bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simplitigs as an efficient and scalable representation of de Bruijn graphs
Authors: Břinda Karel , Baym Michael , Kucherov Gregory 
Published: January 2020

AbstractDe Bruijn graphs play an essential role in computational biology. However, despite their widespread use, they lack a universal scalable representation suitable for different types of genomic data sets. Here, we introduce simplitigs as a compact, efficient and scalable representation and present a fast algorithm for their computation. On examples of several model organisms and two bacterial pan-genomes, we show that, compared to the best existing representation, simplitigs provide a substantial improvement in the cumulative sequence length and their number, especially for graphs with many branching nodes. We demonstrate that this improvement is amplified with more data available. Combined with the commonly used Burrows-Wheeler Transform index of genomic sequences, simplitigs substantially reduce both memory and index loading and query times, as illustrated with large-scale examples of GenBank bacterial pan-genomes.
Optimizing the PBS1 Decoy System to Confer Resistance to Potyvirus Infection in Arabidopsis and Soybean
Authors: Pottinger Sarah E. , Bak Aurelie , Margets Alexandra , Helm Matthew , Tang Lucas , Casteel Clare , Innes Roger W. 
Published: January 2020

ABSTRACTTheArabidopsisresistance protein RPS5 is activated by proteolytic cleavage of the protein kinase PBS1 by thePseudomonas syringaeeffector protease AvrPphB. We have previously shown that replacing seven amino acids at the cleavage site of PBS1 with a motif cleaved by the NIa protease of turnip mosaic virus (TuMV) enables RPS5 activation upon TuMV infection. However, this engineered resistance conferred a trailing necrosis phenotype indicative of a cell death response too slow to contain the virus. We theorized this could result from a positional mismatch within the cell between PBS1TuMV, RPS5 and the NIa protease. To test this, we re-localized PBS1TuMVand RPS5 to cellular sites of NIa accumulation. These experiments revealed that relocation of RPS5 away from the plasma membrane compromised RPS5-dependent cell death inN. benthamiana, even though PBS1 was efficiently cleaved. As an alternative approach, we tested whether overexpression of plasma membrane-localized PBS1TuMVwould enhance RPS5 activation by TuMV. Significantly, over-expressing the PBS1TuMVdecoy protein conferred complete resistance to TuMV when delivered by eitherAgrobacteriumor by aphid transmission, showing that RPS5-mediated defense responses are effective against bacterial and viral pathogens. Lastly, we have now extended this PBS1 decoy approach to soybean by modifying a soybean PBS1 ortholog to be cleaved by the NIa protease of soybean mosaic virus (SMV). Transgenic overexpression of this soybean PBS1 decoy conferred immunity to SMV, demonstrating that we can use endogenous PBS1 proteins in crop plants to engineer economically relevant disease resistant traits.
Palmitvaccenic acid (Δ11-cis-hexadecenoic acid) is synthesized by an OLE1-like desaturase in the arbuscular mycorrhiza fungusRhizophagus irregularis
Authors: Brands Mathias , Cahoon Edgar B. , Dörmann Peter 
Published: January 2020

AbstractArbuscular mycorrhiza (AM) fungi deliver mineral nutrients to the plant host in exchange for reduced carbon in the form of sugars and lipids. Colonization with AM fungi upregulates a specific host lipid synthesis pathway resulting in the production of fatty acids. The fungusRhizophagus irregularisaccumulates predominantly palmitic acid (16:0) and the unusual palmitvaccenic acid (16:1Δ11cis). Here, we present the isolation and characterization ofRiOLE1-LIKE, the desaturase involved in palmitvaccenic acid synthesis, by heterologous expression in yeast and plants. Results are in line with the scenario thatRiOLE1-LIKEencodes an acyl-CoA desaturase with substrate specificity for C15-C18 acyl groups, in particular C16. Phylogenetic analysis ofRiOLE1-LIKErelated sequences revealed that this gene is conserved in AM fungi from the Glomales and Diversisporales, but is absent from non-symbiotic Mortierellaceae and Mucoromycotina fungi, suggesting that 16:1Δ11cisprovides a specific function during AM colonization.
Two-step mechanism of J-domain action in driving Hsp70 function
Authors: Tomiczek Bartłomiej , Delewski Wojciech , Nierzwicki Lukasz , Stolarska Milena , Grochowina Igor , Schilke Brenda , Dutkiewicz Rafal , Uzarska Marta A. , Ciesielski Szymon J. , Czub Jacek , Craig Elizabeth A. , Marszalek Jaroslaw 
Published: January 2020

AbstractJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s discriminate among its multiple JDP partners remain enigmatic. We combined free energy simulations, biochemical assays and evolutionary analyses to address these issues. Our results indicate that the invariant aspartate of the J-domain perturbs a conserved intramolecular Hsp70 network of contacts that crosses domains. This perturbation leads to destabilization of the domain-domain interface - thereby promoting the allosteric transition that triggers ATP hydrolysis. While this mechanistic step is driven by conserved residues, evolutionarily variable residues are key to initial JDP/Hsp70 recognition - via electrostatic interactions between oppositely charged surfaces. We speculate that these variable residues allow an Hsp70 to discriminate amongst JDP partners, as many of them have coevolved. Together, our data points to a two-step mode of J-domain action, a recognition stage followed by a mechanistic stage.Abstract Figure
Economic stress in non-poor Spanish households during the Great Recession
Authors: Ródenas Carmen , Martí Mónica , León Ángel 
Published: January 2020

Purpose
This paper aims to focus on non-poor households that during the Great Recession experienced economic stress (ES). That is, whose economic comfort was reduced taking into account their previous living standards. The paper seeks to determine how the crisis has affected this extensive (and key) social group.

Design/methodology/approach
The analysis has been performed in a dynamic way. The non-poor households ES situation and its changes are studied throughout the period 2008-2016 by taking the four-year intervals provided by the longitudinal Spanish Living Conditions Survey. The authors discuss and select the circumstances to determine whether ES has occurred. To identify which variables determine the probability of suffering ES the authors use a standard logit model.

Findings
The main variable is the tenure status of the dwelling: property with a mortgage or rented multiply the risk of ES by up to 3.5 times. ES falls as the household’s work intensity increases. However, an improvement in the employment situation cannot be associated with a reduction in ES probability. The main socio-demographic variables behave as predicted: woman householder, grow in the number of household members and bad health increase the risk of ES, and the higher the level of education of the householder, the lower the risk.

Originality/value
There are very few studies regarding the people above the poverty line. Exploring and analyzing the factors determining the sensitivity of the largest part of the population to the crisis is very relevant, as the pace of the economic recovery depends largely on them.
The role of corporate governance on CSR disclosure and firm performance in a voluntary environment
Authors: Chijoke-Mgbame Aruoriwo Marian , Mgbame Chijoke Oscar , Akintoye Simisola , Ohalehi Paschal 
Published: January 2020

PurposeThis study aims to investigate the impact of corporate social responsibility disclosure (CSRD) on firm performance and the moderating role of corporate governance on the CSRD–firm performance relationship of listed companies in Nigeria.Design/methodology/approachThe paper uses a panel data set comprising 841 firm-year observations for the period covering 2007-2016. Fixed effect regression analysis was used to examine the relationship between CSRD and firm performance, and the moderating role of corporate governance in the CSRD–firm performance relationship.FindingsThe results of the study show that there are positive performance implications for firms that engage in CSRD. Although this study finds no effect of board size on the CSRD–firm performance relationship, it provides a strong evidence of a positive effect of board independence on the CSR–firm performance relationship.Practical implicationsThe study contributes to the understanding of CSRD–firm performance relationship by providing evidence of the moderating role of corporate governance. It is, therefore, recommended that a stronger regulation be put in place for CSR engagement and the disclosure of same in Nigeria as well as robust measures for the enforcement of corporate governance mechanisms because there are economic benefits to be derived.Originality/valueThe findings contribute to the literature by providing up-to-date and original insights on the CSRD–firm performance relationship within a developing country context. It also uses an uncommon method of measuring CSRD, taking into account the institutional biases that may arise from other methods used in studies on developed countries.
Analysis of content topics, user engagement and library factors in public library social media based on text mining
Authors: Joo Soohyung , Lu Kun , Lee Taehun 
Published: January 2020

PurposeThe purpose of this paper is to explore topics of Facebook posts created by public libraries using the bi-term topic model, and examine the relationships between types of topics and user engagement. The authors further investigated the effects of three library factors, namely, staff size, budget and urbanization degrees, on Facebook content and user engagement based on multilevel generalized linear modeling.Design/methodology/approachThis study suggested a novel method, a combination of the bi-term topic modeling and MGLM, to enhance the understanding of social media in the context of public libraries.FindingsThe findings revealed that posts related to community events, awards and photos were likely to receive more likes and shares, whereas posts about summer reading programs received relatively more comments. In addition, the authors found that a larger staff size and the inclusion of multimedia had positive impacts on user engagement.Originality/valueThis study analyzed the content of public library-generated social media based on text mining. Then, the authors examined the effects of contextual library-level factors on social media practice in public libraries. Based on empirical findings, the study suggested a range of practical implications for effective use of social media in public libraries.
Exploration and refinement of migratory routes in long‐lived birds
Authors: Fayet Annette L. 
Published: January 2020

AbstractIn Focus: Campioni L., Dias M. P., Granadeiro J. P., & Catry P. (2019). An ontogenetic perspective on migratory strategy of a long‐lived pelagic seabird: Timings and destinations change progressively during maturation. Journal of Animal Ecology, 89, 29–43. https://doi.org/10.1111/1365-2656.13044How migration routes develop in long‐lived migratory animals remains poorly understood. Campioni et al. (2019) tracked the migration of immature and breeding Cory's shearwaters and found that the timings and routes gradually changed with age. Young birds followed more exploratory routes at first, but gradually shortened and defined them as they matured, and they returned to the breeding grounds progressively earlier. These findings suggest that long‐lived species start by exploring potentially suitable areas for the non‐breeding season and progressively refine their migration route as they age.
Young children's narrative retell in response to static and animated stories
Authors: Diehm Emily A. , Wood Carla , Puhlman Jane , Callendar Maya 
Published: January 2020

AbstractBackgroundThe format of narrative prompts used within language assessment has remained relatively constant; however, the use of animated video prompts deserves exploration given the increase in access to technology.AimsTo investigate the effect of story presentation format (static picture book versus animated video) on preschool children's narrative retells. It was hypothesized that children would produce more advanced narrative language elements in response to an animated video than a book.Methods & ProceduresA total of 73 children between the ages of 3 and 5 years completed two narrative retells. One of these retells was in response to a 3‐min animated video presented on a computer; the other retell was in response to static pictures presented in a book format. Children's stories were then transcribed and coded for linguistic and narrative elements.Outcomes & ResultsPaired sample t‐tests revealed that children produced significantly longer stories, greater syntactic complexity and lexical variety, and more action verbs when retelling an animated story compared with a book. Furthermore, a post‐hoc analysis revealed that examiners provided significantly fewer prompts when eliciting the retell with animation.Conclusions & ImplicationsTypically developing children demonstrated higher quantity and quality of language within a story retell in response to an animated video than after viewing images from the video presented in a static picture book. Although the extent to which these findings may be similar for children with language disorder has yet to be determined, researchers or clinicians should consider the effect of elicitation procedures on children's retells.
New occurrence of the invasive alien leaf‐footed bug Leptoglossus gonagra (Hemiptera: Coreidae) in South Korea
Authors: Lee Heejo , Kim Mi‐jeong , Bae Yang‐Seop , Kim Dong Eon 
Published: January 2020

AbstractThe invasive alien leaf‐footed bug Leptoglossus gonagra (Fabricius 1775), native to the Americas, is herein recorded from South Korea for the first time. Forty nymphs and adults were collected on 22 September 2016 from arable lands of two separate sites. These individuals were identified based on the analysis of morphological characters and cytochrome oxidase c subunit 1 sequences. A neighbor‐joining tree indicated the existence of two clades: Group A from Brazil, and Group B from Asia and Oceania. Mean genetic distance between clades was 8.11%, range 7.60–8.57%. Within clades, mean genetic distance was 0.42% (0.17–0.83%) in Group A and, 0.45% (0.00–0.83%) in Group B. Colonies of 2nd‐final instar nymphs and adults were found, on top of leaves, flowers, fruits, and between the stems of pumpkins (Cucurbita moschata). Nymphs and adults damaged host plants by sucking their leaves, stems, fruits, and buds. After the first discovery in 2016, we were unable to find the bugs again (in 2017–2019). Therefore, the invasion of this species seems to have occurred only temporarily, during the warm season. We suggest that the species may have failed to overwinter as it is normally distributed in regions warmer than Korea. Nevertheless, possible appearances of this species must be continuously monitored as it is a potential pest of various plants cultivated in South Korea.
Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels
Authors: von Thaden Alina , Nowak Carsten , Tiesmeyer Annika , Reiners Tobias E. , Alves Paulo C. , Lyons Leslie A. , Mattucci Federica , Randi Ettore , Cragnolini Margherita , Galián José , Hegyeli Zsolt , Kitchener Andrew C. , Lambinet Clotilde , Lucas José M. , Mölich Thomas , Ramos Luana , Schockert Vinciane , Cocchiararo Berardino 
Published: January 2020

AbstractThe genomic era has led to an unprecedented increase in the availability of genome‐wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
Parvovirus B19 DNAemia in pregnant women in relation to perinatal death: A nested case‐control study within a large population‐based pregnancy cohort
Authors: Barlinn Regine , Trogstad Lill , Rollag Halvor , Frøen Fredrik , Magnus Per , Dudman Susanne G. 
Published: January 2020

AbstractIntroductionParvovirus B19 (B19V) is the infectious cause of exanthema infectiosum. In Europe around 40% of pregnant women are susceptible to infection. Having small children at home is the main risk factor for contracting an infection during pregnancy. The association between B19V‐infection and perinatal death is not yet settled. The aims of the study were to estimate the association between maternal parvovirus B19 infection in pregnancy and perinatal death, and to assess the significance of a positive B19V PCR in pregnancy.Material and methodsThe study population consists of women included in the Norwegian Mother and Child Cohort Study, a prospective population‐based pregnancy cohort of nearly 100 000 women. Blood samples were obtained during weeks 17‐18 in pregnancy (M1), at birth, and in umbilical cord blood. Within participants in the pregnancy cohort, 138 cases of perinatal death and 1350 controls with live‐born children were included in a nested case‐control study. Samples were analyzed with B19V serology and B19V PCR according to a predefined test algorithm. For cases, medical records and laboratory results from hospitals were combined with the results of B19V serology and PCR. The reported causes of perinatal death were categorized using the classification system: Causes Of Death and Associated Conditions (CODAC).ResultsThe B19V seroconversion rates were 9.8% for cases and 6.8% for control mothers. The odds ratio for maternal B19V infection in cases compared with controls was 1.28 (95% CI 0.35‐4.70), adjusted for age, parity, body mass index and tobacco use. B19V‐PCR‐positive samples were detected at weeks 17‐18 of gestation in both cases and controls. The proportion of positive samples was similar in cases and controls, 24% and 28.2%, respectively. Mothers with PCR‐positive M1 samples transmitted B19V vertically in 9.1% of cases and in 11.9% of the controls. Of all perinatal deaths, 53% were attributed to placental pathology or unknown causes.ConclusionsB19V PCR positivity was high and similar in both cases and controls. In our study B19V DNAemia was not seen to be associated with fatal outcome of pregnancy. The clinical significance of B19V DNA detection during pregnancy is uncertain. Caution is needed when diagnosing a B19V infection based only on B19V DNAemia.
Pharmacodynamic assessment of mycophenolic acid in resting and activated target cell population during the first year after renal transplantation
Authors: Klaasen Rolf Anton , Bergan Stein , Bremer Sara , Hole Kristine , Nordahl Christine Berg , Andersen Anders Mikal , Midtvedt Karsten , Skauby Morten Heier , Vethe Nils Tore 
Published: January 2020

AimsTo explore the pharmacodynamics of mycophenolic acid (MPA) through inosine monophosphate dehydrogenase (IMPDH) capacity measurement and purine levels in peripheral blood mononuclear cells (PBMC) longitudinally during the first year after renal transplantation (TX).MethodsPBMC were isolated from renal recipients 0–4 days prior to and 6–9 days, 5–7 weeks and 1 year after TX (before and 1.5 hours after dose). IMPDH capacity and purine (guanine and adenine) levels were measured in stimulated and nonstimulated PBMC.ResultsTwenty‐nine patients completed the follow‐up period, of whom 24 received MPA. In stimulated PBMC, the IMPDH capacity (pmol 10−6 cells min−1) was median (interquartile range) 127 (95.8–147) before TX and thereafter 44.9 (19.2–93.2) predose and 12.1 (4.64–23.6) 1.5 hours postdose across study days after TX. The corresponding IMPDH capacity in nonstimulated PBMC was 5.71 (3.79–6.93), 3.35 (2.31–5.62) and 2.71 (1.38–4.08), respectively. Predose IMPDH capacity in nonstimulated PBMC increased with time, reaching pre‐TX values at 1 year. In stimulated PBMC, both purines were reduced before (median 39% reduction across days after TX) and after (69% reduction) dose compared to before TX. No alteration in the purine levels was observed in nonstimulated PBMC. Patients needing dose reductions during the first year had lower pre‐dose IMPDH capacity in nonstimulated PBMC (1.87 vs 3.00 pmol 10−6 cells min−1, P = .049) at 6–9 days.ConclusionThe inhibitory effect of MPA was stronger in stimulated PBMC. Nonstimulated PBMC became less sensitive to MPA during the first year after TX. Early IMPDH capacity appeared to be predictive of dose reductions.
First‐in‐human clinical trial to assess the safety, tolerability and pharmacokinetics of P218, a novel candidate for malaria chemoprotection
Authors: Chughlay M. Farouk , Rossignol Emilie , Donini Cristina , El Gaaloul Myriam , Lorch Ulrike , Coates Simon , Langdon Grant , Hammond Tim , Möhrle Jörg , Chalon Stephan 
Published: January 2020

AimsThis first‐in‐human clinical trial of P218, a novel dihydrofolate reductase inhibitor antimalarial candidate, assessed safety, tolerability, pharmacokinetics and food effects in healthy subjects.MethodsThe study consisted of two parts. Part A was a double‐blind, randomized, placebo‐controlled, parallel group, ascending dose study comprising seven fasted cohorts. Eight subjects/cohort were randomized (3:1) to receive either a single oral dose of P218 (10, 30, 100, 250, 500, 750 and 1000 mg) or placebo. Part B was an open‐label, cross‐over, fed/fasted cohort (eight subjects) that received a 250 mg single dose of P218 in two treatment periods.ResultsP218 was generally well tolerated across all doses; 21 treatment‐emergent adverse events occurred in 15/64 subjects. Nine adverse events in five subjects, all of mild intensity, were judged drug related. No clinically relevant abnormalities in ECG, vital signs or laboratory tests changes were observed. P218 was rapidly absorbed, with Cmax achieved between 0.5 and 2 hours post dose. Plasma concentrations declined bi‐exponentially with half‐life values ranging from 3.1 to 6.7 hours (10 and 30 mg), increasing up to 8.9 to 19.6 hours (doses up to 1000 mg). Exposure values increased dose‐proportionally between 100 and 1000 mg for P218 (parent) and three primary metabolites (P218 β‐acyl glucuronide, P218‐OH and P218‐OH β‐acyl glucuronide). Co‐administration of P218 with food reduced Cmax by 35% and delayed absorption by 1 hour, with no significant impact on AUC.ConclusionP218 displayed favourable safety, tolerability and pharmacokinetics. In view of its short half‐life, a long‐acting formulation will be needed for malaria chemoprotection.