bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage
Authors: Arts Peter J. , Kelly J. Daniel , Midgley Claire M. , Anglin Khamal , Lu Scott , Abedi Glen R. , Andino Raul , Bakker Kevin M. , Banman Bryon , Boehm Alexandria B. , Briggs-Hagen Melissa , Brouwer Andrew F. , Davidson Michelle C. , Eisenberg Marisa C. , Garcia-Knight Miguel , Knight Sterling , Peluso Michael J. , Pineda-Ramirez Jesus , Diaz Sanchez Ruth , Saydah Sharon , Tassetto Michel , Martin Jeffrey N. , Wigginton Krista R. 
Published: June 2023

ABSTRACT

Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 10
4
and 1.4 × 10
4
gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications.

IMPORTANCE
This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE.
Predicting variable gene content in
Escherichia coli
using conserved genes
Authors: Nguyen Marcus , Elmore Zachary , Ihle Clay , Moen Francesco S. , Slater Adam D. , Turner Benjamin N. , Parrello Bruce , Best Aaron A. , Davis James J. 
Published: June 2023

ABSTRACT

Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in
Escherichia coli
genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs
,
and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%–90% of all
E. coli
genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943–0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including “hypothetical proteins” was accurately predicted (F1 = 0.902 [0.898–0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse
E. coli
genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876–0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data.

IMPORTANCE

Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%–90% of all publicly available
E. coli
genomes. Overall, the results show that a large portion of the
E. coli
variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.
Reduction of hospital bed cost for inpatient overstay through optimisation of patient flow
Authors: Alharbi Sultanah , Alasmari Abdullah , Hanafy Ehab , Ellawindy Alia 
Published: June 2023

BackgroundOverstay of inpatients is a big challenge to healthcare systems which interferes with the proper utilisation of the available resources and efficient delivery of care. Unnecessary days in the hospital may lead to patient complications including healthcare-associated infections, falls and delirium, which can negatively impact both patient and staff experience. This project aimed to reduce the cost of bed days of inpatient overstay through facilitating the discharge process using a multidisciplinary intervention approach.MethodsThe root causes of inpatient overstay were defined via a multidisciplinary approach. This project applied the extension Deming Cycle method: Find-Organise-Clarify-Understand-Study-Plan-Do-Check-Act (PDCA). Solutions to the root causes which led to process variation were implemented through three PDCA cycles conducted between January 2019 and July 2020.ResultsThere was a significant reduction in the total number of overstay inpatients, the total number of overstay days, and the related bed costs in the first 3 quarters of 2019. A significant and sustained improvement in the emergency department average boarding time was attained in the first half of 2019 (reduced from 11.9 hours to 1.7 hours). A total estimated cost saving of SR30 000 000 (US$8 000 000) in terms of operational efficiency was achieved.ConclusionEarly discharge planning and facilitating the patient discharge process significantly improves the average length of inpatient stay and patient outcomes and decreases hospital costs.
The first international Rome consensus conference on gut microbiota and faecal microbiota transplantation in inflammatory bowel disease
Authors: Lopetuso Loris Riccardo , Deleu Sara , Godny Lihi , Petito Valentina , Puca Pierluigi , Facciotti Federica , Sokol Harry , Ianiro Gianluca , Masucci Luca , Abreu Maria , Dotan Iris , Costello Samuel Paul , Hart Ailsa , Iqbal Tariq H , Paramsothy Sudarshan , Sanguinetti Maurizio , Danese Silvio , Tilg Herbert , Cominelli Fabio , Pizarro Theresa T , Armuzzi Alessandro , Cammarota Giovanni , Gasbarrini Antonio , Vermeire Séverine , Scaldaferri Franco 
Published: June 2023

BackgroundSeveral randomised clinical trials (RCTs) performing faecal microbiota transplantation (FMT) for the management of inflammatory bowel disease (IBD), particularly for ulcerative colitis, have recently been published, but with major variations in study design. These include differences in administered dose, route and frequency of delivery, type of placebo and evaluated endpoints. Although the overall outcomes appear to be promising, they are highly dependent on both donor and recipient factors.ObjectiveTo develop concensus-based statements and recommendations for the evaluation, management and potential treatment of IBD using FMT in order to move towards standardised practices.DesignAn international panel of experts convened several times to generate evidence-based guidelines by performing a deep evaluation of currently available and/or published data. Twenty-five experts in IBD, immunology and microbiology collaborated in different working groups to provide statements on the following key issues related to FMT in IBD: (A) pathogenesis and rationale, (B) donor selection and biobanking, (C) FMT practices and (D) consideration of future studies and perspectives. Statements were evaluated and voted on by all members using an electronic Delphi process, culminating in a plenary consensus conference and generation of proposed guidelines.Results and conclusionsOur group has provided specific statements and recommendations, based on best available evidence, with the end goal of providing guidance and general criteria required to promote FMT as a recognised strategy for the treatment of IBD.
Longitudinal bidirectional link between socioeconomic position and health: a national panel survey analysis
Authors: Benderly Michal , Fluss Ronen , Murad Havi , Averbuch Emma , Freedman Laurence S , Kalter-Leibovici Ofra 
Published: June 2023

BackgroundHealth inequities can stem from socioeconomic position (SEP) leading to poor health (social causation) or poor health resulting in lower SEP (health selection). We aimed to examine the longitudinal bidirectional SEP-health associations and identify inequity risk factors.MethodsLongitudinal Household Israeli Panel survey participants (waves 1–4), age ≥25 years, were included (N=11 461; median follow-up=3 years). Health rated on a 4-point scale was dichotomised as excellent/good and fair/poor. Predictors included SEP parameters (education, income, employment), immigration, language proficiency and population group. Mixed models accounting for survey method and household ties were used.ResultsExamining social causation, male sex (adjusted OR 1.4; 95% CI 1.1 to 1.8), being unmarried, Arab minority (OR 2.4; 95% CI 1.6 to 3.7, vs Jewish), immigration (OR 2.5; 95% CI 1.5 to 4.2, reference=native) and less than complete language proficiency (OR 2.22; 95% CI 1.50 to 3.28) were associated with fair/poor health. Higher education and income were protective, with 60% lower odds of subsequently reporting fair/poor health and 50% lower disability likelihood. Accounting for baseline health, higher education and income were associated with lower likelihood of health deterioration, while Arab minority, immigration and limited language proficiency were associated with higher likelihood. Regarding health selection, longitudinal income was lower among participants reporting poor baseline health (85%; 95% CI 73% to 100%, reference=excellent), disability (94%; 95% CI 88% to 100%), limited language proficiency (86%; 95% CI 81% to 91%, reference=full/excellent), being single (91%; 95% CI 87% to 95%, reference=married), or Arab (88%; 95% CI 83% to 92%, reference=Jews/other).ConclusionPolicy aimed at reducing health inequity should address both social causation (language, cultural, economic and social barriers to good health) and health selection (protecting income during illness and disability).
Capturing Fine-Grained Regional Differences in Language Use through Voting Precinct Embeddings
Authors: Rosenfeld Alex , Hinrichs Lars 
Published: June 2023

Abstract
Linguistic variation across a region of interest can be captured by partitioning the region into areas and using social media data to train embeddings that represent language use in those areas. Recent work has focused on larger areas, such as cities or counties, to ensure that enough social media data is available in each area, but larger areas have a limited ability to find fine-grained distinctions, such as intracity differences in language use. We demonstrate that it is possible to embed smaller areas, which can provide higher resolution analyses of language variation. We embed voting precincts, which are tiny, evenly sized political divisions for the administration of elections. The issue with modeling language use in small areas is that the data becomes incredibly sparse, with many areas having scant social media data. We propose a novel embedding approach that alternates training with smoothing, which mitigates these sparsity issues. We focus on linguistic variation across Texas as it is relatively understudied. We develop two novel quantitative evaluations that measure how well the embeddings can be used to capture linguistic variation. The first evaluation measures how well a model can map a dialect given terms specific to that dialect. The second evaluation measures how well a model can map preference of lexical variants. These evaluations show how embedding models could be used directly by sociolinguists and measure how much sociolinguistic information is contained within the embeddings. We complement this second evaluation with a methodology for using embeddings as a kind of genetic code where we identify “genes” that correspond to a sociological variable and connect those “genes” to a linguistic phenomenon thereby connecting sociological phenomena to linguistic ones. Finally, we explore approaches for inferring isoglosses using embeddings.
A Medieval Climate Anomaly: The Qarakhanid Adaptation
Authors: Misa Henry 
Published: June 2023

Abstract
A synthesis of paleoclimatic, archaeological, and literary evidence from Central Asia (Transoxiana and the Tarim Basin) during the tenth through twelfth centuries suggests that the Qarakhanid state adapted its hybrid economy to a unique climate regime characterized by drought created by the Medieval Climate Anomaly. To adapt, the Qarakhanids expanded the agricultural and pastoral sections of their economy into foothill and highland ecologies and used diplomacy to support a transregional trade network that helped to stimulate drought-stressed oasis economies on both sides of the Tian Shan. New methodological conclusions relevant for the study of interdisciplinary environmental history in general and for the historiography of premodern mobile pastoralist states in particular provide frameworks for future study.
The processes of engagement in information-seeking behavior for individuals with diabetes who developed diabetic foot ulcer: A constructivist grounded theory study
Authors: Costa Idevania G , Camargo-Plazas Pilar 
Published: June 2023

To describe the process of engagement in information seeking behavior for individuals with type 1 and type 2 diabetes. Methodology Constructivist grounded theory. The data was gathered through thirty semi-structured interviews of participants attending a wound care clinic in Southeast, Ontario, Canada. The waiting period taken to seek appropriate help varied from weeks to months. Results “The processes of engagement in information-seeking behavior about diabetes” are organized as follows: 1) discovering diabetes, 2) reactions to the diagnosis, and 3) engaging in self-directed learning. For most participants, the diagnosis of diabetes was unexpected and usually confirmed after a long period of experiencing a diversity of symptoms. The terms used mostly by participants were “I started to wonder” and “Something was wrong with me.” After being diagnosed with diabetes, participants sought information to learn about it. Most of them engaged in self-directed learning to acquire knowledge about their illness. Conclusion Although the Internet is often used to seek information, healthcare providers and support network also played an important role in supporting participants information-seeking behavior learn about diabetes. The unique needs of people with diabetes must be taken into consideration during their diabetes care journey. These findings call for the need to provide education about diabetes from the time they are diagnosed and direct them to reliable resources of information.
High-quality chromosome-level scaffolds of the plant bug Pachypeltis micranthus provide insights into the availability of Mikania micrantha control
Authors: Wang Xiafei , Zhao Ning , Cai Liqiong , Liu Naiyong , Zhu Jiaying , Yang Bin 
Published: June 2023

AbstractBackgroundThe plant bug,Pachypeltis micranthusMu et Liu (Hemiptera: Miridae), is an effective potential biological control agent forMikania micranthaH.B.K. (Asteraceae; one of the most notorious invasive weeds worldwide). However, limited knowledge about this species hindered its practical application and research. Accordingly, sequencing the genome of this mirid bug holds great significance in controllingM. micrantha.ResultsHere, 712.72 Mb high-quality chromosome-level scaffolds ofP. micranthuswere generated, of which 707.51 Mb (99.27%) of assembled sequences were anchored onto 15 chromosome-level scaffolds with contig N50 of 16.84 Mb. TheP. micranthusgenome had the highest GC content (42.43%) and the second highest proportion of repetitive sequences (375.82 Mb, 52.73%) than the three other mirid bugs (i.e.,Apolygus lucorum,Cyrtorhinus lividipennis, andNesidiocoris tenuis). Phylogenetic analysis showed thatP. micranthusclustered with other mirid bugs and diverged from the common ancestor approximately 200 million years ago. Gene family expansion and/or contraction were analyzed, and significantly expanded gene families associated withP. micranthusfeeding and adaptation toM. micranthawere manually identified. Compared with the whole body, transcriptome analysis of the salivary gland revealed that most of the upregulated genes were significantly associated with metabolism pathways and peptidase activity, particularly among cysteine peptidase, serine peptidase, and polygalacturonase; this could be one of the reasons for precisely and highly efficient feeding by the oligophagous bugP. micranthusonM. micrantha.ConclusionCollectively, this work provides a crucial chromosome-level scaffolds resource to study the evolutionary adaptation between mirid bug and their host. It is also helpful in searching for novel environment-friendly biological strategies to controlM. micrantha.
The completeness of the left atrial appendage amputation during routine cardiac surgery
Authors: Radakovic Dejan , Penov Kiril , Lazarus Marc , Madrahimov Nodir , Hamouda Khaled , Schimmer Christoph , Leyh Rainer G. , Bening Constanze 
Published: June 2023

Abstract
Background
Left atrial appendage (LAA) is the origin of most heart thrombi which can lead to stroke or other cerebrovascular event in patients with non-valvular atrial fibrillation (AF). This study aimed to prove safety and low complication rate of surgical LAA amputation using cut and sew technique with control of its effectiveness.

Methods
303 patients who have undergone selective LAA amputation were enrolled in the study in a period from 10/17 to 08/20. The LAA amputation was performed concomitant to routine cardiac surgery on cardiopulmonary bypass with cardiac arrest with or without previous history of AF. The operative and clinical data were evaluated. Extent of LAA amputation was examined intraoperatively by transoesophageal echocardiography (TEE). Six months in follow up, the patients were controlled regarding clinical status and episodes of strokes.

Results
Average age of study population was 69.9 ± 19.2 and 81.9% of patients were male. In only three patients was residual stump after LAA amputation larger than 1 cm with average stump size 0.28 ± 0.34 cm. 3 patients (1%) developed postoperative bleeding. Postoperatively 77 (25.4%) patients developed postoperative AF (POAF), of which 29 (9.6%) still had AF at discharge. On 6 months follow up only 5 patients had NYHA class III and 1 NYHA class IV. Seven patients reported with leg oedema and no patient experienced any cerebrovascular event in early postoperative follow up.

Conclusion
LAA amputation can be performed safely and completely leaving minimal to no LAA residual stump.
External validation of the CREST model to predict early circulatory-etiology death after out-of-hospital cardiac arrest without initial ST-segment elevation myocardial infarction
Authors: Haxhija Zana , Seder David B , May Teresa L , Hassager Christian , Friberg Hans , Lilja Gisela , Ceric Ameldina , Nielsen Niklas , Dankiewicz Josef 
Published: June 2023

Abstract
Background
The CREST model is a prediction model, quantitating the risk of circulatory-etiology death (CED) after cardiac arrest based on variables available at hospital admission, and intend to guide the triage of comatose patients without ST-segment-elevation myocardial infarction after successful cardiopulmonary resuscitation. This study assessed performance of the CREST model in the Target Temperature Management (TTM) trial cohort.

Methods
We retrospectively analyzed data from resuscitated out-of-hospital cardiac arrest (OHCA) patients in the TTM-trial. Demographics, clinical characteristics, and CREST variables (history of coronary artery disease, initial heart rhythm, initial ejection fraction, shock at admission and ischemic time > 25 min) were assessed in univariate and multivariable analysis. The primary outcome was CED. The discriminatory power of the logistic regression model was assessed using the C-statistic and goodness of fit was tested according to Hosmer-Lemeshow.

Results
Among 329 patients eligible for final analysis, 71 (22%) had CED. History of ischemic heart disease, previous arrhythmia, older age, initial non-shockable rhythm, shock at admission, ischemic time > 25 min and severe left ventricular dysfunction were variables associated with CED in univariate analysis. CREST variables were entered into a logistic regression model and the area under the curve for the model was 0.73 with adequate calibration according to Hosmer-Lemeshow test (p = 0.602).

Conclusions
The CREST model had good validity and a discrimination capability for predicting circulatory-etiology death after resuscitation from cardiac arrest without ST-segment elevation myocardial infarction. Application of this model could help to triage high-risk patients for transfer to specialized cardiac centers.