bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revealing roles of S-layer protein (SlpA) in
Clostridioides difficile
pathogenicity by generating the first
slpA
gene deletion mutant
Authors: Wang Shaohua , Courreges Maria C. , Xu Lingjun , Gurung Bijay , Berryman Mark , Gu Tingyue 
Published: May 2024

ABSTRACT

Clostridioides difficile
infection (CDI) with high morbidity and high mortality is an urgent threat to public health, and
C. difficile
pathogenesis studies are eagerly required for CDI therapy. The major surface layer protein, SlpA, was supposed to play a key role in
C. difficile
pathogenesis; however, a lack of isogenic
slpA
mutants has greatly hampered analysis of SlpA functions. In this study, the whole
slpA
gene was successfully deleted for the first time via CRISPR-Cas9 system. Deletion of
slpA
in
C. difficile
resulted in smaller, smother-edged colonies, shorter bacterial cell size, and aggregation in suspension. For life cycle, the mutant demonstrated lower growth (changes of optical density at 600 nm, OD600) but higher cell density (colony-forming unit, CFU), decreased toxins production, and inhibited sporulation. Moreover, the mutant was more impaired in motility, more sensitive to vancomycin and Triton X-100-induced autolysis, releasing more lactate dehydrogenase. In addition, SlpA deficiency led to robust biofilm formation but weak adhesion to human host cells.

IMPORTANCE

Clostridioides difficile
infection (CDI) has been the most common hospital-acquired infection, with a high rate of antibiotic resistance and recurrence incidences, become a debilitating public health threat. It is urgently needed to study
C. difficile
pathogenesis for developing efficient strategies as CDI therapy. SlpA was indicated to play a key role in
C. difficile
pathogenesis. However, analysis of SlpA functions was hampered due to lack of isogenic
slpA
mutants. Surprisingly, the first
slpA
deletion
C. difficile
strain was generated in this study via CRISPR-Cas9, further negating the previous thought about
slpA
being essential. Results in this study will provide direct proof for roles of SlpA in
C. difficile
pathogenesis, which will facilitate future investigations for new targets as vaccines, new therapeutic agents, and intervention strategies in combating CDI.
Early–Middle Devonian paleomagnetic results from the Zhongba microterrane, Tibetan Plateau: Evidence for its origin from the northern margin of Greater India
Authors: Li Shuai , Li Yalin , Tan Xiaodong , Han Zhongpeng , Wang Chengshan , Ma Zining , Xu Yunchuan , Wang Zihao , Xiao Siqi , Cheng Jianbo , Li Zijian , Ma Xingduo , Guo Zichun , Huang Song 
Published: May 2024

Abstract
The initial disintegration of Gondwana during the Paleozoic laid the foundation for the formation of the Tibetan Plateau in the Cenozoic. Determining the relative positions of the microterranes in Gondwana during the Paleozoic not only informs the subsequent drift and accretion processes of these microterranes but is also crucial to the paleogeographic reconstruction of Gondwana. However, the lack of paleomagnetic constraints on the Devonian paleogeography of the microterranes in the northern part of Gondwana makes this effort challenging. Here, we report paleomagnetic results for the first time from the Early–Middle Devonian sediments of the Zhongba microterrane. The site-mean direction is declination (Ds) = 310.7°, inclination (Is) = −67.2°, ks = 31.2, α95 = 8.3°, and n = 11, in stratigraphic coordinates. Positive fold and reversal tests, together with rock magnetism results and microscopic observations, strongly suggest that the remanence carriers are of depositional origin. The paleomagnetic results meet the paleomagnetic reliability criteria and therefore can be used for tectonic reconstructions. Our results constrain the paleolatitude of the Zhongba microterrane to be 50.0°S ± 11.7°S in the Early–Middle Devonian. Combined with published detrital zircon ages as well as paleomagnetic results and geological data, our data indicate that the Zhongba microterrane, which had no tectonic affinity with the Lhasa terrane, was part of the northern margin of Greater India during 408–388 Ma and coupled with the South Qiangtang terrane, Tethyan Himalayas, and other terranes to form the continuous northern continental margin of East Gondwana.
Supplemental Material: Multi-scale, open-system magmatic and sub-solidus processes contribute to the chemical and isotopic characteristics of the Jurassic Guadalupe Igneous Complex, Sierra Nevada, California, USA
Authors: Ratschbacher Barbara C. , al. et 
Published: May 2024

<p>Cathodoluminescence images of zircon grains showing spots analyzed with LA-ICP-MS. Figure S2: Comparison of Mg# in whole rock with Mg# in clinopyroxene and orthopyroxene, amphibole Si versus Mg#, and ranges in anorthite content in plagioclase from samples of various GIC map units. Figure S3: Differences in maximum Hf and Yb/Dy ratio in individual zircon grains from different map units of the GIC and as a function of zonation type. Figure S4: Assimilation-fractional crystallization and mixing calculations. Table S1: Whole-rock Sr and Nd isotope composition and major element composition. Table S2: Whole-rock oxygen isotope composition and major and selected trace element composition. Table S3: Electron microprobe data from clinopyroxene, orthopyroxene, amphibole, feldspar, and titanite. Table S4: Zircon trace element compositions. Table S5: Zircon oxygen isotopes. Table S6: Uncertainties of thermometers used in this study. Text S1: Detailed description of analytical methods and detailed description of thin section observations. File S1: Results of zircon trace element modeling. </p>
A tale of two exemplars: the maternal and newborn mortality transitions of two state clusters in India
Authors: Ram Usha , Ramesh Banadakoppa Manjappa , Blanchard Andrea Katryn , Scott Kerry , Kumar Prakash , Agrawal Ritu , Washington Reynold , Bhushan Himanshu 
Published: May 2024

BackgroundIndia’s progress in reducing maternal and newborn mortality since the 1990s has been exemplary across diverse contexts. This paper examines progress in two state clusters: higher mortality states (HMS) with lower per capita income and lower mortality states (LMS) with higher per capita income.MethodsWe characterised state clusters’ progress in five characteristics of a mortality transition model (mortality levels, causes, health intervention coverage/equity, fertility and socioeconomic development) and examined health policy and systems changes. We conducted quantitative trend analyses, and qualitative document review, interviews and discussions with national and state experts.ResultsBoth clusters reduced maternal and neonatal mortality by over two-thirds and half respectively during 2000–2018. Neonatal deaths declined in HMS most on days 3–27, and in LMS on days 0–2. From 2005 to 2018, HMS improved coverage of antenatal care with contents (ANCq), institutional delivery and postnatal care (PNC) by over three-fold. In LMS, ANCq, institutional delivery and PNC rose by 1.4-fold. C-sections among the poorest increased from 1.5% to 7.1% in HMS and 5.6% to 19.4% in LMS.Fewer high-risk births (to mothers <18 or 36+ years, birth interval <2 years, birth order 3+) contributed 15% and 6% to neonatal mortality decline in HMS and LMS, respectively. Socioeconomic development improved in both clusters between 2005 and 2021; HMS saw more rapid increases than LMS in women’s literacy (1.5-fold), household electricity (by 2-fold), improved sanitation (3.2-fold) and telephone access (6-fold).India’s National (Rural) Health Mission’s financial and administrative flexibility allowed states to tailor health system reforms. HMS expanded public health resources and financial schemes, while LMS further improved care at hospitals and among the poorest.ConclusionTwo state clusters in India progressed in different mortality transitions, with efforts to maximise coverage at increasingly advanced levels of healthcare, alongside socioeconomic improvements. The transition model characterises progress and guides further advances in maternal and newborn survival.
Non-physician anaesthesia providers’ perspectives on task sharing practices in Zambia and Somaliland: a qualitative study
Authors: Karydi Konstantina Ilia , Kabaghe Siston , Blamey Helen , Mohamed Mubarak , Shamambo Naomi , Edgcombe Hilary 
Published: May 2024

IntroductionThe 68th World Health Assembly, in 2015, called for surgical and anaesthesia services strengthening. Acknowledging the healthcare staff shortages, they referred to task sharing, among others, as a more effective use of the healthcare workforce. While task sharing has been increasingly proposed as an important strategy to increase the reach and safety of anaesthesia as well as a means of supporting the workforce in low-resource settings, most data on task sharing relate to non-anaesthetic healthcare contexts. The aim of this study was to understand anaesthetic task sharing as currently experienced and/or envisaged by non-physician anaesthesia providers in Zambia and Somaliland.MethodsAn exploratory qualitative research methodology was used. Participants were recruited initially via contacts of the research team, then through snowballing using a purposive sampling strategy. There were 13 participants: 7 from Somaliland and 6 from Zambia. Semistructured interviews took place synchronously, then were recorded, anonymised, transcribed and analysed thematically. Triangulation and respondents’ validation were used to maximise data validity.ResultsFour major themes were identified in relation to task sharing practices: (1) participants recognised variable components of task sharing in their practice; (2) access to task sharing depends both on sources and resources; (3) implicit barriers may inhibit task sharing practices; (4) there is an appetite among participants for amelioration of current task sharing practices.ConclusionsEmpowering task sharing practices can be achieved only by understanding how these practices work, by identifying gaps and areas of improvement, and by addressing them. The findings from this exploratory study could help the global community understand how anaesthetic task sharing in low-resource settings works and inspire further research on the field. This could inform future modelling of workforce planning strategies in low-resource settings to maximise the effectiveness and professional well-being of the workforce.
Risk of transmission of HIV to infants during breast/chest feeding when mothers/birthing parents living with HIV are on antiretroviral therapy: a protocol for a rapid review
Authors: Djiadeu Pascal , Begum Housne , Archibald Chris , Ekmekjian Taline , Busa Giovanna , Dansoh Jeffery , Van Nguyen Phu , Merckx Joanna , Fleurant Annie 
Published: May 2024

IntroductionHIV is a major public health issue affecting millions globally. Women and girls account for 46% of new HIV infections in 2022 and approximately 1.3 million females become pregnant every year. Vertical transmission of HIV from persons living with HIV (PLHIV) to infants may occur through different modalities, such as through breast/chest feeding. Notably, 82% of PLHIV who chose to breast/chest feed are on antiretroviral therapy (ART) when feeding their infants. Precise estimates of the risk of postpartum transmission to infants during breast/chest feeding at varying viral load levels remain a significant gap in the literature.Methods and analysisA rapid systematic search of electronic databases will be conducted from January 2005 to the present, including Medline, Embase and Global Health. The objective of this rapid review is to explore and assess the available evidence on the effect of varying viral load levels on the risk of HIV transmission to infants during breast/chest feeding when the birthing or gestational parent living with HIV is on ART. Study characteristics will be summarised and reported to support the narrative summary of the findings. The focus will be on the absolute risk of HIV transmission from birthing parent to infant during chest/breast feeding. The findings will also be stratified by month, including the risk of HIV transmission for 6 months and greater than 6 months postpartum. We will ascertain the risk of bias using A Measurement Tool to Assess Systematic Reviews 2, Quality of Prognosis Studies and Downs and Black checklist for the appropriate study type. A summary score will not be calculated, rather the strengths and limitations of the studies will be narratively described.Ethics and disseminationNo human subjects will be involved in the research. The findings of this rapid review will inform a future systematic review and will be disseminated through peer-reviewed publications, presentations and conferences.PROSPERO registration numberCRD42024499393.
Cohort profile: EFTER-COVID – a Danish nationwide cohort for assessing the long-term health effects of the COVID-19 pandemic
Authors: Sørensen Anna Irene Vedel , Bager Peter , Nielsen Nete Munk , Koch Anders , Spiliopoulos Lampros , Hviid Anders , Ethelberg Steen 
Published: May 2024

PurposeTo follow SARS-CoV-2-infected persons up to 18 months after a positive test in order to assess the burden and nature of post acute symptoms and health problems.ParticipantsPersons in Denmark above 15 years of age, who were tested positive for SARS-CoV-2 during 1 September 2020 to 21 February 2023 using a RT-PCR test. As a reference group, three test-negative individuals were selected for every two test-positive individuals by matching on test date.Findings to dateIn total, 2 427 913 invitations to baseline questionnaires have been sent out and 839 528 baseline questionnaires (34.5%) have been completed. Females, the age group 50–69 years, Danish-born and persons, who had received at least one SARS-CoV-2 vaccination booster dose were more likely to participate. Follow-up questionnaires were sent at 2, 4, 6, 9, 12 and 18 months after the test, with response rates at 42%–54%.Future plansNew participants have been recruited on a daily basis from 1 August 2021 to 23 March 2023. Data collection will continue until the last follow-up questionnaires (at 18 months after test) have been distributed in August 2024.
Comprehensive single-cell analysis deciphered microenvironmental dynamics and immune regulator olfactomedin 4 in pathogenesis of gallbladder cancer
Authors: He Huisi , Chen Shuzhen , Yu Yong , Fan Zhecai , Qian Youwen , Dong Yaping , Song Yuting , Zhong Caiming , Sun Xiaojuan , Cao Qiqi , Li Shiyao , Huang Weihan , Li Wenxin , Zhuang Mingzhu , Yang Jinxian , Wang Xianming , Wang Jiaqian , Wu Dongfang , Wang Hongyang , Wen Wen 
Published: May 2024

Objective
Elucidating complex ecosystems and molecular features of gallbladder cancer (GBC) and benign gallbladder diseases is pivotal to proactive cancer prevention and optimal therapeutic intervention.

Design

We performed single-cell transcriptome analysis on 230 737 cells from 15 GBCs, 4 cholecystitis samples, 3 gallbladder polyps, 5 gallbladder adenomas and 16 adjacent normal tissues. Findings were validated through large-scale histological assays, digital spatial profiler multiplexed immunofluorescence (GeoMx), etc. Further molecular mechanism was demonstrated with
in vitro
and
in vivo
studies.

Results
The cell atlas unveiled an altered immune landscape across different pathological states of gallbladder diseases. GBC featured a more suppressive immune microenvironment with distinct T-cell proliferation patterns and macrophage attributions in different GBC subtypes. Notably, mutual exclusivity between stromal and immune cells was identified and remarkable stromal ecosystem (SC) heterogeneity during GBC progression was unveiled. Specifically, SC1 demonstrated active interaction between Fibro-iCAF and Endo-Tip cells, correlating with poor prognosis. Moreover, epithelium genetic variations within adenocarcinoma (AC) indicated an evolutionary similarity between adenoma and AC. Importantly, our study identified elevated olfactomedin 4 (OLFM4) in epithelial cells as a central player in GBC progression. OLFM4 was related to T-cell malfunction and tumour-associated macrophage infiltration, leading to a worse prognosis in GBC. Further investigations revealed that OLFM4 upregulated programmed death-ligand 1 (PD-L1) expression through the MAPK-AP1 axis, facilitating tumour cell immune evasion.

Conclusion
These findings offer a valuable resource for understanding the pathogenesis of gallbladder diseases and indicate OLFM4 as a potential biomarker and therapeutic target for GBC.
Active and non-active progression independent of relapse activity within the first 20 years of relapsing multiple sclerosis
Authors: Maarouf Adil , Stellmann Jan Patrick , Rico Audrey , Boutiere Clemence , Demortiere Sarah , Durozard Pierre , Zaaraoui Wafaa , Ranjeva Jean-Philippe , Pelletier Jean , Audoin Bertrand 
Published: May 2024

BackgroundProgression independent of relapse activity (PIRA) has been described since the early stage of relapsing multiple sclerosis (RMS). However, little is known about the relation between PIRA and inflammatory activity that is particularly important at this stage of the disease.MethodWe included 110 patients in a prospective study within 18 months of RMS onset. MRI examinations and clinical visits were scheduled on the same day for months 0, 6, 12, 24, 36, 60, 84, 120, 180 and 240.ResultsThe mean (SD) age of patients was 30 (6.7) years at inclusion and median (range) follow-up 15 (9–20) years. Analysis of 1118 between-visit intervals revealed 93 confirmed disability accumulation events in 68 (62%) patients: 50 (54%) events related to relapse activity worsening and 43 (46%) PIRA events, including 17 (18%) with MRI activity. The risk of PIRA between two visits (stable event as the reference category) was associated with Expanded Disability Status Scale (EDSS) score (HR: 1.41; 95% CI: 1.18 to 1.69; p<0.001), disease duration (HR: 0.75; 95% CI: 0.62 to 0.90; p<0.005) and new lesions between the visits (HR: 1.09 per lesion; 95% CI: 1.01 to 1.17; p<0.05). As compared with PIRA events with MRI activity, PIRA events without such activity occurred in patients with more disability (mean EDSS score 3, p<0.05), longer disease duration (mean 11 years, p<0.001) and greater number of T2-weighted lesions (p<0.05).ConclusionThis study evidenced that inflammatory activity increases the risk of PIRA in early RMS, arguing that a significant part of PIRA is accessible to treatment targeting inflammation in these patients.
Stone’s sheep (Ovis dalli stonei) lambing and nursery habitat selection
Authors: Enns Grace E. , Jex Bill , Boyce Mark S. 
Published: May 2024

Wildlife conservation often focuses on mitigating disturbance in critical habitats like reproductive ranges. We studied lambing and nursery habitat selection by Stone’s sheep ( Ovis dalli stonei (J.A. Allen, 1897)) in the Cassiar Mountains in British Columbia. We estimated the timing of parturition and delineated lambing and nursery habitats based on movement behaviours of collared females ( n = 18) and vaginal implant transmitters. We identified 23 lambing events in 2018 ( n = 4), 2019 ( n = 13), and 2020 ( n = 6). The median birth date was 17 May and ranged from 3 May to 14 June. Females remained in lambing habitats from 1.5 to 11.3 days with a median of 5.5 days. We examined habitat selection during the lambing and nursery periods at the home-range scale using resource selection functions, and at a finer scale using integrated step-selection analyses. Females selected southwest slopes in rugged terrain at mid-elevations, suggesting selection for warmer micro-climates and features that facilitate predator avoidance. Females avoided habitats near roads during the lambing period but showed selection for habitats near roads during the nursing period. We developed predictive maps of suitable lambing and nursery ranges to inform land planning to help reduce overlap of anthropogenic disturbance with potential reproductive habitats.
Proto-strange quark stars from density-dependent quark mass model
Authors: Issifu Adamu , da Silva Franciele M. , Menezes Débora P. 
Published: May 2024

AbstractIn this paper, we investigate the evolution of strange quark stars (SQS) from birth as proto-strange quark stars to maturity as stable SQSs at a zero temperature. We assume that self-bound free quarks form entirely the compact star and study its evolution through a series of snapshots using a density-dependent quark mass model. We consider $$\beta $$
β
-equilibrated stellar matter at two major stages of the star’s evolution: neutrino trapped regime and neutrino transparent regime during the deleptonization and cooling processes of the star. We fix the entropy density per baryon and the lepton fraction to investigate the nuclear equation of state (EoS), particle distribution, temperature profile inside the star, sound velocity, polytropic index, and the structure of the star. Our results show that stars with higher neutrino concentrations are slightly more massive than the neutrino-poor ones along the evolution lines of the SQS. We obtain EoSs in agreement with the conformal boundary set through sound velocity, and also the 2 M$$_\odot $$

⊙

mass constraint for NSs was satisfied at all stages of the star’s evolution.
Who makes open source code? The hybridisation of commercial and open source practices
Authors: Mehler Peter , Otto Eva Iris , Sapienza Anna 
Published: May 2024

AbstractWhile Free and Open Source (F/OSS) coding has traditionally been described as a separate commons linked to values of openness and sharing, recent research suggests an increasing integration of private corporations into F/OSS practices, blurring the boundaries between F/OSS and commodified coding. However, there is a dearth of empirical, and especially quantitative studies exploring this phenomenon. To address this gap, we model the power dynamics and infrastructural aspects of software production within GitHub, a central hub for F/OSS development, using a large-scale, directed network. Using various network statistics, we detect the ecosystem’s most impactful actors and find a nuanced picture of the influence of individuals, open source organizations, and private corporations in F/OSS practices. We find that the majority of public repositories on GitHub depend on a small core of specialized repositories and users. In accordance with expectations, individuals and open source organizations are more prevalent in this core of elite GitHub users, however, we also find a significant amount of private organizations with an indirect, yet consistent influence within GitHub. In addition, we find that directly influential individuals tend to facilitate sponsorship methods more often than indirectly or non-influential individuals. Our research highlights a hybridization of F/OSS and sheds light on the complex interplay between influence, power, and code production in the multi-language dependency ecosystem of GitHub.
Some classes of functions with low c-differential uniformity over finite fields
Authors: Li Guanghui , Cao Xiwang 
Published: May 2024

Multiplicative differential (and the corresponding [Formula: see text]-differential uniformity) was introduced by Ellingsen et al. in [[Formula: see text]-differentials, multiplicative uniformity and (almost) perfect [Formula: see text]-nonlinearity, IEEE Trans. Inf. Theory 66(9) (2020) 5781–5789], which has attracted lots of attention. Functions with low [Formula: see text]-differential uniformity over finite fields, especially the P[Formula: see text]N and AP[Formula: see text]N functions, have been widely investigated due to their applications in cryptography. In this paper, we first compute the [Formula: see text]-differential uniformity of two classes of permutation polynomials. For one of these, we explicitly determine the [Formula: see text]-DDT entries. For the second type of function, we give bounds for its [Formula: see text]-differential uniformity. Besides, several classes of P[Formula: see text]N or AP[Formula: see text]N functions are presented by employing some known functions and the (generalized) AGW criterion.