bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving the graft ischemia-reperfusion injury during liver transplantation at the single cell resolution
Authors: Wang Linhe , Li Jie , He Shuai , Chen Haitian , He Shujiao , Yin Meixian , Zou DaWei , Xu Jinghong , Chen Shirui , Luo Tao , Yu Xinyu , Bei Jinxin , Guo Zhiyong , He Xiaoshun 
Published: January 2021

ABSTRACTIschemia-reperfusion injury (IRI) remains the major reason for impaired donor graft function and increased mortality post-liver transplantation. The mechanism of IRI involves multiple pathophysiological processes and numerous types of cells. However, a systematic and comprehensive single-cell transcriptional profile of intrahepatic cells during liver transplantation is still unclear. We performed a single-cell transcriptome analysis of 14,313 cells from liver tissues collected from pre-procurement, at the end of preservation and 2 h post-reperfusion. We made detailed annotations of mononuclear phagocyte, endothelial cell, NK/T, B and plasma cell clusters, and we described the dynamic changes of the transcriptome of these clusters during IRI and the interaction between mononuclear phagocyte clusters and other cell clusters. In addition, we found that TNFAIP3 interacting protein 3 (TNIP3), specifically and highly expressed in Kupffer cell clusters post-reperfusion, may have a protective effect on IRI. In summary, our study provides the first dynamic transcriptome map of intrahepatic cell clusters during liver transplantation at single-cell resolution.
Network centrality is the most important variable determining gene sequence evolution rates inSchizosaccharomyces pombe
Authors: Harnqvist Simon 
Published: January 2021

ABSTRACTWhich variables determine the rate of gene and protein sequence evolution is a central question in evolutionary genomics. In the model organism fission yeast(Schizosaccharomyces pombe), the determinants of the rate of sequence evolution have yet to be determined. Previous studies in other organisms have typically found gene expression levels to be most significant, with numerous other variables identified as having a smaller impact. Here, partial least squares regression (PLS) and partial correlation analysis are used to model sequence evolution rates in the fission yeast genome by a range of variables. Variable importance in projection (VIP) scores as well as partial correlation coefficients are calculated for each variable, and used as estimates of the influence of each independent variable on sequence evolution rate. Unlike many previous studies in other organisms, centrality in the PPI network is shown to be the most important variable, and gene expression found to be less influential. Considerable heterogeneity is found in the influence of different gene ontology terms as well as amino acid composition. However, the majority of variance in constraint in fission yeast remains unexplained by this study, indicating that variables not yet considered and stochastics probably have considerable impact on the rate of molecular evolution.
Changes in Behavior and Salivary Serum Amyloid A in cows with Subclinical Mastitis
Authors: Caplen G. , Held S.D.E. 
Published: January 2021

ABSTRACTThe aim of this study was to identify detailed changes in behavior, and in salivary serum amyloid A (SAA), associated with subclinical mastitis. This included standard sickness behaviors (which form part of an adaptive response to conserve energy, minimize heat loss and facilitate recovery following infection and inflammation) and lesser-studied behaviors, that are biologically predicted to change at low-level infection, and therefore particularly relevant for detecting subclinical mastitis (here labelled ‘luxury’ behaviors). SAA is a physiological marker of systemic inflammation, with levels in milk and serum already known to increase during subclinical mastitis. We investigated whether the same was true for SAA in cow saliva. Data were collected for n = 34 commercial barn-housed dairy cows, tested in 17 matched-pairs. Each pair comprised a cow with subclinical mastitis (SCM)and a healthy control (CTRL), identified using somatic cell count (SCC) (SCM: SCC >200 x1000 cells/ml; CTRL: SCC <100 x1000 cells/ml). SCM cows were selected for study ad-hoc, at which point they were paired with a CTRL cow, based upon parity and calving date; consequently, the full data set was accrued over several months. Data were collected for each pair over 3 days: SCC (l4:00-l5:00h) Day 1; behavior (24h from 00:00h) Day 2; salivary serum amyloid-A (SAA) Day 3. We report, for the first time, that an increase in salivary SAA occurs during subclinical mastitis; SAA was higher in SCM cows and demonstrated a positive (weak) correlation with SCC. The behavioral comparisons revealed that SCM cows had reductions in activity (behavioral transitions and distance moved), social exploration, social reactivity (here: likelihood to move away/be displaced following receipt of agonism), performance of social grooming and head butts, and the receipt of agonistic non-contact challenges. In addition, SCM cows received more head swipes, and spent a greater proportion of time lying with their head on their flank than CTRL cows. SCM cows also displayed an altered feeding pattern; they spent a greater proportion of feeding time in direct contact with two conspecifics, and a lower proportion of feeding time at self-locking feed barriers, than CTRL cows. Behavioral measures were found to correlate, albeit loosely, with serum SAA in a direction consistent with predictions for sickness behavior. These included positive correlations with both lying duration and the receipt of all agonistic behavior, and negative correlations with feeding, drinking, the performance of all social and all agonistic behavior, and social reactivity. We conclude that changes in salivary SAA, social behavior, and activity offer potential in the detection of subclinical mastitis and recommend further investigation to substantiate and refine our findings.
Estuarine molecular bycatch as a landscape-wide biomonitoring tool
Authors: Mariani S. , Harper L.R. , Collins R.A. , Baillie C. , Wangensteen O.S. , McDevitt A.D. , Heddell-Cowie M. , Genner M.J. 
Published: January 2021

AbstractEnvironmental DNA analysis is rapidly transforming biodiversity monitoring and bolstering conservation applications worldwide. This approach has been assisted by the development of metabarcoding PCR primers that are suited for detection of a wide range of taxa. However, little effort has gone into exploring the value of the non-target DNA sequences that are generated in every survey, but subsequently discarded. Here we demonstrate that fish-targeted markers widely employed in aquatic biomonitoring can also detect birds and mammals present in the surrounding habitats. We showcase this feature in three temperate estuaries over multiple seasons, where dozens of bird and mammal species offer valuable insights into spatial and temporal faunal variation. Our results indicate that existing metabarcode sequence data sets are suitable for mining and exploration of this ‘molecular by-catch’, and that any future eDNA-based surveys can be designed to accommodate this enhanced property of this widely applicable tool.
Computational identification and characterization of antigenic properties of Rv3899c ofMycobacterium tuberculosisand its interaction with Human leukocyte antigen (HLA)
Authors: Das Ritam , Eniyan Kandasamy , Bajpai Urmi 
Published: January 2021

AbstractTuberculosis (TB) is the second largest infectious disease that kills 1.2 million people annually worldwide. A rise in drug-resistant TB cases demands continued efforts towards the discovery & development of drugs and vaccines. In the recent past, though novel drugs have been added to the current TB regimen [1], research on new vaccine candidates needs a greater thrust. Secretory proteins of H37Rv are frequently studied for their antigenicity and their scope as protein subunit vaccines decrees further analysis. In this study, Rv3899c of H37Rv emerges as a potential vaccine candidate on its evaluation by several bioinformatics tools. It is a non-toxin, secretory protein with an ‘immunoglobulin-like’ fold which does not show similarity with a human protein. We found Rv3899c homologs in several mycobacterial species and its antigenic score (0.54) to compare well with the known immunogens such as ESAT-6 (0.56) and Rv1860 (0.52). Structural examination of Rv3899c predicted ten antigenic peptides, an accessibility profile of the antigenic determinants constituting B-cell epitope rich regions and a low Abundance of Antigenic Regions (AAR) value. Significantly, our study shows ESX-2 secretion system proteins and antigenic PE/PPE proteins of H37Rv as the interacting partners of Rv3899c. Further, molecular docking predicted Rv3899c to interact with human leukocyte antigen HLA-DRB1*04:01 through its antigenically conserved motif (RAAEQQRLQRIVDAVARQEPRISWAAGLRDDGTT). Interestingly, the binding affinity was observed to increase on citrullation of its Arg1 residue. Taken together, the computational characterization and predictive information suggest Rv3899c to be a promising TB vaccine candidate, which should be examined and validated experimentally.
Molecular population genetics ofSex-lethal(Sxl) in theD. melanogasterspecies group - a locus that genetically interacts withWolbachia pipientisinDrosophila melanogaster
Authors: Bauer DuMont Vanessa L. , White Simone L. , Zinshteyn Daniel , Aquadro Charles F. 
Published: January 2021

AbstractSex-lethal(Sxl)is the sex determination switch inDrosophila, and also plays a critical role in germ-line stem cell (GSC) daughter differentiation inDrosophila melanogaster. Three female-sterile alleles atSxlinDrosophila melanogasterwere previously shown to genetically interact to varying degrees with the maternally inherited endosymbiontWolbachia pipientis.Given this genetic interaction andW. pipientis’ability to manipulate reproduction inDrosophila, we carried out a careful study of both the population genetics (within fourDrosophilaspecies) and molecular evolutionary analysis (across 20Drosophilaspecies) ofSxl. Consistent with earlier studies, we find that selective constraint has played a prominent role inSxl’smolecular evolution withinDrosophila, but we also observe patterns that suggest both episodic bursts of protein evolution and recent positive selection atSxl. The episodic nature ofSxl’sprotein evolution is discussed in light of its genetic interaction withW. pipientis.
MBASR: Workflow-simplified ancestral state reconstruction of discrete traits with MrBayes in the R environment
Authors: Heritage Steven 
Published: January 2021

AbstractAncestral state reconstruction (ASR) is a critical tool in comparative biology. Given a phylogenetic tree and observed trait states for taxa at the tree’s tips, ASR aims to model ancestral trait states at the tree’s internal nodes. Thus, the pattern, tempo, and frequency of a character’s evolution can be considered in a phylogenetic framework. Software programs that perform discrete trait ASR analyses are variably complex in terms of workflow steps, input formats, user interfaces, settings and execution commands, and the organization of output.MBASR(acronym forMrBayes Ancestral States with R) is an R language toolkit that highly automates the ASR workflow and uses the machinery of the popular phylogenetics software MrBayes. Input data files are simple, analysis can be setup and run with a single R function, and statistical output is concisely organized and immediately interpretable. Use requires minimal knowledge of the most basic R commands and no experience with the MrBayes program. TheMBASRtoolkit can be freely downloaded from GitHub.
Imaging cytoplasmic lipid dropletsin vivowith fluorescent perilipin 2 and perilipin 3 knockin zebrafish
Authors: Wilson Meredith H. , Ekker Stephen C. , Farber Steven A. 
Published: January 2021

AbstractCytoplasmic lipid droplets are highly dynamic storage organelles; their rapid synthesis, expansion, and degradation, as well as their varied interactions with other organelles allow cells to maintain lipid homeostasis. While the molecular details of lipid droplet dynamics are currently a very active area of investigation, this work has been primarily performed in cultured cells andin vitrosystems. By taking advantage of the powerful transgenic andin vivoimaging opportunities afforded by the zebrafish model system, we have built a suite of tools to allow lipid droplets to be studied in real-time from the subcellular to the whole organism level. Fluorescently-tagging the lipid droplet associated proteins, perilipin 2 and perilipin 3, in the endogenous loci, permits visualization of lipid droplets in the intestine, liver, lateral line and adipose tissue. Using these transgenic lines we have found that perilipin 3 is rapidly loaded on intestinal lipid droplets following a high fat meal and then largely replaced by perilipin 2 a few hours later. These powerful new tools will facilitate studies on the role of lipid droplets in different tissues and under different genetic and physiological manipulations.
Non-targeted multimodal metabolomics data from ovine rumen fluid fractions
Authors: Palevich Nikola , Maclean Paul H. , Cao Mingshu 
Published: January 2021

ABSTRACTFrom an animal production and health perspective, our understanding of the metabolites in ruminant biofluids, particularly rumen fluid across different host species is poorly understood. Metabolomics is a powerful and sensitive approach for investigating low molecular weight metabolite profiles present in rumen biofluids. It can be used to identify potential roles of metabolites in the rumen microbiome and provide and understanding of host-level regulatory mechanisms associated with animal production. The rumen is a strictly anaerobic environment enriched with a complex community of bacteria, protozoa, fungi, archaea and bacteriophages. Here, we present a metabolomic dataset generated using hydrophilic interaction liquid chromatography (HILIC) and semi-polar (C18) chromatography methods coupled to high resolution mass spectrometry (MS), collected in both positive and negative ionization modes, of ovine rumen samples that were fractionated based on molecular weight (20 kDa, 8-10 kDa and 100 Da). This study highlights the potential of HILIC and C18 chromatography combined with non-targeted mass spectrometric methods to detect the polar and semi-polar metabolite species of the ruminal fluid metabolome.
Natural protection from type 1 diabetes in Non Obese Diabetic (NOD) mice is characterised by a unique pancreatic islet phenotype
Authors: Boldison Joanne , Thayer Terri C. , Davies Joanne , Wong F. Susan 
Published: January 2021

AbstractThe non-obese diabetic (NOD) mouse develops spontaneous type 1 diabetes, with some features of disease that are very similar to the human disease. However, a proportion of NOD mice are naturally-protected from developing diabetes, and currently studies characterising this cohort are very limited. Here, using both immunofluorescence and multi-parameter flow cytometry we focus on the pancreatic islet morphology and immune infiltrate observed in naturally-protected NOD mice. We show that naturally-protected NOD mice are characterised by an increased frequency of insulin-containing, smaller sized, pancreatic islets. Although mice remain diabetes free, florid immune infiltrate remains. However, this immune infiltrate is skewed towards a regulatory phenotype in both T and B-cell compartments. Pancreatic islets have an increased frequency of IL-10 producing B cells and associated cell surface markers. Resident memory CD69+CD8+T cells show a significant shift towards reduced CD103 expression, while CD4+T cells have increased FoxP3+CTLA4+expression. These data indicate that naturally-protected NOD mice have a unique islet signature and provide new insight into regulatory mechanisms within pancreatic islets.
GeneFriends 2021: Updated co-expression databases and tools for human and mouse genes and transcripts
Authors: Raina Priyanka , Lopes Inês , Chatsirisupachai Kasit , Farooq Zoya , de Magalhães João Pedro 
Published: January 2021

ABSTRACTGene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have updated the GeneFriends database. Here, we present the latest version of GeneFriends, which includes updated gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples. GeneFriends is freely available athttp://www.genefriends.org/
Prognostic value of liver and kidney function parameters and their correlation with the ratio of urine‐to‐plasma paraquat in patients with paraquat poisoning
Authors: Zhang Shuangyang , Song Shuai , Luo Xuemei , Liu Jianfeng , Liu Mouze , Li Wenqun , Cao Ting , Li Nana , Zeng Cuirong , Zhang Bikui , Cai Hualin 
Published: January 2021

AbstractAcute paraquat poisoning resulting from multiple organ failure usually has a high mortality rate. Liver and kidney, as the key oranges of paraquat detoxification and elimination, their injuries may suppress toxin excretion and enhance the toxicity of paraquat in other organs and worsen the prognosis. Therefore, we intended to explore the prognostic value of liver and kidney function parameters, and further evaluate their correlation with a more stable index urine‐to‐plasma paraquat (urine paraquat concentrations/plasma paraquat concentrations) instead of considering paraquat concentrations in plasma or urine alone. The study included 33 patients with acute paraquat poisoning admitted to four centres in China from January 2018 to December 2019. Seventeen patients (10 male/7 female) survived, whereas 16 patients (7 male/9 female, 48.48%) died from paraquat poisoning. Alanine aminotransferase (ALT) and the blood urea nitrogen (BUN) represent liver and kidney function parameters, respectively. The ratio of urine‐to‐plasma paraquat is negatively correlated with ALT (r = −0.94, P = 0 .02) and BUN (r = −0.82, P = 0.03). For receiver operating characteristic curve (ROC) analysis, ALT, BUN and urine‐to‐plasma paraquat have an AUC over 0.80. The study shows that the functional indexes of liver and kidney, as well as the ratio of urine‐to‐plasma paraquat, could be considered for evaluating the extent of organ injury and excretion rate of paraquat.
A retrospective analysis of the optimal time and psychological impact of decoronation in children and adolescents
Authors: Zhang Lili , Wang Meng , Xue Liang , Zhou Weiwei , Zhang Xin , Jin Luyuan , Xia Dengsheng , Gong Yi 
Published: January 2021

AbstractBackground/AimsDecoronation offers one of the best and most predictable clinical outcomes for dentoalveolar ankylosis. The aim of this study was to determine the factors associated with the efficacy and psychological impact of decoronation for bone preservation.Materials and MethodsThe study included 42 paediatric patients with 42 infrapositioned replanted permanent teeth. Twelve of these teeth were decoronated. Variables such as the time of injury, stage of root development and the extent of infraposition were analysed. The vertical changes in the alveolar bone level of the decoronated teeth were assessed on radiographs using a three‐point scoring system. Parents of 30 patients with teeth that were not decoronated completed a questionnaire addressing their considerations and concerns regarding the treatment of infraposition.ResultsTeeth with root development in stages 2 and 3 showed a significantly higher rate of severe infraposition during the follow‐up visits. Decoronation was performed on 12 teeth within 1.5–5 years (mean 3.8 ± 1.3 years) after replantation and 11 of these cases developed a considerable alveolar bone level. The alveolar bone levels of boys and girls showed improvements of 2.2 and 3.2 mm, respectively. The optimal age for decoronation to have a considerable increase in bone level was 12.12 ± 0.83 years for boys and 11.25 ± 1.77 years for girls. Complicated treatments, followed by parents’ lack knowledge regarding decoronation, children's fear, follow‐up times, and cost were the major concerns regarding decoronation.ConclusionThe optimal time for decoronation should be decided after considering the age, gender, skeletal growth pattern, and the degree of infraposition at the time of decoronation.
Pruritus Intensity Scales across Europe: a prospective validation study
Authors: Storck M. , Sandmann S. , Bruland P. , Pereira M.P. , Steinke S. , Riepe C. , Soto‐Rey I. , Garcovich S. , Augustin M. , Blome C. , Bobko S. , Legat F.J. , Potekaev N. , Lvov A. , Misery L. , Weger W. , Reich A. , Şavk E. , Streit M. , Serra‐Baldrich E. , Szepietowski J.C. , Dugas M. , Ständer S. , Zeidler C. 
Published: January 2021

AbstractBackgroundChronic pruritus (CP) is a subjective symptom, and it is necessary to assess its intensity with validated patient‐reported outcome tools in order to allow determination of the treatment course.ObjectivesSo far, the itch intensity scales were validated in small cohorts and in single languages. Here, we report the validation of the numerical rating scale, the verbal rating scale and the visual analogue scale for the worst and average pruritus intensity in the last 24h in several languages across Europe and across different pruritic dermatoses.MethodsAfter professional translation, the intensity scales were digitized for use as a tablet computer application. Validation was performed in clinics for Dermatology in Austria, France, Germany, Italy, Poland, Russia, Spain, Switzerland and Turkey.ResultsA total of 547 patients with contact dermatitis, chronic nodular prurigo, psoriasis vulgaris, lichen planus or cutaneous T‐cell lymphoma were included. The intensity scales showed a high level of reproducibility and inter‐correlations with each other. The correlation with the Dermatology Life Quality Index was weak to strong in nearly all countries and dermatoses with the exception of France and patients with chronic nodular prurigo, for which no statistically significant correlations were found.ConclusionsThe numerical rating scale, the verbal rating scale und the visual analogue scales are valid instruments with good reproducibility and internal consistency in German (Germany, Austria, Switzerland), French, Italian, Polish, Russian, Spanish and Turkish for different pruritic dermatoses. VAS worst was the best reproducible and consistent measuring instrument in all countries.