bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hericium erinaceuspolysaccharide improves the microstructure, immune function, proliferation and reduces apoptosis of thymus and spleen tissue cells of immunosuppressed mice
Authors: Han Yujiao , Huang Jialiang , Zhao Chunfang , Zhang Feng , Gu Youfang , Wang Chenfang , Jin Erhui 
Published: December 2022

ABSTRACTIn order to study the effect of Hericium erinaceus polysaccharide (HEP) on the immune and antioxidation functions of immunosuppressed mice. The control group received distilled water orally and the model and experimental groups I, II, and III received 0, 80, 160, and 320 mg/kg HEP respectively for a fortnight after re-molding with cyoclphosphnalide (CTX). Compared with the control group, the secretion of IL-2, IL-4, and IFN-γ, the activity or content of T-AOC, T-SOD, and GSH-PX, and the expression of PCNA mRNA in the thymus and spleen were reduced in immunosuppressed mice (P &lt; .05 or P &lt; .01). Compared with immunosuppressed mice, the levels of IL-2, IFN-γ, and GSH-PX and the PCNA mRNA expression of spleen and thymus were increased (P &lt; .05 or P &lt; .01), and the microstructure were also obviously improved in the experimental group III. Overall, 320 mg/kg of HEP significantly improved the immune and antioxidant functions.
Avoidance behavior and experience-dependent tolerance in response to bitter compounds inCaenorhabditis elegans
Authors: Ishikawa Seiryu , Iida Chiharu , Takezawa Yuka , Chiba Kyoko , Kage-Nakadai Eriko 
Published: December 2022

ABSTRACTThis study investigates the mechanisms governing experience-dependent tolerance of bitter compounds in Caenorhabditis elegans. The nematodes showed an aversion to nicotinamide, MgCl2, isoleucine, and arginine in a Gα-dependent manner. Worms furthermore displayed diminished avoidance of MgCl2 upon MgCl2-preconditioning at the larval stages. AIY interneurons have been suggested to be involved in experience-dependent behavioral plasticity.
GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data
Authors: Kim Minsoo , Vo Daniel D , Kumagai Michi E , Jops Connor T , Gandal Michael J 
Published: December 2022

AbstractSummaryWith the continued deluge of results from genome-wide association and functional genomic studies, it has become increasingly imperative to quickly combine and visualize different layers of genetic and genomic data within a given locus to facilitate exploratory and integrative data analyses. While several tools have been developed to visualize locus-level genetic results, the limited speed, scalability and flexibility of current approaches remain a significant bottleneck. Here, we present a Julia package for high-performance genetics and genomics-related data visualization that enables fast, simultaneous plotting of hundreds of association results along with multiple relevant genomic annotations. Leveraging the powerful plotting and layout utilities from Makie.jl facilitates the customization and extensibility of every component of a plot, enabling generation of publication-ready figures.Availability and implementationThe GeneticsMakie.jl package is open source and distributed under the MIT license via GitHub (https://github.com/mmkim1210/GeneticsMakie.jl). The GitHub repository contains installation instructions as well as examples and documentation for built-in functions.Supplementary informationSupplementary data are available at Bioinformatics online.
Variable-selection ANOVA Simultaneous Component Analysis (VASCA)
Authors: Camacho José , Vitale Raffaele , Morales-Jiménez David , Gómez-Llorente Carolina 
Published: December 2022

AbstractMotivationANOVA Simultaneous Component Analysis (ASCA) is a popular method for the analysis of multivariate data yielded by designed experiments. Meaningful associations between factors/interactions of the experimental design and measured variables in the dataset are typically identified via significance testing, with permutation tests being the standard go-to choice. However, in settings with large numbers of variables, like omics (genomics, transcriptomics, proteomics and metabolomics) experiments, the ‘holistic’ testing approach of ASCA (all variables considered) often overlooks statistically significant effects encoded by only a few variables (biomarkers).ResultsWe hereby propose Variable-selection ASCA (VASCA), a method that generalizes ASCA through variable selection, augmenting its statistical power without inflating the Type-I error risk. The method is evaluated with simulations and with a real dataset from a multi-omic clinical experiment. We show that VASCA is more powerful than both ASCA and the widely adopted false discovery rate controlling procedure; the latter is used as a benchmark for variable selection based on multiple significance testing. We further illustrate the usefulness of VASCA for exploratory data analysis in comparison to the popular partial least squares discriminant analysis method and its sparse counterpart.Availability and implementationThe code for VASCA is available in the MEDA Toolbox at https://github.com/josecamachop/MEDA-Toolbox (release v1.3). The simulation results and motivating example can be reproduced using the repository at https://github.com/josecamachop/VASCA/tree/v1.0.0 (DOI 10.5281/zenodo.7410623).Supplementary informationSupplementary data are available at Bioinformatics online.
LapTrack: linear assignment particle tracking with tunable metrics
Authors: Fukai Yohsuke T , Kawaguchi Kyogo 
Published: December 2022

AbstractMotivationParticle tracking is an important step of analysis in a variety of scientific fields and is particularly indispensable for the construction of cellular lineages from live images. Although various supervised machine learning methods have been developed for cell tracking, the diversity of the data still necessitates heuristic methods that require parameter estimations from small amounts of data. For this, solving tracking as a linear assignment problem (LAP) has been widely applied and demonstrated to be efficient. However, there has been no implementation that allows custom connection costs, parallel parameter tuning with ground truth annotations, and the functionality to preserve ground truth connections, limiting the application to datasets with partial annotations.ResultsWe developed LapTrack, a LAP-based tracker which allows including arbitrary cost functions and inputs, parallel parameter tuning and ground-truth track preservation. Analysis of real and artificial datasets demonstrates the advantage of custom metric functions for tracking score improvement from distance-only cases. The tracker can be easily combined with other Python-based tools for particle detection, segmentation and visualization.Availability and implementationLapTrack is available as a Python package on PyPi, and the notebook examples are shared at https://github.com/yfukai/laptrack. The data and code for this publication are hosted at https://github.com/NoneqPhysLivingMatterLab/laptrack-optimisation.Supplementary informationSupplementary data are available at Bioinformatics online.
Oocyte quality evaluation: a review of engineering approaches toward clinical challenges
Authors: Palay Peyman , Fathi Davood , Fathi Rouhollah 
Published: December 2022

AbstractAlthough assisted reproductive technology has been very successful for the treatment of infertility, its steps are still dependent on direct human opinion. An important step of assisted reproductive treatments in lab for women is choosing an oocyte that has a better quality. This step would predict which oocyte has developmental competence leading to healthy baby. Observation of the oocyte morphological quality indicators under microscope by an embryologist is the most common evaluation method of oocyte quality. Such subjective method which relies on embryologist’s experience may vary and leads to misdiagnosis. An alternative solution to eliminate human misjudging in traditional methods and overcome the limitations of them is always using engineering-based procedure. In this review article, we deeply study and categorize engineering-based methods applied for the evaluation of oocyte quality. Then, the challenges in laboratories and clinics settings move forward with translational medicine perspective in mind for all those methods which had been studied were discussed. Finally, a standardized process was presented, which may help improving and focusing the research in this field. Moreover, effective suggestion techniques were introduced that are expected they would be complementary methods to accelerate future researches. The aim of this review was to create a new prospect with the engineering approaches to evaluate oocyte quality and we hope this would help infertile couples to get a baby.
Stabilized generation of human iPSC-derived liver organoids using a modified coating approach
Authors: Kamishibahara Yu , Okamoto Satoshi , Ohkuma Takuya , Taniguchi Hideki 
Published: December 2022

Abstract
Human-induced pluripotent stem cell (hiPSC)-derived hepatic cells are useful tools for regenerative medicine, and various culture substrates are currently used for their differentiation. We differentiated hiPSC-derived hepatic endoderm (HE), endothelial cells (ECs), and mesenchymal cells (MCs) using Laminin-511 (LN) coating to generate liver organoids, hiPSC-liver buds (hiPSC-LBs), which exhibited therapeutic effects when transplanted into disease model animals. Stably producing significant amounts of hiPSC-LBs is necessary for sufficient therapeutic effects. However, general precoating (standard coating) requires quick manipulation, often causing failure for inexperienced cell cultures, we thus tested direct LN addition to the culture medium (Direct coating). Using quantitative gene expression, flow cytometry, albumin secretion, and ammonia metabolism, we demonstrated that Standard and Direct coating similarly induce hiPSC-derived hepatocyte, mesodermal cell, EC, and MC differentiation. Standard and Direct coating-differentiated cells generated iPSC-LBs with equivalent hepatic functions. Furthermore, Direct coating enabled stable induction of differentiation independent of individual culture skills and reduced total amount of LN use as the same differentiated cell quality can be obtained upon LN supplementation at lower concentrations. In summary, the results of this study suggest that Direct coating could enable stable hiPSC-LB production at a low cost, thereby yielding mass cell production using hiPSCs.
Stroke in hemodialysis patients and its association with CHA2DS2-VASC and HAS-BLED scores: a retrospective study
Authors: Sab Marc , Chelala Dania , Aoun Mabel , Azar Rabih , Abdel Massih Tony 
Published: December 2022

ABSTRACTBackgroundIn the general population, the CHA2DS2-VASC and the HAS-BLED scores are helpful to predict cerebrovascular events and hemorrhage in patients with atrial fibrillation (AF). However, their predictive value remains controversial in the dialysis population. This study aims to explore the association between these scores and cerebral cardiovascular events in hemodialysis (HD) patients.MethodsThis is a retrospective study including all HD patients treated between January 2010 and December 2019 in two Lebanese dialysis facilities. Exclusion criteria are patients younger than 18 years old and patients with a dialysis vintage less than 6 months.ResultsA total of 256 patients were included (66.8% men; mean age 69.3 ± 13.9 years). The CHA2DS2-VASc score was significantly higher in patients with stroke (P = .043). Interestingly, this difference was significant in patients without AF (P = .017). Using receiver operating curve analysis, CHA2DS2-VASc score had an area under the curve (AUC) of 0.628 [95% confidence interval (CI): 0.539–0.718) and the best cut-off value for this score was 4. The HAS-BLED score was also significantly higher in patients with a hemorrhagic event (P &lt; .001). AUC for HAS-BLED score was 0.756 (95% CI: 0.686–0.825) and the best cut-off value was also 4.ConclusionsIn HD patients, CHA2DS2-VASc score can be associated with stroke and HAS-BLED score can be associated with hemorrhagic events even in patients without AF. Patients with a CHA2DS2-VASc score ≥4 are at the highest risk for stroke and adverse cardiovascular outcomes, and those with a HAS-BLED score ≥4 are at the highest risk for bleeding.
LidocAine Versus Opioids In MyocarDial infarction: the AVOID-2 randomized controlled trial
Authors: Fernando Himawan , Nehme Ziad , Milne Catherine , O’Brien Jessica , Bernard Stephen , Stephenson Michael , Myles Paul S , Lefkovits Jeffrey , Peter Karlheinz , Brennan Angela , Dinh Diem , Andrew Emily , Taylor Andrew J , Smith Karen , Stub Dion 
Published: December 2022

Abstract

Aims
Opioid analgesia has been shown to interfere with the bioavailability of oral P2Y12 inhibitors prompting the search for safe and effective non-opioid analgesics to treat ischaemic chest pain.

Methods and results
The lidocAine Versus Opioids In MyocarDial infarction trial was a prospective, Phase II, prehospital, open-label, non-inferiority, randomized controlled trial enrolling patients with suspected STEACS with moderate to severe pain [numerical rating scale (NRS) at least 5/10]. Intravenous lidocaine (maximum dose 300 mg) or intravenous fentanyl (up to 50 µg every 5 min) were administered as prehospital analgesia. The co-primary end points were prehospital pain reduction and adverse events requiring intervention. Secondary end points included peak cardiac troponin I, cardiac MRI (cMRI) assessed myocardial infarct size and clinical outcomes to 30 days. A total of 308 patients were enrolled. The median reduction in pain score (NRS) was 4 vs. 3 in the fentanyl and lidocaine arms, respectively, for the primary efficacy end point [estimated median difference −1 (95% confidence interval −1.58, −0.42, P = 0.5 for non-inferiority, P = 0.001 for inferiority of lidocaine)]. Adverse events requiring intervention occurred in 49% vs. 36% of the fentanyl and lidocaine arms which met non-inferiority and superiority favouring lidocaine (P = 0.016 for superiority). No significant differences in myocardial infarct size and clinical outcomes at 30 days were seen.

Conclusion
IV Lidocaine did not meet the criteria for non-inferiority with lower prehospital pain reduction than fentanyl but was safe and better tolerated as analgesia in ST-elevation myocardial infarction (STEMI). Future trials testing non-opioid analgesics in STEMI and whether opioid avoidance improves clinical outcomes are needed.

Trial Registration
CTRN12619001521112p
Gender biases: evidence from a natural experiment in French local elections
Authors: Eyméoud Jean-Benoît , Vertier Paul 
Published: December 2022

AbstractWomen are underrepresented in politics. In this paper, we test one of the potential explanations for this situation: gender biases from voters. We use a natural experiment during French local elections in 2015: for the first time in this country, candidates had to run in pairs, which had to be gender-balanced. We argue that this reform confused some voters, who might have assumed that the first name on the ballot represented the ‘main’ candidate. Since the order of the candidates on the ballot was determined by their alphabetical order, the order of appearance of male and female candidates was as-good-as-random and this setting allows us to isolate gender biases from selection effects. Our main result is that there exists a negative gender bias affecting right-wing candidates, whose vote shares were lower by 1.5 percentage points when the female candidate appeared first on the ballot. The missing votes prevented some pairs of candidates from proceeding to the second round of voting. Using data on newspaper circulation and additional institutional features of the election—namely the fact that candidates can (but do not have to) report additional information about themselves on the ballot—we show that higher levels of information decrease discrimination. We argue that the discrimination we identify is, therefore, likely to be statistical.
Influence of different Lachancea thermotolerans strains in the wine profile in the era of climate challenge
Authors: Vicente Javier , Kelanne Niina , Rodrigo-Burgos Lydia , Navascués Eva , Calderón Fernando , Santos Antonio , Marquina Domingo , Yang Baoru , Benito Santiago 
Published: December 2022

Abstract
The study performed sequential fermentations of red grape juice using several strains of Lachancea thermotolerans and one strain of Saccharomyces cerevisiae. Due to the new conditions imposed by climate change, wine acidity must be affected as well as the volatile profile. Non-Saccharomyces yeasts such as L. thermotolerans are real alternatives to soften the impact of climate change in winemaking. The L. thermotolerans strains included three commercially available strains and two wine-related natural isolates. L. thermotolerans showed significant statistical differences in basic chemical parameters such as lactic acid, malic acid, or ethanol concentrations as well as in the volatile profile. S. cerevisiae clearly produced some volatile compounds in higher amounts than the studied L. thermotolerans strains while others showed the opposite effect. Sequential fermentations involving any of the studied strains of L. thermotolerans with S. cerevisiae showed an increased volatile profile compared to the S. ceresisiae single fermentation, highlighting the synergic effect between the studied species.
Assessing White-Tailed Deer Impacts to Tree Seedling Growth using Citizen Science Data in Minnesota, USA
Authors: Russell Matthew B , Desprez Johanna 
Published: December 2022

AbstractWhite-tailed deer (Odocoileus virginianus Zimmerman) present numerous challenges for maintaining the health of forests in the US Lake States. Although many sources of data exist that provide coarse estimates of deer-browse impacts on plant survival and abundance (e.g., national forest inventories) or examine areas where deer are excluded (e.g., exclosures), few studies exist that use detailed tree seedling measurements across diverse stand conditions and forest types. This study evaluated four years of citizen science data collected in the Assessing Vegetation Impacts from Deer (AVID) program in Minnesota, USA. Results showed that average annual height growth of seedlings for nine browse-palatable species was 1.9 cm. For four of these tree species, annual height growth was not significantly different from zero. These results point to the challenges for the growth and survival of browse-palatable tree species in Minnesota under current deer population levels. Engaging the public through a citizen science project such as AVID showcases the importance of evaluating browse impacts on trees from white-tailed deer while simultaneously providing information to managers and decision makers about this important conservation concern.Study Implications: Citizen scientists can collect data on important conservation issues with ecological implications. This study showcases data provided by volunteers in Minnesota’s Assessing Vegetation Impacts from Deer (AVID) program. These results showed that the growth of nine browse-palatable species grew minimally over a four-year span. Citizen science data like these can be used by state wildlife agencies to better understand forest-wildlife interactions and establish wildlife population harvest goals. Measurements of deer browse can also assist researchers by reducing the costs of data collection and providing a geographically diverse data set with detailed measurements of deer impacts to forest vegetation.
The Unintended Consequences of Arms Embargoes
Authors: Kuo Raymond C , Spindel Jennifer 
Published: December 2022

Abstract
To what extent do arms embargoes curtail the embargoed state's ability to get conventional weapons? We argue that arms embargoes rarely prevent states from receiving conventional weapons, and are one of the few events that push states to switch their supplier base. Using a new dataset on the place of origin of conventional weapons, we provide a more full and complete picture of the effects of arms embargoes imposed by the United Nations and European Union. We show that middlemen, a previously obscured category of states who sell, but do not produce arms, are crucial to skirting embargoes. This article suggests that arms embargoes are a more complicated foreign policy tool than scholars have previously appreciated, and that policymakers need to be cautious in imposing them.
Mitochondrial ATP Production is Required for Endothelial Cell Control of Vascular Tone
Authors: Wilson Calum , Lee Matthew D , Buckley Charlotte , Zhang Xun , McCarron John G 
Published: December 2022

AbstractArteries and veins are lined by nonproliferating endothelial cells that play a critical role in regulating blood flow. Endothelial cells also regulate tissue perfusion, metabolite exchange, and thrombosis. It is thought that endothelial cells rely on ATP generated via glycolysis, rather than mitochondrial oxidative phosphorylation, to fuel each of these energy-demanding processes. However, endothelial metabolism has mainly been studied in the context of proliferative cells, and little is known about energy production in endothelial cells within the fully formed vascular wall. Using intact arteries isolated from rats and mice, we show that inhibiting mitochondrial respiration disrupts endothelial control of vascular tone. Basal, mechanically activated, and agonist-evoked calcium activity in intact artery endothelial cells are each prevented by inhibiting mitochondrial ATP synthesis. Agonist-evoked calcium activity was also inhibited by blocking the transport of pyruvate, the master fuel for mitochondrial energy production, through the mitochondrial pyruvate carrier. The role for mitochondria in endothelial cell energy production is independent of species, sex, or vascular bed. These data show that a mitochondrial ATP supply is necessary for calcium-dependent, nitric oxide-mediated endothelial control of vascular tone, and identifies the critical role of endothelial mitochondrial energy production in fueling perfused blood vessel function.
Limits to transcriptional silencing in Saccharomyces cerevisiae
Authors: Fouet Marc , Rine Jasper 
Published: December 2022

Abstract
Mating-type switching in the budding yeast Saccharomyces cerevisiae relies on the Sir protein complex to silence HML and HMR, the two loci containing copies of the alleles of the mating type locus, MAT. Sir-based transcriptional silencing has been considered locus-specific, but the recent discovery of rare and transient escapes from silencing at HMLα2 with a sensitive assay called to question if these events extend to the whole locus. Adapting the same assay, we measured that transient silencing failures at HML were more frequent for the α2 gene than α1, similarly to their expression level in unsilenced cells. By coupling a mating assay, at HML we found that one of the two genes at that locus can be transiently expressed while the other gene is maintained silent. Thus, transient silencing loss can be a property of the gene rather than the locus. Cells lacking the SIR1 gene experience epigenetic bistability at HML and HMR. Our previous result led us to ask if HML could allow for two independent epigenetic states within the locus in a sir1Δ mutant. A simple construct using a double fluorescent reporter at HMLα1 and HMLα2 ruled out this possibility. Each HML locus displayed a single epigenetic state. We revisited the question of the correlation between the states of two HML loci in diploid cells, and showed they were independent. Finally, we determined the relative strength of gene repression achieved by Sir-based silencing with that achieved by the a1-α2 repressor.