bluuebunny/crossref_metadata_2025_split huggingface dataset:
EVIDENCE OF HIV/HCV COINFECTION AMONG PEOPLE LIVING WITH HIV/AIDS ATTENDING FEDERAL MEDICAL CENTRE, YENAGOA, NIGERIA
Authors: Okonko IO , Shaibu N 
Published: March 2023

ABSTRACTCoinfection of hepatitis C (HCV) may compromise antiretroviral therapy (ART) in Nigeria. In this study, we evaluated the seroprevalence of HIV/HCV coinfection in people living with HIV/AIDs (PLWHA) receiving ART and associated factors. Patients were selected from HIV-1-infected patients enrolled in National HAART Cohort at Federal Medical Centre in Yenagoa, Nigeria. Following the manufacturer’s instructions, medical assessments and anti-HCV antibody serology were obtained for analysis with an ELISA kit (Dia. Pro). A total of 4 of 104 PLWHA tested were anti-HCV antibody positive (4.0%). HIV/HCV coinfections were higher in age groups ≥41 years (4.4%), males (7.0%), CD4 counts 350-499 cells/μl (7.1%) and PVL ≥1000 copies/ml (10.0%). CD4 counts and viral load were an indicator for HIV/HCV coinfections. Socio-demographic variables were not associated (p > 0.05) with HIV/HCV coinfection in univariate analysis; older PLWHA were more likely to be HCV-positive. Males were more prone to HIV/HCV coinfection than females. HIV status did seem to influence the predisposition to HCV infection, as an increase in susceptibility was observed with HIV-infected patients in Yenagoa, Nigeria. The high prevalence of HIV/HCV coinfection in PLWHA in Yenagoa receiving ART demands routine screening for viral hepatitis coinfection, intensive prevention of childhood HCV transmission, and modification of the management of HIV infection.
Identification of the putative causal risk factors and biomarkers of stroke using large-scale genome-wide studies
Authors: Islam Tania , García-Marín Luis M , Rentería Miguel E. , Cuellar-Partida Gabriel , Khan Asaduzzaman , Moni Mohammad Ali 
Published: March 2023

AbstractStroke is a complex neurological disorder, and the risk factors and genetic biomarkers associated with stroke development are not completely understood. This study aims to identify putative causal traits and their biomarkers that influence the risk of stroke. Here the latent causal variable (LCV) method has been used to investigate the potential causal genetic relationships between large-scale genome-wide association studies (GWAS) data of 1504 complex traits from UK Biobank and stroke. Generalised Mendelian randomisation (GSMR) method has also been further used to examine causal inference. These analyses suggest 14 causal traits associated with stroke risk (|GCP|> 0.60; FDR < 0.05), including atrial fibrillation, deep venous thrombosis, gamma-glutamyl transferase, and platelet crit. Gene-based analysis has revealed shared genes, providing novel insights into the genetic biomarkers of the causal traits on stroke risk. Functional enrichment analyses of the shared genes have provided biological pathways underlying biological mechanisms to stroke risk, including “oxidative damage”, “platelet activation”, “cell aging”, and others. This study provides causal evidence of cardiovascular, metabolic, and blood clot-related traits increasing stroke risk. The identified shared gene biomarkers provide valuable insights into the shared genetic biomarkers and underlying mechanisms linking causal traits to stroke risk.
RELATIONSHIP BETWEEN THE LEVEL OF SPIRITUALITY AND BLOOD PRESSURE CONTROL AMONG ADULT HYPERTENSIVE PATIENTS IN RURAL SOUTHWESTERN NIGERIA
Authors: Omonijo Adetunji , Olowoyo Paul , Ibrahim Azeez Oyemomi 
Published: March 2023

SummaryBackgroundSpirituality has been strongly associated with good blood pressure control as it forms a strong coping mechanism in hypertensive patients.PurposeThis hospital-based cross-sectional study was done to determine the relationship between spirituality and blood pressure control among adult hypertensive patients in rural Southwestern Nigeria with a view to achieving good blood pressure control.MethodThe selection was done by systematic random sampling technique. Socio-demographic and clinical information were obtained through semi-structured interviewer-administered questionnaires. The level of spirituality was assessed using the Spiritual Perspective Scale. Data were analysed using the Statistical Package for Social Sciences version 20.0. Statistical significance was set at p ≤ 0.05.ResultsThe mean age of the respondents was 61.1±11.1 years. More than half (52.6%) had high level of spirituality and more than two-thirds (67.1%) of respondents had controlled blood pressure. Respondents with high level of spirituality were 4.76 times more likely to have a good blood pressure control {p<0.001, 95%CI (1.05-14.99)}than those with low level of spirituality.ConclusionProper understanding and effective utilization of this relationship will assist health professionals and researchers in the appropriate integration of this concept into patients’ holistic care with the aim of achieving better blood pressure control among hypertensive patients.
Energy-loss index does not improve risk prediction in aortic stenosis compared to conventional aortic valve area assessment
Authors: Lindow Thomas , Playford David , Strange Geoff , Kozor Rebecca , Ugander Martin 
Published: March 2023

BackgroundEvidence of improved risk assessment in aortic stenosis (AS) by using energy-loss index (ELI) instead of aortic valve area indexed to body surface area (AVAi) is scarce, and positive results have been driven by aortic valve replacement. We aimed to evaluate the prognostic performance of ELI and AVAi in a head-to-head comparison using large-scale, real-world data.MethodsIn the multi-center, mortality-data linked National Echocardiography Database of Australia (NEDA), patients with AS and requisite ascending aortic area measurements were identified. The prognostic value of AVAi and ELI, respectively, was analyzed using Cox regression and the C statistic.ResultsIn patients with mild AS (n=3,179), moderate AS (n=4,194), and severe AS (n=3,120), there were 4,229 deaths of which 2,359 were reported as cardiovascular deaths (median [interquartile range] follow-up 2.5 [1.1–4.5] years]. Decreasing AVAi was associated with increased cardiovascular mortality (hazard ratio [95% confidence interval] 1.18 [1.16– 1.20] per 0.1 cm2/m2downward increment]. Prognostic performance for 5-year mortality did not improve by using ELI instead of AVAi (identical C statistics 0.626 [0.612–0.640]), and the relative performance did not change when analyzing 1-year cardiovascular mortality, or all-cause mortality.ConclusionELI was not associated with improved prognostic performance compared to AVAi in echocardiographic assessment of AS using large-scale, real-world clinical data. AVAi remains a relevant measure for risk prediction in AS, providing information on incremental risk with decreasing area.
Anti-citrullinated protein antibodies with diverse specificities ameliorate collagen antibody-induced arthritis in a time-dependent manner
Authors: Gomez Alejandro M. , Brewer R. Camille , Moon Jae-Seung , Acharya Suman , Kongpachith Sarah , Wang Qian , Jahanbani Shaghayegh , Wong Heidi H. , Lanz Tobias V. , Love Zelda Z. , Min-Oo Gundula , Niedziela-Majka Anita , Robinson William H. 
Published: March 2023

ABSTRACTAnti-citrullinated protein antibodies (ACPAs) are a hallmark of rheumatoid arthritis (RA) and have long been considered to contribute to pathogenesis. In this study, we sequenced the plasmablast antibody repertoires of RA patients and functionally characterized their encoded ACPAs. Recombinantly expressed monoclonal ACPAs bound citrullinated autoantigens, as well as autocitrullinated peptidylarginine deiminase 4 (PAD4). Using the collagen antibody induced arthritis (CAIA) mouse model, we demonstrated that the recombinant ACPAs significantly reduced paw thickness and arthritis severity as compared to isotype-matched control antibodies. Treatment with recombinant ACPAs also significantly reduced bone erosions, synovitis, and cartilage damage in histologic analysis of paws. This amelioration was observed for all the ACPAs tested and was independent of citrullinated antigen specificities. Furthermore, disease amelioration was more prominent when ACPAs were injected at earlier stages of CAIA than at later phases of the model, implying that ACPAs’ anti-inflammatory effects were more preventative than therapeutic. This study highlights a potential protective role for ACPAs in RA.
Mitochondrial phylogeography of grassland caterpillars (Lepidoptera: Lymantriinae:Gynaephora) endemic to the Qinghai-Tibetan Plateau
Authors: Yuan Ming-Long , Bao Ming-Hui , Zhang Qi-Lin , Guo Zhong-Long , Li Min , Wang Juan 
Published: March 2023

AbstractGrassland caterpillars (Lepidoptera: Lymantriinae:Gynaephora) are the most damaging pests to alpine meadows in the Qinghai-Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eightGynaephoraspecies in the QTP to investigate phylogeographic patterns and speciation based on two mitochondrial genes (cox1andnad5). A total of 40 haplotypes were detected in the 39 populations, with >70% of haplotypes specific to single population. The monophyletic QTPGynaephoramigrated from non-QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTPGynaephoraspecies described by morphological characteristics, two species (G. alpherakiiandG. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six species formed two monophyletic clades: Clade A (G. qinghaiensis,G. jiuzhiensis, andG. qumalaiensis) and Clade D (G. aureate,G. rouergensis, andG. minora). These results suggested that the number of the QTPGynaephoraspecies may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation were driven by intensive uplifts of the QTP and associated climate fluctuations during the Pleistocene, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTPGynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTPGynaephora,without population expansion, which may explain the high-altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTPGynaephoraand improves our understanding of the diversity and speciation of QTP insects.
Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level
Authors: Liao Ting-Wei , Huang Lin , Wilson Timothy J. , Ganser Laura R. , Lilley David M. J. , Ha Taekjip 
Published: March 2023

AbstractRiboswitches are found in the 5’-UTR of many bacterial mRNAs. They function as cisacting regulatory elements that control downstream gene expression through ligand-induced conformational changes. Here, we used single-molecule FRET to map the conformational landscape of the SAM/SAH riboswitch and probe how co-transcriptional ligand-induced conformational changes of this translational switch alter ribosome accessibility. The folding of the riboswitch is highly heterogenous, indicating a complex and rugged conformational landscape that enables sampling of the ligand-bound conformation even in the absence of the ligand. Upon ligand binding, the landscape shifts towards the ligand-bound conformation. Mutations at key stabilizing structures alter the ligand-free folding behavior and decrease ligand responsiveness. We also explored translational regulation through folding kinetics by utilizing short oligonucleotides to probe the accessibility of the Shine-Dalgarno sequence within the riboswitch. Additionally, we employed a helicase-based vectorial folding assay to simulate co-transcriptional folding. We find that a competition between ligand binding and ribosome binding is fined tuned via the kinetics of folding. During transcription, the riboswitch takes minutes before reaching equilibrated conformations, and such slow equilibration decreases the effective ligand affinity. Overall, our data demonstrate the significance of conformational polymorphism in RNA function, emphasizing the utilization of complex folding landscapes for regulating ribosome accessibility through ligand induction. Furthermore, we provide direct evidence on how folding kinetics modulate this regulation process.
Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot
Authors: Buckley Sean James , Brauer Chris J. , Unmack Peter J. , Hammer Michael P. , Adams Mark , Beatty Stephen J. , Morgan David L. , Beheregaray Luciano B. 
Published: March 2023

ABSTRACTAnthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic in the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides
Authors: Prunier Grégoire , Cherkaoui Mehdi , Lysiak Albane , Langella Olivier , Blein-Nicolas Mélisande , Lollier Virginie , Benoist Emile , Jean Géraldine , Fertin Guillaume , Rogniaux Hélène , Tessier Dominique 
Published: March 2023

ABSTRACTBackgroundIn proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications is still challenging, currently limited by the number of potential modifications considered in a single analysis and the need to know them in advance. Further developments must be done in the field to help the scientific community to discover new post-translational modifications that play an essential role in disease and to understand how chemical modifications carried by food proteins could impact our health.ResultsTo make progress on this issue, we implemented SpecGlobX (SpecGlob eXTended to eXperimental spectra), a standalone Java application that quickly determines the best spectral alignments of a (possibly very large) list of Peptide-to-Spectrum Matches (PSMs) provided by any open modification search method, or generated by the user. As input, SpecGlobX reads a file containing spectra in MGF or mzML format and a semicolon-delimited spreadsheet describing the PSMs. As output, SpecGlobX returns the best alignment for each PSM, splitting the mass difference between the spectrum and the peptide into one or more shifts while considering the possibility of non-aligned masses (a phenomenon resulting from many situations including neutral losses).SpecGlobX is fast, able to align one million PSMs in about 1.5 minutes on a standard desktop. Firstly, we remind the foundations of the algorithm and detail how we adapted SpecGlob (the method we previously developed following the same aim, but limited to the interpretation of perfect simulated spectra) to the interpretation of imperfect experimental spectra. Then, we highlight the interest of SpecGlobX as a complementary tool downstream to three open modification search methods on a large simulated spectra dataset. Finally, we show on a smaller dataset that SpecGlobX performs equally well on experimental and simulated spectra.ConclusionsSpecGlobX is helpful as a decision support tool, providing keys to interpret peptides carrying complex modifications still poorly considered by current open modification search software. Better alignment of PSMs enhances confidence in the identification of spectra provided by open modification search methods and should improve the interpretation rate of spectra.
Effectiveness of heat tolerance rice cultivars in preserving grain appearance quality under high temperatures - A meta-analysis
Authors: Wakatsuki Hitomi , Takimoto Takahiro , Ishigooka Yasushi , Nishimori Motoki , Sakata Mototaka , Saida Naoya , Akagi Kosuke , Makowski David , Hasegawa Toshihiro 
Published: March 2023

AbstractBackgroundClimate change, particularly rising temperatures, negatively affects rice grain quality, increasing chalky grain percentage (CG) and hampering rice grade and price. Heat-tolerant cultivars have been bred and released since the 2000s, but the effectiveness of heat tolerance in reducing the occurrence of CG has yet to be quantified.ObjectivesThis study aimed to measure the effectiveness of breeding for better heat tolerance in reducing the negative impact of high temperatures on rice quality.MethodsThrough a systematic literature search, we developed a dataset including 1297 field observations covering 48 cultivars from five different heat tolerant ranks (HTRs) at 44 sites across Japan. A linear mixed-effect model (LME) and a random forest model (RF) were fitted to the data to analyze the effect of HTR and climatic factors such as the cumulative mean air temperature above 26 °C (TaHD), mean solar radiation, and mean relative humidity for 20 days after heading on CG.ResultsThe LME model explained 63 % of the variation with a 14% RMSE. The RF partial dependence plot revealed that the logit-transformed CG response to climate factors was linear, supporting the assumption of LME. The statistical analysis showed that CG increased as a function of TaHD (P < 0.001), with significant differences among HTRs (P < 0.001). The strongest effect of TaHD was obtained for the lowest HTR and was found to decrease with increasing HTR. CG also increased with higher relative humidity (P < 0.001) and solar radiation (P < 0.01). Based on our modeling, we estimated that as TaHD increased from 20 to 80 °Cd (equivalent to a mean temperature increase from 27 °C to 30 °C), CG increased by 66 % points (difference in CG) for cultivars with the lowest HTR, 45 % points for cultivars with an intermediate HTR, and 19 % points for cultivars with the highest HTR. Raising HTR by just one step (from intermediate to moderately tolerant) is projected to increase the proportion of first-grade rice at a grain-filling temperature of 27 °C, but tolerance levels need to be improved further in case of stronger warming.ConclusionsThe effect of high temperatures on CG was highly dependent on the cultivar’s HTR. Improvements in HTR effectively reduce the negative impacts of high temperatures on rice grain quality.SignificanceHeat-tolerant cultivars are projected to suppress the prevalence of CG more than threefold compared with heat-sensitive cultivars when grain-filling temperature increases from 27 to 30 °C.
Species-specific stomatal ABA responses in juvenile ferns grown from spores
Authors: Wuyun Tana , Niinemets Ülo , Hõrak Hanna 
Published: March 2023

AbstractAdjustable stomatal pores in leaves control the balance between CO2entry for photosynthesis and water loss via transpiration. The drought and low humidity-induced phytohormone abscisic acid (ABA) is the major regulator of active stomatal closure responses in angiosperms. Whether the ABA signalling pathway for stomatal closure functions similarly in older land plant groups, such as lycophytes and ferns, is still unclear: some studies find no stomatal ABA response in ferns, others find that ABA response is present or triggered by specific environmental conditions. Here we analysed steady-state gas-exchange, stomatal density and stomatal response to exogenously applied ABA in nine fern species grown from spores under controlled growth conditions. We find that ABA responses in ferns are species-specific: stomata in four out of nine species closed in response to ABA. The ABA-sensitive species mostly had slow responses of low magnitude, suggesting reduced ABA-sensitivity of ABA signalling pathway in ferns. Species with larger stomatal conductance tended to close stomata in response to ABA, whereas a relatively strong response of ~35% was also found inCyrtomium falcatum, a fern with low stomatal conductance. Our results show that ferns constitute a diverse group with varying degree of stomatal ABA-sensitivity. Further characterisation of ABA signalling pathway components in diverse fern species is needed to understand the genetic basis for the variable ABA-sensitivity in ferns.
General encoding of canonicalk-mers
Authors: Wittler Roland 
Published: March 2023

AbstractTo index or compare sequences efficiently, oftenk-mers, i.e., substrings of fixed lengthk, are used. For efficient indexing or storage,k-mers are often encoded as integers, e.g., applying some bijective mapping between all possibleσkk-mers and the interval [0,σk−1], whereσis the alphabet size.In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous,canonical k-mers are considered, i.e., the lexicographically smaller of a givenk-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonicalk-mers are not evenly distributed within the interval [0,σk−1].We present a minimal encoding of canonicalk-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0,σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.