrial biome and, due to their extensive area, maintain large stocks of carbon (C). Accordingly, understanding how dryland C cycling will respond to climate change is imperative for accurately forecasting global C cycling and future climate. However, it remains difficult to predict how increased temperature will affect dryland C cycling, as substantial uncertainties surround the potential responses of the two main C fluxes: plant photosynthesis and soil CO2 efflux. In addition to a need for an improved understanding of climate effects on individual dryland C fluxes, there is also notable uncertainty regarding how climate change may influence the relationship between these fluxes.2. To address this important knowledge gap, we measured a growing season's in situphotosynthesis, plant biomass accumulation, and soil CO2 efflux of mature Achnatherum hymenoides (a common and ecologically important C3 bunchgrass growing throughout western North America) exposed to ambient or elevated temperature (+2°C above ambient, warmed via infrared lamps) for three years.3. The 2°C increase in temperature caused a significant reduction in photosynthesis, plant growth, and soil CO2 efflux. Of important note, photosynthesis and soil respiration appeared tightly coupled and the relationship between these fluxes was not altered by the elevated temperature treatment, suggesting C fixation's strong control of both above-ground and below-ground dryland C cycling. Leaf water use efficiency was substantially increased in the elevated temperature treatment compared to the control treatment.4. Taken together, our results suggest notable declines in photosynthesis with relatively subtle warming, reveal strong coupling between above- and below-ground C fluxes in this dryland, and highlight temperature's strong effect on fundamental components of dryland C and water cycles.

Cultural repertoires and food-related household technology within colonia households under conditions of material hardship

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Dean Wesley R

2012-05-01

Full Text Available Abstract Introduction Mexican-origin women in the U.S. living in colonias (new-destination Mexican-immigrant communities along the Texas-Mexico border suffer from a high incidence of food insecurity and diet-related chronic disease. Understanding environmental factors that influence food-related behaviors among this population will be important to improving the well-being of colonia households. This article focuses on cultural repertoires that enable food choice and the everyday uses of technology in food-related practice by Mexican-immigrant women in colonia households under conditions of material hardship. Findings are presented within a conceptual framework informed by concepts drawn from sociological accounts of technology, food choice, culture, and material hardship. Methods Field notes were provided by teams of promotora-researchers (indigenous community health workers and public-health professionals trained as participant observers. They conducted observations on three separate occasions (two half-days during the week and one weekend day within eight family residences located in colonias near the towns of Alton and San Carlos, Texas. English observations were coded inductively and early observations stressed the importance of technology and material hardship in food-related behavior. These observations were further explored and coded using the qualitative data package Atlas.ti. Results Technology included kitchen implements used in standard and adapted configurations and household infrastructure. Residents employed tools across a range of food-related activities identified as forms of food acquisition, storage, preparation, serving, feeding and eating, cleaning, and waste processing. Material hardships included the quality, quantity, acceptability, and uncertainty dimensions of food insecurity, and insufficient consumption of housing, clothing and medical care. Cultural repertoires for coping with material hardship included reliance on

Cultural repertoires and food-related household technology within colonia households under conditions of material hardship.

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Dean, Wesley R; Sharkey, Joseph R; Johnson, Cassandra M; St John, Julie

2012-05-15

BSTRACT: Mexican-origin women in the U.S. living in colonias (new-destination Mexican-immigrant communities) along the Texas-Mexico border suffer from a high incidence of food insecurity and diet-related chronic disease. Understanding environmental factors that influence food-related behaviors among this population will be important to improving the well-being of colonia households. This article focuses on cultural repertoires that enable food choice and the everyday uses of technology in food-related practice by Mexican-immigrant women in colonia households under conditions of material hardship. Findings are presented within a conceptual framework informed by concepts drawn from sociological accounts of technology, food choice, culture, and material hardship. Field notes were provided by teams of promotora-researchers (indigenous community health workers) and public-health professionals trained as participant observers. They conducted observations on three separate occasions (two half-days during the week and one weekend day) within eight family residences located in colonias near the towns of Alton and San Carlos, Texas. English observations were coded inductively and early observations stressed the importance of technology and material hardship in food-related behavior. These observations were further explored and coded using the qualitative data package Atlas.ti. Technology included kitchen implements used in standard and adapted configurations and household infrastructure. Residents employed tools across a range of food-related activities identified as forms of food acquisition, storage, preparation, serving, feeding and eating, cleaning, and waste processing. Material hardships included the quality, quantity, acceptability, and uncertainty dimensions of food insecurity, and insufficient consumption of housing, clothing and medical care. Cultural repertoires for coping with material hardship included reliance on inexpensive staple foods and dishes, and

Unchanged thymidine triphosphate pools and thymidine metabolism in two lines of thymidine kinase 2-mutated fibroblasts.

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Frangini, Miriam; Rampazzo, Chiara; Franzolin, Elisa; Lara, Mari-Carmen; Vilà, Maya R; Martí, Ramon; Bianchi, Vera

2009-02-01

Mitochondrial thymidine kinase (TK2) catalyzes the phosphorylation of thymidine in mitochondria. Its function becomes essential for dTTP synthesis in noncycling cells, where cytosolic dTTP synthesis via R1/R2 ribonucleotide reductase and thymidine kinase 1 is turned down. Mutations in the nuclear gene for TK2 cause a fatal mtDNA depletion syndrome. Only selected cell types are affected, suggesting that the other cells compensate for the TK2 deficiency by adapting the enzyme network that regulates dTTP synthesis outside S-phase. Here we looked for such metabolic adaptation in quiescent cultures of fibroblasts from two TK2-deficient patients with a slow-progressing syndrome. In cell extracts, we measured the activities of TK2, deoxycytidine kinase, thymidine phosphorylase, deoxynucleotidases and the amounts of the three ribonucleotide reductase subunits. Patient cells contained 40% or 5% TK2 activity and unchanged activities of the other enzymes. However, their mitochondrial and cytosolic dTTP pools were unchanged, and also the overall composition of the dNTP pools was normal. TK2-dependent phosphorylation of [(3)H]thymidine in intact cells and the turnover of the dTTP pool showed that even the fibroblasts with 5% residual TK2 activity synthesized dTTP at an almost normal rate. Normal fibroblasts apparently contain more TK2 than needed to maintain dTTP during quiescence, which would explain why TK2-mutated fibroblasts do not manifest mtDNA depletion despite their reduced TK2 activity.

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination

OpenAIRE

Louise S. Matheson; Daniel J. Bolland; Peter Chovanec; Felix Krueger; Simon Andrews; Hashem Koohy; Anne E. Corcoran

2017-01-01

V(D)J recombination is essential for the generation of diverse antigen receptor (AgR) repertoires. In B cells, immunoglobulin kappa (Igκ) light chain recombination follows immunoglobulin heavy chain (Igh) recombination. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. Integration of VDJ-seq data with genome-wide datasets revealed that two chromatin states at the recombination signal sequence (RSS) of VH genes are highly predictive o...

VH repertoire in progeny of long term lymphoid-cultured cells used to reconstitute immunodeficient mice

International Nuclear Information System (INIS)

Denis, K.A.; Timson, L.K.; Witte, O.N.

1989-01-01

VH gene utilization in the progeny of long term lymphoid-cultured cells used for reconstitution of severe combined immunodeficient mice under varying conditions was determined. Hybridomas made from the spleens of these animals were evaluated for clonality and donor origin and a panel of 146 independent hybridomas were subsequently examined for VH expression. Hybridomas derived from the spleens of SCID mice reconstituted with fresh cells, used as a control, utilized VH families in proportion to their numerical representation in the genome. However, hybridomas from the spleens of mice reconstituted with long term cultured cells utilized a predominance of the two VH gene families most proximal to JH, characteristic of cells early in B lymphocyte development. Coinjection of thymocytes with cultured fetal liver cells, to provide good levels of T lymphocytes, did not alter this pattern of VH utilization. Irradiation (3 Gy) of the mice before cultured cell injection, which leads to more complete reconstitution of the B cell compartment, was effective in removing this bias in the VH repertoire. Hybridomas derived from these mice expressed their VH genes more in proportion to family size, characteristic of cells later in B lymphocyte development. In this manner, long term lymphoid-cultured cells can be used to study the transitions that occur in VH repertoire expression which appear to be mediated by either B lymphocyte developmental microenvironment or population size

WORKS FOR CLARINET AND ACCOMPANIMENT IN OLEG NEGRUŢA’S COMPOSITION REPERTOIRE

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MUŞAT SERGHEI

2015-06-01

Full Text Available Oleg Negruţa’s composition repertoire for solo instruments with accompaniment, of which clarinet opuses are highlighted, is important for indigenous musical art. In a vast genre complex, it confirms the composer’s constant commitment to the idea of the Bessarabian professional school. In this sense, as relevant works can be considered the three pieces for clarinet and piano: Improvisation, Fantasy on a Theme by Paganini and Elegy. However, this article is meant to offer details in an analytical way about Negruţa’s specific language and, moreover, to emphasize the author’s mastery of combining folklore elements with others characteristic ofjazz, both being treated according to the canons of academic music.

Next-Generation DNA Sequencing of VH/VL Repertoires: A Primer and Guide to Applications in Single-Domain Antibody Discovery.

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Henry, Kevin A

2018-01-01

Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (V H , V H H or V L ) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform. We include complete protocols and primer sets for amplicon sequencing of V H /V H H/V L repertoires directly from human, mouse, and llama lymphocytes as well as from phage-displayed V H /V H H/V L libraries; these can be easily be adapted to other types of amplicons with little modification. The resulting amplicons are diverse and representative, even using as few as 10 3 input B cells, and their generation is relatively inexpensive, requiring no special equipment and only a limited set of primers. In the absence of heavy-light chain pairing, single-domain antibodies are uniquely amenable to NGS analyses. We present a number of applications of NGS technology useful in discovery of single-domain antibodies from phage display libraries, including: (i) assessment of library functionality; (ii) confirmation of desired library randomization; (iii) estimation of library diversity; and (iv) monitoring the progress of panning experiments. While the case studies presented here are of phage-displayed single-domain antibody libraries, the principles extend to other types of in vitro display libraries.

Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing.

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Valdés-Alemán, Javier; Téllez-Sosa, Juan; Ovilla-Muñoz, Marbella; Godoy-Lozano, Elizabeth; Velázquez-Ramírez, Daniel; Valdovinos-Torres, Humberto; Gómez-Barreto, Rosa E; Martinez-Barnetche, Jesús

2014-01-01

High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.

The effects of a partitioned var gene repertoire of Plasmodium falciparum on antigenic diversity and the acquisition of clinical immunity

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Arinaminpathy Nimalan

2008-01-01

Full Text Available Abstract Background The human malaria parasite Plasmodium falciparum exploits antigenic diversity and within-host antigenic variation to evade the host's immune system. Of particular importance are the highly polymorphic var genes that encode the family of cell surface antigens PfEMP1 (Plasmodium falciparum Erythrocyte Membrane Protein 1. It has recently been shown that in spite of their extreme diversity, however, these genes fall into distinct groups according to chromosomal location or sequence similarity, and that recombination may be confined within these groups. Methods This study presents a mathematical analysis of how recombination hierarchies affect diversity, and, by using simple stochastic simulations, investigates how intra- and inter-genic diversity influence the rate at which individuals acquire clinical immunity. Results The analysis demonstrates that the partitioning of the var gene repertoire has a limiting effect on the total diversity attainable through recombination and that the limiting effect is strongly influenced by the respective sizes of each of the partitions. Furthermore, by associating expression of one of the groups with severe malaria it is demonstrated how a small number of infections can be sufficient to protect against disease despite a seemingly limitless number of possible non-identical repertoires. Conclusion Recombination hierarchies within the var gene repertoire of P. falciparum have a severe effect on strain diversity and the process of acquiring immunity against clinical malaria. Future studies will show how the existence of these recombining groups can offer an evolutionary advantage in spite of their restriction on diversity.

Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules.

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Kalliopi Georgiades

2011-03-01

Full Text Available We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans ("bad bugs" to their closest non-epidemic related species ("controls".We found several significantly different features in the "bad bugs", one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG functional categories revealed a significantly smaller number of genes in the "bad bugs", which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five "bad bugs" showed a greater number of poly (A tails compared to the controls, whereas an elevated number of poly (A tails was found to be strongly correlated to a low GC% content. The "bad bugs" had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA showed that the "bad bugs" had surprisingly more toxin-antitoxin modules than did the controls.We conclude that pathogenic capacity is not the result of "virulence factors" but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution.

Building the repertoire of measures of walking in Rett syndrome

DEFF Research Database (Denmark)

Stahlhut, Michelle; Downs, Jenny; Leonard, Helen

2017-01-01

performance as measured with the FMS-RS was more strongly consistent with other clinical measures supporting its concurrent validity. Test-retest reliability was good for both the FMS-RS and the 2MWT. Therefore, these measures have the potential to be used in clinical practice and research. Implications...... with Rett syndrome (median 18.4 years, range 2.4-60.9 years) were assessed for clinical severity, gross motor skills, and mobility. To measure walking capacity, 27 of this group completed a 2MWT twice on two different assessment days. To assess walking performance, the FMS-RS was administered to the total......BACKGROUND: The repertoire of measures of walking in Rett syndrome is limited. This study aimed to determine measurement properties of a modified two-minute walk test (2MWT) and a modified Rett syndrome-specific functional mobility scale (FMS-RS) in Rett syndrome. METHODS: Forty-two girls and women...

Children show limited movement repertoire when learning a novel motor skill.

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Lee, Mei-Hua; Farshchiansadegh, Ali; Ranganathan, Rajiv

2017-09-27

Examining age differences in motor learning using real-world tasks is often problematic due to task novelty and biomechanical confounds. Here, we investigated how children and adults acquire a novel motor skill in a virtual environment. Participants of three different age groups (9-year-olds, 12-year-olds, and adults) learned to use their upper body movements to control a cursor on a computer screen. Results showed that 9-year-old and 12-year-old children showed poorer ability to control the cursor at the end of practice. Critically, when we investigated the movement coordination, we found that the lower task performance of children was associated with limited exploration of their movement repertoire. These results reveal the critical role of motor exploration in understanding developmental differences in motor learning. © 2017 John Wiley & Sons Ltd.

Using Existing Response Repertoires to Make Sense of Information System Implementation

DEFF Research Database (Denmark)

Jensen, Tina Blegind; Kjærgaard, Annemette Leonhardt

2010-01-01

The implementation of information systems (IS) in organizations often triggers new situations in which users experience a disruption of existing work patterns and routines. Sensemaking becomes central in making users’ meanings explicit, serving as a foundation for further actions and interactions...... with the new technology. The purpose of this paper is to study how users make sense of new technologies by building on existing response repertoires. Empirically, we present findings from a study of an Electronic Patient Record (EPR) system implementation in two Danish hospital wards. Our findings illustrate...... to existing literature by providing a detailed account of how users’ early sensemaking of a technology influences their subsequent actions and reactions towards it. Our findings support managers in understanding users’ perceptions of a new technology, helping them in planning and executing the implementation...

Introduction: Repertoires and Performances of Academic Identity.

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H. Paul

2016-12-01

Full Text Available The idea that academic work requires certain personal qualities, character traits or dispositions is as old as the university. However, no matter how ubiquitous the phenomenon, it is only in recent years, in the wake of a ‘cultural turn’ in the history of science, that historians have begun exploring ideals and practices of scholarly selfhood. This theme issue seeks to make a modest contribution to this emerging field of scholarship with articles that offer conceptual reflection, as well as case studies drawn from the Low Countries. They do so under the banner of ‘scholarly personae’, not with the intention of excluding competing vocabularies, but by way of entry into a new and not yet clearly defined field of study. Introductie: repertoires voor de academische identiteit. Het idee dat academisch onderzoek bepaalde persoonlijke kwaliteiten, karaktertrekken en talenten vereist is zo oud als de universiteit zelf. Toch zijn historici pas recent, in het kielzog van de ‘cultural turn’ in de wetenschapsgeschiedenis, de idealen en praktijken van de academische identiteit gaan onderzoeken. Dit themanummer wil met conceptuele reflecties en casestudies over de Lage Landen een bescheiden bijdrage leveren aan dit opkomende veld van onderzoek. De artikelen gebruiken daarvoor het concept ‘schoarly personae’, niet met de bedoeling om andere benaderingen uit te sluiten, maar bij wijze van ingang in een nieuw en nog niet helder afgebakend onderzoeksgebied.

Introduction: Repertoires and Performances of Academic Identity

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Herman Paul

2016-12-01

Full Text Available The idea that academic work requires certain personal qualities, character traits or dispositions is as old as the university. However, no matter how ubiquitous the phenomenon, it is only in recent years, in the wake of a ‘cultural turn’ in the history of science, that historians have begun exploring ideals and practices of scholarly selfhood. This theme issue seeks to make a modest contribution to this emerging field of scholarship with articles that offer conceptual reflection, as well as case studies drawn from the Low Countries. They do so under the banner of ‘scholarly personae’, not with the intention of excluding competing vocabularies, but by way of entry into a new and not yet clearly defined field of study. Introductie: repertoires voor de academische identiteitHet idee dat academisch onderzoek bepaalde persoonlijke kwaliteiten, karaktertrekken en talenten vereist is zo oud als de universiteit zelf. Toch zijn historici pas recent, in het kielzog van de ‘cultural turn’ in de wetenschapsgeschiedenis, de idealen en praktijken van de academische identiteit gaan onderzoeken. Dit themanummer wil met conceptuele reflecties en casestudies over de Lage Landen een bescheiden bijdrage leveren aan dit opkomende veld van onderzoek. De artikelen gebruiken daarvoor het concept ‘schoarly personae’, niet met de bedoeling om andere benaderingen uit te sluiten, maar bij wijze van ingang in een nieuw en nog niet helder afgebakend onderzoeksgebied.

Statistical inference of the generation probability of T-cell receptors from sequence repertoires.

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Murugan, Anand; Mora, Thierry; Walczak, Aleksandra M; Callan, Curtis G

2012-10-02

Stochastic rearrangement of germline V-, D-, and J-genes to create variable coding sequence for certain cell surface receptors is at the origin of immune system diversity. This process, known as "VDJ recombination", is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Because any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on nonproductive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our probabilistic model predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.

A survey of the gene repertoire of Gigaspora rosea unravels conserved features among Glomeromycota for obligate biotrophy

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Nianwu eTANG

2016-03-01

Full Text Available Arbuscular mycorrhizal (AM fungi are a diverse group of soil fungi (Glomeromycota that form the most ancient mutualistic association termed arbuscular mycorrhizal symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales. Among the 86332 nonredundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for R. irregularis, several metabolic genes were not found, including the fatty acid synthase gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and hundreds of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales and Gigaspora margarita (Diversisporales, reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation

Analysis of the HLA-DR peptidome from human dendritic cells reveals high affinity repertoires and nonconventional pathways of peptide generation

NARCIS (Netherlands)

Ciudad, M Teresa; Sorvillo, Nicoletta; van Alphen, Floris P.J.; Catalán, Diego; Meijer, Sander; Voorberg, Jan; Jaraquemada, Dolores

Dendritic cells (DCs) are the major professional APCs of the immune system; however, their MHC-II-associated peptide repertoires have been hard to analyze, mostly because of their scarce presence in blood and tissues. In vitro matured human monocyte-derived DCs (MoDCs) are widely used as

Urban renewal, migration and memories: The affordances of place-based pedagogies for developing immigrant students’ literate repertoires

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Barbara Comber

2013-02-01

Full Text Available This paper reports on the New literacy demands in the middle years of schooling project in which the affordances of placed-based pedagogy are being explored through teacher inquiries and classroom-based design experiments. The school is located within a large-scale urban renewal project in which houses are being demolished and families relocated. The original school buildings have recently been demolished and replaced by a large ‘Superschool’ which serves a bigger student population from a wider area. Drawing on both quantitative and qualitative data, the teachers reported that the language literacy learning of students (including a majority of students learning English as a second language involved in the project exceeded their expectations. The project provided the motivation for them to develop their oral language repertoires, by involving them in processes such as conducting interviews with adults for their oral histories, through questioning the project manager in regular meetings, and through reporting to their peers and the wider community at school assemblies. At the same time students’ written and multimodal documentation of changes in the neighbourhood and the school grounds extended their literate and semiotic repertoires as they produced books, reports, films, Powerpoints, visual designs and models of structures.

Iron and Lactoferrin Levels Remain Unchanged in Parkin Deficient Mouse Brains: Implications for Parkinson’s Disease Etiology

OpenAIRE

Baker, Hanan

2015-01-01

Parkinson’s disease is a devastating neurodegenerative disease in which loss of dopaminergic neurons in the substantia nigra pars compacta leads to a variety of motor and non-motor deficits. Mutations in the Park2 or parkin gene have been implicated in familial forms of Parkinson’s disease. Parkin is an E3 ubiquitin ligase that plays a role in mitophagy, the degradation of damaged mitochondria. Defects in parkin are thought to impair mitophagy, leading to mitochondrial dysfunction and an incr...

Endometrial natural killer (NK) cells reveal a tissue-specific receptor repertoire.

Science.gov (United States)

Feyaerts, D; Kuret, T; van Cranenbroek, B; van der Zeeuw-Hingrez, S; van der Heijden, O W H; van der Meer, A; Joosten, I; van der Molen, R G

2018-02-13

Is the natural killer (NK) cell receptor repertoire of endometrial NK (eNK) cells tissue-specific? The NK cell receptor (NKR) expression profile in pre-pregnancy endometrium appears to have a unique tissue-specific phenotype, different from that found in NK cells in peripheral blood, suggesting that these cells are finely tuned towards the reception of an allogeneic fetus. NK cells are important for successful pregnancy. After implantation, NK cells encounter extravillous trophoblast cells and regulate trophoblast invasion. NK cell activity is amongst others regulated by C-type lectin heterodimer (CD94/NKG2) and killer cell immunoglobulin-like (KIR) receptors. KIR expression on decidual NK cells is affected by the presence of maternal HLA-C and biased towards KIR2D expression. However, little is known about NKR expression on eNK cells prior to pregnancy. In this study, matched peripheral and menstrual blood (a source of endometrial cells) was obtained from 25 healthy females with regular menstrual cycles. Menstrual blood was collected during the first 36 h of menstruation using a menstrual cup, a non-invasive technique to obtain endometrial cells. KIR and NKG2 receptor expression on eNK cells was characterized by 10-color flow cytometry, and compared to matched pbNK cells of the same female. KIR and HLA-C genotypes were determined by PCR-SSOP techniques. Anti-CMV IgG antibodies in plasma were measured by chemiluminescence immunoassay. KIR expression patterns of eNK cells collected from the same female do not differ over consecutive menstrual cycles. The percentage of NK cells expressing KIR2DL2/L3/S2, KIR2DL3, KIR2DL1, LILRB1 and/or NKG2A was significantly higher in eNK cells compared to pbNK cells, while no significant difference was observed for NKG2C, KIR2DL1/S1, and KIR3DL1. The NKR repertoire of eNK cells was clearly different from pbNK cells, with eNK cells co-expressing more than three NKR simultaneously. In addition, outlier analysis revealed 8 and 15 NKR

Different Somatic Hypermutation Levels among Antibody Subclasses Disclosed by a New Next-Generation Sequencing-Based Antibody Repertoire Analysis

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Kazutaka Kitaura

2017-05-01

Full Text Available A diverse antibody repertoire is primarily generated by the rearrangement of V, D, and J genes and subsequent somatic hypermutation (SHM. Class-switch recombination (CSR produces various isotypes and subclasses with different functional properties. Although antibody isotypes and subclasses are considered to be produced by both direct and sequential CSR, it is still not fully understood how SHMs accumulate during the process in which antibody subclasses are generated. Here, we developed a new next-generation sequencing (NGS-based antibody repertoire analysis capable of identifying all antibody isotype and subclass genes and used it to examine the peripheral blood mononuclear cells of 12 healthy individuals. Using a total of 5,480,040 sequences, we compared percentage frequency of variable (V, junctional (J sequence, and a combination of V and J, diversity, length, and amino acid compositions of CDR3, SHM, and shared clones in the IgM, IgD, IgG3, IgG1, IgG2, IgG4, IgA1, IgE, and IgA2 genes. The usage and diversity were similar among the immunoglobulin (Ig subclasses. Clonally related sequences sharing identical V, D, J, and CDR3 amino acid sequences were frequently found within multiple Ig subclasses, especially between IgG1 and IgG2 or IgA1 and IgA2. SHM occurred most frequently in IgG4, while IgG3 genes were the least mutated among all IgG subclasses. The shared clones had almost the same SHM levels among Ig subclasses, while subclass-specific clones had different levels of SHM dependent on the genomic location. Given the sequential CSR, these results suggest that CSR occurs sequentially over multiple subclasses in the order corresponding to the genomic location of IGHCs, but CSR is likely to occur more quickly than SHMs accumulate within Ig genes under physiological conditions. NGS-based antibody repertoire analysis should provide critical information on how various antibodies are generated in the immune system.

Roaring high and low: composition and possible functions of the Iberian stag's vocal repertoire.

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Daniela Passilongo

Full Text Available We provide a detailed description of the rutting vocalisations of free-ranging male Iberian deer (Cervus elaphus hispanicus, Hilzheimer 1909, a geographically isolated and morphologically differentiated subspecies of red deer Cervus elaphus. We combine spectrographic examinations, spectral analyses and automated classifications to identify different call types, and compare the composition of the vocal repertoire with that of other red deer subspecies. Iberian stags give bouts of roars (and more rarely, short series of barks that are typically composed of two different types of calls. Long Common Roars are mostly given at the beginning or at the end of the bout, and are characterised by a high fundamental frequency (F0 resulting in poorly defined formant frequencies but a relatively high amplitude. In contrast, Short Common Roars are typically given in the middle or at the end of the bout, and are characterised by a lower F0 resulting in relatively well defined vocal tract resonances, but low amplitude. While we did not identify entirely Harsh Roars (as described in the Scottish red deer subspecies (Cervus elaphus scoticus, a small percentage of Long Common Roars contained segments of deterministic chaos. We suggest that the evolution of two clearly distinct types of Common Roars may reflect divergent selection pressures favouring either vocal efficiency in high pitched roars or the communication of body size in low-pitched, high spectral density roars highlighting vocal tract resonances. The clear divergence of the Iberian red deer vocal repertoire from those of other documented European red deer populations reinforces the status of this geographical variant as a distinct subspecies.

Health Benefits In 2016: Family Premiums Rose Modestly, And Offer Rates Remained Stable.

Science.gov (United States)

Claxton, Gary; Rae, Matthew; Long, Michelle; Damico, Anthony; Whitmore, Heidi; Foster, Gregory

2016-10-01

The annual Kaiser Family Foundation/Health Research and Educational Trust Employer Health Benefits Survey found that in 2016, average annual premiums (employer and worker contributions combined) were $6,435 for single coverage and $18,142 for family coverage. The family premium in 2016 was 3 percent higher than that in 2015. On average, workers contributed 18 percent of the premium for single coverage and 30 percent for family coverage. The share of firms offering health benefits (56 percent) and of workers covered by their employers' plans (62 percent) remained statistically unchanged from 2015. Employers continued to offer financial incentives for completing wellness or health promotion activities. Almost three in ten covered workers were enrolled in a high-deductible plan with a savings option-a significant increase from 2014. The 2016 survey included new questions on cost sharing for specialty drugs and on the prevalence of incentives for employees to seek care at alternative settings. Project HOPE—The People-to-People Health Foundation, Inc.

"Nobody Told Me They Didn't Speak English!": Teacher Language Views and Student Linguistic Repertoires in Hutterite Colony Schools in Canada

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Sterzuk, Andrea; Nelson, Cynthia A.

2016-01-01

This article presents a qualitative study of five monolingual teachers' understandings of the linguistic repertoires of their multilingual students. These teachers deliver the Saskatchewan provincial curricula in English to Hutterite colony students who are users of three languages: (a) spoken Hutterisch as a home and community language, (b)…

Massively Parallel RNA Sequencing Identifies a Complex Immune Gene Repertoire in the lophotrochozoan Mytilus edulis

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Philipp, Eva E. R.; Kraemer, Lars; Melzner, Frank; Poustka, Albert J.; Thieme, Sebastian; Findeisen, Ulrike; Schreiber, Stefan; Rosenstiel, Philip

2012-01-01

The marine mussel Mytilus edulis and its closely related sister species are distributed world-wide and play an important role in coastal ecology and economy. The diversification in different species and their hybrids, broad ecological distribution, as well as the filter feeding mode of life has made this genus an attractive model to investigate physiological and molecular adaptations and responses to various biotic and abiotic environmental factors. In the present study we investigated the immune system of Mytilus, which may contribute to the ecological plasticity of this species. We generated a large Mytilus transcriptome database from different tissues of immune challenged and stress treated individuals from the Baltic Sea using 454 pyrosequencing. Phylogenetic comparison of orthologous groups of 23 species demonstrated the basal position of lophotrochozoans within protostomes. The investigation of immune related transcripts revealed a complex repertoire of innate recognition receptors and downstream pathway members including transcripts for 27 toll-like receptors and 524 C1q domain containing transcripts. NOD-like receptors on the other hand were absent. We also found evidence for sophisticated TNF, autophagy and apoptosis systems as well as for cytokines. Gill tissue and hemocytes showed highest expression of putative immune related contigs and are promising tissues for further functional studies. Our results partly contrast with findings of a less complex immune repertoire in ecdysozoan and other lophotrochozoan protostomes. We show that bivalves are interesting candidates to investigate the evolution of the immune system from basal metazoans to deuterostomes and protostomes and provide a basis for future molecular work directed to immune system functioning in Mytilus. PMID:22448234

Diversity and repertoire of IgW and IgM VH families in the newborn nurse shark.

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Rumfelt, Lynn L; Lohr, Rebecca L; Dooley, Helen; Flajnik, Martin F

2004-05-06

Adult cartilaginous fish express three immunoglobulin (Ig) isotypes, IgM, IgNAR and IgW. Newborn nurse sharks, Ginglymostoma cirratum, produce 19S (multimeric) IgM and monomeric/dimeric IgM1gj, a germline-joined, IgM-related VH, and very low amounts of 7S (monomeric) IgM and IgNAR proteins. Newborn IgNAR VH mRNAs are diverse in the complementarity-determining region 3 (CDR3) with non-templated nucleotide (N-region) addition, which suggests that, unlike in many other vertebrates, terminal deoxynucleotidyl transferase (TdT) expressed at birth is functional. IgW is present in the lungfish, a bony fish sharing a common ancestor with sharks 460 million years ago, implying that the IgW VH family is as old as the IgM VH family. This nurse shark study examined the IgM and IgW VH repertoire from birth through adult life, and analyzed the phylogenetic relationships of these gene families. IgM and IgW VH cDNA clones isolated from newborn nurse shark primary and secondary lymphoid tissues had highly diverse and unique CDR3 with N-region addition and VDJ gene rearrangement, implicating functional TdT and RAG gene activity. Despite the clear presence of N-region additions, newborn CDR3 were significantly shorter than those of adults. The IgM clones are all included in a conventional VH family that can be classified into five discrete groups, none of which is orthologous to IgM VH genes in other elasmobranchs. In addition, a novel divergent VH family was orthologous to a published monotypic VH horn shark family. IgW VH genes have diverged sufficiently to form three families. IgM and IgW VH serine codons using the potential somatic hypermutation hotspot sequence occur mainly in VH framework 1 (FR1) and CDR1. Phylogenetic analysis of cartilaginous fish and lungfish IgM and IgW demonstrated they form two major ancient gene groups; furthermore, these VH genes generally diversify (duplicate and diverge) within a species. As in ratfish, sandbar and horn sharks, most nurse shark IgM VH

Degeneracy-driven self-structuring dynamics in selective repertoires.

Science.gov (United States)

Atamas, Sergei P; Bell, Jonathan

2009-08-01

Numerous biological interactions, such as interactions between T cell receptors or antibodies with antigens, interactions between enzymes and substrates, or interactions between predators and prey are often not strictly specific. In such less specific, or "sloppy," systems, referred to here as degenerate systems, a given unit of a diverse resource (antigens, enzymatic substrates, prey) is at risk of being recognized and consumed by multiple consumers (lymphocytes, enzymes, predators). In this study, we model generalized degenerate consumer-resource systems of Lotka-Volterra and Verhulst types. In the degenerate systems of Lotka-Volterra, there is a continuum of types of consumer and resource based on variation of a single trait (characteristic, or preference). The consumers experience competition for a continuum of resource types. This non-local interaction system is modeled with partial differential-integral equations and shows spontaneous self-structuring of the consumer population that depends on the degree of interaction degeneracy between resource and consumer, but does not mirror the distribution of resource. We also show that the classical Verhulst (i.e. logistic) single population model can be generalized to a degenerate model, which shows qualitative behavior similar to that in the degenerate Lotka-Volterra model. These results provide better insight into the dynamics of selective systems in biology, suggesting that adaptation of degenerate repertoires is not a simple "mirroring" of the environment by the "fittest" elements of population.

CARbodies: Human Antibodies Against Cell Surface Tumor Antigens Selected From Repertoires Displayed on T Cell Chimeric Antigen Receptors

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Vanesa Alonso-Camino

2013-01-01

Full Text Available A human single-chain variable fragment (scFv antibody library was expressed on the surface of human T cells after transduction with lentiviral vectors (LVs. The repertoire was fused to a first-generation T cell receptor ζ (TCRζ-based chimeric antigen receptor (CAR. We used this library to isolate antibodies termed CARbodies that recognize antigens expressed on the tumor cell surface in a proof-of-principle system. After three rounds of activation-selection there was a clear repertoire restriction, with the emergence dominant clones. The CARbodies were purified from bacterial cultures as soluble and active proteins. Furthermore, to validate its potential application for adoptive cell therapy, human T cells were transduced with a LV encoding a second-generation costimulatory CAR (CARv2 bearing the selected CARbodies. Transduced human primary T cells expressed significant levels of the CARbodies-based CARv2 fusion protein on the cell surface, and importantly could be specifically activated, after stimulation with tumor cells. This approach is a promising tool for the generation of antibodies fully adapted to the display format (CAR and the selection context (cell synapse, which could extend the scope of current adoptive cell therapy strategies with CAR-redirected T cells.

Repertoire of intensive care unit pneumonia microbiota.

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Sabri Bousbia

Full Text Available Despite the considerable number of studies reported to date, the causative agents of pneumonia are not completely identified. We comprehensively applied modern and traditional laboratory diagnostic techniques to identify microbiota in patients who were admitted to or developed pneumonia in intensive care units (ICUs. During a three-year period, we tested the bronchoalveolar lavage (BAL of patients with ventilator-associated pneumonia, community-acquired pneumonia, non-ventilator ICU pneumonia and aspiration pneumonia, and compared the results with those from patients without pneumonia (controls. Samples were tested by amplification of 16S rDNA, 18S rDNA genes followed by cloning and sequencing and by PCR to target specific pathogens. We also included culture, amoeba co-culture, detection of antibodies to selected agents and urinary antigen tests. Based on molecular testing, we identified a wide repertoire of 160 bacterial species of which 73 have not been previously reported in pneumonia. Moreover, we found 37 putative new bacterial phylotypes with a 16S rDNA gene divergence ≥ 98% from known phylotypes. We also identified 24 fungal species of which 6 have not been previously reported in pneumonia and 7 viruses. Patients can present up to 16 different microorganisms in a single BAL (mean ± SD; 3.77 ± 2.93. Some pathogens considered to be typical for ICU pneumonia such as Pseudomonas aeruginosa and Streptococcus species can be detected as commonly in controls as in pneumonia patients which strikingly highlights the existence of a core pulmonary microbiota. Differences in the microbiota of different forms of pneumonia were documented.

Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome

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Sandhya Verma

2017-06-01

Full Text Available Transcription factors (TFs are the key players in gene expression and their study is highly significant for shedding light on the molecular mechanisms and evolutionary history of organisms. During host–pathogen interaction, extensive reprogramming of gene expression facilitated by TFs is likely to occur in both host and pathogen. To date, the knowledge about TF repertoire in filamentous fungi is in infancy. The necrotrophic fungus Ascochyta rabiei, that causes destructive Ascochyta blight (AB disease of chickpea (Cicer arietinum, demands more comprehensive study for better understanding of Ascochyta-legume pathosystem. In the present study, we performed the genome-wide identification and analysis of TFs in A. rabiei. Taking advantage of A. rabiei genome sequence, we used a bioinformatic approach to predict the TF repertoire of A. rabiei. For identification and classification of A. rabiei TFs, we designed a comprehensive pipeline using a combination of BLAST and InterProScan software. A total of 381 A. rabiei TFs were predicted and divided into 32 fungal specific families of TFs. The gene structure, domain organization and phylogenetic analysis of abundant families of A. rabiei TFs were also carried out. Comparative study of A. rabiei TFs with that of other necrotrophic, biotrophic, hemibiotrophic, symbiotic, and saprotrophic fungi was performed. It suggested presence of both conserved as well as unique features among them. Moreover, cis-acting elements on promoter sequences of earlier predicted A. rabiei secretome were also identified. With the help of published A. rabiei transcriptome data, the differential expression of TF and secretory protein coding genes was analyzed. Furthermore, comprehensive expression analysis of few selected A. rabiei TFs using quantitative real-time polymerase chain reaction revealed variety of expression patterns during host colonization. These genes were expressed in at least one of the time points tested post

Immune Control of Burkholderia pseudomallei––Common, High-Frequency T-Cell Responses to a Broad Repertoire of Immunoprevalent Epitopes

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Arnone Nithichanon

2018-03-01

Full Text Available Burkholderia pseudomallei (Bp is an environmental bacterial pathogen that causes potentially lethal sepsis in susceptible individuals and is considered a Category B, Tier-1 biothreat agent. As such, it is crucial to gain an improved understanding of protective immunity and potential vaccine candidates. The nature of immune correlates dictating why most exposed individuals in endemic regions undergo asymptomatic seroconversion while others succumb to life-threatening sepsis is largely uncharted. Bp seroreactive, immunogenic proteins have previously been identified by antigen microarray. We here set out to conduct an analysis of T-cell recognition of the Bp immunome using serodominant antigens represented in the original antigen microarray, examining immune correlates of disease in healthy seropositive individuals and those with acute disease or in convalescence. By screening a library of 739 overlapping peptides representing the sequences of 20 different Bp antigens, we aimed to define immune correlates of protection at the level of immunoprevalent T-cell epitopes. Responses to a large number of epitopes were common in healthy seropositive individuals: we found remarkably broad responsiveness to Bp epitopes, with 235 of 739 peptides recognized by ≥80% of all tested donors. The cumulative response to Bp epitopes in healthy, seropositive, donors from this endemic region were of the order of thousands of spot forming cells per million cells, making Bp recognition a significant component of the T-cell repertoire. Noteworthy among our findings, analysis revealed 10 highly immunoprevalent T-cell epitopes, able to induce Bp-specific IFNγ responses that were high in responding T-cell frequency within the repertoire, and also common across individuals with different human leukocyte antigen types. Acute melioidosis patients showed poor T-cell responses to the immunoprevalent epitopes, but acquired responsiveness following recovery from infection. Our

The effect of intracellular trafficking of CD1d on the formation of TCR repertoire of NKT cells.

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Shin, Jung Hoon; Park, Se-Ho

2014-05-01

CD1 molecules belong to non-polymorphic MHC class I-like proteins and present lipid antigens to T cells. Five different CD1 genes (CD1a-e) have been identified and classified into two groups. Group 1 include CD1a-c and present pathogenic lipid antigens to αβ T cells reminiscence of peptide antigen presentation by MHC-I molecules. CD1d is the only member of Group 2 and presents foreign and self lipid antigens to a specialized subset of αβ T cells, NKT cells. NKT cells are involved in diverse immune responses through prompt and massive production of cytokines. CD1d-dependent NKT cells are categorized upon the usage of their T cell receptors. A major subtype of NKT cells (type I) is invariant NKT cells which utilize invariant Vα14-Jα18 TCR alpha chain in mouse. The remaining NKT cells (type II) utilize diverse TCR alpha chains. Engineered CD1d molecules with modified intracellular trafficking produce either type I or type II NKT cell-defects suggesting the lipid antigens for each subtypes of NKT cells are processed/generated in different intracellular compartments. Since the usage of TCR by a T cell is the result of antigen-driven selection, the intracellular metabolic pathways of lipid antigen are a key in forming the functional NKT cell repertoire.

Stability of referential signalling across time and locations: testing alarm calls of Australian magpies (Gymnorhina tibicen in urban and rural Australia and in Fiji

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Gisela Kaplan

2013-07-01

Full Text Available In many avian species, vocal repertoire expands and changes throughout life as new syllables are added and sounds adapted to neighbours and circumstances. Referential signals, on the other hand, demand stability and lack of variation so that their meaning can be understood by conspecifics at all times. It is not known how stable such signals may be when the context is changed entirely but the point of reference remains unchanged. We investigated these questions in a rare case of forced translocation of an avian species, the Australian magpie (Gymnorhina tibicen, from Australia to the remote Fijian island of Taveuni decades ago. By using playbacks of vocalisations to 45 magpie groups in Australia, we first established that magpies use functionally referential signals in their alarm call repertoire signalling aerial danger (measured as looking up in response to a specific alarm call even though the speakers were on the ground. With these results in hand, we then used the same playbacks to magpie groups on the island of Taveuni. Our results showed that the meaning of one specific call (eagle alarm call is stable and maintained even in populations that have been isolated from Australian conspecifics over many (at least 10 generations. To our knowledge, this is the first time such a stability of a referential signal has been shown in the natural habitat.

Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species

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Okamura Hiroaki

2009-09-01

Full Text Available Abstract Background In mammals, pheromones play an important role in social and innate reproductive behavior within species. In rodents, vomeronasal receptor type 1 (V1R, which is specifically expressed in the vomeronasal organ, is thought to detect pheromones. The V1R gene repertoire differs dramatically between mammalian species, and the presence of species-specific V1R subfamilies in mouse and rat suggests that V1R plays a profound role in species-specific recognition of pheromones. In ruminants, however, the molecular mechanism(s for pheromone perception is not well understood. Interestingly, goat male pheromone, which can induce out-of-season ovulation in anestrous females, causes the same pheromone response in sheep, and vice versa, suggesting that there may be mechanisms for detecting "inter-species" pheromones among ruminant species. Results We isolated 23 goat and 21 sheep intact V1R genes based on sequence similarity with 32 cow V1R genes in the cow genome database. We found that all of the goat and sheep V1R genes have orthologs in their cross-species counterparts among these three ruminant species and that the sequence identity of V1R orthologous pairs among these ruminants is much higher than that of mouse-rat V1R orthologous pairs. Furthermore, all goat V1Rs examined thus far are expressed not only in the vomeronasal organ but also in the main olfactory epithelium. Conclusion Our results suggest that, compared with rodents, the repertoire of orthologous V1R genes is remarkably conserved among the ruminants cow, sheep and goat. We predict that these orthologous V1Rs can detect the same or closely related chemical compound(s within each orthologous set/pair. Furthermore, all identified goat V1Rs are expressed in the vomeronasal organ and the main olfactory epithelium, suggesting that V1R-mediated ligand information can be detected and processed by both the main and accessory olfactory systems. The fact that ruminant and rodent V1Rs

Diversity and repertoire of IgW and IgM VH families in the newborn nurse shark

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Dooley Helen

2004-05-01

Full Text Available Abstract Background Adult cartilaginous fish express three immunoglobulin (Ig isotypes, IgM, IgNAR and IgW. Newborn nurse sharks, Ginglymostoma cirratum, produce 19S (multimeric IgM and monomeric/dimeric IgM1gj, a germline-joined, IgM-related VH, and very low amounts of 7S (monomeric IgM and IgNAR proteins. Newborn IgNAR VH mRNAs are diverse in the complementarity-determining region 3 (CDR3 with non-templated nucleotide (N-region addition, which suggests that, unlike in many other vertebrates, terminal deoxynucleotidyl transferase (TdT expressed at birth is functional. IgW is present in the lungfish, a bony fish sharing a common ancestor with sharks 460 million years ago, implying that the IgW VH family is as old as the IgM VH family. This nurse shark study examined the IgM and IgW VH repertoire from birth through adult life, and analyzed the phylogenetic relationships of these gene families. Results IgM and IgW VH cDNA clones isolated from newborn nurse shark primary and secondary lymphoid tissues had highly diverse and unique CDR3 with N-region addition and VDJ gene rearrangement, implicating functional TdT and RAG gene activity. Despite the clear presence of N-region additions, newborn CDR3 were significantly shorter than those of adults. The IgM clones are all included in a conventional VH family that can be classified into five discrete groups, none of which is orthologous to IgM VH genes in other elasmobranchs. In addition, a novel divergent VH family was orthologous to a published monotypic VH horn shark family. IgW VH genes have diverged sufficiently to form three families. IgM and IgW VH serine codons using the potential somatic hypermutation hotspot sequence occur mainly in VH framework 1 (FR1 and CDR1. Phylogenetic analysis of cartilaginous fish and lungfish IgM and IgW demonstrated they form two major ancient gene groups; furthermore, these VH genes generally diversify (duplicate and diverge within a species. Conclusion As in ratfish

Defensive repertoire of Drosophila larvae in response to toxic fungi.

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Trienens, Monika; Kraaijeveld, Ken; Wertheim, Bregje

2017-10-01

Chemical warfare including insecticidal secondary metabolites is a well-known strategy for environmental microbes to monopolize a food source. Insects in turn have evolved behavioural and physiological defences to eradicate or neutralize the harmful microorganisms. We studied the defensive repertoire of insects in this interference competition by combining behavioural and developmental assays with whole-transcriptome time-series analysis. Confrontation with the toxic filamentous fungus Aspergillus nidulans severely reduced the survival of Drosophila melanogaster larvae. Nonetheless, the larvae did not behaviourally avoid the fungus, but aggregated at it. Confrontation with fungi strongly affected larval gene expression, including many genes involved in detoxification (e.g., CYP, GST and UGT genes) and the formation of the insect cuticle (e.g., Tweedle genes). The most strongly upregulated genes were several members of the insect-specific gene family Osiris, and CHK-kinase-like domains were over-represented. Immune responses were not activated, reflecting the competitive rather than pathogenic nature of the antagonistic interaction. While internal microbes are widely acknowledged as important, our study emphasizes the underappreciated role of environmental microbes as fierce competitors. © 2017 John Wiley & Sons Ltd.

Three-dimensional Invasion of Human Glioblastoma Cells Remains Unchanged by X-ray and Carbon Ion Irradiation In Vitro

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Eke, Iris; Storch, Katja; Kaestner, Ina; Vehlow, Anne [OncoRay-National Center for Radiation Research in Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden (Germany); Faethe, Christina; Mueller-Klieser, Wolfgang [Institute of Physiology and Pathophysiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz (Germany); Taucher-Scholz, Gisela [Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt (Germany); Temme, Achim; Schackert, Gabriele [Section of Experimental Neurosurgery/Tumor Immunology, Department of Neurosurgery, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden (Germany); Cordes, Nils, E-mail: Nils.Cordes@Oncoray.de [OncoRay-National Center for Radiation Research in Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden (Germany); Department of Radiation Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden (Germany)

2012-11-15

Purpose: Cell invasion represents one of the major determinants that treatment has failed for patients suffering from glioblastoma. Contrary findings have been reported for cell migration upon exposure to ionizing radiation. Here, the migration and invasion capability of glioblastoma cells on and in collagen type I were evaluated upon irradiation with X-rays or carbon ions. Methods and Materials: Migration on and invasion in collagen type I were evaluated in four established human glioblastoma cell lines exposed to either X-rays or carbon ions. Furthermore, clonogenic radiation survival, proliferation (5-bromo-2-deoxyuridine positivity), DNA double-strand breaks ({gamma}H2AX/53BP1-positive foci), and expression of invasion-relevant proteins (eg, {beta}1 integrin, FAK, MMP2, and MMP9) were explored. Migration and invasion assays for primary glioblastoma cells also were carried out with X-ray irradiation. Results: Neither X-ray nor carbon ion irradiation affected glioblastoma cell migration and invasion, a finding similarly observed in primary glioblastoma cells. Intriguingly, irradiated cells migrated unhampered, despite DNA double-strand breaks and reduced proliferation. Clonogenic radiation survival was increased when cells had contact with extracellular matrix. Specific inhibition of the {beta}1 integrin or proliferation-associated signaling molecules revealed a critical function of JNK, PI3K, and p38 MAPK in glioblastoma cell invasion. Conclusions: These findings indicate that X-rays and carbon ion irradiation effectively reduce proliferation and clonogenic survival without modifying the migration and invasion ability of glioblastoma cells in a collagen type I environment. Addition of targeted agents against members of the MAPK and PI3K signaling axis to conventional chemoradiation therapy seems potentially useful to optimize glioblastoma therapy.

MORPHOLOGICAL PECULIARITIES OF MUSIC FOR LISTENING IN THE REPERTOIRE OF THE FIDDLERS-VIOLONISTS FROM THE NORTHERN AREA OF THE REPUBLIC OF MOLDOVA

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SLABARI NICOLAE

2016-06-01

Full Text Available In this article we intend to highlight some characteristic morphological features of the melodies for listening included in the repertoire of the fiddlers- violonists from the north of Moldova, referring, in particular, to the variety and trends of its evolution in the space of time from the second half of the 20th and the beginning of the 21st centuries. By applying this information in the scientific circuit we will contribute to valorizing and completing the image of the fiddler phenomenon at present. The establishment of this repertoire was favored by some socio-political and cultural events of the 20th century, which generated mutation processes, such as globalization, academic schooling, improving the instruments, freedom of communication with musicians from outside the country. As a result, in the investigated space some species are gradually removed from circulation, and others that entered it, are still ongoing a process of crystallization and claim the right to exist. The fiddlers-violinists of the younger generation, tempted by the trendy, increasingly prefer them, being executed at various occasions.

Atazanavir intracellular concentrations remain stable during pregnancy in HIV-infected patients.

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Focà, Emanuele; Calcagno, Andrea; Bonito, Andrea; Simiele, Marco; Domenighini, Elisabetta; D'Avolio, Antonio; Quiros Roldan, Eugenia; Trentini, Laura; Casari, Salvatore; Di Perri, Giovanni; Castelli, Francesco; Bonora, Stefano

2017-11-01

Atazanavir (300 mg) boosted by ritonavir (100 mg) is the preferred third drug in pregnancy. However, there is still discordance on atazanavir dose increase during the third trimester. To evaluate plasma and intracellular atazanavir and ritonavir concentrations in HIV-infected women during pregnancy and after delivery. This was an observational study. HIV-infected pregnant patients treated with atazanavir/ritonavir plus either tenofovir/emtricitabine or abacavir/lamivudine had been prospectively enrolled after having signed a written informed consent form. Plasma and intracellular atazanavir and ritonavir Ctrough (24 ± 3 h after drug intake) were measured at each visit during the first, second and third trimesters and post-partum using validated HPLC-MS and HPLC-photodiode array methods (with direct evaluation of cellular volume). Data are described as median (IQR) and compared through non-parametric tests. Twenty-five patients were enrolled; at baseline, the median age was 32 years (27-35). All patients had plasma HIV RNA  0.05). This is the first demonstration that intracellular atazanavir exposure remains unchanged during pregnancy supporting the standard 300/100 mg atazanavir/ritonavir dosing throughout pregnancy. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)

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Schmid, Christoph D.; Bühlmann, Tobias; Louis, Edward J.; Beck, Hans-Peter

2011-01-01

One of the major virulence factors of the malaria causing parasite is the Plasmodium falciparum encoded erythrocyte membrane protein 1 (PfEMP1). It is translocated to It the membrane of infected erythrocytes and expressed from approximately 60 var genes in a mutually exclusive manner. Switching of var genes allows the parasite to alter functional and antigenic properties of infected erythrocytes, to escape the immune defense and to establish chronic infections. We have developed an efficient method for isolating VAR genes from telomeric and other genome locations by adapting transformation-associated recombination (TAR) cloning, which can then be analyzed and sequenced. For this purpose, three plasmids each containing a homologous sequence representing the upstream regions of the group A, B, and C var genes and a sequence homologous to the conserved acidic terminal segment (ATS) of var genes were generated. Co-transfection with P. falciparum strain ITG2F6 genomic DNA in yeast cells yielded 200 TAR clones. The relative frequencies of clones from each group were not biased. Clones were screened by PCR, as well as Southern blotting, which revealed clones missed by PCR due to sequence mismatches with the primers. Selected clones were transformed into E. coli and further analyzed by RFLP and end sequencing. Physical analysis of 36 clones revealed 27 distinct types potentially representing 50% of the var gene repertoire. Three clones were selected for sequencing and assembled into single var gene containing contigs. This study demonstrates that it is possible to rapidly obtain the repertoire of var genes from P. falciparum within a single set of cloning experiments. This technique can be applied to individual isolates which will provide a detailed picture of the diversity of var genes in the field. This is a powerful tool to overcome the obstacles with cloning and assembly of multi-gene families by simultaneously cloning each member. PMID:21408186

Linguistic repertoires of interdisciplinarity in brazilian journals in the area of psychology

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Mary Jane Paris Spink

2014-12-01

Full Text Available This paper is about manners in which linguistic repertoires of interdisciplinarity for dissemination of scientific knowledge are coordinated. It starts with a contextualization about interdisciplinarity and ways in which disciplines are organized for administrative purposes in Brazil. It seeks to answer the question: how these forms of ordering, controlling and coordinating interdisciplinary operate in the dissemination of scientific knowledge? The analysis of the ways of coordinating interdisciplinarity in scientific dissemination was based on the editorial proposals of journals classified as A1, A2 and B1 in the Qualis of the area of Psychology. The conclusion of this analysis is that scientific journals enact interdisciplinarity in different manners because they use various forms of association based on themes, related areas, and theories or theoretical frameworks. We conclude the analysis with a discussion of the implications of the various manners of coordinating knowledge for the dissemination of information for the public at large.

The effector repertoire of Fusarium oxysporum determines the tomato xylem proteome composition following infection

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Fleur eGawehns

2015-11-01

Full Text Available Plant pathogens secrete small proteins, of which some are effectors that promote infection. During colonization of the tomato xylem vessels the fungus Fusarium oxysporum f. sp. lycopersici (Fol secretes small proteins that are referred to as SIX (Secreted In Xylem proteins. Of these, Six1 (Avr3, Six3 (Avr2, Six5 and Six6 are required for full virulence, denoting them as effectors. To investigate their activities in the plant, the xylem sap proteome of plants inoculated with Fol wild-type or either AVR2, AVR3, SIX2, SIX5 or SIX6 knockout strains was analyzed with nano-Liquid Chromatography-Mass Spectrometry (nLC-MSMS. Compared to mock-inoculated sap 12 additional plant proteins appeared while 45 proteins were no longer detectable in the xylem sap of Fol-infected plants. Of the 285 proteins found in both uninfected and infected plants the abundance of 258 proteins changed significantly following infection. The xylem sap proteome of plants infected with four Fol effector knockout strains differed significantly from plants infected with wild-type Fol, while that of the SIX2-knockout inoculated plants remained unchanged. Besides an altered abundance of a core set of 24 differentially accumulated proteins (DAPs, each of the four effector knockout strains affected specifically the abundance of a subset of DAPs. Hence, Fol effectors have both unique and shared effects on the composition of the tomato xylem sap proteome.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina

2015-01-08

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina; Moitinho-Silva, Lucas; Brü mmer, Franz; Cannistraci, Carlo V.; Ravasi, Timothy; Hentschel, Ute

2015-01-01

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

Behavioural repertoire of working donkeys and consistency of behaviour over time, as a preliminary step towards identifying pain-related behaviours.

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Regan, Fran H; Hockenhull, Jo; Pritchard, Joy C; Waterman-Pearson, Avril E; Whay, Helen R

2014-01-01

The donkey has a reputation for stoicism and its behavioural repertoire in clinical contexts is under-reported. Lack of understanding of the norms of donkey behaviour and how it may vary over time can compromise use of behavioural measures as indicators of pain or emotional state. The objective of this study was to find out whether the behaviour of working donkeys was influenced by gender, the time of day or differed between days with a view to assessing how robust these measures are for inclusion in a working donkey ethogram. Frequency and consistency of postural and event behaviours were measured in 21 adult working donkeys (12 females; 9 males). Instantaneous (scan) and focal sampling were used to measure maintenance, lying, ingestive and investigative behaviours at hourly intervals for ten sessions on each of two consecutive days. High head carriage and biting were seen more frequently in male donkeys than females (Pdonkeys (Pdonkeys expressed an extensive behavioural repertoire, although some differences in behaviour were evident between genders. While most behaviours were consistent over time, some behaviours were influenced by time of day. Few behaviours differed between the two test days. The findings can be used to inform the development of a robust, evidence-based ethogram for working donkeys.

Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito Genomes.

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Suzuki, Yasutsugu; Frangeul, Lionel; Dickson, Laura B; Blanc, Hervé; Verdier, Yann; Vinh, Joelle; Lambrechts, Louis; Saleh, Maria-Carla

2017-08-01

Endogenous viral elements derived from nonretroviral RNA viruses have been described in various animal genomes. Whether they have a biological function, such as host immune protection against related viruses, is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Aedes albopictus cell lines and one from Aedes aegypti cell lines. However, an in-depth characterization of EFVEs in wild-type mosquito populations and individual mosquitoes in vivo has not been performed. We detected the full-length DNA sequence of the previously described EFVEs and their respective transcripts in several A. albopictus and A. aegypti populations from geographically distinct areas. However, EFVE-derived proteins were not detected by mass spectrometry. Using deep sequencing, we detected the production of PIWI-interacting RNA-like small RNAs, in an antisense orientation, targeting the EFVEs and their flanking regions in vivo The EFVEs were integrated in repetitive regions of the mosquito genomes, and their flanking sequences varied among mosquito populations. We bioinformatically predicted several new EFVEs from a Vietnamese A. albopictus population and observed variation in the occurrence of those elements among mosquitoes. Phylogenetic analysis of an A. aegypti EFVE suggested that it integrated prior to the global expansion of the species and subsequently diverged among and within populations. The findings of this study together reveal the substantial structural and nucleotide diversity of flaviviral integrations in Aedes genomes. Unraveling this diversity will help to elucidate the potential biological function of these EFVEs. IMPORTANCE Endogenous viral elements (EVEs) are whole or partial viral sequences integrated in host genomes. Interestingly, some EVEs have important functions for host fitness and

Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system.

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Krebber, A; Bornhauser, S; Burmester, J; Honegger, A; Willuda, J; Bosshard, H R; Plückthun, A

1997-02-14

A prerequisite for the use of recombinant antibody technologies starting from hybridomas or immune repertoires is the reliable cloning of functional immunoglobulin genes. For this purpose, a standard phage display system was optimized for robustness, vector stability, tight control of scFv-delta geneIII expression, primer usage for PCR amplification of variable region genes, scFv assembly strategy and subsequent directional cloning using a single rare cutting restriction enzyme. This integrated cloning, screening and selection system allowed us to rapidly obtain antigen binding scFvs derived from spleen-cell repertoires of mice immunized with ampicillin as well as from all hybridoma cell lines tested to date. As representative examples, cloning of monoclonal antibodies against a his tag, leucine zippers, the tumor marker EGP-2 and the insecticide DDT is presented. Several hybridomas whose genes could not be cloned in previous experimental setups, but were successfully obtained with the present system, expressed high amounts of aberrant heavy and light chain mRNAs, which were amplified by PCR and greatly exceeded the amount of binding antibody sequences. These contaminating variable region genes were successfully eliminated by employing the optimized phage display system, thus avoiding time consuming sequencing of non-binding scFv genes. To maximize soluble expression of functional scFvs subsequent to cloning, a compatible vector series to simplify modification, detection, multimerization and rapid purification of recombinant antibody fragments was constructed.

Quantitative measurement of pathogen specific human memory T cell repertoire diversity using a CDR3β-specific microarray

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Gorski Jack

2007-09-01

Full Text Available Abstract Background Providing quantitative microarray data that is sensitive to very small differences in target sequence would be a useful tool in any number of venues where a sample can consist of a multiple related sequences present in various abundances. Examples of such applications would include measurement of pseudo species in viral infections and the measurement of species of antibodies or T cell receptors that constitute immune repertoires. Difficulties that must be overcome in such a method would be to account for cross-hybridization and for differences in hybridization efficiencies between the arrayed probes and their corresponding targets. We have used the memory T cell repertoire to an influenza-derived peptide as a test case for developing such a method. Results The arrayed probes were corresponded to a 17 nucleotide TCR-specific region that distinguished sequences differing by as little as a single nucleotide. Hybridization efficiency between highly related Cy5-labeled subject sequences was normalized by including an equimolar mixture of Cy3-labeled synthetic targets representing all 108 arrayed probes. The same synthetic targets were used to measure the degree of cross hybridization between probes. Reconstitution studies found the system sensitive to input ratios as low as 0.5% and accurate in measuring known input percentages (R2 = 0.81, R = 0.90, p 0.05. Conclusion This novel strategy appears to be robust and can be adapted to any situation where complex mixtures of highly similar sequences need to be quantitatively resolved.

Expanding the Repertoire of Optogenetically Targeted Cells with an Enhanced Gene Expression System

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Kenji F. Tanaka

2012-08-01

Full Text Available Optogenetics has been enthusiastically pursued in recent neuroscience research, and the causal relationship between neural activity and behavior is becoming ever more accessible. Here, we established knockin-mediated enhanced gene expression by improved tetracycline-controlled gene induction (KENGE-tet and succeeded in generating transgenic mice expressing a highly light-sensitive channelrhodopsin-2 mutant at levels sufficient to drive the activities of multiple cell types. This method requires two lines of mice: one that controls the pattern of expression and another that determines the protein to be produced. The generation of new lines of either type readily expands the repertoire to choose from. In addition to neurons, we were able to manipulate the activity of nonexcitable glial cells in vivo. This shows that our system is applicable not only to neuroscience but also to any biomedical study that requires understanding of how the activity of a selected population of cells propagates through the intricate organic systems.

Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area.

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Tessema, Sofonias K; Monk, Stephanie L; Schultz, Mark B; Tavul, Livingstone; Reeder, John C; Siba, Peter M; Mueller, Ivo; Barry, Alyssa E

2015-01-01

Plasmodium falciparum malaria is a major global health problem that is being targeted for progressive elimination. Knowledge of local disease transmission patterns in endemic countries is critical to these elimination efforts. To investigate fine-scale patterns of malaria transmission, we have compared repertoires of rapidly evolving var genes in a highly endemic area. A total of 3680 high-quality DBLα-sequences were obtained from 68 P. falciparum isolates from ten villages spread over two distinct catchment areas on the north coast of Papua New Guinea (PNG). Modelling of the extent of var gene diversity in the two parasite populations predicts more than twice as many var gene alleles circulating within each catchment (Mugil = 906; Wosera = 1094) than previously recognized in PNG (Amele = 369). In addition, there were limited levels of var gene sharing between populations, consistent with local parasite population structure. Phylogeographic analyses demonstrate that while neutrally evolving microsatellite markers identified population structure only at the catchment level, var gene repertoires reveal further fine-scale geospatial clustering of parasite isolates. The clustering of parasite isolates by village in Mugil, but not in Wosera was consistent with the physical and cultural isolation of the human populations in the two catchments. The study highlights the microheterogeneity of P. falciparum transmission in highly endemic areas and demonstrates the potential of var genes as markers of local patterns of parasite population structure. © 2014 John Wiley & Sons Ltd.

Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire.

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Liu, Ju; Li, Ruihua; Liu, Kun; Li, Liangliang; Zai, Xiaodong; Chi, Xiangyang; Fu, Ling; Xu, Junjie; Chen, Wei

2016-04-22

High-throughput sequencing of the antibody repertoire provides a large number of antibody variable region sequences that can be used to generate human monoclonal antibodies. However, current screening methods for identifying antigen-specific antibodies are inefficient. In the present study, we developed an antibody clone screening strategy based on clone dynamics and relative frequency, and used it to identify antigen-specific human monoclonal antibodies. Enzyme-linked immunosorbent assay showed that at least 52% of putative positive immunoglobulin heavy chains composed antigen-specific antibodies. Combining information on dynamics and relative frequency improved identification of positive clones and elimination of negative clones. and increase the credibility of putative positive clones. Therefore the screening strategy could simplify the subsequent experimental screening and may facilitate the generation of antigen-specific antibodies. Copyright © 2016 Elsevier Inc. All rights reserved.

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

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Sukrit Silas

2017-07-01

Full Text Available Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent to a gene encoding a reverse transcriptase (RT related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium—Arthrospira platensis. Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown.

Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked Evolution of Human Antibody Repertoires to Fusion and Attachment Glycoproteins.

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Sandra Fuentes

2016-04-01

Full Text Available Respiratory Syncytial Virus (RSV is the major cause of pneumonia among infants. Here we elucidated the antibody repertoire following primary RSV infection and traced its evolution through adolescence and adulthood. Whole genome-fragment phage display libraries (GFPDL expressing linear and conformational epitopes in the RSV fusion protein (F and attachment protein (G were used for unbiased epitope profiling of infant sera prior to and following RSV infection. F-GFPDL analyses demonstrated modest changes in the anti-F epitope repertoires post-RSV infection, while G-GFPDL analyses revealed 100-fold increase in number of bound phages. The G-reactive epitopes spanned the N- and C-terminus of the G ectodomain, along with increased reactivity to the central conserved domain (CCD. Panels of F and G antigenic sites were synthesized to evaluate sera from young children (<2 yr, adolescents (14-18 yr and adults (30-45 yr in SPR real-time kinetics assays. A steady increase in RSV-F epitope repertoires from young children to adults was observed using peptides and F proteins. Importantly, several novel epitopes were identified in pre-fusion F and an immunodominant epitope in the F-p27. In all age groups, antibody binding to pre-fusion F was 2-3 folds higher than to post-fusion form. For RSV-G, antibody responses were high following early RSV infection in children, but declined significantly in adults, using either G proteins or peptides. This study identified unlinked evolution of anti-F and anti G responses and supportive evidence for immune pressure driven evolution of RSV-G. These findings could help development of effective countermeasures including vaccines.

Simultaneous determination of the repertoire of classical neurotransmitters released from embryonal carcinoma stem cells using online microdialysis coupled with hydrophilic interaction chromatography–tandem mass spectrometry

International Nuclear Information System (INIS)

Tang, Ya-Bin; Sun, Fan; Teng, Lin; Li, Wen-Bin; An, Shi-Min; Zhang, Chun; Yang, Xin-Jie; Lv, Hao-Yu; Ding, Xu-Ping; Zhu, Liang

2014-01-01

Highlights: • An online MD-HILIC–MS/MS method for simultaneously measuring the repertoire of classical transmitters was developed and validated. • Hydrophilic interaction chromatography (HILIC) was successfully employed to online system. • Stable isotope labeled internal standards and authentic matrix have been applied to guarantee reliable results. • The method features simple procedure (no sample preparation), high recovery (≥73%), high accuracy (89.36% ≤ RE ≤ 116.89%), good reproducibility (2.18% ≤ RSD ≤ 14.56%), and sensitive limits of detection (2 pg for acetylcholine, serotonin, and glutamate, 10 pg for dopamine, norepinephrine, GABA, and glycine). - Abstract: Dynamic, continuous, and simultaneous multi-analysis of transmitters is important for the delineation of the complex interactions between the neuronal and intercellular communications. But the analysis of the whole repertoire of classical transmitters of diverse structure is challenging due to their different physico-chemical properties and to their high polarity feature which leads to poor retention in traditional reversed-phase columns during LC–MS analysis. Here, an online microdialysis coupled with hydrophilic interaction chromatography–tandem mass spectrometry (online MD-HILIC–MS/MS) detection method was developed for the simultaneous measurement of the repertoire of classical transmitters (acetylcholine, serotonin, dopamine, norepinephrine, glutamate, GABA, and glycine). Stable isotope labeled internal standards and authentic matrix have been applied to guarantee reliable results. The method was successfully employed to reveal the characteristics of transmitter release from embryonal carcinoma stem cells. The method features simple procedure (no sample preparation), high recovery (≥73%), high accuracy (89.36% ≤ RE ≤ 116.89%), good reproducibility (2.18% ≤ RSD ≤ 14.56%), and sensitive limits of detection (2 pg for acetylcholine, serotonin, and glutamate, 10 pg

Simultaneous determination of the repertoire of classical neurotransmitters released from embryonal carcinoma stem cells using online microdialysis coupled with hydrophilic interaction chromatography–tandem mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Tang, Ya-Bin [Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Sun, Fan [Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Teng, Lin [Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Department of Cardiology and Institute of Cardiovascular Diseases, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang 443000, Hubei (China); Li, Wen-Bin; An, Shi-Min [Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Zhang, Chun; Yang, Xin-Jie; Lv, Hao-Yu; Ding, Xu-Ping [Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Zhu, Liang, E-mail: zhuliang17@gmail.com [Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); and others

2014-11-07

Highlights: • An online MD-HILIC–MS/MS method for simultaneously measuring the repertoire of classical transmitters was developed and validated. • Hydrophilic interaction chromatography (HILIC) was successfully employed to online system. • Stable isotope labeled internal standards and authentic matrix have been applied to guarantee reliable results. • The method features simple procedure (no sample preparation), high recovery (≥73%), high accuracy (89.36% ≤ RE ≤ 116.89%), good reproducibility (2.18% ≤ RSD ≤ 14.56%), and sensitive limits of detection (2 pg for acetylcholine, serotonin, and glutamate, 10 pg for dopamine, norepinephrine, GABA, and glycine). - Abstract: Dynamic, continuous, and simultaneous multi-analysis of transmitters is important for the delineation of the complex interactions between the neuronal and intercellular communications. But the analysis of the whole repertoire of classical transmitters of diverse structure is challenging due to their different physico-chemical properties and to their high polarity feature which leads to poor retention in traditional reversed-phase columns during LC–MS analysis. Here, an online microdialysis coupled with hydrophilic interaction chromatography–tandem mass spectrometry (online MD-HILIC–MS/MS) detection method was developed for the simultaneous measurement of the repertoire of classical transmitters (acetylcholine, serotonin, dopamine, norepinephrine, glutamate, GABA, and glycine). Stable isotope labeled internal standards and authentic matrix have been applied to guarantee reliable results. The method was successfully employed to reveal the characteristics of transmitter release from embryonal carcinoma stem cells. The method features simple procedure (no sample preparation), high recovery (≥73%), high accuracy (89.36% ≤ RE ≤ 116.89%), good reproducibility (2.18% ≤ RSD ≤ 14.56%), and sensitive limits of detection (2 pg for acetylcholine, serotonin, and glutamate, 10 pg

Mouse lysozyme-M knockout mice reveal how the self-determinant hierarchy shapes the T cell repertoire against this circulating self antigen in wild-type mice

NARCIS (Netherlands)

Sinha, Pratima; Chi, Howard H.; Kim, Hong R.; Clausen, Björn E.; Pederson, Brian; Sercarz, Eli E.; Forster, Irmgard; Moudgil, Kamal D.

2004-01-01

We have studied T cell tolerance to defined determinants within ML-M using wild-type (WT; ML-M+/+) and LysMcre (ML-M-/-) C3H (H-2(k)) mice to determine the relative contribution of ML-M-derived epitopes vs those from other self Ags in selection of the ML-M-specific T cell repertoire. ML-M was

T-cell receptor repertoire of human peripheral CD161hiTRAV1-2+ MAIT cells revealed by next generation sequencing and single cell analysis.

Science.gov (United States)

Held, Kathrin; Beltrán, Eduardo; Moser, Markus; Hohlfeld, Reinhard; Dornmair, Klaus

2015-09-01

Mucosal-associated invariant T (MAIT) cells are a T-cell subset that expresses a conserved TRAV1-2 (Vα7.2) T-cell receptor (TCR) chain and the surface marker CD161. They are involved in the defence against microbes as they recognise small organic molecules of microbial origin that are presented by the non-classical MHC molecule 1 (MR1). MAIT cells express a semi-restricted TCR α chain with TRAV1-2 preferentially linked to TRAJ33, TRAJ12, or TRAJ20 which pairs with a limited set of β chains. To investigate the TCR repertoire of human CD161(hi)TRAV1-2(+) T cells in depth we analysed the α and β chains of this T-cell subset by next generation sequencing. Concomitantly we analysed 132 paired α and β chains from single cells to assess the αβ pairing preferences. We found that the CD161(hi)TRAV1-2(+) TCR repertoire in addition to the typical MAIT TCRs further contains polyclonal elements reminiscent of classical αβ T cells. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek).

Science.gov (United States)

Shrivastava, Divya; Verma, Priyanka; Bhatia, Sabhyata

2014-09-01

Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard's similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.

An Expressive Bodily Movement Repertoire for Marimba Performance, Revealed through Observers' Laban Effort-Shape Analyses, and Allied Musical Features: Two Case Studies

Science.gov (United States)

Broughton, Mary C.; Davidson, Jane W.

2016-01-01

Musicians' expressive bodily movements can influence observers' perception of performance. Furthermore, individual differences in observers' music and motor expertise can shape how they perceive and respond to music performance. However, few studies have investigated the bodily movements that different observers of music performance perceive as expressive, in order to understand how they might relate to the music being produced, and the particular instrument type. In this paper, we focus on marimba performance through two case studies—one solo and one collaborative context. This study aims to investigate the existence of a core repertoire of marimba performance expressive bodily movements, identify key music-related features associated with the core repertoire, and explore how observers' perception of expressive bodily movements might vary according to individual differences in their music and motor expertise. Of the six professional musicians who observed and analyzed the marimba performances, three were percussionists and experienced marimba players. Following training, observers implemented the Laban effort-shape movement analysis system to analyze marimba players' bodily movements that they perceived as expressive in audio-visual recordings of performance. Observations that were agreed by all participants as being the same type of action at the same location in the performance recording were examined in each case study, then across the two studies. A small repertoire of bodily movements emerged that the observers perceived as being expressive. Movements were primarily allied to elements of the music structure, technique, and expressive interpretation, however, these elements appeared to be interactive. A type of body sway movement and more localized sound generating actions were perceived as expressive. These movements co-occurred and also appeared separately. Individual participant data revealed slightly more variety in the types and locations of actions

An expressive bodily movement repertoire for marimba performance, revealed through observers’ Laban effort-shape analyses, and allied musical features: two case studies

Directory of Open Access Journals (Sweden)

Mary C Broughton

2016-08-01

Full Text Available Musicians’ expressive bodily movements can influence observers’ perception of performance. Furthermore, individual differences in observers’ music and motor expertise can shape how they perceive and respond to music performance. However, few studies have investigated the bodily movements that different observers of music performance perceive as expressive, in order to understand how they might relate to the music being produced, and the particular instrument type. In this paper, we focus on marimba performance through two case studies – one solo and one collaborative context. This study aims to investigate the existence of a core repertoire of marimba performance expressive bodily movements, identify key music-related features associated with the core repertoire, and explore how observers’ perception of expressive bodily movements might vary according to individual differences in their music and motor expertise. Of the six professional musicians who observed and analyzed the marimba performances, three were percussionists and experienced marimba players. Following training, observers implemented the Laban effort-shape movement analysis system to analyze marimba players’ bodily movements that they perceived as expressive in audio-visual recordings of performance. Observations that were agreed by all participants as being the same type of action at the same location in the performance recording were examined in each case study, then across the two studies. A small repertoire of bodily movements emerged that the observers perceived as being expressive. Movements were primarily allied to elements of the music structure, technique, and expressive interpretation, however, these elements appeared to be interactive. A type of body sway movement and more localized sound generating actions were perceived as expressive. These movements co-occurred and also appeared separately. Individual participant data revealed slightly more variety in the

An Expressive Bodily Movement Repertoire for Marimba Performance, Revealed through Observers' Laban Effort-Shape Analyses, and Allied Musical Features: Two Case Studies.

Science.gov (United States)

Broughton, Mary C; Davidson, Jane W

2016-01-01

Musicians' expressive bodily movements can influence observers' perception of performance. Furthermore, individual differences in observers' music and motor expertise can shape how they perceive and respond to music performance. However, few studies have investigated the bodily movements that different observers of music performance perceive as expressive, in order to understand how they might relate to the music being produced, and the particular instrument type. In this paper, we focus on marimba performance through two case studies-one solo and one collaborative context. This study aims to investigate the existence of a core repertoire of marimba performance expressive bodily movements, identify key music-related features associated with the core repertoire, and explore how observers' perception of expressive bodily movements might vary according to individual differences in their music and motor expertise. Of the six professional musicians who observed and analyzed the marimba performances, three were percussionists and experienced marimba players. Following training, observers implemented the Laban effort-shape movement analysis system to analyze marimba players' bodily movements that they perceived as expressive in audio-visual recordings of performance. Observations that were agreed by all participants as being the same type of action at the same location in the performance recording were examined in each case study, then across the two studies. A small repertoire of bodily movements emerged that the observers perceived as being expressive. Movements were primarily allied to elements of the music structure, technique, and expressive interpretation, however, these elements appeared to be interactive. A type of body sway movement and more localized sound generating actions were perceived as expressive. These movements co-occurred and also appeared separately. Individual participant data revealed slightly more variety in the types and locations of actions

Profiling the repertoire of phenotypes influenced by environmental cues that occur during asexual reproduction.

Science.gov (United States)

Dombrovsky, Aviv; Arthaud, Laury; Ledger, Terence N; Tares, Sophie; Robichon, Alain

2009-11-01

The aphid Acyrthosiphon pisum population is composed of different morphs, such as winged and wingless parthenogens, males, and sexual females. The combined effect of reduced photoperiodicity and cold in fall triggers the apparition of sexual morphs. In contrast they reproduce asexually in spring and summer. In our current study, we provide evidence that clonal individuals display phenotypic variability within asexual morph categories. We describe that clones sharing the same morphological features, which arose from the same founder mother, constitute a repertoire of variants with distinct behavioral and physiological traits. Our results suggest that the prevailing environmental conditions influence the recruitment of adaptive phenotypes from a cohort of clonal individuals exhibiting considerable molecular diversity. However, we observed that the variability might be reduced or enhanced by external factors, but is never abolished in accordance with a model of stochastically produced phenotypes. This overall mechanism allows the renewal of colonies from a few adapted individuals that survive drastic episodic changes in a fluctuating environment.

Somatic hypermutation of the new antigen receptor gene (NAR) in the nurse shark does not generate the repertoire: possible role in antigen-driven reactions in the absence of germinal centers.

Science.gov (United States)

Diaz, M; Greenberg, A S; Flajnik, M F

1998-11-24

The new antigen receptor (NAR) gene in the nurse shark diversifies extensively by somatic hypermutation. It is not known, however, whether NAR somatic hypermutation generates the primary repertoire (like in the sheep) or rather is used in antigen-driven immune responses. To address this issue, the sequences of NAR transmembrane (Tm) and secretory (Sec) forms, presumed to represent the primary and secondary repertoires, respectively, were examined from the peripheral blood lymphocytes of three adult nurse sharks. More than 40% of the Sec clones but fewer than 11% of Tm clones contained five mutations or more. Furthermore, more than 75% of the Tm clones had few or no mutations. Mutations in the Sec clones occurred mostly in the complementarity-determining regions (CDR) with a significant bias toward replacement substitutions in CDR1; in Tm clones there was no significant bias toward replacements and only a low level of targeting to the CDRs. Unlike the Tm clones where the replacement mutational pattern was similar to that seen for synonymous changes, Sec replacements displayed a distinct pattern of mutations. The types of mutations in NAR were similar to those found in mouse Ig genes rather than to the unusual pattern reported for shark and Xenopus Ig. Finally, an oligoclonal family of Sec clones revealed a striking trend toward acquisition of glutamic/aspartic acid, suggesting some degree of selection. These data strongly suggest that hypermutation of NAR does not generate the repertoire, but instead is involved in antigen-driven immune responses.

The normally expressed kappa immunoglobulin light chain gene repertoire and somatic mutations studied by single-sided specific polymerase chain reaction (PCR); frequent occurrence of features often assigned to autoimmunity

DEFF Research Database (Denmark)

Juul, L; Hougs, L; Andersen, V

1997-01-01

The expressed human kappa light chain gene repertoire utilized by healthy individuals was studied by two different single-sided specific PCR techniques to avoid bias for certain V genes. A total of 103 rearranged kappa sequences from peripheral blood mononuclear cells from healthy individuals were...

The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids

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Ngai John

2006-12-01

Full Text Available Abstract Background Vertebrate odorant receptors comprise at least three types of G protein-coupled receptors (GPCRs: the OR, V1R, and V2R/V2R-like receptors, the latter group belonging to the C family of GPCRs. These receptor families are thought to receive chemosensory information from a wide spectrum of odorant and pheromonal cues that influence critical animal behaviors such as feeding, reproduction and other social interactions. Results Using genome database mining and other informatics approaches, we identified and characterized the repertoire of 54 intact "V2R-like" olfactory C family GPCRs in the zebrafish. Phylogenetic analysis – which also included a set of 34 C family GPCRs from fugu – places the fish olfactory receptors in three major groups, which are related to but clearly distinct from other C family GPCRs, including the calcium sensing receptor, metabotropic glutamate receptors, GABA-B receptor, T1R taste receptors, and the major group of V2R vomeronasal receptor families. Interestingly, an analysis of sequence conservation and selective pressure in the zebrafish receptors revealed the retention of a conserved sequence motif previously shown to be required for ligand binding in other amino acid receptors. Conclusion Based on our findings, we propose that the repertoire of zebrafish olfactory C family GPCRs has evolved to allow the detection and discrimination of a spectrum of amino acid and/or amino acid-based compounds, which are potent olfactory cues in fish. Furthermore, as the major groups of fish receptors and mammalian V2R receptors appear to have diverged significantly from a common ancestral gene(s, these receptors likely mediate chemosensation of different classes of chemical structures by their respective organisms.

Aerosol pH buffering in the southeastern US: Fine particles remain highly acidic despite large reductions in sulfate

Science.gov (United States)

Weber, R. J.; Guo, H.; Russell, A. G.; Nenes, A.

2015-12-01

pH is a critical aerosol property that impacts many atmospheric processes, including biogenic secondary organic aerosol formation, gas-particle phase partitioning, and mineral dust or redox metal mobilization. Particle pH has also been linked to adverse health effects. Using a comprehensive data set from the Southern Oxidant and Aerosol Study (SOAS) as the basis for thermodynamic modeling, we have shown that particles are currently highly acidic in the southeastern US, with pH between 0 and 2. Sulfate and ammonium are the main acid-base components that determine particle pH in this region, however they have different sources and their concentrations are changing. Over 15 years of network data show that sulfur dioxide emission reductions have resulted in a roughly 70 percent decrease in sulfate, whereas ammonia emissions, mainly link to agricultural activities, have been largely steady, as have gas phase ammonia concentrations. This has led to the view that particles are becoming more neutralized. However, sensitivity analysis, based on thermodynamic modeling, to changing sulfate concentrations indicates that particles have remained highly acidic over the past decade, despite the large reductions in sulfate. Furthermore, anticipated continued reductions of sulfate and relatively constant ammonia emissions into the future will not significantly change particle pH until sulfate drops to clean continental background levels. The result reshapes our expectation of future particle pH and implies that atmospheric processes and adverse health effects linked to particle acidity will remain unchanged for some time into the future.

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(DJ Recombination

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Louise S. Matheson

2017-11-01

Full Text Available V(DJ recombination is essential for the generation of diverse antigen receptor (AgR repertoires. In B cells, immunoglobulin kappa (Igκ light chain recombination follows immunoglobulin heavy chain (Igh recombination. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. Integration of VDJ-seq data with genome-wide datasets revealed that two chromatin states at the recombination signal sequence (RSS of VH genes are highly predictive of recombination in mouse pro-B cells. It is unknown whether local chromatin states contribute to Vκ gene choice during Igκ recombination. Here we adapt VDJ-seq to profile the Igκ VκJκ repertoire and present a comprehensive readout in mouse pre-B cells, revealing highly variable Vκ gene usage. Integration with genome-wide datasets for histone modifications, DNase hypersensitivity, transcription factor binding and germline transcription identified PU.1 binding at the RSS, which was unimportant for Igh, as highly predictive of whether a Vκ gene will recombine or not, suggesting that it plays a binary, all-or-nothing role, priming genes for recombination. Thereafter, the frequency with which these genes recombine was shaped both by the presence and level of enrichment of several other chromatin features, including H3K4 methylation and IKAROS binding. Moreover, in contrast to the Igh locus, the chromatin landscape of the promoter, as well as of the RSS, contributes to Vκ gene recombination. Thus, multiple facets of local chromatin features explain much of the variation in Vκ gene usage. Together, these findings reveal shared and divergent roles for epigenetic features and transcription factors in AgR V(DJ recombination and provide avenues for further investigation of chromatin signatures that may underpin V(DJ-mediated chromosomal translocations.

The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals

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Andrésdóttir Valgerdur

2008-11-01

Full Text Available Abstract Background APOBEC3 (A3 proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each A3 gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3. The presence of one A3 gene in mice (Z2–Z3 and seven in humans, A3A-H (Z1a, Z2a-Z1b, Z2b, Z2c-Z2d, Z2e-Z2f, Z2g-Z1c, Z3, suggests extraordinary evolutionary flexibility. To gain insights into the mechanism and timing of A3 gene expansion and into the functional modularity of these genes, we analyzed the genomic sequences, expressed cDNAs and activities of the full A3 repertoire of three artiodactyl lineages: sheep, cattle and pigs. Results Sheep and cattle have three A3 genes, A3Z1, A3Z2 and A3Z3, whereas pigs only have two, A3Z2 and A3Z3. A comparison between domestic and wild pigs indicated that A3Z1 was deleted in the pig lineage. In all three species, read-through transcription and alternative splicing also produced a catalytically active double domain A3Z2-Z3 protein that had a distinct cytoplasmic localization. Thus, the three A3 genes of sheep and cattle encode four conserved and active proteins. These data, together with phylogenetic analyses, indicated that a similar, functionally modular A3 repertoire existed in the common ancestor of artiodactyls and primates (i.e., the ancestor of placental mammals. This mammalian ancestor therefore possessed the minimal A3 gene set, Z1-Z2-Z3, required to evolve through a remarkable series of eight recombination events into the present day eleven Z domain human repertoire. Conclusion The dynamic recombination-filled history of the mammalian A3 genes is consistent with the modular nature of the locus and a model in which most of these events (especially the expansions were selected by ancient pathogenic retrovirus infections.

Epigenetic codes programming class switch recombination

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Bharat eVaidyanathan

2015-09-01

Full Text Available Class switch recombination imparts B cells with a fitness-associated adaptive advantage during a humoral immune response by using a precision-tailored DNA excision and ligation process to swap the default constant region gene of the antibody with a new one that has unique effector functions. This secondary diversification of the antibody repertoire is a hallmark of the adaptability of B cells when confronted with environmental and pathogenic challenges. Given that the nucleotide sequence of genes during class switching remains unchanged (genetic constraints, it is logical and necessary therefore, to integrate the adaptability of B cells to an epigenetic state, which is dynamic and can be heritably modulated before, after or even during an antibody-dependent immune response. Epigenetic regulation encompasses heritable changes that affect function (phenotype without altering the sequence information embedded in a gene, and include histone, DNA and RNA modifications. Here, we review current literature on how B cells use an epigenetic code language as a means to ensure antibody plasticity in light of pathogenic insults.

Analysis of the clonal repertoire of gene-corrected cells in gene therapy.

Science.gov (United States)

Paruzynski, Anna; Glimm, Hanno; Schmidt, Manfred; Kalle, Christof von

2012-01-01

Gene therapy-based clinical phase I/II studies using integrating retroviral vectors could successfully treat different monogenetic inherited diseases. However, with increased efficiency of this therapy, severe side effects occurred in various gene therapy trials. In all cases, integration of the vector close to or within a proto-oncogene contributed substantially to the development of the malignancies. Thus, the in-depth analysis of integration site patterns is of high importance to uncover potential clonal outgrowth and to assess the safety of gene transfer vectors and gene therapy protocols. The standard and nonrestrictive linear amplification-mediated PCR (nrLAM-PCR) in combination with high-throughput sequencing exhibits technologies that allow to comprehensively analyze the clonal repertoire of gene-corrected cells and to assess the safety of the used vector system at an early stage on the molecular level. It enables clarifying the biological consequences of the vector system on the fate of the transduced cell. Furthermore, the downstream performance of real-time PCR allows a quantitative estimation of the clonality of individual cells and their clonal progeny. Here, we present a guideline that should allow researchers to perform comprehensive integration site analysis in preclinical and clinical studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Childhood glaucoma surgery in the 21st Century

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Papadopoulos, M; Edmunds, B; Fenerty, C; Khaw, P T

2014-01-01

Most children with glaucoma will require surgery in their lifetime, often in their childhood years. The surgical management of childhood glaucoma is however challenging, largely because of its greater potential for failure and complications as compared with surgery in adults. The available surgical repertoire for childhood glaucoma has remained relatively unchanged for many years with most progress owing to modifications to existing surgery. Although the surgical approach to childhood glaucoma varies around the world, angle surgery remains the preferred initial surgery for primary congenital glaucoma and a major advance has been the concept of incising the whole of the angle (circumferential trabeculotomy). Simple modifications to the trabeculectomy technique have been shown to considerably minimise complications. Glaucoma drainage devices maintain a vital role for certain types of glaucoma including those refractory to other surgery. Cyclodestruction continues to have a role mainly for patients following failed drainage/filtering surgery. Although the prognosis for childhood glaucoma has improved significantly since the introduction of angle surgery, there is still considerable progress to be made to ensure a sighted lifetime for children with glaucoma all over the world. Collaborative approaches to researching and delivering this care are required, and this paper highlights the need for more high-quality prospective surgical trials in the management of the childhood glaucoma. PMID:24924446

Generation of Novel Traj18-Deficient Mice Lacking Vα14 Natural Killer T Cells with an Undisturbed T Cell Receptor α-Chain Repertoire.

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Nyambayar Dashtsoodol

Full Text Available Invariant Vα14 natural killer T (NKT cells, characterized by the expression of a single invariant T cell receptor (TCR α chain encoded by rearranged Trav11 (Vα14-Traj18 (Jα18 gene segments in mice, and TRAV10 (Vα24-TRAJ18 (Jα18 in humans, mediate adjuvant effects to activate various effector cell types in both innate and adaptive immune systems that facilitates the potent antitumor effects. It was recently reported that the Jα18-deficient mouse described by our group in 1997 harbors perturbed TCRα repertoire, which raised concerns regarding the validity of some of the experimental conclusions that have been made using this mouse line. To resolve this concern, we generated a novel Traj18-deficient mouse line by specifically targeting the Traj18 gene segment using Cre-Lox approach. Here we showed the newly generated Traj18-deficient mouse has, apart from the absence of Traj18, an undisturbed TCRα chain repertoire by using next generation sequencing and by detecting normal generation of Vα19Jα33 expressing mucosal associated invariant T cells, whose development was abrogated in the originally described Jα18-KO mice. We also demonstrated here the definitive requirement for NKT cells in the protection against tumors and their potent adjuvant effects on antigen-specific CD8 T cells.

Bread, milk and a Tattslotto ticket: the interpretive repertoires of young adult gambling in Australia.

Science.gov (United States)

Nekich, Maree Ann; Ohtsuka, Keis

2016-01-01

The discourse of Australian young adults who gamble regularly was analysed to explore key dilemmas and challenges of a generation who grew up with the positive and negative impacts of gambling advertisements. Qualitative interviews of seven young recreational gamblers who regularly frequent gaming machine venues were conducted. The discourse that they used to describe their gambling involvement, motivation, development and subjective views were analysed and three central repertoires: 'Culture not self,' 'If it makes you happy,' and 'No problem here!' were identified. The current findings demonstrate the participants' attempts to understand and legitimise their gambling. Further, it was suggested that young adults face a series of dilemmas when deciding whether to gamble and to what extent they gamble. Their discourse highlights the tension between individual agency, societal expectations and familial influence. The respondents primarily gambled for social reasons in a manner which they perceived as culturally acceptable. The importance of harm minimization and public awareness campaigns directed at young adults was also discussed.

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination.

Science.gov (United States)

Matheson, Louise S; Bolland, Daniel J; Chovanec, Peter; Krueger, Felix; Andrews, Simon; Koohy, Hashem; Corcoran, Anne E

2017-01-01

V(D)J recombination is essential for the generation of diverse antigen receptor (AgR) repertoires. In B cells, immunoglobulin kappa ( Igκ ) light chain recombination follows immunoglobulin heavy chain ( Igh ) recombination. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. Integration of VDJ-seq data with genome-wide datasets revealed that two chromatin states at the recombination signal sequence (RSS) of VH genes are highly predictive of recombination in mouse pro-B cells. It is unknown whether local chromatin states contribute to Vκ gene choice during Igκ recombination. Here we adapt VDJ-seq to profile the Igκ VκJκ repertoire and present a comprehensive readout in mouse pre-B cells, revealing highly variable Vκ gene usage. Integration with genome-wide datasets for histone modifications, DNase hypersensitivity, transcription factor binding and germline transcription identified PU.1 binding at the RSS, which was unimportant for Igh , as highly predictive of whether a Vκ gene will recombine or not, suggesting that it plays a binary, all-or-nothing role, priming genes for recombination. Thereafter, the frequency with which these genes recombine was shaped both by the presence and level of enrichment of several other chromatin features, including H3K4 methylation and IKAROS binding. Moreover, in contrast to the Igh locus, the chromatin landscape of the promoter, as well as of the RSS, contributes to Vκ gene recombination. Thus, multiple facets of local chromatin features explain much of the variation in Vκ gene usage. Together, these findings reveal shared and divergent roles for epigenetic features and transcription factors in AgR V(D)J recombination and provide avenues for further investigation of chromatin signatures that may underpin V(D)J-mediated chromosomal translocations.

The scavenger receptor repertoire in six cnidarian species and its putative role in cnidarian-dinoflagellate symbiosis

Directory of Open Access Journals (Sweden)

Emilie F. Neubauer

2016-11-01

Full Text Available Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians have diverse and complex innate immune repertoires that are just beginning to be described. Scavenger receptors (SR are a diverse superfamily of innate immunity genes that recognize a broad array of microbial ligands and participate in phagocytosis of invading microbes. The superfamily includes subclades named SR-A through SR-I that are categorized based on the arrangement of sequence domains including the scavenger receptor cysteine rich (SRCR, the C-type lectin (CTLD and the CD36 domains. Previous functional and gene expression studies on cnidarian-dinoflagellate symbiosis have implicated SR-like proteins in interpartner communication and regulation. In this study, we characterized the SR repertoire from a combination of genomic and transcriptomic resources from six cnidarian species in the Class Anthozoa. We combined these bioinformatic analyses with functional experiments using the SR inhibitor fucoidan to explore a role for SRs in cnidarian symbiosis and immunity. Bioinformatic searches revealed a large diversity of SR-like genes that resembled SR-As, SR-Bs, SR-Es and SR-Is. SRCRs, CTLDs and CD36 domains were identified in multiple sequences in combinations that were highly homologous to vertebrate SRs as well as in proteins with novel domain combinations. Phylogenetic analyses of CD36 domains of the SR-B-like sequences from a diversity of metazoans grouped cnidarian with bilaterian sequences separate from other basal metazoans. All cnidarian sequences grouped together with moderate support in a subclade separately from bilaterian sequences. Functional experiments were carried out on the sea anemone Aiptasia pallida that engages in a symbiosis with Symbiodinium minutum

Targeted capture massively parallel sequencing analysis of LCIS and invasive lobular cancer: Repertoire of somatic genetic alterations and clonal relationships.

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Sakr, Rita A; Schizas, Michail; Carniello, Jose V Scarpa; Ng, Charlotte K Y; Piscuoglio, Salvatore; Giri, Dilip; Andrade, Victor P; De Brot, Marina; Lim, Raymond S; Towers, Russell; Weigelt, Britta; Reis-Filho, Jorge S; King, Tari A

2016-02-01

Lobular carcinoma in situ (LCIS) has been proposed as a non-obligate precursor of invasive lobular carcinoma (ILC). Here we sought to define the repertoire of somatic genetic alterations in pure LCIS and in synchronous LCIS and ILC using targeted massively parallel sequencing. DNA samples extracted from microdissected LCIS, ILC and matched normal breast tissue or peripheral blood from 30 patients were subjected to massively parallel sequencing targeting all exons of 273 genes, including the genes most frequently mutated in breast cancer and DNA repair-related genes. Single nucleotide variants and insertions and deletions were identified using state-of-the-art bioinformatics approaches. The constellation of somatic mutations found in LCIS (n = 34) and ILC (n = 21) were similar, with the most frequently mutated genes being CDH1 (56% and 66%, respectively), PIK3CA (41% and 52%, respectively) and CBFB (12% and 19%, respectively). Among 19 LCIS and ILC synchronous pairs, 14 (74%) had at least one identical mutation in common, including identical PIK3CA and CDH1 mutations. Paired analysis of independent foci of LCIS from 3 breasts revealed at least one common mutation in each of the 3 pairs (CDH1, PIK3CA, CBFB and PKHD1L1). LCIS and ILC have a similar repertoire of somatic mutations, with PIK3CA and CDH1 being the most frequently mutated genes. The presence of identical mutations between LCIS-LCIS and LCIS-ILC pairs demonstrates that LCIS is a clonal neoplastic lesion, and provides additional evidence that at least some LCIS are non-obligate precursors of ILC. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Strategies for interpersonal and public communication in social movements. Transformations in informal networks and repertoires in the era of social Web

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Rocío Ortiz Galindo

2016-07-01

Full Text Available This work aims to advance in the theoretical analysis of the field of communication and social movements. The article studies the new changes that have emerged in the social Web era. We will review some of the principal works of the literature to observe the communicative strategies in these collectives, which are able to influence in the social change. We will differentiate the area of interpersonal communication (the informal networks and the public communication (the repertoires of collective action. We will use this classification to analyze the communicative strategies which have born in the social cybermovements, in the ICT age.

Evolution of drug resistance in HIV infected patients remaining on a virologically failing cART regimen

DEFF Research Database (Denmark)

Cozzi-Lepri, A; Phillips, AN; Ruiz, L

2007-01-01

OBJECTIVE: To estimate the extent of drug resistance accumulation in patients kept on a virologically failing regimen and its determinants in the clinical setting. DESIGN: The study focused on 110 patients of EuroSIDA on an unchanged regimen who had two genotypic tests performed at two time points...

Norepinephrine-induced apoptotic and hypertrophic responses in H9c2 cardiac myoblasts are characterized by different repertoire of reactive oxygen species generation

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Anita Thakur

2015-08-01

Full Text Available Despite recent advances, the role of ROS in mediating hypertrophic and apoptotic responses in cardiac myocytes elicited by norepinephrine (NE is rather poorly understood. We demonstrate through our experiments that H9c2 cardiac myoblasts treated with 2 µM NE (hypertrophic dose generate DCFH-DA positive ROS only for 2 h; while those treated with 100 µM NE (apoptotic dose sustains generation for 48 h, followed by apoptosis. Though the levels of DCFH fluorescence were comparable at early time points in the two treatment sets, its quenching by DPI, catalase and MnTmPyP suggested the existence of a different repertoire of ROS. Both doses of NE also induced moderate levels of H2O2 but with different kinetics. Sustained but intermittent generation of highly reactive species detectable by HPF was seen in both treatment sets but no peroxynitrite was generated in either conditions. Sustained generation of hydroxyl radicals with no appreciable differences were noticed in both treatment sets. Nevertheless, despite similar profile of ROS generation between the two conditions, extensive DNA damage as evident from the increase in 8-OH-dG content, formation of γ-H2AX and PARP cleavage was seen only in cells treated with the higher dose of NE. We therefore conclude that hypertrophic and apoptotic doses of NE generate distinct but comparable repertoire of ROS/RNS leading to two very distinct downstream responses.

Mining Naïve Rabbit Antibody Repertoires by Phage Display for Monoclonal Antibodies of Therapeutic Utility.

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Peng, Haiyong; Nerreter, Thomas; Chang, Jing; Qi, Junpeng; Li, Xiuling; Karunadharma, Pabalu; Martinez, Gustavo J; Fallahi, Mohammad; Soden, Jo; Freeth, Jim; Beerli, Roger R; Grawunder, Ulf; Hudecek, Michael; Rader, Christoph

2017-09-15

Owing to their high affinities and specificities, rabbit monoclonal antibodies (mAbs) have demonstrated value and potential primarily as basic research and diagnostic reagents, but, in some cases, also as therapeutics. To accelerate access to rabbit mAbs bypassing immunization, we generated a large naïve rabbit antibody repertoire represented by a phage display library encompassing >10 billion independent antibodies in chimeric rabbit/human Fab format and validated it by next-generation sequencing. Panels of rabbit mAbs selected from this library against two emerging cancer targets, ROR1 and ROR2, revealed high diversity, affinity, and specificity. Moreover, ROR1- and ROR2-targeting rabbit mAbs demonstrated therapeutic utility as components of chimeric antigen receptor-engineered T cells, further corroborating the value of the naïve rabbit antibody library as a rich and virtually unlimited source of rabbit mAbs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Protest Leadership and Repertoire: A Comparative Analysis of Peasant Protest in Hunan in the 1990s

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Wu Zhang

2013-01-01

Full Text Available Based on detailed ethnographic fieldwork, this paper compares two cases of peasant protest against heavy taxes and fees in a northern Hunan county in the 1990s. It argues that peasant protest did not arise spontaneously. Rather, it erupted when leaders emerged who used central policy documents on lowering peasant taxes and fees to mobilise peasants. Protest leaders were articulate and public-spirited peasants who had received political training from the local party-state. Furthermore, the number of leaders, their education level, and their relationship with the local party-state explain why the repertoire and the scope of the two protests varied. Protests led by less educated veteran Communist Party cadres tended to be milder and smaller than those led by better-educated peasants more distant from the local party-state. This paper helps us to understand the process of peasant mobilisation in contemporary China and explains why peasant protest varies across cases.

Behavioural repertoire of working donkeys and consistency of behaviour over time, as a preliminary step towards identifying pain-related behaviours.

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Fran H Regan

Full Text Available The donkey has a reputation for stoicism and its behavioural repertoire in clinical contexts is under-reported. Lack of understanding of the norms of donkey behaviour and how it may vary over time can compromise use of behavioural measures as indicators of pain or emotional state. The objective of this study was to find out whether the behaviour of working donkeys was influenced by gender, the time of day or differed between days with a view to assessing how robust these measures are for inclusion in a working donkey ethogram.Frequency and consistency of postural and event behaviours were measured in 21 adult working donkeys (12 females; 9 males. Instantaneous (scan and focal sampling were used to measure maintenance, lying, ingestive and investigative behaviours at hourly intervals for ten sessions on each of two consecutive days. High head carriage and biting were seen more frequently in male donkeys than females (P<0.001. Level head carriage, licking/chewing and head-shaking were observed more frequently in female donkeys (P<0.001. Tail position, ear orientation, foot stamping, rolling/lying and head-shaking behaviours were affected by time of day (P<0.001. However, only two variations in ear orientation were found to be significantly different over the two days of observations (P<0.001. Tail swishing, head shaking, foot stamping, and ears held sideways and downwards were significantly correlated (P<0.001 and are assumed to be behaviours to discourage flies.All donkeys expressed an extensive behavioural repertoire, although some differences in behaviour were evident between genders. While most behaviours were consistent over time, some behaviours were influenced by time of day. Few behaviours differed between the two test days. The findings can be used to inform the development of a robust, evidence-based ethogram for working donkeys.

MicroRNA repertoire for functional genome research in tilapia identified by deep sequencing.

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Yan, Biao; Wang, Zhen-Hua; Zhu, Chang-Dong; Guo, Jin-Tao; Zhao, Jin-Liang

2014-08-01

The Nile tilapia (Oreochromis niloticus; Cichlidae) is an economically important species in aquaculture and occupies a prominent position in the aquaculture industry. MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression involved in diverse biological and metabolic processes. To increase the repertoire of miRNAs characterized in tilapia, we used the Illumina/Solexa sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the different developmental stages of tilapia. Bioinformatic analyses suggest that 197 conserved and 27 novel miRNAs are expressed in tilapia. Sequence alignments indicate that all tested miRNAs and miRNAs* are highly conserved across many species. In addition, we characterized the tissue expression patterns of five miRNAs using real-time quantitative PCR. We found that miR-1/206, miR-7/9, and miR-122 is abundantly expressed in muscle, brain, and liver, respectively, implying a potential role in the regulation of tissue differentiation or the maintenance of tissue identity. Overall, our results expand the number of tilapia miRNAs, and the discovery of miRNAs in tilapia genome contributes to a better understanding the role of miRNAs in regulating diverse biological processes.

Bread, milk and a Tattslotto ticket: the interpretive repertoires of young adult gambling in Australia

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Maree Ann Nekich

2016-05-01

Full Text Available Abstract The discourse of Australian young adults who gamble regularly was analysed to explore key dilemmas and challenges of a generation who grew up with the positive and negative impacts of gambling advertisements. Qualitative interviews of seven young recreational gamblers who regularly frequent gaming machine venues were conducted. The discourse that they used to describe their gambling involvement, motivation, development and subjective views were analysed and three central repertoires: ‘Culture not self,’ ‘If it makes you happy,’ and ‘No problem here!’ were identified. The current findings demonstrate the participants’ attempts to understand and legitimise their gambling. Further, it was suggested that young adults face a series of dilemmas when deciding whether to gamble and to what extent they gamble. Their discourse highlights the tension between individual agency, societal expectations and familial influence. The respondents primarily gambled for social reasons in a manner which they perceived as culturally acceptable. The importance of harm minimization and public awareness campaigns directed at young adults was also discussed.

The repertoire of bitter taste receptor genes in canids.

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Shang, Shuai; Wu, Xiaoyang; Chen, Jun; Zhang, Huanxin; Zhong, Huaming; Wei, Qinguo; Yan, Jiakuo; Li, Haotian; Liu, Guangshuai; Sha, Weilai; Zhang, Honghai

2017-07-01

Bitter taste receptors (Tas2rs) play important roles in mammalian defense mechanisms by helping animals detect and avoid toxins in food. Although Tas2r genes have been widely studied in several mammals, minimal research has been performed in canids. To analyze the genetic basis of Tas2r genes in canids, we first identified Tas2r genes in the wolf, maned wolf, red fox, corsac fox, Tibetan fox, fennec fox, dhole and African hunting dog. A total of 183 Tas2r genes, consisting of 118 intact genes, 6 partial genes and 59 pseudogenes, were detected. Differences in the pseudogenes were observed among nine canid species. For example, Tas2r4 was a pseudogene in the dog but might play a functional role in other canid species. The Tas2r42 and Tas2r10 genes were pseudogenes in the maned wolf and dhole, respectively, and the Tas2r5 and Tas2r34 genes were pseudogenes in the African hunting dog; however, these genes were intact genes in other canid species. The differences in Tas2r pseudogenes among canids might suggest that the loss of intact Tas2r genes in canid species is species-dependent. We further compared the 183 Tas2r genes identified in this study with Tas2r genes from ten additional carnivorous species to evaluate the potential influence of diet on the evolution of the Tas2r gene repertoire. Phylogenetic analysis revealed that most of the Tas2r genes from the 18 species intermingled across the tree, suggesting that Tas2r genes are conserved among carnivores. Within canids, we found that some Tas2r genes corresponded to the traditional taxonomic groupings, while some did not. PIC analysis showed that the number of Tas2r genes in carnivores exhibited no positive correlation with diet composition, which might be due to the limited number of carnivores included in our study.

Negative plant-soil feedbacks increase with plant abundance, and are unchanged by competition.

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Maron, John L; Laney Smith, Alyssa; Ortega, Yvette K; Pearson, Dean E; Callaway, Ragan M

2016-08-01

Plant-soil feedbacks and interspecific competition are ubiquitous interactions that strongly influence the performance of plants. Yet few studies have examined whether the strength of these interactions corresponds with the abundance of plant species in the field, or whether feedbacks and competition interact in ways that either ameliorate or exacerbate their effects in isolation. We sampled soil from two intermountain grassland communities where we also measured the relative abundance of plant species. In greenhouse experiments, we quantified the direction and magnitude of plant-soil feedbacks for 10 target species that spanned a range of abundances in the field. In soil from both sites, plant-soil feedbacks were mostly negative, with more abundant species suffering greater negative feedbacks than rare species. In contrast, the average response to competition for each species was unrelated with its abundance in the field. We also determined how competitive response varied among our target species when plants competed in live vs. sterile soil. Interspecific competition reduced plant size, but the strength of this negative effect was unchanged by plant-soil feedbacks. Finally, when plants competed interspecifically, we asked how conspecific-trained, heterospecific-trained, and sterile soil influenced the competitive responses of our target species and how this varied depending on whether target species were abundant or rare in the field. Here, we found that both abundant and rare species were not as harmed by competition when they grew in heterospecific-trained soil compared to when they grew in conspecific-cultured soil. Abundant species were also not as harmed by competition when growing in sterile vs. conspecific-trained soil, but this was not the case for rare species. Our results suggest that abundant plants accrue species-specific soil pathogens to a greater extent than rare species. Thus, negative feedbacks may be critical for preventing abundant species from

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

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Silas, Sukrit; Makarova, Kira S; Shmakov, Sergey; Páez-Espino, David; Mohr, Georg; Liu, Yi; Davison, Michelle; Roux, Simon; Krishnamurthy, Siddharth R; Fu, Becky Xu Hua; Hansen, Loren L; Wang, David; Sullivan, Matthew B; Millard, Andrew; Clokie, Martha R; Bhaya, Devaki; Lambowitz, Alan M; Kyrpides, Nikos C; Koonin, Eugene V; Fire, Andrew Z

2017-07-11

Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium- Arthrospira platensis Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From

[PALEOPATHOLOGY OF HUMAN REMAINS].

Science.gov (United States)

Minozzi, Simona; Fornaciari, Gino

2015-01-01

Many diseases induce alterations in the human skeleton, leaving traces of their presence in ancient remains. Paleopathological examination of human remains not only allows the study of the history and evolution of the disease, but also the reconstruction of health conditions in the past populations. This paper describes the most interesting diseases observed in skeletal samples from the Roman Imperial Age necropoles found in urban and suburban areas of Rome during archaeological excavations in the last decades. The diseases observed were grouped into the following categories: articular diseases, traumas, infections, metabolic or nutritional diseases, congenital diseases and tumours, and some examples are reported for each group. Although extensive epidemiological investigation in ancient skeletal records is impossible, the palaeopathological study allowed to highlight the spread of numerous illnesses, many of which can be related to the life and health conditions of the Roman population.

Modular Study of the Type III Effector Repertoire in Pseudomonas syringae pv. tomato DC3000 Reveals a Matrix of Effector Interplay in Pathogenesis

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Hai-Lei Wei

2018-05-01

Full Text Available Summary: The bacterial pathogen Pseudomonas syringae pv. tomato DC3000 suppresses the two-tiered innate immune system of Nicotiana benthamiana and other plants by injecting a complex repertoire of type III secretion effector (T3E proteins. Effectorless polymutant DC3000D36E was used with a modularized system for native delivery of the 29 DC3000 T3Es singly and in pairs. Assays of the performance of this T3E library in N. benthamiana leaves revealed a matrix of T3E interplay, with six T3Es eliciting death and eight others variously suppressing the death activity of the six. The T3E library was also interrogated for effects on DC3000D36E elicitation of a reactive oxygen species burst, for growth in planta, and for T3Es that reversed these effects. Pseudomonas fluorescens and Agrobacterium tumefaciens heterologous delivery systems yielded notably different sets of death-T3Es. The DC3000D36E T3E library system highlights the importance of 13 T3Es and their interplay in interactions with N. benthamiana. : Wei et al. used a Pseudomonas syringae strain lacking all known type III effectors with a modularized library expressing the 29 active effectors in the strain’s native repertoire, individually and in pairs, to comprehensively determine effector actions and interplay in inducing and suppressing responses associated with plant pathogenesis and immunity. Keywords: effector-triggered-immunity, pattern-triggered-immunity, Hop proteins, plant immunity, mini-Tn7

Quantifying Distribution of Flow Cytometric TCR-Vβ Usage with Economic Statistics.

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Kornelis S M van der Geest

Full Text Available Measuring changes of the T cell receptor (TCR repertoire is important to many fields of medicine. Flow cytometry is a popular technique to study the TCR repertoire, as it quickly provides insight into the TCR-Vβ usage among well-defined populations of T cells. However, the interpretation of the flow cytometric data remains difficult, and subtle TCR repertoire changes may go undetected. Here, we introduce a novel means for analyzing the flow cytometric data on TCR-Vβ usage. By applying economic statistics, we calculated the Gini-TCR skewing index from the flow cytometric TCR-Vβ analysis. The Gini-TCR skewing index, which is a direct measure of TCR-Vβ distribution among T cells, allowed us to track subtle changes of the TCR repertoire among distinct populations of T cells. Application of the Gini-TCR skewing index to the flow cytometric TCR-Vβ analysis will greatly help to gain better understanding of the TCR repertoire in health and disease.

Narrative Inquiry for Science Education: Teachers' repertoire-making in the case of environmental curriculum

Science.gov (United States)

Hwang, Seyoung

2011-04-01

This paper considers how the school science curriculum can be conceptualised in order to address the contingent and complex nature of environmental and sustainability-related knowledge and understanding. A special concern lies in the development of research perspectives and tools for investigating ways, in which teachers are faced with complex and various situations in the sense-making of science-related issues, and subsequent pedagogic issues. Based on an empirical examination of Korean teachers' sense-making of their curricular practice, the paper develops a narrative approach to teachers' perspectives and knowledge by considering the value of stories as sense-making tools for reflective questioning of what is worth teaching, how and why. By employing the idea of 'repertoire', the study regards teachers' stories about their environment-related personal and teaching experiences as offering angles with which to understand teachers' motivation and reflection in curricular development and implementation. Furthermore, three empirical cases present ways in which the nature of knowledge and understanding is recognised and potentially integrated into pedagogies through teachers' narratives. Finally, the paper argues for the need to reconsider the role of the science teacher in addressing environmental and sustainability-related issues, in ways that facilitate teachers' reflexive interpretation of meanings in cultural texts and the construction of pedagogic text.

Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire

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Chenchen Zhang

2018-04-01

Full Text Available The dietary pattern can influence the immune system directly, but may also modulate it indirectly by regulating the gut microbiota. Here, we investigated the effect of a 3-months lacto-ovo-vegetarian diet on the diversity of gut microbiota and the immune system in healthy omnivorous volunteers, using high-throughput sequencing technologies. The short-term vegetarian diet did not have any major effect on the diversity of the immune system and the overall composition of the metagenome. The prevalence of bacterial genera/species with known beneficial effects on the intestine, including butyrate-producers and probiotic species and the balance of autoimmune-related variable genes/families were, however, altered in the short-term vegetarians. A number of bacterial species that are associated with the expression level of IgA, a key immunoglobulin class that protects the gastrointestinal mucosal system, were also identified. Furthermore, a lower diversity of T-cell repertoire and expression level of IgE, as well as a reduced abundance of inflammation-related genes in the gut microbiota were potentially associated with a control group with long-term vegetarians. Thus, the composition and duration of the diet may have an impact on the balance of pro-/anti-inflammatory factors in the gut microbiota and immune system.

Sex Hormone Receptor Repertoire in Breast Cancer

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Gerald M. Higa

2013-01-01

Full Text Available Classification of breast cancer as endocrine sensitive, hormone dependent, or estrogen receptor (ER positive refers singularly to ERα. One of the oldest recognized tumor targets, disruption of ERα-mediated signaling, is believed to be the mechanistic mode of action for all hormonal interventions used in treating this disease. Whereas ERα is widely accepted as the single most important predictive factor (for response to endocrine therapy, the presence of the receptor in tumor cells is also of prognostic value. Even though the clinical relevance of the two other sex hormone receptors, namely, ERβ and the androgen receptor remains unclear, two discordant phenomena observed in hormone-dependent breast cancers could be causally related to ERβ-mediated effects and androgenic actions. Nonetheless, our understanding of regulatory molecules and resistance mechanisms remains incomplete, further compromising our ability to develop novel therapeutic strategies that could improve disease outcomes. This review focuses on the receptor-mediated actions of the sex hormones in breast cancer.

A theoretical interpersonal style repertoire for middle-level managers

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P. Koortzen

2005-10-01

Full Text Available The development of the interpersonal behaviour of managers has received a good deal of attention, especially in terms of the most appropriate interpersonal styles in the work context and the skills involved in developing and maintaining effective interpersonal relationships. The design of effective interpersonal development programs requires a thorough evaluation of an individual’s interpersonal development needs. In order to do this, evaluators should have an understanding of the most appropriate interpersonal styles for managers. Given the aims of the investigation, the approach that was followed was to evaluate the relevant literature in this field. The theoretical goal was to study and describe the most appropriate theoretical interpersonal style repertoire of middle-level managers using the interpersonal approach, and specifically the 1982 Interpersonal Circle. The conclusions support the notion that dominant, assured, exhibitionistic, social, friendly, warm and trusting styles are the most relevant of the 16 interpersonal segments, while the assured-dominant, social-exhibitionistic and warm-friendly octants are viewed as the most appropriate. Opsomming Die ontwikkeling van die interpersoonlike gedrag van bestuurders het reeds heelwat aandag gekry. Dit geld veral vir aangeleenthede wat verband hou met die mees toepaslike interpersoonlike style binne die werkskonteks en die vaardighede wat die ontwikkeling van effektiewe interpersoonlike verhoudings onderlê. Die ontwikkeling van effektiewe interpersoonlike ontwikkelingsprogramme vereis ’n deeglike evaluering van ’n individu se interpersoonlike ontwikkelingsbehoeftes. Om dit te vermag, is dit nodig vir evalueerders om te verstaan wat die mees toepaslike interpersoonlike style vir bestuurders is. Gegee die doelwitte van die ondersoek is die metode wat gevolg is ’n evaluering van die relevante literatuur in hierdie gebied. Die teoretiese doel was om die mees toepaslike teoretiese

Variability and repertoire size of T-cell receptor V alpha gene segments.

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Becker, D M; Pattern, P; Chien, Y; Yokota, T; Eshhar, Z; Giedlin, M; Gascoigne, N R; Goodnow, C; Wolf, R; Arai, K

The immune system of higher organisms is composed largely of two distinct cell types, B lymphocytes and T lymphocytes, each of which is independently capable of recognizing an enormous number of distinct entities through their antigen receptors; surface immunoglobulin in the case of the former, and the T-cell receptor (TCR) in the case of the latter. In both cell types, the genes encoding the antigen receptors consist of multiple gene segments which recombine during maturation to produce many possible peptides. One striking difference between B- and T-cell recognition that has not yet been resolved by the structural data is the fact that T cells generally require a major histocompatibility determinant together with an antigen whereas, in most cases, antibodies recognize antigen alone. Recently, we and others have found that a series of TCR V beta gene sequences show conservation of many of the same residues that are conserved between heavy- and light-chain immunoglobulin V regions, and these V beta sequences are predicted to have an immunoglobulin-like secondary structure. To extend these studies, we have isolated and sequenced eight additional alpha-chain complementary cDNA clones and compared them with published sequences. Analyses of these sequences, reported here, indicate that V alpha regions have many of the characteristics of V beta gene segments but differ in that they almost always occur as cross-hybridizing gene families. We conclude that there may be very different selective pressures operating on V alpha and V beta sequences and that the V alpha repertoire may be considerably larger than that of V beta.

Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors

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Wei, Junping; Yang, Xiao Yi; Lei, Gangjun; Wang, Tao; Liu, Cong-Xiao; Morse, Michael A.; Gouin, Kenneth; Knott, Simon R. V.; Hartman, Zachary C.

2018-01-01

ABSTRACT Triple-negative breast cancer (TNBC) is an aggressive and molecularly diverse breast cancer subtype typified by the presence of p53 mutations (∼80%), elevated immune gene signatures and neoantigen expression, as well as the presence of tumor infiltrating lymphocytes (TILs). As these factors are hypothesized to be strong immunologic prerequisites for the use of immune checkpoint blockade (ICB) antibodies, multiple clinical trials testing single ICBs have advanced to Phase III, with early indications of heterogeneous response rates of <20% to anti-PD1 and anti-PDL1 ICB. While promising, these modest response rates highlight the need for mechanistic studies to understand how different ICBs function, how their combination impacts functionality and efficacy, as well as what immunologic parameters predict efficacy to different ICBs regimens in TNBC. To address these issues, we tested anti-PD1 and anti-CTLA4 in multiple models of TNBC and found that their combination profoundly enhanced the efficacy of either treatment alone. We demonstrate that this efficacy is due to anti-CTLA4-driven expansion of an individually unique T-cell receptor (TCR) repertoire whose functionality is enhanced by both intratumoral Treg suppression and anti-PD1 blockade of tumor expressed PDL1. Notably, the individuality of the TCR repertoire was observed regardless of whether the tumor cells expressed a nonself antigen (ovalbumin) or if tumor-specific transgenic T-cells were transferred prior to sequencing. However, responsiveness was strongly correlated with systemic measures of tumor-specific T-cell and B-cell responses, which along with systemic assessment of TCR expansion, may serve as the most useful predictors for clinical responsiveness in future clinical trials of TNBC utilizing anti-PD1/anti-CTLA4 ICB. PMID:29721371

Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors.

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Crosby, Erika J; Wei, Junping; Yang, Xiao Yi; Lei, Gangjun; Wang, Tao; Liu, Cong-Xiao; Agarwal, Pankaj; Korman, Alan J; Morse, Michael A; Gouin, Kenneth; Knott, Simon R V; Lyerly, H Kim; Hartman, Zachary C

2018-01-01

Triple-negative breast cancer (TNBC) is an aggressive and molecularly diverse breast cancer subtype typified by the presence of p53 mutations (∼80%), elevated immune gene signatures and neoantigen expression, as well as the presence of tumor infiltrating lymphocytes (TILs). As these factors are hypothesized to be strong immunologic prerequisites for the use of immune checkpoint blockade (ICB) antibodies, multiple clinical trials testing single ICBs have advanced to Phase III, with early indications of heterogeneous response rates of <20% to anti-PD1 and anti-PDL1 ICB. While promising, these modest response rates highlight the need for mechanistic studies to understand how different ICBs function, how their combination impacts functionality and efficacy, as well as what immunologic parameters predict efficacy to different ICBs regimens in TNBC. To address these issues, we tested anti-PD1 and anti-CTLA4 in multiple models of TNBC and found that their combination profoundly enhanced the efficacy of either treatment alone. We demonstrate that this efficacy is due to anti-CTLA4-driven expansion of an individually unique T-cell receptor (TCR) repertoire whose functionality is enhanced by both intratumoral Treg suppression and anti-PD1 blockade of tumor expressed PDL1. Notably, the individuality of the TCR repertoire was observed regardless of whether the tumor cells expressed a nonself antigen (ovalbumin) or if tumor-specific transgenic T-cells were transferred prior to sequencing. However, responsiveness was strongly correlated with systemic measures of tumor-specific T-cell and B-cell responses, which along with systemic assessment of TCR expansion, may serve as the most useful predictors for clinical responsiveness in future clinical trials of TNBC utilizing anti-PD1/anti-CTLA4 ICB.

Scope and Limits of the Notion of "Repertoire of Contention" to Describe, Measure and Explain Conflictivity in XXI Century Chile

Directory of Open Access Journals (Sweden)

Nicolás Orellana Águila

2017-09-01

Full Text Available The aim of this article is to analyze the dynamics of social conflict in Chile during the period 2000-2011. We elaborate catalogues of contention actions from Clacso’s “Cronologías del Conflicto Social”, that are the basis to identify actors, actions, and adversaries. The specific objective is double: on one hand, to take to the limit the theoretical foundations in which a large part of academic interpretations of social conflict are based, evaluating their utility and possible criticisms; on the other, to evaluate whether those who mobilize respond to a heteronomous dynamics of conflict or rather are subjects with an autonomous capacity of action. With this analysis we expect to have enough elements to elaborate an outline of the repertoire of contention in Chile during this Century.

Fundamental roles of the innate-like repertoire of natural antibodies in immune homeostasis

Directory of Open Access Journals (Sweden)

Jaya eVas

2013-02-01

Full Text Available The composition of the early immune repertoire is biased with prominent expression of spontaneously arising B-cell clones that produce IgM with recurrent and often autoreactive binding specificities. Amongst these naturally-arising antibodies (NAbs are IgM antibodies that specifically recognize damaged and senescent cells, often via oxidation-associated neo-determinants. These NAbs are present from birth and can be further boosted by apoptotic cell challenge. Recent studies have shown that IgM NAb to apoptotic cells can enhance phagocytic clearance, as well as suppress pro-inflammatory responses induced via Toll-like receptors, and block pathogenic IgG-immune complex (IC-mediated inflammatory responses. Specific antibody effector functions appear to be involved, as these anti-inflammatory properties are dependent on IgM-mediated recruitment of the early recognition factors of complement. Clinical surveys have suggested that anti-AC IgM NAbs may modulate disease activity in some patients with autoimmune disease. In mechanistic studies, anti-AC NAbs were shown to act in dendritic cells by inhibition of the Mitogen Activated Protein Kinase (MAPK pathway, a primary signal transduction pathway that controls inflammatory responses. This immunomodulatory pathway has an absolute requirement for the induction of MAPK Phosphatase-1. Taken together, recent studies have elucidated the novel properties of a class of protective NAbs, which may directly blunt inflammatory responses through a primitive pathway for regulation of the innate immune system.

A diverse host thrombospondin-type-1 repeat protein repertoire promotes symbiont colonization during establishment of cnidarian-dinoflagellate symbiosis.

Science.gov (United States)

Neubauer, Emilie-Fleur; Poole, Angela Z; Neubauer, Philipp; Detournay, Olivier; Tan, Kenneth; Davy, Simon K; Weis, Virginia M

2017-05-08

The mutualistic endosymbiosis between cnidarians and dinoflagellates is mediated by complex inter-partner signaling events, where the host cnidarian innate immune system plays a crucial role in recognition and regulation of symbionts. To date, little is known about the diversity of thrombospondin-type-1 repeat (TSR) domain proteins in basal metazoans or their potential role in regulation of cnidarian-dinoflagellate mutualisms. We reveal a large and diverse repertoire of TSR proteins in seven anthozoan species, and show that in the model sea anemone Aiptasia pallida the TSR domain promotes colonization of the host by the symbiotic dinoflagellate Symbiodinium minutum . Blocking TSR domains led to decreased colonization success, while adding exogenous TSRs resulted in a 'super colonization'. Furthermore, gene expression of TSR proteins was highest at early time-points during symbiosis establishment. Our work characterizes the diversity of cnidarian TSR proteins and provides evidence that these proteins play an important role in the establishment of cnidarian-dinoflagellate symbiosis.

Stereoselective determination of unchanged and glucuroconjugated eliprodil, a new anti-ischaemic drug, in human plasma and urine by precolumn derivatization and column-switching high-performance liquid chromatography with fluorescence detection.

Science.gov (United States)

Malavasi, B; Ripamonti, M; Rouchouse, A; Ascalone, V

1996-04-05

An HPLC method was developed and validated for the determination in human plasma and urine of the enantiomers of eliprodil, (+/-)-alpha-(4-chlorophenyl)-4[(4-fluorophenyl) methyl]piperidine-1-ethanol hydrochloride, a new anti-ischaemic agent administered as a racemate. Both enantiomers are present in human plasma in unchanged and glucuroconjugated form, whereas only the glucuroconjugated form is excreted into urine; as a consequence, such metabolites in human plasma and urine should be submitted to enzymatic deconjugation with beta-glucuronidase (Escherichia coli) before being extracted. The general method involves a liquid-liquid extraction of eliprodil and internal standard from alkalinized plasma or urine with n-hexane, evaporation of the organic phase and derivatization with (S)-(+)-naphthylethyl isocyanate to give carbamate diastereoisomeric derivatives of (S)-(+)- and (R)-(-)-eliprodil and internal standard; after evaporation of the derivatizing mixture and dissolution of the residue in a small volume of phosphate buffer-acetonitrile (60:40, v/v), an aliquot is injected into a column-switching HPLC system. The derivatized sample extract is purified on a precolumn filled with C8-bonded silica material, which is flushed with acetonitrile-water, then diastereoisomers of eliprodil and the internal standard are automatically transferred by the mobile phase to the analytical column. The analytical column is a C8 type, specially deactivated for basic compounds, the mobile phase is 0.025 M phosphate buffer (pH 2.6)-methanol-acetonitrile (42:2:56) at a flow-rate of 1.2 ml min-1 and fluorimetric detector operating at lambda ex = 275 nm and lambda em = 336 nm is used. The retention times, under these conditions, are about 16 and 17 min for (S)-(+)- and (R)-(-)-eliprodil diastereoisomers, respectively, and about 19 min for the first-eluted diastereoisomer of the internal standard. During the analysis time, the precolumn, reset in a different path from that of the

Cell-specific CO2 fixation rates of two distinct groups of plastidic protists in the Atlantic Ocean remain unchanged after nutrient addition.

Science.gov (United States)

Grob, Carolina; Jardillier, Ludwig; Hartmann, Manuela; Ostrowski, Martin; Zubkov, Mikhail V; Scanlan, David J

2015-04-01

To assess the role of open-ocean ecosystems in global CO2 fixation, we investigated how picophytoplankton, which dominate primary production, responded to episodic increases in nutrient availability. Previous experiments have shown nitrogen alone, or in combination with phosphorus or iron, to be the proximate limiting nutrient(s) for total phytoplankton grown over several days. Much less is known about how nutrient upshift affects picophytoplankton CO2 fixation over the duration of the light period. To address this issue, we performed a series of small volume (8-60 ml) - short term (10-11 h) nutrient addition experiments in different regions of the Atlantic Ocean using NH4 Cl, FeCl3 , K medium, dust and nutrient-rich water from 300 m depth. We found no significant nutrient stimulation of group-specific CO2 fixation rates of two taxonomically and size-distinct groups of plastidic protists. The above was true regardless of the region sampled or nutrient added, suggesting that this is a generic phenomenon. Our findings show that at least in the short term (i.e. daylight period), nutrient availability does not limit CO2 fixation by the smallest plastidic protists, while their taxonomic composition does not determine their response to nutrient addition. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Unchanged content of oxidative enzymes in fast-twitch muscle fibers and V˙O2 kinetics after intensified training in trained cyclists

DEFF Research Database (Denmark)

Christensen, Peter Møller; Gunnarsson, Thomas Gunnar Petursson; Thomassen, Martin

2015-01-01

perturbation during INT. Pulmonary V˙O2 kinetics was determined in eight trained male cyclists (V˙O2-max: 59 ± 4 (means ± SD) mL min(-1) kg(-1)) during MOD (205 ± 12 W ~65% V˙O2-max) and INT (286 ± 17 W ~85% V˙O2-max) exercise before and after a 7-week HIT period (30-sec sprints and 4-min intervals) with a 50...... DW(-1) min(-1)) of CS (56 ± 8 post-HIT vs. 59 ± 10 pre-HIT), HAD (27 ± 6 vs. 29 ± 3) and PFK (340 ± 69 vs. 318 ± 105) and the capillary to fiber ratio (2.30 ± 0.16 vs. 2.38 ± 0.20) was unaltered following HIT. V˙O2 kinetics was unchanged with HIT and the speed of the primary response did not differ...... of oxidative enzymes in fast-twitch fibers, and did not change V˙O2 kinetics....

ALBUM SUARA (REPERTOIRE KATAK SERASAH Leptobrachium hasseltii TSCHUDI, 1883 DI SITU GUNUNG

Directory of Open Access Journals (Sweden)

Sasi Kirono

2016-07-01

Full Text Available This study describes the vocal repertoire of forest litter frog Leptobrachium hasseltii from Situgunung Resort, Mount Gede Pangrango National Park. Two types of calls were identified: advertisement call and aggressive call. Each types were represented by two different characteristics thus four types of calls were examined. The kruskall and wallis test was used to test the difference of nine features. Pearson’s correlation test also used to determine the relationship of all call features to air temperature and body size. Dominant frequency of all call types was relatively similar. Advertisement calls type I was emitted in short duration and fewer notes than advertisement call type II. Aggressive call type I and have longer call duration compared to both of advertisement call. However the introductory note of aggressive call type II was more longer than the others. Aggressive call of L. hasseltii tended to be discrete (territorial and encounter and represented two different continuums. This were caused by the extreme differences of both calls in duration and distance between males when emitting calls. Dominan frequencies of all call types inverse correlated with body size of frogs. Most of temporal features of advertisement call type II correlated with body size and only call duration were longer with increasingly air temperature. Interpulse-interval and pulse period were more longer by increasing the body size, while the introductory note, pulse rate and pulse repetition rate were becoming shortened and it could predict male body size to facilitated competition between males, thus serves as mate selection indicator. Key words: advertisement call, agressif call, Leptobrachium hasseltii, Situgunung resort, social interaction

Directory of Factual and Numeric Databases of Relevance to Aerospace and Defence R and D (Repertoire de Bases de donnees Factuelles ou Numeriques d’interet pour la R and D).

Science.gov (United States)

1992-07-01

Madrid Faculty of Science Institute of Materials Sciences (Instituto de Ciencia de Materiales Facultad de Ciencias, Universidad Autonoma de Madrid) ADDRESS...OF ORGANIZATION: Construcciones Aeronauticas SA CASA ADDRESS/POINT OF CONTACT: Attention: J. Pascual Laboratory Aeropuerto de San Pablo 41007 Sevilla...Factual and Numeric Databases of Relevance to Aerospace and Defence R & D (Repertoire de Bases de donnees Factuelles ou Num~riques d’inte’re^t pour

Variation in singing style use in the reed bunting Emberiza schoeniclus: influencing factors and possible functions

OpenAIRE

Brunner, P; Pasinelli, G

2010-01-01

The two main functions of bird song are territory defence and mate attraction. Considerable progress has been made in understanding how species adjust the use of songs to serve these and other (presumed) functions of bird song, but the striking variety of singing behavior observable in wild birds remains enigmatic. Some species make do with simple songs and small repertoires, while others show large, complex repertoires and still others have evolved several distinct singing styles. In most sp...

Fish remains and humankind: part two

Directory of Open Access Journals (Sweden)

Andrew K G Jones

1998-07-01

Full Text Available The significance of aquatic resources to past human groups is not adequately reflected in the published literature - a deficiency which is gradually being acknowledged by the archaeological community world-wide. The publication of the following three papers goes some way to redress this problem. Originally presented at an International Council of Archaeozoology (ICAZ Fish Remains Working Group meeting in York, U.K. in 1987, these papers offer clear evidence of the range of interest in ancient fish remains across the world. Further papers from the York meeting were published in Internet Archaeology 3 in 1997.

The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires.

Science.gov (United States)

Bergmann, Tobias; Moore, Carrie; Sidney, John; Miller, Donald; Tallmadge, Rebecca; Harman, Rebecca M; Oseroff, Carla; Wriston, Amanda; Shabanowitz, Jeffrey; Hunt, Donald F; Osterrieder, Nikolaus; Peters, Bjoern; Antczak, Douglas F; Sette, Alessandro

2015-11-01

Here we describe a detailed quantitative peptide-binding motif for the common equine leukocyte antigen (ELA) class I allele Eqca-1*00101, present in roughly 25 % of Thoroughbred horses. We determined a preliminary binding motif by sequencing endogenously bound ligands. Subsequently, a positional scanning combinatorial library (PSCL) was used to further characterize binding specificity and derive a quantitative motif involving aspartic acid in position 2 and hydrophobic residues at the C-terminus. Using this motif, we selected and tested 9- and 10-mer peptides derived from the equine herpesvirus type 1 (EHV-1) proteome for their capacity to bind Eqca-1*00101. PSCL predictions were very efficient, with an receiver operating characteristic (ROC) curve performance of 0.877, and 87 peptides derived from 40 different EHV-1 proteins were identified with affinities of 500 nM or higher. Quantitative analysis revealed that Eqca-1*00101 has a narrow peptide-binding repertoire, in comparison to those of most human, non-human primate, and mouse class I alleles. Peripheral blood mononuclear cells from six EHV-1-infected, or vaccinated but uninfected, Eqca-1*00101-positive horses were used in IFN-γ enzyme-linked immunospot (ELISPOT) assays. When we screened the 87 Eqca-1*00101-binding peptides for T cell reactivity, only one Eqca-1*00101 epitope, derived from the intermediate-early protein ICP4, was identified. Thus, despite its common occurrence in several horse breeds, Eqca-1*00101 is associated with a narrow binding repertoire and a similarly narrow T cell response to an important equine viral pathogen. Intriguingly, these features are shared with other human and macaque major histocompatibility complex (MHC) molecules with a similar specificity for D in position 2 or 3 in their main anchor motif.

Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Starting with a system's relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy.

Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells.

Directory of Open Access Journals (Sweden)

Jolene Atia

2016-04-01

Full Text Available Uterine smooth muscle cells remain quiescent throughout most of gestation, only generating spontaneous action potentials immediately prior to, and during, labor. This study presents a method that combines transcriptomics with biophysical recordings to characterise the conductance repertoire of these cells, the 'conductance repertoire' being the total complement of ion channels and transporters expressed by an electrically active cell. Transcriptomic analysis provides a set of potential electrogenic entities, of which the conductance repertoire is a subset. Each entity within the conductance repertoire was modeled independently and its gating parameter values were fixed using the available biophysical data. The only remaining free parameters were the surface densities for each entity. We characterise the space of combinations of surface densities (density vectors consistent with experimentally observed membrane potential and calcium waveforms. This yields insights on the functional redundancy of the system as well as its behavioral versatility. Our approach couples high-throughput transcriptomic data with physiological behaviors in health and disease, and provides a formal method to link genotype to phenotype in excitable systems. We accurately predict current densities and chart functional redundancy. For example, we find that to evoke the observed voltage waveform, the BK channel is functionally redundant whereas hERG is essential. Furthermore, our analysis suggests that activation of calcium-activated chloride conductances by intracellular calcium release is the key factor underlying spontaneous depolarisations.

The penalty points system in Ireland - Does it remain effective 14 years on?

Science.gov (United States)

Downey, C; Donnelly, M

2017-05-23

Road traffic accidents (RTAs) are the leading cause of trauma related mortality in Ireland. The penalty points system (PPS) was introduced in Ireland in 2002 to incentivise safer driving and reduce injury. Its early effect was studied previously 1 which concluded that there was a slight reduction in RTA related femoral shaft fractures (a sensitive indicator of high energy trauma) and a dramatic reduction in RTA related discharges. We hypothesized that over the following 14 years, the penalty points system might lose its effectiveness. Data was again collected from the same HIPE departments from six Dublin teaching hospitals and also University Hospital Waterford (to represent both an urban and a more rural population cohort respectively) examining RTA related femoral shaft fractures over an identical 6 month period (October-April). RTA related discharge data over an identical 6 month period was again acquired and analysed from Beaumont Hospital, Dublin (identical data source to previous study). These results were compared with the identical 6 month period in 2001/02 & 2002/03 (October-April). The total number of RTA related femoral shaft fracture discharges in Dublin decreased from 16 post introduction of PPS in the 2002/03 6-month period to 7 in 2015/16 6-month period. The number remained the same in the Waterford region (n = 5). The total RTA related discharges in Beaumont Hospital, Dublin decreased from 70 post PPS introduction to 57 in the 2015/16 6-month period. This represents an incidence rate of 4.5/1000 discharges (vs 6.9 post introduction) which was a statistically significant reduction (p = 0.014). The mean length of stay for these patients reduced from 13 to 7.7 days. There were consistent reductions in head injury (major & minor), lower limb fracture and facial fracture since the introduction of the PPS. The upper limb, pelvic/acetabular and thoracic injuries remained largely unchanged. Whilst RTA related spinal and abdominal injuries decreased

Temporal mode selectivity by frequency conversion in second-order nonlinear optical waveguides: Erratum

DEFF Research Database (Denmark)

Reddy, Dileep V.; Raymer, M. G.; Mckinstrie, C. J.

2017-01-01

We correct typographical errors in four equations showing the integral forms of the equations of motion and the corresponding perturbative approximation. Subsequently presented derivations, results, and conclusions remain unchanged.......We correct typographical errors in four equations showing the integral forms of the equations of motion and the corresponding perturbative approximation. Subsequently presented derivations, results, and conclusions remain unchanged....

U.S. Navy Ships Food Service Divisions: Modernizing Inventory Management

Science.gov (United States)

2010-06-01

management procedures for receipt, inventory, stowage, and issue of provisions onboard ships have remained relatively unchanged for decades. Culinary ...improve the quality of life for Culinary Specialists 15. NUMBER OF PAGES 87 14. SUBJECT TERMS Inventory management , records keeper, stores onload...remained relatively unchanged for decades. Culinary Specialists are utilizing an antiquated and unreliable inventory management program (the Food

Phenotypic deconstruction of gene circuitry.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2013-06-01

It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

Phenotypic deconstruction of gene circuitry

Science.gov (United States)

Lomnitz, Jason G.; Savageau, Michael A.

2013-06-01

It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

Radiation therapy for age-related macular degeneration

Energy Technology Data Exchange (ETDEWEB)

Takagi, Chikako; Mori, Hideo; Akuta, Keizou [Otsu Red Cross Hospital, Shiga (Japan); Yoshimura, Nagahisa

1998-04-01

We evaluated the effect of low-dose radiation on age-related macular degeneration in 8 affected eyes. Radiation was applied using photons at 4 MV. Each eye received 10 fractions of 2 Gy per day over 2 weeks. At 6 months after treatment, funduscopic or angiographic findings had either improved or remained unchanged in all the eyes. The visual acuity improved by 2 lines or more in 2 eyes (25%), remained unchanged in 5 eyes (63%) and deteriorated in 1 eye (13%). At the last examination, fundus findings had improved in 2 eyes (25%), remained unchanged in 1 eye (13%) and deteriorated in 5 eyes (63%). The visual acuity had improved or unchanged in 2 eyes each (25%) and deteriorated in 4 eyes (50%). There has been no negative side effects of radiation. Above findings show that low-dose radiation is potentially beneficial for subfoveal or juxtafoveal choroidal neovascularizations in age-related macular degeneration on a short term basis. (author)

Average sperm count remains unchanged despite reduction in maternal smoking: results from a large cross-sectional study with annual investigations over 21 years.

Science.gov (United States)

Priskorn, L; Nordkap, L; Bang, A K; Krause, M; Holmboe, S A; Egeberg Palme, D L; Winge, S B; Mørup, N; Carlsen, E; Joensen, U N; Blomberg Jensen, M; Main, K M; Juul, A; Skakkebaek, N E; Jensen, T K; Jørgensen, N

2018-06-01

How are temporal trends in lifestyle factors, including exposure to maternal smoking in utero, associated to semen quality in young men from the general population? Exposure to maternal smoking was associated with lower sperm counts but no overall increase in sperm counts was observed during the study period despite a decrease in this exposure. Meta-analyses suggest a continuous decline in semen quality but few studies have investigated temporal trends in unselected populations recruited and analysed with the same protocol over a long period and none have studied simultaneous trends in lifestyle factors. Cross-sectional population-based study including ~300 participants per year (total number = 6386) between 1996 and 2016. The study is based on men from the Greater Copenhagen area, Denmark, with a median age of 19 years, and unselected with regard to fertility status and semen quality. The men delivered a semen sample, had a blood sample drawn and a physical examination performed and answered a comprehensive questionnaire, including information on lifestyle and the mother's pregnancy. Temporal trends in semen quality and lifestyle were illustrated graphically, and trends in semen parameters and the impact of prenatal and current lifestyle factors were explored in multiple regression analyses. Throughout the study period, 35% of the men had low semen quality. Overall, there were no persistent temporal trends in semen quality, testicular volume or levels of follicle-stimulating hormone over the 21 years studied. The men's alcohol intake was lowest between 2011 and 2016, whereas BMI, use of medication and smoking showed no clear temporal trends. Parental age increased, and exposure in utero to maternal smoking declined from 40% among men investigated in 1996-2000 to 18% among men investigated in 2011-2016. Exposure to maternal smoking was associated with lower sperm counts but no overall increase in sperm counts was observed despite the decrease in this exposure. Information of current and prenatal lifestyle was obtained by self-report, and the men delivered only one semen sample each. The significant decline in in utero exposure to maternal smoking, which was not reflected in an overall improvement of semen quality at the population level, suggest that other unknown adverse factors may maintain the low semen quality among Danish men. The study has received financial support from the ReproUnion; the Research fund of Rigshospitalet, Copenhagen University Hospital; the European Union (Contract numbers BMH4-CT96-0314,QLK4-CT-1999-01422, QLK4-CT-2002-00603, FP7/2007-2013, DEER Grant agreement no. 212844); the Danish Ministry of Health; the Danish Environmental Protection Agency; A.P. Møller and wife Chastine McKinney Møllers foundation; and Svend Andersens Foundation. None of the funders had any role in the study design, collection, analysis or interpretation of data, writing of the paper or publication decisions. N/A.

Longitudinal multiparameter single-cell analysis of macaques immunized with pneumococcal protein-conjugated or unconjugated polysaccharide vaccines reveals distinct antigen specific memory B cell repertoires.

Directory of Open Access Journals (Sweden)

Bin Jia

Full Text Available The efficacy of protein-conjugated pneumococcal polysaccharide vaccines has been well characterized for children. The level of protection conferred by unconjugated polysaccharide vaccines remains less clear, particularly for elderly individuals who have had prior antigenic experience through immunization with unconjugated polysaccharide vaccines or natural exposure to Streptococcus pneumoniae.We compared the magnitude, diversity and genetic biases of antigen-specific memory B cells in two groups of adult cynomolgus macaques that were immunized with a 7-valent conjugated vaccine and boosted after five years with either a 13-valent pneumococcal polysaccharide conjugate vaccine (13vPnC or a 23-valent unconjugated pneumococcal polysaccharide vaccine (23vPS using microengraving (a single-cell analysis method and single-cell RT-PCR.Seven days after boosting, the mean frequency of antigen-specific memory B cells was significantly increased in macaques vaccinated with 13vPnC compared to those receiving 23vPS. The 13vPnC-vaccinated macaques also exhibited a more even distribution of antibody specificities to four polysaccharides in the vaccine (PS4, 6B, 14, 23F that were examined. However, single-cell analysis of the antibody variable region sequences from antigen-specific B cells elicited by unconjugated and conjugated vaccines indicated that both the germline gene segments forming the heavy chains and the average lengths of the Complementary Determining Region 3 (CDR3 were similar.Our results confirm that distinctive differences can manifest between antigen-specific memory B cell repertoires in nonhuman primates immunized with conjugated and unconjugated pneumococcal polysaccharide vaccines. The study also supports the notion that the conjugated vaccines have a favorable profile in terms of both the frequency and breadth of the anamnestic response among antigen-specific memory B cells.

Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2015-01-01

Background: The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. Methods: The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Results: Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Conclusions: Starting with a system’s relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy. PMID:26998346

Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

Directory of Open Access Journals (Sweden)

Phillips Ruth B

2010-10-01

Full Text Available Abstract Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon

Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

Science.gov (United States)

2010-01-01

Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves

Sonographic evolution of hepatocellular carcinoma associated with cirrhosis

International Nuclear Information System (INIS)

Mazzola, G.; Virdone, R.; Orlando, A.; Turri, A.; Caltagirone, M.; Fusco, G.; Parisi, P.; Cottone, M.

1989-01-01

To study the sonographic (US) evolution of hepatocellular carcinoma, 53 tumors in 45 untreated patients were observed regulary with real-time US for a period of 6 to 56 months. At the beginning, 25 tumors were hypoechoic, 18 isoechoic, 4 hyperechoic, and 6 had mixed hypo/hyper echopatterns. At the follow-up, 7 initially hypoechoic tumors had changed to hyperechoic or to mixed echopatterns; 8 hypoechoic tumors had becom isoechoic; 9 of the 25 initially hypoechoic neoplastic lesions had maintained the same echodensity. Ten of the 15 initially isoechoic tumors had changed to mixed echopatterns and 5 had remained unchanged. Three initially isoechoic lesions and a hypoechoic one had turned into diffuse patterns; 2 initially hyperechoic neoplastic lesions had remained unchanged; 1 had switched into hypoechoic, and 1 changed to mixed echopattern; 4 out of 6 tumors with echopattern had remained unchanged, 1 had become hyperechoic and 1 hypoechoic. The current study has proven variou tumors ≤3 cm in diameter to be isoechoic and most tumors >3 in diameter to have mixed hypo/hyper echopatterns. The echogenicity of small hepatocellular carcinomas increases with the tumor growth and remains unchanged when they do not increase in size

Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human.

Science.gov (United States)

Linguiti, Giovanna; Antonacci, Rachele; Tasco, Gianluca; Grande, Francesco; Casadio, Rita; Massari, Serafina; Castelli, Vito; Consiglio, Arianna; Lefranc, Marie-Paule; Ciccarese, Salvatrice

2016-08-15

The bottlenose dolphin (Tursiops truncatus) is a mammal that belongs to the Cetartiodactyla and have lived in marine ecosystems for nearly 60 millions years. Despite its popularity, our knowledge about its adaptive immunity and evolution is very limited. Furthermore, nothing is known about the genomics and evolution of dolphin antigen receptor immunity. Here we report a evolutionary and expression study of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) genes. We have identified in silico the TRG and TRA/TRD genes and analyzed the relevant mature transcripts in blood and in skin from four subjects. The dolphin TRG locus is the smallest and simplest of all mammalian loci as yet studied. It shows a genomic organization comprising two variable (V1 and V2), three joining (J1, J2 and J3) and a single constant (C), genes. Despite the fragmented nature of the genome assemblies, we deduced the TRA/TRD locus organization, with the recent TRDV1 subgroup genes duplications, as it is expected in artiodactyls. Expression analysis from blood of a subject allowed us to assign unambiguously eight TRAV genes to those annotated in the genomic sequence and to twelve new genes, belonging to five different subgroups. All transcripts were productive and no relevant biases towards TRAV-J rearrangements are observed. Blood and skin from four unrelated subjects expression data provide evidence for an unusual ratio of productive/unproductive transcripts which arise from the TRG V-J gene rearrangement and for a "public" gamma delta TR repertoire. The productive cDNA sequences, shared both in the same and in different individuals, include biases of the TRGV1 and TRGJ2 genes. The high frequency of TRGV1-J2/TRDV1- D1-J4 productive rearrangements in dolphins may represent an interesting oligo-clonal population comparable to that found in human with the TRGV9- JP/TRDV2-D-J T cells and in primates. Although the features of the TRG and TRA/TRD loci organization reflect

Construction of naïve camelids VHH repertoire in phage display-based library.

Science.gov (United States)

Sabir, Jamal S M; Atef, Ahmed; El-Domyati, Fotouh M; Edris, Sherif; Hajrah, Nahid; Alzohairy, Ahmed M; Bahieldin, Ahmed

2014-04-01

Camelids have unique antibodies, namely HCAbs (VHH) or commercially named Nanobodies(®) (Nb) that are composed only of a heavy-chain homodimer. As libraries based on immunized camelids are time-consuming, costly and likely redundant for certain antigens, we describe the construction of a naïve camelid VHHs library from blood serum of non-immunized camelids with affinity in the subnanomolar range and suitable for standard immune applications. This approach is rapid and recovers VHH repertoire with the advantages of being more diverse, non-specific and devoid of subpopulations of specific antibodies, which allows the identification of binders for any potential antigen (or pathogen). RNAs from a number of camelids from Saudi Arabia were isolated and cDNAs of the diverse vhh gene were amplified; the resulting amplicons were cloned in the phage display pSEX81 vector. The size of the library was found to be within the required range (10(7)) suitable for subsequent applications in disease diagnosis and treatment. Two hundred clones were randomly selected and the inserted gene library was either estimated for redundancy or sequenced and aligned to the reference camelid vhh gene (acc. No. ADE99145). Results indicated complete non-specificity of this small library in which no single event of redundancy was detected. These results indicate the efficacy of following this approach in order to yield a large and diverse enough gene library to secure the presence of the required version encoding the required antibodies for any target antigen. This work is a first step towards the construction of phage display-based biosensors useful in disease (e.g., TB or tuberculosis) diagnosis and treatment. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov.

Directory of Open Access Journals (Sweden)

Awa Diop

2016-10-01

Full Text Available Background: Microbial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome. Methods: By using three media containing high salt concentration (100, 150, and 200 g/L, the halophilic microbial culturome of a commercial table salt was determined. Results: Eighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp. nov., type strain Awa-1T (=CSUR P1441=DSM 29726, is a moderately halophilic gram-positive, non-spore-forming rod, and is motile by using a flagellum. Strain Awa-1T shows catalase activity but no oxidase activity. It is not only an aerobic bacterium but also able to grow in anaerobic and microaerophilic atmospheres. The draft genome of G. massiliensis is 4,207,226 bp long, composed of 13 scaffolds with 36.05% of G+C content. It contains 3,908 genes (3,839 protein-coding and 69 RNA genes. At least 1,983 (52% orthologous proteins were not shared with the closest phylogenetic species. Hundred twenty-six genes (3.3% were identified as ORFans. Conclusions: Microbial culturomics can dramatically improve the characterization of the food and environmental microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in environment, health, and disease.

Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov.

Science.gov (United States)

Diop, Awa; Khelaifia, Saber; Armstrong, Nicholas; Labas, Noémie; Fournier, Pierre-Edouard; Raoult, Didier; Million, Matthieu

2016-01-01

Microbial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome. By using three media containing high salt concentration (100, 150, and 200 g/L), the halophilic microbial culturome of a commercial table salt was determined. Eighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp. nov., type strain Awa-1 T (=CSUR P1441=DSM 29726), is a moderately halophilic gram-positive, non-spore-forming rod, and is motile by using a flagellum. Strain Awa-1 T shows catalase activity but no oxidase activity. It is not only an aerobic bacterium but also able to grow in anaerobic and microaerophilic atmospheres. The draft genome of G. massiliensis is 4,207,226 bp long, composed of 13 scaffolds with 36.05% of G+C content. It contains 3,908 genes (3,839 protein-coding and 69 RNA genes). At least 1,983 (52%) orthologous proteins were not shared with the closest phylogenetic species. Hundred twenty-six genes (3.3%) were identified as ORFans. Microbial culturomics can dramatically improve the characterization of the food and environmental microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in environment, health, and disease.

Kadav Moun PSA (:60) (Human Remains)

Centers for Disease Control (CDC) Podcasts

2010-02-18

This is an important public health announcement about safety precautions for those handling human remains. Language: Haitian Creole.  Created: 2/18/2010 by Centers for Disease Control and Prevention (CDC).   Date Released: 2/18/2010.

Underlying mechanisms leading to El Niño-to-La Niña transition are unchanged under global warming

Science.gov (United States)

Yun, Kyung-Sook; Yeh, Sang-Wook; Ha, Kyung-Ja

2018-05-01

El Niño's transitions play critical roles in modulating severe weather and climate events. Therefore, understanding the dynamic factors leading to El Niño's transitions and its future projection is a great challenge in predicting the diverse socioeconomic influences of El Niño over the globe. This study focuses on two dynamic factors controlling the El Niño-to-La Niña transition from the present climate and to future climate, using the observation, the historical and the RCP8.5 simulations of Coupled Model Intercomparison phase 5 climate models. The first is the inter-basin coupling between the Indian Ocean and the western North Pacific through the subtropical high variability. The second is the enhanced sensitivity between sea surface temperature and a deep tropical convection in the central tropical Pacific during the El Niño's developing phase. We show that the dynamic factors leading to El Niño-to-La Niña transition in the present climate are unchanged in spite of the increase of greenhouse gas concentrations. We argue that the two dynamic factors are strongly constrained by the climatological precipitation distribution over the central tropical Pacific and western North Pacific as little changed from the present climate to future climate. This implies that two dynamical processes leading to El Niño-to-La Niña transitions in the present climate will also play a robust role in global warming.

The Annuity Puzzle Remains a Puzzle

NARCIS (Netherlands)

Peijnenburg, J.M.J.; Werker, Bas; Nijman, Theo

We examine incomplete annuity menus and background risk as possible drivers of divergence from full annuitization. Contrary to what is often suggested in the literature, we find that full annuitization remains optimal if saving is possible after retirement. This holds irrespective of whether real or

Juveniles' Motivations for Remaining in Prostitution

Science.gov (United States)

Hwang, Shu-Ling; Bedford, Olwen

2004-01-01

Qualitative data from in-depth interviews were collected in 1990-1991, 1992, and 2000 with 49 prostituted juveniles remanded to two rehabilitation centers in Taiwan. These data are analyzed to explore Taiwanese prostituted juveniles' feelings about themselves and their work, their motivations for remaining in prostitution, and their difficulties…

The Changing Role of Salespeople and the Unchanging Feeling toward Selling: Implications for the HEI Programs

Science.gov (United States)

Ballestra, Luca Vincenzo; Cardinali, Silvio; Palanga, Paola; Pacelli, Graziella

2017-01-01

Over the past five decades, several studies have shown that students' reticence toward choosing a sales career has remained constant. Their lack of awareness and misconceptions regarding a sales job are two reasons behind this negative perception and lack of students' "work readiness." Using a conceptual model on student intention to…

Determination of the substrate repertoire of ADAMTS2, 3, and 14 significantly broadens their functions and identifies extracellular matrix organization and TGF-β signaling as primary targets.

Science.gov (United States)

Bekhouche, Mourad; Leduc, Cedric; Dupont, Laura; Janssen, Lauriane; Delolme, Frederic; Vadon-Le Goff, Sandrine; Smargiasso, Nicolas; Baiwir, Dominique; Mazzucchelli, Gabriel; Zanella-Cleon, Isabelle; Dubail, Johanne; De Pauw, Edwin; Nusgens, Betty; Hulmes, David J S; Moali, Catherine; Colige, Alain

2016-05-01

A disintegrin and metalloproteinase with thrombospondin type I motif (ADAMTS)2, 3, and 14 are collectively named procollagen N-proteinases (pNPs) because of their specific ability to cleave the aminopropeptide of fibrillar procollagens. Several reports also indicate that they could be involved in other biological processes, such as blood coagulation, development, and male fertility, but the potential substrates associated with these activities remain unknown. Using the recently described N-terminal amine isotopic labeling of substrate approach, we analyzed the secretomes of human fibroblasts and identified 8, 17, and 22 candidate substrates for ADAMTS2, 3, and 14, respectively. Among these newly identified substrates, many are components of the extracellular matrix and/or proteins related to cell signaling such as latent TGF-β binding protein 1, TGF-β RIII, and dickkopf-related protein 3. Candidate substrates for the 3 ADAMTS have been biochemically validated in different contexts, and the implication of ADAMTS2 in the control of TGF-β activity has been further demonstrated in human fibroblasts. Finally, the cleavage site specificity was assessed showing a clear and unique preference for nonpolar or slightly hydrophobic amino acids. This work shows that the activities of the pNPs extend far beyond the classically reported processing of the aminopropeptide of fibrillar collagens and that they should now be considered as multilevel regulators of matrix deposition and remodeling.-Bekhouche, M., Leduc, C., Dupont, L., Janssen, L., Delolme, F., Vadon-Le Goff, S., Smargiasso, N., Baiwir, D., Mazzucchelli, G., Zanella-Cleon, I., Dubail, J., De Pauw, E., Nusgens, B., Hulmes, D. J. S., Moali, C., Colige, A. Determination of the substrate repertoire of ADAMTS2, 3, and 14 significantly broadens their functions and identifies extracellular matrix organization and TGF-β signaling as primary targets. © FASEB.

Gel-based and gel-free search for plasma membrane proteins in chickpea (Cicer arietinum L.) augments the comprehensive data sets of membrane protein repertoire.

Science.gov (United States)

Barua, Pragya; Subba, Pratigya; Lande, Nilesh Vikram; Mangalaparthi, Kiran K; Prasad, T S Keshava; Chakraborty, Subhra; Chakraborty, Niranjan

2016-06-30

Plasma membrane (PM) encompasses total cellular contents, serving as semi-porous barrier to cell exterior. This living barrier regulates all cellular exchanges in a spatio-temporal fashion. Most of the essential tasks of PMs including molecular transport, cell-cell interaction and signal transduction are carried out by their proteinaceous components, which make the PM protein repertoire to be diverse and dynamic. Here, we report the systematic analysis of PM proteome of a food legume, chickpea and develop a PM proteome reference map. Proteins were extracted from highly enriched PM fraction of four-week-old seedlings using aqueous two-phase partitioning. To address a population of PM proteins that is as comprehensive as possible, both gel-based and gel-free approaches were employed, which led to the identification of a set of 2732 non-redundant proteins. These included both integral proteins having bilayer spanning domains as well as peripheral proteins associated with PMs through posttranslational modifications or protein-protein interactions. Further, the proteins were subjected to various in-silico analyses and functionally classified based on their gene ontology. Finally an inventory of the complete set of PM proteins, identified in several monocot and dicot species, was created for comparative study with the generated PM protein dataset of chickpea. Chickpea, a rich source of dietary proteins, is the second most cultivated legume, which is grown over 10 million hectares of land worldwide. The annual global production of chickpea hovers around 8.5 million metric tons. Recent chickpea genome sequencing effort has provided a broad genetic basis for highlighting the important traits that may fortify other crop legumes. Improvement in chickpea varieties can further strengthen the world food security, which includes food availability, access and utilization. It is known that the phenotypic trait of a cultivar is the manifestation of the orchestrated functions of its

Genomic and transcriptomic insights into the cytochrome P450 monooxygenase gene repertoire in the rice pest brown planthopper, Nilaparvata lugens.

Science.gov (United States)

Lao, Shu-Hua; Huang, Xiao-Hui; Huang, Hai-Jian; Liu, Cheng-Wen; Zhang, Chuan-Xi; Bao, Yan-Yuan

2015-11-01

The cytochrome P450 monooxygenase (P450) gene family is one of the most abundant eukaryotic gene families that encode detoxification enzymes. In this study, we identified an abundance of P450 gene repertoire through genome- and transcriptome-wide analysis in the brown planthopper (Nilaparvata lugens), the most destructive rice pest in Asia. Detailed gene information including the exon-intron organization, size, transcription orientation and distribution in the genome revealed that many P450 loci were closely situated on the same scaffold, indicating frequent occurrence of gene duplications. Insecticide-response expression profiling revealed that imidacloprid significantly increased NlCYP6CS1v2, NLCYP4CE1v2, NlCYP4DE1, NlCYP417A1v2 and NlCYP439A1 expression; while triazophos and deltamethrin notably enhanced NlCYP303A1 expression. Expression analysis at the developmental stage showed the egg-, nymph-, male- and female-specific expression patterns of N. lugens P450 genes. These novel findings will be helpful for clarifying the P450 functions in physiological processes including development, reproduction and insecticide resistance in this insect species. Copyright © 2015 Elsevier Inc. All rights reserved.

Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera

Science.gov (United States)

Karpe, Snehal D.; Jain, Rikesh; Brockmann, Axel; Sowdhamini, Ramanathan

2016-01-01

Abstract We developed a computational pipeline for homology based identification of the complete repertoire of olfactory receptor (OR) genes in the Asian honey bee species, Apis florea. Apis florea is phylogenetically the most basal honey bee species and also the most distant sister species to the Western honey bee Apis mellifera, for which all OR genes had been identified before. Using our pipeline, we identified 180 OR genes in A. florea, which is very similar to the number of ORs identified in A. mellifera (177 ORs). Many characteristics of the ORs including gene structure, synteny of tandemly repeated ORs and basic phylogenetic clustering are highly conserved. The composite phylogenetic tree of A. florea and A. mellifera ORs could be divided into 21 clades which are in harmony with the existing Hymenopteran tree. However, we found a few nonorthologous OR relationships between both species as well as independent pseudogenization of ORs suggesting separate evolutionary changes. Particularly, a subgroup of the OR gene clade XI, which had been hypothesized to code cuticular hydrocarbon receptors showed a high number of species-specific ORs. RNAseq analysis detected a total number of 145 OR transcripts in male and 162 in female antennae. Most of the OR genes were highly expressed on the female antennae. However, we detected five distinct male-biased OR genes, out of which three genes (AfOr11, AfOr18, AfOr170P) were shown to be male-biased in A. mellifera, too, thus corroborating a behavioral function in sex-pheromone communication. PMID:27540087

Strategies for the structural analysis of multi-protein complexes: lessons from the 3D-Repertoire project.

Science.gov (United States)

Collinet, B; Friberg, A; Brooks, M A; van den Elzen, T; Henriot, V; Dziembowski, A; Graille, M; Durand, D; Leulliot, N; Saint André, C; Lazar, N; Sattler, M; Séraphin, B; van Tilbeurgh, H

2011-08-01

Structural studies of multi-protein complexes, whether by X-ray diffraction, scattering, NMR spectroscopy or electron microscopy, require stringent quality control of the component samples. The inability to produce 'keystone' subunits in a soluble and correctly folded form is a serious impediment to the reconstitution of the complexes. Co-expression of the components offers a valuable alternative to the expression of single proteins as a route to obtain sufficient amounts of the sample of interest. Even in cases where milligram-scale quantities of purified complex of interest become available, there is still no guarantee that good quality crystals can be obtained. At this step, protein engineering of one or more components of the complex is frequently required to improve solubility, yield or the ability to crystallize the sample. Subsequent characterization of these constructs may be performed by solution techniques such as Small Angle X-ray Scattering and Nuclear Magnetic Resonance to identify 'well behaved' complexes. Herein, we recount our experiences gained at protein production and complex assembly during the European 3D Repertoire project (3DR). The goal of this consortium was to obtain structural information on multi-protein complexes from yeast by combining crystallography, electron microscopy, NMR and in silico modeling methods. We present here representative set case studies of complexes that were produced and analyzed within the 3DR project. Our experience provides useful insight into strategies that are more generally applicable for structural analysis of protein complexes. Copyright © 2011 Elsevier Inc. All rights reserved.

Forensic considerations when dealing with incinerated human dental remains.

Science.gov (United States)

Reesu, Gowri Vijay; Augustine, Jeyaseelan; Urs, Aadithya B

2015-01-01

Establishing the human dental identification process relies upon sufficient post-mortem data being recovered to allow for a meaningful comparison with ante-mortem records of the deceased person. Teeth are the most indestructible components of the human body and are structurally unique in their composition. They possess the highest resistance to most environmental effects like fire, desiccation, decomposition and prolonged immersion. In most natural as well as man-made disasters, teeth may provide the only means of positive identification of an otherwise unrecognizable body. It is imperative that dental evidence should not be destroyed through erroneous handling until appropriate radiographs, photographs, or impressions can be fabricated. Proper methods of physical stabilization of incinerated human dental remains should be followed. The maintenance of integrity of extremely fragile structures is crucial to the successful confirmation of identity. In such situations, the forensic dentist must stabilise these teeth before the fragile remains are transported to the mortuary to ensure preservation of possibly vital identification evidence. Thus, while dealing with any incinerated dental remains, a systematic approach must be followed through each stage of evaluation of incinerated dental remains to prevent the loss of potential dental evidence. This paper presents a composite review of various studies on incinerated human dental remains and discusses their impact on the process of human identification and suggests a step by step approach. Copyright © 2014 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Isolation of a human anti-epidermal growth factor receptor Fab antibody, EG-19-11, with subnanomolar affinity from naïve immunoglobulin repertoires using a hierarchical antibody library system.

Science.gov (United States)

Hur, Byung-ung; Yoon, Jae-bong; Liu, Li-Kun; Cha, Sang-hoon

2010-11-30

Specific antibodies that possess a subnanomolar affinity are very difficult to obtain from human naïve immunoglobulin repertoires without the use of lengthy affinity optimization procedures. Here, we designed a hierarchical phage-displayed antibody library system to generate an enormous diversity of combinatorial Fab fragments (6×10(17)) and attempted to isolate high-affinity Fabs against the human epidermal growth factor receptor (EGFR). A primary antibody library, designated HuDVFab-8L, comprising 4.5×10(9) human naïve heavy chains and eight unspecified human naïve light chains was selected against the EGFR-Fc protein by biopanning, and four anti-EGFR Fab clones were isolated. Because one of the Fab clones, denoted EG-L2-11, recognized a native EGFR expressed on A431 cells, the heavy chain of the Fab was shuffled with a human naïve light chain repertoire with a diversity of 1.4×10(8) and selected a second time against the EGFR-Fc protein again. One EG-L2-11 variant, denoted EG-19-11, recognized an EGFR epitope that was almost the same as that bound by cetuximab and had a K(D) of approximately 540 pM for soluble EGFR, which is about 7-fold higher than that of the FabC225 derived from cetuximab. This variant was also internalized by A431 cells, likely via receptor-mediated endocytosis, and it efficiently inhibited EGF-mediated tyrosine phosphorylation of the EGFR. These results demonstrate that the use of our hierarchical antibody library system is advantageous in generating fully human antibodies especially with a therapeutic purpose. Copyright © 2010 Elsevier B.V. All rights reserved.

Born Fat: The Relations between Weight Changeability Beliefs and Health Behaviors and Physical Health

Science.gov (United States)

Parent, Mike C.; Alquist, Jessica L.

2016-01-01

Although some popular press and nonscholarly sources have claimed that weight is largely unchangeable, the relationship between this belief and objective measures of health remains unclear. We tested the hypothesis that people who believe weight is unchangeable will have poorer objective and subjective health, and fewer exercise behaviors and…

Development of a remaining lifetime management system for NPPS

International Nuclear Information System (INIS)

Galvan, J.C.; Regano, M.; Hevia Ruperez, F.

1994-01-01

The interest evinced by Spain nuclear power plants in providing a tool to support remaining lifetime management led to UNESA's application to OCIDE in 1992, and the latter's approval, for financing the project to develop a Remaining Lifetime Evaluation System for LWR nuclear power plants. This project is currently being developed under UNESA leadership, and the collaboration of three Spanish engineering companies and a research centre. The paper will describe its objectives, activities, current status and prospects. The project is defined in two phases, the first consisting of the identification and analysis of the main ageing phenomena and their significant parameters and specification of the Remaining Lifetime Evaluation System (RLES), and the second implementation of a pilot application of the RLES to verify its effectiveness. (Author)

Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

Directory of Open Access Journals (Sweden)

Alonso Ángel

2006-03-01

Full Text Available Abstract Background Papillomaviruses (PVs infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the binding of cellular and viral transcription factors to the upstream regulatory region (URR of the virus. It is believed that there is a core of transcription factor binding sites (TFBS common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses. Results We have studied the URR of sixty-one PVs, covering twenty different hosts. We have predicted the TFBS present in the URR and analysed these results by principal component analysis and genetic algorithms. The number and nature of TFBS in the URR might be much broader than thus far described, and different PVs have different repertoires of TFBS. Conclusion There are common fingerprints in the URR in PVs that infect primates, although the ancestors of these viruses diverged a long time ago. Additionally, there are obvious differences between the URR of alpha and beta PVs, despite these PVs infect similar histological cell types in the same host, i.e. human. A thorough analysis of the TFBS in the URR might provide crucial information about the differential biology of cancer-associated PVs.

Neonatal colonisation expands a specific intestinal antigen-presenting cell subset prior to CD4 T-cell expansion, without altering T-cell repertoire.

Directory of Open Access Journals (Sweden)

Charlotte F Inman

Full Text Available Interactions between the early-life colonising intestinal microbiota and the developing immune system are critical in determining the nature of immune responses in later life. Studies in neonatal animals in which this interaction can be examined are central to understanding the mechanisms by which the microbiota impacts on immune development and to developing therapies based on manipulation of the microbiome. The inbred piglet model represents a system that is comparable to human neonates and allows for control of the impact of maternal factors. Here we show that colonisation with a defined microbiota produces expansion of mucosal plasma cells and of T-lymphocytes without altering the repertoire of alpha beta T-cells in the intestine. Importantly, this is preceded by microbially-induced expansion of a signal regulatory protein α-positive (SIRPα(+ antigen-presenting cell subset, whilst SIRPα(-CD11R1(+ antigen-presenting cells (APCs are unaffected by colonisation. The central role of intestinal APCs in the induction and maintenance of mucosal immunity implicates SIRPα(+ antigen-presenting cells as orchestrators of early-life mucosal immune development.

A repertoire of the dominant transcripts from the salivary glands of the blood-sucking bug, Triatoma dimidiata, a vector of Chagas disease

Science.gov (United States)

Kato, Hirotomo; Jochim, Ryan C.; Gomez, Eduardo A.; Sakoda, Ryo; Iwata, Hiroyuki; Valenzuela, Jesus G.; Hashiguchi, Yoshihisa

2010-01-01

Triatoma (T.) dimidiata is a hematophagous Hemiptera and a main vector of Chagas disease. The saliva of this and other blood-sucking insects contains potent pharmacologically active components that assist them in counteracting the host hemostatic and inflammatory systems during blood feeding. To describe the repertoire of potential bioactive salivary molecules from this insect, a number of randomly selected transcripts from the salivary gland cDNA library of T. dimidiata were sequenced and analyzed. This analysis showed that 77.5% of the isolated transcripts coded for putative secreted proteins, and 89.9% of these coded for variants of the lipocalin family proteins. The most abundant transcript was a homologue of procalin, the major allergen of T. protracta saliva, and contributed more than 50% of the transcripts coding for putative secreted proteins, suggesting that it may play an important role in the blood-feeding process. Other salivary transcripts encoding lipocalin family proteins had homology to triabin (a thrombin inhibitor), triafestin (an inhibitor of kallikrein–kinin system), pallidipin (an inhibitor of collagen-induced platelet aggregation) and others with unknown function. PMID:19900580

Remaining life assessment of a high pressure turbine rotor

International Nuclear Information System (INIS)

Nguyen, Ninh; Little, Alfie

2012-01-01

This paper describes finite element and fracture mechanics based modelling work that provides a useful tool for evaluation of the remaining life of a high pressure (HP) steam turbine rotor that had experienced thermal fatigue cracking. An axis-symmetrical model of a HP rotor was constructed. Steam temperature, pressure and rotor speed data from start ups and shut downs were used for the thermal and stress analysis. Operating history and inspection records were used to benchmark the damage experienced by the rotor. Fracture mechanics crack growth analysis was carried out to evaluate the remaining life of the rotor under themal cyclic loading conditions. The work confirmed that the fracture mechanics approach in conjunction with finite element modelling provides a useful tool for assessing the remaining life of high temperature components in power plants.

Postmortem Scavenging of Human Remains by Domestic Cats

Directory of Open Access Journals (Sweden)

Ananya Suntirukpong, M.D.

2017-11-01

Full Text Available Objective: Crime scene investigators, forensic medicine doctors and pathologists, and forensic anthropologists frequently encounter postmortem scavenging of human remains by household pets. Case presentation: The authors present a case report of a partially skeletonized adult male found dead after more than three months in his apartment in Thailand. The body was in an advanced stage of decomposition with nearly complete skeletonization of the head, neck, hands, and feet. The presence of maggots and necrophagous (flesh eating beetles on the body confirmed that insects had consumed much of the soft tissues. Examination of the hand and foot bones revealed canine tooth puncture marks. Evidence of chewing indicated that one or more of the decedent’s three house cats had fed on the body after death. Recognizing and identifying carnivore and rodent activity on the soft flesh and bones of human remains is important in interpreting and reconstructing postmortem damage. Thorough analysis may help explain why skeletal elements are missing, damaged, or out of anatomical position. Conclusion: This report presents a multi-disciplinary approach combining forensic anthropology and forensic medicine in examining and interpreting human remains.

Explosives remain preferred methods for platform abandonment

International Nuclear Information System (INIS)

Pulsipher, A.; Daniel, W. IV; Kiesler, J.E.; Mackey, V. III

1996-01-01

Economics and safety concerns indicate that methods involving explosives remain the most practical and cost-effective means for abandoning oil and gas structures in the Gulf of Mexico. A decade has passed since 51 dead sea turtles, many endangered Kemp's Ridleys, washed ashore on the Texas coast shortly after explosives helped remove several offshore platforms. Although no relationship between the explosions and the dead turtles was ever established, in response to widespread public concern, the US Minerals Management Service (MMS) and National Marine Fisheries Service (NMFS) implemented regulations limiting the size and timing of explosive charges. Also, more importantly, they required that operators pay for observers to survey waters surrounding platforms scheduled for removal for 48 hr before any detonations. If observers spot sea turtles or marine mammals within the danger zone, the platform abandonment is delayed until the turtles leave or are removed. However, concern about the effects of explosives on marine life remains

Decomposition Technique for Remaining Useful Life Prediction

Science.gov (United States)

Saha, Bhaskar (Inventor); Goebel, Kai F. (Inventor); Saxena, Abhinav (Inventor); Celaya, Jose R. (Inventor)

2014-01-01

The prognostic tool disclosed here decomposes the problem of estimating the remaining useful life (RUL) of a component or sub-system into two separate regression problems: the feature-to-damage mapping and the operational conditions-to-damage-rate mapping. These maps are initially generated in off-line mode. One or more regression algorithms are used to generate each of these maps from measurements (and features derived from these), operational conditions, and ground truth information. This decomposition technique allows for the explicit quantification and management of different sources of uncertainty present in the process. Next, the maps are used in an on-line mode where run-time data (sensor measurements and operational conditions) are used in conjunction with the maps generated in off-line mode to estimate both current damage state as well as future damage accumulation. Remaining life is computed by subtracting the instance when the extrapolated damage reaches the failure threshold from the instance when the prediction is made.

Thymic involvement in immune recovery during antiretroviral treatment of HIV infection in adults; comparison of CT and sonographic findings

DEFF Research Database (Denmark)

Kolte, Lilian; Strandberg, Charlotte; Dreves, Anne-Mette

2002-01-01

) repertoire were determined. The study demonstrated no correlation between the 2 scanning methods (r = 0.201, p = 0.358 in patients and r = 0.457, p = 0.184 in controls). Among the patients, no association was found between the sonographically estimated thymic size and immunological parameters such as CD4...... count (r = 0.083, p = 0.706), naive CD4 count (r = 0.067, p = 0.762), CD4 + TREC frequency (r = 0.028, p = 0.900) and CD4 + TCR repertoire (r = -0.057, p = 0.828). These findings show that CT remains superior for assessing thymic size in adults and is preferable to ultrasound when evaluating...

Eye on the B-ALL: B-cell receptor repertoires reveal persistence of numerous B-lymphoblastic leukemia subclones from diagnosis to relapse

Science.gov (United States)

Bashford-Rogers, R J M; Nicolaou, K A; Bartram, J; Goulden, N J; Loizou, L; Koumas, L; Chi, J; Hubank, M; Kellam, P; Costeas, P A; Vassiliou, G S

2016-01-01

The strongest predictor of relapse in B-cell acute lymphoblastic leukemia (B-ALL) is the level of persistence of tumor cells after initial therapy. The high mutation rate of the B-cell receptor (BCR) locus allows high-resolution tracking of the architecture, evolution and clonal dynamics of B-ALL. Using longitudinal BCR repertoire sequencing, we find that the BCR undergoes an unexpectedly high level of clonal diversification in B-ALL cells through both somatic hypermutation and secondary rearrangements, which can be used for tracking the subclonal composition of the disease and detect minimal residual disease with unprecedented sensitivity. We go on to investigate clonal dynamics of B-ALL using BCR phylogenetic analyses of paired diagnosis-relapse samples and find that large numbers of small leukemic subclones present at diagnosis re-emerge at relapse alongside a dominant clone. Our findings suggest that in all informative relapsed patients, the survival of large numbers of clonogenic cells beyond initial chemotherapy is a surrogate for inherent partial chemoresistance or inadequate therapy, providing an increased opportunity for subsequent emergence of fully resistant clones. These results frame early cytoreduction as an important determinant of long-term outcome. PMID:27211266

Increasing plasma fibrinogen, but unchanged levels of intraplatelet cyclic nucleotides, plasma endothelin-1, factor VII, and neopterin during cholesterol lowering with fluvastatin.

Science.gov (United States)

Gottsäter, A; Anwaar, I; Lind, P; Mattiasson, I; Lindgärde, F

1999-04-01

Lipid-lowering statin treatment reduces cardiovascular morbidity and mortality and improves endothelial function in patients with hypercholesterolemia. The aim of the present study was to evaluate plasma levels of fibrinogen, factor VII, and the macrophage-derived inflammatory mediator neopterin during lipid lowering. In addition, the endothelial production of platelet antiaggregatory and vasodilatory factors such as nitric oxide and prostacyclin, and vasoconstrictive factors such as endothelin-1, was assessed. Plasma fibrinogen, factor VII, endothelin-1, and the neopterin and intraplatelet nitric oxide and prostacyclin mediators cyclic 3'-5'guanosine monophosphate (cGMP) and cyclic 3'-5'adenosine monophosphate (cAMP) were measured before and 6 months after the institution of treatment with fluvastatin in 17 patients (eight men and nine women, median age 60 years) with vascular disease and previously untreated hypercholesterolemia. After 6 months, a decrease of 1.62 mmol/l [1.26-2.18 (19%); P factor VII [from 1.14 IE/ml (0.58-1.38) to 1.22 IE/ml (0.96-1.46); NS], or plasma neopterin [from 8.6 nmol/l (7.1-11.5) to 8.7 nmol/l (7.9-11.3); NS]. In conclusion, during cholesterol-lowering treatment with fluvastatin, plasma levels of fibrinogen increased whereas intraplatelet cyclic nucleotide levels and plasma endothelin-1, factor VII and neopterin levels were unchanged.

Why Agricultural Educators Remain in the Classroom

Science.gov (United States)

Crutchfield, Nina; Ritz, Rudy; Burris, Scott

2013-01-01

The purpose of this study was to identify and describe factors that are related to agricultural educator career retention and to explore the relationships between work engagement, work-life balance, occupational commitment, and personal and career factors as related to the decision to remain in the teaching profession. The target population for…

The human vascular endothelial cell line HUV-EC-C harbors the integrated HHV-6B genome which remains stable in long term culture.

Science.gov (United States)

Shioda, Setsuko; Kasai, Fumio; Ozawa, Midori; Hirayama, Noriko; Satoh, Motonobu; Kameoka, Yousuke; Watanabe, Ken; Shimizu, Norio; Tang, Huamin; Mori, Yasuko; Kohara, Arihiro

2018-02-01

Human herpes virus 6 (HHV-6) is a common human pathogen that is most often detected in hematopoietic cells. Although human cells harboring chromosomally integrated HHV-6 can be generated in vitro, the availability of such cell lines originating from in vivo tissues is limited. In this study, chromosomally integrated HHV-6B has been identified in a human vascular endothelial cell line, HUV-EC-C (IFO50271), derived from normal umbilical cord tissue. Sequence analysis revealed that the viral genome was similar to the HHV-6B HST strain. FISH analysis using a HHV-6 DNA probe showed one signal in each cell, detected at the distal end of the long arm of chromosome 9. This was consistent with a digital PCR assay, validating one copy of the viral DNA. Because exposure of HUV-EC-C to chemicals did not cause viral reactivation, long term cell culture of HUV-EC-C was carried out to assess the stability of viral integration. The growth rate was altered depending on passage numbers, and morphology also changed during culture. SNP microarray profiles showed some differences between low and high passages, implying that the HUV-EC-C genome had changed during culture. However, no detectable change was observed in chromosome 9, where HHV-6B integration and the viral copy number remained unchanged. Our results suggest that integrated HHV-6B is stable in HUV-EC-C despite genome instability.

Characterization of the repertoire diversity of the Plasmodium falciparum stevor multigene family in laboratory and field isolates

Directory of Open Access Journals (Sweden)

Holder Anthony A

2009-06-01

Full Text Available Abstract Background The evasion of host immune response by the human malaria parasite Plasmodium falciparum has been linked to expression of a range of variable antigens on the infected erythrocyte surface. Several genes are potentially involved in this process with the var, rif and stevor multigene families being the most likely candidates and coding for rapidly evolving proteins. The high sequence diversity of proteins encoded by these gene families may have evolved as an immune evasion strategy that enables the parasite to establish long lasting chronic infections. Previous findings have shown that the hypervariable region (HVR of STEVOR has significant sequence diversity both within as well as across different P. falciparum lines. However, these studies did not address whether or not there are ancestral stevor that can be found in different parasites. Methods DNA and RNA sequences analysis as well as phylogenetic approaches were used to analyse the stevor sequence repertoire and diversity in laboratory lines and Kilifi (Kenya fresh isolates. Results Conserved stevor genes were identified in different P. falciparum isolates from different global locations. Consistent with previous studies, the HVR of the stevor gene family was found to be highly divergent both within and between isolates. Importantly phylogenetic analysis shows some clustering of stevor sequences both within a single parasite clone as well as across different parasite isolates. Conclusion This indicates that the ancestral P. falciparum parasite genome already contained multiple stevor genes that have subsequently diversified further within the different P. falciparum populations. It also confirms that STEVOR is under strong selection pressure.

Fuel element production at BWX technologies

International Nuclear Information System (INIS)

Pace, Brett

1997-01-01

Effective July 1, 1997, the Government Group portion of the Babcock and Wilcox company was incorporated separately to become BWX Technologies, Inc. (BWXT) a wholly-owned subsidiary of the Babcock and Wilcox Company. The names of the divisions and other business units of the former Babcock and Wilcox Government Group (Advanced Systems Operations, Naval Nuclear Fuel Division, and Nuclear Equipment Division) will remain unchanged, but they are now known as divisions or business units of BWXT. The management of all units and their reporting relationships will likewise remain unchanged. (author)

Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum.

Science.gov (United States)

Rao, Soumya; Nandineni, Madhusudan R

2017-01-01

Colletotrichum truncatum, a major fungal phytopathogen, causes the anthracnose disease on an economically important spice crop chilli (Capsicum annuum), resulting in huge economic losses in tropical and sub-tropical countries. It follows a subcuticular intramural infection strategy on chilli with a short, asymptomatic, endophytic phase, which contrasts with the intracellular hemibiotrophic lifestyle adopted by most of the Colletotrichum species. However, little is known about the molecular determinants and the mechanism of pathogenicity in this fungus. A high quality whole genome sequence and gene annotation based on transcriptome data of an Indian isolate of C. truncatum from chilli has been obtained. Analysis of the genome sequence revealed a rich repertoire of pathogenicity genes in C. truncatum encoding secreted proteins, effectors, plant cell wall degrading enzymes, secondary metabolism associated proteins, with potential roles in the host-specific infection strategy, placing it next only to the Fusarium species. The size of genome assembly, number of predicted genes and some of the functional categories were similar to other sequenced Colletotrichum species. The comparative genomic analyses with other species and related fungi identified some unique genes and certain highly expanded gene families of CAZymes, proteases and secondary metabolism associated genes in the genome of C. truncatum. The draft genome assembly and functional annotation of potential pathogenicity genes of C. truncatum provide an important genomic resource for understanding the biology and lifestyle of this important phytopathogen and will pave the way for designing efficient disease control regimens.

A Bayesian Framework for Remaining Useful Life Estimation

Data.gov (United States)

National Aeronautics and Space Administration — The estimation of remaining useful life (RUL) of a faulty component is at the center of system prognostics and health management. It gives operators a potent tool in...

Review of the Dinosaur Remains from the Middle Jurassic of Scotland, UK

Directory of Open Access Journals (Sweden)

Neil D. L. Clark

2018-02-01

Full Text Available Dinosaurs are rare from the Middle Jurassic worldwide. The Isle of Skye, is the only place in Scotland thus far to have produced dinosaur remains. These remains consist mainly of footprints, but also several bones and teeth. These Bajocian and Bathonian remains represent an important collection of a basal eusauropod, early examples of non-neosauropod and possible basal titanosauriform eusauropods, and theropod remains that may belong to an early coelurosaur and a possible megalosaurid, basal tyrannosauroid, or dromaeosaurid. The footprints from here also suggest a rich and diverse dinosaur fauna for which further better diagnosable remains are likely to be found.

Dynamic evolution of bitter taste receptor genes in vertebrates

Directory of Open Access Journals (Sweden)

Jones Gareth

2009-01-01

Full Text Available Abstract Background Sensing bitter tastes is crucial for many animals because it can prevent them from ingesting harmful foods. This process is mainly mediated by the bitter taste receptors (T2R, which are largely expressed in the taste buds. Previous studies have identified some T2R gene repertoires, and marked variation in repertoire size has been noted among species. However, the mechanisms underlying the evolution of vertebrate T2R genes remain poorly understood. Results To better understand the evolutionary pattern of these genes, we identified 16 T2R gene repertoires based on the high coverage genome sequences of vertebrates and studied the evolutionary changes in the number of T2R genes during birth-and-death evolution using the reconciled-tree method. We found that the number of T2R genes and the fraction of pseudogenes vary extensively among species. Based on the results of phylogenetic analysis, we showed that T2R gene families in teleost fishes are more diverse than those in tetrapods. In addition to the independent gene expansions in teleost fishes, frogs and mammals, lineage-specific gene duplications were also detected in lizards. Furthermore, extensive gains and losses of T2R genes were detected in each lineage during their evolution, resulting in widely differing T2R gene repertoires. Conclusion These results further support the hypotheses that T2R gene repertoires are closely related to the dietary habits of different species and that birth-and-death evolution is associated with adaptations to dietary changes.

Remaining life diagnosis method and device for nuclear reactor

International Nuclear Information System (INIS)

Yamamoto, Michiyoshi.

1996-01-01

A neutron flux measuring means is inserted from the outside of a reactor pressure vessel during reactor operation to forecast neutron-degradation of materials of incore structural components in the vicinity of portions to be measured based on the measured values, and the remaining life of the reactor is diagnosed by the forecast degraded state. In this case, the neutron fluxes to be measured are desirably fast and/or medium neutron fluxes. As the positions where the measuring means is to be inserted, for example, the vicinity of the structural components at the periphery of the fuel assembly is selected. Aging degradation characteristics of the structural components are determined by using the aging degradation data for the structural materials. The remaining life is analyzed based on obtained aging degradation characteristics and stress evaluation data of the incore structural components at portions to be measured. Neutron irradiation amount of structural components at predetermined positions can be recognized accurately, and appropriate countermeasures can be taken depending on the forecast remaining life thereby enabling to improve the reliability of the reactor. (N.H.)

Industry remains stuck in a transitional mode

International Nuclear Information System (INIS)

Garb, F.A.

1991-01-01

The near future for industry remains foggy for several obvious reasons. The shake-up of the Soviet Union and how the pieces will reform remains unclear. How successful efforts are to privatize government oil company operations around the world has yet to be determined. A long sought peace in the Middle East seems to be inching closer, but will this continue? If it does continue, what impact will it have on world energy policy? Will American companies, which are now transferring their attention to foreign E and P, also maintain an interest in domestic activities? Is the U.S. economy really on the upswing? We are told that the worst of the recession is over, but try telling this to thousands of workers in the oil patch who are being released monthly by the big players in domestic operations. This paper reports that 1992 should be a better year than 1991, if measured in opportunity. There are more exploration and acquisition options available, both domestically and internationally, than there have been in years. Probably more opportunities exist than there are players-certainly more than can be funded with current financial resources

Data-driven remaining useful life prognosis techniques stochastic models, methods and applications

CERN Document Server

Si, Xiao-Sheng; Hu, Chang-Hua

2017-01-01

This book introduces data-driven remaining useful life prognosis techniques, and shows how to utilize the condition monitoring data to predict the remaining useful life of stochastic degrading systems and to schedule maintenance and logistics plans. It is also the first book that describes the basic data-driven remaining useful life prognosis theory systematically and in detail. The emphasis of the book is on the stochastic models, methods and applications employed in remaining useful life prognosis. It includes a wealth of degradation monitoring experiment data, practical prognosis methods for remaining useful life in various cases, and a series of applications incorporated into prognostic information in decision-making, such as maintenance-related decisions and ordering spare parts. It also highlights the latest advances in data-driven remaining useful life prognosis techniques, especially in the contexts of adaptive prognosis for linear stochastic degrading systems, nonlinear degradation modeling based pro...

Work-related factors influencing home care nurse intent to remain employed.

Science.gov (United States)

Tourangeau, Ann E; Patterson, Erin; Saari, Margaret; Thomson, Heather; Cranley, Lisa

Health care is shifting out of hospitals into community settings. In Ontario, Canada, home care organizations continue to experience challenges recruiting and retaining nurses. However, factors influencing home care nurse retention that can be modified remain largely unexplored. Several groups of factors have been identified as influencing home care nurse intent to remain employed including job characteristics, work structures, relationships and communication, work environment, responses to work, and conditions of employment. The aim of this study was to test and refine a model that identifies which factors are related to home care nurse intentions to remain employed for the next 5 years with their current home care employer organization. A cross-sectional survey design was implemented to test and refine a hypothesized model of home care nurse intent to remain employed. Logistic regression was used to determine which factors influence home care nurse intent to remain employed. Home care nurse intent to remain employed for the next 5 years was associated with increasing age, higher nurse-evaluated quality of care, having greater variety of patients, experiencing greater meaningfulness of work, having greater income stability, having greater continuity of client care, experiencing more positive relationships with supervisors, experiencing higher work-life balance, and being more satisfied with salary and benefits. Home care organizations can promote home care nurse intent to remain employed by (a) ensuring nurses have adequate training and resources to provide quality client care, (b) improving employment conditions to increase income stability and satisfaction with pay and benefits, (c) ensuring manageable workloads to facilitate improved work-life balance, and (d) ensuring leaders are accessible and competent.

Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection.

Directory of Open Access Journals (Sweden)

Evgeny A Glazov

Full Text Available MicroRNA (miRNA and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral infection we used Illumina's ultrahigh throughput sequencing approach. We sequenced three small RNA libraries prepared from cell line derived from the adult bovine kidney under normal conditions and upon infection of the cell line with Bovine herpesvirus 1. We used a bioinformatics approach to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected 219 out of 356 known bovine miRNAs and 115 respective miRNA* sequences. In addition we identified five new bovine orthologs of known mammalian miRNAs and discovered 268 new cow miRNAs many of which are not identifiable in other mammalian genomes and thus might be specific to the ruminant lineage. In addition we found seven new bovine mirtron candidates. We also discovered 10 small nucleolar RNA (snoRNA loci that give rise to small RNA with possible miRNA-like function. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. New miRNA sequences and the original sequencing data have been submitted to miRNA repository (miRBase and NCBI GEO archive respectively. We envisage that these resources will facilitate functional annotation of the bovine genome and promote further functional and comparative genomics studies of small regulatory RNA in mammals.

Red Assembly: the work remains

Directory of Open Access Journals (Sweden)

Leslie Witz

installed. What to do at this limit, at the transgressive encounter between saying yes and no to history, remains the challenge. It is the very challenge of what insistently remains.

3D-Printable Antimicrobial Composite Resins

NARCIS (Netherlands)

Yue, Jun; Zhao, Pei; Gerasimov, Jennifer Y.; van de Lagemaat, Marieke; Grotenhuis, Arjen; Rustema-Abbing, Minie; van der Mei, Henny C.; Busscher, Henk J.; Herrmann, Andreas; Ren, Yijin

2015-01-01

3D printing is seen as a game-changing manufacturing process in many domains, including general medicine and dentistry, but the integration of more complex functions into 3D-printed materials remains lacking. Here, it is expanded on the repertoire of 3D-printable materials to include antimicrobial

An analysis of the alleged skeletal remains of Carin Göring.

Directory of Open Access Journals (Sweden)

Anna Kjellström

Full Text Available In 1991, treasure hunters found skeletal remains in an area close to the destroyed country residence of former Nazi leader Hermann Göring in northeastern Berlin. The remains, which were believed to belong to Carin Göring, who was buried at the site, were examined to determine whether it was possible to make a positive identification. The anthropological analysis showed that the remains come from an adult woman. The DNA analysis of several bone elements showed female sex, and a reference sample from Carin's son revealed mtDNA sequences identical to the remains. The profile has one nucleotide difference from the Cambridge reference sequence (rCRS, the common variant 263G. A database search resulted in a frequency of this mtDNA sequence of about 10% out of more than 7,000 European haplotypes. The mtDNA sequence found in the ulna, the cranium and the reference sample is, thus, very common among Europeans. Therefore, nuclear DNA analysis was attempted. The remains as well as a sample from Carin's son were successfully analysed for the three nuclear markers TH01, D7S820 and D8S1179. The nuclear DNA analysis of the two samples revealed one shared allele for each of the three markers, supporting a mother and son relationship. This genetic information together with anthropological and historical files provides an additional piece of circumstantial evidence in our efforts to identify the remains of Carin Göring.

Does hypertension remain after kidney transplantation?

Directory of Open Access Journals (Sweden)

Gholamreza Pourmand

2015-05-01

Full Text Available Hypertension is a common complication of kidney transplantation with the prevalence of 80%. Studies in adults have shown a high prevalence of hypertension (HTN in the first three months of transplantation while this rate is reduced to 50- 60% at the end of the first year. HTN remains as a major risk factor for cardiovascular diseases, lower graft survival rates and poor function of transplanted kidney in adults and children. In this retrospective study, medical records of 400 kidney transplantation patients of Sina Hospital were evaluated. Patients were followed monthly for the 1st year, every two months in the 2nd year and every three months after that. In this study 244 (61% patients were male. Mean ± SD age of recipients was 39.3 ± 13.8 years. In most patients (40.8% the cause of end-stage renal disease (ESRD was unknown followed by HTN (26.3%. A total of 166 (41.5% patients had been hypertensive before transplantation and 234 (58.5% had normal blood pressure. Among these 234 individuals, 94 (40.2% developed post-transplantation HTN. On the other hand, among 166 pre-transplant hypertensive patients, 86 patients (56.8% remained hypertensive after transplantation. Totally 180 (45% patients had post-transplantation HTN and 220 patients (55% didn't develop HTN. Based on the findings, the incidence of post-transplantation hypertension is high, and kidney transplantation does not lead to remission of hypertension. On the other hand, hypertension is one of the main causes of ESRD. Thus, early screening of hypertension can prevent kidney damage and reduce further problems in renal transplant recipients.

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

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Jeliazko R. Jeliazkov

2018-03-01

Full Text Available Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody’s antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recent homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity.

And the Dead Remain Behind

Directory of Open Access Journals (Sweden)

Peter Read

2013-08-01

Full Text Available In most cultures the dead and their living relatives are held in a dialogic relationship. The dead have made it clear, while living, what they expect from their descendants. The living, for their part, wish to honour the tombs of their ancestors; at the least, to keep the graves of the recent dead from disrepair. Despite the strictures, the living can fail their responsibilities, for example, by migration to foreign countries. The peripatetic Chinese are one of the few cultures able to overcome the dilemma of the wanderer or the exile. With the help of a priest, an Australian Chinese migrant may summon the soul of an ancestor from an Asian grave to a Melbourne temple, where the spirit, though removed from its earthly vessel, will rest and remain at peace. Amongst cultures in which such practices are not culturally appropriate, to fail to honour the family dead can be exquisitely painful. Violence is the cause of most failure.

Molecular genetic identification of skeletal remains of apartheid ...

African Journals Online (AJOL)

The Truth and Reconciliation Commission made significant progress in examining abuses committed during the apartheid era in South Africa. Despite information revealed by the commission, a large number of individuals remained missing when the commission closed its proceedings. This provided the impetus for the ...

Palmar, Patellar, and Pedal Human Remains from Pavlov

Czech Academy of Sciences Publication Activity Database

Trinkaus, E.; Wojtal, P.; Wilczyński, J.; Sázelová, Sandra; Svoboda, Jiří

2017-01-01

Roč. 2017, June (2017), s. 73-101 ISSN 1545-0031 Institutional support: RVO:68081758 Keywords : Gravettian * human remains * isolated bones * anatomically modern humans * Upper Paleolithic Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology http://paleoanthro.org/media/journal/content/PA20170073.pdf

Robotics to enable older adults to remain living at home.

Science.gov (United States)

Pearce, Alan J; Adair, Brooke; Miller, Kimberly; Ozanne, Elizabeth; Said, Catherine; Santamaria, Nick; Morris, Meg E

2012-01-01

Given the rapidly ageing population, interest is growing in robots to enable older people to remain living at home. We conducted a systematic review and critical evaluation of the scientific literature, from 1990 to the present, on the use of robots in aged care. The key research questions were as follows: (1) what is the range of robotic devices available to enable older people to remain mobile, independent, and safe? and, (2) what is the evidence demonstrating that robotic devices are effective in enabling independent living in community dwelling older people? Following database searches for relevant literature an initial yield of 161 articles was obtained. Titles and abstracts of articles were then reviewed by 2 independent people to determine suitability for inclusion. Forty-two articles met the criteria for question 1. Of these, 4 articles met the criteria for question 2. Results showed that robotics is currently available to assist older healthy people and people with disabilities to remain independent and to monitor their safety and social connectedness. Most studies were conducted in laboratories and hospital clinics. Currently limited evidence demonstrates that robots can be used to enable people to remain living at home, although this is an emerging smart technology that is rapidly evolving.

Robotics to Enable Older Adults to Remain Living at Home

Directory of Open Access Journals (Sweden)

Alan J. Pearce

2012-01-01

Full Text Available Given the rapidly ageing population, interest is growing in robots to enable older people to remain living at home. We conducted a systematic review and critical evaluation of the scientific literature, from 1990 to the present, on the use of robots in aged care. The key research questions were as follows: (1 what is the range of robotic devices available to enable older people to remain mobile, independent, and safe? and, (2 what is the evidence demonstrating that robotic devices are effective in enabling independent living in community dwelling older people? Following database searches for relevant literature an initial yield of 161 articles was obtained. Titles and abstracts of articles were then reviewed by 2 independent people to determine suitability for inclusion. Forty-two articles met the criteria for question 1. Of these, 4 articles met the criteria for question 2. Results showed that robotics is currently available to assist older healthy people and people with disabilities to remain independent and to monitor their safety and social connectedness. Most studies were conducted in laboratories and hospital clinics. Currently limited evidence demonstrates that robots can be used to enable people to remain living at home, although this is an emerging smart technology that is rapidly evolving.

Dinosaur remains from the type Maastrichtian: An update

NARCIS (Netherlands)

Weishampel, David B.; Mulder, Eric W A; Dortangs, Rudi W.; Jagt, John W M; Jianu, Coralia Maria; Kuypers, Marcel M M; Peeters, Hans H G; Schulp, Anne S.

1999-01-01

Isolated cranial and post-cranial remains of hadrosaurid dinosaurs have been collected from various outcrops in the type area of the Maastrichtian stage during the last few years. In the present contribution, dentary and maxillary teeth are recorded from the area for the first time. Post-cranial

Decontamination and management of human remains following incidents of hazardous chemical release.

Science.gov (United States)

Hauschild, Veronique D; Watson, Annetta; Bock, Robert

2012-01-01

To provide specific guidance and resources for systematic and orderly decontamination of human remains resulting from a chemical terrorist attack or accidental chemical release. A detailed review and health-based decision criteria protocol is summarized. Protocol basis and logic are derived from analyses of compound-specific toxicological data and chemical/physical characteristics. Guidance is suitable for civilian or military settings where human remains potentially contaminated with hazardous chemicals may be present, such as sites of transportation accidents, terrorist operations, or medical examiner processing points. Guidance is developed from data-characterizing controlled experiments with laboratory animals, fabrics, and materiel. Logic and specific procedures for decontamination and management of remains, protection of mortuary affairs personnel, and decision criteria to determine when remains are sufficiently decontaminated are presented. Established procedures as well as existing materiel and available equipment for decontamination and verification provide reasonable means to mitigate chemical hazards from chemically exposed remains. Unique scenarios such as those involving supralethal concentrations of certain liquid chemical warfare agents may prove difficult to decontaminate but can be resolved in a timely manner by application of the characterized systematic approaches. Decision criteria and protocols to "clear" decontaminated remains for transport and processing are also provided. Once appropriate decontamination and verification have been accomplished, normal procedures for management of remains and release can be followed.

76 FR 14057 - Notice of Inventory Completion: University of Wyoming, Anthropology Department, Human Remains...

Science.gov (United States)

2011-03-15

...: University of Wyoming, Anthropology Department, Human Remains Repository, Laramie, WY AGENCY: National Park... Anthropology Department, Human Remains Repository, Laramie, WY. The human remains and associated funerary... the human remains was made by University of Wyoming, Anthropology Department, Human Remains Repository...

Modular Study of the Type III Effector Repertoire in Pseudomonas syringae pv. tomato DC3000 Reveals a Matrix of Effector Interplay in Pathogenesis.

Science.gov (United States)

Wei, Hai-Lei; Zhang, Wei; Collmer, Alan

2018-05-08

The bacterial pathogen Pseudomonas syringae pv. tomato DC3000 suppresses the two-tiered innate immune system of Nicotiana benthamiana and other plants by injecting a complex repertoire of type III secretion effector (T3E) proteins. Effectorless polymutant DC3000D36E was used with a modularized system for native delivery of the 29 DC3000 T3Es singly and in pairs. Assays of the performance of this T3E library in N. benthamiana leaves revealed a matrix of T3E interplay, with six T3Es eliciting death and eight others variously suppressing the death activity of the six. The T3E library was also interrogated for effects on DC3000D36E elicitation of a reactive oxygen species burst, for growth in planta, and for T3Es that reversed these effects. Pseudomonas fluorescens and Agrobacterium tumefaciens heterologous delivery systems yielded notably different sets of death-T3Es. The DC3000D36E T3E library system highlights the importance of 13 T3Es and their interplay in interactions with N. benthamiana. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Methodology for Extraction of Remaining Sodium of Used Sodium Containers

International Nuclear Information System (INIS)

Jung, Minhwan; Kim, Jongman; Cho, Youngil; Jeong, Jiyoung

2014-01-01

Sodium used as a coolant in the SFR (Sodium-cooled Fast Reactor) reacts easily with most elements due to its high reactivity. If sodium at high temperature leaks outside of a system boundary and makes contact with oxygen, it starts to burn and toxic aerosols are produced. In addition, it generates flammable hydrogen gas through a reaction with water. Hydrogen gas can be explosive within the range of 4.75 vol%. Therefore, the sodium should be handled carefully in accordance with standard procedures even though there is a small amount of target sodium remainings inside the containers and drums used for experiment. After the experiment, all sodium experimental apparatuses should be dismantled carefully through a series of draining, residual sodium extraction, and cleaning if they are no longer reused. In this work, a system for the extraction of the remaining sodium of used sodium drums has been developed and an operation procedure for the system has been established. In this work, a methodology for the extraction of remaining sodium out of the used sodium container has been developed as one of the sodium facility maintenance works. The sodium extraction system for remaining sodium of the used drums was designed and tested successfully. This work will contribute to an establishment of sodium handling technology for PGSFR. (Prototype Gen-IV Sodium-cooled Fast Reactor)

Robotics to Enable Older Adults to Remain Living at Home

OpenAIRE

Pearce, Alan J.; Adair, Brooke; Miller, Kimberly; Ozanne, Elizabeth; Said, Catherine; Santamaria, Nick; Morris, Meg E.

2012-01-01

Given the rapidly ageing population, interest is growing in robots to enable older people to remain living at home. We conducted a systematic review and critical evaluation of the scientific literature, from 1990 to the present, on the use of robots in aged care. The key research questions were as follows: (1) what is the range of robotic devices available to enable older people to remain mobile, independent, and safe? and, (2) what is the evidence demonstrating that robotic devices are effec...

Mummified remains from the Archaeological Museum in Zagreb, Croatia - Reviewing peculiarities and limitations of human and non-human radiological identification and analysis in mummified remains.

Science.gov (United States)

Petaros, Anja; Janković, Ivor; Cavalli, Fabio; Ivanac, Gordana; Brkljačić, Boris; Čavka, Mislav

2015-10-01

Forensic protocols and medico-legal techniques are increasingly being employed in investigations of museological material. The final findings of such investigations may reveal interesting facts on historical figures, customs and habits, as well as provide meaningful data for forensic use. Herein we present a case review where forensic experts were requested to identify taxonomic affinities, stage of preservation and provide skeletal analysis of mummified non-human archaeological remains, and verify whether two mummified hands are human or not. The manuscript offers a short review on the process and particularities of radiological species identification, the impact of post-mortem changes in the analysis and imaging of mummified remains as well as the macroscopical interpretation of trauma, pathology and authenticity in mummified remains, which can all turn useful when dealing with forensic cases. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

A Unique T-Cell Receptor Amino Acid Sequence Selected by Human T-Cell Lymphotropic Virus Type 1 Tax301-309-Specific Cytotoxic T Cells in HLA-A24:02-Positive Asymptomatic Carriers and Adult T-Cell Leukemia/Lymphoma Patients.

Science.gov (United States)

Ishihara, Yuko; Tanaka, Yukie; Kobayashi, Seiichiro; Kawamura, Koji; Nakasone, Hideki; Gomyo, Ayumi; Hayakawa, Jin; Tamaki, Masaharu; Akahoshi, Yu; Harada, Naonori; Kusuda, Machiko; Kameda, Kazuaki; Ugai, Tomotaka; Wada, Hidenori; Sakamoto, Kana; Sato, Miki; Terasako-Saito, Kiriko; Kikuchi, Misato; Kimura, Shun-Ichi; Tanihara, Aki; Kako, Shinichi; Uchimaru, Kaoru; Kanda, Yoshinobu

2017-10-01

We previously reported that the T-cell receptor (TCR) repertoire of human T-cell lymphotropic virus type 1 (HTLV-1) Tax 301-309 -specific CD8 + cytotoxic T cells (Tax 301-309 -CTLs) was highly restricted and a particular amino acid sequence motif, the PDR motif, was conserved among HLA-A*24:02-positive (HLA-A*24:02 + ) adult T-cell leukemia/lymphoma (ATL) patients who had undergone allogeneic hematopoietic cell transplantation (allo-HSCT). Furthermore, we found that donor-derived PDR + CTLs selectively expanded in ATL long-term HSCT survivors with strong CTL activity against HTLV-1. On the other hand, the TCR repertoires in Tax 301-309 -CTLs of asymptomatic HTLV-1 carriers (ACs) remain unclear. In this study, we directly identified the DNA sequence of complementarity-determining region 3 (CDR3) of the TCR-β chain of Tax 301-309 -CTLs at the single-cell level and compared not only the TCR repertoires but also the frequencies and phenotypes of Tax 301-309 -CTLs between ACs and ATL patients. We did not observe any essential difference in the frequencies of Tax 301-309 -CTLs between ACs and ATL patients. In the single-cell TCR repertoire analysis of Tax 301-309 -CTLs, 1,458 Tax 301-309 -CTLs and 140 clones were identified in this cohort. Tax 301-309 -CTLs showed highly restricted TCR repertoires with a strongly biased usage of BV7, and PDR, the unique motif in TCR-β CDR3, was exclusively observed in all ACs and ATL patients. However, there was no correlation between PDR + CTL frequencies and HTLV-1 proviral load (PVL). In conclusion, we have identified, for the first time, a unique amino acid sequence, PDR, as a public TCR-CDR3 motif against Tax in HLA-A*24:02 + HTLV-1-infected individuals. Further investigations are warranted to elucidate the role of the PDR + CTL response in the progression from carrier state to ATL. IMPORTANCE ATL is an aggressive T-cell malignancy caused by HTLV-1 infection. The HTLV-1 regulatory protein Tax aggressively promotes the

Career Motivation in Newly Licensed Registered Nurses: What Makes Them Remain

Science.gov (United States)

Banks, Zarata Mann; Bailey, Jessica H.

2010-01-01

Despite vast research on newly licensed registered nurses (RNs), we don't know why some newly licensed registered nurses remain in their current jobs and others leave the nursing profession early in their career. Job satisfaction, the most significant factor emerging from the literature, plays a significant role in nurses' decisions to remain in…

Thymic commitment of regulatory T cells is a pathway of TCR-dependent selection that isolates repertoires undergoing positive or negative selection.

Science.gov (United States)

Coutinho, A; Caramalho, I; Seixas, E; Demengeot, J

2005-01-01

The seminal work of Le Douarin and colleagues (Ohki et al. 1987; Ohki et al. 1988; Salaun et al. 1990; Coutinho et al. 1993) first demonstrated that peripheral tissue-specific tolerance is centrally established in the thymus, by epithelial stromal cells (TEC). Subsequent experiments have shown that TEC-tolerance is dominant and mediated by CD4 regulatory T cells (Treg) that are generated intrathymically by recognition of antigens expressed on TECs (Modigliani et al. 1995; Modigliani et al. 1996a). From these and other observations, in 1996 Modigliani and colleagues derived a general model for the establishment and maintenance of natural tolerance (MM96) (Modigliani et al. 1996b), with two central propositions: (1) T cell receptor (TCR)-dependent sorting of emergent repertoires generates TEC-specific Treg displaying the highest TCR self-affinities below deletion thresholds, thus isolating repertoires undergoing positive and negative selection; (2) Treg are intrathymically committed (and activated) for a unique differentiative pathway with regulatory effector functions. The model explained the embryonic/perinatal time window of natural tolerance acquisition, by developmental programs determining (1) TCR multireactivity, (2) the cellular composition in the thymic stroma (relative abundance of epithelial vs hemopoietic cells), and (3) the dynamics of peripheral lymphocyte pools, built by accumulation of recent thymic emigrants (RTE) that remain recruitable to regulatory functions. We discuss here the MM96 in the light of recent results demonstrating the promiscuous expression of tissue-specific antigens by medullary TECs (Derbinski et al. 2001; Anderson et al. 2002; Gotter et al. 2004) and indicating that Treg represent a unique differentiative pathway (Fontenot et al. 2003; Hori et al. 2003; Khattri et al. 2003), which is adopted by CD4 T cells with high avidity for TEC-antigens (Bensinger et al. 2001; Jordan et al. 2001; Apostolou et al. 2002). In the likelihood that

Chronic alcoholism in rats induces a compensatory response, preserving brain thiamine diphosphate, but the brain 2-oxo acid dehydrogenases are inactivated despite unchanged coenzyme levels.

Science.gov (United States)

Parkhomenko, Yulia M; Kudryavtsev, Pavel A; Pylypchuk, Svetlana Yu; Chekhivska, Lilia I; Stepanenko, Svetlana P; Sergiichuk, Andrej A; Bunik, Victoria I

2011-06-01

Thiamine-dependent changes in alcoholic brain were studied using a rat model. Brain thiamine and its mono- and diphosphates were not reduced after 20 weeks of alcohol exposure. However, alcoholism increased both synaptosomal thiamine uptake and thiamine diphosphate synthesis in brain, pointing to mechanisms preserving thiamine diphosphate in the alcoholic brain. In spite of the unchanged level of the coenzyme thiamine diphosphate, activities of the mitochondrial 2-oxoglutarate and pyruvate dehydrogenase complexes decreased in alcoholic brain. The inactivation of pyruvate dehydrogenase complex was caused by its increased phosphorylation. The inactivation of 2-oxoglutarate dehydrogenase complex (OGDHC) correlated with a decrease in free thiols resulting from an elevation of reactive oxygen species. Abstinence from alcohol following exposure to alcohol reactivated OGDHC along with restoration of the free thiol content. However, restoration of enzyme activity occurred before normalization of reactive oxygen species levels. Hence, the redox status of cellular thiols mediates the action of oxidative stress on OGDHC in alcoholic brain. As a result, upon chronic alcohol consumption, physiological mechanisms to counteract the thiamine deficiency and silence pyruvate dehydrogenase are activated in rat brain, whereas OGDHC is inactivated due to impaired antioxidant ability. © 2011 The Authors. Journal of Neurochemistry © 2011 International Society for Neurochemistry.

Fossil human remains from Bolomor Cave (Valencia, Spain).

Science.gov (United States)

Arsuaga, Juan Luis; Fernández Peris, Josep; Gracia-Téllez, Ana; Quam, Rolf; Carretero, José Miguel; Barciela González, Virginia; Blasco, Ruth; Cuartero, Felipe; Sañudo, Pablo

2012-05-01

Systematic excavations carried out since 1989 at Bolomor Cave have led to the recovery of four Pleistocene human fossil remains, consisting of a fibular fragment, two isolated teeth, and a nearly complete adult parietal bone. All of these specimens date to the late Middle and early Late Pleistocene (MIS 7-5e). The fibular fragment shows thick cortical bone, an archaic feature found in non-modern (i.e. non-Homo sapiens) members of the genus Homo. Among the dental remains, the lack of a midtrigonid crest in the M(1) represents a departure from the morphology reported for the majority of Neandertal specimens, while the large dimensions and pronounced shoveling of the marginal ridges in the C(1) are similar to other European Middle and late Pleistocene fossils. The parietal bone is very thick, with dimensions that generally fall above Neandertal fossils and resemble more closely the Middle Pleistocene Atapuerca (SH) adult specimens. Based on the presence of archaic features, all the fossils from Bolomor are attributed to the Neandertal evolutionary lineage. Copyright © 2012 Elsevier Ltd. All rights reserved.

On random age and remaining lifetime for populations of items

DEFF Research Database (Denmark)

Finkelstein, M.; Vaupel, J.

2015-01-01

We consider items that are incepted into operation having already a random (initial) age and define the corresponding remaining lifetime. We show that these lifetimes are identically distributed when the age distribution is equal to the equilibrium distribution of the renewal theory. Then we...... develop the population studies approach to the problem and generalize the setting in terms of stationary and stable populations of items. We obtain new stochastic comparisons for the corresponding population ages and remaining lifetimes that can be useful in applications. Copyright (c) 2014 John Wiley...

Evolution of drug resistance in HIV infected patients remaining on a virologically failing cART regimen

DEFF Research Database (Denmark)

Cozzi-Lepri, A; Phillips, AN; Ruiz, L

2007-01-01

OBJECTIVE: To estimate the extent of drug resistance accumulation in patients kept on a virologically failing regimen and its determinants in the clinical setting. DESIGN: The study focused on 110 patients of EuroSIDA on an unchanged regimen who had two genotypic tests performed at two time points...... (t0 and t1) when viral load was > 400 copies/ml. METHODS: Accumulation of resistance between t0 and t1 was measured using genotypic susceptibility scores (GSS) obtained by counting the total number of active drugs (according to the Rega system v6.4.1) among all licensed antiretrovirals as of 1...... January 2006. Patients were grouped according to the number of active drugs in the failing regimen at t0 (GSS_f-t0). RESULTS: At t0, patients had been on the failing combination antiretroviral therapy (cART) for a median of 11 months (range, 6-50 months). Even patients with extensive resistance...

Mineral remains of early life on Earth? On Mars?

Science.gov (United States)

Iberall, Robbins E.; Iberall, A.S.

1991-01-01

The oldest sedimentary rocks on Earth, the 3.8-Ga Isua Iron-Formation in southwestern Greenland, are metamorphosed past the point where organic-walled fossils would remain. Acid residues and thin sections of these rocks reveal ferric microstructures that have filamentous, hollow rod, and spherical shapes not characteristic of crystalline minerals. Instead, they resemble ferric-coated remains of bacteria. Because there are no earlier sedimentary rocks to study on Earth, it may be necessary to expand the search elsewhere in the solar system for clues to any biotic precursors or other types of early life. A study of morphologies of iron oxide minerals collected in the southern highlands during a Mars sample return mission may therefore help to fill in important gaps in the history of Earth's earliest biosphere. -from Authors

A Study on Generic Representation of Skeletal Remains Replication of Prehistoric Burial

Directory of Open Access Journals (Sweden)

C.-W. Shao

2015-08-01

Full Text Available Generic representation of skeletal remains from burials consists of three dimensions which include physical anthropologists, replication technicians, and promotional educators. For the reason that archaeological excavation is irreversible and disruptive, detail documentation and replication technologies are surely needed for many purposes. Unearthed bones during the process of 3D digital scanning need to go through reverse procedure, 3D scanning, digital model superimposition, rapid prototyping, mould making, and the integrated errors generated from the presentation of colours and textures are important issues for the presentation of replicate skeleton remains among professional decisions conducted by physical anthropologists, subjective determination of makers, and the expectations of viewers. This study presents several cases and examines current issues on display and replication technologies for human skeletal remains of prehistoric burials. This study documented detail colour changes of human skeleton over time for the reference of reproduction. The tolerance errors of quantification and required technical qualification is acquired according to the precision of 3D scanning, the specification requirement of rapid prototyping machine, and the mould making process should following the professional requirement for physical anthropological study. Additionally, the colorimeter is adopted to record and analyse the “colour change” of the human skeletal remains from wet to dry condition. Then, the “colure change” is used to evaluate the “real” surface texture and colour presentation of human skeletal remains, and to limit the artistic presentation among the human skeletal remains reproduction. The“Lingdao man No.1”, is a well preserved burial of early Neolithic period (8300 B.P. excavated from Liangdao-Daowei site, Matsu, Taiwan , as the replicating object for this study. In this study, we examined the reproduction procedures step by

Uses and Gratifications of Social Media: A Comparison of Facebook and Instant Messaging

Science.gov (United States)

Quan-Haase, Anabel; Young, Alyson L.

2010-01-01

Users have adopted a wide range of digital technologies into their communication repertoire. It remains unclear why they adopt multiple forms of communication instead of substituting one medium for another. It also raises the question: What type of need does each of these media fulfill? In the present article, the authors conduct comparative work…

Shotgun microbial profiling of fossil remains

DEFF Research Database (Denmark)

Der Sarkissian, Clio; Ermini, Luca; Jónsson, Hákon

2014-01-01

the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach...... to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial...... community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using...

Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host–Gut Microbiome Interactions

Directory of Open Access Journals (Sweden)

Tatsuo Ichinohe

2018-04-01

Full Text Available The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype. Over the past several years, high-throughput next-generation sequencing has been developed as a powerful tool to profile T- and B-cell receptor repertoires in a given individual at the single-cell level. Sophisticated immuno-bioinformatic analyses by use of this innovative methodology have been already implemented in clinical development of antibody engineering, vaccine design, and cellular immunotherapy. In this article, we aim to discuss the possible application of high-throughput immune receptor sequencing in the field of nutritional and intestinal immunology. Although there are still unsolved caveats, this emerging technology combined with single-cell transcriptomics/proteomics provides a critical tool to unveil the previously unrecognized principle of host–microbiome immune homeostasis. Accumulation of such knowledge will lead to the development of effective ways for personalized immune modulation through deeper understanding of the mechanisms by which the intestinal environment affects our immune ecosystem.

Diethylstilbestrol alters positive and negative selection of T cells in the thymus and modulates T-cell repertoire in the periphery

International Nuclear Information System (INIS)

Brown, Nicole; Nagarkatti, Mitzi; Nagarkatti, Prakash S.

2006-01-01

Prenatal exposure to diethylstilbestrol (DES) is known to cause altered immune functions and increased susceptibility to autoimmune disease in humans. In the current study, we investigated the effects of DES on T-cell differentiation in the thymus using the HY-TCR transgenic (Tg) mouse model in which the female mice exhibit positive selection of T cells bearing the Tg TCR, while the male mice show negative selection of such T cells. In female HY-TCR-Tg mice, exposure to DES showed more pronounced decrease in thymic cellularity when compared to male mice. Additionally, female mice also showed a significant decrease in the proportion of double-positive (DP) T cells in the thymus and HY-TCR-specific CD8 + T cells in the periphery. Male mice exhibiting negative selection also showed decreased thymic cellularity following DES exposure. Moreover, the male mice showed increased proportion of double-negative (DN) T cells in the thymus and decreased proportion of CD8 + T cells. The density of expression of HY-TCR on CD8 + cells was increased following DES exposure in both females and males. Finally, the proliferative response of thymocytes to mitogens and peripheral lymph node T cells to male H-Y antigen was significantly altered in female and male mice following DES treatment. Taken together, these data suggest that DES alters T-cell differentiation in the thymus by interfering with positive and negative selection processes, which in turn modulates the T-cell repertoire in the periphery

Diethylstilbestrol alters positive and negative selection of T cells in the thymus and modulates T-cell repertoire in the periphery

Energy Technology Data Exchange (ETDEWEB)

Brown, Nicole [Department of Microbiology and Immunology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298 (United States); Nagarkatti, Mitzi [Department of Microbiology and Immunology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298 (United States); Nagarkatti, Prakash S [Department of Pharmacology and Toxicology, PO Box 980613, Virginia Commonwealth University Medical Center, Richmond, VA 23298-0613 (United States)

2006-04-15

Prenatal exposure to diethylstilbestrol (DES) is known to cause altered immune functions and increased susceptibility to autoimmune disease in humans. In the current study, we investigated the effects of DES on T-cell differentiation in the thymus using the HY-TCR transgenic (Tg) mouse model in which the female mice exhibit positive selection of T cells bearing the Tg TCR, while the male mice show negative selection of such T cells. In female HY-TCR-Tg mice, exposure to DES showed more pronounced decrease in thymic cellularity when compared to male mice. Additionally, female mice also showed a significant decrease in the proportion of double-positive (DP) T cells in the thymus and HY-TCR-specific CD8{sup +} T cells in the periphery. Male mice exhibiting negative selection also showed decreased thymic cellularity following DES exposure. Moreover, the male mice showed increased proportion of double-negative (DN) T cells in the thymus and decreased proportion of CD8{sup +} T cells. The density of expression of HY-TCR on CD8{sup +} cells was increased following DES exposure in both females and males. Finally, the proliferative response of thymocytes to mitogens and peripheral lymph node T cells to male H-Y antigen was significantly altered in female and male mice following DES treatment. Taken together, these data suggest that DES alters T-cell differentiation in the thymus by interfering with positive and negative selection processes, which in turn modulates the T-cell repertoire in the periphery.

The Transcriptome of the Zoanthid Protopalythoa variabilis (Cnidaria, Anthozoa) Predicts a Basal Repertoire of Toxin-like and Venom-Auxiliary Polypeptides.

Science.gov (United States)

Huang, Chen; Morlighem, Jean-Étienne Rl; Zhou, Hefeng; Lima, Érica P; Gomes, Paula B; Cai, Jing; Lou, Inchio; Pérez, Carlos D; Lee, Simon Ming; Rádis-Baptista, Gandhi

2016-10-05

Protopalythoa is a zoanthid that, together with thousands of predominantly marine species, such as hydra, jellyfish, and sea anemones, composes the oldest eumetazoan phylum, i.e., the Cnidaria. Some of these species, such as sea wasps and sea anemones, are highly venomous organisms that can produce deadly toxins for preying, for defense or for territorial disputes. Despite the fact that hundreds of organic and polypeptide toxins have been characterized from sea anemones and jellyfish, practically nothing is known about the toxin repertoire in zoanthids. Here, based on a transcriptome analysis of the zoanthid Protopalythoa variabilis, numerous predicted polypeptides with canonical venom protein features are identified. These polypeptides comprise putative proteins from different toxin families: neurotoxic peptides, hemostatic and hemorrhagic toxins, membrane-active (pore-forming) proteins, protease inhibitors, mixed-function venom enzymes, and venom auxiliary proteins. The synthesis and functional analysis of two of these predicted toxin products, one related to the ShK/Aurelin family and the other to a recently discovered anthozoan toxin, displayed potent in vivo neurotoxicity that impaired swimming in larval zebrafish. Altogether, the complex array of venom-related transcripts that are identified in P. variabilis, some of which are first reported in Cnidaria, provides novel insight into the toxin distribution among species and might contribute to the understanding of composition and evolution of venom polypeptides in toxiferous animals. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.

Science.gov (United States)

Corrie, Brian D; Marthandan, Nishanth; Zimonja, Bojan; Jaglale, Jerome; Zhou, Yang; Barr, Emily; Knoetze, Nicole; Breden, Frances M W; Christley, Scott; Scott, Jamie K; Cowell, Lindsay G; Breden, Felix

2018-07-01

Next-generation sequencing allows the characterization of the adaptive immune receptor repertoire (AIRR) in exquisite detail. These large-scale AIRR-seq data sets have rapidly become critical to vaccine development, understanding the immune response in autoimmune and infectious disease, and monitoring novel therapeutics against cancer. However, at present there is no easy way to compare these AIRR-seq data sets across studies and institutions. The ability to combine and compare information for different disease conditions will greatly enhance the value of AIRR-seq data for improving biomedical research and patient care. The iReceptor Data Integration Platform (gateway.ireceptor.org) provides one implementation of the AIRR Data Commons envisioned by the AIRR Community (airr-community.org), an initiative that is developing protocols to facilitate sharing and comparing AIRR-seq data. The iReceptor Scientific Gateway links distributed (federated) AIRR-seq repositories, allowing sequence searches or metadata queries across multiple studies at multiple institutions, returning sets of sequences fulfilling specific criteria. We present a review of the development of iReceptor, and how it fits in with the general trend toward sharing genomic and health data, and the development of standards for describing and reporting AIRR-seq data. Researchers interested in integrating their repositories of AIRR-seq data into the iReceptor Platform are invited to contact support@ireceptor.org. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Market values summary/October market review/current market data

International Nuclear Information System (INIS)

Anon.

1994-01-01

This article is the October uranium market summary. During this period, volume increased to 2.2 Mlb U3O8 on the spot concentrates market. The unrestricted and restricted exchange values remained steady at $7.00 and $9.05 per pound U3O8 respectively. There were two UF6 deals during this period, and with supply more than adequate to meet the demand, the restricted UF6 price remained unchanged at $29.00 per kgU as UF6. The unrestricted value increased slightly to $24.50. The conversion value was unchanged, and the enrichment services market/prices weakened. Both active supply and demand decreased during this period

USING CONDITION MONITORING TO PREDICT REMAINING LIFE OF ELECTRIC CABLES

International Nuclear Information System (INIS)

LOFARO, R.; SOO, P.; VILLARAN, M.; GROVE, E.

2001-01-01

Electric cables are passive components used extensively throughout nuclear power stations to perform numerous safety and non-safety functions. It is known that the polymers commonly used to insulate the conductors on these cables can degrade with time; the rate of degradation being dependent on the severity of the conditions in which the cables operate. Cables do not receive routine maintenance and, since it can be very costly, they are not replaced on a regular basis. Therefore, to ensure their continued functional performance, it would be beneficial if condition monitoring techniques could be used to estimate the remaining useful life of these components. A great deal of research has been performed on various condition monitoring techniques for use on electric cables. In a research program sponsored by the U.S. Nuclear Regulatory Commission, several promising techniques were evaluated and found to provide trendable information on the condition of low-voltage electric cables. These techniques may be useful for predicting remaining life if well defined limiting values for the aging properties being measured can be determined. However, each technique has advantages and limitations that must be addressed in order to use it effectively, and the necessary limiting values are not always easy to obtain. This paper discusses how condition monitoring measurements can be used to predict the remaining useful life of electric cables. The attributes of an appropriate condition monitoring technique are presented, and the process to be used in estimating the remaining useful life of a cable is discussed along with the difficulties that must be addressed

Neanderthal infant and adult infracranial remains from Marillac (Charente, France).

Science.gov (United States)

Dolores Garralda, María; Maureille, Bruno; Vandermeersch, Bernard

2014-09-01

At the site of Marillac, near the Ligonne River in Marillac-le-Franc (Charente, France), a remarkable stratigraphic sequence has yielded a wealth of archaeological information, palaeoenvironmental data, as well as faunal and human remains. Marillac must have been a sinkhole used by Neanderthal groups as a hunting camp during MIS 4 (TL date 57,600 ± 4,600BP), where Quina Mousterian lithics and fragmented bones of reindeer predominate. This article describes three infracranial skeleton fragments. Two of them are from adults and consist of the incomplete shafts of a right radius (Marillac 24) and a left fibula (Marillac 26). The third fragment is the diaphysis of the right femur of an immature individual (Marillac 25), the size and shape of which resembles those from Teshik-Tash and could be assigned to a child of a similar age. The three fossils have been compared with the remains of other Neanderthals or anatomically Modern Humans (AMH). Furthermore, the comparison of the infantile femora, Marillac 25 and Teshik-Tash, with the remains of several European children from the early Middle Ages clearly demonstrates the robustness and rounded shape of both Neanderthal diaphyses. Evidence of peri-mortem manipulations have been identified on all three bones, with spiral fractures, percussion pits and, in the case of the radius and femur, unquestionable cutmarks made with flint implements, probably during defleshing. Traces of periostosis appear on the fibula fragment and on the immature femoral diaphysis, although their aetiology remains unknown. Copyright © 2014 Wiley Periodicals, Inc.

REPERTOIRE (DIRECTORY).

Science.gov (United States)

JOUBERT, MADELEINE

THIS DIRECTORY DESCRIBES, IN FRENCH, THE STRUCTURE, OBJECTIVES, ADMISSION REQUIREMENTS, AFFILIATIONS, EDUCATIONAL ACTIVITIES, AND PUBLICATIONS OF 62 ADULT EDUCATION ORGANIZATIONS AND INSTITUTIONS SERVING FRENCH-SPEAKING CANADA. IT INCLUDES DATA ON TYPE OF ORGANIZATION OR INSTITUTION, SCOPE OF ACTIVITY, REGION (WHERE SPECIFIED), FINANCIAL SUPPORT,…

Comparison of decomposition rates between autopsied and non-autopsied human remains.

Science.gov (United States)

Bates, Lennon N; Wescott, Daniel J

2016-04-01

Penetrating trauma has been cited as a significant factor in the rate of decomposition. Therefore, penetrating trauma may have an effect on estimations of time-since-death in medicolegal investigations and on research examining decomposition rates and processes when autopsied human bodies are used. The goal of this study was to determine if there are differences in the rate of decomposition between autopsied and non-autopsied human remains in the same environment. The purpose is to shed light on how large incisions, such as those from a thorocoabdominal autopsy, effect time-since-death estimations and research on the rate of decomposition that use both autopsied and non-autopsied human remains. In this study, 59 non-autopsied and 24 autopsied bodies were studied. The number of accumulated degree days required to reach each decomposition stage was then compared between autopsied and non-autopsied remains. Additionally, both types of bodies were examined for seasonal differences in decomposition rates. As temperature affects the rate of decomposition, this study also compared the internal body temperatures of autopsied and non-autopsied remains to see if differences between the two may be leading to differential decomposition. For this portion of this study, eight non-autopsied and five autopsied bodies were investigated. Internal temperature was collected once a day for two weeks. The results showed that differences in the decomposition rate between autopsied and non-autopsied remains was not statistically significant, though the average ADD needed to reach each stage of decomposition was slightly lower for autopsied bodies than non-autopsied bodies. There was also no significant difference between autopsied and non-autopsied bodies in the rate of decomposition by season or in internal temperature. Therefore, this study suggests that it is unnecessary to separate autopsied and non-autopsied remains when studying gross stages of human decomposition in Central Texas

Remaining useful life estimation based on discriminating shapelet extraction

International Nuclear Information System (INIS)

Malinowski, Simon; Chebel-Morello, Brigitte; Zerhouni, Noureddine

2015-01-01

In the Prognostics and Health Management domain, estimating the remaining useful life (RUL) of critical machinery is a challenging task. Various research topics including data acquisition, fusion, diagnostics and prognostics are involved in this domain. This paper presents an approach, based on shapelet extraction, to estimate the RUL of equipment. This approach extracts, in an offline step, discriminative rul-shapelets from an history of run-to-failure data. These rul-shapelets are patterns that are selected for their correlation with the remaining useful life of the equipment. In other words, every selected rul-shapelet conveys its own information about the RUL of the equipment. In an online step, these rul-shapelets are compared to testing units and the ones that match these units are used to estimate their RULs. Therefore, RUL estimation is based on patterns that have been selected for their high correlation with the RUL. This approach is different from classical similarity-based approaches that attempt to match complete testing units (or only late instants of testing units) with training ones to estimate the RUL. The performance of our approach is evaluated on a case study on the remaining useful life estimation of turbofan engines and performance is compared with other similarity-based approaches. - Highlights: • A data-driven RUL estimation technique based on pattern extraction is proposed. • Patterns are extracted for their correlation with the RUL. • The proposed method shows good performance compared to other techniques

Generating Two-Dimensional Repertoire of siRNA Linc-ROR and siRNA mRNA ARF6 from the lincRNA-RoR/miR-145/ARF6 expression Pathway that involved in the progression of Triple Negative Breast Cancer

Science.gov (United States)

Aditya Parikesit, Arli; Nurdiansyah, Rizki

2018-01-01

The research for finding the cure for breast cancer is currently entering the interesting phase of the transcriptomics based method. With the application of Next Generation Sequencing (NGS), molecular information on breast cancer could be gathered. Thus, both in silico and wet lab research has determined that the role of lincRNA-RoR/miR-145/ARF6 expression Pathway could not be ignored as one of the cardinal starting points for Triple-Negative Breast Cancer (TNBC). As the most hazardous type of breast cancer, TNBC should be treated with the most advanced approach that available in the scientific community. Bioinformatics approach has found the possible siRNA-based drug candidates for TNBC. It was found that siRNA that interfere with lincRNA-ROR and mRNA ARF6 could be a feasible opportunity as the drug candidate for TNBC. However, this claim should be validated with more thorough thermodynamics and kinetics computational approach as the comprehensive way to comprehend their molecular repertoire. In this respect, the claim was validated using various tools such as the RNAfold server to determine the 2D structure, Barriers server to comprehend the RNA folding kinetics, RNAeval server to validate the siRNA-target interaction. It was found that the thermodynamics and kinetics repertoire of the siRNA are indeed rational and feasible. In this end, our computation approach has proven that our designed siRNA could interact with lincRNA-RoR/miR-145/ARF6 expression Pathway.

Highly efficient DNA extraction method from skeletal remains

Directory of Open Access Journals (Sweden)

Irena Zupanič Pajnič

2011-03-01

Full Text Available Background: This paper precisely describes the method of DNA extraction developed to acquire high quality DNA from the Second World War skeletal remains. The same method is also used for molecular genetic identification of unknown decomposed bodies in routine forensic casework where only bones and teeth are suitable for DNA typing. We analysed 109 bones and two teeth from WWII mass graves in Slovenia. Methods: We cleaned the bones and teeth, removed surface contaminants and ground the bones into powder, using liquid nitrogen . Prior to isolating the DNA in parallel using the BioRobot EZ1 (Qiagen, the powder was decalcified for three days. The nuclear DNA of the samples were quantified by real-time PCR method. We acquired autosomal genetic profiles and Y-chromosome haplotypes of the bones and teeth with PCR amplification of microsatellites, and mtDNA haplotypes 99. For the purpose of traceability in the event of contamination, we prepared elimination data bases including genetic profiles of the nuclear and mtDNA of all persons who have been in touch with the skeletal remains in any way. Results: We extracted up to 55 ng DNA/g of the teeth, up to 100 ng DNA/g of the femurs, up to 30 ng DNA/g of the tibias and up to 0.5 ng DNA/g of the humerus. The typing of autosomal and YSTR loci was successful in all of the teeth, in 98 % dekalof the femurs, and in 75 % to 81 % of the tibias and humerus. The typing of mtDNA was successful in all of the teeth, and in 96 % to 98 % of the bones. Conclusions: We managed to obtain nuclear DNA for successful STR typing from skeletal remains that were over 60 years old . The method of DNA extraction described here has proved to be highly efficient. We obtained 0.8 to 100 ng DNA/g of teeth or bones and complete genetic profiles of autosomal DNA, Y-STR haplotypes, and mtDNA haplotypes from only 0.5g bone and teeth samples.

"SINCE I MUST PLEASE THOSE BELOW": HUMAN SKELETAL REMAINS RESEARCH AND THE LAW.

Science.gov (United States)

Holland, Thomas D

2015-01-01

The ethics of non-invasive scientific research on human skeletal remains are poorly articulated and lack a single, definitive analogue in western law. Laws governing invasive research on human fleshed remains, as well as bio-ethical principles established for research on living subjects, provide effective models for the establishment of ethical guidelines for non-invasive research on human skeletal remains. Specifically, non-invasive analysis of human remains is permissible provided that the analysis and collection of resulting data (1) are accomplished with respect for the dignity of the individual, (2) do not violate the last-known desire of the deceased, (3) do not adversely impact the right of the next of kin to perform a ceremonious and decent disposal of the remains, and (4) do not unduly or maliciously violate the privacy interests of the next of kin.

Intrinsic positive end-expiratory pressure during one-lung ventilation of patients with pulmonary hyperinflation. Influence of low respiratory rate with unchanged minute volume.

Science.gov (United States)

Szegedi, L L; Barvais, L; Sokolow, Y; Yernault, J C; d'Hollander, A A

2002-01-01

We measured lung mechanics and gas exchange during one-lung ventilation (OLV) of patients with chronic obstructive pulmonary disease, using three respiratory rates (RR) and unchanged minute volume. We studied 15 patients about to undergo lung surgery, during anaesthesia, and placed in the lateral position. Ventilation was with constant minute volume, inspiratory flow and FIO2. For periods of 15 min, RR of 5, 10, and 15 bpm were applied in a random sequence and recordings were made of lung mechanics and an arterial blood gas sample was taken. Data were analysed with the repeated measures ANOVA and paired t-test with Bonferroni correction. PaO2 changes were not significant. At the lowest RR, PaCO2 decreased (from 42 (SD 4) mm Hg at RR 15-41 (4) mm Hg at RR 10 and 39 (4) mm Hg at RR 5, P<0.01), and end-tidal carbon dioxide increased (from 33 (5) mm Hg at RR 15 to 35 (5) mm Hg at RR 10 and 36 (6) mm Hg at RR 5, P<0.01). Intrinsic positive end-expiratory pressure (PEEPi) was reduced even with larger tidal volumes (from 6 (4) cm H2O at RR 15-5 (4) cm H2O at RR 10, and 3 (3) cm H2O at RR 5, P<0.01), most probably caused by increased expiratory time at the lowest RR. A reduction in RR reduces PEEPi and hypercapnia during OLV in anaesthetized patients with chronic obstructive lung disease.

The repertoire of glycosphingolipids recognized by Vibrio cholerae.

Directory of Open Access Journals (Sweden)

John Benktander

Full Text Available The binding of cholera toxin to the ganglioside GM1 as the initial step in the process leading to diarrhea is nowadays textbook knowledge. In contrast, the knowledge about the mechanisms for attachment of Vibrio cholerae bacterial cells to the intestinal epithelium is limited. In order to clarify this issue, a large number of glycosphingolipid mixtures were screened for binding of El Tor V. cholerae. Several specific interactions with minor complex non-acid glycosphingolipids were thereby detected. After isolation of binding-active glycosphingolipids, characterization by mass spectrometry and proton NMR, and comparative binding studies, three distinct glycosphingolipid binding patterns were defined. Firstly, V. cholerae bound to complex lacto/neolacto glycosphingolipids with the GlcNAcβ3Galβ4GlcNAc sequence as the minimal binding epitope. Secondly, glycosphingolipids with a terminal Galα3Galα3Gal moiety were recognized, and the third specificity was the binding to lactosylceramide and related compounds. V. cholerae binding to lacto/neolacto glycosphingolipids, and to the other classes of binding-active compounds, remained after deletion of the chitin binding protein GbpA. Thus, the binding of V. cholerae to chitin and to lacto/neolacto containing glycosphingolipids represents two separate binding specificities.

SPIN SUSCEPTIBILITY IN HIGH - TC SUPERCONDUCTIVITY

African Journals Online (AJOL)

USER

2012-07-05

Jul 5, 2012 ... remains unchanged as a result of which the oxygen site will remain deficient ... kinetic energy, a hole's spin hooks up with the random Cu moment to form a ... reach out to each other magnetically to form spin singlet pairs with ...

Predicting the Remaining Useful Life of Rolling Element Bearings

DEFF Research Database (Denmark)

Hooghoudt, Jan Otto; Jantunen, E; Yi, Yang

2018-01-01

Condition monitoring of rolling element bearings is of vital importance in order to keep the industrial wheels running. In wind industry this is especially important due to the challenges in practical maintenance. The paper presents an attempt to improve the capability of prediction of remaining...

The effect of simulating porcelain firing on the elemental composition, microstructure, and mechanical properties of electroformed gold restorations

Directory of Open Access Journals (Sweden)

Youssef S. Al Jabbari

2016-09-01

Conclusion: Although microstructure and elemental composition of electroformed Au crowns remain unchanged, the mechanical properties are significantly affected by the thermal treatment of porcelain firing.

Screw Remaining Life Prediction Based on Quantum Genetic Algorithm and Support Vector Machine

Directory of Open Access Journals (Sweden)

Xiaochen Zhang

2017-01-01

Full Text Available To predict the remaining life of ball screw, a screw remaining life prediction method based on quantum genetic algorithm (QGA and support vector machine (SVM is proposed. A screw accelerated test bench is introduced. Accelerometers are installed to monitor the performance degradation of ball screw. Combined with wavelet packet decomposition and isometric mapping (Isomap, the sensitive feature vectors are obtained and stored in database. Meanwhile, the sensitive feature vectors are randomly chosen from the database and constitute training samples and testing samples. Then the optimal kernel function parameter and penalty factor of SVM are searched with the method of QGA. Finally, the training samples are used to train optimized SVM while testing samples are adopted to test the prediction accuracy of the trained SVM so the screw remaining life prediction model can be got. The experiment results show that the screw remaining life prediction model could effectively predict screw remaining life.

Authentic leadership: becoming and remaining an authentic nurse leader.

Science.gov (United States)

Murphy, Lin G

2012-11-01

This article explores how chief nurse executives became and remained authentic leaders. Using narrative inquiry, this qualitative study focused on the life stories of participants. Results demonstrate the importance of reframing, reflection in alignment with values, and the courage needed as nurse leaders progress to authenticity.

20 CFR 408.330 - How long will your application remain in effect?

Science.gov (United States)

2010-04-01

... effect? 408.330 Section 408.330 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SPECIAL BENEFITS FOR CERTAIN WORLD WAR II VETERANS Filing Applications Filing Your Application § 408.330 How long will your application remain in effect? Your application for SVB will remain in effect from the date it is filed until...

Structural remains at the early mediaeval fort at Raibania, Orissa

Directory of Open Access Journals (Sweden)

Bratati Sen

2013-11-01

Full Text Available The fortifications of mediaeval India occupy an eminent position in the history of military architecture. The present paper deals with the preliminary study of the structural remains at the early mediaeval fort at Raibania in the district of Balasore in Orissa. The fort was built of stone very loosely kept together. The three-walled fortification interspersed by two consecutive moats, a feature evidenced at Raibania, which is unparallel in the history of ancient and mediaeval forts and fortifications in India. Several other structures like the Jay-Chandi Temple Complex, a huge well, numerous tanks and remains of an ancient bridge add to the uniqueness of the Fort in the entire eastern region.

76 FR 14058 - Notice of Inventory Completion: University of Wyoming, Anthropology Department, Human Remains...

Science.gov (United States)

2011-03-15

...: University of Wyoming, Anthropology Department, Human Remains Repository, Laramie, WY AGENCY: National Park... in the possession and control of the University of Wyoming Anthropology Department, Human Remains... made by University of Wyoming, Anthropology Department, Human Remains Repository, professional staff in...

Evolution of drug resistance in HIV-infected patients remaining on a virologically failing combination antiretroviral therapy regimen

DEFF Research Database (Denmark)

Cozzi-Lepri, Alessandro; Phillips, Andrew N; Ruiz, Lidia

2007-01-01

OBJECTIVE: To estimate the extent of drug resistance accumulation in patients kept on a virologically failing regimen and its determinants in the clinical setting. DESIGN: The study focused on 110 patients of EuroSIDA on an unchanged regimen who had two genotypic tests performed at two time points...... (t0 and t1) when viral load was > 400 copies/ml. METHODS: Accumulation of resistance between t0 and t1 was measured using genotypic susceptibility scores (GSS) obtained by counting the total number of active drugs (according to the Rega system v6.4.1) among all licensed antiretrovirals as of 1...... January 2006. Patients were grouped according to the number of active drugs in the failing regimen at t0 (GSS_f-t0). RESULTS: At t0, patients had been on the failing combination antiretroviral therapy (cART) for a median of 11 months (range, 6-50 months). Even patients with extensive resistance...

76 FR 34122 - Missouri Disaster Number MO-00048

Science.gov (United States)

2011-06-10

... Injury Loans Only): Missouri: Crawford, Dent, Gasconade, Iron, Madison, Sainte Genevieve, Washington... remains unchanged. (Catalog of Federal Domestic Assistance Numbers 59002 and 59008) James E. Rivera...

76 FR 33395 - Tennessee Disaster Number TN-00051

Science.gov (United States)

2011-06-08

... Counties: (Physical Damage and Economic Injury Loans): Carroll, Crockett, Hardin, Henry, Madison... remains unchanged. (Catalog of Federal Domestic Assistance Numbers 59002 and 59008) James E. Rivera...

75 FR 27009 - Tennessee Disaster Number TN-00039

Science.gov (United States)

2010-05-13

..., Houston, Madison, Obion. Contiguous Counties: (Economic Injury Loans Only): Tennessee: Henry, Weakley... remains unchanged. (Catalog of Federal Domestic Assistance Numbers 59002 and 59008) James E. Rivera...

Drivers and barriers for bioenergy trade

NARCIS (Netherlands)

Junginger, Martin; Schouwenberg, Peter Paul; Nikolaisen, Lars; Andrade, Onofre

2014-01-01

There are several drivers responsible for the strong increase in biomass trade over the past decade: concerns regarding the effects of climate change remain unchanged, and policy targets for renewable energy for 2020 have so far remained (largely) intact despite the economic crisis. At the same

T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire.

Science.gov (United States)

Beausang, John F; Wheeler, Amanda J; Chan, Natalie H; Hanft, Violet R; Dirbas, Frederick M; Jeffrey, Stefanie S; Quake, Stephen R

2017-11-28

Tumor-infiltrating T cells play an important role in many cancers, and can improve prognosis and yield therapeutic targets. We characterized T cells infiltrating both breast cancer tumors and the surrounding normal breast tissue to identify T cells specific to each, as well as their abundance in peripheral blood. Using immune profiling of the T cell beta-chain repertoire in 16 patients with early-stage breast cancer, we show that the clonal structure of the tumor is significantly different from adjacent breast tissue, with the tumor containing ∼2.5-fold greater density of T cells and higher clonality compared with normal breast. The clonal structure of T cells in blood and normal breast is more similar than between blood and tumor, and could be used to distinguish tumor from normal breast tissue in 14 of 16 patients. Many T cell sequences overlap between tissue and blood from the same patient, including ∼50% of T cells between tumor and normal breast. Both tumor and normal breast contain high-abundance "enriched" sequences that are absent or of low abundance in the other tissue. Many of these T cells are either not detected or detected with very low frequency in the blood, suggesting the existence of separate compartments of T cells in both tumor and normal breast. Enriched T cell sequences are typically unique to each patient, but a subset is shared between many different patients. We show that many of these are commonly generated sequences, and thus unlikely to play an important role in the tumor microenvironment. Copyright © 2017 the Author(s). Published by PNAS.

The repertoire of G protein-coupled receptors in the human parasite Schistosoma mansoni and the model organism Schmidtea mediterranea

Directory of Open Access Journals (Sweden)

Zamanian Mostafa

2011-12-01

Full Text Available Abstract Background G protein-coupled receptors (GPCRs constitute one of the largest groupings of eukaryotic proteins, and represent a particularly lucrative set of pharmaceutical targets. They play an important role in eukaryotic signal transduction and physiology, mediating cellular responses to a diverse range of extracellular stimuli. The phylum Platyhelminthes is of considerable medical and biological importance, housing major pathogens as well as established model organisms. The recent availability of genomic data for the human blood fluke Schistosoma mansoni and the model planarian Schmidtea mediterranea paves the way for the first comprehensive effort to identify and analyze GPCRs in this important phylum. Results Application of a novel transmembrane-oriented approach to receptor mining led to the discovery of 117 S. mansoni GPCRs, representing all of the major families; 105 Rhodopsin, 2 Glutamate, 3 Adhesion, 2 Secretin and 5 Frizzled. Similarly, 418 Rhodopsin, 9 Glutamate, 21 Adhesion, 1 Secretin and 11 Frizzled S. mediterranea receptors were identified. Among these, we report the identification of novel receptor groupings, including a large and highly-diverged Platyhelminth-specific Rhodopsin subfamily, a planarian-specific Adhesion-like family, and atypical Glutamate-like receptors. Phylogenetic analysis was carried out following extensive gene curation. Support vector machines (SVMs were trained and used for ligand-based classification of full-length Rhodopsin GPCRs, complementing phylogenetic and homology-based classification. Conclusions Genome-wide investigation of GPCRs in two platyhelminth genomes reveals an extensive and complex receptor signaling repertoire with many unique features. This work provides important sequence and functional leads for understanding basic flatworm receptor biology, and sheds light on a lucrative set of anthelmintic drug targets.

Unsustainable Growth, Hyper-Competition, and Worth in Life Science Research: Narrowing Evaluative Repertoires in Doctoral and Postdoctoral Scientists' Work and Lives.

Science.gov (United States)

Fochler, Maximilian; Felt, Ulrike; Müller, Ruth

There is a crisis of valuation practices in the current academic life sciences, triggered by unsustainable growth and "hyper-competition." Quantitative metrics in evaluating researchers are seen as replacing deeper considerations of the quality and novelty of work, as well as substantive care for the societal implications of research. Junior researchers are frequently mentioned as those most strongly affected by these dynamics. However, their own perceptions of these issues are much less frequently considered. This paper aims at contributing to a better understanding of the interplay between how research is valued and how young researchers learn to live, work and produce knowledge within academia. We thus analyze how PhD students and postdocs in the Austrian life sciences ascribe worth to people, objects and practices as they talk about their own present and future lives in research. We draw on literature from the field of valuation studies and its interest in how actors refer to different forms of valuation to account for their actions. We explore how young researchers are socialized into different valuation practices in different stages of their growing into science. Introducing the concept of "regimes of valuation" we show that PhD students relate to a wider evaluative repertoire while postdocs base their decisions on one dominant regime of valuing research. In conclusion, we discuss the implications of these findings for the epistemic and social development of the life sciences, and for other scientific fields.

Political, energy events will remain interwoven

International Nuclear Information System (INIS)

Jones, D.P.

1991-01-01

This paper reports that it is possible to discuss the significance of political and energy events separately, but, in truth, they are intricately interwoven. Furthermore, there are those who will argue that since the two are inseparable, the future is not predictable; so why bother in the endeavor. It is possible that the central point of the exercise may have been missed-yes, the future is unpredictable exclamation point However, the objective of prediction is secondary. The objective of understanding the dynamic forces of change is primary exclamation point With this view of recent history, it is perhaps appropriate to pause and think about the future of the petroleum industry. The future as shaped by political, energy, economic, environmental and technological forces will direct our lives and markets during this decade. Most importantly, what will be the direction that successful businesses take to remain competitive in a global environment? These are interesting issues worthy of provocative thoughts and innovative ideas

Some remaining problems in HCDA analysis

International Nuclear Information System (INIS)

Chang, Y.W.

1981-01-01

The safety assessment and licensing of liquid-metal fast breeder reactors (LMFBRs) requires an analysis on the capability of the reactor primary system to sustain the consequences of a hypothetical core-disruptive accident (HCDA). Although computational methods and computer programs developed for HCDA analyses can predict reasonably well the response of the primary containment system, and follow up the phenomena of HCDA from the start of excursion to the time of dynamic equilibrium in the system, there remain areas in the HCDA analysis that merit further analytical and experimental studies. These are the analysis of fluid impact on reactor cover, three-dimensional analysis, the treatment of the perforated plates, material properties under high strain rates and under high temperatures, the treatment of multifield flows, and the treatment of prestressed concrete reactor vessels. The purpose of this paper is to discuss the structural mechanics of HCDA analysis in these areas where improvements are needed

Safety provision for nuclear power plants during remaining running time

International Nuclear Information System (INIS)

Rossnagel, Alexander; Hentschel, Anja

2012-01-01

With the phasing-out of the industrial use of nuclear energy for the power generation, the risk of the nuclear power plants has not been eliminated in principle, but only for a limited period of time. Therefore, the remaining nine nuclear power plants must also be used for the remaining ten years according to the state of science and technology. Regulatory authorities must substantiate the safety requirements for each nuclear power plant and enforce these requirements by means of various regulatory measures. The consequences of Fukushima must be included in the assessment of the safety level of nuclear power plants in Germany. In this respect, the regulatory authorities have the important tasks to investigate and assess the security risks as well as to develop instructions and orders.

76 FR 32387 - Tennessee Disaster Number TN-00053

Science.gov (United States)

2011-06-06

... Only): Tennessee: Carroll, Haywood, Madison. All other information in the original declaration remains unchanged. (Catalog of Federal Domestic Assistance Numbers 59002 and 59008) James E. Rivera, Associate...

The experiences of remaining nurse tutors during the transformation ...

African Journals Online (AJOL)

The transformation of public services and education in South Africa is part of the political and socioeconomic transition to democracy. Changes are occurring in every fi eld, including that of the health services. A qualitative study was undertaken to investigate the experiences of the remaining nurse tutors at a school of ...

Numerical investigation on the variation of welding stresses after material removal from a thick titanium alloy plate joined by electron beam welding

International Nuclear Information System (INIS)

Liu, Chuan; Zhang, Jianxun; Wu, Bing; Gong, Shuili

2012-01-01

Highlights: → After less materials removal from the top, stresses on the bottom remain unchanged. → The transverse stress within the weld decreases significantly with material removal. → Local material removal does not influence the longitudinal stress significantly. -- Abstract: The stress modification after material removal from a 50 mm thick titanium alloy plate jointed by electron beam welding (EBW) was investigated through the finite element method (FEM). The welding experiment and milling process were carried out to experimentally determine the stresses induced by EBW and their modification after local material removal. The modification of as-welded stresses due to the local material removal method and the whole layer removal method was discussed with the finite element analysis. Investigated results showed that with less materials removal from the top, the stresses on the bottom surface remain almost unchanged; after material removal from the top and bottom part, the transverse stress on the newly-formed surface decreases significantly as compared to the as-welded stresses at the same locations; however, the stress modification only occurs at the material removal region in the case of local region removal method; the longitudinal stress decreases with the whole layer removal method while remains almost unchanged with the local region removal method.

Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains

DEFF Research Database (Denmark)

Wales, Nathan; Andersen, Kenneth; Cappellini, Enrico

2014-01-01

Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate a...... extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated...... on the interactions between humans and past plant communities....

Effects of antithrombotic drugs in patients with left ventricular thrombi: assessment with indium-111 platelet imaging and two-dimensional echocardiography

International Nuclear Information System (INIS)

Stratton, J.R.; Ritchie, J.L.

1984-01-01

Patients with left ventricular thrombi not caused by recent myocardial infarction were prospectively studied by indium-111 platelet imaging and two-dimensional echocardiography to determine the reproducibility of these techniques and the short-term effects of sulfinpyrazone (200 mg four times daily), aspirin (325 mg three times daily) plus dipyridamole (75 mg three times daily), and full-dose warfarin. At baseline, all patients underwent indium-111 platelet imaging and echocardiography, and the results were positive for thrombus. In six patients on no antithrombotic drug therapy, repeat platelet scans and echocardiographic studies at 6.0 +/- 3.3 weeks remained positive and were unchanged. In seven patients studied on sulfinpyrazone, three platelet scans became negative, two became equivocal, and two were unchanged; the presence and size of thrombus was constant by echocardiography in all seven patients. Of the six patients studied on aspirin plus dipyridamole, one platelet scan became negative, those of three became equivocal, and two were unchanged; all echocardiographic findings remained positive, but one patient had decreased thrombus size. Among four warfarin-treated patients, three had resolution of platelet deposition and one was unchanged; by echocardiography, thrombus resolved in one patient, was decreased in size in one, and was unchanged in two. We conclude that, in the absence of antithrombotic drug therapy, platelet imaging and echocardiographic findings are stable in patients with left ventricular thrombi not caused by recent myocardial infarction. Sulfinpyrazone, aspirin plus dipyridamole, and warfarin all interrupt platelet deposition in some patients with chronic left ventricular thrombi

Chloroquine resistant P. falciparum prevalence is low and unchanged between 1990 and 2005 in Guinea-Bissau

DEFF Research Database (Denmark)

Ursing, Johan; Schmidt, Berit Aydin; Lebbad, Marianne

2007-01-01

Chloroquine resistant malaria was first reported in Guinea-Bissau in 1990 but chloroquine remains the most commonly used antimalarial in the country. Since 1990, we have conducted nearly annual standardized WHO in vitro micro-tests to assess chloroquine resistance. We have identified pfcrt 76T...... and other genetic polymorphisms in samples from 1992, 1993, 1995, 2004 and 2005. We have also monitored drug prescriptions for febrile illnesses. The mean proportion of in vitro tests indicating chloroquine resistance was 33% (range 14-54%) with the exception of an outlying value year 2000. The proportion...... of chloroquine resistant P. falciparum detected by in vitro testing did not increase over time. Pfcrt 76T was associated with chloroquine resistance but pfmdr1 86Y was not. The mean pfcrt 76T prevalence varied between 13% and 38%. The prevalence of SNPs at Pfcrt positions 76, 271, 326 and pfmdr1 position 86 did...

The Artificial Leaf: Recent Progress and Remaining Challenges

Directory of Open Access Journals (Sweden)

Mark D Symes

2016-12-01

Full Text Available The prospect of a device that uses solar energy to split water into H2 and O2 is highly attractive in terms of producing hydrogen as a carbon-neutral fuel. In this mini review, key research milestones that have been reached in this field over the last two decades will be discussed, with special focus on devices that use earth-abundant materials. Finally, the remaining challenges in the development of such “artificial leaves” will be highlighted.

Study on remain actinides recovery in pyro reprocessing

International Nuclear Information System (INIS)

Suharto, Bambang

1996-01-01

The spent fuel reprocessing by dry process called pyro reprocessing have been studied. Most of U, Pu and MA (minor actinides) from the spent fuel will be recovered and be fed back to the reactor as new fuel. Accumulation of remain actinides will be separated by extraction process with liquid cadmium solvent. The research was conducted by computer simulation to calculate the stage number required. The calculation's results showed on the 20 stages extractor more than 99% actinides can be separated. (author)

Direct dating of Early Upper Palaeolithic human remains from Mladec.

Science.gov (United States)

Wild, Eva M; Teschler-Nicola, Maria; Kutschera, Walter; Steier, Peter; Trinkaus, Erik; Wanek, Wolfgang

2005-05-19

The human fossil assemblage from the Mladec Caves in Moravia (Czech Republic) has been considered to derive from a middle or later phase of the Central European Aurignacian period on the basis of archaeological remains (a few stone artefacts and organic items such as bone points, awls, perforated teeth), despite questions of association between the human fossils and the archaeological materials and concerning the chronological implications of the limited archaeological remains. The morphological variability in the human assemblage, the presence of apparently archaic features in some specimens, and the assumed early date of the remains have made this fossil assemblage pivotal in assessments of modern human emergence within Europe. We present here the first successful direct accelerator mass spectrometry radiocarbon dating of five representative human fossils from the site. We selected sample materials from teeth and from one bone for 14C dating. The four tooth samples yielded uncalibrated ages of approximately 31,000 14C years before present, and the bone sample (an ulna) provided an uncertain more-recent age. These data are sufficient to confirm that the Mladec human assemblage is the oldest cranial, dental and postcranial assemblage of early modern humans in Europe and is therefore central to discussions of modern human emergence in the northwestern Old World and the fate of the Neanderthals.

New fossil remains of Homo naledi from the Lesedi Chamber, South Africa

Science.gov (United States)

Hawks, John; Elliott, Marina; Schmid, Peter; Churchill, Steven E; de Ruiter, Darryl J; Roberts, Eric M; Hilbert-Wolf, Hannah; Garvin, Heather M; Williams, Scott A; Delezene, Lucas K; Feuerriegel, Elen M; Randolph-Quinney, Patrick; Kivell, Tracy L; Laird, Myra F; Tawane, Gaokgatlhe; DeSilva, Jeremy M; Bailey, Shara E; Brophy, Juliet K; Meyer, Marc R; Skinner, Matthew M; Tocheri, Matthew W; VanSickle, Caroline; Walker, Christopher S; Campbell, Timothy L; Kuhn, Brian; Kruger, Ashley; Tucker, Steven; Gurtov, Alia; Hlophe, Nompumelelo; Hunter, Rick; Morris, Hannah; Peixotto, Becca; Ramalepa, Maropeng; van Rooyen, Dirk; Tsikoane, Mathabela; Boshoff, Pedro; Dirks, Paul HGM; Berger, Lee R

2017-01-01

The Rising Star cave system has produced abundant fossil hominin remains within the Dinaledi Chamber, representing a minimum of 15 individuals attributed to Homo naledi. Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi. Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi, and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species. DOI: http://dx.doi.org/10.7554/eLife.24232.001 PMID:28483039

25 CFR 291.15 - How long do Class III gaming procedures remain in effect?

Science.gov (United States)

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false How long do Class III gaming procedures remain in effect... ENTERPRISES CLASS III GAMING PROCEDURES § 291.15 How long do Class III gaming procedures remain in effect? Class III gaming procedures remain in effect for the duration specified in the procedures or until...

The potential and biological test on cloned cassava crop remains on local sheep

Science.gov (United States)

Ginting, R.; Umar, S.; Hanum, C.

2018-02-01

This research aims at knowing the potential of cloned cassava crop remains dry matter and the impact of the feeding of the cloned cassava crop remains based complete feed on the consumption, the body weight gain, and the feed conversion of the local male sheep with the average of initial body weight of 7.75±1.75 kg. The design applied in the first stage research was random sampling method with two frames of tile and the second stage research applied Completely Randomized Design (CRD) with three (3) treatments and four (4) replicates. These treatments consisted of P1 (100% grass); P2 (50% grass, 50% complete feed pellet); P3 (100% complete feed from the raw material of cloned cassava crop remaining). Statistical tests showed that the feeding of complete feed whose raw material was from cloned cassava crop remains gave a highly significant impact on decreasing feed consumption, increasing body weight, lowering feed conversion, and increasing crude protein digestibility. The conclusion is that the cloned cassava crop remains can be used as complete sheep feed to replace green grass and can give the best result.

Population cycles: generalities, exceptions and remaining mysteries

Science.gov (United States)

2018-01-01

Population cycles are one of nature's great mysteries. For almost a hundred years, innumerable studies have probed the causes of cyclic dynamics in snowshoe hares, voles and lemmings, forest Lepidoptera and grouse. Even though cyclic species have very different life histories, similarities in mechanisms related to their dynamics are apparent. In addition to high reproductive rates and density-related mortality from predators, pathogens or parasitoids, other characteristics include transgenerational reduced reproduction and dispersal with increasing-peak densities, and genetic similarity among populations. Experiments to stop cyclic dynamics and comparisons of cyclic and noncyclic populations provide some understanding but both reproduction and mortality must be considered. What determines variation in amplitude and periodicity of population outbreaks remains a mystery. PMID:29563267

Intersubunit distances in full-length, dimeric, bacterial phytochrome Agp1, as measured by pulsed electron-electron double resonance (PELDOR) between different spin label positions, remain unchanged upon photoconversion.

Science.gov (United States)

Kacprzak, Sylwia; Njimona, Ibrahim; Renz, Anja; Feng, Juan; Reijerse, Edward; Lubitz, Wolfgang; Krauss, Norbert; Scheerer, Patrick; Nagano, Soshichiro; Lamparter, Tilman; Weber, Stefan

2017-05-05

Bacterial phytochromes are dimeric light-regulated histidine kinases that convert red light into signaling events. Light absorption by the N-terminal photosensory core module (PCM) causes the proteins to switch between two spectrally distinct forms, Pr and Pfr, thus resulting in a conformational change that modulates the C-terminal histidine kinase region. To provide further insights into structural details of photoactivation, we investigated the full-length Agp1 bacteriophytochrome from the soil bacterium Agrobacterium fabrum using a combined spectroscopic and modeling approach. We generated seven mutants suitable for spin labeling to enable application of pulsed EPR techniques. The distances between attached spin labels were measured using pulsed electron-electron double resonance spectroscopy to probe the arrangement of the subunits within the dimer. We found very good agreement of experimental and calculated distances for the histidine-kinase region when both subunits are in a parallel orientation. However, experimental distance distributions surprisingly showed only limited agreement with either parallel- or antiparallel-arranged dimer structures when spin labels were placed into the PCM region. This observation indicates that the arrangements of the PCM subunits in the full-length protein dimer in solution differ significantly from that in the PCM crystals. The pulsed electron-electron double resonance data presented here revealed either no or only minor changes of distance distributions upon Pr-to-Pfr photoconversion. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Prognostic modelling options for remaining useful life estimation by industry

Science.gov (United States)

Sikorska, J. Z.; Hodkiewicz, M.; Ma, L.

2011-07-01

Over recent years a significant amount of research has been undertaken to develop prognostic models that can be used to predict the remaining useful life of engineering assets. Implementations by industry have only had limited success. By design, models are subject to specific assumptions and approximations, some of which are mathematical, while others relate to practical implementation issues such as the amount of data required to validate and verify a proposed model. Therefore, appropriate model selection for successful practical implementation requires not only a mathematical understanding of each model type, but also an appreciation of how a particular business intends to utilise a model and its outputs. This paper discusses business issues that need to be considered when selecting an appropriate modelling approach for trial. It also presents classification tables and process flow diagrams to assist industry and research personnel select appropriate prognostic models for predicting the remaining useful life of engineering assets within their specific business environment. The paper then explores the strengths and weaknesses of the main prognostics model classes to establish what makes them better suited to certain applications than to others and summarises how each have been applied to engineering prognostics. Consequently, this paper should provide a starting point for young researchers first considering options for remaining useful life prediction. The models described in this paper are Knowledge-based (expert and fuzzy), Life expectancy (stochastic and statistical), Artificial Neural Networks, and Physical models.

Highly skewed T-cell receptor V-beta chain repertoire in the bone marrow is associated with response to immunosuppressive drug therapy in children with very severe aplastic anemia

Energy Technology Data Exchange (ETDEWEB)

Schuster, F R; Hubner, B [Clinic of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf (Germany); Führer, M [Department of Pediatric Oncology and Hematology, Dr von Haunersches Children' s Hospital, University of Munich, Munich (Germany); Eckermann, O; Gombert, M [Clinic of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf (Germany); Dornmair, K [Department for Clinical Neuroimmunology, University of Munich, Munich (Germany); Binder, V; Reuther, S; Krell, P [Clinic of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf (Germany); Keller, T [Acomed, statistical analysis GmbH, Leipzig (Germany); Borkhardt, A [Clinic of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Medical Faculty, Heinrich Heine University, Düsseldorf (Germany)

2011-03-01

One of the major obstacles of immunosuppressive therapy (IST) in children with severe aplastic anemia (SAA) comes from the often months-long unpredictability of bone-marrow (BM) recovery. In this prospective study in children with newly diagnosed very severe AA (n=10), who were enrolled in the therapy study SAA-BFM 94, we found a dramatically reduced diversity of both CD4+ and CD8+ BM cells, as scored by comprehensive V-beta chain T-cell receptor (TCR) analysis. Strongly skewed TCR V-beta pattern was highly predictive for good or at least partial treatment response (n=6, CD8+ complexity scoring median 35.5, range 24–73). In contrast, IST in patients with rather moderate reduction of TCR V-beta diversity (n=4, CD8+ complexity scoring median 109.5, range 82–124) always failed (P=0.0095). If confirmed in a larger series of patients, TCR V-beta repertoire in BM may help to assign children with SAA up-front either to IST or to allogeneic stem-cell transplantation.

Highly skewed T-cell receptor V-beta chain repertoire in the bone marrow is associated with response to immunosuppressive drug therapy in children with very severe aplastic anemia

International Nuclear Information System (INIS)

Schuster, F R; Hubner, B; Führer, M; Eckermann, O; Gombert, M; Dornmair, K; Binder, V; Reuther, S; Krell, P; Keller, T; Borkhardt, A

2011-01-01

One of the major obstacles of immunosuppressive therapy (IST) in children with severe aplastic anemia (SAA) comes from the often months-long unpredictability of bone-marrow (BM) recovery. In this prospective study in children with newly diagnosed very severe AA (n=10), who were enrolled in the therapy study SAA-BFM 94, we found a dramatically reduced diversity of both CD4+ and CD8+ BM cells, as scored by comprehensive V-beta chain T-cell receptor (TCR) analysis. Strongly skewed TCR V-beta pattern was highly predictive for good or at least partial treatment response (n=6, CD8+ complexity scoring median 35.5, range 24–73). In contrast, IST in patients with rather moderate reduction of TCR V-beta diversity (n=4, CD8+ complexity scoring median 109.5, range 82–124) always failed (P=0.0095). If confirmed in a larger series of patients, TCR V-beta repertoire in BM may help to assign children with SAA up-front either to IST or to allogeneic stem-cell transplantation

Silicon photonics: some remaining challenges

Science.gov (United States)

Reed, G. T.; Topley, R.; Khokhar, A. Z.; Thompson, D. J.; Stanković, S.; Reynolds, S.; Chen, X.; Soper, N.; Mitchell, C. J.; Hu, Y.; Shen, L.; Martinez-Jimenez, G.; Healy, N.; Mailis, S.; Peacock, A. C.; Nedeljkovic, M.; Gardes, F. Y.; Soler Penades, J.; Alonso-Ramos, C.; Ortega-Monux, A.; Wanguemert-Perez, G.; Molina-Fernandez, I.; Cheben, P.; Mashanovich, G. Z.

2016-03-01

This paper discusses some of the remaining challenges for silicon photonics, and how we at Southampton University have approached some of them. Despite phenomenal advances in the field of Silicon Photonics, there are a number of areas that still require development. For short to medium reach applications, there is a need to improve the power consumption of photonic circuits such that inter-chip, and perhaps intra-chip applications are viable. This means that yet smaller devices are required as well as thermally stable devices, and multiple wavelength channels. In turn this demands smaller, more efficient modulators, athermal circuits, and improved wavelength division multiplexers. The debate continues as to whether on-chip lasers are necessary for all applications, but an efficient low cost laser would benefit many applications. Multi-layer photonics offers the possibility of increasing the complexity and effectiveness of a given area of chip real estate, but it is a demanding challenge. Low cost packaging (in particular, passive alignment of fibre to waveguide), and effective wafer scale testing strategies, are also essential for mass market applications. Whilst solutions to these challenges would enhance most applications, a derivative technology is emerging, that of Mid Infra-Red (MIR) silicon photonics. This field will build on existing developments, but will require key enhancements to facilitate functionality at longer wavelengths. In common with mainstream silicon photonics, significant developments have been made, but there is still much left to do. Here we summarise some of our recent work towards wafer scale testing, passive alignment, multiplexing, and MIR silicon photonics technology.

Green business will remain green

International Nuclear Information System (INIS)

Marcan, P.

2008-01-01

It all started with two words. Climate change. The carbon dioxide trading scheme, which was the politicians' idea on solving the number one global problem, followed. Four years ago, when the project was begun, there was no data for project initiation. Quotas for polluters mainly from energy production and other energy demanding industries were distributed based on spreadsheets, maximum output and expected future development of economies. Slovak companies have had a chance to profit from these arrangements since 2005. Many of them took advantage of the situation and turned the excessive quotas into an extraordinary profit which often reached hundreds of million Sk. The fact that the price of free quotas offered for sale dropped basically to 0 in 2006 only proved that the initial distribution was too generous. And the market reacted to the first official measurements of emissions. Slovak companies also contributed to this development. However, when planning the maximum emission volumes for 2008-2012 period, in spite of the fact that actual data were available, their expectations were not realistic. A glance at the figures in the proposal of the Ministry of Environment is sufficient to realize that there will be no major change in the future. And so for many Slovak companies business with a green future will remain green for the next five years. The state decided to give to selected companies even more free space as far as emissions are concerned. The most privileged companies can expect quotas increased by tens of percent. (author)

Ghost Remains After Black Hole Eruption

Science.gov (United States)

2009-05-01

NASA's Chandra X-ray Observatory has found a cosmic "ghost" lurking around a distant supermassive black hole. This is the first detection of such a high-energy apparition, and scientists think it is evidence of a huge eruption produced by the black hole. This discovery presents astronomers with a valuable opportunity to observe phenomena that occurred when the Universe was very young. The X-ray ghost, so-called because a diffuse X-ray source has remained after other radiation from the outburst has died away, is in the Chandra Deep Field-North, one of the deepest X-ray images ever taken. The source, a.k.a. HDF 130, is over 10 billion light years away and existed at a time 3 billion years after the Big Bang, when galaxies and black holes were forming at a high rate. "We'd seen this fuzzy object a few years ago, but didn't realize until now that we were seeing a ghost", said Andy Fabian of the Cambridge University in the United Kingdom. "It's not out there to haunt us, rather it's telling us something - in this case what was happening in this galaxy billions of year ago." Fabian and colleagues think the X-ray glow from HDF 130 is evidence for a powerful outburst from its central black hole in the form of jets of energetic particles traveling at almost the speed of light. When the eruption was ongoing, it produced prodigious amounts of radio and X-radiation, but after several million years, the radio signal faded from view as the electrons radiated away their energy. HDF 130 Chandra X-ray Image of HDF 130 However, less energetic electrons can still produce X-rays by interacting with the pervasive sea of photons remaining from the Big Bang - the cosmic background radiation. Collisions between these electrons and the background photons can impart enough energy to the photons to boost them into the X-ray energy band. This process produces an extended X-ray source that lasts for another 30 million years or so. "This ghost tells us about the black hole's eruption long after

43 CFR 10.11 - Disposition of culturally unidentifiable human remains.

Science.gov (United States)

2010-10-01

... AMERICAN GRAVES PROTECTION AND REPATRIATION REGULATIONS Human Remains, Funerary Objects, Sacred Objects, or... religious leaders of all Indian tribes and Native Hawaiian organizations: (i) From whose tribal lands, at... objects; (ii) The names and appropriate methods to contact any traditional religious leaders who should be...

Updated Estimates of the Remaining Market Potential of the U.S. ESCO Industry

Energy Technology Data Exchange (ETDEWEB)

Larsen, Peter H. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Energy Analysis and Environmental Impacts Div.; Carvallo Bodelon, Juan Pablo [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Energy Analysis and Environmental Impacts Div.; Goldman, Charles A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Energy Analysis and Environmental Impacts Div.; Murphy, Sean [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Energy Analysis and Environmental Impacts Div.; Stuart, Elizabeth [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Energy Analysis and Environmental Impacts Div.

2017-04-01

The energy service company (ESCO) industry has a well-established track record of delivering energy and economic savings in the public and institutional buildings sector, primarily through the use of performance-based contracts. The ESCO industry often provides (or helps arrange) private sector financing to complete public infrastructure projects with little or no up-front cost to taxpayers. In 2014, total U.S. ESCO industry revenue was estimated at $5.3 billion. ESCOs expect total industry revenue to grow to $7.6 billion in 2017—a 13% annual growth rate from 2015-2017. Researchers at Lawrence Berkeley National Laboratory (LBNL) were asked by the U.S. Department of Energy Federal Energy Management Program (FEMP) to update and expand our estimates of the remaining market potential of the U.S. ESCO industry. We define remaining market potential as the aggregate amount of project investment by ESCOs that is technically possible based on the types of projects that ESCOS have historically implemented in the institutional, commercial, and industrial sectors using ESCO estimates of current market penetration in those sectors. In this analysis, we report U.S. ESCO industry remaining market potential under two scenarios: (1) a base case and (2) a case “unfettered” by market, bureaucratic, and regulatory barriers. We find that there is significant remaining market potential for the U.S. ESCO industry under both the base and unfettered cases. For the base case, we estimate a remaining market potential of $92-$201 billion ($2016). We estimate a remaining market potential of $190-$333 billion for the unfettered case. It is important to note, however, that there is considerable uncertainty surrounding the estimates for both the base and unfettered cases.

Remaining childless : Causes and consequences from a life course perspective

NARCIS (Netherlands)

Keizer, R.

2010-01-01

Little is know about childless individuals in the Netherlands, although currently one out of every five Dutch individuals remains childless. Who are they? How did they end up being childless? How and to what extent are their life outcomes influenced by their childlessness? By focusing on individual

Risk-based management of remaining life of power plant components

International Nuclear Information System (INIS)

Roos, E.; Jovanovic, A.S.; Maile, K.; Auerkari, P.

1999-01-01

The paper describes application of different modules of the MPA-System ALIAS in risk-based management of remaining life of power plant components. The system allows comprehensive coverage of all aspects of the remaining life management, including also the risk analysis and risk management. In addition, thanks to the modular character of the system it is also possible to implement new methods: In the case described here, a new (probabilistic) method for determination of the next inspection time for the components exposed to creep loading has been developed and implemented in the system. Practical application of the method has shown (a) that the mean values obtained by the method fall into the range of results obtained by other methods (based on expert knowledge), and (b) that it is possible to quantify the probability of aberration from the mean values. This in turn allows quantifying the additional risks linked to e.g. prolonging of inspection intervals. (orig.) [de

1-(Benzofuran-2-yl)-2-(3,3,3-trifluoropropyl)aminopentane HCl, 3-F-BPAP, antagonizes the enhancer effect of (-)-BPAP in the shuttle box and leaves the effect of (-)-deprenyl unchanged.

Science.gov (United States)

Knoll, Joseph; Miklya, Ildikó; Knoll, Berta; Yasusa, Takuya; Shimazu, Seiichiro; Yoneda, Fumio

2002-09-13

The subcutaneous administration of 1 mg/kg tetrabenazine, once daily for 5 days, which depletes the catecholamine stores in the brain, significantly inhibits in rats the acquisition of a two-way conditioned avoidance reflex in the shuttle box. Enhancer substances, the tryptamine-derived selective and highly potent enhancer, R-(-)-1-(benzofuran-2-yl)-2-propylaminopentane HCl [(-)-BPAP] (0.05-10 mg/kg), the beta-phenylethylamine (PEA)-derived enhancer, (-)-deprenyl (1-5 mg/kg) and the (-)-deprenyl analogue, free of MAO-B inhibitory potency, (-)-1-phenyl-2-propylaminopentane HCl [(-)-PPAP], (1-5 mg/kg), antagonize in a dose-dependent manner the inhibition of learning caused by tetrabenazine. 1-(Benzofuran 2 yl)-2-(3,3,3-trifluoropropyl)aminopentane HCl [3 F BPAP], a newly synthetized analogue of (-)-BPAP with low specific activity, significantly antagonized the enhancer effect of (-)-BPAP but left the effect of (-)-deprenyl and (-)-PPAP unchanged. This is the first proof for a difference in the mechanism of action between a PEA-derived enhancer substance and its tryptamine-derived peer.

A method for defleshing human remains using household bleach.

Science.gov (United States)

Mann, Robert W; Berryman, Hugh E

2012-03-01

Medical examiners and forensic anthropologists are often faced with the difficult task of removing soft tissue from the human skeleton without damaging the bones, teeth and, in some cases, cartilage. While there are a number of acceptable methods that can be used to remove soft tissue including macerating in water, simmering or boiling, soaking in ammonia, removing with scissors, knife, scalpel or stiff brush, and dermestid beetles, each has its drawback in time, safety, or potential to damage bone. This technical report using the chest plate of a stabbing victim presents a safe and effective alternative method for removing soft tissue from human remains, in particular the chest plate, following autopsy, without damaging or separating the ribs, sternum, and costal cartilage. This method can be used to reveal subtle blunt force trauma to bone, slicing and stabbing injuries, and other forms of trauma obscured by overlying soft tissue. Despite the published cautionary notes, when done properly household bleach (3-6% sodium hypochlorite) is a quick, safe, and effective method for examining cartilage and exposing skeletal trauma by removing soft tissue from human skeletal remains. 2011 American Academy of Forensic Sciences. Published 2011. This article is a U.S. Government work and is in the public domain in the U.S.A.

Determination of Remaining Useful Life of Gas Turbine Blade

Directory of Open Access Journals (Sweden)

Meor Said Mior Azman

2016-01-01

Full Text Available The aim of this research is to determine the remaining useful life of gas turbine blade, using service-exposed turbine blades. This task is performed using Stress Rupture Test (SRT under accelerated test conditions where the applied stresses to the specimen is between 400 MPa to 600 MPa and the test temperature is 850°C. The study will focus on the creep behaviour of the 52000 hours service-exposed blades, complemented with creep-rupture modelling using JMatPro software and microstructure examination using optical microscope. The test specimens, made up of Ni-based superalloy of the first stage turbine blades, are machined based on International Standard (ISO 24. The results from the SRT will be analyzed using these two main equations – Larson-Miller Parameter and Life Fraction Rule. Based on the results of the remaining useful life analysis, the 52000h service-exposed blade has the condition to operate in the range of another 4751 hr to 18362 hr. The microstructure examinations shows traces of carbide precipitation that deteriorate the grain boundaries that occurs during creep process. Creep-rupture life modelling using JMatPro software has shown good agreement with the accelerated creep rupture test with minimal error.

New paleoradiological investigations of ancient human remains from North West Lombardy archaeological excavations

Energy Technology Data Exchange (ETDEWEB)

Licata, Marta; Borgo, Melania; Armocida, Giuseppe; Nicosia, Luca; Ferioli, Elena [University of Insubria (Varese), Department of Biotechnology and Life Sciences, Varese (Italy)

2016-03-15

Since its birth in 1895, radiology has been used to study ancient mummies. The purpose of this article is to present paleoradiological investigations conducted on several medieval human remains in Varese province. Anthropological (generic identification) and paleopathological analyses were carried out with the support of diagnostic imaging (X-ray and CT scans). Human remains were discovered during excavations of medieval archaeological sites in northwest Lombardy. Classical physical anthropological methods were used for the macroscopic identification of the human remains. X-ray and CT scans were performed on the same scanner (16-layer Hitachi Eclos 16 X-ray equipment). Radiological analysis permitted investigating (1) the sex, (2) age of death, (3) type of trauma, (4) therapeutic interventions and (5) osteomas in ancient human remains. In particular, X-ray and CT examinations showed dimorphic facial traits on the mummified skull, and the same radiological approaches allowed determining the age at death from a mummified lower limb. CT analyses allow investigating different types of traumatic lesions in skulls and postcranial skeleton portions and reconstructing the gait and functional outcomes of a fractured femur. Moreover, one case of possible Gardner's syndrome (GS) was postulated from observing multiple osteomas in an ancient skull. Among the medical tests available to the clinician, radiology is the most appropriate first-line procedure for a diagnostic approach to ancient human remains because it can be performed without causing any significant damage to the specimen. (orig.)

New paleoradiological investigations of ancient human remains from North West Lombardy archaeological excavations

International Nuclear Information System (INIS)

Licata, Marta; Borgo, Melania; Armocida, Giuseppe; Nicosia, Luca; Ferioli, Elena

2016-01-01

Since its birth in 1895, radiology has been used to study ancient mummies. The purpose of this article is to present paleoradiological investigations conducted on several medieval human remains in Varese province. Anthropological (generic identification) and paleopathological analyses were carried out with the support of diagnostic imaging (X-ray and CT scans). Human remains were discovered during excavations of medieval archaeological sites in northwest Lombardy. Classical physical anthropological methods were used for the macroscopic identification of the human remains. X-ray and CT scans were performed on the same scanner (16-layer Hitachi Eclos 16 X-ray equipment). Radiological analysis permitted investigating (1) the sex, (2) age of death, (3) type of trauma, (4) therapeutic interventions and (5) osteomas in ancient human remains. In particular, X-ray and CT examinations showed dimorphic facial traits on the mummified skull, and the same radiological approaches allowed determining the age at death from a mummified lower limb. CT analyses allow investigating different types of traumatic lesions in skulls and postcranial skeleton portions and reconstructing the gait and functional outcomes of a fractured femur. Moreover, one case of possible Gardner's syndrome (GS) was postulated from observing multiple osteomas in an ancient skull. Among the medical tests available to the clinician, radiology is the most appropriate first-line procedure for a diagnostic approach to ancient human remains because it can be performed without causing any significant damage to the specimen. (orig.)

Scientific Management Still Endures in Education

Science.gov (United States)

Ireh, Maduakolam

2016-01-01

Some schools in America have changed, while others remain unchanged due largely to the accretion of small adjustments in what remains a very traditional enterprise. The problem is rooted in the propagation and adoption of scientific management by educators who applied and/or continues to apply it to education to restore order and for…

Explaining why nurses remain in or leave bedside nursing: a critical ethnography.

Science.gov (United States)

Mahon, Paula; McPherson, Gladys

2014-09-01

To describe the application of critical ethnography to explain nurses' decisions to remain in or leave bedside nursing, and to describe researcher positioning and reflexivity. Enquiry into hospital nurses' decisions to remain in or leave bedside nursing positions has been conducted from a variety of theoretical perspectives by researchers adopting a range of methodological approaches. This research helps to explain how work environments can affect variables such as job satisfaction and turnover, but provides less insight into how personal and professional factors shape decisions to remain in or leave bedside nursing. A critical theoretical perspective was taken to examine the employment decisions made by nurses in a paediatric intensive care unit (PICU). Data was collected from nurses (n=31) through semi-structured interviews and unobtrusive observation. The authors describe critical ethnography as a powerful research framework for enquiry that allowed them to challenge assumptions about why nurses remain in or leave their jobs, and to explore how issues of fairness and equity contribute to these decisions. Critical ethnography offers a powerful methodology for investigations into complex interactions, such as those between nurses in a PICU. In adopting this methodology, researchers should be sensitised to manifestations of power, attend to their stance and location, and reflexion. The greatest challenges from this research included how to make sense of the insider position, how to acknowledge assumptions and allow these to be challenged, and how to ensure that power relationships in the environment and in the research were attended to.

"Recent" macrofossil remains from the Lomonosov Ridge, central Arctic Ocean

Science.gov (United States)

Le Duc, Cynthia; de Vernal, Anne; Archambault, Philippe; Brice, Camille; Roberge, Philippe

2016-04-01

The examination of surface sediment samples collected from 17 sites along the Lomonosov Ridge at water depths ranging from 737 to 3339 meters during Polarstern Expedition PS87 in 2014 (Stein, 2015), indicates a rich biogenic content almost exclusively dominated by calcareous remains. Amongst biogenic remains, microfossils (planktic and benthic foraminifers, pteropods, ostracods, etc.) dominate but millimetric to centrimetric macrofossils occurred frequently at the surface of the sediment. The macrofossil remains consist of a large variety of taxa, including gastropods, bivalvia, polychaete tubes, scaphopods, echinoderm plates and spines, and fish otoliths. Among the Bivalvia, the most abundant taxa are Portlandia arctica, Hyalopecten frigidus, Cuspidaria glacilis, Policordia densicostata, Bathyarca spp., and Yoldiella spp. Whereas a few specimens are well preserved and apparently pristine, most mollusk shells displayed extensive alteration features. Moreover, most shells were covered by millimeter scale tubes of the serpulid polychaete Spirorbis sp. suggesting transport from low intertidal or subtidal zone. Both the ecological affinity and known geographic distribution of identified bivalvia as named above support the hypothesis of transportation rather than local development. In addition to mollusk shells, more than a hundred fish otoliths were recovered in surface sediments. The otoliths mostly belong to the Gadidae family. Most of them are well preserved and without serpulid tubes attached to their surface, suggesting a local/regional origin, unlike the shell remains. Although recovered at the surface, the macrofaunal assemblages of the Lomonosov Ridge do not necessarily represent the "modern" environments as they may result from reworking and because their occurrence at the surface of the sediment may also be due to winnowing of finer particles. Although the shells were not dated, we suspect that their actual ages may range from modern to several thousands of

Studies on protozoa in ancient remains - A Review

Directory of Open Access Journals (Sweden)

Liesbeth Frías

2013-02-01

Full Text Available Paleoparasitological research has made important contributions to the understanding of parasite evolution and ecology. Although parasitic protozoa exhibit a worldwide distribution, recovering these organisms from an archaeological context is still exceptional and relies on the availability and distribution of evidence, the ecology of infectious diseases and adequate detection techniques. Here, we present a review of the findings related to protozoa in ancient remains, with an emphasis on their geographical distribution in the past and the methodologies used for their retrieval. The development of more sensitive detection methods has increased the number of identified parasitic species, promising interesting insights from research in the future.

Thymic function and T cell parameters in a natural human experimental model of seasonal infectious diseases and nutritional burden

Directory of Open Access Journals (Sweden)

Morgan Gareth

2011-06-01

Full Text Available Abstract Background The study exploits a natural human experimental model of subsistence farmers experiencing chronic and seasonally modified food shortages and infectious burden. Two seasons existed, one of increased deprivation and infections (Jul-Dec, another of abundance and low infections (Jan-Jun; referred to as the hungry/high infection and harvest/low infection seasons respectively. Prior analysis showed a 10-fold excess in infectious disease associated mortality in young adults born in the hungry/high infection versus harvest/low infection season, and reduced thymic output and T cell counts in infancy. Here we report findings on the role of early life stressors as contributors to the onset of T cell immunological defects in later life. Methods We hypothesised that season of birth effects on thymic function and T cell immunity would be detectable in young adults since Kaplan-Meier survival curves indicated this to be the time of greatest mortality divergence. T cell subset analyses by flow-cytometry, sjTRECs, TCRVβ repertoire and telomere length by PCR, were performed on samples from 60 males (18-23 y selected to represent births in the hungry/high infection and harvest/low infection Results Total lymphocyte counts were normal and did not differ by birth season. CD3+ and CD4+ but not CD8+ counts were lower for those born during the hungry/high infection season. CD8+ telomere length also tended to be shorter. Overall, CD8+ TCRVβ repertoire skewing was observed with 'public' expressions and deletions seen in TCRVβ12/22 and TCRVβ24, respectively but no apparent effect of birth season. Conclusions We conclude that, although thymic function was unchanged, the CD4+ and CD3+ counts, and CD8+ telomere length results suggested that aspects of adult T cell immunity were under the influence of early life stressors. The endemicity of CMV and HBV suggested that chronic infections may modulate immunity through T cell repertoire development. The

75 FR 5108 - Notice of Inventory Completion: University of Wyoming, Anthropology Department, Human Remains...

Science.gov (United States)

2010-02-01

... Wyoming, Anthropology Department, Human Remains Repository, Laramie, WY AGENCY: National Park Service... funerary objects in the possession and control of the University of Wyoming, Anthropology Department, Human... of Wyoming, Anthropology Department, Human Remains Repository professional staff in consultation with...

Molecular fingerprinting of complex grass allergoids: size assessments reveal new insights in epitope repertoires and functional capacities.

Science.gov (United States)

Starchenka, S; Bell, A J; Mwange, J; Skinner, M A; Heath, M D

2017-01-01

that modification allows shorter-course therapy options as a result of providing an IgG epitope repertoire important for efficacy. Additionally, the work paves the way to help further develop methods for standardising allergoid platforms.

30-day mortality after coronary artery bypass grafting and valve surgery has greatly improved over the last decade, but the 1-year mortality remains constant

Directory of Open Access Journals (Sweden)

Laura Sommer Hansen

2015-01-01

Full Text Available Introduction: European system for cardiac operative risk evaluation (EuroSCORE is a valuable tool in control of the quality of cardiac surgery. However, the validity of the risk score for the individual patient may be questioned. The present study was carried out to investigate whether the continued fall in short-term mortality reflects an actual improvement in late mortality, and subsequently, to investigate EuroSCORE as predictor of 1-year mortality. Methods: A population-based cohort study of 25,602 patients from a 12-year period from three public university hospitals undergoing coronary artery bypass grafting (CABG or valve surgery. Analysis was carried out based on EuroSCORE, age and co-morbidity factors (residual EuroSCORE. Results: During the period the average age increased from 65.1 ± 10.0 years to 68.9 ± 10.7 years (P < 0.001, one-way ANOVA, and the number of females increased from 26.0% to 28.2% (P = 0.0012, Chi-square test. The total EuroSCORE increased from 4.67 to 5.68 while the residual EuroSCORE decreased from 2.64 to 1.83. Thirty-day mortality decreased from 4.07% in 1999-2000 to 2.44% in 2011-2012 (P = 0.0056; Chi-square test, while 1-year mortality was unchanged (6.50% in 1999-2000 vs. 6.25% in 2011-2012 [P = 0.8086; Chi-square test]. Discussion: The study demonstrates that both co-morbidity and age has a great impact on 30-day mortality. However, with time the impact of co-morbidity seems less. Thus, age is more important than co-morbidity in late mortality. The various developments in short and long-term mortality are not readily explained. Conclusion: Although 30-day mortality of CABG and valve surgery patients has decreased during the 12-year period, the 1-year mortality remains the same.

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

Science.gov (United States)

Gadala-Maria, Daniel; Yaari, Gur; Uduman, Mohamed; Kleinstein, Steven H

2015-02-24

Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential response to infection and vaccination. Repertoire properties can now be studied at large-scale through next-generation sequencing of rearranged Ig genes. Accurate analysis of these repertoire-sequencing (Rep-Seq) data requires identifying the germline variable (V), diversity (D), and joining (J) gene segments used by each Ig sequence. Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles. However, existing databases are likely to be incomplete and novel polymorphisms are hard to differentiate from the frequent occurrence of somatic hypermutations in Ig sequences. Here we develop a Tool for Ig Genotype Elucidation via Rep-Seq (TIgGER). TIgGER analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This information is then used to improve the initial V segment assignments from existing tools, like IMGT/HighV-QUEST. The application of TIgGER to Rep-Seq data from seven subjects identified 11 novel V segment alleles, including at least one in every subject examined. These novel alleles constituted 13% of the total number of unique alleles in these subjects, and impacted 3% of V(D)J segment assignments. These results reinforce the highly polymorphic nature of human Ig V genes, and suggest that many novel alleles remain to be discovered. The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses.

Expanding the knowledge on lignocellulolytic and redox enzymes of worker and soldier castes from the lower termite Coptotermes gestroi

Directory of Open Access Journals (Sweden)

João Paulo Lourenço Franco Cairo

2016-10-01

Full Text Available Termites are considered one of the most efficient decomposers of lignocelluloses on Earth due to their ability to produce, along with its microbial symbionts, a repertoire of carbohydrate-active enzymes (CAZymes. Recently, a set of Pro-oxidant, Antioxidant, and Detoxification enzymes (PAD were also correlated with the metabolism of carbohydrates and lignin in termites. The lower termite Coptotermes gestroi is considered the main urban pest in Brazil, causing damage to wood constructions. Recently, analysis of the enzymatic repertoire of C. gestroi unveiled the presence of different CAZymes. Because the gene profile of CAZy/PAD enzymes endogenously synthesized by C. gestroi and also by their symbiotic protists remains unclear, the aim of this study was to explore the eukaryotic repertoire of these enzymes in worker and soldier castes of C. gestroi. Our findings showed that worker and soldier castes present similar repertoires of CAZy/PAD enzymes, and also confirmed that endo-glucanases (GH9 and beta-glucosidases (GH1 were the most important glycoside hydrolase families related to lignocellulose degradation in both castes. Classical cellulases such as exo-glucanases (GH7 and endo-glucanases (GH5 and GH45, as well as classical xylanases (GH10 and GH11, were found in both castes only taxonomically related to protists, highlighting the importance of symbiosis in C. gestroi. Moreover, our analysis revealed the presence of Auxiliary Activity enzyme families (AAs, which could be related to lignin modifications in termite digestomes. In conclusion, this report expanded the knowledge on genes and proteins related to CAZy/PAD enzymes from worker and soldier castes of lower termites, revealing new potential enzyme candidates for second-generation biofuel processes.

Expanding the Knowledge on Lignocellulolytic and Redox Enzymes of Worker and Soldier Castes from the Lower Termite Coptotermes gestroi.

Science.gov (United States)

Franco Cairo, João P L; Carazzolle, Marcelo F; Leonardo, Flávia C; Mofatto, Luciana S; Brenelli, Lívia B; Gonçalves, Thiago A; Uchima, Cristiane A; Domingues, Romênia R; Alvarez, Thabata M; Tramontina, Robson; Vidal, Ramon O; Costa, Fernando F; Costa-Leonardo, Ana M; Paes Leme, Adriana F; Pereira, Gonçalo A G; Squina, Fabio M

2016-01-01

Termites are considered one of the most efficient decomposers of lignocelluloses on Earth due to their ability to produce, along with its microbial symbionts, a repertoire of carbohydrate-active enzymes (CAZymes). Recently, a set of Pro-oxidant, Antioxidant, and Detoxification enzymes (PAD) were also correlated with the metabolism of carbohydrates and lignin in termites. The lower termite Coptotermes gestroi is considered the main urban pest in Brazil, causing damage to wood constructions. Recently, analysis of the enzymatic repertoire of C. gestroi unveiled the presence of different CAZymes. Because the gene profile of CAZy/PAD enzymes endogenously synthesized by C. gestroi and also by their symbiotic protists remains unclear, the aim of this study was to explore the eukaryotic repertoire of these enzymes in worker and soldier castes of C. gestroi . Our findings showed that worker and soldier castes present similar repertoires of CAZy/PAD enzymes, and also confirmed that endo-glucanases (GH9) and beta-glucosidases (GH1) were the most important glycoside hydrolase families related to lignocellulose degradation in both castes. Classical cellulases such as exo-glucanases (GH7) and endo-glucanases (GH5 and GH45), as well as classical xylanases (GH10 and GH11), were found in both castes only taxonomically related to protists, highlighting the importance of symbiosis in C. gestroi . Moreover, our analysis revealed the presence of Auxiliary Activity enzyme families (AAs), which could be related to lignin modifications in termite digestomes. In conclusion, this report expanded the knowledge on genes and proteins related to CAZy/PAD enzymes from worker and soldier castes of lower termites, revealing new potential enzyme candidates for second-generation biofuel processes.

A code of ethics for evidence-based research with ancient human remains.

Science.gov (United States)

Kreissl Lonfat, Bettina M; Kaufmann, Ina Maria; Rühli, Frank

2015-06-01

As clinical research constantly advances and the concept of evolution becomes a strong and influential part of basic medical research, the absence of a discourse that deals with the use of ancient human remains in evidence-based research is becoming unbearable. While topics such as exhibition and excavation of human remains are established ethical fields of discourse, when faced with instrumentalization of ancient human remains for research (i.e., ancient DNA extractions for disease marker analyses) the answers from traditional ethics or even more practical fields of bio-ethics or more specific biomedical ethics are rare to non-existent. The Centre for Evolutionary Medicine at the University of Zurich solved their needs for discursive action through the writing of a self-given code of ethics which was written in dialogue with the researchers at the Institute and was published online in Sept. 2011: http://evolutionäremedizin.ch/coe/. The philosophico-ethical basis for this a code of conduct and ethics and the methods are published in this article. © 2015 Wiley Periodicals, Inc.

Some social and forensic aspects of exhumation and reinterment of industrial revolution remains.

Science.gov (United States)

Duff, E J; Johnson, J S

1974-03-23

The aetiological aspects of exhumed remains from two burial sites were examined using 1839 and 1879 as years of comparison. We tried to discover whether the sample of recovered remains was representative of those buried. The state of the remains varied according to the type of soil and coffin material in which they were buried. At the earlier date most deaths were caused by infectious lesions rather than degenerative ones and 76% of those who died were below employable age-whereas in 1879 the commonest causes of death were tuberculosis ("phthisis") and bronchitis, and 42% died before they could be employed. The registration of deaths were recorded more accurately at the later date, and it was easier to build up a picture of the age, sex, and occupation of the people who died.

Greater repertoire and temporal variability of cross-frequency coupling (CFC modes in resting-state neuromagnetic recordings among children with reading difficulties

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Stavros I Dimitriadis

2016-04-01

Full Text Available AbstractCross-frequency, phase-to-amplitude coupling (PAC between neuronal oscillations at rest may serve as the substrate that supports information exchange between functionally specialized neuronal populations both within and between cortical regions. The study utilizes novel algorithms to identify prominent instantaneous modes of cross-frequency coupling and their temporal stability in resting state magnetoencephalography (MEG data from 23 students experiencing severe reading difficulties (RD and 27 age-matched non-impaired readers (NI.Phase coherence estimates were computed in order to identify the prominent mode of PAC interaction for each sensor, sensor pair, and pair of frequency bands (from δ to γ at successive temporal segments of the continuous MEG record. The degree of variability in the characteristic frequency-pair PACf1-f2 modes over time was also estimated. Results revealed a wider repertoire of prominent PAC interactions in RD as compared to NI students, suggesting an altered functional substrate for information exchange between neuronal assemblies in the former group. Moreover, RD students showed significant variability in PAC modes over time. This temporal instability of PAC values was particularly prominent: (a within and between right hemisphere temporal and occipitotemporal sensors and, (b between left hemisphere frontal, temporal, and occipitotemporal sensors and corresponding right hemisphere sites. Altered modes of neuronal population coupling may help account for extant data revealing reduced, task-related neurophysiological and hemodynamic activation in left hemisphere regions involved in the reading network in RD. Moreover, the spatial distribution of pronounced instability of cross-frequency coupling modes in this group may provide an explanation for previous reports suggesting the presence of inefficient compensatory mechanisms to support reading.

Cryptanalysis of a spatiotemporal chaotic cryptosystem

International Nuclear Information System (INIS)

Rhouma, Rhouma; Belghith, Safya

2009-01-01

This paper proposes three different attacks on a recently proposed chaotic cryptosystem in [Li P, Li Z, Halang WA, Chen G. A stream cipher based on a spatiotemporal chaotic system. Chaos, Solitons and Fractals 2007;32:1867-76]. The cryptosystem under study displays weakness in the generation of the keystream. The encryption is made by generating a keystream mixed with blocks generated from the plaintext. The so obtained keystream remains unchanged for every encryption procedure. Moreover, its generation does neither depend on the plaintext nor on the ciphertext, that's to say, the keystream remains unchangeable for every plaintext with the same length. Guessing the keystream leads to guessing the key. This paper presents three possible attacks able to break the whole cryptosystem based on this drawback in generating the keystream.

Effects of prolonged recombinant human erythropoietin administration on muscle membrane transport systems and metabolic marker enzymes

DEFF Research Database (Denmark)

Juel, C; Thomsen, J J; Rentsch, R L

2007-01-01

on the expression of muscle membrane transport proteins. Likewise, improvements in performance may involve upregulation of metabolic enzymes. Since Epo is known to augment performance we tested the effect of rHuEpo on some marker enzymes that are related to aerobic capacity. For these purposes eight subjects...... performance by approximately 54%. Membrane transport systems and carbonic anhydrases involved in pH regulation remained unchanged. Of the Na(+), K(+)-pump isoforms only the density of the alpha2 subunit was decreased (by 22%) after treatment. The marker enzymes cytochrom c and hexokinase remained unchanged......Adaptations to chronic hypoxia involve changes in membrane transport proteins. The underlying mechanism of this response may be related to concomitant occurring changes in erythropoietin (Epo) levels. We therefore tested the direct effects of recombinant human erythropoietin (rHuEpo) treatment...

Improved glucose tolerance after high-load strength training in patients undergoing dialysis

DEFF Research Database (Denmark)

Mølsted, Stig; Harrison, Adrian Paul; Eidemak, Inge

2013-01-01

glucose tolerance (n = 9). Conclusion: The conducted strength training was associated with a significant improvement in glucose tolerance in patients with impaired glucose tolerance or type 2 diabetes undergoing dialysis. The effect was apparently not associated with muscle hypertrophy, whereas the muscle...... a week. Muscle fiber size, composition and capillary density were analyzed in biopsies obtained in the vastus lateralis muscle. Glucose tolerance and the insulin response were measured by a 2-hour oral glucose tolerance test. Results: All outcome measures remained unchanged during the control period....... After strength training the relative area of type 2X fibers was decreased. Muscle fiber size and capillary density remained unchanged. After the strength training, insulin concentrations were significantly lower in patients with impaired glucose tolerance or type 2 diabetes (n = 14) (fasting insulin...

Nuclear remains an economic and ecologic asset

International Nuclear Information System (INIS)

Le Ngoc, Boris

2015-01-01

The author herein outlines the several benefits of nuclear energy and nuclear industry for France. He first outlines that France possesses 97 per cent of de-carbonated electricity thanks to nuclear energy (77 pc) and renewable energies (20 pc, mainly hydraulic), and that renewable energies must be developed in the building and transport sectors to be able to get rid of the environmentally and financially costly fossil energies. He outlines that reactor maintenance and the nuclear fuel cycle industry are fields of technological leadership for the French nuclear industry which is, after motor industry and aircraft industry, the third industrial sector in France. He indicates that nuclear electricity is to remain the most competitive one, and that nuclear energy and renewable energies must not be opposed to it but considered as complementary in the struggle against climate change, i.e. to reduce greenhouse gas emissions and to get rid of the prevalence of fossil energies

The Soriya Band: A Case Study of Cambodian American Rock Music in Southern California

OpenAIRE

Seng, Sophea

2016-01-01

Following the 1975-1979 genocide, Cambodian exiles in the U.S. recreated cultural institutions through music. Music remains significant in rebuilding cultural life in diasporic Cambodian communities. Live bands perform contemporary and classic ballads during Cambodian New Year in April, at wedding parties and in restaurants on weekend nights. Live rock bands continue to dot community celebrations as survivors collectively create musical repertoires and schedule practices to perform at festive...

The first Neanderthal remains from an open-air Middle Palaeolithic site in the Levant.

Science.gov (United States)

Been, Ella; Hovers, Erella; Ekshtain, Ravid; Malinski-Buller, Ariel; Agha, Nuha; Barash, Alon; Mayer, Daniella E Bar-Yosef; Benazzi, Stefano; Hublin, Jean-Jacques; Levin, Lihi; Greenbaum, Noam; Mitki, Netta; Oxilia, Gregorio; Porat, Naomi; Roskin, Joel; Soudack, Michalle; Yeshurun, Reuven; Shahack-Gross, Ruth; Nir, Nadav; Stahlschmidt, Mareike C; Rak, Yoel; Barzilai, Omry

2017-06-07

The late Middle Palaeolithic (MP) settlement patterns in the Levant included the repeated use of caves and open landscape sites. The fossil record shows that two types of hominins occupied the region during this period-Neandertals and Homo sapiens. Until recently, diagnostic fossil remains were found only at cave sites. Because the two populations in this region left similar material cultural remains, it was impossible to attribute any open-air site to either species. In this study, we present newly discovered fossil remains from intact archaeological layers of the open-air site 'Ein Qashish, in northern Israel. The hominin remains represent three individuals: EQH1, a nondiagnostic skull fragment; EQH2, an upper right third molar (RM 3 ); and EQH3, lower limb bones of a young Neandertal male. EQH2 and EQH3 constitute the first diagnostic anatomical remains of Neandertals at an open-air site in the Levant. The optically stimulated luminescence ages suggest that Neandertals repeatedly visited 'Ein Qashish between 70 and 60 ka. The discovery of Neandertals at open-air sites during the late MP reinforces the view that Neandertals were a resilient population in the Levant shortly before Upper Palaeolithic Homo sapiens populated the region.

Mammalian remains from an Indian site on Curaçao

NARCIS (Netherlands)

Hooijer, D.A.

1963-01-01

The animal remains (mostly of shells, fish, and turtles) collected by Mr. H. R. VAN HEEKEREN and Mr. C. J. DU RY at the Indian site Sint Jan II, Curaçao, in March, 1960, include a few specimens of mammals. As was the case with the Indian site Santa Cruz, on Aruba (HOOIJER, 1960), several forms are

RHM 1(2).indb

African Journals Online (AJOL)

mike

Research in Hospitality Management 2012, 1(2): 53–63 ... Strategies used to incorporate source materials also remained largely unchanged, with learners ..... score (as is the case in IELTS). ...... Introduction: situating the concept of practice.

Flexural vibrations of finite composite poroelastic cylinders

Indian Academy of Sciences (India)

We know from daily experience that many man-made structures consist of ..... The physical parameters of these composite cylinders following Eq. (38) are given in ... Titanium implants remain virtually unchanged in appearance, which offers ...

Skeletal Indicators of Shark Feeding on Human Remains: Evidence from Florida Forensic Anthropology Cases.

Science.gov (United States)

Stock, Michala K; Winburn, Allysha P; Burgess, George H

2017-11-01

This research examines a series of six Florida forensic anthropology cases that exhibit taphonomic evidence of marine deposition and shark-feeding activities. In each case, we analyzed patterns of trauma/damage on the skeletal remains (e.g., sharp-force bone gouges and punctures) and possible mechanisms by which they were inflicted during shark predation/scavenging. In some cases, shark teeth were embedded in the remains; in the absence of this evidence, we measured interdental distance from defects in the bone to estimate shark body length, as well as to draw inferences about the potential species responsible. We discuss similarities and differences among the cases and make comparisons to literature documenting diagnostic shark-inflicted damage to human remains from nearby regions. We find that the majority of cases potentially involve bull or tiger sharks scavenging the remains of previously deceased, adult male individuals. This scavenging results in a distinctive taphonomic signature including incised gouges in cortical bone. © 2017 American Academy of Forensic Sciences.

Cognitive bias in forensic anthropology: visual assessment of skeletal remains is susceptible to confirmation bias.

Science.gov (United States)

Nakhaeizadeh, Sherry; Dror, Itiel E; Morgan, Ruth M

2014-05-01

An experimental study was designed to examine cognitive biases within forensic anthropological non-metric methods in assessing sex, ancestry and age at death. To investigate examiner interpretation, forty-one non-novice participants were semi randomly divided into three groups. Prior to conducting the assessment of the skeletal remains, two of the groups were given different extraneous contextual information regarding the sex, ancestry and age at death of the individual. The third group acted as a control group with no extraneous contextual information. The experiment was designed to investigate if the interpretation and conclusions of the skeletal remains would differ amongst participants within the three groups, and to assess whether the examiners would confirm or disagree with the given extraneous context when establishing a biological profile. The results revealed a significant biasing effect within the three groups, demonstrating a strong confirmation bias in the assessment of sex, ancestry and age at death. In assessment of sex, 31% of the participants in the control group concluded that the skeleton remains were male. In contrast, in the group that received contextual information that the remains were male, 72% concluded that the remains were male, and in the participant group where the context was that the remains were of a female, 0% of the participants concluded that the remains were male. Comparable results showing bias were found in assessing ancestry and age at death. These data demonstrate that cognitive bias can impact forensic anthropological non-metric methods on skeletal remains and affects the interpretation and conclusions of the forensic scientists. This empirical study is a step in establishing an evidence base approach for dealing with cognitive issues in forensic anthropological assessments, so as to enhance this valuable forensic science discipline. Copyright © 2013 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights

Using of microvertebrate remains in reconstruction of late quaternary (Holocene paleoclimate, Eastern Iran

Directory of Open Access Journals (Sweden)

Mansour Aliabadian

2015-09-01

Full Text Available   Introduction   Study of quaternary microvertebrate remains in eastern Iran, according to a few of the sediments is very important. Reconstruction of quaternary climate in many parts of West and North West of Iran as the biggest karst state is possible, such as cave Kani Mikaiel (Hashemi et al. 2005, 2006, 2007ab, 2008 2010, Jangjoo et al . 2010, Yafteh cave (Otte et al. 2007, Hashemi et al. 2015. However, such studies were very poor in eastern and north-eastern Iran (Hashemi and darvish 2006 Hashemi et al. 2008, 2015. Investigation of taxonomic identification quantification and distribution of micromammals revealed that these remains are useful in paleontology and archaeological research, because their abundance is useful for paleobiostratigraphy and dating of continental sediments. The recent research is about reconstruction of paleoclimate in two archeological sites of Konar sandal (KS (Jiroft and Tapeh Naderi (TN (Mashhad based on the microvertebrate and especially Tatera indica species. In these sites we attempted to solve the palaeoenvironment condition by analysis of rodent remains which hold the greatest potential to monitoring of ecological parameters (Hoover et al. 1977 Getz 1961 Reig 1970 Merritt 1974. Combining of a rich network of data with using of morphological and morphometric methods reconstruction of paleoenvironment documentation and investigation of their relationship with the environment is the main result of this research .       Material & Methods   In both zooarchaeological samples which are composed of juveniles and young individual rodent, (KS, NISP=800 and TN, NISP=3 cranial and postcranial remains were sorted anatomically and washed with water. Dental pattern of mandible and maxillary tooth rows were drowns using a drawing tube connecting to a stereomicroscope (Olympus SZH-10. All recovered teeth fragments were measured based on the greatest dental length and width of the upper and lower jaw molars

Using of microvertebrate remains in reconstruction of late quaternary (Holocene paleoclimate, Eastern Iran

Directory of Open Access Journals (Sweden)

Narges Hashemi

2015-10-01

Full Text Available Introduction   Study of quaternary microvertebrate remains in eastern Iran, according to a few of the sediments is very important. Reconstruction of quaternary climate in many parts of West and North West of Iran as the biggest karst state is possible, such as cave Kani Mikaiel (Hashemi et al. 2005, 2006, 2007a;b, 2008; 2010, Jangjoo et al . 2010, Yafteh cave (Otte et al. 2007, Hashemi et al. 2015. However, such studies were very poor in eastern and north-eastern Iran (Hashemi and darvish 2006; Hashemi et al. 2008, 2015. Investigation of taxonomic identification; quantification and distribution of micromammals revealed that these remains are useful in paleontology and archaeological research, because their abundance is useful for paleobiostratigraphy and dating of continental sediments. The recent research is about reconstruction of paleoclimate in two archeological sites of Konar sandal (KS (Jiroft and Tapeh Naderi (TN (Mashhad based on the microvertebrate and especially Tatera indica species. In these sites we attempted to solve the palaeoenvironment condition by analysis of rodent remains which hold the greatest potential to monitoring of ecological parameters (Hoover et al. 1977; Getz 1961; Reig 1970; Merritt 1974. Combining of a rich network of data with using of morphological and morphometric methods; reconstruction of paleoenvironment; documentation and investigation of their relationship with the environment is the main result of this research .       Material & Methods   In both zooarchaeological samples which are composed of juveniles and young individual rodent, (KS, NISP=800 and TN, NISP=3 cranial and postcranial remains were sorted anatomically and washed with water. Dental pattern of mandible and maxillary tooth rows were drowns using a drawing tube connecting to a stereomicroscope (Olympus SZH-10. All recovered teeth fragments were measured based on the greatest dental length and width of the upper and lower jaw molars when

Generation-specific incentives and disincentives for nurse faculty to remain employed.

Science.gov (United States)

Tourangeau, Ann E; Wong, Matthew; Saari, Margaret; Patterson, Erin

2015-05-01

The aims of this paper are to: (1) describe work characteristics that nurse faculty report encourage them to remain in or leave their academic positions; and (2) determine if there are generational differences in work characteristics selected. Nurse faculty play key roles in preparing new nurses and graduate nurses. However, educational institutions are challenged to maintain full employment in faculty positions. A cross-sectional, descriptive survey design was employed. Ontario nurse faculty were asked to select, from a list, work characteristics that entice them to remain in or leave their faculty positions. Respondent data (n = 650) were collected using mailed surveys over four months in 2011. While preferred work characteristics differed across generations, the most frequently selected incentives enticing nurse faculty to stay were having: a supportive director/dean, reasonable workloads, supportive colleagues, adequate resources, manageable class sizes and work/life balance. The most frequently selected disincentives included: unmanageable workloads, unsupportive organizations, poor work environments, exposure to bullying, belittling and other types of incivility in the workplace and having an unsupportive director/dean. This research yields new and important knowledge about work characteristics that nurse faculty report shape their decisions to remain in or leave their current employment. Certain work characteristics were rated as important among all generations. Where similarities exist, broad strategies addressing work characteristics may effectively promote nurse faculty retention. However, where generational differences exist, retention-promoting strategies should target generation-specific preferences. © 2014 John Wiley & Sons Ltd.

The Human Remains from HMS Pandora

Directory of Open Access Journals (Sweden)

D.P. Steptoe

2002-04-01

Full Text Available In 1977 the wreck of HMS Pandora (the ship that was sent to re-capture the Bounty mutineers was discovered off the north coast of Queensland. Since 1983, the Queensland Museum Maritime Archaeology section has carried out systematic excavation of the wreck. During the years 1986 and 1995-1998, more than 200 human bone and bone fragments were recovered. Osteological investigation revealed that this material represented three males. Their ages were estimated at approximately 17 +/-2 years, 22 +/-3 years and 28 +/-4 years, with statures of 168 +/-4cm, 167 +/-4cm, and 166cm +/-3cm respectively. All three individuals were probably Caucasian, although precise determination of ethnicity was not possible. In addition to poor dental hygiene, signs of chronic diseases suggestive of rickets and syphilis were observed. Evidence of spina bifida was seen on one of the skeletons, as were other skeletal anomalies. Various taphonomic processes affecting the remains were also observed and described. Compact bone was observed under the scanning electron microscope and found to be structurally coherent. Profiles of the three skeletons were compared with historical information about the 35 men lost with the ship, but no precise identification could be made. The investigation did not reveal the cause of death. Further research, such as DNA analysis, is being carried out at the time of publication.

DNA analyses of the remains of the Prince Branciforte Barresi family.

Science.gov (United States)

Rickards, O; Martínez-Labarga, C; Favaro, M; Frezza, D; Mallegni, F

2001-01-01

The five skeletons found buried in the church of Militello di Catania, Sicily, were tentatively identified by morphological analysis and historical reports as the remains of Prince Branciforte Barresi, two of his children, his brother and another juvenile member of the family (sixteenth and seventeenth centuries). In order to attempt to clarify the degree of relationships of the five skeletons, sex testing and mitochondrial DNA (mtDNA) sequence analysis of the hypervariable segments I and II (HV1 and HV2) of control region were performed. Moreover, the 9 bp-deletion marker of region V (COII/tRNAlys) was examined. Molecular genetic analyses were consistent with historical expectations, although they did not directly demonstrate that these are in fact the remains of the Prince and his relatives, due to the impossibility of obtaining DNA from living maternal relatives of the Prince.

Enhanced Contaminated Human Remains Pouch: initial development and preliminary performance assessments

Energy Technology Data Exchange (ETDEWEB)

Iseli, A.M.; Kwen, H.D.; Ul-Alam, M.; Balasubramanian, M.; Rajagopalan, S.

2011-11-07

The objective is to produce a proof of concept prototype Enhanced Contaminated Human Remains Pouch (ECHRP) with self-decontamination capability to provide increased protection to emergency response personnel. The key objective was to decrease the concentration of toxic chemicals through the use of an absorbent and reactive nanocellulose liner. Additionally, nanomaterials with biocidal properties were developed and tested as a 'stand-alone' treatment. The setting was a private company research laboratory. The main outcome measures were production of a functional prototype. A functional prototype capable of mitigating the threats due to sulfur mustard, Soman, and a large variety of liquid and vapor toxic industrial chemicals was produced. Stand-alone biocidal treatment efficacy was validated. The ECHRP provides superior protection from both chemical and biological hazards to various emergency response personnel and human remains handlers.

Cues-Pause-Point Language Training: Teaching Echolalics Functional Use of Their Verbal Labeling Repertoires.

Science.gov (United States)

McMorrow, Martin J.; And Others

1987-01-01

A cues-pause-point procedure was used to train two severely retarded females to remain quiet before, during, and briefly after the presentation of questions and then to verbalize on the basis of environmental cues whose labels represented the correct responses. Echolalia was rapidly replaced by correct responding on the trained stimuli. (Author/JW)

Properties and effects of remaining carbon from waste plastics gasifying on iron scale reduction.

Science.gov (United States)

Zhang, Chongmin; Chen, Shuwen; Miao, Xincheng; Yuan, Hao

2011-06-01

The carbonous activities of three kinds of carbon-bearing materials gasified from plastics were tested with coal coke as reference. The results showed that the carbonous activities of these remaining carbon-bearing materials were higher than that of coal-coke. Besides, the fractal analyses showed that the porosities of remaining carbon-bearing materials were higher than that of coal-coke. It revealed that these kinds of remaining carbon-bearing materials are conducive to improve the kinetics conditions of gas-solid phase reaction in iron scale reduction. Copyright © 2011 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Prevalence of remaining horizontal instability in high-grade acromioclavicular joint injuries surgically managed.

Science.gov (United States)

Cisneros, Luis Natera; Reiriz, Juan Sarasquete

2017-04-01

To determine the prevalence of remaining horizontal instability in high-grade acromioclavicular joint (ACJ) injuries surgically managed by means of four different surgical strategies and to assess its relation to the clinical outcomes and the quality of life. In this multicentric non-randomized retrospective study, 53 patients with high-grade ACJ injuries surgically managed (by means of open or arthroscopic surgery) were clinically and radiographically assessed at 24 months or more after shoulder surgery. The presence of post-surgical remaining horizontal instability was evaluated by means of Alexander or axillary X-ray views. The study population was divided into two groups: patients with evidence of post-surgical remaining horizontal instability and patients without evidence of post-surgical remaining horizontal instability at the last follow-up visit. The relationship between remaining horizontal instability and the quality-of-life questionnaires was analyzed. 18.87% (10/53) of the Alexander or axillary X-rays views showed post-surgical remaining horizontal instability at the last follow-up visit (INSTAB-group). Results of the questionnaires were: (1) physical SF36 score (INSTAB-group 57.02 ± 3.17  and NO-INSTAB-group 57.66 ± 3.30, p = 0.583); (2) mental SF36 score (INSTAB-group 53.95 ± 3.98  and NO-INSTAB-group 55.71 ± 3.30, p = 0.150); (3) NRS for pain (INSTAB-group 1.30 ± 1.49 and NO-INSTAB-group 0.83  ± 1.08, p = 0.260); (4) DASH questionnaire (INSTAB-group 5.27 ± 5.42 and NO-INSTAB-group 3.06 ± 2.30, p = 0.049); (5) Constant score (INSTAB-group 93.4 ± 3.5 and NO-INSTAB-group 94.83  ± 4.3, p = 0.333); and Global satisfaction (INSTAB-group 8.7  ± 0.95 and NO-INSTAB-group 8.64 ± 1.03, p = 0.874). Independently of the type of procedure, post-surgical remaining horizontal instability was present in almost one-fifth of the patients, and this group of patients showed a significantly worse DASH score. The

Reactive Oxygen is a Major Factor Regulating Cell Division and Angiogenesis in Breast Cancer

National Research Council Canada - National Science Library

Arnold, Rebecca

2001-01-01

.... We investigated the generation of the H2O2 and O2%. While O2 levels appeared to remain unchanged, 11202 levels increased significantly over control cell lines in several of the tumor cell lines...

Seven transmembrane G protein-coupled receptor repertoire of gastric ghrelin cells

DEFF Research Database (Denmark)

Engelstoft, Maja S; Park, Won-Mee; Sakata, Ichiro

2013-01-01

The molecular mechanisms regulating secretion of the orexigenic-glucoregulatory hormone ghrelin remain unclear. Based on qPCR analysis of FACS-purified gastric ghrelin cells, highly expressed and enriched 7TM receptors were comprehensively identified and functionally characterized using in vitro......, ex vivo and in vivo methods. Five Gαs-coupled receptors efficiently stimulated ghrelin secretion: as expected the β1-adrenergic, the GIP and the secretin receptors but surprisingly also the composite receptor for the sensory neuropeptide CGRP and the melanocortin 4 receptor. A number of Gαi....../o-coupled receptors inhibited ghrelin secretion including somatostatin receptors SSTR1, SSTR2 and SSTR3 and unexpectedly the highly enriched lactate receptor, GPR81. Three other metabolite receptors known to be both Gαi/o- and Gαq/11-coupled all inhibited ghrelin secretion through a pertussis toxin-sensitive Gαi...

Three Antagonistic Cyclic di-GMP-Catabolizing Enzymes Promote Differential Dot/Icm Effector Delivery and Intracellular Survival at the Early Steps of Legionella pneumophila Infection

Science.gov (United States)

Allombert, Julie; Lazzaroni, Jean-Claude; Baïlo, Nathalie; Gilbert, Christophe; Charpentier, Xavier; Doublet, Patricia

2014-01-01

Legionella pneumophila is an intracellular pathogen which replicates within protozoan cells and can accidently infect alveolar macrophages, causing an acute pneumonia in humans. The second messenger cyclic di-GMP (c-di-GMP) has been shown to play key roles in the regulation of various bacterial processes, including virulence. While investigating the function of the 22 potential c-di-GMP-metabolizing enzymes of the L. pneumophila Lens strain, we found three that directly contribute to its ability to infect both protozoan and mammalian cells. These three enzymes display diguanylate cyclase (Lpl0780), phosphodiesterase (Lpl1118), and bifunctional diguanylate cyclase/phosphodiesterase (Lpl0922) activities, which are all required for the survival and intracellular replication of L. pneumophila. Mutants with deletions of the corresponding genes are efficiently taken up by phagocytic cells but are partially defective for the escape of the Legionella-containing vacuole (LCV) from the host degradative endocytic pathway and result in lower survival. In addition, Lpl1118 is required for efficient endoplasmic reticulum recruitment to the LCV. Trafficking and biogenesis of the LCV are dependent upon the orchestrated actions of several type 4 secretion system Dot/Icm effectors proteins, which exhibit differentially altered translocation in the three mutants. While translocation of some effectors remained unchanged, others appeared over- and undertranslocated. A general translocation offset of the large repertoire of Dot/Icm effectors may be responsible for the observed defects in the trafficking and biogenesis of the LCV. Our results suggest that L. pneumophila uses cyclic di-GMP signaling to fine-tune effector delivery and ensure effective evasion of the host degradative pathways and establishment of a replicative vacuole. PMID:24379287

International standards to document remaining autonomic function after spinal cord injury

DEFF Research Database (Denmark)

Krassioukov, Andrei; Biering-Sørensen, Fin; Donovan, William

2012-01-01

This is the first guideline describing the International Standards to document remaining Autonomic Function after Spinal Cord Injury (ISAFSCI). This guideline should be used as an adjunct to the International Standards for Neurological Classification of Spinal Cord Injury (ISNCSCI) including the ...

Leprosy: ancient disease remains a public health problem nowadays.

Science.gov (United States)

Noriega, Leandro Fonseca; Chiacchio, Nilton Di; Noriega, Angélica Fonseca; Pereira, Gilmayara Alves Abreu Maciel; Vieira, Marina Lino

2016-01-01

Despite being an ancient disease, leprosy remains a public health problem in several countries -particularly in India, Brazil and Indonesia. The current operational guidelines emphasize the evaluation of disability from the time of diagnosis and stipulate as fundamental principles for disease control: early detection and proper treatment. Continued efforts are needed to establish and improve quality leprosy services. A qualified primary care network that is integrated into specialized service and the development of educational activities are part of the arsenal in the fight against the disease, considered neglected and stigmatizing.

Clonal progression during the T cell-dependent B cell antibody response depends on the immunoglobulin DH gene segment repertoire.

Directory of Open Access Journals (Sweden)

Ahmad eTrad

2014-08-01

Full Text Available The diversity of the third complementarity determining region of the Ig H chain is constrained by natural selection of immunoglobulin diversity (DH sequence. To test the functional significance of this constraint in the context of thymus-dependent (TD immune responses, we immunized BALB/c mice with WT or altered DH sequence with 2-phenyloxazolone-coupled chicken serum albumin (phOx-CSA. We chose this antigen because studies of the humoral immune response to the hapten phOx were instrumental in the development of the current theoretical framework on which our understanding of the forces driving TD responses is based. To allow direct comparison, we used the classic approach of generating monoclonal Ab (mAb from various stages of the immune response to phOx to assess the effect of changing the sequence of the DH on clonal expansion, class switching and affinity maturation, which are hallmarks of TD responses. Compared to WT, TD-induced humoral IgM as well as IgG antibody production in the D-altered D-DFS and D-iD strains were significantly reduced. An increased prevalence of IgM producing hybridomas from late primary, secondary, and tertiary memory responses suggested either impaired class switch recombination (CSR or impaired clonal expansion of class switched B cells with phOx reactivity. Neither of the D-altered strains demonstrated the restriction in the VH/VL repertoire, the elimination of VH1 family-encoded antibodies, the focusing of the distribution of CDR-H3 lengths, or the selection for the normally dominant Ox1 clonotype which all are hallmarks of the anti-phOx response in WT mice. These changes in clonal selection and expansion as well as class switch recombination indicate that the genetic constitution of the DH locus, which has been selected by evolution, can strongly influence the functional outcome of a TD humoral response.

Ancestral and derived attributes of the dlx gene repertoire, cluster structure and expression patterns in an African cichlid fish

Directory of Open Access Journals (Sweden)

Renz Adina J

2011-01-01

Full Text Available Abstract Background Cichlid fishes have undergone rapid, expansive evolutionary radiations that are manifested in the diversification of their trophic morphologies, tooth patterning and coloration. Understanding the molecular mechanisms that underlie the cichlids' unique patterns of evolution requires a thorough examination of genes that pattern the neural crest, from which these diverse phenotypes are derived. Among those genes, the homeobox-containing Dlx gene family is of particular interest since it is involved in the patterning of the brain, jaws and teeth. Results In this study, we characterized the dlx genes of an African cichlid fish, Astatotilapia burtoni, to provide a baseline to later allow cross-species comparison within Cichlidae. We identified seven dlx paralogs (dlx1a, -2a, -4a, -3b, -4b, -5a and -6a, whose orthologies were validated with molecular phylogenetic trees. The intergenic regions of three dlx gene clusters (dlx1a-2a, dlx3b-4b, and dlx5a-6a were amplified with long PCR. Intensive cross-species comparison revealed a number of conserved non-coding elements (CNEs that are shared with other percomorph fishes. This analysis highlighted additional lineage-specific gains/losses of CNEs in different teleost fish lineages and a novel CNE that had previously not been identified. Our gene expression analyses revealed overlapping but distinct expression of dlx orthologs in the developing brain and pharyngeal arches. Notably, four of the seven A. burtoni dlx genes, dlx2a, dlx3b, dlx4a and dlx5a, were expressed in the developing pharyngeal teeth. Conclusion This comparative study of the dlx genes of A. burtoni has deepened our knowledge of the diversity of the Dlx gene family, in terms of gene repertoire, expression patterns and non-coding elements. We have identified possible cichlid lineage-specific changes, including losses of a subset of dlx expression domains in the pharyngeal teeth, which will be the targets of future functional

Common variants at 6q22 and 17q21 are associated with intracranial volume

NARCIS (Netherlands)

M.A. Ikram (Arfan); M. Fornage (Myriam); G.D. Smith; S. Seshadri (Sudha); R. Schmidt (Reinhold); S. Debette (Stéphanie); H.A. Vrooman (Henri); S. Sigurdsson (Stefan); S. Ropele (Stefan); H.R. Taal (Rob); D.O. Mook-Kanamori (Dennis); L.H. Coker (Laura); W.T. Longstreth Jr; W.J. Niessen (Wiro); A.L. DeStefano (Anita); A. Beiser (Alexa); A.P. Zijdenbos; M.V. Struchalin (Maksim); C.R. Jack Jr. (Clifford); F. Rivadeneira Ramirez (Fernando); A.G. Uitterlinden (André); D.S. Knopman (David); A.L. Hartikainen; C.E. Pennell (Craig); E. Thiering (Eelisabeth); E.A.P. Steegers (Eric); H. Hakonarson (Hakon); J. Heinrich (Joachim); C. Palmer (Cameron); M.-R. Jarvelin (Marjo-Riitta); M.I. McCarthy (Mark); S.F.A. Grant (Struan); B.S. Pourcain (Beate); N.J. Timpson (Nicholas); G.D. Smith; U. Sovio (Ulla); M.A. Nalls (Michael); R. Au (Rhoda); A. Hofman (Albert); H. Gudnason (Haukur); A. van der Lugt (Aad); T.B. Harris (Tamara); W.M. Meeks (William); M.W. Vernooij (Meike); M.A. van Buchem (Mark); D.J. Catellier (Diane); V.W.V. Jaddoe (Vincent); V. Gudnason (Vilmundur); B.G. Windham (B Gwen); P.A. Wolf (Philip); C.M. van Duijn (Cornelia); T.H. Mosley (Thomas); R. Schmidt (Reinhold); L.J. Launer (Lenore); M.M.B. Breteler (Monique); C. DeCarli (Charles); L.S. Adair (Linda); W.Q. Ang (Wei); M. Atalay (Mustafa); C.E.M. van Beijsterveldt (Toos); N.E. Bergen (Nienke); P.J. Benke (Paul); D. Berry (Diane); L. Coin (Lachlan); O.S.P. Davis (Oliver S.); P. Elliott (Paul); C. Flexeder (Claudia); T.M. Frayling (Timothy); R. Gaillard (Romy); M. Groen-Blokhuis (Maria); L.-K. Goh; C.M.A. Haworth (Claire M.); D. Hadley (David); J. Hedebrand (Johannes); A. Hinney (Anke); J.N. Hirschhorn (Joel); J.W. Holloway (John); J.J. Holst; J.J. Hottenga (Jouke Jan); M. Horikoshi (Momoko); V. Huikari (Ville); E. Hypponen (Elina); T.O. Kilpeläinen (Tuomas); M. Kirin (Mirna); M. Kowgier (Matthew); T.A. Lakka (Timo); L.A. Lange (Leslie); D.A. Lawlor (Debbie); T. Lehtimäki (Terho); A. Lewin (Alex); C.M. Lindgren (Cecilia); V. Lindi (Virpi); R. Maggi (Reedik); J.A. Marsh (Julie); C.M. Middeldorp (Christel); I.Y. Millwood (Iona); J.C. Murray (Jeffrey); M. Nivard (Michel); C. Nohr (Christian); I. Ntalla (Ioanna); E. Oken (Emily); K. Panoutsopoulou (Kalliope); J. Pararajasingham (Jennifer); A. Rodriguez (Alfredo Chapin); R.M. Salem (Rany); S. Sebert (Sylvain); N. Siitonen (Niina); D.P. Strachan (David); Y.Y. Teo (Yik Ying); B. Valcárcel (Beatriz); G.A.H.M. Willemsen (Gonneke); E. Zeggini (Eleftheria); D.I. Boomsma (Dorret); C. Cooper (Charles); M.H. Gillman (Matthew); B. Hocher (Berthold); T.A. Lakka (Timo); K.L. Mohlke (Karen); G.V. Dedoussis (George); K.K. Ong (Ken); E. Pearson (Ewan); T.S. Price (Thomas); C. Power (Christopher); O. Raitakari (Olli); S-M. Saw (Seang-Mei); A. Scherag (Andre); O. Simell (Olli); T.I.A. Sørensen (Thorkild); J.F. Wilson (James)

2012-01-01

textabstractDuring aging, intracranial volume remains unchanged and represents maximally attained brain size, while various interacting biological phenomena lead to brain volume loss. Consequently, intracranial volume and brain volume in late life reflect different genetic influences. Our

Developing criteria for performance-based concrete specifications.

Science.gov (United States)

2013-07-01

For more than 50 years now, concrete technology has advanced, but CDOT specifications for durability have : remained mostly unchanged. The minimum cement content for a given strength is derived from mix design : guidelines that were developed before ...

Structural remains at the early mediaeval fort at Raibania, Orissa

OpenAIRE

Sen, Bratati

2013-01-01

The fortifications of mediaeval India occupy an eminent position in the history of military architecture. The present paper deals with the preliminary study of the structural remains at the early mediaeval fort at Raibania in the district of Balasore in Orissa. The fort was built of stone very loosely kept together. The three-walled fortification interspersed by two consecutive moats, a feature evidenced at Raibania, w...

SMART POINT CLOUD: DEFINITION AND REMAINING CHALLENGES

Directory of Open Access Journals (Sweden)

F. Poux

2016-10-01

Full Text Available Dealing with coloured point cloud acquired from terrestrial laser scanner, this paper identifies remaining challenges for a new data structure: the smart point cloud. This concept arises with the statement that massive and discretized spatial information from active remote sensing technology is often underused due to data mining limitations. The generalisation of point cloud data associated with the heterogeneity and temporality of such datasets is the main issue regarding structure, segmentation, classification, and interaction for an immediate understanding. We propose to use both point cloud properties and human knowledge through machine learning to rapidly extract pertinent information, using user-centered information (smart data rather than raw data. A review of feature detection, machine learning frameworks and database systems indexed both for mining queries and data visualisation is studied. Based on existing approaches, we propose a new 3-block flexible framework around device expertise, analytic expertise and domain base reflexion. This contribution serves as the first step for the realisation of a comprehensive smart point cloud data structure.

Shippingport Spent Fuel Canister (SSFC) Design Report Project W-518

International Nuclear Information System (INIS)

JOHNSON, D.M.

2000-01-01

The SSFC Design Report Describes A spent fuel canister for Shippingport Core 2 blanket fuel assemblies. The design of the SSFC is a minor modification of the MCO. The modification is limited to the Shield Plug which remains unchanged with regard to interfaces with the canister shell. The performance characteristics remain those for the MCO, which bounds the payload of the SSFC

On use of radial evanescence remain term in kinematic hardening

International Nuclear Information System (INIS)

Geyer, P.

1995-10-01

A fine modelling of the material' behaviour can be necessary to study the mechanical strength of nuclear power plant' components under cyclic loads. Ratchetting is one of the last phenomena for which numerical models have to be improved. We discuss in this paper on use of radial evanescence remain term in kinematic hardening to improve the description of ratchetting in biaxial loading tests. It's well known that Chaboche elastoplastic model with two non linear kinematic hardening variables initially proposed by Armstrong and Frederick, usually over-predicts accumulation of ratchetting strain. Burlet and Cailletaud proposed in 1987 a non linear kinematic rule with a radial evanescence remain term. The two models lead to identical formulation for proportional loadings. In the case of a biaxial loading test (primary+secondary loading), Burlet and Cailletaud model leads to accommodation, when Chaboche one's leads to ratchetting with a constant increment of strain. So we can have an under-estimate with the first model and an over-estimate with the second. An easy method to improve the description of ratchetting is to combine the two kinematic rules. Such an idea is already used by Delobelle in his model. With analytical results in the case of tension-torsion tests, we show in a first part of the paper, the interest of radial evanescence remain term in the non linear kinematic rule to describe ratchetting: we give the conditions to get adaptation, accommodation or ratchetting and the value of the strain increment in the last case. In the second part of the paper, we propose to modify the elastoplastic Chaboche model by coupling the two types of hardening by means of two scalar parameters which can be identified independently on biaxial loading tests. Identification of these two parameters returns to speculate on the directions of strain in order to adjust the ratchetting to experimental observations. We use the experimental results on the austenitic steel 316L at room

Adaptive antibody diversification through N-linked glycosylation of the immunoglobulin variable region.

Science.gov (United States)

van de Bovenkamp, Fleur S; Derksen, Ninotska I L; Ooijevaar-de Heer, Pleuni; van Schie, Karin A; Kruithof, Simone; Berkowska, Magdalena A; van der Schoot, C Ellen; IJspeert, Hanna; van der Burg, Mirjam; Gils, Ann; Hafkenscheid, Lise; Toes, René E M; Rombouts, Yoann; Plomp, Rosina; Wuhrer, Manfred; van Ham, S Marieke; Vidarsson, Gestur; Rispens, Theo

2018-02-20

A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N -linked glycans, a process conditional on the introduction of consensus amino acid motifs ( N -glycosylation sites) during somatic hypermutation. High levels of variable domain glycans have been associated with autoantibodies in rheumatoid arthritis, as well as certain follicular lymphomas. However, the role of these glycans in the humoral immune response remains poorly understood. Interestingly, studies have reported both positive and negative effects on antibody affinity. Our aim was to elucidate the role of variable domain glycans during antigen-specific antibody responses. By analyzing B-cell repertoires by next-generation sequencing, we demonstrate that N -glycosylation sites are introduced at positions in which glycans can affect antigen binding as a result of a specific clustering of progenitor glycosylation sites in the germline sequences of variable domain genes. By analyzing multiple human monoclonal and polyclonal (auto)antibody responses, we subsequently show that this process is subject to selection during antigen-specific antibody responses, skewed toward IgG4, and positively contributes to antigen binding. Together, these results highlight a physiological role for variable domain glycosylation as an additional layer of antibody diversification that modulates antigen binding.

The neuro-immunological interface in an evolutionary perspective: the dynamic relationship between effector and recognition systems.

Science.gov (United States)

Ottaviani, E; Valensin, S; Franceschi, C

1998-04-16

The evolutionary perspective indicates that an immune-neuroendocrine effector system integrating innate immunity, stress and inflammation is present in invertebrates. This defense network, centered on the macrophage and exerting primitive and highly promiscuous recognition units, is very effective, ancestral and appears to have been conserved throughout evolution from invertebrates to higher vertebrates. It would seem that there was a "big bang" in the recognition system of lower vertebrates, and T and B cell repertoires, MHC and antibodies suddenly appeared. We argue that this phenomenon is the counterpart of the increasing complexity of the internal circuitry and recognition units in the effector system. The immediate consequences were a progressive enlargement of the pathogen repertoire and new problems regarding self/not-self discrimination. Probably not by chance, a new organ appeared, capable of purging cells able of excessive self recognition. This organ, the thymus, appears to be the result of a well known evolutionary strategy of re-using pre-existing material (neuroendocrine cells and mediators constituting the thymic microenvironment). This bricolage at an organ level is similar to the effect we have already described at the level of molecules and functions of the defense network, and has a general counterpart at genetic level. Thus, in vertebrates, the conserved immune-neuroendocrine effector system remains of fundamental importance in defense against pathogens, while its efficiency has increased through synergy with the new, clonotipical recognition repertoire.

Regulatory perspective on remaining challenges for utilization of pharmacogenomics-guided drug developments.

Science.gov (United States)

Otsubo, Yasuto; Ishiguro, Akihiro; Uyama, Yoshiaki

2013-01-01

Pharmacogenomics-guided drug development has been implemented in practice in the last decade, resulting in increased labeling of drugs with pharmacogenomic information. However, there are still many challenges remaining in utilizing this process. Here, we describe such remaining challenges from the regulatory perspective, specifically focusing on sample collection, biomarker qualification, ethnic factors, codevelopment of companion diagnostics and means to provide drugs for off-target patients. To improve the situation, it is important to strengthen international harmonization and collaboration among academia, industries and regulatory agencies, followed by the establishment of an international guideline on this topic. Communication with a regulatory agency from an early stage of drug development is also a key to success.

Quantum Dots for Cancer Research: Current Status, Remaining Issues, and Future Perspectives

International Nuclear Information System (INIS)

Fang, Min; Peng, Chun-wei; Pang, Dai-Wen; Li, Yan

2012-01-01

Cancer is a major threat to public health in the 21st century because it is one of the leading causes of death worldwide. The mechanisms of carcinogenesis, cancer invasion, and metastasis remain unclear. Thus, the development of a novel approach for cancer detection is urgent, and real-time monitoring is crucial in revealing its underlying biological mechanisms. With the optical and chemical advantages of quantum dots (QDs), QD-based nanotechnology is helpful in constructing a biomedical imaging platform for cancer behavior study. This review mainly focuses on the application of QD-based nanotechnology in cancer cell imaging and tumor microenvironment studies both in vivo and in vitro, as well as the remaining issues and future perspectives

A Panel of Recombinant Mucins Carrying a Repertoire of Sialylated O-Glycans Based on Different Core Chains for Studies of Glycan Binding Proteins

Directory of Open Access Journals (Sweden)

Reeja Maria Cherian

2015-08-01

Full Text Available Sialylated glycans serve as key elements of receptors for many viruses, bacteria, and bacterial toxins. The microbial recognition and their binding specificity can be affected by the linkage of the terminal sugar residue, types of underlying sugar chains, and the nature of the entire glycoconjugate. Owing to the pathobiological significance of sialylated glycans, we have engineered Chinese hamster ovary (CHO cells to secrete mucin-type immunoglobulin-fused proteins carrying terminal α2,3- or α2,6-linked sialic acid on defined O-glycan core saccharide chains. Besides stably expressing P-selectin glycoprotein ligand-1/mouse immunoglobulin G2b cDNA (PSGL-1/mIgG2b, CHO cells were stably transfected with plasmids encoding glycosyltransferases to synthesize core 2 (GCNT1, core 3 (B3GNT6, core 4 (GCNT1 and B3GNT6, or extended core 1 (B3GNT3 chains with or without the type 1 chain-encoding enzyme B3GALT5 and ST6GAL1. Western blot and liquid chromatography-mass spectrometry analysis confirmed the presence of core 1, 2, 3, 4, and extended core 1 chains carrying either type 1 (Galb3GlcNAc or type 2 (Galb4GlcNAc outer chains with or without α2,6-linked sialic acids. This panel of recombinant mucins carrying a repertoire of sialylated O-glycans will be important tools in studies aiming at determining the fine O-glycan binding specificity of sialic acid-specific microbial adhesins and mammalian lectins.

The use of fish remains in sediments for the reconstruction of paleoproductivity

Energy Technology Data Exchange (ETDEWEB)

Drago, T; Santos, A M P; Pinheiro, J [Institute Nacional de Recursos Biologicos (INRB), L-IPIMAR, Av. 5 de Outubro s/n 8700-305 OLHaO (Portugal); Ferreira-Bartrina, V [Centra de Investigacion CientIfica y de Educacion Superior de Ensenada- CICESE, Km. 107 Carretera Tijuana, C.P.22860, Ensenada, B.C. (Mexico)], E-mail: tdrago@ipimar.pt

2009-01-01

The majority of the works concerning fish productivity are based in fish landing records. However, in order to understand the causes of variability in fish productivity (natural and/or anthropogenic) it is essential to have information from periods when human impacts (e.g., fisheries) are considered unimportant. This can be achieved through the use of fish remains, i.e. scales, vertebrae and otoliths, from sediment records. The obtained data can be used to develop time series of fish stocks revealing the history of fish population dynamics over the last centuries or millennia. The majority of these works are located in Eastern Boundary Current Systems (e.g., Benguela, Peru-Humboldt, California), because these are associated with coastal upwelling and high productivity, which in some cases is at the origin of low bottom oxygen levels, leading to scale preservation. A search for fish remains in the Portuguese margin sediments is in progress in the context of the ongoing research project POPEI (High-resolution oceanic paleoproductivity and environmental changes; correlation with fish populations), which intend to fill the gap in studies of this type for the Canary Current System. In this paper we review some general ideas of the use of fish remains, related studies, methodologies and data processing, as well as presenting the first results of POPEI.

Common variants at 6q22 and 17q21 are associated with intracranial volume

NARCIS (Netherlands)

Arfan Ikram, M.; Fornage, M.; Smith, A.V.; Seshadri, S.; Schmidt, R.; Debette, S.; Vrooman, H.A.; Sigurdsson, S.; Ropele, S.; Taal, H.R.; Mook-Kanamori, D.O.; Coker, L.H.; Longstreth, Jr. W.T.; Niessen, W.J.; DeStefano, A.L.; Beiser, A.; Zijdenbos, A.P.; Struchalin, M.; Jack, C.R.; Rivadeneira, F.; Uitterlinden, A.G.; Knopman, D.S.; Hartikainen, A.-L.; Pennell, C.E.; Thiering, E.; Steegers, E.A.P.; Hakonarson, H.; Heinrich, J.; Palmer, L.J.; Jarvelin, M.-R.; McCarthy, M.I.; Grant, S.F.A.; St Pourcain, B.; Timpson, N.J.; Smith, G.D.; Sovio, U.; van Beijsterveldt, C.E.M.; Groen-Blokhuis, M.M.; Hottenga, J.J.; Middeldorp, C.M.; Nivard, M.G.; Willemsen, G.; Boomsma, D.I.; Nalls, M.A.; Au, R.; Hofman, A.; Gudnason, H.; van der Lugt, A.; Harris, T.B.; Meeks, W.M.; Vernooij, M.W.; van Buchem, M.A.; Catellier, D.; Jaddoe, V.W.V.; Gudnason, V.; Windham, B.G.; Wolf, P.A.; van Duijn, C.M.; Mosley, T.H.; Schmidt, H.; Launer, L.J.; Breteler, M.M.B.; DeCarli, C.S.

2012-01-01

During aging, intracranial volume remains unchanged and represents maximally attained brain size, while various interacting biological phenomena lead to brain volume loss. Consequently, intracranial volume and brain volume in late life reflect different genetic influences. Our genome-wide

A multidisciplinary reconstruction of Palaeolithic nutrition that holds promise for the prevention and treatment of diseases of civilisation

NARCIS (Netherlands)

Kuipers, Remko S.; Joordens, Josephine C. A.; Muskiet, Frits A. J.

Evolutionary medicine acknowledges that many chronic degenerative diseases result from conflicts between our rapidly changing environment, our dietary habits included, and our genome, which has remained virtually unchanged since the Palaeolithic era. Reconstruction of the diet before the

Acidification of the osteoclastic resorption compartment provides insight into the coupling of bone formation to bone resorption

DEFF Research Database (Denmark)

Karsdal, M.A.; Henriksen, K.; Sorensen, M.G.

2005-01-01

Patients with defective osteoclastic acidification have increased numbers of osteoclasts, with decreased resorption, but bone formation that remains unchanged. We demonstrate that osteoclast survival is increased when acidification is impaired, and that impairment of acidification results in inhi...

76 FR 32387 - Kentucky Disaster Number KY-00040

Science.gov (United States)

2011-06-06

... Damage and Economic Injury Loans): Ballard, Daviess, Henderson, Lawrence, McLean, Pike. Contiguous..., Morgan, Muhlenberg, Ohio. Illinois: Alexander. Indiana: Spencer, Vanderburgh, Warrick. Virginia: Buchanan, Dickenson, Wise. West Virginia: Mingo. All other information in the original declaration remains unchanged...

Role of cytochrome P450s in insecticide resistance: impact on the control of mosquito-borne diseases and use of insecticides on Earth

OpenAIRE

David, Jean-Philippe; Ismail, Hanafy Mahmoud; Chandor-Proust, Alexia; Paine, Mark John Ingraham

2013-01-01

The fight against diseases spread by mosquitoes and other insects has enormous environmental, economic and social consequences. Chemical insecticides remain the first line of defence but the control of diseases, especially malaria and dengue fever, is being increasingly undermined by insecticide resistance. Mosquitoes have a large repertoire of P450s (over 100 genes). By pinpointing the key enzymes associated with insecticide resistance we can begin to develop new tools to aid the implementat...

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells

OpenAIRE

Soucie, E.L.; Weng, Z.; Geirsdottir, L.; Molawi, K.; Maurizio, J.; Fenouil, R.; Mossadegh-Keller, N.; Gimenez, G.; VanHille, L.; Beniazza, M.; Favret, J.; Berruyer, C.; Perrin, P.; Hacohen, N.; Andrau, J.C.

2016-01-01

Differentiated macrophages can self-renew in tissues and expand long-term in culture, but the gene regulatory mechanisms that accomplish self-renewal in the differentiated state have remained unknown. Here we show that in mice, the transcription factors MafB and c-Maf repress a macrophage-specific enhancer repertoire associated with a gene network controlling self-renewal. Single cell analysis revealed that, in vivo, proliferating resident macrophages can access this network by transient down...

[Sexuality of our seniors: happy end or new beginning?].

Science.gov (United States)

Degauquier, C; Absil, A S; Meuris, S; Psalti, I; Jurysta, F

2012-01-01

Comparing surveys from successive periods demonstrates that elderly people now enjoy a better and more varied sexual life than previous generations. The proportion of older people who remain sexually active has significantly increased, and the practices of masturbation or oral sex have spread considerably. The generation effect has an incidence upon sexual behaviour: older people's repertoire of sexual practices differs from that of younger people, in the sense that it focuses less on sexual intercourse and oral sex. Women and men, beyond the common trends towards sexuality characterised by a more open repertoire of sexual practices, differ in terms of sexual interest and subjective sexual wellbeing. The cessation of sexual activity by individuals who had previously been sexually active is often the result of a cascade of reactions, such as the occurrence of a sexual dysfunction in one or both partners, anticipation of failure, increased anxiety, lack of adaptation of sexuality and/or avoidance behaviour.

A predictive model of muscle excitations based on muscle modularity for a large repertoire of human locomotion conditions

Directory of Open Access Journals (Sweden)

Jose eGonzalez-Vargas

2015-09-01

Full Text Available Humans can efficiently walk across a large variety of terrains and locomotion conditions with little or no mental effort. It has been hypothesized that the nervous system simplifies neuromuscular control by using muscle synergies, thus organizing multi-muscle activity into a small number of coordinative co-activation modules. In the present study we investigated how muscle modularity is structured across a large repertoire of locomotion conditions including five different speeds and five different ground elevations. For this we have used the non-negative matrix factorization technique in order to explain EMG experimental data with a low-dimensional set of four motor components. In this context each motor components is composed of a non-negative factor and the associated muscle weightings. Furthermore, we have investigated if the proposed descriptive analysis of muscle modularity could be translated into a predictive model that could: 1 Estimate how motor components modulate across locomotion speeds and ground elevations. This implies not only estimating the non-negative factors temporal characteristics, but also the associated muscle weighting variations. 2 Estimate how the resulting muscle excitations modulate across novel locomotion conditions and subjects.The results showed three major distinctive features of muscle modularity: 1 the number of motor components was preserved across all locomotion conditions, 2 the non-negative factors were consistent in shape and timing across all locomotion conditions, and 3 the muscle weightings were modulated as distinctive functions of locomotion speed and ground elevation. Results also showed that the developed predictive model was able to reproduce well the muscle modularity of un-modeled data, i.e. novel subjects and conditions. Muscle weightings were reconstructed with a cross-correlation factor greater than 70% and a root mean square error less than 0.10. Furthermore, the generated muscle excitations

Mild traumatic brain injury diagnosis frequently remains unrecorded in subjects with craniofacial fractures.

Science.gov (United States)

Puljula, Jussi; Cygnel, Hanna; Mäkinen, Elina; Tuomivaara, Veli; Karttunen, Vesa; Karttunen, Ari; Hillbom, Matti

2012-12-01

Traumatic brain injuries (TBI) in subjects with craniofacial fractures are usually diagnosed by emergency room physicians. We investigated how often TBI remains unrecorded in these subjects, and whether diagnostic accuracy has improved after the implementation of new TBI guidelines. All subjects with craniofacial fractures admitted to Oulu University Hospital in 1999 and in 2007 were retrospectively identified. New guidelines for improving the diagnostic accuracy of TBI were implemented between 2000 and 2006. Clinical symptoms of TBI were gathered from notes on hospital charts and compared to the recorded diagnoses at discharge. Logistic regression was used to identify independent predictors for TBI to remain unrecorded. Of 194 subjects with craniofacial fracture, 111(57%) had TBI, 40 in 1999 and 71 in 2007. Fifty-one TBIs (46%) remained unrecorded at discharge, 48 being mild and 3 moderate-to-severe. Subjects with unrecorded TBI were significantly less frequently referred to follow-up visits. Failures to record the TBI diagnosis were less frequent (29/71, 41%) in 2007 than in 1999 (22/40, 55%), but the difference was not statistically significant. The most significant independent predictor for this failure was the clinical specialty (other than neurology/neurosurgery) of the examining physician (palcohol intoxication did not hamper the diagnosis of TBI. TBIs remain frequently unrecorded in subjects with craniofacial fractures. Recording of mild TBI slightly but insignificantly improved after the implementation of new guidelines. Copyright © 2012 Elsevier Ltd. All rights reserved.

Yellow Fever Remains a Potential Threat to Public Health.

Science.gov (United States)

Vasconcelos, Pedro F C; Monath, Thomas P

2016-08-01

Yellow fever (YF) remains a serious public health threat in endemic countries. The recent re-emergence in Africa, initiating in Angola and spreading to Democratic Republic of Congo and Uganda, with imported cases in China and Kenya is of concern. There is such a shortage of YF vaccine in the world that the World Health Organization has proposed the use of reduced doses (1/5) during emergencies. In this short communication, we discuss these and other problems including the risk of spread of YF to areas free of YF for decades or never before affected by this arbovirus disease.

Tuberculosis remains a challenge despite economic growth in Panama.

Science.gov (United States)

Tarajia, M; Goodridge, A

2014-03-01

Tuberculosis (TB) is a disease associated with inequality, and wise investment of economic resources is considered critical to its control. Panama has recently secured its status as an upper-middle-income country with robust economic growth. However, the prioritisation of resources for TB control remains a major challenge. In this article, we highlight areas that urgently require action to effectively reduce TB burden to minimal levels. Our conclusions suggest the need for fund allocation and a multidisciplinary approach to ensure prompt laboratory diagnosis, treatment assurance and workforce reinforcement, complemented by applied and operational research, development and innovation.

Left ventricular remodeling in the first year after acute myocardial infarction and the predictive value of N-terminal pro brain natriuretic peptide

DEFF Research Database (Denmark)

Nilsson, Jens C; Groenning, Bjoern A; Nielsen, Gitte

2002-01-01

), whereas the remaining 18 patients (43%) had stable conditions regarding these LV measures. LV ejection fraction at baseline was significantly reduced in all patient categories but was unchanged over time. Elevated NT-proBNP level at baseline was identified as an independent predictor of increase in LVEDVI...... during follow-up examination (P =.007). A baseline level of NT-proBNP >115 pmol/L identified patients who later had LV dilatation develop with a sensitivity and specificity of 89% and 68% (area under curve = 0.77). CONCLUSION: In this 1-year follow-up study of patients with a first transmural MI......, approximately 30% had significant increments develop in LVEDVI and LVESVI, and LV ejection fraction remained unchanged. Patients in whom LV dilatation developed could be identified early after the MI with elevated plasma levels of NT-proBNP...

Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

Directory of Open Access Journals (Sweden)

Fabian Haß

2017-10-01

Full Text Available The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs, have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.

The Insta-Dead: The rhetoric of the human remains trade on Instagram

Directory of Open Access Journals (Sweden)

Damien Huffer

2017-07-01

Full Text Available There is a thriving trade, and collector community, around human remains that is facilitated by posts on new social media such as Instagram, Facebook, Etsy, and, until recently, eBay. In this article, we examine several thousand Instagram posts and perform some initial text analysis on the language and rhetoric of these posts to understand something about the function of this community, what they value and how they trade, buy, and sell, human remains. Our results indicate a well-connected network of collectors and dealers both specialist and generalist, with a surprisingly wide-reaching impact on the 'enthusiasts' who, through their rhetoric, support the activities of this collecting community, in the face of legal and ethical issues generated by its existence.

Perceived organizational support and intention to remain: The mediating roles of career success and self-esteem.

Science.gov (United States)

Liu, Jingying; Liu, Yan-Hui

2016-04-01

The aim of this study was to explore the relationships among perceived organizational support, career success, self-esteem and intention to remain. A cross-sectional study was designed, and subjects were recruited from six nonprofit organizations in China in spring 2015. A convenience sample of 610 nurses answered a survey with questions related to their ideas about their work. Structural equation modelling analyses were conducted. The results revealed that perceived organizational support was positively associated with intention to remain and career success, which, in turn, mediated the relationship between perceived organizational support and intention to remain. We also found that self-esteem mediated the relationships between perceived organizational support and career success and between career success and intention to remain. Higher perceived organizational support, career success and self-esteem can increase intention to remain in Chinese nurses. © 2015 John Wiley & Sons Australia, Ltd.

Calibration of C-14 dates: some remaining uncertainties and limitations

International Nuclear Information System (INIS)

Burleigh, R.

1975-01-01

A brief review is presented of the interpretation of radiocarbon dates in terms of calendar years. An outline is given of the factors that make such correlations necessary and of the work that has so far been done to make them possible. The calibration of the C-14 timescale very largely depends at present on the bristlecone pine chronology, but it is clear that many detailed uncertainties still remain. These are discussed. (U.K.)

Spontaneous recovery of locomotion induced by remaining fibers after spinal cord transection in adult rats.

Science.gov (United States)

You, Si-Wei; Chen, Bing-Yao; Liu, Hui-Ling; Lang, Bing; Xia, Jie-Lai; Jiao, Xi-Ying; Ju, Gong

2003-01-01

A major issue in analysis of experimental results after spinal cord injury is spontaneous functional recovery induced by remaining nerve fibers. The authors investigated the relationship between the degree of locomotor recovery and the percentage and location of the fibers that spared spinal cord transection. The spinal cords of 12 adult rats were transected at T9 with a razor blade, which often resulted in sparing of nerve fibers in the ventral spinal cord. The incompletely-transected animals were used to study the degree of spontaneous recovery of hindlimb locomotion, evaluated with the BBB rating scale, in correlation to the extent and location of the remaining fibers. Incomplete transection was found in the ventral spinal cord in 42% of the animals. The degree of locomotor recovery was highly correlated with the percentage of the remaining fibers in the ventral and ventrolateral funiculi. In one of the rats, 4.82% of remaining fibers in unilateral ventrolateral funiculus were able to sustain a certain recovery of locomotion. Less than 5% of remaining ventrolateral white matter is sufficient for an unequivocal motor recovery after incomplete spinal cord injury. Therefore, for studies with spinal cord transection, the completeness of sectioning should be carefully checked before any conclusion can be reached. The fact that the degree of locomotor recovery is correlated with the percentage of remaining fibers in the ventrolateral spinal cord, exclusive of most of the descending motor tracts, may imply an essential role of propriospinal connections in the initiation of spontaneous locomotor recovery.

Systematic in-vitro evaluation of the NCI/NIH Developmental Therapeutics Program Approved Oncology Drug Set for the identification of a candidate drug repertoire for MLL-rearranged leukemia

Directory of Open Access Journals (Sweden)

Hoeksema KA

2011-09-01

Full Text Available Kimberley A Hoeksema1, Aarthi Jayanthan1, Todd Cooper2, Lia Gore3, Tanya Trippett4, Jessica Boklan6, Robert J Arceci5, Aru Narendran11Division of Pediatric Oncology, Alberta Children's Hospital, Calgary, AB, Canada; 2Aflac Cancer Center and Blood Disorders Service, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA; 3Center for Cancer and Blood Disorders, Children's Hospital, University of Colorado Denver, Aurora, CO, USA; 4Memorial Sloan-Kettering Cancer Center, New York, NY, USA; 5Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; 6Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ, USAAbstract: Despite significant progress made in the overall cure rate, the prognosis for relapsed and refractory malignancies in children remains extremely poor. Hence, there is an urgent need for studies that enable the timely selection of appropriate agents for Phase I clinical studies. The Pediatric Oncology Experimental Therapeutics Investigators' Consortium (POETIC is systematically evaluating libraries of known and novel compounds for activity against subsets of high-risk pediatric malignancies with defined molecular aberrations for future clinical development. In this report, we describe the in-vitro activity of a diverse panel of approved oncology drugs against MLL-rearranged pediatric leukemia cell lines. Agents in the Approved Oncology Drug Set II (National Cancer Institute/National Institutes of Health Developmental Therapeutics Program were evaluated by in-vitro cytotoxicity assays in pediatric acute lymphoblastic leukemia and acute myeloid leukemia cell lines with MLL gene rearrangements. Validation studies were carried out with patient leukemia cells in culture. Comparative analysis for toxicity against nonmalignant cells was evaluated in normal bone marrow stromal cells and normal human lymphocytes. Results from this study show that 42 of the 89 agents tested have

Stable isotopes, niche partitioning and the paucity of elasmosaur remains in the Maastrichtian type area

NARCIS (Netherlands)

Schulp, Anne S.; Janssen, Renée; Van Baal, Remy R.; Jagt, John W M; Mulder, Eric W A; Vonhof, Hubert B.

2017-01-01

Remains of elasmosaurid plesiosaurs are exceedingly rare in the type-Maastrichtian strata (Late Cretaceous, southeast Netherlands and northeast Belgium), in stark contrast to relatively common skeletal remains of mosasaurs. Here, we present an analysis of δ13C stable isotope values for tooth enamel

Remaining useful life assessment of lithium-ion batteries in implantable medical devices

Science.gov (United States)

Hu, Chao; Ye, Hui; Jain, Gaurav; Schmidt, Craig

2018-01-01

This paper presents a prognostic study on lithium-ion batteries in implantable medical devices, in which a hybrid data-driven/model-based method is employed for remaining useful life assessment. The method is developed on and evaluated against data from two sets of lithium-ion prismatic cells used in implantable applications exhibiting distinct fade performance: 1) eight cells from Medtronic, PLC whose rates of capacity fade appear to be stable and gradually decrease over a 10-year test duration; and 2) eight cells from Manufacturer X whose rates appear to be greater and show sharp increase after some period over a 1.8-year test duration. The hybrid method enables online prediction of remaining useful life for predictive maintenance/control. It consists of two modules: 1) a sparse Bayesian learning module (data-driven) for inferring capacity from charge-related features; and 2) a recursive Bayesian filtering module (model-based) for updating empirical capacity fade models and predicting remaining useful life. A generic particle filter is adopted to implement recursive Bayesian filtering for the cells from the first set, whose capacity fade behavior can be represented by a single fade model; a multiple model particle filter with fixed-lag smoothing is proposed for the cells from the second data set, whose capacity fade behavior switches between multiple fade models.

Effect of interaction of embedded crack and free surface on remaining fatigue life

Directory of Open Access Journals (Sweden)

Genshichiro Katsumata

2016-12-01

Full Text Available Embedded crack located near free surface of a component interacts with the free surface. When the distance between the free surface and the embedded crack is short, stress at the crack tip ligament is higher than that at the other area of the cracked section. It can be easily expected that fatigue crack growth is fast, when the embedded crack locates near the free surface. To avoid catastrophic failures caused by fast fatigue crack growth at the crack tip ligament, fitness-for-service (FFS codes provide crack-to-surface proximity rules. The proximity rules are used to determine whether the cracks should be treated as embedded cracks as-is, or transformed to surface cracks. Although the concepts of the proximity rules are the same, the specific criteria and the rules to transform embedded cracks into surface cracks differ amongst FFS codes. This paper focuses on the interaction between an embedded crack and a free surface of a component as well as on its effects on the remaining fatigue lives of embedded cracks using the proximity rules provided by the FFS codes. It is shown that the remaining fatigue lives for the embedded cracks strongly depend on the crack aspect ratio and location from the component free surface. In addition, it can be said that the proximity criteria defined by the API and RSE-M codes give overly conservative remaining lives. On the contrary, the WES and AME codes always give long remaining lives and non-conservative estimations. When the crack aspect ratio is small, ASME code gives non-conservative estimation.

Non-steroidal anti-inflammatory drugs and renal response to exercise

DEFF Research Database (Denmark)

Olsen, Niels Vidiendal; Jensen, N G; Hansen, J M

1999-01-01

baseline values or exercise-induced decreases in renal plasma flow or glomerular filtration rate. Indomethacin, but not nabumetone, decreased sodium excretion, urine flow rate and free water clearance. The renal response to exercise, however, remained unchanged. In contrast with nabumatone, indomethacin...

Celiac disease and pulmonary hemosiderosis in a patient with chronic granulomatous disease

NARCIS (Netherlands)

Hartl, Dominik; Belohradsky, Bernd H.; Griese, Matthias; Nicolai, Thomas; Krauss-Etschmann, Susanne; Roos, Dirk; Wintergerst, Uwe

2004-01-01

We report on a patient with the hitherto undescribed combination of chronic granulomatous disease, pulmonary hemosiderosis, and celiac disease. The hemosiderosis resolved with a gluten-free diet and glucocorticosteroid pulse therapy, but the restrictive lung function pattern remained unchanged. Lung

Proteolytic Degradation of Bovine Submaxillary Mucin (BSM) and Its Impact on Adsorption and Lubrication at a Hydrophobic Surface

DEFF Research Database (Denmark)

Madsen, Jan Busk; Svensson, Birte; Abou Hachem, Maher

2015-01-01

in the secondary structure owing to the removal ofterminal domains, but the overall random coil conformation adopted by the central glycosylated domain remained dominant and essentially unchanged. Surface adsorption properties as characterized by optical wave guide light mode spectroscopy (OWLS) showed...