bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory Divergence as a Mechanism for X-Autosome Incompatibilities in Caenorhabditis Nematodes
Authors: Viswanath Athmaja , Cutter Asher D 
Published: April 2023

Abstract
The world's astounding biodiversity results from speciation, the process of formation of distinct species. Hybrids between species often have reduced fitness due to negative epistatic interactions between divergent genetic factors, as each lineage accumulated substitutions independently in their evolutionary history. Such negative genetic interactions can manifest as gene misexpression due to divergence in gene regulatory controls from mutations in cis-regulatory elements and trans-acting factors. Gene misexpression due to differences in regulatory controls can ultimately contribute to incompatibility within hybrids through developmental defects such as sterility and inviability. We sought to quantify the contributions of regulatory divergence to postzygotic reproductive isolation using sterile interspecies hybrids of two Caenorhabditis nematodes: Caenorhabditis briggsae and Caenorhabditis nigoni. We analyzed previous transcriptome profiles for two introgression lines with distinct homozygous X-linked fragments from C. briggsae in a C. nigoni genomic background that confers male sterility, owing to defects in spermatogenesis (Li R, et al. 2016. Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-chromosome introgression. Genome Res. 26:1219–1232). Our analysis identified hundreds of genes that show distinct classes of nonadditive expression inheritance and regulatory divergence. We find that these nonoverlapping introgressions affect many of the same genes in the same way and demonstrate that the preponderance of transgressive gene expression is due to regulatory divergence involving compensatory and joint effects of cis- and trans-acting factors. The similar transcriptomic responses to nonoverlapping genetic perturbations of the X-chromosome implicate multiway incompatibilities as an important feature contributing to hybrid male sterility in this system.
Validity, Reliability, Responsiveness, and Feasibility of the Life-Space Assessment Administered via Telephone in Community-Dwelling Older Adults
Authors: Ullrich Phoebe , Hummel Merit , Hauer Klaus , Bauer Jürgen M , Werner Christian 
Published: April 2023

Abstract

Background and Objectives
The life-space assessment (LSA) is the most commonly used questionnaire to assess life-space mobility (LSM) in older adults, with well-established psychometric properties for face-to-face (FF) administration. However, these properties have not yet been explicitly studied when the LSA is administered by telephone. The aim of this study was to evaluate the concurrent and construct validity, test–retest reliability, responsiveness, and feasibility of a telephone-based LSA version (TE-LSA) in older adults.

Research Design and Methods
Fifty community-dwelling older adults (age = 79.3 ± 5.3 years) participated in the study. Concurrent validity was assessed against the FF-LSA construct validity by testing 15 a priori hypotheses on expected associations with LSM determinants, test–retest reliability via 2 telephone surveys 1 week apart, responsiveness after 8.5 ± 1.8 months in participants with improved, stable, and worsened mobility defined by 2 external criteria, and feasibility by the completion rate/time and ceiling/floor effects.

Results
Good to excellent agreement between the 2 different administration methods was found (intraclass correlation coefficient [ICC2,1] = 0.73–0.98). Twelve of 15 (80%) hypotheses on construct validity were confirmed. ICCs for test–retest reliability were good to excellent (ICC2,1 = 0.62–0.94). Minimal detectable change for the TE-LSA total score was 20 points. Standardized response means were large for worsened (0.88), moderate for improved (0.68), and trivial for stable participants (0.04). Completion rate was 100% and mean completion time was 5.5 ± 3.3 min. No ceiling or floor effects were observed for the TE-LSA total score.

Discussion and Implications
Telephone administration of the LSA is valid, reliable, responsive, and feasible for assessing LSM in community-dwelling older adults.
Inequalities in end-stage renal disease: underprivileged and ethnic minority members are at higher risk
Authors: Wilf-Miron Rachel , Myers Vicki , Saban Mor , Novikov Ilya , Kimron Lizie , Ziv Arnona , Kalter-Leibovici Ofra 
Published: April 2023

Abstract

Background
Incidence of end-stage renal disease (ESRD) is higher in Israel than the European average. Socio-economic differences in ESRD have been reported globally, but many countries lack a national register. Using national data, we assessed which socio-demographic factors are associated with 5-year incidence of ESRD in Israel, where there is universal access to renal replacement therapy (RRT).

Methods
Data on all incident ESRD cases aged ≥20 years receiving chronic RRT between 1 January 2014 and 31 December 2018 (N = 7883) were collected from Israel’s National Dialysis & Renal Transplant Register. Individual-level data on ESRD cases requiring RRT included residential area, age, gender, ethnicity (Jewish or Arab) and ESRD cause (diabetes, other, unknown/missing). Area-level data included age and sex distribution, socio-economic status (SES) and proportion of Arab population. The associations between individual-level socio-demographic characteristics and ESRD cause were tested in bivariate comparisons. The risk of developing ESRD during the study period (from all and specific causes) was estimated using multiple Poisson regression models with negative binomial distribution, using four parameters, namely sex, ethnicity, SES category and age strata, based on area-level distribution of these parameters, and with the whole population (aged ≥20 years) as the denominator.

Results
A socio-economic gradient was seen for ESRD from all causes, more marked for diabetic aetiology [rate ratio (RR)=0.45, 95% CI: 0.39–0.52 highest vs lowest SES categories] than from other (RR = 0.64, 95% CI: 0.55–0.75) or unknown cause (RR = 0.79, 95% CI: 0. 62–0.99). Based on population area-level data, predominantly Arab neighbourhoods showed higher risk for ESRD requiring RRT for all causes, with the strongest association for diabetes (RR = 1.69, 95% CI: 1.53–1.86) adjusted for SES, age and sex.

Conclusions
A strong socio-economic gradient was demonstrated for ESRD requiring RRT. Arab ethnicity was associated with higher risk for ESRD, especially due to diabetes. Our findings suggest the need for allocation of health resources according to needs and culturally appropriate interventions for improving control of modifiable risk factors for chronic renal failure.
Efficacy of vancomycin lock therapy for totally implantable venous access port-related infection due to coagulase-negative staphylococci in 100 patients with cancer
Authors: Lafaurie Matthieu , Montlahuc Claire , Kerneis Solen , de Lastours Victoire , Abgrall Sophie , Manceron Véronique , Couzigou Carine , Chabrol Amélie , de Raigniac Axelle , Lescure Xavier , Longuet Pascale , Lesprit Philippe , Vanjak Dominique , Lepeule Raphael ,   Groupe des référents en Infectiologie d’Ile de France (GRIF), Abgrall S , Bleibtreu A , Canoui E , Caseris M , Chabrol A , Chopin D , Couzigou C , De Coninck L , Diamantis S , Dournon N , Dubert M , Dollat M , Escaut L , Fihman V , Galy A , Gros H , Kerneis S , Lafaurie M , de Lastours V , Lebeaux D , L Lecapitaine A , Lefort A , Lepeule R , Longuet P , Munier A L , Ourghanlian C , Pourbaix A , de Raigniac A , Saidani M , Sayne N , Surgers L , Therby A , Wemmert C 
Published: April 2023

Abstract

Objectives
Data on the efficacy of vancomycin catheter lock therapy (VLT) for conservative treatment of totally implantable venous access port-related infections (TIVAP-RI) due to CoNS are scarce. The aim of this study was to evaluate the effectiveness of VLT in the treatment of TIVAP-RI due to CoNS in cancer patients.

Methods
This prospective, observational, multicentre study included adults with cancer treated with VLT for a TIVAP-RI due to CoNS. The primary endpoint was the success of VLT, defined as no TIVAP removal nor TIVAP-RI recurrence within 3 months after initiation of VLT. The secondary endpoint was 3 month mortality. Risk factors for VLT failure were also analysed.

Results
One hundred patients were included [men 53%, median age 63 years (IQR 53–72)]. Median duration of VLT was 12 days (IQR 9–14). Systemic antibiotic therapy was administered in 87 patients. VLT was successful in 44 patients. TIVAP could be reused after VLT in 51 patients. Recurrence of infection after completion of VLT occurred in 33 patients, among which TIVAP was removed in 27. Intermittent VLT (antibiotic solution left in place in the TIVAP lumen part of the time) was identified as a risk factor for TIVAP-RI recurrence. At 3 months, 26 deaths were reported; 1 (4%) was related to TIVAP-RI.

Conclusions
At 3 months, success of VLT for TIVAP-RI due to CoNS was low. However, removing TIVAP was avoided in nearly half the patients. Continuous locks should be preferred to intermittent locks. Identifying factors of success is essential to select patients who may benefit from VLT.
The antioxidant defence ofDekkera bruxellensisagainst hydrogen peroxide and its relationship to nitrate metabolism
Authors: Xavier Mariana Rodrigues , Teles Gilberto Henrique , de Carvalho Jennyfer Martins , Vieira Leucio Duarte , Pita Will de Barros , Antonio de Morais Marcos 
Published: April 2023

AbstractAims. The yeast Dekkera bruxellensis is a Crabtree-positive yeast that tends towards the oxidative/respiratory metabolism in aerobiosis. However, it is more sensitive to H2O2 than Saccharomyces cerevisiae. In order to investigate this metabolic paradox, the present work aimed to uncover the biological defence mechanism used by this yeast to tolerate the presence of exogenous H2O2. Methods and Results. Growth curves and spot tests were performed to establish the values of minimal inhibitory concentration and minimal biocidal concentration of H2O2 for different combinations of carbon and nitrogen sources. Cells in exponential growth phase in different culture conditions were used to measure superoxide and thiols [protein (PT) and non-PT], enzyme activities and gene expression. Conclusions. The combination of glutathione peroxidase (Gpx) and sulfhydryl-containing PT formed the preferred defence mechanism against H2O2, which was more efficiently active under respiratory metabolism. However, the action of this mechanism was suppressed when the cells were metabolizing nitrate (NO3). Significance and Impact of Study. These results were relevant to figure out the fitness of D. bruxellensis to metabolize industrial substrates containing oxidant molecules, such as molasses and plant hydrolysates, in the presence of a cheaper nitrogen source such as NO3.
Gustation in insects: taste qualities and types of evidence used to show taste function of specific body parts
Authors: King B H , Gunathunga Panchalie B 
Published: April 2023

AbstractThe insect equivalent of taste buds are gustatory sensilla, which have been found on mouthparts, pharynxes, antennae, legs, wings, and ovipositors. Most gustatory sensilla are uniporous, but not all apparently uniporous sensilla are gustatory. Among sensilla containing more than one neuron, a tubular body on one dendrite is also indicative of a taste sensillum, with the tubular body adding tactile function. But not all taste sensilla are also tactile. Additional morphological criteria are often used to recognize if a sensillum is gustatory. Further confirmation of such criteria by electrophysiological or behavioral evidence is needed. The five canonical taste qualities to which insects respond are sweet, bitter, sour, salty, and umami. But not all tastants that insects respond to easily fit in these taste qualities. Categories of insect tastants can be based not only on human taste perception, but also on whether the response is deterrent or appetitive and on chemical structure. Other compounds that at least some insects taste include, but are not limited to: water, fatty acids, metals, carbonation, RNA, ATP, pungent tastes as in horseradish, bacterial lipopolysaccharides, and contact pheromones. We propose that, for insects, taste be defined not only as a response to nonvolatiles but also be restricted to responses that are, or are thought to be, mediated by a sensillum. This restriction is useful because some of the receptor proteins in gustatory sensilla are also found elsewhere.
Exact Monte Carlo likelihood-based inference for jump-diffusion processes
Authors: Gonçalves Flávio B , Łatuszyński Krzysztof , Roberts Gareth O 
Published: April 2023

AbstractStatistical inference for discretely observed jump-diffusion processes is a complex problem which motivates new methodological challenges. Thus, existing approaches invariably resort to time-discretisations which inevitably lead to approximations in inference. In this paper, we give the first general collection of methodologies for exact (in this context meaning discretisation-free) likelihood-based inference for discretely observed finite activity jump-diffusions. The only sources of error involved are Monte Carlo error and convergence of expectation maximisation (EM) or Markov chain Monte Carlo (MCMC) algorithms. We shall introduce both frequentist and Bayesian approaches, illustrating the methodology through simulated and real examples.
The Snapdragon Genomes Reveal the Evolutionary Dynamics of the S-Locus Supergene
Authors: Zhu Sihui , Zhang Yu’e , Copsy Lucy , Han Qianqian , Zheng Dongfeng , Coen Enrico , Xue Yongbiao 
Published: April 2023

Abstract
The genus Antirrhinum has been used as a model to study self-incompatibility extensively. The multi-allelic S-locus, carrying a pistil S-RNase and dozens of S-locus F-box (SLF) genes, underlies the genetic control of self-incompatibility (SI) in Antirrhinum hispanicum. However, there have been limited studies on the genomic organization of the S-locus supergene due to a lack of high-quality genomic data. Here, we present the chromosome-level reference and haplotype-resolved genome assemblies of a self-incompatible A. hispanicum line, AhS7S8. For the first time, 2 complete A. hispanicum S-haplotypes spanning ∼1.2 Mb and containing a total of 32 SLFs were reconstructed, whereas most of the SLFs derived from retroelement-mediated proximal or tandem duplication ∼122 Mya. Back then, the S-RNase gene and incipient SLFs came into linkage to form the pro-type of type-1 S-locus in the common ancestor of eudicots. Furthermore, we detected a pleiotropic cis-transcription factor (TF) associated with regulating the expression of SLFs, and two miRNAs may control the expression of this TF. Interspecific S-locus and intraspecific S-haplotype comparisons revealed the dynamic nature and polymorphism of the S-locus supergene mediated by continuous gene duplication, segmental translocation or loss, and TE-mediated transposition events. Our data provide an excellent resource for future research on the evolutionary studies of the S-RNase-based self-incompatibility system.
Quantitative haplotype-resolved analysis of mitochondrial DNA heteroplasmy in Human single oocytes, blastoids, and pluripotent stem cells
Authors: Bi Chongwei , Wang Lin , Fan Yong , Yuan Baolei , Alsolami Samhan , Zhang Yingzi , Zhang Pu-Yao , Huang Yanyi , Yu Yang , Izpisua Belmonte Juan Carlos , Li Mo 
Published: April 2023

Abstract
Maternal mitochondria are the sole source of mtDNA for every cell of the offspring. Heteroplasmic mtDNA mutations inherited from the oocyte are a common cause of metabolic diseases and associated with late-onset diseases. However, the origin and dynamics of mtDNA heteroplasmy remain unclear. We used our individual Mitochondrial Genome sequencing (iMiGseq) technology to study mtDNA heterogeneity, quantitate single nucleotide variants (SNVs) and large structural variants (SVs), track heteroplasmy dynamics, and analyze genetic linkage between variants at the individual mtDNA molecule level in single oocytes and human blastoids. Our study presented the first single-mtDNA analysis of the comprehensive heteroplasmy landscape in single human oocytes. Unappreciated levels of rare heteroplasmic variants well below the detection limit of conventional methods were identified in healthy human oocytes, of which many are reported to be deleterious and associated with mitochondrial disease and cancer. Quantitative genetic linkage analysis revealed dramatic shifts of variant frequency and clonal expansions of large SVs during oogenesis in single-donor oocytes. iMiGseq of a single human blastoid suggested stable heteroplasmy levels during early lineage differentiation of naïve pluripotent stem cells. Therefore, our data provided new insights of mtDNA genetics and laid a foundation for understanding mtDNA heteroplasmy at early stages of life.
Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR
Authors: FitzPatrick Vincent D , Leemans Christ , van Arensbergen Joris , van Steensel Bas , Bussemaker Harmen J 
Published: April 2023

Abstract
Classic promoter mutagenesis strategies can be used to study how proximal promoter regions regulate the expression of particular genes of interest. This is a laborious process, in which the smallest sub-region of the promoter still capable of recapitulating expression in an ectopic setting is first identified, followed by targeted mutation of putative transcription factor binding sites. Massively parallel reporter assays such as survey of regulatory elements (SuRE) provide an alternative way to study millions of promoter fragments in parallel. Here we show how a generalized linear model (GLM) can be used to transform genome-scale SuRE data into a high-resolution genomic track that quantifies the contribution of local sequence to promoter activity. This coefficient track helps identify regulatory elements and can be used to predict promoter activity of any sub-region in the genome. It thus allows in silico dissection of any promoter in the human genome to be performed. We developed a web application, available at cissector.nki.nl, that lets researchers easily perform this analysis as a starting point for their research into any promoter of interest.
Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul
Authors: Flack Nicole , Drown Melissa , Walls Carrie , Pratte Jay , McLain Adam , Faulk Christopher 
Published: April 2023

Abstract
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul’s zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
DisseminatedTalaromyces marneffeiInfection With STAT3-Hyper-IgE Syndrome: A Case Series and Literature Review
Authors: Li Zhengtu , Yang Jinglu , Qiu Ye , Yang Feng , Tang Mengxin , Li Shaoqiang , Zhan Yangqing , Li Yongming , Tang Sufang , Jing Cheng , Ye Feng 
Published: April 2023

AbstractBackgroundLittle is known about the clinical characteristics of talaromycosis with hyper–immunoglobulin E syndrome (HIES).MethodsWe conducted a multicenter retrospective study, which included 7 hospitals from 2016 to 2022. Five consecutive cases of human immunodeficiency virus (HIV)–negative patients with systemic Talaromyces marneffei infections due to STAT3-HIES were identified. A systematic literature review of original articles published in English identified an additional 7 cases. Clinical characteristics and laboratory parameters were collected.ResultsForty-two percent (5/12) of patients were young adults. The main symptoms of 10 patients were similar: fever (75%), cough (75%) and dyspnea (33%), but two patients mainly had gastrointestinal symptoms. Most patients had a history of infections since infancy. T marneffei was cultured from the bronchoalveolar lavage fluid (50%) and 25% of patients were next-generation sequencing positive. Eight patients had significantly elevated serum immunoglobulin E, increased B cells and decreased natural killer cells. There were ten different STAT3 mutations, three of which were reported for the first time in this study. Chest computed tomography examinations showed multiple exudations with cavities in the lungs. Voriconazole combined with thymosin was effective. Despite given antifungal agents, most had poor outcomes and the case fatality rate was as high as 25%.ConclusionsSTAT3-HIES is most likely a susceptibility factor for T marneffei infections among HIV-negative patients, which has a high case fatality rate. Increased awareness among clinicians is necessary to help in early diagnosis.
Ministerial Advisers as Power Resources: Exploring Expansion, Stability and Contraction in Westminster Ministers’ Offices
Authors: Pickering Heath , Craft Jonathan , Brans Marleen 
Published: April 2023

Abstract
In this article, we argue that the entourage of ministerial advisers available to prime ministers and other ministers is an institutional power resource that can serve as a useful indicator to measure the changing nature of the political executive. Two novel contributions are made utilising four new datasets on ministerial advisers coupled with a comparative analysis of 21 governments in Australia, Britain, Canada and New Zealand, in varying dates between 1997 and 2020. First, by using ministerial advisers as a proxy indicator, we chart how the offices of executive politicians can either expand, remain stable or contract. As a corrective to the general long-term narrative that ministers’ offices continually expand, our evidence shows this expansion has in some cases been interrupted and more generally manifests in different patterns from one government to the next. Second, we interrogate these patterns against the background of four typical assumptions from the party family, government tenure, parliamentary control and leadership stability literature. The new datasets, typology and analysis provide fresh comparative insights to advance our understanding about the evolving nature of the political executive in the four classic Westminster family countries.