bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing Ebola Virus Disease Surveillance And Prevention In Counties Without Confirmed Cases In Rural Liberia: Experiences From Sinoe County During The Flare-Up In Monrovia, April To June, 2016
Authors: Weah Vera Darling , Doedeh John S. , Wiah Samson Q. , Nyema Emmanuel , Lombeh Siafa , Naiene Jeremias 
Published: May 2017

AbstractIntroductionDuring the flare-ups of Ebola virus disease (EVD) in Liberia, Sinoe County reactivated the multi-sectorial EVD control strategy in order to be ready to respond to the eventual reintroduction of cases.This paper describes the impacts of the interventions implemented in Sinoe County during the last flare-up in Monrovia, from April 1 to June 9, 2016, using the resources provided during the original outbreak that ended one year back.MethodsWe conducted a descriptive study to describe the key interventions implemented in Sinoe County, the capacity available, the implications for the reactivation of the multi-sectoral EVD control strategy, and the results of the same. We also conducted a cross-sectional study to analyze the impact of the interventions on the surveillance and on infection prevention and control (IPC).ResultsThe attrition of the staff trained during the original outbreak was low, and most of the supplies, equipment, and infrastructure from the original outbreak remained available.With an additional US$1755, improvements were observed in the IPC indicators of triage, which increased from a mean of 60% during the first assessment to 77% (P=0.002). Additionally, personal/staff training improved from 78% to 89% (P=0.04).The percentage of EVD death alerts per expected deaths investigated increased from 26% to 63% (P<0.0001).DiscussionThe small attrition of the trained staff and the availability of most of the supplies, equipment, and infrastructure made the reactivation of the multi-sectoral EVD control strategy fast and affordable. The improvement of the EVD surveillance was possibly affected by the community engagement activities, awareness and mentoring of the health workers, and improved availability of clinicians in the facilities during the flare-up. The community engagement may contribute to the report of community-based events, specifically community deaths. The mentoring of the staff during the supportive supervisions also contributed to improve the IPC indicators.
Cooperation & Liaison between Universities & Editors (CLUE): Recommendations on Best Practice
Authors:   CLUE Working Group, Wager Elizabeth , Kleinert Sabine , Garfinkel Michele , Bahr Volker , Bazdaric Ksenija , Farthing Michael , Graf Chris , Hammatt Zoë , Horn Lyn , King Susan , Parrish Debra , Pulverer Bernd , Taylor Paul , van Meer Gerrit 
Published: May 2017

SummaryJournals and research institutions have common interests regarding the trustworthiness of research publications but their specific roles and responsibilities differ. These draft recommendations aim to address issues surrounding cooperation and liaison between journals and institutions about possible and actual problems with reported research. The proposals will be discussed at various meetings including the World Conference on Research Integrity in May 2017. We will also consider comments and suggestions posted on this preprint.The main recommendations are that:National registers of individuals or departments responsible for research integrity at institutions should be created.Institutions should develop mechanisms for assessing the validity of research reports that are independent from processes to determine whether individual researchers have committed misconduct.Essential research data and peer review records should be retained for at least 10 years.While journals should normally raise concerns with authors in the first instance, they also need criteria to determine when to contact the institution before, or at the same time as, alerting the authors in cases of suspected data fabrication or falsification to prevent the destruction of evidence.Anonymous or pseudonymous allegations made to journals or institutions should be judged on their merit and not dismissed automatically.Institutions should release relevant sections of reports of research trustworthiness or misconduct investigations to all journals that have published research that was the subject of the investigation.
Could the recent zika epidemic have been predicted?
Authors: Muñoz Ángel G. , Thomson Madeleine C. , Stewart-Ibarra Anna M. , Vecchi Gabriel A. , Chourio Xandre , Nájera Patricia , Moran Zelda , Yang Xiaosong 
Published: May 2017

AbstractGiven knowledge at the time, the recent 2015-2016 zika virus (ZIKV) epidemic probably could not have been predicted. Without the prior knowledge of ZIKV being already present in South America, and given the lack of understanding of key epidemiologic processes and long-term records of ZIKV cases in the continent, the best related prediction was for potential risk of anAedes-borne disease epidemic. Here we use a recently published two-vector capacity model to assess the predictability of the conditions conducive to epidemics of diseases like zika, chikungunya or dengue, transmitted by the independent or concurrent presence ofAedes aegyptiandAedes albopictus. We compare the potential risk of transmission forcing the model with the observed climate and with state-of-the-art operational forecasts from the North American Multi Model Ensemble (NMME), finding that the predictive skill of this new seasonal forecast system is highest for multiple countries in Latin America and the Caribbean during the December-February and March-May seasons, and slightly lower –but still of potential use to decision-makers– for the rest of the year. In particular, we find that above-normalsuitable conditionsfor the occurrence of the zika epidemic at the beginning of 2015 could have been successfully predicted for several zika hotspots, and in particular for Northeast Brazil: the heart of the epidemic. Nonetheless, the initiation and spread of an epidemic depends on the effect of multiple factors beyond climate conditions, and thus this type of approach must be considered as a guide and not as a formal predictive tool of vector-borne epidemics.
Morphometrics reveals complex and heritable apple leaf shapes
Authors: Migicovsky Zoë , Li Mao , Chitwood Daniel H. , Myles Sean 
Published: May 2017

AbstractApple (Malus spp.) is a widely grown and valuable fruit crop. Leaf shape and size are important for flowering in apple and may also be early indicators for other agriculturally valuable traits. We examined 9,000 leaves from 869 unique apple accessions using linear measurements and comprehensive morphometric techniques. We identified allometric variation in the length-to-width aspect ratio between accessions and species of apple. The allometric variation was due to variation in the width of the leaf blade, not length. Aspect ratio was highly correlated with the primary axis of morphometric variation (PC1) quantified using elliptical Fourier descriptors (EFDs) and persistent homology (PH). While the primary source of variation was aspect ratio, subsequent PCs corresponded to complex shape variation not captured by linear measurements. After linking the morphometric information with over 122,000 genome-wide SNPs, we found high narrow-sense heritability values even at later PCs, indicating that comprehensive morphometrics can capture complex, heritable phenotypes. Thus, techniques such as EFDs and PH are capturing heritable biological variation that would be missed using linear measurements alone, and which could potentially be used to select for a hidden phenotype only detectable using comprehensive morphometrics.
Thoracolumbar intervertebral disc area morphometry in elderly Chinese men and women: radiographic quantifications at baseline and changes at year-4 follow-up
Authors: Wáng Jùn-Qīng , Káplár Zoltán , Deng Min , Griffith James F. , Leung Jason C. S. , Kwok Anthony WL , Kwok Timothy , Leung Ping Chung , Wáng Yì-Xiáng J. 
Published: May 2017

The manuscript submitted does not contain information about medical device(s)/drug(s). No benefits in any form have been or will be received from a commercial party related directly or indirectly to the subject of this manuscript.Study Design:A population-based radiographic study with longitudinal follow-up.Objective:To develop a quantitative index for lumbar disc space narrowing (DSN) evaluation in elderly subjects; to determine how DSN in the elderly is influenced by osteoporosis and gender.Summary of Background Data:There is paucity of research on quantitative classification of lumbar DSN based on disc areal morphometry.Methods:With the database of Osteoporotic Fractures in Men (Hong Kong) and Osteoporotic Fractures in Women (Hong Kong) Studies and those who attended the year-4 follow-up (n = 1519 for men and n = 1546 for women), data of 491 women and 592 men were randomly selected. The anterior, middle, and posterior heights, anteroposterior diameter and area of intervertebral discs (T4T5 to L4L5) were measured on lateral radiographs. Disc Area Index for Lumbar Spine (DAIL, disc area divided by the mean of the sum of square of the adjacent upper and lower vertebrae mid-height anterior-posterior diameter) was developed and compared with semi-quantitative DSN expert grading.Results:DAIL correlated with semi-quantitative grading, with sensitivity and specificity varying from 87.3% to 96.8% for grade-1 DSN (<30% reduction in disc height), and 92.9 % to 100% for grade-3 DSN (>60% reduction in disc height). The thoracolumbar disc area loss among men and women during 4-years’ follow-up period varied between 1.32% and 3.56%, and it was greater for women (mean: 2.44%) than for men (mean: 1.90%,p=0.044). Majority of lumbar DSN progressions during 72 to 76 years old were progression from normal disc space to grade-1DSN. Osteoporosis was associated with greater disc area decrease, both for thoracic and lumbar discs.Conclusion:Lumbar DSN can be quantified using DAIL. In elderly Chinese, intervertebral disc narrowing over a 4-year period was greater in women than men, and associated with the presence of osteoporosis.
A CRISPR-based yeast two-hybrid system for investigating RNA-protein interactions
Authors: Hass Evan P. , Zappulla David C. 
Published: May 2017

ABSTRACTDespite the great importance of RNA-protein interactions in cells, there is a very limited set of approaches available for identifying proteins that bind to a specific RNA. We report here combining the use of CRISPR technology with the yeast two-hybrid protein-protein interaction system in order to create an advantageous method for investigating RNA-protein interactions. In thisCRISPR-assistedRNA/RBPyeast (CARRY) two-hybrid system, an RNA of interest is targeted to the promoters of standard yeast two-hybrid reporter genes by fusing it to the CRISPR guide RNA in a strain expressing catalytically deactivated Cas9 (dCas9). If the promoter-tethered RNA binds to a protein fused to Gal4 transcriptional activation domain (GAD), then the reporter genes become transcribed, just as in the standard protein-protein yeast two-hybrid assay. We used the CARRY two-hybrid system to analyze MS2 bacteriophage RNA hairpin binding to the MS2 coat protein (MCP). We tested MS2 hairpin mutants with a range of biochemically determined binding affinities for MCP and found that CARRY two-hybrid detected all binding interactions with dissociation constants ≤300 nM. In summary, this new CRISPR-based yeast two-hybrid system provides an easily operable, much-needed new tool for identifying proteins that bind to a particular RNA.
Changes of gene expression but not cytosine methylation are associated with plasticity of male parental care reflecting behavioural state, social context, and individual flexibility
Authors: Cunningham CB , Ji L , McKinney EC , Benowitz KM , Schmitz RJ , Moore AJ 
Published: May 2017

AbstractBehaviour is often on the front line of plasticity in response to different environments. At the genetic level, behavioural changes are likely to be associated with changes of gene expression. Most studies to date have focused on gene expression differences associated with discrete behavioural states reflecting development or age-related changes, such as honey bee castes. However, more rapidly flexible behaviour is often observed in response to social context or simple individual variation. The differences in genetic influences for the different forms of plasticity are poorly understood. In this study we contrasted gene expression during male parental care of the burying beetle,Nicrophorus vespilloides, in a factorial design. MaleN. vespilloidesmales typically do not provide care when females are present. However, male care is inducible by the removing female and has parental effects equivalent to female care. We used this experimental manipulation to isolate gene expression and cytosine methylation associated with differences of behavioural state, differences of social context, or differences of individual flexibility for expressing care. The greatest number of differentially expressed genes was associated with behavioural state, followed by differences of social contexts, and lastly differences of individual variation. DNA methylation has been hypothesized to regulate the transcriptional architecture that regulates behavioural transitions. We tested this hypothesis by quantifying differences of cytosine methylation that were associated with differences of behavioural state and individual flexibility. Changes of cytosine methylation were not associated with changes of gene expression. Our results suggest a hierarchical association between gene expression and the different sources of variation that influence behaviour, but that this process is not controlled by DNA methylation despite reflecting levels of plasticity in behaviour. Our results further suggest that the extent that a behaviour is transient plays an underappreciated role in determining the molecular mechanisms that underpin the behaviour.
NQO1 binds and supports SIRT1 function
Authors: Tsvetkov Peter , Adler Julia , Adamovich Yaarit , Asher Gad , Reuven Nina , Shaul Yosef 
Published: May 2017

AbstractSilent information regulator 2-related enzyme 1 (SIRT1) is an NAD+-dependent class III deacetylase and a key component of the cellular metabolic sensing pathway. The requirement of NAD+for SIRT1 activity led us to assume that NQO1, an NADH oxidoreductase producing NAD+, regulates SIRT1 activity. We show here that SIRT1 is capable of increasing NQO1 (NAD(P)H Dehydrogenase Quinone 1) transcription and protein levels. NQO1 physically interacts with SIRT1 but not with an enzymatically dead SIRT1 H363Y mutant. The interaction of NQO1 with SIRT1 is markedly increased under mitochondrial inhibition. Interestingly, under this condition the nuclear pool of NQO1 is elevated. Depletion of NQO1 compromises the role of SIRT1 in inducing transcription of several target genes and eliminates the protective role of SIRT1 following mitochondrial inhibition. Our results suggest that SIRT1 and NQO1 form a regulatory loop where SIRT1 regulates NQO1 expression and NQO1 binds and mediates the protective role of SIRT1 during mitochondrial stress. The interplay between an NADH oxidoreductase enzyme and an NAD+dependent deacetylase may act as a rheostat in sensing mitochondrial stress.
Systematic analysis of RNA-seq-based gene co-expression across multiple plants
Authors: Yu Hua , Jiao Bingke , Liang Chengzhi 
Published: May 2017

AbstractThe complex cellular network was formed by the interacting gene modules. Building the high-quality RNA-seq-based Gene Co-expression Network (GCN) is critical for uncovering these modules and understanding the phenotypes of an organism. Here, we established and analyzed the RNA-seq-based GCNs in two monocot species rice and maize, and two eudicot speciesArabidopsisand soybean, and subdivided them into co-expressed modules. Taking rice as an example, we associated these modules with biological functions and agronomic traits by enrichment analysis, and discovered a large number of conditin-specific or tissue-specific modules. In addition, we also explored the regulatory mechanism of the modules by enrichment of the known cis-elements, transcription factors and miRNA targets. Their coherent enrichment with the inferred functions of the modules revealed their synergistic effect on the gene expression regulation. Moreover, the comparative analysis of gene co-expression was performed to identify conserved and species-specific functional modules across 4 plant species. We discovered that the modules shared across 4 plants participate in the basic biological processes, whereas the species-specific modules were involved in the spatiotemporal-specific processes linking the genotypes to phenotypes. Our research provides the massive modules relating to the cellular activities and agronomic traits in several model and crop plant species.
CRootBox: A structural-functional modelling framework for root systems
Authors: Schnepf Andrea , Leitner Daniel , Landl Magdalena , Lobet Guillaume , Mai Trung Hieu , Morandage Shehan , Sheng Cheng , Zörner Mirjam , Vanderborght Jan , Vereecken Harry 
Published: May 2017

ABSTRACTBackground and AimsRoot architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural models have been widely used and been further developed into functional-structural models that simulate the fate of water and solutes in the soil-root system. We present a root architectural model, CRootBox, as a flexible framework to model architecture and its interactions with static and dynamic soil environments.MethodsCRootBox is a C++ -based root architecture model with Python binding, so that CRootBox can be included via a shared library into any Python code. Output formats include VTP, DGF, RSML and CSV. We further created a database of published root architectural parameters. The capabilities of CRootBox for the unconfined growth of single root systems, as well as the different parameter sets, are highlighted into a freely available web application.Key resultsWe demonstrate the use of CRootBox for 5 different cases (1) free growth of individual root systems (2) growth of root systems in containers as a way to mimic experimental setups, (3), field scale simulation, (4) root growth as affected by heterogeneous, static soil conditions, and (5) coupling CRootBox with Soil Physics with Python code to dynamically compute water flow in soil, root water uptake, and water flow inside roots.ConclusionsIn conclusion, we present a fast and flexible functional-structural root model which is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of root on soil. In the future, we plan to extend this approach to the aboveground part of the plant.
Side effects and the need for secrecy: characterising discontinuation of modern contraception and its causes in Ethiopia using mixed methods
Authors: Alvergne Alexandra , Stevens Rose , Gurmu Eshetu 
Published: May 2017

AbstractBackgroundContraceptive discontinuation is a major barrier to reducing global unmet needs for family planning, but the reasons why women discontinue contraception are poorly understood. Here we use data from Ethiopia to investigate (i) the magnitude of contraceptive discontinuation in 2005-2011, (ii) how the risk of discontinuation varies with method type and education level and (iii) the barriers to continuation. Our main hypothesis is that contraceptive discontinuation is driven by the experience of physiological side-effects associated with the use of hormonal contraception, rather than a lack of education.MethodsWe used a mixed methods explanatory sequential design to explain the quantitative results in more details through the qualitative data. First, we analysed quantitative data from the 2011 Ethiopian Demographic and Health Survey to study patterns of contraceptive discontinuation and method choice using multilevel multiprocess models. Second, we conducted semi-structured interviews and focus group discussions in the 3 most populated regions of Ethiopia with individuals of reproductive age and health professionals.ResultsThe analysis of EDHS data shows that the rate of discontinuation has not reduced in the period 2005-2011 and remains high. Discontinuation mainly takes the form of abandonment, and is a function of method type and wealth but not of educational level. Interviews with women and health professionals reveal that the experience of debilitating physiological side effects, the need for secrecy and poverty are important barriers to continuation.ConclusionsOur findings together suggest that physiological and social side-effects of contraceptive use, not education, are the root causes of contraceptive discontinuation in Ethiopia. We argue that to tackle discontinuation due to side-effects, dispelling misconceptions through educating women is not addressing the root causes of discontinuation, and that priority should be given to both engaging men and questioning the appropriateness of medical technology to the physiology of Ethiopian women, especially those living in poverty.
Cell dynamics underlying oriented growth of theDrosophilawing imaginal disc
Authors: Dye Natalie A. , Popović Marko , Spannl Stephanie , Etournay Raphaël , Kainmüller Dagmar , Myers Eugene W. , Jülicher Frank , Eaton Suzanne 
Published: May 2017

ABSTRACTQuantitative analysis of the dynamic cellular mechanisms shaping theDrosophilawing during its larval growth phase has been limited, impeding our ability to understand how morphogen patterns regulate tissue shape. Such analysis requires imaging explants under conditions that maintain both growth and patterning, as well as methods to quantify how much cellular behaviors change tissue shape. Here, we demonstrate a key requirement for the steroid hormone 20-hydroxyecdysone (20E) in the maintenance of numerous patterning systemsin vivoand in explant culture. We find that low concentrations of 20E support prolonged proliferation in explanted wing discs in the absence of insulin, incidentally providing novel insight into the hormonal regulation of imaginal growth. We use 20E-containing media to directly observe growth and apply recently developed methods for quantitatively decomposing tissue shape changes into cellular contributions. We discover that while cell divisions drive tissue expansion along one axis, their contribution to expansion along the orthogonal axis is cancelled by cell rearrangements and cell shape changes. This finding raises the possibility that anisotropic mechanical constraints contribute to growth orientation in the wing disc.
Control of AMPA receptor activity by the extracellular loops of auxiliary proteins
Authors: Riva Irene , Eibl Clarissa , Volkmer Rudolf , Carbone Anna L. , Plested Andrew J. R. 
Published: May 2017

AbstractAt synapses throughout the mammalian brain, AMPA receptors form complexes with auxiliary proteins, including TARPs. However, how TARPs modulate AMPA receptor gating remains poorly understood. We built structural models of TARP-AMPA receptor complexes for TARPs γ2 and γ8, combining recent structural studies and de novo structure predictions. These models, combined with peptide binding assays, provide evidence for multiple interactions between GluA2 and variable extracellular loops of TARPs. Substitutions and deletions of these loops had surprisingly rich effects on the kinetics of glutamate-activated currents, without any effect on assembly. Critically, by altering the two interacting loops of γ2 and γ8, we could entirely remove all allosteric modulation of GluA2, without affecting formation of AMPA receptor-TARP complexes. Likewise, substitutions in the linker domains of GluA2 completely removed any effect of Y2 on receptor kinetics, indicating a dominant role for this previously overlooked site proximal to the AMPA receptor channel gate.