bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic evidence of an early evolutionary divergence event in wildSaccharomyces cerevisiae
Authors: Bendixsen Devin P , Gettle Noah , Gilchrist Ciaran , Zhang Zebin , Stelkens Rike 
Published: June 2020

AbstractComparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer’s yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high quality long read genomes of non-domesticated yeast strains isolated from primeval forests and other natural environments in China and Taiwan. In a comprehensive analysis of our new genome assemblies, along with other long readSaccharomycetesgenomes available, we show that the newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity of Brewer’s yeast, confirming predictions made from short read genomic data. Three of these strains (termed the East Asian Clade IX Complex here) share a recent ancestry and evolutionary history suggesting an early divergence from otherS. cerevisiaestrains before the larger radiation of the species, and prior to its domestication. Our genomic analyses reveal that the wild East Asian strains contain elevated levels of structural variations. The new genomic resources provided here contribute to our understanding of the natural diversity ofS. cerevisiae, expand the intraspecific genetic variation found in this this heavily domesticated microbe, and provide a foundation for understanding its origin and global colonization history.Significance statementBrewer’s yeast (Saccharomyces cerevisiae) is a domesticated microbe and research model organism with a global distribution, and suspected origin in East Asia. So far only limited genomic resources are available from non-domesticated lineages. This study provides seven new, high quality long read genomes of strains isolated from primeval forests and other natural environments in China and Taiwan. Comparative genomics reveal elevated levels of structural variation in this group, and early phylogenetic branching prior to the global radiation of the species. These new genomic resources expand our understanding of the evolutionary history of Brewer’s yeast, and illustrate what the ancestors of this highly successful microbe may have looked like.
Behavioral, Biochemical and Histopathological effects of Standardised Pomegranate extract with Vinpocetine, Propolis or Cocoa in a rat model of Parkinson’s disease
Authors: Ali Azza A. , Kamal Mona M. , Khalil Mona G. , Ali Shimaa A. , Elariny Hemat A. , Bekhit Amany , Wahid Ahmed 
Published: June 2020

AbstractIntroductionParkinsonism is a neurodegenerative disorder. Pomegranate (POM) has been previously shown to have a dopaminergic neuroprotective effect against Parkinsonism.ObjectiveThe aim of the current study is to compare the efficacy of POM, vinpocetine, Propolis, Cocoa or L-dopa using RT-induced Parkinsonism rat model.MethodsRats were divided into seven groups; one normal and five RT model groups. One of the RT (2.5 mg/kg sc) groups served as non-treated parkinsonism model whereas the others were treated with either L-dopa (10 mg/kg PO) or with POM (150 mg/kg PO) together with each of the following; vinpocetine (VIN) (20 mg/kg PO), Propolis (300 mg/kg PO), Cocoa (24 mg/kg PO). Motor and cognitive performances were examined using three tests (catalepsy, open-field, Y-maze). Striatal dopamine, norepinephrine, serotonin, acetylcholinesterase, GABA, Glutamate, GSK 3B, BDNF levels were assessed as well as MDA, SOD, TAC, IL-1β, TNF-α, iNOs and caspase-3. Also, histopathological examinations of different brain regions were determined.ResultsTreatment with L-dopa alone or with all POM combination groups alleviated the deficits in locomotor activities, cognition, monoamine levels, acetylcholinesterase activity, oxidative stress, and inflammatory markers as well as caspase-3 expression induced by RT.ConclusionCombinations of POM with each of VIN, Propolis or Cocoa have a promising disease-modifying antiparkinsonian therapy even without being given as an adjuvant to L-dopa.
PeskAAS: A near-real-time, open-source monitoring and analytics system for small-scale fisheries
Authors: Tilley Alexander , Lopes Joctan Dos Reis , Wilkinson Shaun P. 
Published: June 2020

AbstractSmall-scale fisheries are responsible for landing half of world’s fish catch, yet there are very sparse data on these fishing activities and associated fisheries production in time and space. Fisheries-dependent data underpin scientific guidance of management and conservation of fisheries systems, but it is inherently difficult to generate robust and comprehensive data for small-scale fisheries, particularly given their dispersed and diverse nature. In tackling this challenge, we use open source software components including the Shiny R package to build PeskAAS; an adaptable and scalable digital application that enables the collation, classification, analysis and visualisation of small-scale fisheries catch and effort data. We piloted and refined this system in Timor-Leste; a small island developing nation. The features that make PeskAAS fit-for-purpose are that it is: (i) fully open-source and free to use (ii) component-based, flexible and able to integrate vessel tracking data with catch records; (iii) able to perform spatial and temporal filtering of fishing productivity by fishing method and habitat; (iv) integrated with species-specific length-weight parameters from FishBase; (v) controlled through a click-button dashboard, that was co-designed with fisheries scientists and government managers, that enables easy to read data summaries and interpretation of context-specific fisheries data. With limited training and code adaptation, the PeskAAS workflow has been used as a framework on which to build and adapt systematic, standardised data collection for small-scale fisheries in other contexts. Automated analytics of these data can provide fishers, managers and researchers with insights into a fisher’s experience of fishing efforts, fisheries status, catch rates, economic efficiency and geographic preferences and limits that can potentially guide management and livelihood investments.
In Silicodesign and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins
Authors: Kathwate Gunderao H 
Published: June 2020

AbstractCOVID 19 is disease caused by novel corona virus, SARS-CoV2 originated in China most probably of Bat origin. Till date, no specific vaccine or drug has been discovered to tackle the infections caused by SARS-CoV2. In response to this pandemic, we utilized bioinformatics knowledge to develop efficient vaccine candidate against SARS-CoV2. Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Predicted BCR and TCR epitopes were antigenic in nature non-toxic and probably non-allergen. Modelled and refined tertiary structure was predicted as valid for further use. Protein-Protein interaction prediction of TLR2/4 and designed vaccine indicates promising binding. Designed multiepitope vaccine has induced cell mediated and humoral immunity along with increased interferon gamma response. Macrophages and dendritic cells were also found increased over the vaccine exposure.In silicocodon optimization and cloning in expression vector indicates that vaccine can be efficiently expressed inE. coli. In conclusion, predicted vaccine is a good antigen, probable no allergen and has potential to induce cellular and humoral immunity.
Examining and fine-tuning the selection of glycan compositions with GlyConnect Compozitor
Authors: Robin Thibault , Mariethoz Julien , Lisacek Frédérique 
Published: June 2020

AbstractA key point in achieving accurate intact glycopeptide identification is the definition of the glycan composition file that is used to match experimental with theoretical masses by a glycoproteomics search engine. At present, these files are mainly built from searching the literature and/or querying data sources focused on posttranslational modifications. Most glycoproteomics search engines include a default composition file that is readily used when processing mass spectrometry data. We introduce here a glycan composition visualising and comparative tool associated with the GlyConnect database and called GlyConnect Compozitor. It has web interface through which the database can be queried to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarising information searched in the database. These results provide a guide for selecting or deselecting compositions in a file in order to reflect the context of a study as closely as possible. As part of the tool collection of the Glycomics@ExPASy initiative, Compozitor is hosted athttps://glyconnect.expasy.org/compozitor/where it can be run as a web application. It is also directly accessible from the GlyConnect database.
Denisovan ancestry and population history of early East Asians
Authors: Massilani Diyendo , Skov Laurits , Hajdinjak Mateja , Gunchinsuren Byambaa , Tseveendorj Damdinsuren , Yi Seonbok , Lee Jungeun , Nagel Sarah , Nickel Birgit , Devièse Thibaut , Higham Tom , Meyer Matthias , Kelso Janet , Peter Benjamin M. , Pääbo Svante 
Published: June 2020

AbstractWe present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.
Oocyte spindle assembly depends on multiple interactions between HP1 and the CPC
Authors: Wang Lin-Ing , DeFosse Tyler , Jang Janet K. , Battaglia Rachel A. , Wagner Victoria F. , McKim Kim S. 
Published: June 2020

AbstractThe chromosomes in the oocytes of many animals appear to promote bipolar spindle assembly. InDrosophilaoocytes, spindle assembly requires the chromosome passenger complex (CPC), which consists of INCENP, Borealin, Survivin and Aurora B. To determine what recruits the CPC to the chromosomes and its role in spindle assembly, we developed a strategy to manipulate the function and localization of INCENP, which is critical for recruiting the Aurora B kinase. We found that an interaction between Borealin and the chromatin is crucial for the recruitment of the CPC to the chromosomes and is sufficient to build kinetochores and recruit spindle microtubules. We also found that HP1 moves from the chromosomes to the spindle microtubules along with the CPC. We propose that the interaction with HP1 promotes the movement of the CPC from the chromosomes to the microtubules. In addition, within the central spindle, rather than at the centromeres, the CPC and HP1 are required for homologous chromosome bi-orientation.
Early phylodynamics analysis of the COVID-19 epidemic in France
Authors: Danesh Gonché , Elie Baptiste , Michalakis Yannis , Sofonea Mircea T , Bal Antonin , Behillil Sylvie , Destras Grégory , Boutolleau David , Burrel Sonia , Marcelin Anne-Geneviève , Plantier Jean-Christophe , Thibault Vincent , Simon-Loriere Etienne , van der Werf Sylvie , Lina Bruno , Josset Laurence , Enouf Vincent , Alizon Samuel ,   the COVID SMIT PSL group
Published: June 2020

AbstractFrance was one of the first countries to be reached by the COVID-19 pandemic. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (ℛt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. Different models suggest a slowing down of the epidemic in Mar, which would be consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the effective infection duration andℛtare in line with those estimated from contact tracing data. Finally, based on the available sequence data, we estimate that the French epidemic wave originated between mid-Jan and early Feb. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context and calls for further analyses with denser sampling.
Perfluoroalkyl Substances are increased in patients with Late-Onset Ulcerative colitis and induce Intestinal Barrier defects ex vivo in Murine Intestinal tissue
Authors: Fart Frida , Salihović Samira , McGlinchey Aidan , Gareau Melanie G. , Orešič Matej , Halfvarson Jonas , Hyötyläinen Tuulia , Schoultz Ida 
Published: June 2020

AbstractBackgroundEnvironmental factors are strongly implicated in late-onset of inflammatory bowel disease. Here, we investigate whether high exposure to perfluoroalkyl substances correlates with (1) late-onset inflammatory bowel disease, and (2) disturbances of the bile acid pool. We further explore the effect of the specific perfluoroalkyl substance perfluoronoctanoic acid on intestinal barrier function in murine tissue.MethodsSerum levels of perfluoroalkyl substances and bile acids were assessed by ultra-performance liquid chromatography coupled to a triple-quadrupole mass spectrometer in matched samples from patients with ulcerative colitis (n=20) and Crohn’s disease (n=20) diagnosed at the age of ≥55 years. Age and sex-matched blood donors (n=20), were used as healthy controls. Ex vivo Ussing chamber experiments were performed to assess the effect of perfluoronoctanoic acid on ileal and colonic murine tissue (n=9).ResultsThe total amount of perfluoroalkyl substances was significantly increased in patients with ulcerative colitis compared to healthy controls and patients with Crohn’s disease (p<0.05). Ex vivo exposure to perfluoronoctanoic acid induced a significanlty altered ileal and colonic barrier function. The distribution of bile acids, as well as the correlation pattern between (1) perfluoroalkyl substances and (2) bile acids, differed between patient and control groups.ConclusionOur results demonstrate that perfluoroalkyl substances levels are increased in patients with late-onset ulcerative colitis and may contribute to the disease by inducing a dysfunctional intestinal barrier.
Microvascular blood flow changes of the abductor pollicis brevi muscle during sustained static exercise
Authors: Giovannella Martina , Urtane Evelina , Karadeniz Umut , Rubins Uldis , Weigel Udo M. , Marcinkevics Zbignevs , Durduran Turgut 
Published: June 2020

ABSTRACTA practical assessment of the health of the palm muscle, abductor pollicis brevis (APB), is important for diagnosis of different conditions. Here we have developed a protocol and a probe to utilize diffuse correlation spectroscopy (DCS) to characterize microvascular blood flow changes in the APB during and after sustained isometric exercise, during and after thumb abduction at at 55% of maximum voluntary contraction (MVC). Blood flow in the APB decreased during exercise in the subjects (n=13) with high MVC (n=7) and stayed constant in the ones with low MVC (n=6) suggesting that the mechanical occlusion due to increased intramuscular pressure exceeded the vasodilation elicited by the higher demand. Blood flow changes during exercise negatively correlated with the absolute force applied by each subject. Muscular blood flow increased after exercise compared to the values reached during exercise. In conclusion, DCS allows the study of the response of a small muscle to static exercise.
Genetic polymorphisms mediating behavioural and immune response to pathogens may moderate the impact of the COVID-19 pandemic: a pilot study
Authors: Rajkumar Ravi Philip 
Published: June 2020

AbstractBackgroundThe COVID-19 pandemic has affected the entire world, but there are wide variations in prevalence and mortality across nations. Genetic variants which influence behavioural or immune responses to pathogens, selected for by pathogen pressure, may influence this variability. Two relevant polymorphisms in this context are the s allele of the serotonin transporter promoter (5-HTTLPR) and the G allele of the interleukin-6 gene (IL-6 rs1800795).MethodsThe frequencies of the 5-HTTLPR s allele and IL-6 rs1800795 G allele were obtained from published data. The correlations between these allele frequencies and the prevalence and mortality rates of COVID-19 were examined across 44 nations.ResultsThe IL-6 rs1800795 G allele was negatively correlated with COVID-19 prevalence (ρ = −0.466, p < 0.01) and mortality (ρ = −0.591, p<0.001) across nations. The 5-HTTLPR s allele was negatively correlated with COVID-19 mortality rates (ρ = −0.437, p = 0.023).ConclusionsThese results suggest that a significant relationship exists between genetic variants that influence behavioural and immune responses to pathogens and indices of the impact of COVID-19 across nations. Further investigation of these variants and their correlates may permit the development of better preventive or therapeutic strategies in the management of the COVID-19 pandemic.
Cytokeratin-18 has potential as a biomarker of drug-induced liver injury in European and African patients on treatment for tuberculosis
Authors: Rupprechter Sarah AE , Sloan Derek J , Oosthuyzen Wilna , Bachmann Till T , Hill Adam T , Dhaliwal Kevin , Templeton Kate , Matovu Joshua , Sekaggya-Wiltshire Christine , Dear James W 
Published: June 2020

AbstractPatients on anti-tuberculosis (anti-TB) therapy are at risk of developing drug-induced liver injury (DILI). Cytokeratin-18 (K18) is an exploratory DILI biomarker that has been developed predominately in Caucasian populations and not African populations in whom TB is common. Our aim was to determine the K18 concentration in different populations with mycobacterial infection and investigate whether K18 has potential as a biomarker of anti-TB DILI.European patients receiving anti-TB therapy were recruited at the Royal Infirmary of Edinburgh, UK (ALISTER - ClinicalTrials.gov Identifier: NCT03211208). African patients with HIV-TB coinfection, receiving anti-TB and anti-retroviral therapy (ART), were recruited at the Infectious Diseases Institute, Kampala, Uganda (SAEFRIF - NCT03982277). Serial blood samples, demographic and clinical data were collected. K18 was quantified using the M65 ELISA.The study had 235 participants (healthy volunteers (n=28); ALISTER: active TB (n=30), latent TB (n=88), non-tuberculous mycobacterial infection (n=25); SAEFRIF: HIV-TB coinfection (n=64)). There was no difference in K18 across the groups and treatment did not affect K18 in the absence of DILI. Alanine transaminase activity (ALT) and K18 were correlated (r=0.42, 95%CI=0.34-0.49, P<0.0001). Variability was higher for K18 than ALT. There were two DILI cases: baseline ALT was 18 and 28 IU/1, peak ALT 431 and 194 IU/L; baseline K18 58 and 219 U/L, peak K18 1247 and 3490 U/L, respectively.Circulating K18 was comparable in UK and Ugandan patients. K18 correlated with ALT and increased with DILI. Further work should determine the diagnostic and prognostic utility of K18 in this global context-of-use.
Stewardship regulation and earnings quality: evidence from Japan
Authors: Routledge James 
Published: June 2020

Purpose
This paper aims to examine if compliance with the Japanese Stewardship Code by institutional investors is related to the earnings quality of their investee companies. It extends the study by Lu et al. who considered this question for large UK companies with high-quality board governance and a rich information environment. This study provides new insights by exploiting the contrasting Japanese setting.

Design/methodology/approach
The association between Code-compliant institutional investor shareholding and discretionary accruals is examined for Japanese companies in the Nikkei 225 Index. The study period is from the introduction of the Code in 2015 to 2017.

Findings
A negative association is found between the level of institutional investor Code-compliant shareholding and discretionary accruals, which is robust to tests that address endogeneity. The findings suggest Code-compliant institutional investor shareholding mitigates opportunistic income-increasing earnings management and promotes conservative accounting. Consistent results are found for benchmark beating and accruals quality as alternative earnings quality measures.

Originality/value
This study offers new insights regarding the efficacy of the Stewardship Code’s policy approach. The findings suggest the stewardship regulatory model is effective when internal governance is weak and external monitoring by institutional investors is a viable substitute or complement.
Acceptability of low-sodium mozzarella coated with zein and essential oils
Authors: Pereira Lívio Antônio Silva , Bemfeito Raquel Martino , Bemfeito Carla Martino , e Silva Priscila de Castro , Rodrigues Jéssica Ferreira , Gonçalves Michelle Carlota , Pinheiro Ana Carla Marques , Piccoli Roberta Hilsdorf 
Published: June 2020

PurposeThe main purpose of this paper was to evaluate the influence of the zein coating containing essential oils on the sensory characteristics of sodium-reduced mozzarellas.Design/methodology/approachMozzarellas were prepared by dipping in brine containing 5, 10, 15 or 20% of NaCl (w/v) that correspond, respectively, to 25, 50, 75 and 100% of NaCl content used in industry. These salted mozzarellas and another one, unsalted, were coated by an edible zein film added with 3% of a mixture of thyme and garlic essential oils (1:1). They were subjected to sensory analysis in relation to salty taste and overall impression. The mozzarella without salt reduction (20% NaCl w/v), coated or uncoated with the edible film, was also subjected to the analysis of water loss and microbiological quality, in order to evaluate the impact of this film on product quality.FindingsThe zein coating added with oils did not compromise the sensory acceptance of the mozzarella prepared with up to 50% of salt reduction. Water loss and microbial growth were lower in zein-coated mozzarella than in uncoated mozzarella. These results showed that this film could be applied as natural additive, contributing to the microbiological and sensory characteristics of the mozzarella.Originality/valueThis paper contributes to reducing the lack of studies in relation to new technologies for food preservation and sodium reduction. In addition, the zein coating containing essential oils can be tested on other food categories.