bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of dairy cow temperament on milk yield: a systematic review and meta-analysis
Authors: Marçal-Pedroza Maria G , Canozzi Maria Eugênia Andrighetto , Campos Mariana M , Sant’Anna Aline C 
Published: April 2023

Abstract
The temperament of dairy cows interferes in milk yield and quality, but there is a lack of consensus throughout the literature. Thus, systematic review (SR) and meta-analysis (MA) methodologies were used to assess the effects of dairy cow temperament on milk yield. Our literature search included four electronic databases (CABI Abstracts, Web of Science, PubMed, and Scopus) and bibliographies of the publications included on MA. As inclusion criteria, we considered publications about the temperament of lactating cows and its effect on daily milk yield and total milk yield (whole lactation). A random effect-MA was carried out separately for daily milk yield and total milk yield related to each class of cows’ temperament, ‘low’ (low reactivity, calm animals), ‘intermediate’ (intermediate reactivity), and ‘high’ (high reactivity, reactive animals). A total of eight publications reporting 75 trials were included in the analyses for daily milk yield, and three publications reporting nine trials for total milk yield. For daily and total milk yield the heterogeneity between publications was high (I2 = 99.9%). Cows of European breeds with intermediate temperament produced less milk daily than the calm (P = 0.020) and reactive ones (P &lt; 0.001). In the case of primiparous cows, those with intermediate temperament produced less milk daily (P &lt; 0.001) than the reactive ones, while for multiparous, the intermediate produced less than calm (P = 0.032) and reactive cows (P &lt; 0.001). Regarding the stage of lactation, cows evaluated throughout lactation with a calm temperament tended (P = 0.081) to produce more milk than the intermediate ones, but less than the reactive ones (P &lt; 0.001). For total milk yield, reactive cows tended to produce more than the calm (P = 0.082) and intermediate (P = 0.001) ones. Among European and primiparous cows, reactive cows produced more than the intermediate (P = 0.001). According to our results, we cannot confirm what we expected, that calmer cows would be the most productive for both daily and total yield.
Genomic evaluation of carcass traits of Korean beef cattle Hanwoo using a single-step marker effect model
Authors: Koo Yangmo , Alkhoder Hatem , Choi Tae-Jeong , Liu Zengting , Reents Reinhard 
Published: April 2023

Abstract
Hanwoo beef cattle are well known for the flavor and tenderness of their meat. Genetic improvement programs have been extremely successful over the last 40 yr. Recently, genomic selection was initiated in Hanwoo to enhance genetic progress. Routine genomic evaluation based on the single-step breeding value model was implemented in 2020 for all economically important traits. In this study, we tested a single-step marker effect model for the genomic evaluation of four carcass traits, namely, carcass weight (CW), eye muscle area, backfat thickness, and marbling score. In total, 8,023,666 animals with carcass records were jointly evaluated, including 29,965 genotyped animals. To assess the prediction stability of the single-step model, carcass data from the last 4 yr were removed in a forward validation study. The estimated genomic breeding values (GEBV) of the validation animals and other animals were compared between the truncated and full evaluations. A parallel conventional best linear unbiased prediction (BLUP) evaluation with either the full or the truncated dataset was also conducted for comparison with the single-step model. The estimates of the marker effect from the truncated evaluation were highly correlated with those from the full evaluation, ranging from 0.88 to 0.92. The regression coefficients of the estimates of the marker effect for the full and truncated evaluations were close to their expected value of 1, indicating unbiased estimates for all carcass traits. Estimates of the marker effect revealed three chromosomal regions (chromosomes 4, 6, and 14) harboring the major genes for CW in Hanwoo. For validation of cows or steers, the single-step model had a much higher R2 value for the linear regression model than the conventional BLUP model. Based on the regression intercept and slope of the validation, the single-step evaluation was neither inflated nor deflated. For genotyped animals, the estimated GEBV from the full and truncated evaluations were more correlated than the estimated breeding values from the two conventional BLUP evaluations. The single-step model provided a more accurate and stable evaluation over time.
Black queen cell virus detected in Canadian mosquitoes
Authors: Baril Cole , LeMoine Christophe M R , Cassone Bryan J 
Published: April 2023

AbstractBlack queen cell virus (BQCV) is a ubiquitous honeybee virus and a significant pathogen to queen bee (Apis mellifera) larvae. However, many aspects of the virus remain poorly understood, including the transmission dynamics. In this study, we used next-generation sequencing to identify BQCV in Aedes vexans (n = 4,000) collected in 2019 and 2020 from Manitoba, Canada. We assembled de novo the nearly complete (&gt;96%) genome sequence of the virus, which is the first available from North America and the first report of BQCV being harbored by mosquitoes. Phylogenetic tree reconstructions indicated that the genome had 95.5% sequence similarity to a BQCV isolate from Sweden. Sequences of a potential vector (Varroa destructor) and a microsporidian associated with BQCV (Nosema apis) were not identified in the mosquito samples, however, we did detect sequences of plant origin. We, therefore, hypothesize that the virus was indirectly acquired by mosquitoes foraging at the same nectar sources as honeybees.
Spontaneous resolution of traumatic bronchial tear after thoracic crush injury
Authors: Schwarze Erik , Chang Donald D , Cleary Corbin J , Rakitin Ilya 
Published: April 2023

AbstractTraumatic bronchial tears are rare life-threatening injuries. Here, we report a 28-year old male who presented after sustaining a crush injury to his thoracic cavity, resulting in a spiral left mainstem bronchial tear secondary to high intraluminal pressure. While preparing for surgery, a preoperative bronchoscopy found that the bronchial tear had re-approximated and effectively sealed the laceration. No operative intervention was performed and the patient subsequently underwent a full recovery. While most bronchial tears undergo surgical intervention, our report describes the successful management of a bronchial tear injury with a non-operative approach and supportive care.
GOLVEN peptides regulate lateral root spacing as part of a negative feedback loop on the establishment of auxin maxima
Authors: Jourquin Joris , Fernandez Ana Ibis , Wang Qing , Xu Ke , Chen Jian , Šimura Jan , Ljung Karin , Vanneste Steffen , Beeckman Tom 
Published: April 2023

Abstract
Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it was unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.
Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover
Authors: Mazzolini Andrea , Mora Thierry , Walczak Aleksandra M. 
Published: April 2023

Chronic infections of the human immunodeficiency virus (HIV) create a very complex coevolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely unknown and could help in disease treatment and vaccine development. Here we study a longitudinal dataset of ten HIV-infected people, where both the B-cell receptors and the virus are deeply sequenced. We focus on simple measures of turnover, which quantify how much the composition of the viral strains and the immune repertoire change between time points. At the single-patient level, the viral–host turnover rates do not show any statistically significant correlation, however, they correlate if one increases the amount of statistics by aggregating the information across patients. We identify an anti-correlation: large changes in the viral pool composition come with small changes in the B-cell receptor repertoire. This result seems to contradict the naïve expectation that when the virus mutates quickly, the immune repertoire needs to change to keep up. However, a simple model of antagonistically evolving populations can explain this signal. If it is sampled at intervals comparable with the sweep time, one population has had time to sweep while the second cannot start a counter-sweep, leading to the observed anti-correlation.
This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
A high-throughput multiplex array for antigen-specific serology with automated analysis
Authors: Rosenberg A.F , Killian J.T. , Green T.J. , Akther J. , Hossain M.E. , Shang Q. , Qiu S. , Guang Y. , Randall T.D. , Lund F.E. , King R.G. 
Published: April 2023

AbstractHigh-throughput customizable CBA automated script-based analysisThe utility of high-throughput systems to evaluate antigen-specific antibody (Ab) has been highlighted by the SARS-CoV-2 pandemic. Pathogen-specific Ab levels are often used to assess protection following vaccination and, in the case of novel pathogens, an indication of prior exposure. Several platforms exist to visualize antigen-specific Ab, however most are not quantitative and are difficult to scale for population level studies. Additionally, the sensitivity across platforms differs making direct comparisons between studies difficult. Cytometric bead arrays (CBA) are an attractive platform for antigen-specific Ab measurements as they can be used to assess Ab reactivity against several antigens and of several isotypes to be performed simultaneously. Additionally, CBAs exhibit high sensitivity and can be designed to provide quantitative measurements. Using commercially available particles, a biotin-Streptavidin bead loading strategy, and the inclusion of indirect standards, we describe a flexible system that can be modified to include a variety of antigens. Here we describe two arrays, focused on antigens derived from either β-coronaviruses or influenza virus. To support the high-throughput capacity of this system, we developed a suit of automated software tools, the CBA Toolbox, to process raw data into antigen-reactive IgM, IgA, and IgG concentrations. We describe quality control requirements, assay performance, and normalizations to accurately quantitate antigen-specific Ig.
Elevation and topography shape the diversity of mesoscale landscape-level woody plant species found in temperate evergreen forests
Authors: Watanabe Shuntaro , Maesako Yuri , Inada Tomoya 
Published: April 2023

AbstractPlant species richness is influenced by complex interactions between biotic and abiotic factors that operate on different spatial scales. Since spatial scales vary continuously in nature, it is expected that multiple factors simultaneously affect species richness and composition at an intermediate spatial scale (i.e., the mesoscale landscape level). Previous studies have shown that local topography and elevation are important factors for shaping mesoscale landscape-level plant species richness; however, the relative importance of these factors has rarely been examined. Here, we used spatially explicit woody plant survey data to investigate the relative importance of topography, elevation, and disturbance at the mesoscale landscape level. We found that topography and elevation are important drivers of plant species richness and composition at the mesoscale landscape level and affect different components (i.e., the number of species and species composition, respectively). Our study also found that closely-related species coexisted along the elevational gradient, suggesting that niche partitioning among closely-related species is a fundamentally important feature of mesoscale species richness pattern. Furthermore, we found that specialization in a habitat of closely-related species can be established even within a limited environmental gradient. This suggests that biotic interactions among closely-related species may be an important factor driving habitat specialization, and biotic interactions may play an important role in shaping landscape-scale biodiversity patterns.
Physcomitrella SUN2 mediates MTOC association to the nuclear envelope and facilitates chromosome alignment during spindle assembly
Authors: Yoshida Mari W. , Oguri Noiri , Goshima Gohta 
Published: April 2023

AbstractPlant cells lack centrosomes and instead utilise acentrosomal microtubule organising centres (MTOCs) to rapidly increase the number of microtubules at the onset of spindle assembly. Although several proteins required for MTOC formation have been identified, how the MTOC is positioned at the right place is not known. Here, we show that the inner nuclear membrane protein SUN2 is required for MTOC association with the nuclear envelope (NE) during mitotic prophase in the mossPhyscomitrium patens. In actively dividing protonemal cells, microtubules accumulate around the NE during prophase. In particular, regional MTOC is formed at the apical surface of the nucleus. However, microtubule accumulation around the NE was impaired and apical MTOCs were mislocalised insun2knockout (KO) cells. In addition, chromosome distribution in the nucleus was skewed, suggesting that SUN2 mediates the linking of microtubules with chromosomes. Upon nuclear envelope breakdown (NEBD), the mitotic spindle was assembled with mislocalised MTOC, which were a source of microtubules insun2KO plants. However, completion of chromosome alignment in the spindle was delayed; in severe cases, the chromosome was transiently detached from the spindle body. SUN2 tended to localise to the apical surface of the nucleus during prophase in a microtubule-dependent manner. Based on these results, we propose that SUN2 facilitates the attachment of microtubules to chromosomes during spindle assembly by linking them prior to NEBD. Furthermore, this study suggests that trans-NE microtubule-chromosome linking, a well-known function of SUN in animals and yeast, is conserved in plants.
Staphylococcus aureusbiofilm secreted factors cause mucosal damage, mast cell infiltration and goblet cell hyperplasia in a rat rhinosinusitis model
Authors: Houtak Ghais , Nepal Roshan , Bouras George , Shaghayegh Gohar , Bennett Catherine , Finnie John , Fenix Kevin , Psaltis Alkis James , Wormald Peter-John , Vreugde Sarah 
Published: April 2023

AbstractChronic Rhinosinusitis (CRS) is an inflammatory condition of the paranasal sinus mucosa. Despite being a common health issue, the exact cause of CRS is yet to be understood. However, research suggests thatStaphylococcus aureus, particularly in the biofilm form, drives the disease. This study aimed to investigate the impact of long-term exposure to secreted factors ofStaphylococcus aureusbiofilm (SABSF), harvested from clinical isolates of non-CRS carriers and CRS patients, on the nasal mucosa in a rat model.Wistar rats were randomised (n=5/group) to receive daily intranasal instillations of 40 μL (200 μg/μL) SABSF for 28 days or vehicle control withS. aureusisolated from the sinuses of a non-CRS carrier, a type 2 endotype CRS with nasal polyps (CRSwNP) patient, and a non-type 2 endotype CRS without nasal polyps (CRSsNP) patient. The sinonasal samples of the rats were then analysed through histopathology and transcriptome profiling.The results showed that all three intervention groups displayed significant lymphocytic infiltration (p≤0.05). However, only the SABSF collected from the CRSwNP patient caused significant mucosal damage, mast cell infiltration, and goblet cell hyperplasia compared to the control. The transcriptomics results indicated that SABSF significantly enriched multiple inflammatory pathways and showed distinct transcriptional expression differences between the control group and the SABSF collected from CRS patients (p≤0.05). Additionally, the SABSF challenges induced the expression of IgA and IgG but not IgE.In conclusion, thisin vivostudy indicates that long-term exposure to SABSF leads to an inflammatory response in the nasal mucosa with increased severity forS. aureusisolated from a CRSwNP patient. The findings of this study shed light on the role ofS. aureusin the development of CRS and could inform future research and treatment efforts.
Impact of pathogen genetics on clinical phenotypes in a population ofTalaromyces marneffeifrom Vietnam
Authors: Sephton-Clark Poppy , Nguyen Thu , Hoa Ngo Thi , Ashton Philip , van Doorn H. Rogier , Ly Vo Trieu , Le Thuy , Cuomo Christina A. 
Published: April 2023

AbstractTalaromycosis, a severe and invasive fungal infection caused byTalaromyces marneffei, is difficult to treat and impacts those living in endemic regions of southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome wide association study approaches to a cohort of 336T. marneffeiisolates collected from patients who enrolled in the Itraconazole versus Amphotericin B for Talaromycosis (IVAP) trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multi-strain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered duringT. marneffeiinfection, providing an initial view of how pathogen genetics affects disease outcomes.
Regulation of Human PINK1 ubiquitin kinase by Serine167, Serine228 and Cysteine412 phosphorylation
Authors: Waddell Andrew D. , Ojha Hina , Agarwal Shalini , Clarke Christopher J. , Terriente-Felix Ana , Zhou Houjiang , Kakade Poonam , Knebel Axel , Shaw Andrew M. , Gourlay Robert , Varghese Joby , Soares Renata F. , Toth Rachel , Macartney Thomas , Eyers Patrick A. , Morrice Nick , Bayliss Richard , Whitworth Alexander J. , Eyers Claire E. , Muqit Miratul M. K. 
Published: April 2023

AbstractLoss-of-function mutations in the human PINK1 kinase (hPINK1) are causative of early-onset Parkinson’s disease (PD). Activation ofhPINK1 induces phosphorylated ubiquitin to initiate removal of damaged mitochondria by autophagy. Previously we solved the structure of the insect PINK1 orthologue,Tribolium castaneumPINK1, and showed that autophosphorylation of Ser205 was critical for ubiquitin interaction and phosphorylation (Kumar, Tamjar, Waddell et al., 2017). Here we report new findings on the regulation ofhPINK1 by phosphorylation. We reconstituteE. coliexpressedhPINK1 activityin vitroby direct incorporation of phosphoserine at the equivalent site Serine 228 (pSer228), providing direct evidence for a role for Ser228 phosphorylation inhPINK1 activation. Furthermore, using mass spectrometry, we identify six novel Ser/Thr autophosphorylation sites including regulatory Serine167 phosphorylation (pSer167), which in addition to pSer228 is required for ubiquitin recognition and phosphorylation. Strikingly, we also detect phosphorylation of a conserved Cysteine412 (pCys412) residue in thehPINK1 activation segment. Structural modelling suggests that pCys412 inhibits ubiquitin recognition and we demonstrate that mutation of Cys412 to Ala rendershPINK1 more active towards ubiquitin when expressed in human cells. These results outline new insights intohPINK1 activation by pSer167 and pSer228 and a novel inhibitory mechanism mediated by pCys412. These findings will aid in the development of small molecule activators ofhPINK1.
A survey of Rare Disease awareness among healthcare professionals and researchers in India
Authors: Vashishta Laxmikant , Bapat Purna , Bhattacharya Yashodhara , Choudhury Mohua Chakraborty , Chirmule Narendra , D’Costa Susan , Jindani Shilpa , Rao Manohar , Sheth Smritie 
Published: April 2023

AbstractRare diseases (RDs) are diseases that occur infrequently and affect a small fraction of the population. Although these diseases individually affect small number of people, together they affect 400 million people globally at any given time. In India, where resources are scarce, healthcare infrastructure and policy framework are focused on mitigating diseases that affect many people. Further, the level of RD awareness among healthcare professionals, researchers, and general public is considerably low. As a result, many cases of RDs remain unreported, undiagnosed, and untreated. To frame policies regarding RDs, it is crucial to understand the current level of RD awareness among healthcare professional and researchers, as they are key stakeholders in diagnosis, treatment, policy making, and drug development. We conducted an exploratory survey to understand the current level of RD awareness among healthcare professionals and researchers based on identification of an RD, time for diagnosis, treatment options, and relationship with family history and geographic location. We noted that our respondents have considerably low level of RD awareness. They correctly identified the importance of family history but failed to realize the association with geographic location. After presenting the survey findings, we have made recommendation to improve RD awareness in India. Our findings will be helpful to design awareness campaigns and frame relevant policies.