bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brucella
NpeA is a secreted Type IV effector containing an N-WASP-binding short linear motif that promotes niche formation
Authors: Giménez Agostina , Del Giudice Mariela G. , López Paula V. , Guaimas Francisco , Sámano-Sánchez Hugo , Gibson Toby J. , Chemes Lucía B. , Arregui Carlos O. , Ugalde Juan E. , Czibener Cecilia 
Published: June 2024

ABSTRACT

The modulation of actin polymerization is a common theme among microbial pathogens. Even though microorganisms show a wide repertoire of strategies to subvert the activity of actin, most of them converge in the ones that activate nucleating factors, such as the Arp2/3 complex.
Brucella
spp. are intracellular pathogens capable of establishing chronic infections in their hosts. The ability to subvert the host cell response is dependent on the capacity of the bacterium to attach, invade, avoid degradation in the phagocytic compartment, replicate in an endoplasmic reticulum-derived compartment and egress. Even though a significant number of mechanisms deployed by
Brucella
in these different phases have been identified and characterized, none of them have been described to target actin as a cellular component. In this manuscript, we describe the identification of a novel virulence factor (NpeA) that promotes niche formation. NpeA harbors a short linear motif (SLiM) present within an amphipathic alpha helix that has been described to bind the GTPase-binding domain (GBD) of N-WASP and stabilizes the autoinhibited state. Our results show that NpeA is secreted in a Type IV secretion system-dependent manner and that deletion of the gene diminishes the intracellular replication capacity of the bacterium.
In vitro
and
ex vivo
experiments demonstrate that NpeA binds N-WASP and that the short linear motif is required for the biological activity of the protein.

IMPORTANCE

The modulation of actin-binding effectors that regulate the activity of this fundamental cellular protein is a common theme among bacterial pathogens. The neural Wiskott–Aldrich syndrome protein (N-WASP) is a protein that several pathogens target to hijack actin dynamics. The highly adapted intracellular bacterium
Brucella
has evolved a wide repertoire of virulence factors that modulate many activities of the host cell to establish successful intracellular replication niches, but, to date, no effector proteins have been implicated in the modulation of actin dynamics. We present here the identification of a virulence factor that harbors a short linear motif (SLiM) present within an amphipathic alpha helix that has been described to bind the GTPase-binding domain (GBD) of N-WASP stabilizing its autoinhibited state. We demonstrate that this protein is a Type IV secretion effector that targets N-WASP-promoting intracellular survival and niche formation.
Draft genome sequence of
Vibrio
sp. PBL-C16, isolated from Batu Laut Beach in Selangor, Malaysia
Authors: Kahar Ummirul Mukminin , Goh Kian Mau , Zakaria Iffah Izzati , Radzlin Nurfatini , Mohd Ruslan Izzatul Husna , Azizan Suha 
Published: June 2024

ABSTRACT

Vibrio
sp. PBL-C16 is a bacterium that was isolated from Batu Laut Beach in Selangor, Malaysia. Here, we present a high-quality annotated draft genome of strain PBL-C16 and suggest its potential glycoside hydrolase enzymes for polysaccharide degradation.
Transparency interventions to improve health system outcomes in low and middle-income countries: a narrative systematic review
Authors: Gholami Masoomeh , Takian Amirhossein , Kabir Mohammad Javad , Olyaeemanesh Alireza , Mohammadi Mehrdad 
Published: June 2024

ObjectivesThis study aimed to identify the types of transparency interventions in the health systems of the low-income and middle-income countries and the outcomes of such interventions in those systems.MethodWe searched major medical databases including PubMed, Embase and Scopus, for any kind of interventional study on transparency in health systems. We also looked for additional sources of information in organisational websites, grey literature and reference checking. Using the PRISMA algorithm for identifying related studies, we included 24 articles.ResultsOur initial search, from 1980 to August 2021, retrieved 407 articles, 24 of which were narratively analysed. Response to a problem (mostly corruption) was the main reason for the initiation of a transparency intervention. Transparency interventions differed in terms of types, performance methods, collaboration partners and outcomes. They help improve the health system mostly in the short term and in some cases, long term.ConclusionAlthough our findings revealed that transparency initiatives could reduce some problems such as counterfeit drugs and corruption, and improve health indicators in a short term, still their sustainability remains a concern. Health systems need robust interventions with clearly defined and measured outcomes, especially sustainable outcomes to tackle corruption fundamentally.
Cohort profile: longitudinal and population comparison of children who are HIV-exposed uninfected and children who are HIV unexposed in Kenya (HOPE study)
Authors: Njuguna Irene N , King'e Maureen , Moraa Helen , Kumar Manasi , Benki-Nugent Sarah , Wagner Anjuli Dawn , McGrath Christine J , Dorsey Shannon , Ndegwa Serah , Onyango Alvin , Wamalwa Dalton , John-Stewart Grace 
Published: June 2024

PurposeGlobally, the number of children/adolescents exposed to HIV but uninfected (HIV-exposed uninfected, HEU) is growing. The HEU outcomes: population-evaluation and screening strategies study was designed to provide population-level evidence of the impact of HIV and recent antiretroviral therapy regimen exposure on neurodevelopmental, hearing and mental health outcomes from infancy to adolescence.ParticipantsThe study includes a prospective mother–infant cohort and cross-sectional child/youth–caregiver cohorts conducted in Kenya.Between 2021 and 2022, the study enrolled 2000 mother–infant pairs (1000 HEU and 1000 HIV-unexposed uninfected (HUU)) for longitudinal follow-up. Infants were eligible if they were aged 4–10 weeks and healthy. Mothers were eligible if their HIV status was known and were ≥18 years. Study visits are 6 monthly until the child reaches age 3 years.Cross-sectional cohorts spanning ages 3–18 years started enrolment in 2022. Target enrolment is 4400 children/youth (4000 HEU and 400 HUU). Children and youth are eligible if they are HIV negative, maternal HIV status and timing of diagnosis is known, and caregivers are ≥18 years.Data on infant/child/youth growth, neurodevelopment, mental health, morbidity and hearing are collected at enrolment using standardised tools. Dry blood spots samples are collected for telomere length assessment at baseline and yearly for the longitudinal cohort. Growth z-scores, neurodevelopmental scores, telomere length and prevalence of developmental and hearing problems will be compared between HEU/HUU populations.Findings to dateFull cohort enrolment for the longitudinal cohort is complete and participants are in follow-up. At 1 year of age, comparing HEU to HUU neurodevelopment using the Malawi developmental assessment tool, we found that HEU infants had higher language scores and comparable scores in fine motor, gross motor and social scores. The cross-sectional cohort has enrolled over 2000 participants and recruitment is ongoing.Future plansLongitudinal cohort follow-up and enrolment to the cross-sectional study will be completed in June 2024.
Evaluating a Modified Use of the Kaiser Permanente Early-onset Sepsis Risk Calculator to Reduce Antibiotic Exposure: a Retrospective Study
Authors: Alhindi Mohammed Yasir , Almalki Faisal Ghazi , Al Saif Saif , Almalahi Abdulaziz , Alsaegh Mawaddah Hesham , Mustafa Ahmed , AlQurashi Mansour Abdullah 
Published: June 2024

BackgroundEarly-onset neonatal sepsis (EONS) remains an important disease entity due to very serious adverse outcomes if left untreated. Lack of diagnostic tools in identifying healthy from diseased neonates, and clinicians’ fear of the missing positive-culture sepsis babies, or babies with clinical sepsis have led to overtreating and unnecessary antibiotic exposure. Kaiser Permanente EONS risk calculator is an internally validated tool that can predict EONS. This sepsis risk calculator (SRC) classifies neonates into three subgroups: (1) ill-appearing, (2) equivocal and (3) well-appearing. We propose a modification to this tool that aims to use it solely for well-appearing babies. This modification represents a more conservative approach to decrease antibiotic exposure and offers an alternative for those hesitant to fully implement this tool.MethodsThis is a dual-centre retrospective study where data were extracted from the electronic medical records. Our primary outcome was to validate the modified use of the SRC with a two-by-two table. Specificity, negative predictive value and expected antibiotic reduction were used to evaluate the tool’s feasibility.ResultAmong 770 babies suspected of EONS, the feasibility of the modified use was tested. The expected antibiotic exposure reduction rate on the modification was 40.4% overall. The proposed modification resulted in a specificity and negative predictive value of 99.28% (95% CI: 97.92% to 99.85%) and 99.5% (95% CI: 99% to 99.8%), respectively.ConclusionThe modified use of the sepsis risk calculator has shown that it can safely reduce antibiotic exposure in well-appearing babies. The modified use is used as a ‘rule out’ test that can identify very low risk of EONS babies, and safely minimise antibiotic exposure. Further prospective studies are needed to examine the efficacy of this use, and quality improvement projects are required to evaluate its applicability in different clinical settings.
Characterizations of multi-kingdom gut microbiota in immune checkpoint inhibitor-treated hepatocellular carcinoma
Authors: Zhu Chengpei , Zhang Chenchen , Wang Shanshan , Xun Ziyu , Zhang Dongya , Lan Zhou , Zhang Longhao , Chao Jiashuo , Liang Yajun , Pu Zilun , Ning Cong , Sang Xinting , Yang Xiaobo , Wang Hanping , Jiang Xianzhi , Zhao Haitao 
Published: June 2024

BackgroundThe association between gut bacteria and the response to immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) has been studied; however, multi-kingdom gut microbiome alterations and interactions in ICI-treated HCC cohorts are not fully understood.MethodsFrom November 2018 to April 2022, patients receiving ICI treatment for advanced HCC were prospectively enrolled. Herein, we investigated the multi-kingdom microbiota characterization of the gut microbiome, mycobiome, and metabolome using metagenomic, ITS2, and metabolomic data sets of 80 patients with ICI-treated HCC.ResultsOur findings demonstrated that bacteria and metabolites differed significantly between the durable clinical benefit (DCB) and non-durable clinical benefit (NDB) groups, whereas the differences were smaller for fungi. The overall diversity of bacteria and fungi before treatment was higher in the DCB group than in the NDB group, and the difference in diversity began to change with the use of immunotherapy after 6–8 weeks. We also explored the alterations of gut microbes in the DCB and NDB groups, established 18 bacterial species models as predictive biomarkers for predicting whether immunotherapy is of sustained benefit (area under the curve=75.63%), and screened two species of bacteria (Actinomyces_sp_ICM47, andSenegalimassilia_anaerobia) and one metabolite (galanthaminone) as prognostic biomarkers for predicting survival in patients with HCC treated with ICI.ConclusionsIn this study, the status and characterization of the multi-kingdom microbiota, including gut bacteria, fungi, and their metabolites, were described by multiomics sequencing for the first time in patients with HCC treated with ICI. Our findings demonstrate the potential of bacterial taxa as predictive biomarkers of ICI clinical efficacy, and bacteria and their metabolites as prognostic biomarkers.
Using Defence Engagement (Health) to progress the Women Peace and Security agenda
Authors: Kinkaid Victoria , Masti M , Whitaker J , Russell A , McCrae L 
Published: June 2024

Since the unanimous passing of United Nations Security Council Resolution 1325, which calls on member states to address gender inequality, many countries and the wider North Atlantic Treaty Organisation community have championed the Women Peace and Security agenda to empower women and reduce violence within fragile states. When women are empowered and actively involved in decision-making, there is less violence, and more peace and stability in that society, which benefits all members.Defence Medical Services are uniquely positioned to progress this agenda, particularly through its Defence Engagement activities. The UK’s military medical community has more women in leadership than the wider military community. Our personnel can and should be used to model and empower military healthcare workers in partner nations. This paper forms part of a special issue ofBMJ Military Healthdedicated to Defence Engagement.
Plasma effects on resonant phenomena
Authors: Pradhan Anil 
Published: June 2024

The effect of autoionizing resonances in atomic systems and processes is reviewed. Theoretical framework for treating resonances in the coupled channel approximation using the R-matrix method, as well as approximations related to plasma applications are described. The former entails large-scale atomic computations, and the latter is based on a new method for including collisional, Stark, thermal, and other broadening mechanisms. We focus particularly on the problem of opacities calculations in high-energy-density plasmas such as stellar interiors and inertial confinement fusion devices. The treatment is generally relevant to radiative and collisional processes as the cross sections become energy-temperature-density dependent. While the computational difficulty increases considerably, the reaction rates are significantly affected. The related issue of the Boltzmann–Saha equation-of-state and its variants in local thermodynamic equilibrium is also explored as the intermediary between atomic data on the one hand and plasma environments on the other.
Exploring Trade-offs in Explainable AI
Authors: Brown Dene , Hawe Glenn 
Published: June 2024

Machine Learning (ML) models are increasingly used in systems that involve physical human interaction or decision-making systems that impact human health and safety. Ensuring that these systems are safe and reliable is an important topic of current AI research.
For many ML models it is unclear how a prediction (output) is arrived at from the provided features (input). Critical systems cannot blindly trust the predictions of such "black box" models, but instead need additional reassurance via insight into the model's reasoning. A range of methods exist within the field of Explainable AI (XAI) to make the reasoning of black box ML models more understandable and transparent.
The explanations provided by XAI methods may be evaluated in a number of (competing) ways. In this paper, we investigate the trade-off between selected metrics for an XAI method called UnRAvEL, which is similar to the popular LIME approach. Our results show that by weighting the terms within the acquisition function used in UnRAvEL, different trade-offs can be achieved.
Mode Change Management for Adaptive Cyber-physical Systems
Authors: García-Gordillo Miguel , Valls Joan J. , Coronel Javier , Sáez Sergio 
Published: June 2024

Cyber-physical systems are usually integrated with a highly changing environment. Because of the variability of their environment, these systems need to adapt their behaviour at runtime to achieve the expected results. In the case of distributed solutions, this behaviour must be consistent across the continuum, increasing the complexity of the design due to the need to synchronise the different components distributed in the multiple nodes.
A multimode application approach could be used to solve this need, assuming it is implemented as a distributed system. The approach involves applications with multiple behaviours (or operational modes) and a mechanism to change from one mode to another.
This article describes an operational mode change management solution based on that approach and the reference architecture presented in the TRANSACT project. This architecture integrates CPS end devices at the edge of the network with edge computing servers and cloud computing facilities. Static and dynamic views are included to describe the solution, and specific use case scenarios are added for better understanding.
Neutrophil Extracellular Traps in Myocardial Tissue Drive Cardiac Dysfunction and Adverse Outcomes in Patients With Heart Failure With Dilated Cardiomyopathy
Authors: Ichimura Shohei , Misaka Tomofumi , Ogawara Ryo , Tomita Yusuke , Anzai Fumiya , Sato Yu , Miura Shunsuke , Yokokawa Tetsuro , Sato Takamasa , Oikawa Masayoshi , Kobayashi Atsushi , Yoshihisa Akiomi , Takeishi Yasuchika 
Published: June 2024

BACKGROUND:
The immune systems and chronic inflammation are implicated in the pathogenesis of dilated cardiomyopathy (DCM) and heart failure. However, the significance of neutrophil extracellular traps (NETs) in heart failure remains to be elucidated.

METHODS:
We enrolled consecutive 62 patients with heart failure with idiopathic DCM who underwent endomyocardial biopsy. Biopsy specimens were subjected to fluorescent immunostaining to detect NETs, and clinical and outcome data were collected. Ex vivo and in vivo experiments were conducted.

RESULTS:
The numbers of NETs per myocardial tissue area and the proportion of NETs per neutrophil were significantly higher in patients with DCM compared with non-DCM control subjects without heart failure, and the numbers of NETs were negatively correlated with left ventricular ejection fraction. Patients with DCM with NETs (n=32) showed lower left ventricular ejection fraction and higher BNP (B-type natriuretic peptide) than those without NETs (n=30). In a multivariable Cox proportional hazard model, the presence of NETs was independently associated with an increased risk of adverse cardiac events in patients with DCM. To understand specific underlying mechanisms, extracellular flux analysis in ex vivo revealed that NETs-containing conditioned medium from wild-type neutrophils or purified NET components led to impaired mitochondrial oxygen consumption of cardiomyocytes, while these effects were abolished when PAD4 (peptidyl arginine deiminase 4) in neutrophils was genetically ablated. In a murine model of pressure overload, NETs in myocardial tissue were predominantly detected in the acute phase and persisted throughout the ongoing stress. Four weeks after transverse aortic constriction, left ventricular ejection fraction was reduced in wild-type mice, whereas PAD4-deficient mice displayed preserved left ventricular ejection fraction without inducing NET formation.

CONCLUSIONS:
NETs in myocardial tissue contribute to cardiac dysfunction and adverse outcomes in patients with heart failure with DCM, potentially through mitochondrial dysfunction of cardiomyocytes.
Associations of Plasma Metabolites With Risks of Incident Stroke and Its Subtypes in Chinese Adults
Authors: Niu Rundong , Wang Hao , Peng Rong , Wang Wei , Lin Yuhui , Xiao Yang , Zhou Lue , Xu Xuedan , Mu Xuanwen , Zhang Xiaomin , He Meian , Li Wending , Wu Tangchun , Qiu Gaokun 
Published: June 2024

Background
Metabolomics studies have identified various metabolic markers associated with stroke risk, yet much uncertainty persists regarding heterogeneity in these associations between different stroke subtypes. We aimed to examine metabolic profiles associated with incident stroke and its subtypes in Chinese adults.

Methods and Results

We performed a nested case–control study within the Dongfeng‐Tongji cohort, including 1029 and 266 incident cases of ischemic stroke (IS) and hemorrhagic stroke (HS), respectively, with a mean follow‐up period of 6.1±2.3 years. Fifty‐five metabolites in fasting plasma were measured by ultra‐high‐performance liquid chromatography–mass spectrometry. We examined the associations of metabolites with the risks of total stroke, IS, and HS, with a focus on the comparison of associations of plasma metabolite with IS and HS, using conditional logistic regression. We found that increased levels of asymmetrical/symmetrical dimethylarginine and glutamate were significantly associated with elevated risk of total stroke (odds ratios and 95%, 1.20 [1.08–1.34] and 1.22 [1.09–1.36], respectively; both Benjamini‐Hochberg‐adjusted
P
<0.05). When examining stroke subtypes, asymmetrical/symmetrical dimethylarginine was nominally associated with both IS and HS (odds ratios [95% CIs]: 1.16 [1.03–1.31] and 1.39 [1.07–1.81], respectively), while glutamate was associated with only IS (odds ratios [95% CI]: 1.26 [1.11–1.43]). The associations of glutamate with IS risk were significantly stronger among participants with hypertension and diabetes than among those without these diseases (both
P
for interaction <0.05).

Conclusions
This study validated the positive associations of asymmetrical/symmetrical dimethylarginine and glutamate with stroke risk, mainly that of IS, in a Chinese population, and revealed a novel unanimous association of with both IS and HS. Our findings provided potential intervention targets for stroke prevention.
Delving into the diversity of genus Ironus Bastian, 1865 with special reference to Ironus dentifurcatus Argo & Heyns, 1972 (Ironidae: Enoplida), collected from coal mines
Authors: Asif Mohammad , Mahboob Mohammad , Rehman P. Fazal , Tahseen Qudsia 
Published: June 2024

Summary
In the exploration of nematode diversity within the coal mine spoil of Sonebhadra district, an isolate of Ironus dentifurcatus Argo & Heyns, 1972 was collected from the soil surrounding the roots of Prosopis juliflora. This study aims to unravel taxonomic intricacies of I. dentifurcatus through analysis of morphometric data, morphological characteristics utilising both light and scanning electron microscopy, and genetic scrutiny employing the SSU 18s rDNA gene marker. The study adds valuable information to the evolutionary history of I. dentifurcatus by constructing a comprehensive phylogenetic tree. This analysis is further augmented by an exploration of phylogeography and genetic divergence within the genus Ironus Bastian, 1865. The results reveal the genetic variability within the species of Ironus and the possible adaptative radiations in the group.
On the Self-Styled ‘Refutation’ of the ‘Seditious Jesus Hypothesis’
Authors: Bermejo-Rubio Fernando 
Published: June 2024

Abstract
The hypothesis according to which Jesus and his group were somehow involved in anti-Roman resistance has been systematically opposed by some quarters through the centuries. One of the most recent examples is Jesse P. Nickel’s The Things that Make for Peace: Jesus and Eschatological Violence, a book whose author boldly claims to have ‘refuted’ that hypothesis. The present article surveys this volume, concluding that it contains several misunderstandings of the field and method, as well as serious misrepresentations of the hypothesis under discussion, to the extent that everything indicates that it is influenced by theological presuppositions. These conclusions are not limited because Nickel’s book is representative of a much wider trend within the field.
Western Anti-Judaism Goes East
Authors: Minov Sergey 
Published: June 2024

Abstract
The article explores history of the reception of anti-Jewish hagiographical traditions of Western origin among Syriac Christians during the Islamic period by focusing on the textual tradition of the Miracles of the Virgin, a Western collection of Marian legends that was translated into Arabic during the thirteenth century and later on, during the nineteenth century, into Syriac. As an illustration, Syriac text and English translation of two relevant narratives from this work are offered: the Story of a young Frankish Jew and the Story of a Jewish boy.