bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-fractional Davey–Stewartson equation: Lie point symmetries, similarity reductions, conservation laws and traveling wave solutions
Authors: Guo Baoyong , Fang Yong , Dong Huanhe 
Published: July 2023

Abstract
As a celebrated nonlinear water wave equation, the Davey–Stewartson equation is widely studied by researchers, especially in the field of mathematical physics. On the basis of the Riemann–Liouville fractional derivative, the time-fractional Davey–Stewartson equation is investigated in this paper. By application of the Lie symmetry analysis approach, the Lie point symmetries and symmetry groups are obtained. At the same time, the similarity reductions are derived. Furthermore, the equation is converted to a system of fractional partial differential equations and a system of fractional ordinary differential equations in the sense of Riemann–Liouville fractional derivative. By virtue of the symmetry corresponding to the scalar transformation, the equation is converted to a system of fractional ordinary differential equations in the sense of Erdélyi–Kober fractional integro-differential operators. By using Noether’s theorem and Ibragimov’s new conservation theorem, the conserved vectors and the conservation laws are derived. Finally, the traveling wave solutions are achieved and plotted.
Current fluctuations in a semi-infinite line
Authors: Saha Soumyabrata , Sadhu Tridib 
Published: July 2023

Abstract
We present the application of a fluctuating hydrodynamic theory to study current fluctuations in diffusive systems on a semi-infinite line in contact with a reservoir with slow coupling. We show that the distribution of the time-integrated current across the boundary at large times follows a large deviation principle with a rate function that depends on the coupling strength with the reservoir. The system exhibits a long-term memory of its initial state, which was earlier reported on an infinite line and can be described using quenched and annealed averages of the initial state. We present an explicit expression for the rate function for independent particles, which we verify using an exact solution of the microscopic dynamics. For the symmetric simple exclusion process, we present expressions for the first three cumulants of both quenched and annealed averages.
ReCo: automated NGS

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unting of single and combinatorial CRISPR gRNAs
Authors: Wegner Martin , Kaulich Manuel 
Published: July 2023

Abstract

Summary
CRISPR screens are increasingly performed to associate genotypes with genotypes. So far, however, their analysis required specialized computational knowledge to transform high-throughput next-generation sequencing (NGS) data into sequence formats amenable for downstream analysis. We developed ReCo, a stand-alone and user-friendly analytics tool for generating read-count tables of single and combinatorial CRISPR library and screen-based NGS data. Together with cutadapt and bowtie2 for rapid sequence trimming and alignment, ReCo enables the automated generation of read count tables from staggered NGS reads for the downstream identification of gRNA-induced phenotypes.

Availability and implementation
ReCo is published under the MIT license and available at: https://github.com/KaulichLab/ReCo.
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data
Authors: Li Chen , Chen Xiaoyang , Chen Shengquan , Jiang Rui , Zhang Xuegong 
Published: July 2023

AbstractMotivationSingle-cell chromatin accessibility sequencing (scCAS) technology provides an epigenomic perspective to characterize gene regulatory mechanisms at single-cell resolution. With an increasing number of computational methods proposed for analyzing scCAS data, a powerful simulation framework is desirable for evaluation and validation of these methods. However, existing simulators generate synthetic data by sampling reads from real data or mimicking existing cell states, which is inadequate to provide credible ground-truth labels for method evaluation.ResultsWe present simCAS, an embedding-based simulator, for generating high-fidelity scCAS data from both cell- and peak-wise embeddings. We demonstrate simCAS outperforms existing simulators in resembling real data and show that simCAS can generate cells of different states with user-defined cell populations and differentiation trajectories. Additionally, simCAS can simulate data from different batches and encode user-specified interactions of chromatin regions in the synthetic data, which provides ground-truth labels more than cell states. We systematically demonstrate that simCAS facilitates the benchmarking of four core tasks in downstream analysis: cell clustering, trajectory inference, data integration, and cis-regulatory interaction inference. We anticipate simCAS will be a reliable and flexible simulator for evaluating the ongoing computational methods applied on scCAS data.Availability and implementationsimCAS is freely available at https://github.com/Chen-Li-17/simCAS.
Alpha-ketoglutarate supplementation reduces inflammation and thrombosis in type 2 diabetes by suppressing leukocyte and platelet activation
Authors: Agarwal Sakshi , Ghosh Riya , Verma Garima , Khadgawat Rajesh , Guchhait Prasenjit 
Published: July 2023

Abstract
The interplay between platelets and leukocytes contributes to the pathogenesis of inflammation, thrombosis, and cardiovascular diseases (CVDs) in type 2 diabetes (T2D). Our recent studies described alpha-ketoglutarate (αKG), a Krebs cycle intermediate metabolite as an inhibitor to platelets and leukocytes activation by suppressing phosphorylated-Akt (pAkt) through augmentation of prolyl hydroxylase-2 (PHD2). Dietary supplementation with a pharmacological concentration of αKG significantly inhibited lung inflammation in mice with either SARS-CoV-2 infection or exposed to hypoxia treatment. We therefore investigated if αKG supplementation could suppress hyperactivation of these blood cells and reduce thromboinflammatory complications in T2D. Our study describes that dietary supplementation with αKG (8 mg/100 g body wt. daily) for 7 days significantly reduced the activation of platelets and leukocytes (neutrophils and monocytes), and accumulation of IL1β, TNFα, and IL6 in peripheral blood of T2D mice. αKG also reduced the infiltration of platelets and leukocytes, and accumulation of inflammatory cytokines in lungs by suppressing pAkt and pP65 signaling. In a cross-sectional investigation, our study also described the elevated platelet–leukocyte aggregates and pro-inflammatory cytokines in circulation of T2D patients. T2D platelets and leukocytes showed an increased aggregation and thrombus formation in vitro. Interestingly, a pre-incubation of T2D blood samples with octyl αKG significantly suppressed the activation of these blood cells and ameliorated aggregate/thrombus formation in vitro. Thus, suggesting a potential therapeutic role of αKG against inflammation, thrombosis, and CVDs in T2D.
Impact of Concomitant 5-Aminosalicylic Acid Therapy on Vedolizumab Efficacy and Safety in Inflammatory Bowel Disease: Post Hoc Analyses of Clinical Trial Data
Authors: Ungaro Ryan C , Kadali Harisha , Zhang Wenwen , Adsul Shashi , Reinisch Walter 
Published: July 2023

Abstract

Background and Aims
The benefit of continuing 5-aminosalicylic acid [5-ASA] treatment when escalating to advanced therapies in patients with inflammatory bowel disease [IBD] is unclear. Vedolizumab is a gut-selective monoclonal anti-α4β7-integrin antibody used to treat moderate to severe IBD. Clinical trial data were analysed post hoc to assess the impact of 5-ASA co-treatment on vedolizumab efficacy and safety in patients with IBD.

Methods
Data were analysed from patients aged 18–80 years with moderate to severe ulcerative colitis [UC]/Crohn’s disease [CD] receiving intravenous [IV]/subcutaneous [SC] vedolizumab. Efficacy data were from four studies [GEMINI 1 and 2 and VISIBLE 1 and 2]; safety data were from seven studies [GEMINI 1‒3 and long-term, VISIBLE 1, 2, and open-label extension]. The impact of 5-ASA co-treatment on clinical and endoscopic outcomes at Weeks 6 and 52 was assessed using multivariate analysis (adjusted odds ratios [aORs] with 95% confidence intervals [CIs]).

Results
There were no significant differences in UC clinical remission [Mayo score ≤2, no subscore &gt;1] rates with vs without 5-ASA at Week 6 [20.7% vs 20.4%, respectively; aOR 0.77, 95% CI 0.43–1.38] or at Week 52 [45.1% vs 40.6%; aOR 1.14, 0.70–1.86], and in CD clinical remission [CD activity index score ≤150] rates at Week 6 [41.4% vs 35.1%; 1.26, 0.86–1.85] or at Week 52 [49.6% vs 37.8%; 1.35, 0.91–1.99]. The incidence of enteric and all infections in vedolizumab IV/SC-treated patients was low with and without 5-ASA.

Conclusion
Continuation of concomitant oral 5-ASA after starting vedolizumab had no significant impact on clinical and endoscopic outcomes.

Clinical trial identifiers
GEMINI 1: NCT00783718, EudraCT 2008-002782-32; GEMINI 2: NCT00783692, EudraCT 2008-00278-33; GEMINI 3: NCT01224171, EudraCT 2009-016488-12; GEMINI long-term safety study: NCT00790933, EudraCT 2008-002784-14; VISIBLE 1: NCT02611830, EudraCT 2015-000480-14; VISIBLE 2: NCT02611817, EudraCT 2015-000481-58; VISIBLE open-label extension: NCT02620046, EudraCT 2015-000482-31.
Challenges in diagnosing pulmonary embolism in an adult with Fontan physiology: a case report
Authors: Teng Catherine , Shrestha Ribesh , Phillips Jason 
Published: July 2023

Abstract

Background
With the increasing longevity of congenital heart disease patients and limited number of adult congenital heart disease specialists, it is becoming increasingly imperative for general cardiologists to understand not only the unique physiology of Fontan patients but also imaging protocol considerations when treating this group of patients.

Case summary
Here, we present a patient with a history of congenital tricuspid atresia status after the Fontan procedure who presented for gut translocation–related bacteraemia. Importantly, the patient was falsely diagnosed with pulmonary embolism resulting from inaccurate acquisition of computed tomography imaging.

Discussion
This case illustrates the complex intricacies that clinicians should consider when facing the challenge of treating Fontan patients.
Acute pulmonary hypertension due to microthrombus formation following COVID-19 vaccination: a case report
Authors: Nakagawa Akiko , Nakamura Norihito , Torii Sho , Goto Shinya 
Published: July 2023

Abstract

Background
Several side effects have been reported after mRNA COVID-19 vaccinations. Nonetheless, the risk of pulmonary hypertension (PH) is rarely reported. Most cases with acute PH following vaccination were due to macropulmonary embolism secondary to deep vein thrombosis. However, acute PH due to microthrombus formation after COVID-19 vaccination has not been reported before, although a microthrombus has been considered to lead to the dysfunction of multiple organs, particularly in patients infected with COVID-19.

Case summary
A 63-year-old woman without any past medical history presented to our hospital with facial and bilateral pedal oedema and progressive dyspnoea on exertion. Her symptoms began the day after her second COVID-19 vaccination and developed gradually, which prompted her to seek consultation in our hospital 6 weeks later. An echocardiogram revealed substantially elevated right heart pressure, and cardiac catheterization revealed high pulmonary artery pressure (mean PAP, 30 mmHg). Contrast-enhanced computed tomography and venous echography revealed no apparent thrombus, and ventilation/perfusion (V/Q) scintigraphy revealed no V/Q mismatch. However, elevated D-dimer indicated the presence of a coagulation–fibrinolysis system in her body; thus, heparin therapy was initiated intravenously on Day 3 for 4 days, followed by direct oral anticoagulants ended on Day 16. Her symptoms substantially improved as her D-dimer level decreased, and a follow-up cardiac catheterization on Day 14 revealed a decline in mean PAP (15 mmHg).

Discussion
Our case suggests that the presence of acute PH is likely due to microangiopathy. Further studies are required to reveal the relationship between immune responses and microthrombus formation after COVID-19 vaccination.
Lifestyle interventions to change trajectories of obesity-related cardiovascular risk from childhood onset to manifestation in adulthood: a joint scientific statement of the task force for childhood health of the European Association of Preventive Cardiology and the European Childhood Obesity Group
Authors: Hanssen Henner , Moholdt Trine , Bahls Martin , Biffi Alessandro , Siegrist Monika , Lewandowski Adam J , Biondi-Zoccai Giuseppe , Cavarretta Elena , Kokkvoll Ane , Løchen Maja-Lisa , Maestrini Viviana , Pinto Rita Salvador , Palermi Stefano , Thivel David , Wojcik Malgorzata , Hansen Dominique , Van Craenenbroeck Emeline M , Weghuber Daniel , Kraenkel Nicolle , Tiberi Monica 
Published: July 2023

Abstract
There is an immediate need to optimize cardiovascular (CV) risk management and primary prevention of childhood obesity to timely and more effectively combat the health hazard and socioeconomic burden of CV disease from childhood development to adulthood manifestation. Optimizing screening programs and risk management strategies for obesity-related CV risk in childhood has high potential to change disease trajectories into adulthood. Building on a holistic view on the aetiology of childhood obesity, this document reviews current concepts in primary prevention and risk management strategies by lifestyle interventions. As an additional objective, this scientific statement addresses the high potential for reversibility of CV risk in childhood and comments on the use of modern surrogate markers beyond monitoring weight and body composition. This scientific statement also highlights the clinical importance of quantifying CV risk trajectories and discusses the remaining research gaps and challenges to better promote childhood health in a population-based approach. Finally, this document provides an overview on the lessons to be learned from the presented evidence and identifies key barriers to be targeted by researchers, clinicians, and policymakers to put into practice more effective primary prevention strategies for childhood obesity early in life to combat the burden of CV disease later in life.
Interannual dynamics of Tuber melanosporum and fungal communities in productive black truffle orchards amended with truffle nests
Authors: Garcia-Barreda Sergi , Marco Pedro , Bonito Gregory , Parladé Javier , Sánchez Sergio , González Vicente , Larena Inmaculada , Benucci Gian Maria Niccolò 
Published: July 2023

Abstract
Truffle growers devote great efforts to improve black truffle productivity, developing agronomic practices such as ‘truffle nests’ (peat amendments that are supplemented with truffle spore inoculum). It has been hypothesized that improved fruiting associated with nests is linked to stimulation of truffle mycelia previously established in soil or to changes generated in soil fungal community. To assess this, we used real-time PCR to quantify black truffle extraradical mycelium during 2 years after nests installation. We also characterized the fungal community via high-throughput amplicon sequencing of the ITS region of rRNA genes. We found that neither the abundance of truffle mycelium in nests nor in the soil—nest interphase was higher than in the bulk soil, which indicates that nests do not improve mycelial growth. The fungal community in nests showed lower richness and Shannon index and was compositionally different from that of soil, which suggests that nests may act as an open niche for fungal colonization that facilitates truffle fruiting. The ectomycorrhizal fungal community showed lower richness in nests. However, no negative relationships between amount of truffle mycelium and reads of other ectomycorrhizal fungi were found, thus countering the hypothesis that ectomycorrhizal competition plays a role in the nest effect.
The genome sequence of the Champagne Epernay Geisenheim wine yeast reveals its hybrid nature
Authors: Bernardi Beatrice , Michling Florian , Muno-Bender Judith , Matti Katrin , Wendland Jürgen 
Published: July 2023

Abstract
Lager yeasts are hybrids between Saccharomyces cerevisiae and S. eubayanus. Wine yeast biodiversity, however, has only recently been discovered to include besides pure S. cerevisiae strains also hybrids between different Saccharomyces yeasts as well as introgressions from non-Saccharomyces species. Here, we analysed the genome of the Champagne Epernay Geisenheim (CEG) wine yeast. This yeast is an allotetraploid (4n − 1) hybrid of S. cerevisiae harbouring a substantially reduced S. kudriavzevii genome contributing only 1/3 of a full genome equivalent. We identified a novel oligopeptide transporter gene, FOT4, in CEG located on chromosome XVI. FOT genes were originally derived from Torulaspora microellipsoides and FOT4 arose by non-allelic recombination between adjacent FOT1 and FOT2 genes. Fermentations of CEG in Riesling and Müller-Thurgau musts were compared with the S. cerevisiae Geisenheim wine yeast GHM, which does not carry FOT genes. At low temperature (10°C), CEG completed fermentations faster and produced increased levels of higher alcohols (e.g. isoamyl alcohol). At higher temperature (18°C), CEG produced higher amounts of the pineapple-like alkyl esters i-butyric and propionic acid ethyl esters compared to GHM. The hybrid nature of CEG thus provides advantages in grape must fermentations over S. cerevisiae wine yeasts, especially with regard to aroma production.
Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast
Authors: Robinson DeElegant , Vanacloig-Pedros Elena , Cai Ruoyi , Place Michael , Hose James , Gasch Audrey P 
Published: July 2023

Abstract
Variation in gene copy number can alter gene expression and influence downstream phenotypes; thus copy-number variation provides a route for rapid evolution if the benefits outweigh the cost. We recently showed that genetic background significantly influences how yeast cells respond to gene overexpression, revealing that the fitness costs of copy-number variation can vary substantially with genetic background in a common-garden environment. But the interplay between copy-number variation tolerance and environment remains unexplored on a genomic scale. Here, we measured the tolerance to gene overexpression in four genetically distinct Saccharomyces cerevisiae strains grown under sodium chloride stress. Overexpressed genes that are commonly deleterious during sodium chloride stress recapitulated those commonly deleterious under standard conditions. However, sodium chloride stress uncovered novel differences in strain responses to gene overexpression. West African strain NCYC3290 and North American oak isolate YPS128 are more sensitive to sodium chloride stress than vineyard BC187 and laboratory strain BY4743. Consistently, NCYC3290 and YPS128 showed the greatest sensitivities to overexpression of specific genes. Although most genes were deleterious, hundreds were beneficial when overexpressed—remarkably, most of these effects were strain specific. Few beneficial genes were shared between the sodium chloride-sensitive isolates, implicating mechanistic differences behind their sodium chloride sensitivity. Transcriptomic analysis suggested underlying vulnerabilities and tolerances across strains, and pointed to natural copy-number variation of a sodium export pump that likely contributes to strain-specific responses to overexpression of other genes. Our results reveal extensive strain-by-environment interactions in the response to gene copy-number variation, raising important implications for the accessibility of copy-number variation-dependent evolutionary routes under times of stress.
Power of neutrality tests for detecting natural selection
Authors: Tanaka Tomotaka , Hayakawa Toshiyuki , Teshima Kosuke M 
Published: July 2023

Abstract
Detection of natural selection is one of the main interests in population genetics. Thus, many tests have been developed for detecting natural selection using genomic data. Although it is recognized that the utility of tests depends on several evolutionary factors, such as the timing of selection, strength of selection, frequency of selected alleles, demographic events, and initial frequency of selected allele when selection started acting (softness of selection), the relationships between such evolutionary factors and the power of tests are not yet entirely clear. In this study, we investigated the power of 4 tests: Tajiama's D, Fay and Wu's H, relative extended haplotype homozygosity (rEHH), and integrated haplotype score (iHS), under ranges of evolutionary parameters and demographic models to quantitatively expand the understanding of approaches for detecting selection. The results show that each test detects selection within a limited parameter range, and there are still wide ranges of parameters for which none of these tests work effectively. In addition, the parameter space in which each test shows the highest power overlaps the empirical results of previous research. These results indicate that our present perspective of adaptation is limited to only a part of actual adaptation.
The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species
Authors: Lipinska Agnieszka P , Krueger-Hadfield Stacy A , Godfroy Olivier , Dittami Simon M , Ayres-Ostrock Lígia , Bonthond Guido , Brillet-Guéguen Loraine , Coelho Susana , Corre Erwan , Cossard Guillaume , Destombe Christophe , Epperlein Paul , Faugeron Sylvain , Ficko-Blean Elizabeth , Beltrán Jessica , Lavaut Emma , Le Bars Arthur , Marchi Fabiana , Mauger Stéphane , Michel Gurvan , Potin Philippe , Scornet Delphine , Sotka Erik E , Weinberger Florian , Cabral de Oliveira Mariana , Guillemin Marie-Laure , Plastino Estela M , Valero Myriam 
Published: July 2023

Abstract
Macroalgal (seaweed) genomic resources are generally lacking as compared with other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole-genome assemblies for two species (Gracilaria chilensis and Gracilaria gracilis), a draft genome assembly of Gracilaria caudata, and genome annotation of the previously published Gracilaria vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.