bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of concentrations of lead (Pb) in meat from wild-shot common pheasants killed using shotgun pellets principally composed of lead, iron (Fe), bismuth (Bi) and zinc (Zn)
Authors: Green Rhys E. , Taggart Mark A. , Guiu Maider , Waller Hayley , Pap Sabolc , Sheldon Rob , Pain Deborah J. 
Published: May 2023

AbstractThe source of almost all of the lead (Pb) found in meat from carcasses of wild-shot small game animals is often thought to be small embedded fragments of the lead shotgun pellets usually used by hunters to kill them. Available circumstantial evidence supports this conjecture, but an unknown proportion of the lead in game meat might be biologically-incorporated and absorbed by the game animal from ingested shotgun pellets and other environmental sources, such as soil and residues from mining. A critical test comparing lead concentrations in meat from animals known to have been killed using different types of shotgun ammunition has not been performed until now. We compared lead concentrations in samples of edible meat from carcasses of 27 wild-shot common pheasants (Phasianus colchicus) from which only lead shotgun pellets were recovered post mortem with concentrations for 20 birds from which only iron pellets were recovered. Shotgun pellets were removed from the meat samples before analysis. The mean concentration of lead was about 30 times greater in the meat of pheasants shot with lead than those shot with iron and was similar to mean concentrations of lead reported previously from Europe-wide samples of meat from wild-shot small game animals, including pheasants, killed using unknown types of ammunition. These results support the hypothesis that changing the type of shotgun ammunition in use for hunting from lead to iron would greatly reduce the concentration of lead in meat from wild-shot small game.
MethPhaser: methylation-based haplotype phasing of human genomes
Authors: Fu Yilei , Aganezov Sergey , Mahmoud Medhat , Beaulaurier John , Juul Sissel , Treangen Todd J. , Sedlazeck Fritz J 
Published: May 2023

AbstractThe assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limited by read length and stretches of homozygosity along the genome. To overcome this limitation, we designed MethPhaser, the first method that utilizes methylation signals from Oxford Nanopore Technologies to extend SNV-based phasing. Across control samples, we extend the phase length N50 by almost 3-fold while minimally increasing the phasing error by ∼0.02%. Nevertheless, methylation signals have limitations, such as random signals on sex chromosomes or tissue purity. To assess the latter, we also applied MethPhaser on blood samples from 4 patients, still showing improvements over SNV-only phasing. MethPhaser further improves phasing acrossHLAand multiple other medically relevant genes, improving our understanding of how mutations interact across multiple phenotypes. MethPhaser is available athttps://github.com/treangenlab/methphaser.
RIP140 regulates HES1 oscillatory expression and mitogenic activity in colon cancer cells
Authors: Sfeir Nour , Kajdan Marilyn , Jalaguier Stéphan , Bonnet Sandrine , Teyssier Catherine , Pyrdziak Samuel , Yuan Rong , Bousquet Emilie , Maraver Antonio , Bernex Florence , Pirot Nelly , Boissiere Florence , Castet-Nicolas Audrey , Lapierre Marion , Cavaillès Vincent 
Published: May 2023

ABSTRACTBackgroundThe transcription factor RIP140 (Receptor Interacting Protein of 140 kDa) regulates intestinal homeostasis and tumorigenesis through the Wnt signaling. In this study, we have investigated its effect on the Notch/HES1 signaling pathway.MethodsThe impact on HES1 expression and activity was evaluated in colorectal cancer (CRC) cell lines and in transgenic mice, invalidated or not for theRip140gene in the intestinal epithelium. A tumor microarray and transcriptomic data sets were used to investigate RIP140 and HES1 expression in relation with patient survival. Statistical comparisons were performed with Mann-Whitney or Kruskal-Wallis orChi2tests.ResultsIn CRC cells, RIP140 positively regulatedHES1gene expression at the transcriptional level via an RBPJ/NICD-mediated mechanism. In support of thesein vitrodata, RIP140 and HES1 expression significantly correlated in mouse intestine and in a cohort of CRC samples, analyzed by immunohistochemistry, thus supporting the positive regulation ofHES1gene expression by RIP140.Interestingly, when the Notch pathway is fully activated, RIP140 exerted a strong inhibition ofHES1gene transcription controlled by the level of HES1 itself. Moreover, RIP140 directly interacts with HES1 and reversed its mitogenic activity in human CRC cells. In line with this observation, HES1 levels were associated with a better patient survival only when tumors expressed high levels of RIP140.ConclusionsOur data identify RIP140 as a key regulator of the Notch/HES1 signaling pathway with a dual effect onHES1gene expression at the transcriptional level and a strong impact on colon cancer cell proliferation.
A Hydroponic-Based Bioassay to FacilitatePlasmodiophora brassicaePhenotyping
Authors: Salih Rasha , Brochu Anne-Sophie , Labbé Caroline , Strelkov Stephen E. , Franke Coreen , Bélanger Richard , Pérez-López Edel 
Published: May 2023

ABSTRACTClubroot, caused by the obligate parasitePlasmodiophora brassicae, is one of the most devastating diseases affecting the canola/oilseed rape (Brassica napus) industry worldwide. Currently, the planting of clubroot-resistant (CR) cultivars is the most effective strategy used to restrict the spread and the economic losses linked to the disease. However, virulentP. brassicaeisolates have been able to infect many of the currently available CR cultivars, and the options to manage the disease are becoming limited. Another challenge has been achieving consistency in evaluating host reactions toP. brassicaeinfection, with most bioassays conducted in soil and/or potting medium, which requires significant space and can be labour intensive. Visual scoring of clubroot symptom development can also be influenced by user bias. Here, we have developed a hydroponic bioassay using well-characterizedP. brassicaesingle-spore isolates representative of clubroot virulence in Canada, as well as field isolates from three Canadian provinces, in combination with canola inbred homozygous lines carrying resistance genetics representative of CR cultivars available to growers in Canada. To improve the efficiency and consistency of disease assessment, symptom severity scores were compared with clubroot evaluations based on the scanned root area. According to the results, this bioassay offers a reliable, less expensive, and reproducible option to evaluateP. brassicaevirulence, as well as a means to identify which canola resistance profile(s) may be effective against particular isolates. This bioassay will contribute to the breeding of new CR canola cultivars and the identification of virulence genes inP. brassicaethat could trigger resistance and have been very elusive to this day.
Resolving genotype-phenotype discrepancies of the Kidd blood group system using long-read nanopore sequencing
Authors: Gueuning M , Thun GA , Trost N , Schneider L , Sigurdardottir S , Engström C , Larbes N , Merki Y , Frey BM , Gassner C , Meyer S , Mattle-Greminger MP 
Published: May 2023

AbstractDue to substantial improvement in read accuracy, third-generation long-read sequencing holds great potential in blood group diagnostics, particularly in cases where traditional genotyping or sequencing techniques, primarily targeting exons, fail to explain serological phenotypes. In this study, we employed Oxford Nanopore sequencing to resolve all genotype-phenotype discrepancies in the Kidd blood group system (JK, encoded bySLC14A1) observed over seven years of routine high-throughput donor genotyping using a mass spectrometry based platform at Blood Transfusion Service Zurich. Discrepant results from standard serological typing and donor genotyping were confirmed by commercial PCR-SSP kits. To resolve discrepancies, we amplified the entire coding region ofSLC14A1(∼24 kb, exons 3 to 10) in two overlapping long-range PCRs in all samples. Amplicons were barcoded and sequenced on a MinION flow cell. Sanger sequencing and bridge-PCRs were used to confirm findings. Among 11,972 donors with both serological and genotype data available for the Kidd system, we identified 10 cases with unexplained conflicting results. Five were linked to known weak and null alleles caused by variants not included in the routine donor genotyping. In two cases, we identified novel null alleles on theJK*01(Gly40Asp; c.119G>A) andJK*02(Gly242Glu; c.725G>A) haplotype, respectively. Remarkably, the remaining three cases were associated with a yet unknown deletion of ∼5 kb spanning exons 9-10 of theJK*01allele, which other molecular methods had failed to detect. Overall, nanopore sequencing demonstrated reliable and accurate performance for detecting both single-nucleotide and structural variants. It possesses the potential to become a robust tool in the molecular diagnostic portfolio, particularly for addressing challenging structural variants such as hybrid genes, deletions and duplications.
Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates
Authors: Ye Zhiqiang , Pfrender Michael E. , Lynch Michael 
Published: May 2023

AbstractStudies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. Here, we compared population-genomics data betweenD. pulexandD. pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region.D. pulicariahas lower genome-wide nucleotide diversity, a smaller effective population size, higher incidence of private alleles, and substantially more linkage-disequilibrium thanD. pulex. Functional enrichment analysis revealed that positively selected genes inD. pulicariaare enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended lifespan inD. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Additionally, genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats.
Early cellular and molecular signatures correlate with severity of West Nile Virus infection
Authors: Lee Ho-Joon , Zhao Yujiao , Fleming Ira , Mehta Sameet , Wang Xiaomei , Wyk Brent Vander , Ronca Shannon E. , Kang Heather , Chou Chih-Hung , Fatou Benoit , Smolen Kinga K. , Levy Ofer , Clish Clary B. , Xavier Ramnik J. , Steen Hanno , Hafler David A. , Love J. Christopher , Shalek Alex K. , Guan Leying , Murray Kristy O. , Kleinstein Steven H. , Montgomery Ruth R. 
Published: May 2023

ABSTRACTInfection with West Nile Virus (WNV) can drive a wide range of responses, from asymptomatic to flu-like symptoms/fever or severe cases of encephalitis and death. To identify cellular and molecular signatures distinguishing WNV severity, we employed systems profiling of peripheral blood from asymptomatic and severely ill individuals infected with WNV. We interrogated immune responses longitudinally from acute infection through convalescence at 3 months and 1 year employing multiplexed single cell protein and transcriptional profiling (CyTOF and Seq-Well) complemented with matched serum proteomics and metabolomics. At the acute time point, we detected both an elevated proportion of pro-inflammatory markers in innate immune cell types and reduced frequency of regulatory T cell activity in participants with severe infection compared to those with asymptomatic infection. Single-cell transcriptomics of paired samples revealed that asymptomatic donors had higher expression of genes associated with innate immune pathways, in particular anti-inflammatory CD16+monocytes at the acute time point. A multi-omics analysis identified factors--beyond those from individual analyses--that distinguished immune state trajectory between severity groups. Here we highlighted the potential of systems immunology using multiple cell-type and cell-state-specific analyses to identify correlates of infection severity and host cellular activity contributing to an effective anti-viral response.
UV-induced feather color change reflects its porphyrin content
Authors: Hasegawa Masaru , Arai Emi , Ito Shosuke , Wakamatsu Kazumasa 
Published: May 2023

AbstractPigmentary coloration is widespread in animals. Its evolutionary and ecological features are often attributed to the property of predominant pigments; therefore, most research has focused on predominant pigments such as carotenoids in carotenoid-based coloration. However, coloration results from predominant pigments and many other minority pigments, and the importance of the latter is overlooked. Here, we focused on porphyrin, an “uncommon” pigment found in bird feathers, and investigate its importance in the context of feather color changes in the barn swallowHirundo rustica. We found that the “pheomelanin-based coloration” of the barn swallow faded after the irradiation of UV light, and this effect was particularly strong in the feathers of young swallows (nestlings and fledglings, here). We also found that it is not the predominant pigment, pheomelanin, but protoporphyrin IX pigment that showed the same pattern of depigmentation after the irradiation of UV light, particularly in the feathers of young swallows. In fact, the abovementioned age-dependent feather color change was statistically explained by the amount of porphyrin in the feathers. The current study demonstrates that a minority pigment, porphyrin, explains within-season dynamic color change, an ecological feature of feather coloration. The porphyrin-mediated rapid color change would benefit young birds, in which feather coloration affects the parental food allocation during a few weeks before independence, but not later. Future studies should not ignore these minor but essential pigments and their evolutionary and ecological functions.Significance statementPredominant pigments are assumed to determine animal coloration and its ecological features. It is then not surprising that the evolutionary and ecological features of animal coloration are often attributed to the chemical properties of predominant pigments. However, coloration results from predominant pigments and several other minority pigments. By irradiating UV light on reddish throat feathers of the barn swallowHirundo rustica, we examined within-season dynamic color change in relation to a minority pigment, porphyrin, which has not previously been examined but is a candidate pigment for feather color change, because porphyrin can be easily photodegraded. We found that not the predominant pigment, pheomelanin, but porphyrin pigments explained the feather color change. Minor pigments and their chemical properties should not be dismissed to understand the ecological and evolutionary functions of animal coloration.
ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection
Authors: Eliad Berta , Schneider Noa , Zgayer Orna Ben-Naim , Amichan Yarden , Glaser Fabian , Erdmann Emily A. , Rajendren Suba , Hundley Heather A. , Lamm Ayelet T. 
Published: May 2023

ABSTRACTAdenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, inCaenorhabditis elegans, it is not, making them invaluable for RNA editing research. InC. elegans, ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established inC. elegans. In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. Inadbp-1mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels andde-novoediting, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.
Glycocalyx dynamics and membrane curvature under cytosolic pressure
Authors: Gandhi Jay G. , Koch Donald L. , Paszek Matthew J. 
Published: May 2023

ABSTRACTThe glycocalyx is a soft material composed of glycosylated proteins and lipids decorating the plasma membrane of cells. Although the glycocalyx is a mechanical conduit between the plasma membrane and the cell surroundings, the coupled dynamics of the glycocalyx and membrane are poorly understood in most cell processes. Here, we construct a dynamic model to predict the coupled mechanical behaviors of the glycocalyx and membrane due to internal cytosolic pressure in a cell interacting with an external substrate. We report how the glycocalyx constituents bear cytosolic loads, physically rearrange, and shape the cell membrane. Simulations of the model predict that highly flexible, polymeric elements in the glycocalyx are uniformly compressed in the cell-substrate contact zone. However, more rigid, fiber-like glycocalyx constituents dynamically rearrange over timescales on the order of 10 milliseconds, concentrating into clusters. This spatial heterogeneity allows close apposition of the plasma membrane with the substrate, a geometry that would be favorable for subsequent adhesive bond formation. Clustered glycocalyx constituents imprint nanotopographical features on the plasma membrane with longitudinal dimensions of 200 – 300 nm. Analysis of the membrane topographies reveals curvatures that could be sufficient to elicit biological responses through curvature sensing proteins, such as BAR-domain proteins. Together, our simulations suggest how instabilities in the compressed glycocalyx could mediate downstream adhesive and signaling processes in the bleb-substrate interface.
A mixed amplicon metabarcoding and sequencing approach for surveillance of drug resistance to levamisole and benzimidazole inHaemonchusspp
Authors: Francis Emily Kate , Antonopoulos Alistair , Westman Mark Edward , McKay-Demeler Janina , Laing Roz , Šlapeta Jan 
Published: May 2023

AbstractAnthelmintic resistant parasitic nematodes present a significant threat to sustainable livestock production worldwide. The ability to detect the emergence of anthelmintic resistance at an early stage, and therefore determine which drugs remain most effective, is crucial for minimising production losses. Despite many years of research into the molecular basis of anthelmintic resistance, no molecular-based tools are commercially available for the diagnosis of resistance as it emerges in field settings. We described a mixed deep amplicon sequencing approach to determine the frequency of the levamisole (LEV) resistant single nucleotide polymorphism (SNP) withinarc-8 exon 4 (S168T) inHaemonchusspp., coupled with benzimidazole (BZ) resistance SNPs withinβ-tubulinisotype-1 and ITS-2 nemabiome. This constitutes the first multi-drug and multi-species molecular diagnostic developed for helminths of veterinary importance. Of the ovine, bovine, caprine and camelid Australian field isolates we tested, S168T was detected in the majority ofHaemonchusspp. populations from sheep and goats, but rarely at a frequency greater than 16%; an arbitrary threshold we set based on whole genome sequencing of LEV resistantH. contortusGWBII. Overall, BZ resistance was far more prevalent inHaemonchusspp. than LEV resistance, confirming that LEV is still an important anthelmintic class for small ruminants in New South Wales. The mixed amplicon metabarcoding approach described herein, paves the way towards the use of large scale sequencing as a surveillance technology in the field, the results of which can be translated into evidence-based recommendations for the livestock sector.
Investigation on fin cooling for lithium-polymer batteries
Authors: Yasar Onur , Ekici Selcuk , Yalcin Enver , Karakoç Tahir Hikmet 
Published: May 2023

Purpose
Lithium-polymer batteries have common usage in aviation industry especially unmanned aerial vehicles (UAV). Overheating is a serious problem in lithium-polymer batteries. Various cooling methods are performed to keep lithium-polymer batteries in the desired temperature range. The purpose of this paper is to examine pouch type lithium-polymer battery with plate fins by using particle image velocimetry (PIV) and computational fluid dynamics (CFD) for UAV.

Design/methodology/approach
Battery models were produced with a 3D printer. The upper surfaces of fabricated battery models were covered with plate fins with different fin heights and fin thicknesses. Velocities were obtained with PIV and CFD. Temperature dissipations were acquired with numerical simulations.

Findings
At the end of the study, the second battery model gave the lowest temperature values among the battery models. Temperature values of the seventh battery model were the highest temperatures. Fin cooling reduced the maximum cell temperatures noticeably. Numerical simulations agreed with PIV measurements well.

Practical implications
This paper takes into account two essential tools such as PIV and CFD, for fluid mechanics, which are significant in the aviation industry and engineering life.

Originality/value
The originality of this paper depends on investigation of both PIV and CFD for UAV and developing a cooling method that can be feasible for landing and take-off phases for UAV.