bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in antibiotic resistance patterns for children and adults treated at 166 non-affiliated US facilities using EHR data
Authors: Sivasankar Shivani , Goldman Jennifer L , Hoffman Mark A 
Published: January 2023

Abstract

Background
Antibiotic resistance (AR) is a global public health threat. Surveillance of baseline AR and trends and emerging resistance among priority bacterial isolates with respect to the age of the patients and the type of healthcare setting are required due to differences in antimicrobial need and use in these populations.

Methods
We performed a retrospective study using deidentified electronic health record (EHR) data in the Cerner Health Facts™ data warehouse. Antibiotic susceptibility data were extracted for all bacterial isolates of interest at 166 non-affiliated healthcare facilities reporting microbiology susceptibility results of the FDA recommended antibiotics between the years 2012 to 2017. We assessed and visualized the slope coefficient from linear regression to compare changes in resistance over time for the four patient care groups.

Results
The trends in resistance rates to clinically relevant antibiotics were influenced by age and care setting. For example, ertapenem-resistant Enterobacter cloacae isolates from children overall increased significantly compared with adults (0.7% to 9.8%, 2.1% to 2.8%, P = 0.00013) and isolates from children in paediatric facilities increased significantly compared with facilities treating adults and children (0.1% to 27.1%, 0.9% to 3.8%, P = 0.0002).

Conclusions
Large-scale analysis of EHR data from 166 facilities shows that AR patterns for some bug-drug combinations vary by care setting and patient age. We describe novel data visualizations to interpret large-scale EHR data on the prevalence and trends of AR that should influence antimicrobial prescribing and antimicrobial stewardship programme interventions.
Can’t keep it SECRET: system evaluation of carbapenem restriction against empirical therapy
Authors: Wells Drew A , Johnson Asia J , Lukas Jack G , Hobbs Diana A , Cleveland Kerry O , Twilla Jennifer D , Hobbs Athena L V 
Published: January 2023

Abstract

Objectives
Carbapenems are appealing agents for empirical use given their broad spectrum of activity; however, selective use is vital in minimizing the risk for development of carbapenem-resistant pathogens. We aimed to examine the impact of carbapenem restriction criteria and a pre-authorization process on utilization and cost savings across a health system.

Methods
This retrospective study was conducted across five adult hospitals. The pre-implementation period was 8 February 2020 to 30 April 2020 and the post-implementation period was 8 February 2022 to 30 April 2022. The primary outcome was to compare the number of orders for carbapenems between the study periods for both the intervention and non-intervention hospitals. Secondary outcomes included projected annual cost and an estimated cost-savings evaluation using a stratified analysis for the intervention and non-intervention facilities to account for more resource-limited settings.

Results
The total number of carbapenem orders decreased between study periods at the intervention hospital (246 versus 61, P &lt; 0.01). At the non-intervention hospitals, orders decreased, although not significantly (333 versus 279, P = 0.58). Meropenem orders decreased by 66% compared with 12% for the intervention and the non-intervention hospitals, respectively (P &lt; 0.001). Annual estimated cost for all facilities was $255 561 in the pre-implementation period compared with $29 593 in the post-implementation period (P &lt; 0.001). Using a stratified analysis to account for available resources, the estimated annual cost saving was $225 968 for the system.

Conclusions
Implementation of carbapenem restriction at the intervention hospital decreased utilization and provided significant cost savings. Furthermore, resource-limited facilities can still experience significant cost savings using a stratified antimicrobial stewardship intervention approach.
Spontaneous rupture of splenic artery pseudoaneurysm
Authors: Hordiychuk Andriy , Mehanna Daniel 
Published: December 2022

Abstract
False aneurysm or visceral artery pseudoaneurysm (VAPA) results from a tear in the vessel wall due to trauma with subsequent periarterial haematoma formation. VAPA is relatively rare, with a reported incidence of 0.1–0.2%, although the actual incidence is not known since many are asymptomatic. Splenic artery pseudoaneurysm is even more rare pathology. Only around 200 cases have been described in the literature. The case report below describes a spontaneous rupture of splenic artery pseudoaneurysm.
Implementing evidence-based interventions for managing pediatric hydrocephalus: a systematic review protocol
Authors: Ikwuegbuenyi Chibuikem A , Zolo Yvan , Nyalundja Arsene Daniel , Ngoma Placide , Abu-Bonsrah Nancy , Kanmounye Ulrick Sidney , Groves Mari L 
Published: January 2023

Abstract

Background
Pediatric hydrocephalus (PH) accounts for one of the most frequent neurological conditions in children and with a high burden in developing countries. The plurality of its etiological mechanisms has led to several therapeutic modalities, including the endoscopic third ventriculostomy, which has shown significant benefits. This study aims to determine the availability of PH treatment modalities worldwide using an implementation science framework.

Methods
This systematic review will be conducted following AMSTAR guidelines and reported following PRISMA guidelines. A comprehensive search from database inception to the date the search is run will be conducted in Medline, Embase and Global Index Medicus. Conference abstracts, scoping, systematic reviews (SRs), book chapters and non-French/English publications will be excluded. After the screening process, data will be extracted, and its quality analyzed. Newcastle-Ottawa Scale and Cochrane risk of bias 2.00 tool will be employed to assess the risk of bias. Odds or risk ratios and mean differences with their 95% confidence interval will measure the effect. The I2 statistic will describe effect heterogeneity in meta-analysis data. No Ethic approval is required.

Study Implications
Evidence-based practice is a complex problem-solving approach derived from high-quality evidence. Their implementation models are well reported in neurosciences in resource-limited countries. This SR will use the Framework for Reach, Effectiveness, Adoption, Implementation and Maintenance to conceptualize the public health impact of PH treatment modalities. We will identify reasons for the low use of an evidence-based strategy to inform policy.

Systematic Review Registration
The protocol has been registered on the International Prospective Register of Systematic Reviews (PROSPERO CRD42022354804).
Time-dependent boundary conditions for data-driven coronal global and spherical wedge-shaped models
Authors: Feng Xueshang , Lv Jiakun , Xiang Changqing , Jiang Chaowei 
Published: December 2022

ABSTRACT
The development of an efficient and accurate method for boundary condition treatments is of fundamental importance to data-driven magnetohydrodynamic (MHD) modelling of the global solar corona and solar active region. Particularly, in a 3D spherical wedge-shaped volume, suitable to the numerical study of solar active region, the transverse terms calls for a delicate treatment at the computational domain’s edges and corners, and properly prescribed conditions for boundaries joining regions of different flow properties, so as to take account of the joint effect of incoming and outgoing waves. To provide a solution to the determination of boundary conditions, in this paper a systematic tactics is formulated for handling edges and corners and the prescribed conditions for inner/outer/edge/corner boundaries are proposed through the combination (CBC-ILW) of the time-dependent characteristic boundary conditions (CBCs) and the inverse Lax-Wendroff (ILW) procedure. First, a data-driven 3D MHD simulation has been carried out to study the dynamic evolution of the solar corona from 1Rs to 6.7Rs during the period between 2018 May 16 and August 6. The simulated results of the global coronal evolution provide a good comparison with observed coronal images during the period investigated. Then, the validity of 3D MHD-CBC-ILW is verified for a 3D spherical wedge model, by producing almost the same results as those taken out of the global model on a 3D spherical wedge-shaped volume.
scAVENGERS: a genotype-based deconvolution of individuals in multiplexed single-cell ATAC-seq data without reference genotypes
Authors: Han Seungbeom , Kim Kyukwang , Park Seongwan , Lee Andrew J , Chun Hyonho , Jung Inkyung 
Published: December 2022

Abstract
Genetic differences inferred from sequencing reads can be used for demultiplexing of pooled single-cell RNA-seq (scRNA-seq) data across multiple donors without WGS-based reference genotypes. However, such methods could not be directly applied to single-cell ATAC-seq (scATAC-seq) data owing to the lower read coverage for each variant compared to scRNA-seq. We propose a new software, scATAC-seq Variant-based EstimatioN for GEnotype ReSolving (scAVENGERS), which resolves this issue by calling more individual-specific germline variants and using an optimized mixture model for the scATAC-seq. The benchmark conducted with three synthetic multiplexed scATAC-seq datasets of peripheral blood mononuclear cells and prefrontal cortex tissues showed outstanding performance compared to existing methods in terms of accuracy, doublet detection, and a portion of donor-assigned cells. Furthermore, analyzing the effect of the improved sections provided insight into handling pooled single-cell data in the future. Our source code of the devised software is available at GitHub: https://github.com/kaistcbfg/scAVENGERS.
Thirty years since the Maastricht Treaty
Authors: Tizzano Antonio 
Published: January 2023

Abstract
2022 marks the thirtieth anniversary of the Maastricht Treaty on European Union (TEU), signed in that city in the Netherlands on 7 February 1992. Even though many may have almost forgotten about this Treaty, or may simply remember it as part of the sequence of textual revisions that have contributed to the process of European integration since 1985, it in fact represented an important turning point in the history of the EU s integration process.
What is the J-sign and why is it important?
Authors: Rousseau-Saine Alexis , Nault Marie-Lyne , Hiemstra Laurie A. 
Published: January 2023

Purpose of review
Recurrent lateral patellofemoral instability is a complex condition that requires a thorough evaluation to optimize treatment. The J-sign test is classically part of the physical examination, but its significance and importance remain unclear. This review aims to describe how to perform the test and classify the observation as well as to analyze the most recent literature on its clinical applications.

Recent findings
The J-sign test has been described as positive (present) or negative (absent), and classified using the quadrant method and the Donnell classification. Suboptimal inter-rater reliability has been shown for both classifications, making comparison between clinicians and studies challenging. The J-sign is most predominantly associated with patella alta, trochlear dysplasia, lateral force vector, and rotational abnormalities. A growing number of studies have shown a correlation between a positive J-sign and lower clinical outcome scores and higher rate of surgical failure.

Summary
The J-sign is an important aspect of the physical examination in patients with recurrent lateral patellofemoral instability. Although there is no consensus on how to perform or classify the test, it can be used as a marker of severity of patellofemoral instability and is one of the tools available to guide the treatment plan.
Proteins with amino acid repeats constitute rapidly evolvable and human-specific essentialome
Authors: Singh Anjali Kumari , Amar Ishita , Ramadasan Harikrishnan , Kappagantula Keertana Sai , Chavali Sreenivas 
Published: December 2022

AbstractProtein products of essential genes, indispensable for organismal survival, are highly conserved and bring about fundamental functions. Interestingly, proteins that contain amino acid homorepeats that tend to evolve rapidly are enriched in eukaryotic essentialomes. Why are proteins with hypermutable homorepeats enriched in conserved and functionally vital essential proteins? We solve this function versus evolutionary paradox by demonstrating that human essential proteins with homorepeats bring about cross-talk across biological processes through high interactability and have distinct regulatory functions affecting expansive global regulation. Importantly, essential proteins with homorepeats rapidly diverge with the amino acid substitutions frequently affecting functional sites, likely facilitating rapid adaptability. Strikingly, essential proteins with homorepeats influence human-specific embryonic and brain development, implying that the presence of homorepeats could contribute to the emergence of human-specific processes. Thus, we propose that homorepeat containing essential proteins affecting species-specific traits can be potential intervention targets across pathologies including cancers and neurological disorders.
Virtual motivation: The psychological and transfer of learning effects of immersive virtual reality practice
Authors: Markwell Logan T. , Velten Joei R. , Partridge Julie A. , Porter Jared M. 
Published: December 2022

AbstractPrevious research has shown practice within an immersive virtual reality (VR) environment improves real-world (RW) performance. Increased user motivation is one possible advantage of practicing in VR. One recent study showed that an enriched gaming environment led to higher levels of engagement, resulting in a direct learning benefit. The purpose of this study was to compare the intrinsic motivation, engagement, and transfer of learning differences between VR practice and RW practice of the same motor skill. Participants (n= 61) were randomly assigned to a RW practice group (n= 30) or a VR practice group (n= 31) in which they performed a golf putting task. Analyses showed VR practice led to a significantly greater increase in average IMI score than RW practice. Analyses for performance showed there was a significant (p< .001) improvement in accuracy (i.e., radial error) from pre to posttest, but the two groups did not differ from one another. Overall, these results partially support our hypotheses and suggest that VR practice led to a greater increase in motivation compared to RW practice. Additionally, these results suggest that VR practice was similarly effective at improving accuracy compared to RW practice. Future research directions are discussed.
Genotyping ofOrientia tsutsugamushicirculating in and around Vellore (South India) using TSA 56 gene
Authors: Kumaraswamy Janaki , Govindasamy Punitha , Nagarajan Lakshmi Surya , Gunasekaran Karthik , Abhilash KPP , Prakash John Antony Jude 
Published: January 2023

AbstractThe immunodominant TSA 56 gene ofOrientia tsutsugamushi, (scrub typhus agent) has four variable regions (VD-I to VD-IV) making it useful for genotyping. As of date the genotyping data from India is based on partial 56kDa gene sequence analysis. The complete TSA 56 gene sequence is important for knowing the circulating strains and for designing region specific diagnostics and vaccines. This study was undertaken to determineOrientia tsutsugamushigenotypes circulating in and around Vellore using complete and partial TSA 56 gene. Of the 379 whole blood samples from suspected scrub typhus patients, 162 were positive by 47 kDa qPCR. Long protocol to amplify the complete TSA 56 gene (≈1605 bp) was performed on 21 samples. On the same 21 samples the partial gene sequence was also amplified using the Horinouchi (≈650bp) and the Furuya (≈480 bp) protocol. Using a combination of Sanger and Nanopore technology complete sequence was obtained for 9 and near complete (1551 to 1596 bp) for 4 respectively. As Furuya protocol gave multiple bands we obtained 480 bp sequences from the 13 complete gene sequences byin silicoanalysis. In contrast, 650bp sequences were obtained for 11 samples while for the remaining two we derived the 650 bp sequences from the complete gene sequences (Long protocol). Phylogenetic analysis of the complete gene (Long protocol) which includes VD-I to VD-IV region and partial gene (Horinouchi) which amplifies the VD-I to VD-III regions showed identical genotypes. Twelve belonged to TA763 genotype and one belongs to Karp genotype. The Furuya sequence (in silico) correctly identified the Karp genotype and 10 of the TA763 genotypes. Two TA763 genotypes (identified by complete and 650 bp partial gene analysis) were misidentified by Furuya sequence analysis as Karp genotype.The limited analysis showed the commonestOrientia tsutsugamushigenotypes circulating in and around Vellore is TA763 and that the 650 bp (Sanger) sequencing could be a cost effective method for identifying the scrub typhus genotypes. However, these results need to be validated by larger prospective multi-centric studies.
Bridging the gap – estimation of 2022/2023 SARS-CoV-2 healthcare burden in Germany based on multidimensional data from a rapid epidemic panel
Authors: Harries M , Jaeger V.K , Rodiah I , Hassenstein M.J. , Ortmann J , Dreier M , von Holt I , Brinkmann M , Dulovic A , Gornyk D , Hovardovska O , Kuczewski C , Kurosinki MA , Schlotz M , Schneiderhan-Marra N , Strengert M , Krause G , Sester M , Klein F , Petersmann A , Karch A , Lange B 
Published: December 2022

AbstractThroughout the SARS-CoV-2 pandemic, Germany lacked an adaptive population panel for epidemic diseases and a modelling platform to rapidly incorporate panel estimates.We evaluated how a cross-sectional analysis of 9922 participants of the MuSPAD study in June/July 2022 combined with a newly developed modelling platform could bridge the gap and analyzed antibody levels, neutralizing serum activity and interferon-gamma release response of serum samples. We categorized the population into four groups with differing protection against severe course of disease (validated by neutralizing serum activity), and found that 30% were in the group with highest protection, and 85% in either the highest categories or second highest group regarding protection level.Estimated hospitalizations due to SARS-CoV-2 were predicted to be between 30 to 300% of the peak in 02/2021 dependent on assumed variant characteristics. We showed the feasibility of a rapid epidemic panel able to evaluate complex endpoints for SARS-CoV-2 and inform scenario modelling.
Phages are important unrecognized players in the ecology of the oral pathogenPorphyromonas gingivalis
Authors: Matrishin Cole B. , Haase Elaine M. , Dewhirst Floyd E. , Mark Welch Jessica L. , Miranda-Sanchez Fabiola , MacFarland Donald C. , Kauffman Kathryn M. 
Published: December 2022

AbstractBackgroundPorphyromonas gingivalis(hereafter “Pg”) is an oral pathogen that can act as a keystone driver of inflammation and periodontal disease. AlthoughPgis most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized byPg. Insights into the factors shaping the striking strain-level variation inPg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. A key force shaping strain level diversity in all microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, althoughPghas been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology ofPg.ResultsHere we systematically addressed the question of whetherPgare infected by phages - and we found that they are. We found that prophages are common inPg, they are genomically diverse, and they encode genes that have the potential to alterPgphysiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems inPg, and thatPgstrains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a modelPgstrain are active in culture, producing extracellular viral particles in broth cultures.DiscussionThis work definitively establishes that phages are a major unrecognized force shaping the ecology and intraspecies strain-level diversity of the well-studied oral pathogenPg. The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known aboutPg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly.
Copy number variants alter local and global mutational tolerance
Authors: Avecilla Grace , Spealman Pieter , Matthews Julia , Caudal Elodie , Schacherer Joseph , Gresham David 
Published: December 2022

AbstractCopy number variants (CNVs), duplications and deletions of genomic content, contribute to evolutionary adaptation, but can also confer deleterious effects, and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs of differing sizes and structures. Here, we investigatedSaccharomyces cerevisiae(yeast) strains that have CNVs of variable structures but with multiple copies of the geneGAP1. Although beneficial in glutamine-limited chemostats, CNVs result in decreased fitness compared with the euploid ancestor in rich media. We used transposon mutagenesis to investigate mutational tolerance and genetic interactions with CNVs. We find that CNVs confer novel mutational tolerance in amplified essential genes and novel genetic interactions. We validated a novel genetic interaction withBMH1. CNV strains have increased mutational tolerance in genes related to translation, and reduced mutational tolerance in genes related to mitochondrial function. We performed RNAseq and found that transcriptional dosage compensation does not affect the majority of genes amplified by CNVs. Furthermore, we do not find that CNV strains exhibit previously described transcriptional signatures of aneuploidy. Instead, CNV strains exhibit downregulation of genes involved in cellular respiration, nucleoside biosynthetic processes, and small molecule metabolism, and upregulation of genes involved in transposition, nucleic acid metabolic processes, and siderophore transport. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs with implications for genome evolution and CNV associated diseases, such as cancer.