bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined Maternal Exposure to Cypermethrin and Stress Affect Embryonic Brain and Placental Outcomes in Mice
Authors: Elser Benjamin A , Kayali Khaled , Dhakal Ram , O’Hare Bailey , Wang Kai , Lehmler Hans-Joachim , Stevens Hanna E 
Published: March 2020

Abstract
Prenatal exposure to cypermethrin is a risk factor for adverse neurodevelopmental outcomes in children. In addition, maternal psychological stress during pregnancy has significant effects on fetal neurodevelopment and may influence end-stage toxicity to offspring by altering maternal xenobiotic metabolism. As such, this study examined effects of maternal exposure to alpha-cypermethrin and stress, alone and in combination, on offspring development, with a focus on fetal neurotoxicity. CD1 mouse dams were administered 10 mg/kg alpha-cypermethrin or corn oil vehicle via oral gavage from embryonic day 11 (E11) to E14. In addition, dams from each treatment were subjected to a standard model of restraint stress from E12 to E14. Cypermethrin treatment impaired fetal growth, reduced fetal forebrain volume, and increased ventral forebrain proliferative zone volume, the latter effects driven by combined exposure with stress. Cypermethrin also impaired migration of GABAergic progenitors, with different transcriptional changes alone and in combination with stress. Stress and cypermethrin also interacted in effects on embryonic microglia morphology. In addition, levels of cypermethrin were elevated in the serum of stressed dams, which was accompanied by interacting effects of cypermethrin and stress on hepatic expression of cytochrome P450 enzymes. Levels of cypermethrin in amniotic fluid were below the limit of quantification, suggesting minimal transfer to fetal circulation. Despite this, cypermethrin increased placental malondialdehyde levels and increased placental expression of genes responsive to oxidative stress, effects significantly modified by stress exposure. These findings suggest a role for interaction between maternal exposures to cypermethrin and stress on offspring neurodevelopment, involving indirect mechanisms in the placenta and maternal liver.
Integration of urine proteomics and renal single-cell genomics identifies an interferon-gamma response gradient in lupus nephritis
Authors: Fava Andrea , Buyon Jill , Mohan Chandra , Zhang Ting , Belmont H. Michael , Izmirly Peter , Clancy Robert , Trujillo Jose Monroy , Fine Derek , Zhang Yuji , Magder Laurence , Rao Deepak A. , Arazi Arnon , Berthier Celine C. , Davidson Anne , Diamond Betty , Hacohen Nir , Wofsy David ,   the Accelerating Medicines Partnership in SLE network, Raychaudhuri Soumya , Petri Michelle 
Published: March 2020

AbstractLupus nephritis, one of the most serious manifestations of systemic lupus erythematosus (SLE), has both a heterogeneous clinical and pathological presentation. For example, proliferative nephritis identifies a more aggressive disease class that requires immunosuppression. However, the current classification system relies on the static appearance of histopathological morphology which does not capture differences in the inflammatory response. Therefore, a biomarker grounded in the disease biology is needed to understand the molecular heterogeneity of lupus nephritis and identify immunologic mechanism and pathways. Here, we analyzed the patterns of 1000 urine protein biomarkers in 30 patients with active lupus nephritis. We found that patients stratify over a chemokine gradient inducible by interferon-gamma. Higher values identified patients with proliferative lupus nephritis. After integrating the urine proteomics with the single-cell transcriptomics of kidney biopsies, it was observed that the urinary chemokines defining the gradient were predominantly produced by infiltrating CD8 T cells, along with natural killer and myeloid cells. The urine chemokine gradient significantly correlated with the number of kidney-infiltrating CD8 cells. These findings suggest that urine proteomics can capture the complex biology of the kidney in lupus nephritis. Patient-specific pathways may be noninvasively tracked in the urine in real time, enabling diagnosis and personalized treatment.
Functionally non-redundant paralogsspe-47andspe-50encode FB-MO associated proteins and interact withhim-8
Authors: Clark Jessica N. , Prajapati Gaurav , Aldaco Fermina , Sokolich Thomas J. , Keung Steven , Austin Sarojani , Valdés Ángel A. , LaMunyon Craig W. 
Published: March 2020

AbstractThe activation ofC. elegansspermatids to crawling spermatozoa is affected by a number of genes includingspe-47.Here, we investigate a paralog tospe-47:spe-50, which has a highly conserved sequence and expression, but which is not functionally redundant tospe-47.Phylogenetic analysis indicates that the duplication event that produced the paralogs occurred prior to the radiation of theCaenorhabditisspecies included in the analysis, allowing a long period for the paralogs to diverge in function. Furthermore, we observed that knockout mutations in both genes, either alone or together, have little effect on sperm function. However, hermaphrodites harboring both knockout mutations combined with a third mutation in thehim-8gene are nearly self-sterile due to a sperm defect, even though they have numerous apparently normal sperm within their spermathecae. We suggest that the sperm in these triple mutants are defective in fusing with oocytes, and that the effect of thehim-8mutation is due to its role in chromatin remodeling.
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Authors: Nurk Sergey , Walenz Brian P. , Rhie Arang , Vollger Mitchell R. , Logsdon Glennis A. , Grothe Robert , Miga Karen H. , Eichler Evan E. , Phillippy Adam M. , Koren Sergey 
Published: March 2020

AbstractComplete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced PacBio HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultra-long Oxford Nanopore reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of 9 complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance towards the complete assembly of human genomes.AvailabilityHiCanu is implemented within the Canu assembly framework and is available fromhttps://github.com/marbl/canu.
In-hospital Death Following Successful OHCA Resuscitation: Causes of early and late mortality and the impact of withdrawal of care
Authors: Li Shu , Lazaridis Christos , Goldenberg Fernando D. , Shah Atman P. , Tataris Katie , Beiser David G. , Sharp Willard W. 
Published: March 2020

AbstractObjectiveIn-hospital mortality in patients successfully resuscitated following out-of-hospital cardiac arrest (OHCA) is high. The factors and timings of these deaths is not well known. To better understand in hospital post-OHCA mortality we developed a novel categorization system of in hospital death and studied the factors and timings associated with these deaths.MethodsThis was a single-centered retrospective observational human study in adult non-traumatic OHCA patients in a university affiliated hospital. Through an expert consensus process, a novel classification system of hospital death was developed.ResultsTwo hundred and forty-one patients were enrolled in the study. Death was categorized as due to withdrawal of life sustaining treatment (WOLST) 159 (66.0%), recurrent in-hospital cardiac arrest 51 (21.1%), or due to neurological criteria 31 (12.9%). Subcategorization of factors associated with WOLST into 7 categories was done by defined criteria. Inter-reliability of this system was 0.858. 50% of WOLST decisions were due to neurological injury. Early death (≤ 3 days) was associated with recurrent in-hospital cardiac arrest and WOLST in the setting of refractory shock or multi-organ injury. Late in-hospital death (> 3 days) was primarily due to WOLST decisions in the setting of isolated neurological injury.ConclusionsOHCA in hospital mortality occurred in a bimodal pattern with early deaths due to recurrent arrest and multiorgan injury while late deaths were due to isolated neurological injury. The majority of deaths occurred in the setting of WOLST decisions. Further study of the influence of these factors on post OHCA survival are needed.
Rapidly induced drug adaptation mediates escape from BRAF inhibition in single melanoma cells
Authors: Yang Chen , Tian Chengzhe , Hoffman Timothy E. , Jacobsen Nicole K. , Spencer Sabrina L. 
Published: March 2020

AbstractDespite increasing numbers of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Here we track the response of thousands of single melanoma cells to BRAF inhibitors and show that a subset escapes drug within the first 3 days of treatment. Cell-cycle re-entry occurs via a non-genetic mechanism involving activation of mTORC1 and ATF4, validated in cultures of patient biopsies. These escapees cycle periodically in drug, incur significant DNA damage, and out-proliferate non-escapees over extended treatment. Our work reveals a mutagenesis-prone, expanding subpopulation of early drug escapees that may seed development of permanent drug resistance.
Glycolytic metabolism of pathogenic T cells enables early detection of GvHD by13C-MRI
Authors: Assmann Julian C. , Farthing Don E. , Saito Keita , Maglakelidze Natella , Oliver Brittany , Warrick Kathrynne A. , Sourbier Carole , Ricketts Christopher J. , Meyer Thomas J. , Pavletic Steven Z. , Linehan W. Marston , Krishna Murali C. , Gress Ronald E. , Buxbaum Nataliya P. 
Published: March 2020

AbstractGraft-versus-host disease (GvHD) is a prominent barrier to allogeneic hematopoietic stem cell transplantation (HSCT). Definitive diagnosis of GvHD is invasive and biopsies of involved tissues pose a high risk of bleeding and infection. Our previous studies in a chronic GvHD mouse model demonstrated that alloreactive CD4+T cells are distributed to target organs ahead of overt symptoms, meanwhile CD4+T cell activation is tied to increased glycolysis. Thus, we hypothesized that metabolic imaging of glycolysis would allow non-invasive detection of insipient GvHD in target organs infiltrated by glycolytic effector memory CD4+T cells. We metabolically characterized CD4+T cell subsets on day 14 post-transplant before the onset of chronic GvHD in a pre-clinical mouse model and performed13C hyperpolarized magnetic resonance imaging (MRI) to quantify glycolytic activity in the liver of mice over the course of the disease. Intracellular metabolic screening andex vivometabolic profiling of CD4+T cell subsets at day 14 confirmed that activated CD4+T cells were highly glycolytic. Concurrently, hyperpolarized13C-pyruvate MRI of the liver showed high conversion of pyruvate to lactate, indicative of increased glycolytic activity, that distinguished allogeneic from syngeneic HSCT recipients prior to the development of overt chronic GvHD. Furthermore, single cell sequencing of T cells in patients undergoing allogeneic HSCT indicated that similar metabolic changes may play a role in acute GvHD, providing a rationale for testing this imaging approach in the clinical post-HSCT setting. Our imaging approach is amenable to clinical translation and may allow early, non-invasive diagnosis of GvHD.
Testing the efficacy of lionfish traps in the northern Gulf of Mexico
Authors: Harris Holden E. , Fogg Alexander Q. , Gittings Stephen R. , Ahrens Robert N. M. , Allen Micheal S. , Patterson William F. 
Published: March 2020

AbstractSpearfishing is currently the primary approach for removing invasive Indo-Pacific lionfish(Pterois volitans/milescomplex) to mitigate their impacts to western Atlantic marine ecosystems. However, a substantial portion of lionfish spawning biomass is beyond the depth limits of SCUBA. Innovative technologies may offer an alternative means to target lionfish and allow for the development of a deepwater lionfish trap fishery, but the removal efficiency and potential environmental impacts of traps have not been evaluated. We tested a collapsible non-containment trap (the ‘Gittings trap’) near artificial reefs in the northern Gulf of Mexico. A total of 327 lionfish and 28 native fishes (4 of which regulated species) recruited to traps (i.e., number of fish observed within the trap footprint) during 82 trap sets, catching 144 lionfish and 29 native species. Lionfish recruitment was highest for single (versus paired) traps deployed <15 m from reefs with a 1-day soak time, for which mean lionfish and native species recruitment per trap were approximately 5 and 0.1, respectively. Gittings traps selected for larger lionfish (mean size 277 mm total length) compared to spearfishing (mean size 258 mm). Community impacts from Gittings traps appeared minimal given recruitment patterns and catch rates were >10X higher for lionfish versus native fishes. Gittings traps did not move on the bottom during two major storm events; however, further testing will be necessary to test trap movement with surface buoys. Additional research should also focus on design and operational modifications to improve Gittings trap deployment success (68% successfully opened on the seabed) and reduce lionfish escapement (56% escaped from traps upon retrieval). While removal efficiency for lionfish (12–24%) was far below that of spearfishing, study results demonstrate Gittings traps are suitable for future testing on deepwater natural reefs, which constitute >90% of the region’s reef habitat.
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions
Authors: Zhou Peng , Li Zhi , Magnusson Erika , Gomez Cano Fabio , Crisp Peter A. , Noshay Jaclyn M. , Grotewold Erich , Hirsch Candice N. , Briggs Steven P. , Springer Nathan M. 
Published: March 2020

Abstract
The regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potential transcriptional regulation. Here, we analyzed a large number of publically available maize (Zea mays) transcriptome data sets including &gt;6000 RNA sequencing samples to generate 45 coexpression-based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, and tissue-and-genotype samples). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes. By examining the power of our coexpression-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets, we found that presence/absence changes rather than quantitative changes in TF gene expression are more likely associated with changes in target gene expression. Integrating information from our TF-target predictions and previous expression quantitative trait loci (eQTL) mapping results provided support for 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. This study highlights the utility of developing multiple GRNs within a species to detect putative regulators of important plant pathways and provides potential targets for breeding or biotechnological applications.
A comparison of bank and credit union growth around the financial crisis
Authors: Lu Wenling , Swisher Judith 
Published: March 2020

PurposeThe purpose of this research is to examine the growth rates of commercial banks and credit unions around the financial crisis and recovery. Credit unions are analyzed as a group and by field of membership. Specifically, this research analyzes the growth rates of assets, deposits, and loans.Design/methodology/approachThis research employs univariate tests of differences to examine the median growth rates for commercial banks and credit unions. Unbalanced pool regressions analyze growth rates during the pre-crisis, crisis, and recovery periods, controlling for size, net charge-offs, and unemployment.FindingsUnivariate test results that control for size show that banks grow at faster rates than credit unions for most of the pre-crisis years. However, medium sized credit unions grow at faster rates for most of the crisis and recovery years. Results of unbalanced pool regressions suggest that, overall, credit unions grow at slower rates than do banks. However, during the crisis and recovery, credit union growth is significantly greater than that of banks, after controlling for net charge-offs, size, and unemployment. Credit union growth varies by field of membership type.Originality/valueAlthough a large volume of research examines commercial bank performance around the financial crisis, only a few papers assess the performance of credit unions. And very few papers compare commercial banks and credit unions. This paper explores how the recent financial crisis influenced the growth of commercial banks and credit unions from 2005 to 2013.
A qualitative study investigating food choices and perceived psychosocial influences on eating behaviours in secondary school students
Authors: Calvert Sian , Dempsey Robert C. , Povey Rachel 
Published: March 2020

PurposeChildhood obesity is a major global health concern. Understanding children's and adolescent’s eating behaviours and promoting healthier behaviours is key for reducing the negative health outcomes associated with obesity. The current study explored the perceptions of healthy eating behaviours and the influences on eating behaviours amongst 11-to-13-year-old secondary school students.Design/methodology/approachNine semi-structured same-sex focus group discussions were conducted in schools located in deprived areas of England, with the discussions subjected to a thematic framework analysis.FindingsThree main constructs were identified in the analysis as follows: (1)eating patterns and lifestyle, (2)social influencesand (3)environmental influences. Participants understood what healthy eating behaviours are and the benefits of eating healthy; yet, they reported irregular mealtimes and consuming unhealthy snacks. Students reported that their parents and fellow student peers were strong influences on their own eating behaviours, with girls subjected to being teased by male students for attempting to eat healthily. Finally, students perceived that unhealthy foods were cheaper, tasted better and were readily available in their social environments compared to healthier options, making healthier behaviours less likely to occur.Originality/valueFindings indicate that students had a good understanding of healthy eating behaviours but did not always practise them and are seemingly influenced by their social and environmental context. The promotion of healthier eating in this age group needs to challenge the misperceptions associated with the accessibility and social acceptability of unhealthy food items.
Scholarly publication venue recommender systems
Authors: Dehdarirad Hossein , Ghazimirsaeid Javad , Jalalimanesh Ammar 
Published: March 2020

PurposeThe purpose of this investigation is to identify, evaluate, integrate and summarize relevant and qualified papers through conducting a systematic literature review (SLR) on the application of recommender systems (RSs) to suggest a scholarly publication venue for researcher's paper.Design/methodology/approachTo identify the relevant papers published up to August 11, 2018, an SLR study on four databases (Scopus, Web of Science, IEEE Xplore and ScienceDirect) was conducted. We pursued the guidelines presented by Kitchenham and Charters (2007) for performing SLRs in software engineering. The papers were analyzed based on data sources, RSs classes, techniques/methods/algorithms, datasets, evaluation methodologies and metrics, as well as future directions.FindingsA total of 32 papers were identified. The most data sources exploited in these papers were textual (title/abstract/keywords) and co-authorship data. The RS classes in the selected papers were almost equally used. DBLP was the main dataset utilized. Cosine similarity, social network analysis (SNA) and term frequency–inverse document frequency (TF–IDF) algorithm were frequently used. In terms of evaluation methodologies, 24 papers applied only offline evaluations. Furthermore, precision, accuracy and recall metrics were the popular performance metrics. In the reviewed papers, “use more datasets” and “new algorithms” were frequently mentioned in the future work part as well as conclusions.Originality/valueGiven that a review study has not been conducted in this area, this paper can provide an insight into the current status in this area and may also contribute to future research in this field.
Kinh and ethnic tourism stakeholder participation and collaboration in tourism planning in Sapa, Vietnam
Authors: Nguyen Huy Van , Diane Lee , Newsome David 
Published: March 2020

PurposeThis paper aims to explore the Kinh and ethnic stakeholders’ participation and collaboration in tourism planning in Sapa, Vietnam.Design/methodology/approachThe primary data collection involved semi-structured interviews with 33 key tourism stakeholders, and data were analyzed using qualitative content analysis.FindingsThe findings reveal that in terms of participation and collaboration in tourism planning, there is little difference between the Kinh and ethnic groups. Tourism planning is viewed as a top-down approach, and both groups at the community level have very limited participation in tourism planning activities. However, at the on-site management level, there are opposing views between high (Kinh) and low (ethnic) management levels about participation in tourism planning. Both groups recognize the need for interdependence regarding collaboration in tourism planning. They also share similar aspects in regard to facilitating and hindering their participation in tourism planning.Research limitations/implicationsThe limitations of this study include the use of a qualitative method, which limited the number of respondents. Future research could benefit from the application of quantitative research methods to include a greater number of local tourism stakeholders.Practical implicationsThis study contributes to a better understanding of tourism planning in the Vietnamese context and has some practical implications for destination management and policymaking.Originality/valueThis is the first study to investigate the perspectives of Kinh and ethnic groups in term of participation and collaboration in tourism planning in the Vietnamese context.