bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History
Authors: Johri Parul , Pfeifer Susanne P , Jensen Jeffrey D 
Published: May 2023

Abstract
Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.
Clostridioides difficileInfection: Clinical Practice and Health Outcomes in 6 Large Tertiary Hospitals in Eastern Australia
Authors: Stewart Adam G , Chen Sharon C A , Hamilton Kate , Harris-Brown Tiffany , Korman Tony M , Figtree Melanie , Worth Leon J , Kok Jen , Van der Poorten David , Byth Karen , Slavin Monica A , Paterson David L 
Published: May 2023

AbstractBackgroundClostridioides difficile infection (CDI) is associated with significant morbidity and mortality in both healthcare and community settings. We aimed to define the predisposing factors, risks for severe disease, and mortality determinants of CDI in eastern Australia over a 1-year period.MethodsThis is an observational retrospective study of CDI in hospitalized patients aged ≥18 years in 6 tertiary institutions from 1 January 2016 to 31 December 2016. Patients were identified through laboratory databases and medical records of participating institutions. Clinical, imaging, and laboratory data were input into an electronic database hosted at a central site.ResultsA total of 578 patients (578 CDI episodes) were included. Median age was 65 (range, 18–99) years and 48.2% were male. Hospital-onset CDI occurred in 64.0%. Recent antimicrobial use (41.9%) and proton pump inhibitor use (35.8%) were common. Significant risk factors for severe CDI were age &lt;65 years (P &lt; .001), malignancy within the last 5 years (P &lt; .001), and surgery within the previous 30 days (P &lt; .001). Significant risk factors for first recurrence included severe CDI (P = .03) and inflammatory bowel disease (P = .04). Metronidazole was the most common regimen for first episodes of CDI with 65.2% being concordant with Australian treatment guidelines overall. Determinants for death at 60 days included age ≥65 years (P = .01), severe CDI (P &lt; .001), and antibiotic use within the prior 30 days (P = .02). Of those who received metronidazole as first-line therapy, 10.1% died in the 60-day follow-up period, compared to 9.8% of those who received vancomycin (P = .86).ConclusionsPatients who experience CDI are vulnerable and require early diagnosis, clinical surveillance, and effective therapy to prevent complications and improve outcomes.
The competitive advantage of sanctioning institutions revisited: A multilab replication
Authors: Lo Iacono Sergio , Przepiorka Wojtek , Buskens Vincent , Corten Rense , van Assen Marcel , van de Rijt Arnout 
Published: May 2023

Abstract
Is peer sanctioning a sustainable solution to the problem of human cooperation? We conducted an exact multilab replication (N = 1,008; 7 labs × 12 groups × 12 participants) of an experiment by Gürerk, Irlenbusch, and Rockenbach published in Science in 2006 (Gürerk Ö, Irlenbusch B, Rockenbach B. The competitive advantage of sanctioning institutions. 2006. Science. 312(5770):108–111). In GIR2006 (N = 84; 1 lab × 7 groups × 12 participants), groups that allowed members to reward cooperators and punish defectors were found to outgrow and outperform groups without a peer-sanctioning institution. We find GIR2006 replicated in accordance with all preregistered replication criteria in five of the seven labs we sampled. There, the majority of participants joined groups with a sanctioning institution, and participants cooperated and profited more on average than in groups without a sanctioning institution. In the two other labs, results were weaker but still favored sanctioning institutions. These findings establish the competitive advantage of sanctioning institutions as a robust phenomenon within the European context.
Translating Akkadian to English with neural machine translation
Authors: Gutherz Gai , Gordin Shai , Sáenz Luis , Levy Omer , Berant Jonathan 
Published: May 2023

Abstract
Cuneiform is one of the earliest writing systems in recorded human history (ca. 3,400 BCE–75 CE). Hundreds of thousands of such texts were found over the last two centuries, most of which are written in Sumerian and Akkadian. We show the high potential in assisting scholars and interested laypeople alike, by using natural language processing (NLP) methods such as convolutional neural networks (CNN), to automatically translate Akkadian from cuneiform Unicode glyphs directly to English (C2E) and from transliteration to English (T2E). We show that high-quality translations can be obtained when translating directly from cuneiform to English, as we get 36.52 and 37.47 Best Bilingual Evaluation Understudy 4 (BLEU4) scores for C2E and T2E, respectively. For C2E, our model is better than the translation memory baseline in 9.43, and for T2E, the difference is even higher and stands at 13.96. The model achieves best results in short- and medium-length sentences (c. 118 or less characters). As the number of digitized texts grows, the model can be improved by further training as part of a human-in-the-loop system which corrects the results.
Reasoning about climate change
Authors: Bago Bence , Rand David G , Pennycook Gordon 
Published: May 2023

Abstract
Why is disbelief in anthropogenic climate change common despite broad scientific consensus to the contrary? A widely held explanation involves politically motivated (system 2) reasoning: Rather than helping uncover the truth, people use their reasoning abilities to protect their partisan identities and reject beliefs that threaten those identities. Despite the popularity of this account, the evidence supporting it (i) does not account for the fact that partisanship is confounded with prior beliefs about the world and (ii) is entirely correlational with respect to the effect of reasoning. Here, we address these shortcomings by (i) measuring prior beliefs and (ii) experimentally manipulating participants’ extent of reasoning using cognitive load and time pressure while they evaluate arguments for or against anthropogenic global warming. The results provide no support for the politically motivated system 2 reasoning account over other accounts: Engaging in more reasoning led people to have greater coherence between judgments and their prior beliefs about climate change—a process that can be consistent with rational (unbiased) Bayesian reasoning—and did not exacerbate the impact of partisanship once prior beliefs are accounted for.
Reliability of C-reactive protein as an inflammatory marker in patients with immune-mediated inflammatory diseases and liver dysfunction
Authors: Ross Yael , Ballou Stanley 
Published: May 2023

Abstract

Objectives
CRP is an acute-phase reactant widely used clinically as a marker of inflammation. CRP is a protein synthesized by hepatocytes. Previous studies have shown lower CRP levels in response to infections in patients with chronic liver disease. We hypothesized that CRP levels would also be lower during active immune-mediated inflammatory diseases (IMIDs) in patients with liver dysfunction.

Methods
This retrospective cohort study used Slicer Dicer in Epic, our electronic medical record system, to search for patients with IMIDs both with and without concomitant liver disease. Patients with liver disease were excluded if there was no clear documentation of liver disease staging. Patients were also excluded if a CRP level was not available during disease flare or active disease. Arbitrarily, we considered normal CRP as ≤0.7 mg/dl, mild elevation of CRP as ≥0.8 and &lt;3mg/dl, and elevated CRP as ≥3mg/dl.

Results
We identified 68 patients with both liver disease and IMIDs (RA, PsA and PMR) and 296 patients with autoimmune disease and without liver disease. Presence of liver disease had the lowest odds ratio (odds ratio = 0.25, P &lt; 0.0001) of having an elevated CRP during flare. Each specific IMID, except SLE and IBD, had higher median CRP levels during active disease episodes in patients without liver disease than in those with liver disease.

Discussion
Overall, IMID patients with liver disease had lower serum CRP levels during active disease than their counterparts without liver dysfunction. This observation has implications for clinical use of CRP level as a reliable marker of disease activity in patients with IMIDs and liver dysfunction.
Association of the AAV-PRO questionnaire with established outcome measures in AAV
Authors: Maunz Annika , Jacoby Johann , Henes Joerg , Robson Joanna C , Hellmich Bernhard , Löffler Christian 
Published: May 2023

Abstract

Objectives
The ANCA-associated vasculitis (AAV) patient-reported outcome (AAV-PRO) questionnaire was developed to capture the impact of AAV and its treatment. We investigated the association of specific AAV-PRO domains with disease activity and extent, damage, depression, health-related quality of life, and treatment.

Methods
In a prospective longitudinal study, AAV-PRO, Beck’s depression inventory (BDI), Short Form 36 (SF-36), BVAS and Vasculitis Damage Index (VDI) were completed at baseline (t1) and after 3–6 months (t2). In addition, patient data (including diagnosis, therapies, relapses, and organ manifestations) were recorded. Data were analysed by t-tests and correlation-based regression analyses.

Results
A total of 156 patients with AAV participated. The mean BVAS at the time of enrolment was 1.4 ± 3.74. The median AAV-PRO domain scores were higher in patients reporting ‘active disease‘ compared with those reporting ‘in remission’ (P &lt; 0.001). In the correlation analyses, all AAV-PRO domain scores correlated strongly with the BDI (all r ≥ 0.319, all P ≤ 0.001) as well as with all eight SF-36 subdomains (all |r|≥0.267, all P ≤ 0.001). The regression analyses showed that AAV-PRO domains were strongly predicted by the BDI and SF-36 domains (|β| ≥ 0.240 for the strongest predictor of each domain). In the longitudinal comparison (t1/t2), there were no significant changes in the overall results.

Conclusion
Our data show convergent validity for all AAV-PRO subdomains, using the established questionnaires BDI and SF-36. The AAV-PRO domains scores were not correlated with clinician-derived instruments (including the BVAS and the VDI). Thus, we regard the AAV-PRO questionnaire as a valuable measure of outcomes that might complement traditional end-points in clinical trials.
The European Dimension of the ‘talks process’ in Northern Ireland
Authors: Lagana Giada 
Published: May 2023

Abstract
Analysis of efforts to develop peace in Northern Ireland often attributes the foundation of the peace process to the dialogue between the then Sinn Fein president, Gerry Adams, and the Social Democratic and Labour Party’s (SDLP) former leader, John Hume, in the late 1980s. However, it has been recognized that attempts to forge peace have a longer timeline, involving the interplay of several national and international historical contexts in which the European Community (EC) / European Union (EU) dimension and the role of the EU institutions in restoring peace and reconciliation has been generally neglected. The objective of this article is therefore to examine the European dimension of the Northern Ireland talks process, addressing the whole range of relationships affecting the political stalemate in the years preceding the signing of Belfast/Good Friday Agreement (GFA). Drawing on never-before-seen United Kingdom (UK) government and EC/EU archival documents and semi-structured élite interviews, this article highlights how the original dialogue on power-sharing and devolution in Northern Ireland included a much stronger EU dimension that it is publicly acknowledged. This article constitutes an emblematic case-study on the ‘Europeanisation’ of British politics in Northern Ireland, with findings uncovering a new and subtle dimension of the EC/EU role in the Northern Ireland peace process.
Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant
Authors: Koh Eileen Y , Ong Jasmine , Wang Yifan , Toh Xinyu , Fernandez Charlene Judith , Huangfu Taoqi , Hall Robyn N , Toh Steffie , Lim Kelvin , Sng Wendy , Lim Hwee Ping , Ho Kelvin , Chang Siow Foong , Yap Him Hoo 
Published: May 2023

Abstract
Rabbit haemorrhagic disease (RHD) is a significant and debilitating viral disease affecting lagomorphs. In September 2020, Singapore reported its first cases of RHD virus (RHDV) infection in domesticated rabbits. The initial findings reported that the outbreak strain belonged to genotype GI.2 (RHDV2/RHDVb), and epidemiological investigations could not identify the definitive source of the virus origin. Further recombination detection and phylogenetic analyses of the Singapore outbreak strain revealed that the RHDV was a GI.2 structural (S)/GI.4 non-structural (NS) recombinant variant. Sequence analyses on the National Centre for Biotechnology Information (NCBI) database showed high homology to recently emerged Australian variants, which were prevalent in local Australian lagomorph populations since 2017. Time-structured and phylogeographic analyses for the S and NS genes revealed a close genetic relationship between the Singapore RHDV strain and the Australian RHDV variants. More thorough epidemiological inquiries are necessary to ascertain how an Australian RHDV was introduced into the Singapore rabbit population, and opportune development of RHDV diagnostics and vaccines will be important to safeguard lagomorphs from future RHDV infection and disease management.
Genome Resource for the Highly Virulent Xanthomonas oryzae pv. oryzae Strain HN2011 from China
Authors: Zhao Pu , Li Quanlin , Yin Han , Du Zhenglin , Zhai Wenxue , Xia Zhihui , Zhou Yongli 
Published: May 2023

Xanthomonas oryzae pv. oryzae ( Xoo) is the causal bacterium of rice bacterial blight (BB), which is one of the most destructive bacterial diseases of rice worldwide. Although more than 40 BB resistance genes ( Xa genes) have been identified, only a few conferring broad resistance (e.g., Xa4 and Xa21) have been widely used for rice breeding in Asia. The narrow genetic basis for the BB resistance of rice cultivars has resulted in the emergence of new pathogenic strains that can overcome the resistance of commonly grown rice cultivars derived from breeding programs. For example, Xoo strain HN2011, which was isolated in Hainan (China), can overcome the resistance mediated by multiple BB resistance genes, including Xa4 and Xa21. We herein present the complete genome sequence of HN2011 generated by Nanopore sequencing. The genomic data will be useful for elucidating the genomic variations of Xoo and will contribute to clarifying the interaction between Xoo and rice. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Current Concepts in Sternoclavicular Joint Injuries
Authors: Hesse Daniel , Paull Thomas , Cole Peter A. 
Published: May 2023

Summary:
Sternoclavicular joint (SCJ) injuries account for <3% of shoulder injuries. Anterior dislocations are far more common than posterior dislocations, but proper recognition is essential as posterior injuries are potentially life-threatening. The computed tomography scan is the gold standard in determining the direction of the SCJ injury and, furthermore, can help to determine the difference between medial clavicle fractures through an open physis and pure dislocations. Because the medial clavicle is one of the last physes to close and does not fuse until as late as 25 years of age in men, SCJ injuries in this age group most often represent physeal injuries; however, the treatment is similar to that for SCJ dislocations. Closed reduction maneuvers may be successful for the acute posterior SCJ dislocation, but operative reduction and repair is the gold standard of treatment. Anterior dislocations are not amenable to closed reduction due to deforming forces which cause recurrent dislocation but are believed to best be treated with closed management with the expectation for resolution of pain. Operative management of painful or unstable chronic dislocations includes medial clavicle resection and ligament reconstruction with allograft tendon in the setting of sternoclavicular instability.

Level of Evidence:
Therapeutic Level V. See Instructions for Authors for a complete description of levels of evidence.
Impact of a Dedicated Orthopaedic Trauma Room on Elective Arthroplasty Case Volume
Authors: Smith Austin , Chatterji Rishi , Diedring Benjamin , Waldron Jacob , Sharma Rajan , Fahs Adam , Knesek David , Klein Alan , Afsari Alan , Best Benjamin 
Published: May 2023

Objective:
To examine the effects of implementing a dedicated orthopaedic trauma room (DOTR) on elective arthroplasty volume.

Design:
Retrospective cohort study.

Setting:
Level I academic trauma center.

Intervention:
A retrospective analysis was performed for two 3-year intervals before and after DOTR introduction on January 20, 2013, at a Level I trauma center. Surgeons were included if they performed elective primary total hip arthroplasty (THA), total knee arthroplasty (TKA), total shoulder arthroplasty (TSA), or reverse total shoulder arthroplasty (RTSA) regularly from 2010 to 2015.

Main Outcome Measures:
Change in elective arthroplasty volume after the implementation of a DOTR.

Results:
A total of 2339 cases were performed by surgeons A-E, with an average of 303.3 cases per year pre-DOTR and an average of 476.3 cases per year post-DOTR. On average, within our institution, there were 75.79 per 10,000 cases/year in Michigan pre-DOTR and 104.2 per 10,000 cases/year in Michigan post-DOTR. Surgeons A-E averaged 173.0 more cases per year and increased their average proportion of elective arthroplasty case volume in Michigan. There was a statistically significant market share increase of 9.8 per 10,000 cases/year in Michigan, at our hospital in the post-DOTR periods (P = 0.039) (CI [0.5442, 19.21], SE = 4.523). This market share increase of 9.8 cases/10,000 cases was the yearly increase in market share that our average surgeons saw after the DOTR implementation, this took into account the observed annual increase in arthroplasty volume statewide during those years.

Conclusion:
Implementation of a DOTR was associated with increases in the total number, annual mean, and annual proportion of elective arthroplasty cases performed in Michigan for both elective surgeons and the institution as a whole. These findings reveal a benefit of DOTR implementation to elective arthroplasty surgeons and health systems on a larger scale, in the form of increased arthroplasty case volume.
Potential biomarkers for diagnosis and disease evaluation of idiopathic pulmonary fibrosis
Authors: Wang Qing , Xie Zhaoliang , Wan Nansheng , Yang Lei , Jin Zhixian , Jin Fang , Huang Zhaoming , Chen Min , Wang Huiming , Feng Jing 
Published: May 2023

Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease characterized by progressive lung fibrogenesis and histological features of usual interstitial pneumonia. IPF has a poor prognosis and presents a spectrum of disease courses ranging from slow evolving disease to rapid deterioration; thus, a differential diagnosis remains challenging. Several biomarkers have been identified to achieve a differential diagnosis; however, comprehensive reviews are lacking. This review summarizes over 100 biomarkers which can be divided into six categories according to their functions: differentially expressed biomarkers in the IPF compared to healthy controls; biomarkers distinguishing IPF from other types of interstitial lung disease; biomarkers differentiating acute exacerbation of IPF from stable disease; biomarkers predicting disease progression; biomarkers related to disease severity; and biomarkers related to treatment. Specimen used for the diagnosis of IPF included serum, bronchoalveolar lavage fluid, lung tissue, and sputum. IPF-specific biomarkers are of great clinical value for the differential diagnosis of IPF. Currently, the physiological measurements used to evaluate the occurrence of acute exacerbation, disease progression, and disease severity have limitations. Combining physiological measurements with biomarkers may increase the accuracy and sensitivity of diagnosis and disease evaluation of IPF. Most biomarkers described in this review are not routinely used in clinical practice. Future large-scale multicenter studies are required to design and validate suitable biomarker panels that have diagnostic utility for IPF.