bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotic susceptibility patterns of pathogens isolated from hospitalized patients with advanced HIV disease (AHD) in Bihar, India
Authors: Kumar Vikash , Murali Shreyas , Goldberg Jacob , Alonso Beatriz , Moretó-Planas Laura , Reid Anthony , Harshana Amit , Burza Sakib , Mahajan Raman 
Published: January 2024

Abstract

Objectives
To describe the prevalence of common bacterial pathogens and antibiotic susceptibility patterns amongst advanced HIV disease (AHD) patients admitted between May 2019 and March 2021 to a Médecins Sans Frontières (MSF)-supported AHD inpatient unit in Bihar, India.

Methods
A retrospective analysis of routinely collected demographic, clinical and microbiological data. Antibacterial susceptibility testing was done by an accredited referral laboratory using the modified Kirby–Bauer disc diffusion method.

Results
A total of 238 isolates from 577 patients were identified through culture testing. Patient median (IQR) age was 38 (31–45) years, and 75% were male. Predominant sample types included blood (600; 38%), urine (266; 17%) and sputum (178; 11%). Of the isolated bacteria, Escherichia coli (80; 13.9%) was the most prevalent, followed by Klebsiella pneumonia (54; 9.4%), Pseudomonas aeruginosa (22; 3.8%), Klebsiella oxytoca (10; 1.7%), Proteus mirabilis (9; 1.6%), and Acinetobacter baumannii (7; 1.2%). The resistance pattern showed that most bacterial isolates were highly resistant to commonly prescribed antibiotics such as third-generation cephalosporins, fluoroquinolones and co-trimoxazole. Most pathogens were moderately resistant to antibiotics from the WHO Watch group, such as meropenem and piperacillin/tazobactam. In contrast, isolates were more susceptible to aminoglycosides, such as amikacin, gentamicin and nitrofurantoin.

Conclusions
In Bihar, inpatients with AHD displayed a concerning array of antibiotic-resistant infections. This study provides a starting point from which further work on antimicrobial resistance in this vulnerable cohort of patients can be conducted.
Barriers and facilitators to the implementation of family cancer history collection tools in oncology clinical practices
Authors: Allen Caitlin G , Neil Grace , Halbert Chanita Hughes , Sterba Katherine R , Nietert Paul J , Welch Brandon , Lenert Leslie 
Published: January 2024

Abstract

Introduction
This study aimed to identify barriers and facilitators to the implementation of family cancer history (FCH) collection tools in clinical practices and community settings by assessing clinicians’ perceptions of implementing a chatbot interface to collect FCH information and provide personalized results to patients and providers.

Objectives
By identifying design and implementation features that facilitate tool adoption and integration into clinical workflows, this study can inform future FCH tool development and adoption in healthcare settings.

Materials and methods
Quantitative data were collected using survey to evaluate the implementation outcomes of acceptability, adoption, appropriateness, feasibility, and sustainability of the chatbot tool for collecting FCH. Semistructured interviews were conducted to gather qualitative data on respondents' experiences using the tool and recommendations for enhancements.

Results
We completed data collection with 19 providers (n = 9, 47%), clinical staff (n = 5, 26%), administrators (n = 4, 21%), and other staff (n = 1, 5%) affiliated with the NCI Community Oncology Research Program. FCH was systematically collected using a wide range of tools at sites, with information being inserted into the patient’s medical record. Participants found the chatbot tool to be highly acceptable, with the tool aligning with existing workflows, and were open to adopting the tool into their practice.

Discussion and conclusions
We further the evidence base about the appropriateness of scripted chatbots to support FCH collection. Although the tool had strong support, the varying clinical workflows across clinic sites necessitate that future FCH tool development accommodates customizable implementation strategies. Implementation support is necessary to overcome technical and logistical barriers to enhance the uptake of FCH tools in clinical practices and community settings.
Screening in Women With BRCA Mutations Revisited
Authors: Greenwood Heather I , Dodelzon Katerina 
Published: January 2024

Abstract
Patients with BRCA1 or BRCA2 gene mutations are at high risk for the development of breast cancer. This article reviews the current evidence for breast cancer screening of patients with BRCA1 or BRCA2 pathogenic gene mutations if they have not undergone prophylactic mastectomy. It will review the current evidence-based imaging recommendations for different modalities and ages of screening initiation in screening this patient population at high risk. Special considerations in transgender BRCA1 and BRCA2 mutation carriers are also discussed.
Collagen mutation and age contribute to differential craniofacial phenotypes in mouse models of osteogenesis imperfecta
Authors: Sung Hsiao H , Spresser Wyatt J , Hoffmann Joseph P , Dai Zongrui , Van der Kraan Peter M , Caird Michelle S , Davidson Esmeralda Blaney , Kozloff Kenneth M 
Published: January 2024

Abstract
Craniofacial and dentoalveolar abnormalities are present in all types of osteogenesis imperfecta (OI). Mouse models of the disorder are critical to understand these abnormalities and underlying OI pathogenesis. Previous studies on severely affected OI mice report a broad spectrum of craniofacial phenotypes, exhibiting some similarities to the human disorder. The Brtl/+ and G610c/+ are moderately severe and mild-type IV OI, respectively. Little is known about the aging effects on the craniofacial bones of these models and their homology to human OI. This study aimed to analyze the Brtl/+ and G610c/+ craniofacial morphometries during aging to establish suitability for further OI craniofacial bone intervention studies. We performed morphological measurements on the micro-CT-scanned heads of 3-wk-old, 3-mo-old, and 6-mo-old female Brtl/+ and G610c/+ mice. We observed that Brtl/+ skulls are shorter in length than WT (P &lt; .05), whereas G610c/+ skulls are similar in length to their WT counterparts. The Brtl/+ mice exhibit alveolar bone with a porotic-like appearance that is not observed in G610c/+. As they age, Brtl/+ mice show severe bone resorption in both the maxilla and mandible (P &lt; .05). By contrast, G610c/+ mice experience mandibular resorption consistently across all ages, but maxillary resorption is only evident at 6 mo (P &lt; .05). Western blot shows high osteoclastic activities in the Brtl/+ maxilla. Both models exhibit delayed pre-functional eruptions of the third molars (P &lt; .05), which are similar to those observed in some bisphosphonate-treated OI subjects. Our study shows that the Brtl/+ and G610c/+ mice display clear features found in type IV OI patients; both show age-related changes in the craniofacial growth phenotype. Therefore, understanding the craniofacial features of these models and how they age will allow us to select the most accurate mouse model, mouse age, and bone structure for the specific craniofacial bone treatment of differing OI groups.
18F-Sodium fluoride PET-CT visualizes disease activity in chronic nonbacterial osteitis in adults
Authors: Leerling Anne T , Smit Frits , Spӓth Zita , Cañete Ana Navas , de Geus-Oei Lioe-Fee , van de Burgt Alina , Dekkers Olaf M , van der Bruggen Wouter , Appelman-Dijkstra Natasha M , Vriens Dennis , Winter Elizabeth M 
Published: January 2024

Abstract
Chronic nonbacterial osteitis (CNO) is a rare disease spectrum, which lacks biomarkers for disease activity. Sodium fluoride-18 positron emission tomography/computed tomography ([18F]NaF-PET/CT) is a sensitive imaging tool for bone diseases and yields quantitative data on bone turnover. We evaluated the capacities of [18F]NaF-PET/CT to provide structural and functional assessment in adult CNO. A coss-sectional study was performed including 43 adult patients with CNO and 16 controls (patients referred for suspected, but not diagnosed with CNO) who underwent [18F]NaF-PET/CT at our expert clinic. Structural features were compared between patients and controls, and maximal standardized uptake values (SUVmax [g/mL]) were calculated for bone lesions, soft tissue/joint lesions, and reference bone. SUVmax was correlated with clinical disease activity in patients. Structural assessment revealed manubrial and costal sclerosis/hyperostosis and calcification of the costoclavicular ligament as typical features associated with CNO. SUVmax of CNO lesions was higher compared with in-patient reference bone (mean paired difference: 11.4; 95% CI: 9.4–13.5; p &lt; .001) and controls (mean difference: 12.4; 95%CI: 9.1–15.8; p &lt; .001). The highest SUVmax values were found in soft tissue and joint areas such as the costoclavicular ligament and manubriosternal joint, and these correlated with erythrocyte sedimentation rate in patients (correlation coefficient: 0.546; p &lt; .002). Our data suggest that [18F]NaF-PET/CT is a promising imaging tool for adult CNO, allowing for detailed structural evaluation of its typical bone, soft-tissue, and joint features. At the same time, [18F]NaF-PET/CT yields quantitative bone remodeling data that represent the pathologically increased bone turnover and the process of new bone formation. Further studies should investigate the application of quantified [18F]NaF uptake as a novel biomarker for disease activity in CNO, and its utility to steer clinical decision making.
Agricultural issues with climate change—case studies with 3 soybean pests: Johnsongrass, kudzu bug, and charcoal rot
Authors: Carley Danesha Seth , Cook Jennifer , Emerine Sherrie 
Published: January 2024

Abstract
Agricultural production and crop yields are threatened around the world by the emergence and spread of agronomical pests, including diseases, insects, and weeds. Due to changes in precipitation, carbon dioxide levels, and warming temperatures being experienced throughout most of the world, new challenges are emerging for pest management in virtually all major cropping systems. While precise environmental impacts due to climate change are impossible to predict, they will require innovative and new solutions for pest management. In this article, we explore the challenges of 3 problem pest species with soybean: Johnsongrass, kudzu bug, and charcoal rot. Understanding pest responses to climate change is vital for better understanding the new agricultural innovations that will be required to manage them in the future.
Discontinuation of Contact Precautions for Methicillin-resistant Staphylococcus aureus in a Pediatric Healthcare System
Authors: Most Zachary M , Phillips Bethany , Sebert Michael E 
Published: January 2024

Abstract

Background
Many hospitals caring for adult patients have discontinued the requirement for contact precautions (CP) for patients with methicillin-resistant Staphylococcus aureus (MRSA) infection or colonization without reported negative effects. It is not clear whether this experience can be extrapolated to pediatric facilities.

Methods
CP for MRSA were discontinued in all locations except the neonatal intensive care unit at a 3-hospital pediatric healthcare system in September 2019. All hospitalized patients underwent surveillance for LabID healthcare facility-onset MRSA infections. Analysis was done using interrupted time series (ITS) from September 2017 through August 2023 and aggregate before-and-after rate ratios.

Results
There were 234 incident healthcare facility-onset MRSA infections during 766 020 patient days of surveillance. After discontinuation of CP for MRSA there was no change in the ITS slope (0.06, 95% CI: −0.35 to 0.47, P = .78) or intercept (0.21, 95% CI: −0.36 to 0.78, P = .47) of the LabID healthcare facility-onset MRSA infection incidence density rate. Additionally, there was no change in the aggregate incidence density rate of these MRSA LabID events (aggregate rate ratio = 0.98, 95% CI: 0.74 to 1.28). MRSA nasal colonization among patients being screened before cardiac surgery did not change (aggregate rate ratio = 0.94, 95% CI: 0.60 to 1.48). The prevalence rate of contact isolation days decreased by 14.0%.

Conclusions
Discontinuation of CP for pediatric patients with MRSA was not associated with increased MRSA infection over 4 years. Our experience supports considering discontinuation of CP for MRSA in similar pediatric healthcare settings in the context of good adherence to horizontal infection prevention measures.
Necessary conditions for the formation of filaments and star clusters in the cold neutral medium
Authors: Pillsworth Rachel , Pudritz Ralph E 
Published: January 2024

ABSTRACT
Star formation takes place in filamentary molecular clouds which arise by physical processes that take place in the cold neutral medium (CNM). We address the necessary conditions for this diffuse (n ≈ 30 cm−3), cold (T ≈ 60 K), magnetized gas undergoing shock waves, and supersonic turbulence, to produce filamentary structures capable of fragmenting into cluster forming regions. Using ramses and a magnetized CNM environment as our initial conditions, we simulate a 0.5 kpc turbulent box to model a uniform gas with magnetic field strength of 7 μG, varying the 3D velocity dispersion via decaying turbulence. We use a surface density of 320 M⊙ pc−2, representative of the inner 4.0 kpc central molecular zone of the Milky Way and typical luminous galaxies. Filamentary molecular clouds are formed dynamically via shocks within a narrow range of velocity dispersions in the CNM of 5–10 km s−1 with a preferred value at 8 km s−1. Cluster sink particles appear in filaments which exceed their critical line mass, occurring optimally for velocity dispersions of 8 km s−1. Tracking the evolution of magnetic fields, we find that they lead to double the dense star-forming gas than in purely hydro runs. Perpendicular orientations between magnetic field and filaments can increase the accretion rates onto filaments and hence their line masses. Because magnetic fields help support gas, magnetohydrodynamic runs result in average temperatures an order of magnitude higher than unmagnetized counterparts. Finally, we find magnetic fields delay the onset of cluster formation by ∝ 0.4 Myr.
Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems
Authors: Rakesh Siuli , Aravind L , Krishnan Arunkumar 
Published: January 2024

Abstract
The DndABCDE systems catalysing the unusual phosphorothioate (PT) DNA backbone modification, and the DndFGH systems, which restrict invasive DNA, have enigmatic and paradoxical features. Using comparative genomics and sequence-structure analyses, we show that the DndABCDE module is commonly functionally decoupled from the DndFGH module. However, the modification gene-neighborhoods encode other nucleases, potentially acting as the actual restriction components or suicide effectors limiting propagation of the selfish elements. The modification module's core consists of a coevolving gene-pair encoding the DNA-scanning apparatus – a DndD/CxC-clade ABC ATPase and DndE with two ribbon-helix-helix (MetJ/Arc) DNA-binding domains. Diversification of DndE’s DNA-binding interface suggests a multiplicity of target specificities. Additionally, many systems feature DNA cytosine methylase genes instead of PT modification, indicating the DndDE core can recruit other nucleobase modifications. We show that DndFGH is a distinct counter-invader system with several previously uncharacterized domains, including a nucleotide kinase. These likely trigger its restriction endonuclease domain in response to multiple stimuli, like nucleotides, while blocking protective modifications by invader methylases. Remarkably, different DndH variants contain a HerA/FtsK ATPase domain acquired from multiple sources, including cellular genome-segregation systems and mobile elements. Thus, we uncovered novel HerA/FtsK-dependent defense systems that might intercept invasive DNA during replication, conjugation, or packaging.
THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration
Authors: Yang Wen-Qing , Ge Jian-Yang , Zhang Xiaofeng , Zhu Wen-Yu , Lin Lin , Shi Yigong , Xu Beisi , Liu Ru-Juan 
Published: January 2024

Abstract
The mechanisms by which the relatively conserved spliceosome manages the enormously large number of splicing events that occur in humans (∼200 000 versus ∼300 in yeast) are poorly understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G) on the G72 of U6 snRNA (the catalytic center of the spliceosome) promotes efficient pre-mRNA splicing activity in human cells. This modification was identified to be conserved among vertebrates. Further, THUMPD2 was demonstrated as the methyltransferase responsible for U6 m2G72 by explicitly recognizing the U6-specific sequences and structural elements. The knock-out of THUMPD2 eliminated U6 m2G72 and impaired the pre-mRNA splicing activity, resulting in thousands of changed alternative splicing events of endogenous pre-mRNAs in human cells. Notably, the aberrantly spliced pre-mRNA population elicited the nonsense-mediated mRNA decay pathway. We further show that THUMPD2 was associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome regulates global pre-mRNA splicing and impacts physiology and disease.
Predicting the spread of SARS-CoV-2 variants: An artificial intelligence enabled early detection
Authors: Levi Retsef , Zerhouni El Ghali , Altuvia Shoshy 
Published: January 2024

Abstract
During more than 3 years since its emergence, SARS-CoV-2 has shown great ability to mutate rapidly into diverse variants, some of which turned out to be very infectious and have spread throughout the world causing waves of infections. At this point, many countries have already experienced up to six waves of infections. Extensive academic work has focused on the development of models to predict the pandemic trajectory based on epidemiological data, but none has focused on predicting variant-specific spread. Moreover, important scientific literature analyzes the genetic evolution of SARS-CoV-2 variants and how it might functionally affect their infectivity. However, genetic attributes have not yet been incorporated into existing epidemiological modeling that aims to capture infection trajectory. Thus, this study leverages variant-specific genetic characteristics together with epidemiological information to systematically predict the future spread trajectory of newly detected variants. The study describes the analysis of 9.0 million SARS-CoV-2 genetic sequences in 30 countries and identifies temporal characteristic patterns of SARS-CoV-2 variants that caused significant infection waves. Using this descriptive analysis, a machine-learning-enabled risk assessment model has been developed to predict, as early as 1 week after their first detection, which variants are likely to constitute the new wave of infections in the following 3 months. The model’s out-of-sample area under the curve (AUC) is 86.3% for predictions after 1 week and 90.8% for predictions after 2 weeks. The methodology described in this paper could contribute more broadly to the development of improved predictive models for variants of other infectious viruses.
Slowly but surely: Exposure of communities and infrastructure to subsidence on the US east coast
Authors: Ohenhen Leonard O , Shirzaei Manoochehr , Barnard Patrick L 
Published: January 2024

Abstract
Coastal communities are vulnerable to multihazards, which are exacerbated by land subsidence. On the US east coast, the high density of population and assets amplifies the region's exposure to coastal hazards. We utilized measurements of vertical land motion rates obtained from analysis of radar datasets to evaluate the subsidence-hazard exposure to population, assets, and infrastructure systems/facilities along the US east coast. Here, we show that 2,000 to 74,000 km2 land area, 1.2 to 14 million people, 476,000 to 6.3 million properties, and &gt;50% of infrastructures in major cities such as New York, Baltimore, and Norfolk are exposed to subsidence rates between 1 and 2 mm per year. Additionally, our analysis indicates a notable trend: as subsidence rates increase, the extent of area exposed to these hazards correspondingly decreases. Our analysis has far-reaching implications for community and infrastructure resilience planning, emphasizing the need for a targeted approach in transitioning from reactive to proactive hazard mitigation strategies in the era of climate change.
GASZ self-interaction clusters mitochondria into the intermitochondrial cement for proper germ cell development
Authors: Miao Junru , Wang Chuanyun , Chen Wei , Wang Yongsheng , Kakasani Shalin , Wang Yuan 
Published: January 2024

Abstract
Mitochondrial features and activities vary in a cell type- and developmental stage-dependent manner to critically impact cell function and lineage development. Particularly in male germ cells, mitochondria are uniquely clustered into intermitochondrial cement (IMC), an electron-dense granule in the cytoplasm to support proper spermatogenesis. But it remains puzzling how mitochondria assemble into such a stable structure as IMC without limiting membrane during development. Here, we showed that GASZ (germ cell-specific, ankyrin repeat, SAM and basic leucine zipper domain containing protein), a mitochondrion-localized germ cell-specific protein, self-interacted with each other to cluster mitochondria and maintain protein stability for IMC assembling. When the self-interaction of GASZ was disrupted by either deleting its critical interaction motif or using a blocking peptide, the IMC structure was destabilized, which in turn led to impaired spermatogenesis. Notably, the blocked spermatogenesis was reversible once GASZ self-interaction was recovered. Our findings thus reveal a critical mechanism by which mitochondrion-based granules are properly assembled to support germ cell development while providing an alternative strategy for developing nonhormonal male contraceptives by targeting IMC protein interactions.