bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prioritizing transcriptomic and epigenomic experiments by using an optimization strategy that leverages imputed data
Authors: Schreiber Jacob , Bilmes Jeffrey , Noble William Stafford 
Published: July 2019

AbstractSuccessful science often involves not only performing experiments well, but also choosing well among many possible experiments. In a hypothesis generation setting, choosing an experiment well means choosing an experiment whose results are interesting or novel. In this work, we formalize this selection procedure in the context of genomics and epigenomics data generation. Specifically, we consider the task faced by a scientific consortium such as the National Institutes of Health ENCODE Consortium, whose goal is to characterize all of the functional elements in the human genome. Given a list of possible cell types or tissue types (“biosamples”) and a list of possible high throughput sequencing assays, we ask “Which experiments should ENCODE perform next?” We demonstrate how to represent this task as an optimization problem, where the goal is to maximize the information gained in each successive experiment. Compared with previous work that has addressed a similar problem, our approach has the advantage that it can use imputed data to tailor the selected list of experiments based on data collected previously by the consortium. We demonstrate the utility of our proposed method in simulations, and we provide a general software framework, named Kiwano, for selecting genomic and epigenomic experiments.
STAT5-dependent regulation of CDC25A by miR-16 controls proliferation and differentiation in FLT3-ITD acute myeloid leukemia
Authors: Sueur Gabrielle , Boutet Alison , Gotanègre Mathilde , Mansat-De Mas Véronique , Besson Arnaud , Manenti Stéphane , Bertoli Sarah 
Published: July 2019

AbstractWe recently identified the CDC25A phosphatase as a key actor in proliferation and differentiation in acute myeloid leukemia which expresses the FLT3-ITD mutation. In this paper we demonstrate that CDC25A level is controlled by a complex STAT5/miR-16 transcription and translation pathway working downstream of this receptor. First, we established by CHIP analysis that STAT5 is directly involved in FLT3-ITD-dependentCDC25Agene transcription. In addition, we determined that miR-16 expression is repressed by FLT3-ITD activity, and that STAT5 participates in this repression. In accordance with these results, miR-16 expression was significantly reduced in a panel of AML primary samples carrying the FLT3-ITD mutation when compared with FLT3wt cells. The expression of a miR-16 mimic reduced CDC25A protein and mRNA levels, and RNA interference-mediated down modulation of miR-16 restored CDC25A expression in response to FLT3-ITD inhibition. Finally, decreasing miR-16 expression partially restored the proliferation of cells treated with the FLT3 inhibitor AC220, while the expression of miR-16 mimic stopped this proliferation and induced monocytic differentiation of AML cells. In summary, we identified a FLT3-ITD/STAT5/miR-16/CDC25A axis essential for AML cell proliferation and differentiation.
The in vivo endothelial cell translatome is highly heterogeneous across vascular beds
Authors: Cleuren Audrey C.A. , van der Ent Martijn A. , Jiang Hui , Hunker Kristina L. , Yee Andrew , Siemieniak David R. , Molema Grietje , Aird William C. , Ganesh Santhi K. , Ginsburg David 
Published: July 2019

AbstractEndothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression following EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single cell suspensions for fluorescence-activated cell sorting (FACS) or single cell RNA sequencing analysis. Comparison of our EC-TRAP to published single cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.SignificanceEndothelial cells (ECs), which line all vertebrate blood vessels, are highly heterogeneous across different tissues. The present study uses a genetic approach to specifically tag mRNAs within ECs of the mouse, thereby allowing recovery and sequence analysis to evaluate the EC-specific gene expression program directly from intact organs. Our findings demonstrate marked heterogeneity in EC gene expression across different vascular beds under both normal and disease conditions, with a more accurate picture than can be achieved using other methods. The data generated in these studies advance our understanding of EC function in different blood vessels and provide a valuable resource for future studies.
Evolved for success in novel environments: The round goby genome
Authors: Adrian-Kalchhauser Irene , Blomberg Anders , Larsson Tomas , Musilova Zuzana , Peart Claire R , Pippel Martin , Solbakken Monica Hongroe , Suurväli Jaanus , Walser Jean-Claude , Wilson Joanna Yvonne , Rosenblad Magnus Alm , Burguera Demian , Gutnik Silvia , Michiels Nico , Töpel Mats , Pankov Kirill , Schloissnig Siegfried , Winkler Sylke 
Published: July 2019

AbstractSince the beginning of global trade, hundreds of species have colonized territories outside of their native range. Some of these species proliferate at the expense of native ecosystems, i.e., have become invasive. Invasive species constitute powerfulin situexperimental systems to study fast adaptation and directional selection on short ecological timescales. They also present promising case studies for ecological and evolutionary success in novel environments.We seize this unique opportunity to study genomic substrates for ecological success and adaptability to novel environments in a vertebrate. We report a highly contiguous long-read based genome assembly for the most successful temperate invasive fish, the benthic round goby (Neogobius melanostomus), and analyse gene families that may promote its impressive ecological success.Our approach provides novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns in epigenetic regulators, and the presence of genes that may have contributed to the round goby’s capacity to invade cold and salty waters.A recurring theme across all analyzed gene families are gene expansions. This suggests that gene duplications may promote ecological flexibility, superior performance in novel environments, and underlie the impressive colonization success of the round goby.Gobiidaegenerally feature fascinating adaptations and are excellent colonizers. Further long-read genome approaches across the goby family may reveal whether the ability to conquer new habitats relates more generally to gene copy number expansions.
H3K4me3 is neither instructive for, nor informed by, transcription
Authors: Murray Struan C , Lorenz Philipp , Howe Françoise S , Wouters Meredith , Brown Thomas , Xi Shidong , Fischl Harry , Khushaim Walaa , Rayappu Joseph Regish , Angel Andrew , Mellor Jane 
Published: July 2019

AbstractH3K4me3 is a near-universal histone modification found predominantly at the 5’ region of genes, with a well-documented association with gene activity. H3K4me3 has been ascribed roles as both an instructor of gene expression and also a downstream consequence of expression, yet neither has been convincingly proven on a genome-wide scale. Here we test these relationships using a combination of bioinformatics, modelling and experimental data from budding yeast in which the levels of H3K4me3 have been massively ablated. We find that loss of H3K4me3 has no effect on the levels of nascent transcription or transcript in the population. Moreover, we observe no change in the rates of transcription initiation, elongation, mRNA export or turnover, or in protein levels, or cell-to-cell variation of mRNA. Loss of H3K4me3 also has no effect on the large changes in gene expression patterns that follow galactose induction. Conversely, loss of RNA polymerase from the nucleus has no effect on the pattern of H3K4me3 deposition and little effect on its levels, despite much larger changes to other chromatin features. Furthermore, large genome-wide changes in transcription, both in response to environmental stress and during metabolic cycling, are not accompanied by corresponding changes in H3K4me3. Thus, despite the correlation between H3K4me3 and gene activity, neither appear to be necessary to maintain levels of the other, nor to influence their changes in response to environmental stimuli. When we compare gene classes with very different levels of H3K4me3 but highly similar transcription levels we find that H3K4me3-marked genes are those whose expression is unresponsive to environmental changes, and that their histones are less acetylated and dynamically turned-over. Constitutive genes are generally well-expressed, which may alone explain the correlation between H3K4me3 and gene expression, while the biological role of H3K4me3 may have more to do with this distinction in gene class.
Analysis and correction on frictional temperature rise testing of brake based on preset thermometry method
Authors: Zhao Shaodi , Yin Yan , Bao Jiusheng , Xiao Xingming , Li Zengsong , Chen Guoan 
Published: July 2019

Purpose
The friction between brake pair causes an intense temperature rise on interface during braking, which affects the braking performance seriously. Therefore, building an accurate testing method for frictional temperature rise (FTR) is a prerequisite.

Design/methodology/approach
Facing braking conditions of automobiles, an experimental system for testing of FTR based on preset thermometry method (PTM) was established. The FTR was collected by the PTM and the variation laws as well as the cause of errors were analyzed by experiments. The deviations between tested and real temperature were corrected based on tribology and heat theories. Finally, an online prediction method for FTR was pointed out.

Findings
After correction, the temperature curve accords well with the laws of tribology and thermal theories. The corrected FTR at braking end point is approximately equal to the authentic temperature test by hand thermometer.

Originality/value
This study eliminated the hysteresis phenomenon of temperature rise sequence and lays a foundation for online accurate monitoring and warning of brake friction temperature rise. It has important theoretical and practical value for expanding the monitoring and improvement of brake performance.
Ninety and not out—Understanding our oldest old
Authors: Gibson Diane , Goss John 
Published: July 2019

AbstractObjectiveThis paper draws attention to the rapidly growing number of Australian nonagenarians, presents previously unpublished information on this sub‐group of older people and explores the implications for future patterns of service delivery, planning and policy.MethodsStatistical analyses of Census data and other Australian Bureau of Statistics Surveys using Table Builder Pro, combined with analysis of de‐identified Australian Institute of Health and Welfare (AIHW) unit record data on aged care and AIHW GRIM (mortality) data.ResultsMale nonagenarians almost doubled from 2006 to 2016, while their female counterparts grew by 55%. This cohort is the first to reap cumulative advantage from the dramatic reduction in death rates from 1970. Their demographic circumstances reveal both changes and continuities compared to the previous cohort.ConclusionMen and women aged 90 and over use a substantial proportion of aged care services, and their characteristics and circumstances are highly relevant to planning current and future aged care services.
Cellular immune responses in amniotic fluid of women with preterm labor and intra‐amniotic infection or intra‐amniotic inflammation
Authors: Gomez‐Lopez Nardhy , Romero Roberto , Galaz Jose , Xu Yi , Panaitescu Bogdan , Slutsky Rebecca , Motomura Kenichiro , Gill Navleen , Para Robert , Pacora Percy , Jung Eunjung , Hsu Chaur‐Dong 
Published: July 2019

AbstractProblemPreterm birth is commonly preceded by preterm labor, a syndrome that is causally linked to both intra‐amniotic infection and intra‐amniotic inflammation. However, the stereotypical cellular immune responses in these two clinical conditions are poorly understood.Method of studyAmniotic fluid samples (n = 26) were collected from women diagnosed with preterm labor and intra‐amniotic infection (amniotic fluid IL‐6 concentrations ≥2.6 ng/mL and culturable microorganisms, n = 10) or intra‐amniotic inflammation (amniotic fluid IL‐6 concentrations ≥2.6 ng/mL without culturable microorganisms, n = 16). Flow cytometry was performed to evaluate the phenotype and number of amniotic fluid leukocytes. Amniotic fluid concentrations of classical pro‐inflammatory cytokines, type 1 and type 2 cytokines, and T‐cell chemokines were determined using immunoassays.ResultsWomen with spontaneous preterm labor and intra‐amniotic infection had (a) a greater number of total leukocytes, including neutrophils and monocytes/macrophages, in amniotic fluid; (b) a higher number of total T cells and CD4+ T cells, but not CD8+ T cells or B cells, in amniotic fluid; and (c) increased amniotic fluid concentrations of IL‐6, IL‐1β, and IL‐10, compared to those with intra‐amniotic inflammation. However, no differences in amniotic fluid concentrations of T‐cell cytokines and chemokines were observed between these two clinical conditions.ConclusionThe cellular immune responses observed in women with preterm labor and intra‐amniotic infection are more severe than in those with intra‐amniotic inflammation, and neutrophils, monocytes/macrophages, and CD4+ T cells are the main immune cells responding to microorganisms that invade the amniotic cavity. These findings provide insights into the intra‐amniotic immune mechanisms underlying the human syndrome of preterm labor.
Effects of Lonicera japonica extract supplementation on in vitro ruminal fermentation, methane emission, and microbial population
Authors: Yejun Lee , Su Kyoung Lee , Shin Ja Lee , Jong‐Su Eun , Sung Sill Lee 
Published: July 2019

AbstractLonicera japonica (LJ; honeysuckle) is used in traditional folk medicine in Korea and is a rich source of ascorbic acid and phenolic components that are reported to have antioxidant and antibiotic properties. We performed an in vitro experiment to assess the effects of LJ extracts (LJE) on ruminal fermentation. Timothy hay (0.3 g dry matter [DM]) was incubated with buffer, ruminal fluid, and 0%, 3%, 5%, 7%, and 9% LJE. Batch culture fermentation was conducted separately for 12, 24, and 48 hr to determine gas production (GP), ruminal fermentation characteristics, and microbial population characteristics. The effects on GP were generally similar to those on DM degradability, with a linear decrease observed at 9% extract at 24 hr. NH3‐N showed a linear increase with increasing extract concentrations at 12 hr, whereas a decrease was observed at 24 hr. Extract supplementation decreased methane (CH4) production at 12, 24, and 48 hr. In addition, the abundance of fibrolytic bacteria and ciliate‐associated methanogen was reduced at all concentrations of extracts. These results indicate that LJE have the potential to serve as a ruminal fermentation modifier to suppress CH4 production with minimal effects on nutrient digestion in the rumen.
Endometriosis infiltrating the pelvic floor muscles with histopathological correlation—A case report
Authors: Crispi Jr Claudio P. , Crispi Claudio P. , de Paula Crispi Fernanda , Cardeman Leon , Salomao Alice C. C. Brandão , de Freitas Fonseca Marlon 
Published: July 2019

AbstractWe report the case of a 29‐year‐old woman with deep infiltrating endometriosis who underwent robotic nerve‐sparing surgery for resection of all visible lesions infiltrating pelvic and extrapelvic sites. Painful symptoms included severe dysmenorrhea, menstrual dyschezia and stranguria, with no improvement in response to hormonal treatment. The location on physical examination of a painful retrocervical nodule was identified by magnetic resonance imaging to be infiltrating the right parametrium/paracervix. During surgery, this nodule was recognized as an important retrocervical/rectovaginal lesion infiltrating the pelvic floor (i.e. levator ani and coccygeus), and was histopathologically confirmed as endometriosis infiltrating the skeletal pelvic floor muscles. A Pubmed search of the MEDLINE database in March (2019) found no publication reporting histopathologic confirmation of endometriosis infiltrating the pelvic floor muscles.
Forum on teaching Asian religions in the American South
Authors: Mikles Natasha L. , Esaki Brett J. , Battaglia Lisa 
Published: July 2019

AbstractThis series of three essays by educators from Georgia, Texas, and Alabama examines teaching Asian Religions in the American South. Through reflection on individual experience, each essay offers concrete strategies for the classroom that can be utilized by fellow educators working in the American South, but can also inform pedagogy in other North American regions. Introducing the idea of the “imagined student,” Esaki discusses teaching African American students and tailoring Asian religions courses towards their interests by producing positive buy‐in, while also acknowledging their potential isolation from White peers interested in similar topics. Mikles builds on Esaki's idea of the imagined student to discuss her own experience teaching Mexican and Vietnamese American students in Texas, while presenting specific strategies to overcome preconceived educator bias about students in Southern classrooms. Battaglia closes out the series by suggesting the use of a phenomenological approach for students to sympathetically enter into an Asian religious worldview. She offers specific exercises that can help students unpack their own assumptions – their “invisible backpack” – and approach Asian religions on their own terms.
Cross-country analysis of correlation between protection of women’s economic and social rights, health improvement and sustainabledevelopment
Authors: Alaei Kamiar , Akgüngör Sedef , Chao Weng-Fong , Hasan Sayyida , Marshall Allyson , Schultz Emily , Alaei Arash 
Published: July 2019

ObjectiveThe goal of this study is to assess the correlation between protection of women’s economic and social rights (WESR), health improvement and sustainable development.MethodsA cross-country analysis of 162 countries was employed to assess development, health and human rights of the countries by measuring associated variables. Data sets for the health, human rights and economic and social rights of these countries were from 2004 to 2010. The dependent variables are health and human development and the independent variables are the human rights variables. Regression analysis and principle axis factoring were used for extraction and varimax method for rotation. Country grouping was made using cluster analysis. Potential biases, resulting from measurement differences in human rights values, were eliminated by using z-transformation to standardise variables.ResultsRegression results reveal that WESR variable is correlated with the health outcomes. Cluster analysis separated the countries into three clusters, based on the WESR variable. Countries where WESR were ‘highly respected’ (44 countries) are categorised into cluster 1; countries where WESR were ‘moderately respected’ (51 countries) are categorised into cluster 2 and countries where WESR were ‘poorly respected’ (63 countries) are categorised into cluster 3. Countries were then compared in their respective clusters based on health and human development variables. It was found that the countries which ‘highly respected’ WESR had better average health values compared with the second and third clusters. Our findings demonstrate that countries with a strong women’s rights status ultimately had better health outcomes.ConclusionWESR status has correlation with the health and human development. When women’s rights are highly respected, the nation is more likely to have higher health averages and accelerated development.
Process and outcomes evaluation of a pre-academic arts program for individuals with mental health conditions: a mixed methods study protocol
Authors: Salomon-Gimmon Maayan , Orkibi Hod , Elefant Cochavit 
Published: July 2019

IntroductionTheGarageis a multidisciplinary pre-academic arts school for people with artistic abilities who are coping with mental health conditions (MHC). The programme, supported by the National Insurance Institute and the Ministry of Health in Israel, is an innovative rehabilitation service designed to impart and enhance artistic-professional skills and socioemotional abilities to ultimately facilitate participants’ integration into higher education and the job market.Methods and analysisThis mixed methods longitudinal study will include an embedded design in which the qualitative data are primary and the quantitative data are secondary, thus providing complementary information. The study will examine the contribution of the Garage to changes in participants’ personal recovery, well-being, creative self-concept and community integration as well as possible mechanisms that may account for these changes. Qualitative data will be collected using focus groups with graduates and students (a total of ~60 participants). Quantitative data will be ‎collected by self-report questionnaires only from students attending the programme (before, during and at the end of the academic year). Data on the graduates’ integration into higher education and the job market after completing the programme will also be collected from the management team. The qualitative data will be analysed following the grounded theory approach and the quantitative data will be analysed with correlations, paired tests to examine pre–post changes and regression analyses. A merged data analysis will be conducted for data integration.Ethics and disseminationThe University’s Human Research Ethics Committee approved the design and procedures of the study (approval #357–16). All participants will sign an informed consent form where it is clarified that participation in the study is on a voluntary basis, and anonymity and confidentiality are guaranteed. The results will be submitted for peer-reviewed journal publications, presented at conferences and disseminated to the funder and the programme’s management team.