bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional characterization of two TolC in the resistance to drugs and metals and in the virulence of
Riemerella anatipestifer
Authors: Huang Li , Guo Fang , Li Xiao , Wang Mengying , Zhu Dekang , Wang Mingshu , Jia Renyong , Chen Shun , Zhao Xinxin , Zhang Shaqiu , Gao Qun , Yang Qiao , Wu Ying , Huang Juan , Tian Bin , Ou Xumin , Sun Di , Mao Sai , Zhang Ling , Yu YanLing , Götz Friedrich , Cheng Anchun , Liu Mafeng 
Published: December 2023

ABSTRACT

TolC is an outer membrane protein that is responsible for the efflux of multi-substrates in Gram-negative bacteria.
Riemerella anatipestifer
CH-1 encodes two TolC proteins, B739_0871 (TolCA) and B739_1784 (TolCB). TolCB was previously involved in the export of manganese (Mn). However, whether TolCB has other substrates is unclear, and the functions of TolCA remain to be characterized. Here, we show that deletion of
tolCA
renders the bacteria hypersensitive to the gentamicin, the SDS, and various metals, such as Mn(II), Zn(II), Cu(II), Fe(II), Co(II), and Ni(II). By contrast, the deletion of
tolCB
only conferred high sensitivity to Mn. Consistently, the deletion of
tolCA
led to intracellular accumulation of the various tested metals, while the deletion of
tolCB
only led to Mn accumulation under conditions of excess Mn. Moreover, the
tolCA
deletion mutant (∆
tolCA
) but not the
tolCB
deletion mutant (∆
tolCB
) was more sensitive to the NaOCl than the wild type (WT). Strikingly, the ∆
tolCA
but not ∆
tolCB
decreased the frequency of clones resistant to several tested antibiotics. In the duck infection model, the ∆
tolCA
but not ∆
tolCB
decreased virulence and colonization of
R. anatipestifer
CH-1, possibly due to increased sensitivity of ∆
tolCA
to non-inactivated duck serum as compared to the WT. Finally, genome mining revealed that homologs of
tolCA
and
tolCB
are highly conserved across
R. anatipestifer
strains and also present in other members of
Flavobacteriaceae
. Taken together, our results revealed that compared with TolCB, TolCA has a wider range of efflux substrates and functions in
R. anatipestifer
CH-1.

IMPORTANCE

Riemerella anatipestifer
(RA) is a notorious duck pathogen, characterized by a multitude of serotypes that exhibit no cross-reaction with one another. Moreover, RA is resistant to various antibacterial agents. Consequently, understanding the mechanisms behind resistance and identifying potential targets for drug development have become pressing needs. In this study, we show that the two TolC proteins play a role in the resistance to different drugs and metals and in the virulence. The results suggest that TolCA has a wider range of efflux substrates than TolCB. Except for gentamicin, neither TolCA nor TolCB was involved in the efflux of the other tested antibiotics. Strikingly, TolCA but not TolCB enhanced the frequency of resistance-conferring mutations. Moreover, TolCA was involved in RA virulence. Given its conservation in RA, TolCA has potential as a drug target for the development of therapeutics against RA infections.
Species identification and strain discrimination of fermentation yeasts
Saccharomyces cerevisiae
and
Saccharomyces uvarum
using Raman spectroscopy and convolutional neural networks
Authors: Wang Kaidi , Chen Jing , Martiniuk Jay , Ma Xiangyun , Li Qifeng , Measday Vivien , Lu Xiaonan 
Published: December 2023

ABSTRACT

Reliable typing of yeast strains is of great importance to the alcoholic beverage industry to ensure a reliable fermentation process and high-quality products.
Saccharomyces cerevisiae
is the most used yeast species in wine, sake, and ale beer fermentation, whereas
Saccharomyces uvarum
is more commonly used for cider fermentation and, due to its cryotolerance, white wine production. We propose a promising method for species identification and strain discrimination of
S. cerevisiae
and
S. uvarum
using Raman spectroscopy in combination with convolutional neural networks (CNNs). Raman spectra collected from various
S. cerevisiae
and
S. uvarum
strains were accurately classified at the species level using random forest. Cultivation time and temperature did not significantly affect the spectral reproducibility and discrimination capability. An overall accuracy of 91.9% was achieved to discriminate 27 yeast isolates at the strain level using a CNN model. Raman-CNN further identified eight yeast isolates spiked in grape juice with an accuracy of 98.1%. Raman spectral signatures derived from diverse protein and lipid compositions may contribute to this discrimination. The proposed approach also precisely predicted the concentration of a specific yeast strain within a yeast mixture with an
R
2
of 0.9913 and an average error of 4.09%. The entire analysis can be completed within 1 hour following cultivation and only requires simple sample preparation and low consumable cost. Taken together, Raman spectroscopy coupled with CNN is a robust, accurate, and reliable approach for typing of fermentation yeast strains.

IMPORTANCE

The use of
S. cerevisiae and S. uvarum
yeast starter cultures is a common practice in the alcoholic beverage fermentation industry. As yeast strains from different or the same species have variable fermentation properties, rapid and reliable typing of yeast strains plays an important role in the final quality of the product. In this study, Raman spectroscopy combined with CNN achieved accurate identification of
S. cerevisiae
and
S. uvarum
isolates at both the species and strain levels in a rapid, non-destructive, and easy-to-operate manner. This approach can be utilized to test the identity of commercialized dry yeast products and to monitor the diversity of yeast strains during fermentation. It provides great benefits as a high-throughput screening method for agri-food and the alcoholic beverage fermentation industry. This proposed method has the potential to be a powerful tool to discriminate
S. cerevisiae and S. uvarum
strains in taxonomic, ecological studies and fermentation applications.
Amino acid substitution L232F in non-structural protein 6 identified as a possible human-adaptive mutation in clade B MERS coronaviruses
Authors: So Ray T. Y. , Chu Daniel K. W. , Hui Kenrie P. Y. , Mok Chris K. P. , Shum Marcus H. H. , Sanyal Sumana , Nicholls John M. , Ho John C. W. , Cheung Man-chun , Ng Ka-chun , Yeung Hin-Wo , Chan Michael C. W. , Poon Leo L. M. , Zhao Jincun , Lam Tommy T. Y. , Peiris Malik 
Published: December 2023

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV) causes zoonotic disease. Dromedary camels are the source of zoonotic infection. We performed sequence analysis of clade B MERS-CoV after excluding potential bias arising multiple sequences from a single zoonotic transmission chain and identified a substitution of amino acid leucine to phenylalanine in the codon 232 position of the non-structural protein 6 (nsp6) (nsp6 L232F) that occurs preferentially in human clade B MERS-CoV, with a rate of 16.9% (20/118) in human sequences vs a 0.6% (1/160) in camel sequences. Using a human clade B MERS-CoV strain GD01 as backbone, we generated a pair of isogenic recombinant MERS-CoV with nsp6 232L and 232F residues, respectively, and showed that the nsp6 L232F substitution confers higher replication competence in
ex vivo
culture of human nasal and bronchial tissues and in lungs of mice experimentally infected
in vivo
. Mechanistically, the nsp6 L232F substitution was found to associate with higher exocytic virus egress, while innate immune responses, autophagic restriction, and zippering activity of the endoplasmic reticulum remained unaffected. Our study suggests an adaptive mutation that occurs in clade B MERS-CoV associated with inter-species transmission to humans that may facilitate higher viral replication in the human respiratory tract. This highlights the importance of MERS-CoV as a zoonotic threat and the need for continued virus surveillance in camels and humans.

IMPORTANCE

Viral host adaptation plays an important role in inter-species transmission of coronaviruses and influenza viruses. Multiple human-adaptive mutations have been identified in influenza viruses but not so far in MERS-CoV that circulates widely in dromedary camels in the Arabian Peninsula leading to zoonotic transmission. Here, we analyzed clade B MERS-CoV sequences and identified an amino acid substitution L232F in nsp6 that repeatedly occurs in human MERS-CoV. Using a loss-of-function reverse genetics approach, we found the nsp6 L232F conferred increased viral replication competence
in vitro
, in cultures of the upper human respiratory tract
ex vivo,
and in lungs of mice infected
in vivo
. Our results showed that nsp6 L232F may be an adaptive mutation associated with zoonotic transmission of MERS-CoV. This study highlighted the capacity of MERS-CoV to adapt to transmission to humans and also the need for continued surveillance of MERS-CoV in camels.
Complete genome sequence of
Cutibacterium acnes
type II CCSM0331, isolated from a healthy woman’s skin
Authors: Ma Laiji , Li Yan , Niu Yujie , Yang Suzhen , Shao Li 
Published: December 2023

ABSTRACT

The complete genome sequence of
Cutibacterium acnes
Type II strain CCSM0331, which was isolated from the healthy facial skin, is reported. The assembled 2.5-Mbp genome comprised a single circular chromosome. These data will provide valuable information on the beneficial role of
C. acnes
as a skin commensal bacteria.
Complete genome sequence of Australian soil bacterium
Rouxiella badensis
DAR84756 resolved with Oxford Nanopore long-read and Illumina sequences
Authors: Paul Saina , Anderson Peter J. , Maynard Gregg J. , Dyall-Smith Michael , Kudinha Timothy 
Published: December 2023

ABSTRACT

The complete genome sequence of the bacterium
Rouxiella badensis
DAR84756, isolated from soil in Orange, NSW, Australia, was resolved using a combination of Nanopore long-read and Illumina short-read sequencing. The genome consists of a single, circular chromosome of 5,004,491 bp and a plasmid of 40,722 bp.
High-resolution X-ray fluorescence-based provenance mapping of Eocene fluvial distributary fans that fed ancient Gosiute Lake, Wyoming, USA
Authors: Smith M.E. , Gregorich H.G. , Gipson L.A. , Krueger R.C. , Carroll A.R. , Parrish E.C. , Walters A.P. , Honig S. , Schwaderer C. , Meyers S. , Singer B.S. , Lowenstein T.K. , Arnuk W.D. 
Published: December 2023

Abstract
The Green River Formation of Wyoming, USA, is host to the world’s largest known lacustrine sodium carbonate deposits, which accumulated in a closed basin during the early Eocene greenhouse. Alkaline brines are hypothesized to have been delivered to ancient Gosiute Lake by the Aspen paleoriver that flowed from the Colorado Mineral Belt. To precisely trace fluvial provenance in the resulting deposits, we conducted X-ray fluorescence analyses and petrographic studies across a suite of well-dated sandstone marker beds of the Wilkins Peak Member of the Green River Formation. Principal component analysis reveals strong correlation among elemental abundances, grain composition, and sedimentary lithofacies. To isolate a detrital signal, elements least affected by authigenic minerals, weathering, and other processes were included in a principal component analysis, the results of which are consistent with petrographic sandstone modes and detrital zircon chronofacies of the basin. Sandstone marker beds formed during eccentricity-paced lacustrine lowstands and record the migration of fluvial distributary channel networks from multiple catchments around a migrating depocenter, including two major paleorivers. The depositional topography of these convergent fluvial fans would have inversely defined bathymetric lows during subsequent phases of lacustrine inundation, locations where trona could accumulate below a thermocline. Provenance mapping verifies fluvial connectivity to the Aspen paleoriver and to sources of alkalinity in the Colorado Mineral Belt across Wilkins Peak Member deposition, and shows that the greatest volumes of sediment were delivered from the Aspen paleoriver during deposition of marker beds A, B, D, and I, each of which were deposited coincident with prominent “hyperthermal” isotopic excursions documented in oceanic cores.
Manifold child, family and social variables are associated with injury among New Zealand preschool children
Authors: Underwood Lisa , Kool Bridget , Pillai Avinesh , Kingi Te Kani , Morton Susan , Ameratunga Shanthi 
Published: December 2023

AimApproaches to understanding child injury tend to focus on short-term proximal influences. Previous analyses have found higher rates of injury among Māori and Pacific children in Aotearoa New Zealand (NZ). This study aimed to investigate how combinations of situations and multiple events act across the life-course to either protect preschool children from, or place them at risk of, repeated injuries requiring medical attention.MethodsLongitudinal data were used to identify parent-reported injuries requiring medical attention among 6114 preschool NZ children. The environments experienced by children with multiple and/or severe injury were explored using multivariable analyses.ResultsEight percent of children (n=505) experienced 1–3 injuries with at least one hospitalisation or ≥4 injuries (high injurygroup) from birth to 4.5 years of age. After accounting for antenatal, sociodemographic and psychosocial variables, children of Māori mothers (OR=0.7, 95% CI 0.5 to 0.97) and children of Asian mothers (OR=0.5, 95% CI 0.3 to 0.7) were less likely to be in thehigh injurygroup than children of European mothers. After adjusting for maternal ethnicity and child variables (gender, temperament, level of activity and behaviour difficulties), cumulative exposure to factors in four domains was associated with injury category: maternal, family, social and service use.ConclusionThis study identified social and economic opportunities to lower rates of injury among preschool children, that might reduce associated direct and indirect costs. Our findings in relation to ethnicity go against the standard public rhetoric and provide support for shifting the apportioning of blame for child injury from individuals to wider environmental exposures for which public health and societal solutions are required.
Comparison of kinetic changes during helicopter medical evacuations: civilian versus military flights
Authors: Naude Claire , Bujon Cécile , Boussen Salah , Serre Thierry , Bélot Frédérik 
Published: December 2023

BackgroundHelicopter evacuation is crucial for providing medical care to casualties. Previous civilian studies have demonstrated that air transport can enhance survival rates compared with ground transport. However, there has been limited research on specific accelerations during helicopter flights, particularly in military flights. This study aims to analyse and compare the accelerations endured during civilian and military helicopter evacuations.MethodsAccelerations were recorded during evacuation flights from the site of injury to the first medical responders in civilian helicopter EC135 T1, and military Puma SA.330 and Caiman NH90 TTH helicopters. The research investigated global acceleration and compared acceleration distributions along the vertical, lateral and longitudinal axes. A specific comparative study of the take-off phases was also performed.ResultsThe analysis showed that vertical loads caused the most extreme accelerations for all types of helicopter but these extreme accelerations were rare and lasted for less than 1 s. Military flights show similar acceleration intensities to civilian flights, but accelerations are higher during short periods of the take-off phase.ConclusionsThe findings suggest that helicopter evacuations during military operations are as safe as civilian evacuations and highlight the importance of patient positioning in the aircraft. However, further research should investigate the haemodynamic response to accelerations experienced during actual evacuation flights.
Inequalities in intimate partner violence screening and receiving information among diverse groups of women: an online survey during COVID-19 lockdowns
Authors: Agronsky Beatris , Alfayumi-Zeadna Samira , Sergienko Ruslan , Daoud Nihaya 
Published: December 2023

BackgroundResearch shows violence against women likely increases during emergencies. COVID-19’s emergence exacerbated intimate partner violence (IPV), suggesting that healthcare services (HCS) should have increased IPV screening efforts and referrals of victims to support services. However, little is known about the prevalence of IPV screening and information provision during COVID-19 lockdowns.MethodsWe examined prevalence of ‘ever been screened’ (ES) for IPV and ‘receiving information about support services’ (RI) in HCS during COVID-19 lockdowns and compared these among non-immigrant Jewish women, immigrant Jewish and other women, and Palestinian women citizens in Israel. We collected data during Israel’s second and third COVID-19 lockdowns (October 2020–February 2021) using a structured, online, self-administrated Arabic-language and Hebrew-language questionnaire. Eligibility criteria included women ≥18 years old, citizens of Israel, in a current intimate relationship (permanent or occasional) who used social media or smartphones. In total, 519 women completed the survey: 73 Palestinian, 127 Jewish immigrants and others, and 319 non-immigrant Jewish.ResultsOverall, 37.2% of women reported any IPV, of whom just 26.9% reported ES, 39.4% reported RI and 13.5% reported both (ES&RI). Palestinian women reported higher IPV rates (49.3%) compared with non-immigrant Jewish (34.2%) and immigrant Jewish and other (37.8%) women; however, they reported lower ES (OR 0.64, 90% CI (0.34 to 1.86) and RI 0.29 (0.17 to 0.50).ConclusionsIn a survey during COVID-19 lockdowns, only about one-quarter of women who reported IPV were ES for IPV, or RI about support services, suggesting strengthened IPV screening is needed in HCS during emergencies, particularly targeting minority women, who report higher IPV but receive fewer services.
Co-design of patient information leaflets for germline predisposition to cancer: recommendations for clinical practice from the UK Cancer Genetics Group (UKCGG), Cancer Research UK (CRUK) funded CanGene-CanVar Programme and the Association of Genetic Nurse Counsellors (AGNC)
Authors: Kohut Kelly , Speight Beverley , Young Julie , Way Rosalind , Wiggins Jennifer , Monje-Garcia Laura , Eccles Diana M , Foster Claire , Turner Lesley , Snape Katie , Hanson Helen ,   on behalf of the CanGene-CanVar Patient Reference Panel
Published: December 2023

BackgroundTesting for germline pathogenic variants (GPVs) in cancer predisposition genes is increasingly offered as part of routine care for patients with cancer. This is often urgent in oncology clinics due to potential implications on treatment and surgical decisions. This also allows identification of family members who should be offered predictive genetic testing. In the UK, it is common practice for healthcare professionals to provide a patient information leaflet (PIL) at point of care for diagnostic genetic testing in patients with cancer, after results disclosure when a GPV is identified, and for predictive testing of at-risk relatives. Services usually create their own PIL, resulting in duplication of effort and wide variability regarding format, content, signposting and patient input in co-design and evaluation.MethodsRepresentatives from UK Cancer Genetics Group (UKCGG), Cancer Research UK (CRUK) funded CanGene-CanVar programme and Association of Genetic Nurse Counsellors (AGNC) held a 2-day meeting with the aim of making recommendations for clinical practice regarding co-design of PIL for germline cancer susceptibility genetic testing. Lynch syndrome and haematological malignancies were chosen as exemplar conditions.ResultsMeeting participants included patient representatives including as co-chair, multidisciplinary clinicians and other experts from across the UK. High-level consensus for UK recommendations for clinical practice was reached on several aspects of PIL using digital polling, including that PIL should be offered, accessible, co-designed and evaluated with patients.ConclusionsRecommendations from the meeting are likely to be applicable for PIL co-design for a wide range of germline genetic testing scenarios.
Efficacy of iliopsoas plane block for patients undergoing hip arthroscopy: a prospective, triple-blind, randomized, placebo-controlled trial
Authors: Jessen Christian , Brix Lone Dragnes , Nielsen Thomas Dahl , Espelund Ulrick Skipper , Lund Bent , Bendtsen Thomas Fichtner 
Published: December 2023

BackgroundIntraoperative stretching of the hip joint capsule often generates severe pain during the first 3 hours after hip arthroscopy. The short-lived severe pain mandates high opioid consumption, which may result in adverse events and delay recovery. The femoral nerve nociceptors are located anteriorly in the hip joint capsule. A femoral nerve block reduces pain and opioid demand after hip arthroscopy. It impedes, however, ambulation and home discharge after outpatient surgery. The iliopsoas plane block selectively anesthetizes the femoral sensory nerve branches innervating the hip joint capsule without compromising ambulation. We aimed to assess reduction of opioid consumption after iliopsoas plane block during the short-lived painful postsurgical period of time after hip arthroscopy.MethodsIn a randomized, triple-blind trial, 50 patients scheduled for hip arthroscopy in general anesthesia were allocated to active or placebo iliopsoas plane block. The primary outcome was opioid consumption during the first three postoperative hours in the postanesthesia care unit. Secondary outcomes included pain, nausea, and ability to ambulate.ResultsForty-nine patients were analyzed for the primary outcome. The mean 3-hour intravenous morphine equivalent consumption in the iliopsoas plane block group was 10.4 mg vs 23.8 mg in the placebo group (p<0.001). No intergroup differences were observed for the secondary outcomes during the postoperative follow-up.ConclusionAn iliopsoas plane block reduces opioid consumption after hip arthroscopy. The reduction of opioid consumption during the clinically relevant 3-hour postsurgical period of time was larger than 50% for active versus placebo iliopsoas plane block in this randomized, triple-blind trial.