bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attraction Versus Capture II: Efficiency of the BG-Sentinel Trap Under Semifield Conditions and Characterizing Response Behaviors of Male Aedes aegypti (Diptera: Culicidae)
Authors: Amos Brogan A , Ritchie Scott A , Cardé Ring T 
Published: May 2020

AbstractAedes aegypti (L.) is an important vector of viruses causing dengue, Zika, chikungunya, and yellow fever and as such presents a serious threat to public health in tropical regions. Control programs involving ‘rear and release’ of modified male Ae. aegypti are underway and require effective trapping methods for surveillance of both the released insects and the impacted wild mosquito population. The BG-Sentinel trap (BGS) is widely used in Ae. aegypti surveillance but its level of efficiency, that is, what proportion of the mosquitoes encountering the trap are captured, is unknown. This is especially true for male mosquitoes, the behavior of which is incompletely understood. We tested the efficiency of two versions of the BGS for capturing male Ae. aegypti under semifield conditions with and without CO2 and a human skin odor mimic lure and with these baits combined. A navy-blue BGS trap emitting CO2 and a human skin odor mimic captured 18% of the released male Ae. aegypti, with a capture efficiency of 9 % (of the total encounters with the trap). Male Ae. aegypti had multiple encounters with the BGS that did not result in capture; they crossed over the trap entrance without being captured or landed on the sides of the trap. Swarming behavior around the BGS was also recorded, even when only a visual cue was present. Understanding male Ae. aegypti behaviors during an encounter with the BGS can inform improvement of trap design and therefore capture efficiency for surveillance in control programs.
Effectiveness of interventions targeting air travellers for delaying local outbreaks of SARS-CoV-2
Authors: Clifford Samuel , Pearson Carl A B , Klepac Petra , Van Zandvoort Kevin , Quilty Billy J ,   CMMID COVID-19 working group, Eggo Rosalind M , Flasche Stefan 
Published: May 2020

AbstractBackgroundWe evaluated if interventions aimed at air travellers can delay local severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community transmission in a previously unaffected country.MethodsWe simulated infected air travellers arriving into countries with no sustained SARS-CoV-2 transmission or other introduction routes from affected regions. We assessed the effectiveness of syndromic screening at departure and/or arrival and traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduces the average number of secondary cases. We use stochastic simulations to account for uncertainty in both arrival and secondary infections rates, and present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. We report the median expected delay achievable in each scenario and an inner 50% interval.ResultsUnder baseline assumptions, introducing exit and entry screening in combination with traveller sensitisation can delay a local SARS-CoV-2 outbreak by 8 days (50% interval: 3–14 days) when the rate of importation is 1 infected traveller per week at time of introduction. The additional benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by 7 days (50% interval: 2–13 days). In the absence of screening, with less effective sensitisation, or a higher rate of importation, these delays shrink rapidly to &lt;4 days.ConclusionSyndromic screening and traveller sensitisation in combination may have marginally delayed SARS-CoV-2 outbreaks in unaffected countries.
Phylogeny and gene expression of the complete NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Triticum aestivum
Authors: Wang Huadun , Wan Yongfang , Buchner Peter , King Robert , Ma Hongxiang , Hawkesford Malcolm J 
Published: May 2020

AbstractNPF genes encode membrane transporters involved in the transport of a large variety of substrates including nitrate and peptides. The NPF gene family has been described for many plants, but the whole NPF gene family for wheat has not been completely identified. The release of the wheat reference genome has enabled the identification of the entire wheat NPF gene family. A systematic analysis of the whole wheat NPF gene family was performed, including responses of specific gene expression to development and nitrogen supply. A total of 331 NPF genes (113 homoeologous groups) have been identified in wheat. The chromosomal location of the NPF genes is unevenly distributed, with predominant occurrence in the long arms of the chromosomes. The phylogenetic analysis indicated that wheat NPF genes are closely clustered with Arabidopsis, Brachypodium, and rice orthologues, and subdivided into eight subfamilies. The expression profiles of wheat NPF genes were examined using RNA-seq data, and a subset of 44 NPF genes (homoeologous groups) with contrasting expression responses to nitrogen and/or development in different tissues were identified. The systematic identification of gene composition, chromosomal locations, evolutionary relationships, and expression profiles contributes to a better understanding of the roles of the wheat NPF genes and lays the foundation for further functional analysis in wheat.
Original Research by Young Twinkle Students (ORBYTS): ephemeris refinement of transiting exoplanets
Authors: Edwards Billy , Changeat Quentin , Yip Kai Hou , Tsiaras Angelos , Taylor Jake , Akhtar Bilal , AlDaghir Josef , Bhattarai Pranup , Bhudia Tushar , Chapagai Aashish , Huang Michael , Kabir Danyaal , Khag Vieran , Khaliq Summyyah , Khatri Kush , Kneth Jaidev , Kothari Manisha , Najmudin Ibrahim , Panchalingam Lobanaa , Patel Manthan , Premachandran Luxshan , Qayyum Adam , Rana Prasen , Shaikh Zain , Syed Sheryar , Theti Harnam , Zaidani Mahmoud , Saraf Manasvee , de Mijolla Damien , Caines Hamish , Kokori Anatasia , Rocchetto Marco , Mallonn Matthias , Bachschmidt Matthieu , Bosch Josep M , Bretton Marc , Chatelain Philippe , Deldem Marc , Di Sisto Romina , Evans Phil , Fernández-Lajús Eduardo , Guerra Pere , Grau Horta Ferran , Kang Wonseok , Kim Taewoo , Leroy Arnaud , Lomoz František , de Haro Juan Lozano , Hentunen Veli-Pekka , Jongen Yves , Molina David , Montaigut Romain , Naves Ramon , Raetz Manfred , Sauer Thomas , Watkins Americo , Wünsche Anaël , Zibar Martin , Dunn William , Tessenyi Marcell , Savini Giorgio , Tinetti Giovanna , Tennyson Jonathan 
Published: May 2020

ABSTRACT
We report follow-up observations of transiting exoplanets that have either large uncertainties (&gt;10 min) in their transit times or have not been observed for over 3 yr. A fully robotic ground-based telescope network, observations from citizen astronomers, and data from TESS have been used to study eight planets, refining their ephemerides and orbital data. Such follow-up observations are key for ensuring accurate transit times for upcoming ground- and space-based telescopes, which may seek to characterize the atmospheres of these planets. We find deviations from the expected transit time for all planets, with transits occurring outside the 1σ uncertainties for seven planets. Using the newly acquired observations, we subsequently refine their periods and reduce the current predicted ephemeris uncertainties to 0.28–4.01 min. A significant portion of this work has been completed by students at two high schools in London as part of the Original Research By Young Twinkle Students (ORBYTS) programme.
Development of a single-stranded DNA-binding protein fluorescent fusion toolbox
Authors: Dubiel Katarzyna , Henry Camille , Spenkelink Lisanne M , Kozlov Alexander G , Wood Elizabeth A , Jergic Slobodan , Dixon Nicholas E , van Oijen Antoine M , Cox Michael M , Lohman Timothy M , Sandler Steven J , Keck James L 
Published: May 2020

AbstractBacterial single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA and help to recruit heterologous proteins to their sites of action. SSBs perform these essential functions through a modular structural architecture: the N-terminal domain comprises a DNA binding/tetramerization element whereas the C-terminus forms an intrinsically disordered linker (IDL) capped by a protein-interacting SSB-Ct motif. Here we examine the activities of SSB-IDL fusion proteins in which fluorescent domains are inserted within the IDL of Escherichia coli SSB. The SSB-IDL fusions maintain DNA and protein binding activities in vitro, although cooperative DNA binding is impaired. In contrast, an SSB variant with a fluorescent protein attached directly to the C-terminus that is similar to fusions used in previous studies displayed dysfunctional protein interaction activity. The SSB-IDL fusions are readily visualized in single-molecule DNA replication reactions. Escherichia coli strains in which wildtype SSB is replaced by SSB-IDL fusions are viable and display normal growth rates and fitness. The SSB-IDL fusions form detectible SSB foci in cells with frequencies mirroring previously examined fluorescent DNA replication fusion proteins. Cells expressing SSB-IDL fusions are sensitized to some DNA damaging agents. The results highlight the utility of SSB-IDL fusions for biochemical and cellular studies of genome maintenance reactions.
G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress
Authors: Somasekharan Syam Prakash , Zhang Fan , Saxena Neetu , Huang Jia Ni , Kuo I-Chih , Low Caitlin , Bell Robert , Adomat Hans , Stoynov Nikolay , Foster Leonard , Gleave Martin , Sorensen Poul H 
Published: May 2020

AbstractCells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into RNA granules reduces their translation, but it remains unclear whether RBPs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress adaptation in cancer. To study transcript partitioning under cell stress, we catalogued mRNAs enriched in prostate carcinoma PC-3 cell PSs, as defined by polysome fractionation and RNA sequencing (RNAseq), and compared them to mRNAs complexed with the known SG-nucleator protein, G3BP1, as defined by spatially-restricted enzymatic tagging and RNAseq. By comparing these compartments before and after short-term arsenite-induced oxidative stress, we identified three major categories of transcripts, namely those that were G3BP1-associated and PS-depleted, G3BP1-dissociated and PS-enriched, and G3BP1-associated but also PS-enriched. Oxidative stress profoundly altered the partitioning of transcripts between these compartments. Under arsenite stress, G3BP1-associated and PS-depleted transcripts correlated with reduced expression of encoded mitochondrial proteins, PS-enriched transcripts that disassociated from G3BP1 encoded cell cycle and cytoprotective proteins whose expression increased, while transcripts that were both G3BP1-associated and PS-enriched encoded proteins involved in diverse stress response pathways. Therefore, G3BP1 guides transcript partitioning to reprogram mRNA translation and support stress adaptation.
EpiRegio: analysis and retrieval of regulatory elements linked to genes
Authors: Baumgarten Nina , Hecker Dennis , Karunanithi Sivarajan , Schmidt Florian , List Markus , Schulz Marcel H 
Published: May 2020

Abstract
A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding regions, but their mechanisms of gene regulation are often unknown. An additional challenge is to reliably identify the target genes of the regulatory regions, which is an essential step in understanding their impact on gene expression. Here we present the EpiRegio web server, a resource of regulatory elements (REMs). REMs are genomic regions that exhibit variations in their chromatin accessibility profile associated with changes in expression of their target genes. EpiRegio incorporates both epigenomic and gene expression data for various human primary cell types and tissues, providing an integrated view of REMs in the genome. Our web server allows the analysis of genes and their associated REMs, including the REM’s activity and its estimated cell type-specific contribution to its target gene’s expression. Further, it is possible to explore genomic regions for their regulatory potential, investigate overlapping REMs and by that the dissection of regions of large epigenomic complexity. EpiRegio allows programmatic access through a REST API and is freely available at https://epiregio.de/.
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values
Authors: Orlando Gabriele , Raimondi Daniele , Kagami Luciano Porto , Vranken Wim F 
Published: May 2020

AbstractNuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino acid residue, chemical shifts present multi-dimensional and complexly cross-correlated information, making them difficult to analyse. The ShiftCrypt method, based on neural network auto-encoder architecture, compresses the per-amino acid chemical shift information in a single, interpretable, amino acid-type independent value that reflects the biophysical state of a residue. We here present the ShiftCrypt web server, which makes the method readily available. The server accepts chemical shifts input files in the NMR Exchange Format (NEF) or NMR-STAR format, executes ShiftCrypt and visualises the results, which are also accessible via an API. It also enables the ”biophysically-based” pairwise alignment of two proteins based on their ShiftCrypt values. This approach uses Dynamic Time Warping and can optionally include their amino acid code information, and has applications in, for example, the alignment of disordered regions. The server uses a token-based system to ensure the anonymity of the users and results. The web server is available at www.bio2byte.be/shiftcrypt.
Estradiol and mortality in women with end-stage kidney disease
Authors: Ramesh Sharanya , James Matthew T , Holroyd-Leduc Jayna M , Wilton Stephen B , Seely Ellen W , Hemmelgarn Brenda R , Tonelli Marcello , Wheeler David C , Ahmed Sofia B 
Published: May 2020

Abstract

Background
Young women with end-stage kidney disease (ESKD) have early menopause compared with women in the general population and the highest mortality among the dialysis population. We hypothesized that low estrogen status was associated with death in women with ESKD.

Methods
We measured estradiol and sex hormone levels in female ESKD patients initiating hemodialysis from 2005 to 2012 in four Canadian centers. We divided women into quintiles based on estradiol levels and tested for associations between the estradiol level and cardiovascular (CV), non-CV and all-cause mortality. Participants were further dichotomized by age.

Results
A total of 482 women (60 ± 15 years of age, 53% diabetic, estradiol 116 ± 161 pmol/L) were followed for a mean of 2.9 years, with 237 deaths (31% CV). Estradiol levels were as follows (mean ± standard deviation): Quintile 1: 19.3 ± 0.92 pmol/L; Quintile 2: 34.6 ± 6.6 pmol/L; Quintile 3: 63.8 ± 10.6 pmol/L; Quintile 4: 108.9 ± 19.3; Quintile 5: 355 ± 233 pmol/L. Compared with Quintile 1, women in Quintiles 4 and 5 had significantly higher adjusted all-cause mortality {hazard ratio [HR] 2.12 [95% confidence interval (CI) 1.38–3.25] and 1.92 [1.19–3.10], respectively}. Similarly, compared with Quintile 1, women in Quintile 5 had higher non-CV mortality [HR 2.16 (95% CI 1.18–3.96)]. No associations were observed between estradiol levels and CV mortality. When stratified by age, higher quintiles were associated with greater all-cause mortality (P for trend &lt;0.001) and non-CV mortality (P for trend = 0.02), but not CV mortality in older women.

Conclusions
In women with ESKD treated with hemodialysis, higher estradiol levels were associated with greater all-cause and non-CV mortality. Further studies are required to determine the mechanism for the observed increased risk.
Meaning of empowerment in peritoneal dialysis: focus groups with patients and caregivers
Authors: Baumgart Amanda , Manera Karine E , Johnson David W , Craig Jonathan C , Shen Jenny I , Ruiz Lorena , Wang Angela Yee-Moon , Yip Terence , Fung Samuel K S , Tong Matthew , Lee Achilles , Cho Yeoungjee , Viecelli Andrea K , Sautenet Benedicte , Teixeira-Pinto Armando , Brown Edwina A , Brunier Gillian , Dong Jie , Scholes-Robertson Nicole , Dunning Tony , Mehrotra Rajnish , Naicker Saraladevi , Pecoits-Filho Roberto , Perl Jeffrey , Wilkie Martin , Tong Allison 
Published: May 2020

Abstract

Background
While peritoneal dialysis (PD) can offer patients more independence and flexibility compared with in-center hemodialysis, managing the ongoing and technically demanding regimen can impose a burden on patients and caregivers. Patient empowerment can strengthen capacity for self-management and improve treatment outcomes. We aimed to describe patients’ and caregivers’ perspectives on the meaning and role of patient empowerment in PD.

Methods
Adult patients receiving PD (n = 81) and their caregivers (n = 45), purposively sampled from nine dialysis units in Australia, Hong Kong and the USA, participated in 14 focus groups. Transcripts were thematically analyzed.

Results
We identified six themes: lacking clarity for self-management (limited understanding of rationale behind necessary restrictions, muddled by conflicting information); PD regimen restricting flexibility and freedom (burden in budgeting time, confined to be close to home); strength with supportive relationships (gaining reassurance with practical assistance, comforted by considerate health professionals, supported by family and friends); defying constraints (reclaiming the day, undeterred by treatment, refusing to be defined by illness); regaining lost vitality (enabling physical functioning, restoring energy for life participation); and personal growth through adjustment (building resilience and enabling positive outlook, accepting the dialysis regimen).

Conclusions
Understanding the rationale behind lifestyle restrictions, practical assistance and family support in managing PD promoted patient empowerment, whereas being constrained in time and capacity for life participation outside the home undermined it. Education, counseling and strategies to minimize the disruption and burden of PD may enhance satisfaction and outcomes in patients requiring PD.
Adult diffuse glioma GWAS by molecular subtype identifies variants inD2HGDHandFAM20C
Authors: Eckel-Passow Jeanette E , Drucker Kristen L , Kollmeyer Thomas M , Kosel Matt L , Decker Paul A , Molinaro Annette M , Rice Terri , Praska Corinne E , Clark Lauren , Caron Alissa , Abyzov Alexej , Batzler Anthony , Song Jun S , Pekmezci Melike , Hansen Helen M , McCoy Lucie S , Bracci Paige M , Wiemels Joseph , Wiencke John K , Francis Stephen , Burns Terry C , Giannini Caterina , Lachance Daniel H , Wrensch Margaret , Jenkins Robert B 
Published: May 2020

AbstractBackgroundTwenty-five germline variants are associated with adult diffuse glioma, and some of these variants have been shown to be associated with particular subtypes of glioma. We hypothesized that additional germline variants could be identified if a genome-wide association study (GWAS) were performed by molecular subtype.MethodsA total of 1320 glioma cases and 1889 controls were used in the discovery set and 799 glioma cases and 808 controls in the validation set. Glioma cases were classified into molecular subtypes based on combinations of isocitrate dehydrogenase (IDH) mutation, telomerase reverse transcriptase (TERT) promoter mutation, and 1p/19q codeletion. Logistic regression was applied to the discovery and validation sets to test for associations of variants with each of the subtypes. A meta-analysis was subsequently performed using a genome-wide P-value threshold of 5 × 10−8.ResultsNine variants in or near D-2-hydroxyglutarate dehydrogenase (D2HGDH) on chromosome 2 were genome-wide significant in IDH-mutated glioma (most significant was rs5839764, meta P = 2.82 × 10−10). Further stratifying by 1p/19q codeletion status, one variant in D2HGDH was genome-wide significant in IDH-mutated non-codeleted glioma (rs1106639, meta P = 4.96 × 10−8). Further stratifying by TERT mutation, one variant near FAM20C (family with sequence similarity 20, member C) on chromosome 7 was genome-wide significant in gliomas that have IDH mutation, TERT mutation, and 1p/19q codeletion (rs111976262, meta P = 9.56 × 10−9). Thirty-six variants in or near GMEB2 on chromosome 20 near regulator of telomere elongation helicase 1 (RTEL1) were genome-wide significant in IDH wild-type glioma (most significant was rs4809313, meta P = 2.60 × 10−10).ConclusionsPerforming a GWAS by molecular subtype identified 2 new regions and a candidate independent region near RTEL1, which were associated with specific glioma molecular subtypes.
Differences in Smoking Topography and Subjective Responses to Smoking Among African American and White Menthol and Non-Menthol Smokers
Authors: Gunawan Tommy , Juliano Laura M 
Published: May 2020

AbstractIntroductionIt has been suggested that menthol increases exposure to harmful elements of smoking and makes smoking more rewarding, easier to initiate, and harder to quit. Isolating the direct effects of menthol is challenging as African American (AA) race and menthol preference are highly overlapping. This study evaluated smoking behavior and subjective responses among a balanced sample of AA and white menthol and non-menthol smokers. In addition, smoking topography (ST) was compared to naturalistic smoking (NS) and interactions with menthol and race were explored.Aims and MethodsSmokers (N = 100) smoked and rated their preferred brand of cigarettes via ST or NS during two laboratory visits (counterbalanced).ResultsControlling for baseline differences among the groups (eg, nicotine dependence), menthol smokers took shorter and smaller puffs and AA smokers took longer puffs, but there were no differences in total puff volume, carbon monoxide, or other ST parameters. Menthol smokers reported greater urge reduction and lower sensory stimulation. The smoking method (ST vs. NS) had no effects on smoking behavior or exposure. Cigarettes smoked via ST were rated stronger. Differences in satisfaction based on the smoking method interacted with race and menthol status. Ratings of aversion differed by race and menthol status.ConclusionsMenthol was not associated with increased smoke exposure or reward (except for urge reduction). ST caused minimal experimental reactivity relative to NS. Additional research that isolates the effects of menthol and examines potential interactive effects with race and other variables is needed to better understand its role in smoking-related health disparities.ImplicationsMenthol and non-menthol smokers differed on some demographic variables and menthol preference was associated with greater nicotine dependence and greater urge reduction after smoking. Menthol was not associated with greater smoke exposure. Future research that investigates the unique risks associated with menthol and examines potential interactive effects with race and other related variables is warranted to better understand the role of menthol in smoking-related health disparities.