bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sex Differences in Hydration Biomarkers and Test–Retest Reliability Following Passive Dehydration
Authors: Doherty Colin S. , Fortington Lauren V. , Barley Oliver R. 
Published: January 2024

This study investigated (a) differences between males and females for changes in serum, tear, and urine osmolality, hematocrit, and urine specific gravity following acute passive dehydration and (b) assessed the reliability of these biomarkers separately for each sex. Fifteen males (age: 26.3 ± 3.5 years, body mass: 76 ± 7 kg) and 15 females (age: 28.8 ± 6.4 years, body mass: 63 ± 7 kg) completed a sauna protocol twice (5–28 days apart), aiming for 4% body mass loss (BML). Urine, blood, and tear markers were collected pre- and postdehydration, and change scores were calculated. Male BML was significantly greater than that of females in Trial 1 (3.53% ± 0.55% vs. 2.53% ± 0.43%, p < .001) and Trial 2 (3.36% ± 0.66% vs. 2.53% ± 0.44%, p = .01). Despite significant differences in BML, change in hematocrit was the only change marker that displayed a significant difference in Trial 1 (males: 3% ± 1%, females: 2% ± 1%, p = .004) and Trial 2 (males: 3% ± 1%, females: 1% ± 1%, p = .008). Regression analysis showed a significant effect for sex (male) predicting change in hematocrit (β = 0.8, p = .032) and change in serum osmolality (β = −3.3, p = .005) when controlling for BML but not for urinary or tear measures. The intraclass correlation coefficients for females (ICC 2, 1) were highest for change in urine specific gravity (ICC = .62, p = .006) and lowest for change in tear osmolarity (ICC = −.14, p = .689), whereas for males, it was posthematocrit (ICC = .65, p = .003) and post tear osmolarity (ICC = .18, p = .256). Generally, biomarkers showed lower test–retest reliability in males compared with females but, overall, were classified as poor–moderate in both sexes. These findings suggest that the response and reliability of hydration biomarkers are sex specific and highlight the importance of accounting for BML differences.
BadR directly represses the expression of the glycerol utilization operon in the Lyme disease pathogen
Authors: Zhang Jun-Jie , Raghunandanan Sajith , Wang Qian , Priya Raj , Alanazi Fuad , Lou Yongliang , Yang X. Frank 
Published: January 2024

ABSTRACT

Glycerol utilization as a carbohydrate source by
Borreliella burgdorferi
, the Lyme disease spirochete, is critical for its successful colonization and persistence in the tick vector. The expression of the
glpFKD
(
glp
) operon, which encodes proteins for glycerol uptake/utilization, must be tightly regulated during the enzootic cycle of
B. burgdorferi
. Previous studies have established that the second messenger cyclic di-GMP (c-di-GMP) is required for the activation of
glp
expression, while an alternative sigma factor RpoS acts as a negative regulator for
glp
expression. In the present study, we report identification of a
cis
element within the 5´ untranslated region of
glp
that exerts negative regulation of
glp
expression. Further genetic screen of known and predicted DNA-binding proteins encoded in the genome of
B. burgdorferi
uncovered that overexpressing
Borrelia
host adaptation regulator (BadR), a known global regulator, dramatically reduced
glp
expression. Similarly, the
badR
mutant significantly increased
glp
expression. Subsequent electrophoretic mobility shift assay analyses demonstrated that BadR directly binds to this
cis
element, thereby repressing
glp
independent of RpoS-mediated repression. The efficiency of BadR binding was further assessed in the presence of c-di-GMP and various carbohydrates. This finding highlights multi-layered positive and negative regulatory mechanisms employed by
B. burgdorferi
to synchronize
glp
expression throughout its enzootic cycle.

IMPORTANCE

Borreliella burgdorferi
, the Lyme disease pathogen, must modulate its gene expression differentially to adapt successfully to its two disparate hosts. Previous studies have demonstrated that the glycerol uptake and utilization operon,
glpFKD
, plays a crucial role in spirochetal survival within ticks. However, the
glpFKD
expression must be repressed when
B. burgdorferi
transitions to the mammalian host. In this study, we identified a specific
cis
element responsible for the repression of
glpFKD
. We further pinpointed
Borrelia
host adaptation regulator as the direct binding protein to this
cis
element, thereby repressing
glpFKD
expression. This discovery paves the way for a deeper exploration of how zoonotic pathogens sense distinct hosts and switch their carbon source utilization during transmission.
Risk factors for recognized and unrecognized SARS-CoV-2 infection: a seroepidemiologic analysis of the Prospective Urban Rural Epidemiology (PURE) study
Authors: Leong Darryl P. , Loeb Mark , Mony Prem K. , Rangarajan Sumathy , Mushtaha Maha , Miller Matthew S. , Dias Mary , Yegorov Sergey , V Mamatha , Telci Caklili Ozge , Temizhan Ahmet , Szuba Andrzej , Abat Marc Evans M. , Mat-Nasir Nafiza , Diaz Maria Luz , Khansaheb Hamda , Lopez-Jaramillo Patricio , Duong MyLinh , Teo Koon K. , Poirier Paul , Oliveira Gustavo , Avezum Álvaro , Yusuf Salim 
Published: January 2024

ABSTRACT

There are limited data on individual risk factors for SARS-CoV-2 infection (including unrecognized infection). In this seroepidemiologic substudy of an ongoing prospective cohort study of community-dwelling adults, participants were thoroughly characterized pre-pandemic. The SARS-CoV-2 infection was ascertained by serology. Among 8,719 participants from 11 high-, middle-, and low-income countries, 3,009 (35%) were seropositive for SARS-CoV-2. Characteristics independently associated with seropositivity were younger age (odds ratio, OR; 95% confidence interval, CI, per five-year increase: 0.95; 0.91–0.98) and body mass index >25 kg/m
2
(OR, 95% CI: 1.16, 1.01–1.34). Smoking (as compared with never smoking, OR, 95% CI: 0.83, 0.70–0.97) and COVID-19 vaccination (OR, 95% CI: 0.70, 0.60–0.82) were associated with a reduced risk of seropositivity. Among seropositive participants, 83% were unaware of having been infected with SARS-CoV-2. Seropositivity and a lack of awareness of infection were more common in lower-income countries. The COVID-19 vaccination reduces the risk of SARS-CoV-2 infection (including recognized and unrecognized infections). Overweight or obesity is an independent risk factor for SARS-CoV-2 infection. Infection and lack of infection awareness are more common in lower-income countries.

IMPORTANCE
In this large, international study, evidence of SARS-CoV-2 infection was obtained by testing blood specimens from 8,719 community-dwelling adults from 11 countries. The key findings are that (i) the large majority (83%) of community-dwelling adults from several high-, middle-, and low-income countries with blood test evidence of SARS-CoV-2 infection were unaware of this infection—especially in lower-income countries; and (ii) overweight/obesity predisposes to SARS-CoV-2 infection, while COVID-19 vaccination is associated with a reduced risk of SARS-CoV-2 infection. These observations are not attributable to other individual characteristics, highlighting the importance of the COVID-19 vaccination to prevent not only severe infection but possibly any infection. Further research is needed to understand the mechanisms by which overweight/obesity might increase the risk of SARS-CoV-2 infection.
Shewanella
phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family
Authors: Wang Hongmin , Zheng Kaiyang , Wang Min , Ma Keran , Ren Linyi , Guo Ruizhe , Ma Lina , Zhang Hong , Liu Yundan , Xiong Yao , Wu Miaolan , Shao Hongbing , Sung Yeong Yik , Mok Wen Jye , Wong Li Lian , McMinn Andrew , Liang Yantao 
Published: January 2024

ABSTRACT

Shewanella
is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few
Shewanella
phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel
Shewanella
phage, vB_SbaS_Y11, that infects
Shewanella KR11
and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR
AcrVA2
gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to
Pseudomonas
virus H66 and
Pseudomonas
phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named
Ranviridae
.

IMPORTANCE

The Gram-negative
Shewanella
bacterial genus currently includes about 80 species of mostly aquatic
Gammaproteobacteria
, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a
Shewanella
phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR
AcrVA2
gene and belongs to a potential virus family,
Ranviridae
. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of
Shewanella
phage populations.
Klebsiella pneumoniae
DedA family proteins have redundant roles in divalent cation homeostasis and resistance to phagocytosis
Authors: Tiwari Vijay , Sharma Amit , Braga Reygan , Garcia Emily , Appiah Ridhwana , Fleeman Renee , Abuaita Basel H. , Patrauchan Marianna , Doerrler William T. 
Published: January 2024

ABSTRACT

The DedA superfamily is a highly conserved family of membrane proteins. Deletion of
Escherichia coli yqjA
and
yghB
, encoding related DedA family proteins, results in sensitivity to elevated temperature, antibiotics, and alkaline pH. The human pathogen
Klebsiella pneumoniae
possesses genes encoding DedA family proteins with >90% amino acid identity to
E. coli
YqjA and YghB. We hypothesized that the deletion of
K. pneumoniae yqjA
and
yghB
will impact its physiology and may reduce its virulence. The
K. pneumoniae
Δ
yqjA
Δ
yghB
mutant (strain VT101) displayed a growth defect at 42°C and alkaline pH sensitivity, not unlike its
E. coli
counterpart. However, VT101 retained mostly wild-type resistance to antibiotics. We found VT101 was sensitive to the chelating agent EDTA, the anionic detergent SDS, and agents capable of alkalizing the bacterial cytoplasm such as bicarbonate or chloroquine. We could restore growth at alkaline pH and at elevated temperature by addition of 0.5–2 mM Ca
2+
or Mg
2+
to the culture media. VT101 displayed a slower uptake of calcium, which was dependent upon calcium channel activity. VT201, with similar deletions as VT101 but derived from a virulent
K. pneumoniae
strain, was highly susceptible to phagocytosis by alveolar macrophages and displayed a defect in the production of capsule. These findings suggest divalent cation homeostasis and virulence are interlinked by common functions of the DedA family.

IMPORTANCE

Klebsiella pneumoniae
is a dangerous human pathogen. The DedA protein family is found in all bacteria and is a membrane transporter often required for virulence and antibiotic resistance.
K. pneumoniae
possesses homologs of
E. coli
YqjA and YghB, with 60% amino acid identity and redundant functions, which we have previously shown to be required for tolerance to biocides and alkaline pH. A
K. pneumoniae
strain lacking
yqjA
and
yghB
was found to be sensitive to alkaline pH, elevated temperature, and EDTA/SDS and displayed a defect in calcium uptake. Sensitivity to these conditions was reversed by addition of calcium or magnesium to the growth medium. Introduction of Δ
yqjA
and Δ
yghB
mutations into virulent
K. pneumoniae
resulted in the loss of capsule, increased phagocytosis by macrophages, and a partial loss of virulence. These results show that targeting the
Klebsiella
DedA family results in impaired divalent cation transport and, in turn, loss of virulence.
Late Mesozoic subduction-accretion in the southern Qiangtang: Insights from the Sumxi igneous complex of west-central Tibet
Authors: Wang Chao , Ding Lin , Cai Fulong , Zeng Deng , Li Jinxiang , Zhang Liyun , Yue Yahui 
Published: January 2024

Abstract
Knowledge of the evolution of the Bangong-Nujiang Tethyan Ocean is crucial for reconstructing the paleography of the Tethyan Realm, given its significance as a key component of the eastern Tethys. Nonetheless, there has been uncertainty regarding both the timing and the processes involved in the closure of this ocean. This study focused on a 110–106 Ma igneous complex comprising basalts–basaltic andesites, trachyandesites, and granodiorites from the Sumxi area in the western part of the Qiangtang terrane of west-central Tibet. The basalts–basaltic andesites have SiO2 contents of 52.5–58.7 wt% and MgO contents of 2.89–4.63 wt%, and exhibit some arc-like geochemical signatures. However, these rocks also have elevated Nb contents (&gt;10 ppm) and Nb/La ratios (&gt;0.5), as well as enriched Sr-Nd isotopic composition [εNd(t) = −7.40 to −6.00], implying that they are products of a mantle source metasomatized by adakitic melts. The trachyandesites are characterized by intermediate compositions (SiO2 = 63.6–65.2 wt%), high Mg number (40–60), and more enriched εNd(t) values (−8.37 to −7.49). Comparing their geochemical composition to that of mélange rocks, it is postulated that these trachyandesites were formed through the partial melting of a mantle source including mélange matrix rocks within a subduction zone. The granodiorites exhibit adakitic geochemical features (Sr = 830.14–1032.70 ppm, Y = 14.86–15.37 ppm, Sr/Y = 54–68), indicating that they originated from the partial melting of a thickened lower crust in a continental arc setting. Our results, in combination with a synthesis of tectonomagmatism along the Bangong-Nujiang suture zone, provide convincing evidence for subduction of an oceanic plateau and subsequent slab roll-back. The Sumxi igneous complex, with its clear arc affinity, suggests that the Bangong-Nujiang Tethyan Ocean, or at least its western part, remained open until the late Early Cretaceous (ca. 106 Ma).
Hydrologic windows into the crystalline basement and their controls on groundwater flow patterns across the Paradox Basin, western USA
Authors: Person M. , McIntosh J.C. , Kim J.-H. , Noyes C. , Bailey L. , Lingrey S. , Krantz R. , Lucero D. , Reiners P.W. , Ferguson G. 
Published: January 2024

Abstract
Conceptual models of sedimentary basin groundwater flow systems typically assume that the crystalline basement acts as an impermeable boundary and can be neglected. In this study, we use hydrologic models constrained by isotopic and geochemical datasets to argue that the La Sal Mountains, Utah, USA, act as a hydrologic window into the Paradox Basin’s lower aquifer system and underlying crystalline basement. We conducted a sensitivity study in which we varied crystalline basement/laccolith permeability as well as fault zone connectivity along a cross-sectional transect from the La Sal Mountains to Lisbon Valley. When the crystalline basement/laccolith units are set at relatively permeable levels (10–14 m2), simulated tracers that include total dissolved solids, oxygen isotopic composition of pore fluids (δ18O), and groundwater residence times are in closest agreement with field measurements. Model results indicate that pore fluids in the basal aquifer system underlying the Paradox Formation confining unit are a mixture of relatively young meteoric fluids and older Paradox Formation brines. The presence of faults did not significantly modify fluid exchange between the upper and lower aquifer systems. This was due, in part, to underpressuring within the Paradox Formation. Our study concludes that the Paradox Basin represents a regional recharge area for the Colorado Plateau, with groundwater discharge occurring along the Colorado River within the Grand Canyon some 375 km away to the southwest. This is only possible with a permeable crystalline basement. Our findings help explain the genesis of Mississippi Valley-type ore deposits of the US Midcontinent, where the presence of a permeable basement may be useful in addressing issues related to solute mass and energy balance.
Correlating mantle cooling with tectonic transitions on early Earth
Authors: Gunawardana Prasanna M. , Chowdhury Priyadarshi , Morra Gabriele , Cawood Peter A. 
Published: January 2024

Abstract
The dominant tectonic mode operating on early Earth (before ca. 2.5 Ga) remains elusive, with an increasing body of evidence suggesting that non-plate tectonic modes were likely more prevalent at that time. Thus, how plate tectonics evolved after that remains contentious. We performed two-dimensional numerical modeling of mantle convection at temperatures appropriate for the Hadean–Archean eons and show that subduction and rift systems may have spontaneously emerged on Earth from an earlier drip-and-rift–dominated tectonic mode in response to the secular cooling of the mantle. This cooling of the mantle was mediated by repeated events of rifting and dripping that likely occurred over a few hundred million years. As the mantle cooled, its effective viscosity and the thickness and strength of the lithosphere increased, which helped establish rigid plates and initiate plate tectonics on Earth.
Robotic surgery in the management of synchronous esophageal and gastric perforation after endoscopic dilation
Authors: Donado Jimenez Maria Jose , Jimenez Maria Carolina , Cubas Robert 
Published: January 2024

Upper gastrointestinal perforation is a feared complication of diagnostic and therapeutic endoscopy, with an incidence of perforation between 0.3% and 5%. Even though is rare, the mortality rate can be as high as 40%. Currently, there is no consensus on the best therapeutic strategy and it usually depends on patient stability, the extent of perforation, time to diagnosis, surgeon experience and available resourcesWe present a case of a patient who presented to our institution to undergo an ambulatory oesophageal dilation. After dilation, the patient developed two full-thickness gastric perforations and a full-thickness oesophageal perforation without haemodynamic instability. All perforations were diagnosed and treated with a combination of intraoperative endoscopy and robotic surgery with excellent outcomes.We demonstrate that a robotic approach combined with intraoperative diagnostic endoscopy is a safe and feasible treatment option for esophageal and gastric perforations in a stable patient without large extraluminal contamination.
Coaches of youth field sports as delivery agents of injury prevention programmes: how are we training the trainers? A scoping review
Authors: Guilfoyle Lauren , Kenny Ian C , O'Sullivan Kieran , Campbell Mark J , Warrington Giles D , Glynn Liam G , Comyns Tom 
Published: January 2024

ObjectiveTo systematically map the coach education (CE) component of injury prevention programmes (IPPs) for youth field sports by identifying and synthesising the design, content and facilitation strategies used to address competency drivers and behaviour change.DesignScoping review.Data sourcesPubMed, PsycInfo, EMBASE, CINAHL, SportDiscus and Google Scholar electronic databases were searched using keywords related to IPPs and youth field sports.Eligibility criteria for selecting studiesStudies of IPPs in youth field sports, that provided ‘train-the-trainer’ education to coaches as designated delivery agents.Results20 studies from two field sports (soccer/football; n=17, Rugby Union; n=3) fulfilled the eligibility criteria. Eleven CE interventions occurred in the preseason and 18 occurred at one time-point (single day). Five studies cited use of a behavioural change theory or model in the design of their CE, most frequently the Health Action Process Approach model (n=5); and use of behavioural change techniques varied. Twelve of twenty studies (60%) reported some form of ongoing support to coaches following the CE primary intervention concurrent with IPP implementation.ConclusionCE that occurs on 1 day (one time-point) is most popular for preparing coaches as delivery agents of IPPs in youth field sports. While recognising pragmatic barriers, more expansive in-service training, support and feedback may enhance the effective implementation of IPPs.Trial registration numberhttps://doi.org/10.17605/OSF.IO/FMHGD
Genome-wide DNA methylation risk scores for schizophrenia derived from blood and brain tissues further explain the genetic risk in patients stratified by polygenic risk scores for schizophrenia and bipolar disorder
Authors: Ohi Kazutaka , Shimada Mihoko , Soda Midori , Nishizawa Daisuke , Fujikane Daisuke , Takai Kentaro , Kuramitsu Ayumi , Muto Yukimasa , Sugiyama Shunsuke , Hasegawa Junko , Kitaichi Kiyoyuki , Ikeda Kazutaka , Shioiri Toshiki 
Published: January 2024

BackgroundGenetic and environmental factors contribute to the pathogenesis of schizophrenia (SZ) and bipolar disorder (BD). Among genetic risk groups stratified by combinations of Polygenic Risk Score (PRS) deciles for SZ, BD and SZ versus BD, genetic SZ risk groups had high SZ risk and prominent cognitive impairments. Furthermore, epigenetic alterations are implicated in these disorders. However, it was unclear whether DNA Methylation Risk Scores (MRSs) for SZ risk derived from blood and brain tissues were associated with SZ risk, particularly the PRS-stratified genetic SZ risk group.MethodsEpigenome-wide association studies (EWASs) of SZ risk in whole blood were preliminarily conducted between 66 SZ patients and 30 healthy controls (HCs) and among genetic risk groups (individuals with low genetic risk for SZ and BD in HCs (n=30) and in SZ patients (n=11), genetic BD risk in SZ patients (n=25) and genetic SZ risk in SZ patients (n=30)) stratified by combinations of PRSs for SZ, BD and SZ versus BD. Next, differences in MRSs based on independent EWASs of SZ risk in whole blood, postmortem frontal cortex (FC) and superior temporal gyrus (STG) were investigated among our case‒control and PRS-stratified genetic risk status groups.ResultsAmong case‒control and genetic risk status groups, 33 and 351 genome-wide significant differentially methylated positions (DMPs) associated with SZ were identified, respectively, many of which were hypermethylated. Compared with the low genetic risk in HCs group, the genetic SZ risk in SZ group had 39 genome-wide significant DMPs, while the genetic BD risk in SZ group had only six genome-wide significant DMPs. The MRSs for SZ risk derived from whole blood, FC and STG were higher in our SZ patients than in HCs in whole blood and were particularly higher in the genetic SZ risk in SZ group than in the low genetic risk in HCs and genetic BD risk in SZ groups. Conversely, the MRSs for SZ risk based on our whole-blood EWASs among genetic risk groups were also associated with SZ in the FC and STG. There were no correlations between the MRSs and PRSs.ConclusionsThese findings suggest that the MRS is a potential genetic marker in understanding SZ, particularly in patients with a genetic SZ risk.