bluuebunny/crossref_metadata_2025_split huggingface dataset:
Narratives, Knowledge Objects, and the Making of Great Power Competition
Authors: Müller Thomas 
Published: September 2024

AbstractWhat makes great power relations more (or less) competitive? One key argument in International Relations (IR) is that interpretations matter and shape how competitive great power relations are. This article seeks to further develop this argument. Drawing on objectual IR and the sociology of expectations, it proposes a constructivist framework that unpacks two crucial, yet surprisingly little studied aspects of the making of great power competition: (i) the constitution and organization of great power relations as a contest over scarce goods and (ii) the interplay of narratives and knowledge objects that underpins it. To illustrate the framework and contribute to theory development, the article reconstructs the dynamics of two prominent dimensions of great power competition in the past decade: The tensions between NATO and Russia in Europe and the economic competition between the United States and China. It shows that the making of great power competition involves three interrelated elements: the framing of relations among powerful states as contests over some valued goods, the production of knowledge about the distribution of these goods, and governance arrangements stipulating rules for the contests. What underpins the three elements is an interplay of narratives and knowledge objects: General narratives of what the competition is about and what is at stake preconfigure which knowledge objects are regarded as pertinent. The pertinent knowledge objects, in turn, shape the specific narratives that are told about how the competition unfolds.
The imperative of teamwork in antimicrobial stewardship (AMS) interventions: insights from an ethnographic study with practitioners in Spain
Authors: Moreno Lozano Cristina 
Published: September 2024

Abstract
Teamwork—the activity of working together in a group towards a similar goal—is a defining feature of the practice of clinical medicine carried out in hospitals and other healthcare facilities. This Viewpoint suggests that teamwork is a defining feature of antimicrobial stewardship (AMS) programmes, and identifies six elements that characterise AMS team dynamics. These insights arise from an original ethnographic study of AMS carried out in Spain, where these programmes are known as Programas para la Optimización de Antimicrobianos. The study used qualitative research methods including ethnographic observations in public hospitals and scientific and educational fora, in-depth interviews and archival research. It calls for a reflection on the part of the global community of AMS practitioners on the role of team dynamics in building sustainable AMS interventions and the inclusion of teamwork skills in training curricula aimed at future practitioners.
Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting
Authors: Stoesser N , George R , Aiken Z , Phan H T T , Lipworth S , Quan T P , Mathers A J , De Maio N , Seale A C , Eyre D W , Vaughan A , Swann J , Peto T E A , Crook D W , Cawthorne J , Dodgson A , Walker A S ,   TRACE Investigators Group, Aiken Zoie , Akinremi Oluwafemi , Ali Aiysha , Cawthorne Julie , Cleary Paul , Crook Derrick W , Decraene Valerie , Dodgson Andrew , Doumith Michel , Ellington Matthew J , George Ryan , Grimshaw John , Guiver Malcolm , Hill Robert , Hopkins Katie L , Jones Rachel , Lenney Cheryl , Mathers Amy J , McEwan Ashley , Moore Ginny , Mumford Andrew , Neilson Mark , Neilson Sarah , Peto Tim E A , Phan Hang T T , Regan Mark , Seale Anna C , Stoesser Nicole , Turner-Gardner Jay , Watts Vicky , Sarah Walker A , Walker Jimmy , Welfare William , Woodford Neil , Wyllie David H 
Published: September 2024

Abstract

Background
Healthcare-associated wastewater and asymptomatic patient reservoirs colonized by carbapenemase-producing Enterobacterales (CPE) contribute to nosocomial CPE dissemination, but the characteristics and dynamics of this remain unclear.

Methods
We systematically sampled wastewater sites (n = 4488 samples; 349 sites) and patients (n = 1247) across six wards over 6–12 months to understand blaKPC-associated CPE (KPC-E) diversity within these reservoirs and transmission in a healthcare setting. Up to five KPC-E-positive isolates per sample were sequenced (Illumina). Recombination-adjusted phylogenies were used to define genetically related strains; assembly and mapping-based approaches were used to characterize antimicrobial resistance genes, insertion sequences (ISs) and Tn4401 types/target site sequences. The accessory genome was evaluated in some of the largest clusters, and those crossing reservoirs.

Results
Wastewater site KPC-E-positivity was substantial [101/349 sites (28.9%); 228/5601 (4.1%) patients cultured]. Thirteen KPC-E species and 109 strains were identified using genomics, and 24% of wastewater and 26% of patient KPC-E-positive samples harboured one or more strains. Most diversity was explained by the individual niche, suggesting localized factors are important in selection and spread. Tn4401 + flanking target site sequence diversity was greater in wastewater sites (P &lt; 0.001), which might favour Tn4401-associated transposition/evolution. Shower/bath- and sluice/mop-associated sites were more likely to be KPC-E-positive (adjusted OR = 2.69; 95% CI: 1.44–5.01; P = 0.0019; and adjusted OR = 2.60; 95% CI: 1.04–6.52; P = 0.0410, respectively). Different strains had different blaKPC dissemination dynamics.

Conclusions
We identified substantial and diverse KPC-E colonization of wastewater sites and patients in this hospital setting. Reservoir and niche-specific factors (e.g. microbial interactions, selection pressures), and different strains and mobile genetic elements likely affect transmission dynamics. This should be considered in surveillance and control strategies.
DxGoals: A Software Tool for Determining and Analyzing Clinically Meaningful Classification Accuracy Goals for Diagnostic Tests
Authors: Nguyen Ngoc-Ty , Pennello Gene A 
Published: September 2024

Abstract

Background
To evaluate diagnostic tests for low prevalence conditions, classification accuracy metrics such as sensitivity, specificity, and positive likelihood ratio (PLR) and negative likelihood ratio (NLR) are advantageous because they are prevalence-independent and thus estimable in studies enriched for the condition. However, classification accuracy goals are often chosen without a clear understanding of whether they are clinically meaningful. Pennello (2021) proposed a risk stratification framework for determining classification accuracy goals. A software application is needed to determine the goals and provide data analysis.

Methods
We introduce DxGoals, a freely available, R-Shiny software application for determining, visualizing, and analyzing classification accuracy goals for diagnostic tests. Given prevalence p for the target condition and specification that a test's positive and negative predictive values PPVand NPV=1−cNPV should satisfy PPV&gt;PPV* and cNPV&lt;cNPV*, DxGoals uses Bayes Theorem to determine equivalent goals for PLR and NLR and implied goals for sensitivity and specificity. When study data are provided, DxGoals analyzes whether the determined goals are met with statistical significance. When comparing 2 tests, DxGoals translates a superiority or noninferiority goals for the differences PPV−p and p−cNPV to equivalent goals for PLR and NLR and analyzes the goals when data are provided.

Results
We illustrate DxGoals on tests for penicillin allergy, ovarian cancer, and cervical cancer. The inputs cNPV*,p, and PPV* were informed by clinical management guidelines.

Conclusions
DxGoals facilitates determination, visualization, and analysis of clinically meaningful standalone and comparative classification accuracy goals. It is a potentially useful tool for diagnostic test evaluation.
Total Copper and Labile Bound Copper Fraction as a Selective and Sensitive Tool in the Evaluation of Wilson Disease
Authors: Bornhorst Joshua A , Bitzer Anna C , Day Patrick L , Wermers Michelle , Smith Carin Y , Pazdernik Vanessa K , Pelto Ryan , Sankaran Banu , Quicquaro Adam , Jannetto Paul J 
Published: September 2024

Abstract

Background
A dual filtration-based method for determination of serum labile bound copper (LBC) and LBC fraction (LBC/total copper) was developed. Reduced total copper, elevated LBC, and elevated LBC fraction have been reported in Wilson disease (WD).

Methods
To evaluate the diagnostic performance of these markers, samples were obtained from 21 WD treatment-naïve (WD-TN, no WD treatment or &lt;28 days of treatment) patients, 46 WD standard-of-care–treated (WD-SOC) patients, along with 246 patients representing other potential disorders of copper status. These were then compared to 213 reference interval population patients.

Results
Receiver operating characteristic curves for the reference population vs WD-TN yielded areas under the curve for total copper, LBC, and LBC fraction, of 0.99, 0.81, and 0.98, respectively. Using Youden cutoffs, sensitivity/specificity for WD-TN was 95%/97% for total copper, 71%/85% for LBC, and 95%/94% for LBC fraction. LBC values, but not total copper and LBC fraction, differed substantially between WD-TN and WD-SOC cohorts.
We propose a dual model wherein total copper and LBC fraction results must agree to be classified as a “positive” or “negative” result for WD. This correctly classified 19/21 WD-TN patients as positive, and 194/213 reference interval patients as negative. The remaining “indeterminate” patients (representing approximately 9% of the reference and the WD-TN populations) exhibited conflicting total copper and LBC fraction results. When indeterminate results are excluded, this model exhibited apparent 100% sensitivity/specificity.

Conclusions
Agreement of total serum copper and LBC fraction classification may constitute an effective “rule-in” and “rule-out” assessment for WD-TN patients.
Cardiac Troponin to Adjudicate Subclinical Heart Failure in Diabetic Patients and a Murine Model of Metabolic Syndrome
Authors: Brown Hannah M , Spies Nicholas C , Jia Wentong , Moley John , Lawless Sydney , Roemmich Brittany , Brestoff Jonathan R , Zaydman Mark A , Farnsworth Christopher W 
Published: September 2024

Abstract

Background
Cardiovascular disease, kidney health, and metabolic disease (CKM) syndrome is associated with significant morbidity and mortality, particularly from congestive heart failure (CHF). Guidelines recommend measurement of cardiac troponin (cTn) to identify subclinical heart failure (HF) in diabetics/CKM. However, appropriate thresholds and the impact from routine screening have not been elucidated.

Methods
cTnI was assessed using the Abbott high sensitivity (hs)-cTnI assay in outpatients with physician-ordered hemoglobin A1c (Hb A1c) and associated with cardiac comorbidities/diagnoses, demographics, and estimated glomerular filtration rate (eGFR). Risk thresholds used in CKM staging guidelines of &gt;10 and &gt;12 ng/L for females and males, respectively, were used. Multivariate logistic regression was applied. hs-cTnI was assessed in a high-fat-diet induced murine model of obesity and diabetes.

Results
Of 1304 patients, 8.0% females and 15.7% males had cTnI concentrations above the risk thresholds. Thirty-one (4.2%) females and 23 (4.1%) males had cTnI above the sex-specific 99% upper reference limit. A correlation between hs-cTnI and Hb A1c (R = 0.2) and eGFR (R = −0.5) was observed. hs-cTnI concentrations increased stepwise based on A1C of &lt;5.7% (median = 1.5, IQR:1.3–1.8), 5.7%–6.4% (2.1, 2.0–2.4), 6.5%–8.0% (2.8, 2.5–3.2), and &gt;8% (2.8, 2.2–4.3). Male sex (P &lt; 0.001), eGFR (P &lt; 0.001), and CHF (P = 0.004) predicted elevated hs-cTnI. Obese and diabetic mice had increased hs-cTnI (7.3 ng/L, 4.2–10.4) relative to chow-fed mice (2.6 ng/L, 1.3–3.8).

Conclusion
A high proportion of outpatients with diabetes meet criteria for subclinical HF using hs-cTnI measurements. Glucose control is independently associated with elevated cTnI, a finding replicated in a murine model of metabolic syndrome.
The effect of vitamin D3 and omega-3 combination, taken orally, on triglycerides, lining of intestine, and the biodiversity of gut microbiota in healthy rats
Authors: Abdulrazzaq Shaymaa B , Abu-Samak Mahmoud , Omar Amin , Barakat Muna , Alzaghari Lujain F , Mosleh Ibrahim , Al-Najjar Moath , Al-Najjar Mohammad A A 
Published: September 2024

Abstract

Aim
The gut microbiota plays a key role in host health. An intake of omega-3 and vitamin D3 in a separate manner is vital for maintaining good health of gut microbiota and controlling some illness manifestations. The aim of this study is to investigate the potential change in biodiversity of the gut microbiome in healthy rats supplemented with vitamin D3, omega-3 alone and their combination and to reflect onto the triglyceride levels in serum and fecal samples.

Methods and results
Using the 16S rRNA gene Miseq Illumina NGS, and monitoring triglyceride levels in serum and fecal samples coupled with several clinical parameters, we examined the effect of orally taken combination of omega-3 and vitamin D3 alongside the separate intake of supplements on gut microbiota in 24 healthy white Wistar rats for six weeks. The study findings showed that combination treatment encouraged the growth of opportunistic Clostridia class during day 21 and 42 of treatment by 7.7 and 7.4 folds, respectively, exhibited incomplete absorption levels for both supplements when used concomitantly, demonstrated a damaging effect on the gut intestinal lining wall thickness (126 µm) when compared to control group (158  µm), increasing lumen diameter (400 µm), and showed higher triglyceride level in fecal samples.

Conclusions
These findings indicate that omega-3 and vitamin D3 supplements as combination intake reveal unfavorable effects, thus, it is advised to conduct further in-depth studies to clarify the presence or absence of any chemical interaction between both supplements’ molecules and to investigate based on human model to attain a superior perspective.
Sheep and goats as reservoirs of colistin-resistant E. coli: first detection of ETEC ST10 and E. coli ST6396 mcr-1 positive strains in North Africa
Authors: Boukli-Hacene Fella , Djouadi Lydia Neïla , Raddaoui Anis , Hachem Yousra , Boumerdassi Hanane , Achour Wafa , Nateche Farida 
Published: September 2024

Abstract

Aim
This study aimed to screen and characterize colistin-resistant strains isolated from different livestock species in Algeria, including sheep, goats, and dromedaries.

Methods and results
A total of 197 rectal and nasal swabs were screened for colistin-resistant Gram-negative bacilli. Twenty one isolates were selected, identified, and their antibiotic resistance was phenotypically and genotypically characterized. The majority (15/21) were affiliated to Escherichia coli, from which 4 strains isolated from sheep (n = 2) and goats (n = 2) and belonging to phylogroup A and ST10 and ST6396 lineages, respectively, carried the mcr-1 gene. The remaining isolates were identified as belonging to the following genera: Raoultella, Enterobacter, Klebsiella, and Pseudomonas.

Conclusion
This study highlights the presence of virulent and multiresistant Gram-negative bacilli in farm animals, increasing the risk of transmitting potentially fatal infections to humans.
Language, 6-mercaptopurine adherence, and relapse in children with acute lymphoblastic leukemia
Authors: Robles Joanna , Chen Yanjun , Hageman Lindsey , Aristizabal Paula , Landier Wendy , Bhatia Smita , Wadhwa Aman 
Published: September 2024

Abstract
Hispanic children with acute lymphoblastic leukemia (ALL) have lower 6-mercaptopurine (6MP) adherence and greater hazard of relapse compared with non-Hispanic White children. We examined the association between Spanish language and 6MP adherence, and hazard of relapse. 6MP adherence was measured electronically over a 6-month period. Participants were grouped by the language of demographic questionnaire completion: Non-Hispanic White-English Speaking (ES, n = 159), Hispanic-Spanish Speaking (Hispanic-SS, n = 59), and Hispanic-ES (n = 109). Hispanic-ES had significantly lower fitted median 6MP adherence compared with non-Hispanic White-ES participants (88.3%, 95% CI = 84.7% to 91.2% vs 95.0%, 95% CI = 93.6% to 96.2%, P &lt; .001). There was no difference in fitted median 6MP adherence between Hispanic-ES and Hispanic-SS participants (88.3%, 95% CI = 84.1% to 91.5% vs 88.3%, 95% CI = 84.7% to 91.2%, P = .9) or adjusted hazard of relapse for Hispanic-SS participants (HR = 0.9, 95%CI = 0.3 to 2.4, P = .8). Spanish language use among Hispanic patients with ALL is not associated with lower 6MP adherence or greater relapse risk. Factors related to Hispanic ethnicity, apart from language, appear to influence adherence.
Machine learning of metabolite–protein interactions from model-derived metabolic phenotypes
Authors: Habibpour Mahdis , Razaghi-Moghadam Zahra , Nikoloski Zoran 
Published: September 2024

Abstract
Unraveling metabolite–protein interactions is key to identifying the mechanisms by which metabolism affects the function of other cellular layers. Despite extensive experimental and computational efforts to identify the regulatory roles of metabolites in interaction with proteins, it remains challenging to achieve a genome-scale coverage of these interactions. Here, we leverage established gold standards for metabolite–protein interactions to train supervised classifiers using features derived from genome-scale metabolic models and matched data on protein abundance and reaction fluxes to distinguish interacting from non-interacting pairs. Through a comprehensive comparative study, we explore the impact of different features and assess the effect of gold standards for non-interacting pairs on the performance of the classifiers. Using data sets from Escherichia coli and Saccharomyces cerevisiae, we demonstrate that the features constructed by integrating fluxomic and proteomic data with metabolic phenotypes predicted from genome-scale metabolic models can be effectively used to train classifiers, accurately predicting metabolite–protein interactions in the context of metabolism. Our results reveal that the high performance of classifiers trained on these features is unaffected by the method used to generate gold standards for non-interacting pairs. Overall, our study introduces valuable features that improve the performance of identifying metabolite–protein interactions in the context of metabolism.
Diagnostic Dilemmas: A Review of Reported Cases of Human Herpesvirus 6 Encephalitis in Immunocompetent Adults
Authors: Webb Gemma , Leong Mei Yen Michelle , Bishop Emma , Sehu Marjoree 
Published: September 2024

Abstract
Human herpesvirus 6 (HHV-6) is associated with its presentation in the pediatric population as roseola infantum. Rarely, it is the causative agent of encephalitis, with most cases reported among the immunocompromised population due to reactivation. This review article analyzes the published records of cases labeled HHV-6 encephalitis in immunocompetent adults, aiming to understand the diagnostic methods behind each case and explore the complexities of such a diagnosis. We note significant variability in the methods used to come to a diagnosis of HHV-6 encephalitis, as well as inconsistent approaches to treatment of this condition. Given the rarity of HHV-6 encephalitis in immunocompetent adults, there are no clearly structured diagnostic guidelines for this condition in this patient population. We highlight several diagnostic methods that provide more convincing evidence of true HHV-6 encephalitis and may provide a basis for further development of guidelines for the diagnosis and treatment of this condition.
Multispecies Cocirculation of Adenoviruses Identified by Next-Generation Sequencing During an Acute Gastroenteritis Outbreak in Coastal Kenya in 2023
Authors: Lambisia Arnold W , Mutunga Martin , Katama Esther N , Agoti Charles N , Houldcroft Charlotte J 
Published: September 2024

Abstract

Background
Although 7 human adenovirus (HAdV) species are known to exist, only F (types 40 and 41) and G are identified as diarrheal disease agents. The role of other HAdV species in diarrheal disease remains unclear, and data on their prevalence are limited. We describe HAdV species and types in hospitalized children with diarrhea in coastal Kenya.

Methods
Three hundred twenty-nine stool samples collected between June 2022 and August 2023 from children aged &lt;13 years were screened for HAdV using quantitative polymerase chain reaction (qPCR). Positive HAdV cases were genotyped by adenovirus primers from the RespiCoV panel by amplification, next-generation sequencing, and phylogenetic analysis.

Results
Sixty-five samples (20%) tested HadV positive, of which 5 HAdV species were identified. Other than HAdV F, other species included A, B, C, and D; these were detected as either mono-detections or coinfections. Six HAdV F identified by NGS had been missed by our qPCR typing method. This appeared to be as a result of a 133-nucleotide deletion in the long fiber protein, which abrogated a primer and probe binding site. Based on grading of diarrheal disease severity using VESIKARI scores, 93% of the HAdV cases presented with severe disease. One child with an HAdV F infection died.

Conclusions
Our study shows the enormous diversity and clinical characteristics of HAdV species in children with diarrhea in coastal Kenya. These data offer an opportunity to improve current diagnostic assays and increase knowledge of HAdV in Africa for control of outbreaks in the future.
Sendai virus-mediated RNA delivery restores fertility to congenital and chemotherapy-induced infertile female mice
Authors: Kanatsu-Shinohara Mito , Morimoto Hiroko , Liu Tianjiao , Tamura Masaru , Shinohara Takashi 
Published: September 2024

Abstract
Current infertility treatment strategies focus on mature gametes, leaving a significant proportion of cases with gamete progenitors that stopped complete differentiation. On the other hand, recent advancements in next-generation sequencing have identified many candidate genes that may promote maturation of germ cells. Although gene therapy has shown success in mice, concerns about the integration of DNA vectors into oocytes hinder clinical applications. Here, we present the restoration of fertility in female mice through Sendai virus (SeV)-mediated RNA delivery. Ovaries lacking Kitl expression exhibit only primordial follicles due to impaired signaling to oocytes expressing the KIT tyrosine kinase. Despite SeVs being immunogenic and larger than the blood-follicle barrier, the administration of Kitl-expressing SeVs reinitiated oogenesis in genetically infertile mice that have only primordial follicles, resulting in the birth of normal offspring through natural mating. This virus also effectively addressed iatrogenic infertility induced by busulfan, a widely used cancer chemotherapy agent. Offspring born through SeV administration and natural mating displayed normal genomic imprinting patterns and fertility. Since SeVs pose no genotoxicity risk, the successful restoration of fertility by SeVs represents a promising approach for treating congenital infertility with somatic cell defects and protecting fertility of cancer patients who may become infertile due to loss of oocytes during cancer therapy.