bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of serum anti‐Müllerian hormone concentrations following treatment with vitamin D in Holstein Friesian heifers
Authors: Koca Davut , Nak Yavuz , Sendag Sait , Nak Deniz , Avcılar Talha , Sahin Mustafa Eren , Arslan Talha , Ozyigit Musa Ozgur , Wehrend Axel 
Published: October 2023

AbstractAnti‐Müllerian hormone (AMH) levels in the blood of dairy cattle are associated with the count of antral follicles (AFC), ovarian function. Numerous studies, particularly in human medicine, have shown that vitamin D3 (Vit D3) has a positive effect on AMH levels. To our knowledge, the effects of Vit D3 on serum AMH levels in heifers have not been investigated. The goal of the current study was to evaluate the concentrations of serum AMH in dairy heifers following Vit D3 treatment. The study included 20 healthy non‐pregnant Holstein Friesian heifers. These animals came to estrus at least once. All heifers received a single intramuscular dosage of 5 million IU Vit D3 (Cholecalciferol). Blood samples were collected from the coccygeal veins of all animals before and after Vit D3 injection (days 7, 14, and 28) for the measurement of AMH and 25(OH)D concentrations. In our analysis, we observed that after exogenous Vit D3 administration, circular 25(OH)D increased constantly (up to day 28 after Vit D3 injection) in all animals. On day 28, AMH concentrations saw a 10% increase in comparison with those measured the day before the Vit D3 injection. However, a comparison of AMH concentrations measured across days did not reveal statistically significant differences between Day 0, 7, 14, and 28 levels (p = .10). Furthermore, no statistical correlation was observed between the pairs (age‐AMH) and (weight‐AMH). Considering all times, no correlation was found between 25(OH)D and blood AMH levels. These findings demonstrated that exogenous Vit D3 did not affect serum AMH in Holstein Friesian heifers.
Social security pension and the effect on household saving
Authors: Halvorsen Elin , Jia Zhiyang , Kruse Herman , Vigtel Trond C. 
Published: October 2023

AbstractIn this paper, we examine the substitution between pension wealth and household saving. To identify the effect of reductions in social security pension wealth on household saving, we utilize variations in changes in social security pension wealth induced by Norway's 2011 reform across different cohorts, time periods, and sectors. Our study focuses on the saving behaviors of individuals between the ages of 57 and 61, and we find that the annual saving rate increased by around 1.4 percentage points after the reform. When considering the overall life‐cycle changes in household saving, this corresponds to a crowd‐out effect of about 50 percent of the total loss in pension wealth.
Uncertainty Analysis of Friction and Wear-Rate of Cylinder Liner–Piston Ring Tribo Pair Under Boundary Lubrication Conditions
Authors: Baby Ajith Kurian , P. K. Rajendrakumar , Lawrence K. Deepak 
Published: October 2023

Abstract
Uncertainty analyses can improve the reliability and validity of the assessment of friction and wear-rate of tribosystems. This work analyses the various sources of uncertainty in the estimation of friction and wear-rate of liner-ring pairs using a linear reciprocating tribometer (LRT) as per the analytical method suggested by Guide to the Expression of Uncertainty in Measurement (GUM) and simulation approach using Monte Carlo simulation (MCS) method. The uncertainty analysis was conducted by performing sliding wear experiments using a hypereutectic Al–Si cylinder liner specimen against the chrome-coated piston ring as the counter specimen. The experiments were performed to mimic the engine’s condition under a boundary layer lubrication regime. The type A and type B uncertainty components of the tribosystem, such as uncertainty involved in the measurement of mass, linear dimensions of the specimen, radius of the specimen, normal force, stroke length, and frictional force, were evaluated to study their influence on the assessment of the friction and wear-rate. The probability density function of all these uncertainty sources was simulated using the MCS approach to compute the 95% coverage interval for friction and wear-rate directly. The variation in absolute value between the coverage interval limits computed by the GUM framework and predicted by the Monte Carlo method for wear-rate was 11.83%, and for friction coefficient, it was 12.005%.
DegU-mediated suppression of carbohydrate uptake in
Listeria monocytogenes
increases adaptation to oxidative stress
Authors: Chen Mianmian , Ren Gengjia , Zhang Xian , Yang Lifeng , Ding Qiang , Sun Jing , Xia Jing , Xu Jiali , Jiang Lingli , Fang Weihuan , Cheng Changyong , Song Houhui 
Published: October 2023

ABSTRACT

The foodborne bacterial pathogen
Listeria monocytogenes
exhibits remarkable survival capabilities under challenging conditions, severely threatening food safety and human health. The orphan regulator DegU is a pleiotropic regulator required for bacterial environmental adaptation. However, the specific mechanism of how DegU participates in oxidative stress tolerance remains unknown in
L. monocytogenes
. In this study, we demonstrate that DegU suppresses carbohydrate uptake under stress conditions by altering global transcriptional profiles, particularly by modulating the transcription of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS)-related genes, such as
ptsH
,
ptsI
, and
hprK
. Specifically, in the absence of
degU
, the transcripts of
ptsI
are significantly upregulated and those of
hprK
are significantly downregulated in response to copper ion-induced stress. Overexpression of
ptsI
significantly increases bacterial growth
in vitro
, while overexpression of
hprK
leads to a decrease in growth. We further demonstrate that DegU directly senses oxidative stress, downregulates
ptsI
transcription, and upregulates
hprK
transcription. Additionally, through an electrophoretic mobility shift assay, we demonstrate that DegU directly regulates the transcription of
ptsI
and
hprK
by binding to specific regions within their respective promoter sequences. Notably, the putative pivotal DegU binding sequence for
ptsI
is located from 38 to 68 base pairs upstream of the
ptsH
transcription start site (TSS), whereas for
hprK
, it is mapped from 36 to 124 base pairs upstream of the
hprK
TSS. In summary, we elucidate that DegU plays a significant role in suppressing carbohydrate uptake in response to oxidative stress through the direct regulation of
ptsI
and
hprK
.

Importance

Understanding the adaptive mechanisms employed by
Listeria monocytogenes
in harsh environments is of great significance. This study focuses on investigating the role of DegU in response to oxidative stress by examining global transcriptional profiles. The results highlight the noteworthy involvement of DegU in this stress response. Specifically, DegU acts as a direct sensor of oxidative stress, leading to the modulation of gene transcription. It downregulates
ptsI
transcription while it upregulates
hprK
transcription through direct binding to their promoters. Consequently, these regulatory actions impede bacterial growth, providing a defense mechanism against stress-induced damage. These findings gained from this study may have broader implications, serving as a reference for studying adaptive mechanisms in other pathogenic bacteria and aiding in the development of targeted strategies to control
L. monocytogenes
and ensure food safety.
Bacterial bioconvection confers context-dependent growth benefits and is robust under varying metabolic and genetic conditions
Authors: Shoup Daniel , Ursell Tristan 
Published: October 2023

ABSTRACT

Microbes often respond to environmental cues by adopting collective behaviors—like biofilms or swarming—that benefit the population. During “bioconvection,” microbes gather in dense groups and plume downward through fluid environments, driving flow and mixing on the scale of millions of cells. Though bioconvection was observed a century ago, the effects of differing physical and chemical inputs and its potential selective advantages for different species of microbes remain largely unexplored. In
Bacillus subtilis
, vertical oxygen gradients that originate from air-liquid interfaces create cell-density inversions that drive bioconvection. Here, we develop
Escherichia coli
as a complementary model for the study of bioconvection. In the context of a still fluid, we found that motile and chemotactic genotypes of both
E. coli
and
B. subtilis
bioconvect and show increased growth compared to immotile or non-chemotactic genotypes, whereas in a well-mixed fluid, there is no growth advantage to motility or chemotaxis. We found that fluid depth, cell concentration, and carbon availability affect the emergence and timing of bioconvective patterns. Also, whereas
B. subtilis
requires oxygen gradients to bioconvect,
E. coli
deficient in aerotaxis (Δ
aer
) or energy-taxis (Δ
tsr
) still bioconvects, as do cultures that lack an air-liquid interface. Thus, in two distantly related microbes, bioconvection may confer context-dependent growth benefits, and
E. coli
bioconvection is robustly elicited by multiple types of chemotaxis. These results greatly expand the set of physical and metabolic conditions in which this striking collective behavior can be expected and demonstrate its potential to be a generic force for behavioral selection across ecological contexts.

IMPORTANCE

Individual microorganisms frequently move in response to gradients in their fluid environment, with corresponding metabolic benefits. At a population level, such movements can create density variations in a fluid that couple to gravity and drive large-scale convection and mixing called bioconvection. In this work, we provide evidence that this collective behavior confers a selective benefit on two distantly related species of bacteria. We develop new methods for quantifying this behavior and show that bioconvection in
Escherichia coli
is surprisingly robust to changes in cell concentration, fluid depth, interface conditions, metabolic sensing, and carbon availability. These results greatly expand the set of conditions known to elicit this collective behavior and indicate its potential to be a selective pressure across ecological contexts.
PSGL-1 is an evolutionarily conserved antiviral restriction factor
Authors: Jiang Chao , Mei Miao , Liu Ying , Hou Min , Jiao Jun , Tan Ya , Tan Xu 
Published: October 2023

ABSTRACT

The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to protect the hosts from morbidity, mortality, and even extinction associated with viral infections. There are a number of restriction factors identified so far to counteract HIV infection of the humans. PSGL-1 is a recently characterized human restriction factor that acts both early and late in the viral life cycle, the latter of which is antagonized by the HIV-1 Vpu protein. Here we show
in vitro
and in a knockout mouse model that PSGL-1’s antiviral function is conserved in mice for combating the murine leukemia virus (MLV). In counter-strike, the glycogag or glycoMA proteins encoded by MLV can interact with mouse PSGL-1, which leads to Cul3-KLHL20 E3 ligase-dependent ubiquitination and degradation of PSGL-1. The amino acids involved in this interaction demonstrate the evidence of positive selection, manifesting the evolution pressure from the antagonism between PSGL-1 and glycogag/glycoMA. Our data support that PSGL-1 is an evolutionarily conserved antiviral restriction factor.

Importance
Studying the co-evolution between viruses and humans is important for understanding why we are what we are now as well as for developing future antiviral drugs. Here we pinned down an evolutionary arms race between retroviruses and mammalian hosts at the molecular level by identifying the antagonism between a host antiviral restriction factor PSGL-1 and viral accessory proteins. We show that this antagonism is conserved from mouse to human and from mouse retrovirus to HIV. Further studying this antagonism might provide opportunities for developing new antiviral therapies.
Rapid evolution of pre-zygotic reproductive barriers in allopatric populations
Authors: Mahilkar Anjali , Nagendra Prachitha , Venkataraman Pavithra , Deshmukh Saniya , Saini Supreet 
Published: October 2023

ABSTRACT
Adaptive divergence leading to speciation is the major evolutionary process generating diversity in life forms. The most commonly observed form of speciation is allopatric speciation which requires that gene flow be prevented between populations by physical or temporal barriers, as they adapt to their respective environments. Eventually, these adaptive responses lead to accumulation of mutations in different lines. The increased genetic distance between the lines is known to lead to the populations becoming reproductively isolated. A widely accepted theory is that speciation simply occurs as a by-product of adaptive response of the populations. Several examples of allopatric speciation from ecology and laboratory exist. However, we know little about the nature (pre- or post-zygotic) of barriers that arise first in this process. Understanding the first barriers that arise between populations is key to understanding how the process of speciation initiates. In recent years, fungi have been used as model organisms to answer questions related to the evolution of reproductive isolation. Here, we show rapid evolution of pre-zygotic barriers between allopatric yeast populations. We further demonstrate that these pre-zygotic barriers arise due to altered mating kinetics of the evolved population. Moreover, our non-adaptive evolution experiments with yeast under limited selection pressure also show rapid emergence of reproductive isolation. Overall, our results show that evolution of pre-zygotic reproductive barriers can occur as a result of natural selection or drift.

IMPORTANCE

A population diversifies into two or more species—such a process is known as speciation. In sexually reproducing microorganisms, which barriers arise first—pre-mating or post-mating? In this work, we quantify the relative strengths of these barriers and demonstrate that pre-mating barriers arise first in allopatrically evolving populations of yeast,
Saccharomyces cerevisiae
. These defects arise because of the altered kinetics of mating of the participating groups. Thus, our work provides an understanding of how adaptive changes can lead to diversification among microbial populations.
Genomic analysis of almost 8,000
Salmonella
genomes reveals drivers and landscape of antimicrobial resistance in China
Authors: Wang Yanan , Xu Xuebin , Zhu Baoli , Lyu Na , Liu Yue , Ma Sufang , Jia Shulei , Wan Bo , Du Yongkun , Zhang Gaiping , Gao George F. 
Published: October 2023

ABSTRACT

Foodborne
Salmonella
infection remains a major public health concern worldwide. With rising antimicrobial resistance, genomic surveillance is key to tracking outbreaks and monitoring transmission, but there is no comprehensive national surveillance scheme for
Salmonella
involving humans, food, animals, and the environment in China. Moreover, the association between antimicrobial resistance and climate, social, and economic factors has rarely been investigated. Here, we use 1,962
Salmonella
isolates collected from 22 Chinese provinces and add 6,035 publicly available genomes to build a Chinese local
Salmonella
genome database version 2 (CLSGDB v2) representing 30 Chinese provinces, covering 1905–2022. Using the CLSGDB v2, we mapped the landscape and spatiotemporal dynamics of antimicrobial resistance markers, virulome, and mobilome in
Salmonella
. We identified 317
mcr
positive and 745 azithromycin resistance genes positive
Salmonella
isolates out of 7,997 isolates. We further uncovered the geographic distribution veil of
mcr-1
,
fosA7
,
fosA3
,
mph(A)
, and
bla
CTX-M-55
genes in China, all of them resistant to the critically important antimicrobials including colistin, fosfomycin, azithromycin, and the third-generation cephalosporins. Interestingly, economic, climatic, and social factors can drive the rise of antimicrobial resistance was observed. Finally, we release the CLSGDB v2 as an open-access database and thus can assist surveillance studies tracking 164
Salmonella enterica
serovars and 295 sequence types across the globe. The CLSGDB v2 is freely available at
https://nmdc.cn/clsgdbv2
.

IMPORTANCE

We established the largest Salmonella genome database from China and presented the landscape and spatiotemporal dynamics of antimicrobial resistance genes. We also found that economic, climatic, and social factors can drive the rise of antimicrobial resistance. The Chinese local Salmonella genome database version 2 was released as an open-access database (
https://nmdc.cn/clsgdbv2
) and thus can assist surveillance studies across the globe. This database will help inform interventions for AMR, food safety, and public health.
Factors associated with the increased incidence of necrotising enterocolitis in extremely preterm infants in Sweden between two population-based national cohorts (2004–2007 vs 2014–2016)
Authors: Challis Pontus , Källén Karin , Björklund Lars , Elfvin Anders , Farooqi Aijaz , Håkansson Stellan , Ley David , Norman Mikael , Normann Erik , Serenius Fredrik , Sävman Karin , Hellström-Westas Lena , Um-Bergström Petra , Ådén Ulrika , Abrahamsson Thomas , Domellöf Magnus 
Published: October 2023

ObjectiveTo investigate potential risk factors behind the increased incidence of necrotising enterocolitis (NEC) in Swedish extremely preterm infants.DesignRegistry data from two population-based national cohorts were studied. NEC diagnoses (Bell stage ≥II) were validated against hospital records.PatientsAll liveborn infants <27 weeks of gestation 2004–2007 (n=704) and 2014–2016 (n=895) in Sweden.Main outcome measuresNEC incidence.ResultsThe validation process resulted in a 28% reduction of NEC cases but still confirmed a higher NEC incidence in the later epoch compared with the earlier (73/895 (8.2%) vs 27/704 (3.8%), p=0.001), while the composite of NEC or death was lower (244/895 (27.3%) vs 229/704 (32.5%), p=0.022). In a multivariable Cox regression model, censored for mortality, there was no significant difference in early NEC (0–7 days of life) between epochs (HR=0.9 (95% CI 0.5 to 1.9), p=0.9), but being born in the later epoch remained an independent risk factor for late NEC (>7 days) (HR=2.7 (95% CI 1.5 to 5.0), p=0.001). In propensity score analysis, a significant epoch difference in NEC incidence (12% vs 2.8%, p<0.001) was observed only in the tertile of infants at highest risk of NEC, where the 28-day mortality was lower in the later epoch (35% vs 50%, p=0.001). More NEC cases were diagnosed with intramural gas in the later epoch (33/73 (45.2%) vs 6/26 (23.1%), p=0.047).ConclusionsThe increase in NEC incidence between epochs was limited to cases occurring after 7 days of life and was partly explained by increased survival in the most extremely preterm infants. Misclassification of NEC is common.
HLA-DPA1*02:01~B1*01:01is a risk haplotype for primary sclerosing cholangitis mediating activation of NKp44+ NK cells
Authors: Zecher Britta F , Ellinghaus David , Schloer Sebastian , Niehrs Annika , Padoan Benedetta , Baumdick Martin E , Yuki Yuko , Martin Maureen P , Glow Dawid , Schröder-Schwarz Jennifer , Niersch Jennifer , Brias Sébastien , Müller Luisa M , Habermann Robin , Kretschmer Paul , Früh Tristan , Dänekas Janis , Wehmeyer Malte H , Poch Tobias , Sebode Marcial ,   International PSC Study Group (IPSCSG), Ellinghaus Eva , Degenhardt Frauke , Körner Christian , Hoelzemer Angelique , Fehse Boris , Oldhafer Karl J , Schumacher Udo , Sauter Guido , Carrington Mary , Franke Andre , Bunders Madeleine J , Schramm Christoph , Altfeld Marcus 
Published: October 2023

ObjectivePrimary sclerosing cholangitis (PSC) is characterised by bile duct strictures and progressive liver disease, eventually requiring liver transplantation. Although the pathogenesis of PSC remains incompletely understood, strong associations with HLA-class II haplotypes have been described. As specific HLA-DP molecules can bind the activating NK-cell receptor NKp44, we investigated the role of HLA-DP/NKp44-interactions in PSC.DesignLiver tissue, intrahepatic and peripheral blood lymphocytes of individuals with PSC and control individuals were characterised using flow cytometry, immunohistochemical and immunofluorescence analyses. HLA-DPA1 and HLA-DPB1 imputation and association analyses were performed in 3408 individuals with PSC and 34 213 controls. NK cell activation on NKp44/HLA-DP interactions was assessed in vitro using plate-bound HLA-DP molecules and HLA-DPB wildtype versus knock-out human cholangiocyte organoids.ResultsNKp44+NK cells were enriched in livers, and intrahepatic bile ducts of individuals with PSC showed higher expression of HLA-DP. HLA-DP haplotype analysis revealed a highly elevated PSC risk forHLA-DPA1*02:01~B1*01:01(OR 1.99, p=6.7×10−50). Primary NKp44+NK cells exhibited significantly higher degranulation in response to plate-bound HLA-DPA1*02:01-DPB1*01:01 compared with control HLA-DP molecules, which were inhibited by anti-NKp44-blocking. Human cholangiocyte organoids expressing HLA-DPA1*02:01-DPB1*01:01 after IFN-γ-exposure demonstrated significantly increased binding to NKp44-Fc constructs compared with unstimulated controls. Importantly, HLA-DPA1*02:01-DPB1*01:01-expressing organoids increased degranulation of NKp44+NK cells compared with HLA-DPB1-KO organoids.ConclusionOur studies identify a novel PSC risk haplotypeHLA-DP A1*02:01~DPB1*01:01and provide clinical and functional data implicating NKp44+NK cells that recognise HLA-DPA1*02:01-DPB1*01:01 expressed on cholangiocytes in PSC pathogenesis.
How long is Long-COVID? Symptomatic improvement between 12 and 18 months in a prospective cohort study
Authors: Barker-Davies Robert M , O’Sullivan O , Holdsworth D A , Ladlow P , Houston A , Chamley R , Greenhalgh A , Nicol E D , Bennett A N 
Published: October 2023

IntroductionCOVID-19 infection can precede, in a proportion of patients, a prolonged syndrome including fatigue, exercise intolerance, mood and cognitive problems. This study aimed to describe the profile of fatigue-related, exercise-related, mood-related and cognitive-related outcomes in a COVID-19-exposed group compared with controls.Methods113 serving UK Armed Forces participants were followed up at 5, 12 (n=88) and 18 months (n=70) following COVID-19. At 18 months, 56 were in the COVID-19-exposed group with 14 matched controls. Exposed participants included hospitalised (n=25) and community (n=31) managed participants. 43 described at least one of the six most frequent symptoms at 5 months: fatigue, shortness of breath, chest pain, joint pain, exercise intolerance and anosmia. Participants completed a symptom checklist, patient-reported outcome measures (PROMs), the National Institute for Health cognitive battery and a 6-minute walk test (6MWT). PROMs included the Fatigue Assessment Scale (FAS), Generalised Anxiety Disorder-7 (GAD-7), Patient Health Questionnaire-9 (PHQ-9) and Patient Checklist-5 (PCL-5) for post-traumatic stress.ResultsAt 5 and 12 months, exposed participants presented with higher PHQ-9, PCL-5 and FAS scores than controls (ES (effect size) ≥0.25, p≤0.04). By 12 months, GAD-7 was not significantly different to controls (ES <0.13, p=0.292). Remaining PROMs lost significant difference by 18 months (ES ≤0.11, p≥0.28). No significant differences in the cognitive scales were observed at any time point (F=1.96, p=0.167). At 5 and 12 months, exposed participants recorded significantly lower distances on the 6MWT (ηp2≥0.126, p<0.01). 6MWT distance lost significant difference by 18 months (ηp2<0.039, p>0.15).ConclusionsThis prospective cohort-controlled study observed adverse outcomes in depression, post-traumatic stress, fatigue and submaximal exercise performance up to 12 months but improved by 18-month follow-up, in participants exposed to COVID-19 compared with a matched control group.