bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated Plasma Complement Factors inCRB1-associated Inherited Retinal Dystrophies
Authors: Moekotte Lude , de Boer Joke H. , Hiddingh Sanne , de Ligt Aafke , Nguyen Xuan-Thanh-An , Hoyng Carel B. , Inglehearn Chris F. , McKibbin Martin , Lamey Tina M. , Thompson Jennifer A. , Chen Fred K. , McLaren Terri L. , AlTalbishi Alaa , Panneman Daan M. , Boonen Erica G.M. , Banfi Sandro , Bocquet Béatrice , Meunier Isabelle , Baere Elfride De , Koenekoop Robert , Ołdak Monika , Rivolta Carlo , Roberts Lisa , Ramesar Raj , Strupaitė-Šileikienė Rasa , Kohl Susanne , Farrar G. Jane , van Vugt Marion , van Setten Jessica , Roosing Susanne , van den Born L. Ingeborgh , Boon Camiel J.F. , van Genderen Maria M. , Kuiper Jonas J.W. 
Published: November 2023

AbstractObjectiveTo determine the profile of inflammation-related proteins and complement system factors in serum ofCRB1-associated inherited retinal dystrophies (CRB1-IRDs).DesignA case-control study.Subjects, Participants, and/or ControlsA cohort of 30 DutchCRB1-IRD patients and 29 Dutch healthy controls (HC) (Cohort I), and a second cohort of 123CRB1-IRD patients from 14 countries and 1292 controls (Cohort II) were used in this study.MethodsQuantitative 370-plex targeted proteomics in blood plasma and genotyping of the single nucleotide variant (SNV) rs7535263 in theCFHgene.Main Outcome MeasuresPlasma concentrations of inflammation-related proteins and the genotype of the SNV rs7535263.ResultsCRB1-IRD patients showed increased plasma levels of complement system and coagulation cascade proteins compared to healthy controls. Complement Factor I [CFI], Serpin Family D1 [SERPIND1], and Complement Factor H [CFH] were significantly elevated (q<0.05, adjusted for age and sex), which correlated (Pearson’s correlation coefficient >0.6) with higher levels of plasma Complement Component 3 [C3] (q = 0.064). The most enriched pathway in patients was the “Complement cascade” (R-HSA-166658,Padj=P= 3.03 × 10-15). An analysis of the genotype ofCFHvariant rs7535263, which is in close physical proximity to theCRB1gene and is associated with other retinal conditions by influencing plasma complement levels, revealed significantly skewed allele distribution specifically in Dutch patients (A allele of rs7535263, odds ratio (OR) [95%CI = 2.85 [1.35-6.02],P= 6.19 × 10-3), but not in a global case-control cohort (P= 0.12). However,CRB1missense variants that are common in patients display strong linkage disequilibrium (LD) with rs7535263 inCFHin the UK Biobank (D’ = 0.97 for p.(Cys948Tyr); D’ = 1.0 for p.(Arg764Cys)), indicating that genetic linkage may influence plasma complement factor levels inCRB1-IRD patients. After accounting for theCFHgenotype in the proteomic analyses, we also detected significantly elevated plasma levels of Complement Factor H Related 2 [CFHR2] inCRB1-IRD patients (q = 0.04).ConclusionsCRB1-IRDs are characterized by changes in plasma levels of complement factors and proteins of the innate immune system, which is influenced by common functional variants in theCFH-CFHRlocus. This indicates that innate immunity is implicated inCRB1-IRDs.
Development of a Liver Disease-Specific Large Language Model Chat Interface using Retrieval Augmented Generation
Authors: Ge Jin , Sun Steve , Owens Joseph , Galvez Victor , Gologorskaya Oksana , Lai Jennifer C. , Pletcher Mark J. , Lai Ki 
Published: November 2023

AbstractBackgroundLarge language models (LLMs) have significant capabilities in clinical information processing tasks. Commercially available LLMs, however, are not optimized for clinical uses and are prone to generating incorrect or hallucinatory information. Retrieval-augmented generation (RAG) is an enterprise architecture that allows embedding of customized data into LLMs. This approach “specializes” the LLMs and is thought to reduce hallucinations.MethodsWe developed “LiVersa,” a liver disease-specific LLM, by using our institution’s protected health information (PHI)-complaint text embedding and LLM platform, “Versa.” We conducted RAG on 30 publicly available American Association for the Study of Liver Diseases (AASLD) guidelines and guidance documents to be incorporated into LiVersa. We evaluated LiVersa’s performance by comparing its responses versus those of trainees from a previously published knowledge assessment study regarding hepatitis B (HBV) treatment and hepatocellular carcinoma (HCC) surveillance.ResultsLiVersa answered all 10 questions correctly when forced to provide a “yes” or “no” answer. Full detailed responses with justifications and rationales, however, were not completely correct for three of the questions.DiscussionsIn this study, we demonstrated the ability to build disease-specific and PHI-compliant LLMs using RAG. While our LLM, LiVersa, demonstrated more specificity in answering questions related to clinical hepatology – there were some knowledge deficiencies due to limitations set by the number and types of documents used for RAG. The LiVersa prototype, however, is a proof of concept for utilizing RAG to customize LLMs for clinical uses and a potential strategy to realize personalized medicine in the future.
Chronotropic Incompetence among People with HIV Improves with Exercise Training in the Exercise for Healthy Aging Study
Authors: Durstenfeld Matthew S. , Wilson Melissa P. , Jankowski Catherine M. , Ditzenberger Grace L. , Longenecker Chris T. , Erlandson Kristine M. 
Published: November 2023

AbstractBackgroundPeople with HIV (PWH) have lower exercise capacity compared to HIV uninfected peers, which may be explained by chronotropic incompetence (CI), the inability to increase heart rate during exercise.MethodsThe Exercise for Healthy Aging Study included adults ages 50-75 with and without HIV. Participants completed 12 weeks of moderate intensity exercise, before randomization to moderate or high intensity for 12 additional weeks. We compared adjusted heart rate reserve (AHRR; CI <80%) on cardiopulmonary exercise testing by HIV serostatus, and change from baseline to 12 and 24 weeks using mixed effects models.ResultsAmong 32 PWH and 37 controls (median age 56, 7% female, mean BMI 28 kg/m2), 28% of PWH compared to 11% of controls had CI at baseline (p=0.067). AHRR was lower among PWH (91 vs 102%; difference 11%, 95% CI 2.5-19.7; p=0.01). At week 12, AHRR normalized among PWH (+8%, 95% CI 4-11; p<0.001) and was sustained at week 24 (+5, 95%CI 1-9; p=0.008) compared to no change among controls (95%CI –4 to 4; p=0.95; pinteraction=0.004). After 24 weeks of exercise, only 15% PWH and 10% of controls had CI (p=0.70).ConclusionsChronotropic incompetence contributes to reduced exercise capacity among PWH and improves with exercise training.
Dynamic Simulation Modeling to Analyze the Impact of Whole Genome Sequencing National Implementation Scenarios in Lung cancer on Time-to-Treatment, Costs and Patient Demand
Authors: van de Ven Michiel , Koffijberg Hendrik , Retèl Valesca P.J. , van Harten Wim H. , IJzerman Maarten J. 
Published: November 2023

AbstractBackgroundAlthough Whole Genome Sequencing (WGS) is increasingly proposed to unravel molecular origins of advanced cancers, it is less clear if and how WGS should be routinely offered in the health service. The objective of this study is to investigate how the cost per patient and time-to-treatment is affected if WGS were implemented in the national health system and how these outcomes differ among subgroups of patients with lung cancer. This first-ever study used health systems simulation modeling to analyze implementation scenarios ensuring sustainable access to cancer treatment.MethodsA base case and three scenarios (varying stage of disease and hospitals offering WGS) the optimal placement of WGS in the diagnostic pathway was simulated using a dynamic simulation model. The model simulated lung cancer patients undergoing molecular diagnostic procedures in one or multiple hospitals. The model also included patient and healthcare provider heterogeneity as well as referral patterns of lung cancer (LC) patients using patient-level data obtained from the Netherlands Cancer Registry. Model outcomes were the time-to-treatment, total diagnostic cost, and the demand for WGS sequencing capacity including the expertise of a molecular tumor board.ResultsThe time-to-treatment ranged between 20-46 days for all four scenarios considered. The cost of molecular diagnostic testing per patient ranged from €621 in the base case to €1930 in the scenario where all LC patients (stage I-IV) receive upfront WGS. Compared to the base case, upfront testing using WGS in all LC patients led to a 33% reduction in the time-to-treatment, a 210% increase in the cost per patient and a six-fold increase in total diagnostic costs.ConclusionsThis first-ever study investigating implementation scenario’s demonstrated that upfront WGS for all lung cancer patients can reduce the time to treatment yet at a higher cost. However, upfront WGS also reduces diagnostic pathway complexity, which may improve care planning and treatment efficiency. The model is versatile in its approach to study the impact of price discounts or the amount of actionable targets tested for and further analysis showed discounts on consumables up to 50% imply WGS would the preferred strategy.
Measures of retention in HIV care: A protocol for a mixed methods study
Authors: Rehman Nadia , Garcia Michael Cristian , Jones Aaron , Ma Jinhui , Mertz Dominik , Mbuagbaw Lawrence 
Published: November 2023

AbstractIntroductionRetention in HIV care is necessary to achieve adherence to antiretroviral therapy, viral load suppression, and optimal health outcomes. There is no standard definition for retention in HIV care, which compromises consistent and reliable reporting and comparison of retention across facilities, jurisdictions, and studies.ObjectiveThe objective of this study is to explore how stakeholders involved in HIV care define retention in HIV care and their preferences on measuring retention.MethodsWe will use an exploratory sequential mixed methods design involving HIV stakeholder groups such as people living with HIV, people involved in providing care for PLHIV, and people involved in decision-making about PLHIV. In the qualitative phase of the study, we with conduct 20-25 in-depth interviews to collect perspectives of HIV stakeholders on using their preferred retention measures. The interview guide has being provided as an online Supplementary Appendix 1.The findings from the qualitative phase will inform the development of survey items for the quantitative phase. Survey participants (n=385) will be invited to rate the importance of each approach to measuring retention on a seven-point Likert scale. We will merge the findings from the qualitative and quantitative findings phase to inform a consensus-building framework for a standard definition of retention in care.Ethical Issues and DisseminationThis study has received ethics approval from the Hamilton Integrated Research Ethics Board. The findings will be disseminated through peer-reviewed publications, conference presentations, and among stakeholder groups.Limitations1. This study has limitation, we won’t be able to arrive at a standard definition, a Delphi technique amongst the stakeholders will be utilized using the framework to reach a consensus globally accepted definition.
Transitions of care between jail-based medications for opioid use disorder and ongoing treatment in the community: A retrospective cohort study
Authors: Krawczyk Noa , Lim Sungwoo , Cherian Teena , Goldfeld Keith S. , Katyal Monica , Rivera Bianca D. , McDonald Ryan , Khan Maria , Wiewel Ellen , Braunstein Sarah , Murphy Sean M. , Jalali Ali , Jeng Philip J. , Kutscher Eric , Khatri Utsha G. , Rosner Zachary , Vail William L. , MacDonald Ross , Lee Joshua D. 
Published: November 2023

AbstractBackground and AimsOffering medications for opioid use disorder (MOUD) in carceral settings can significantly reduce overdose risk. However, it is unknown whether and to what extent individuals in U.S. jail settings continue MOUD once they leave incarceration, and what factors influence treatment continuity.DesignRetrospective cohort study of linked jail-based electronic health records and community OUD treatment claims.SettingNew York City JailParticipantsIncarcerations of individuals with OUD discharged from jail to the community between May 1, 2011 and December 31, 2017ComparatorsReceiving vs. not receiving MOUD (methadone or buprenorphine) at the time of release from jailMeasurementsWe measured continuity of community-based MOUD treatment within one month of release, among those with and without MOUD during release from jail. We tested for effect modification based on MOUD receipt prior to incarceration and assessed factors associated with treatment discontinuation upon re-entry.FindingsOf 28,298 eligible incarcerations, 52.8% received MOUD at release. 30% of incarcerations with MOUD had a community-based MOUD claim within 30 days of release, compared to 7% of incarcerations without MOUD (Risk Ratio: 2.62 (2.44-2.82)). Most (69%) of those with MOUD claims prior to incarceration who received in-jail MOUD continued MOUD in the community, compared to only 9% of those without prior MOUD. Among incarcerations with MOUD at release, those who were younger, Non-Hispanic Black and with no history of MOUD treatment were less likely to continue treatment following release.ConclusionsMOUD maintenance in jail is strongly associated with MOUD continuity in the community upon release. Still, findings highlight a continued gap in MOUD upon-reentry, especially among those who initiate MOUD in jail. In the wake of worsening overdose deaths and troubling disparities, improving continuty of evidence-based care among this population must be an urgent policy priority.
Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event
Authors: Gschwind Rémi , Petitjean Marie , Fournier Claudine , Lao Julie , Clermont Olivier , Nordmann Patrice , Mellmann Alexander , Denamur Erick , Poirel Laurent , Ruppé Etienne 
Published: November 2023

AbstractBeta-lactam degradation by beta-lactamases is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase encoding genes can be transferred between closely-related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) has never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Peudomonadota and Bacteroidota phyla.AnEscherichia colistrain was isolated from a patient in Münster (Germany). Its genome was sequenced (Illumina and Nanopore). The ESBL encoding gene was cloned and the corresponding enzyme was characterised. Distribution of the gene among bacteria was studied with BLASTN using RefSeq Genomes databases. Frequency of its closest homolog in the Global Microbial Gene Catalog (GMGC) was also analysed.TheblaMUN-1gene found in theE. colistrain, encoded for an Ambler subclass A2 beta-lactamase with 82.2% amino acid identity to TLA-1 and it was found to confer an ESBL phenotype.blaMUN-1was found in four copies, two chromosomal copies and two located on a phage-plasmid p0111. Each copy was found on a 7.6kb genomic island associated with mobility.blaMUN-1was found distributed among the Bacteroidales order and inSutterella wardsworthensis(Pseudomonadota). Its closest homolog in the GMGC was found predominantly and frequently in the Human gut sub-catalog (found in 26.8% of the samples).This is the first reported case of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. While the gene was frequently found in the human gut, inter-phylum transfer was rare, suggesting that inter-phylum barriers are strong but not impassable.
UnderstandingCampylobacter coliisolates from the Vietnamese meat production network; a pilot study
Authors: Lehri Burhan , Navoly Georgina , Corser Abigail , Nashar Fauzy , Willcocks Sam , Ngoc Pham Thi , Wren Brendan W. , Huong Luu Quynh , Stabler Richard A. 
Published: November 2023

AbstractChanging farming practices and the associated increase in the use of antibiotics are amongst the main drivers shaping the global increase of Campylobacter infections. The effects farming practices have onCampylobacterspecies, need to be studied at the global scale, particularly in emerging middle-income countries, where the demand for low-cost poultry meat is rising. WhileC. jejunicauses the majority of poultry associated diarrhoea,C. colicauses a significant amount of disease but are relatively understudied. In this study we characterised sevenC. colistrains isolated from poultry farms and markets in Hanoi, Vietnam. Comprehensive data sets of bacterial Whole-Genome Sequencing; and phenotypic assays, such as, growth, motility, antimicrobial resistant testing along with virulence testing were performed to reveal the genetic relatedness and pathophysiological characteristics of sevenC. colistrains. Six isolates were classified as multi-drug resistant, with all isolates resistant to ciprofloxacin, nalidixic acid and tetracycline, but susceptible to phenicols. All isolates had similar growth rates, while five were hyper-motile. Lethality of the isolates towards a tractable host-model system, larvae of the greater wax mothGalleria mellonella, often used to determineCampylobactervirulence was demonstrated for the first time forC. coli. Multilocus sequence typing data correlates with North American, European, and Asian isolates from patients suffering from gastroenteritis, emphasising the global spread of these strains. This work demonstrates thatC. coli, with high levels of antimicrobial resistance, is an understudied global threat.Data summaryGenBank database with accession numbers JAKGTW000000000, JAKGTV000000000, JAKGTS000000000, JAKGTU000000000, JAKGTT000000000, JAKGTR000000000 and CP091310https://www.ncbi.nlm.nih.gov/nuccore/JAKGTW000000000https://www.ncbi.nlm.nih.gov/nuccore/JAKGTV000000000https://www.ncbi.nlm.nih.gov/nuccore/JAKGTS000000000https://www.ncbi.nlm.nih.gov/nuccore/JAKGTU000000000https://www.ncbi.nlm.nih.gov/nuccore/JAKGTT000000000https://www.ncbi.nlm.nih.gov/nuccore/JAKGTR000000000https://www.ncbi.nlm.nih.gov/nuccore/CP091310.1The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Robotic process automation and artificial intelligence capabilities driving digital strategy: a resource-based view
Authors: Moderno Osvaldo Braz dos Santos , Braz Antonio Carlos , Nascimento Paulo Tromboni de Souza 
Published: November 2023

PurposeResearch of currently limited literature sees Robotic Process Automation (RPA) as an important tool at the tactical level. However, the literature has not considered its potential contribution to creating competitive advantages. This paper aims to link RPA and Resource-based view (RBV) literature, proposing a conceptual framework boosting RPA research as part of an organizational AI strategy.Design/methodology/approach This study applied a Systematic Literature Review (SRL), combining bibliometrics and content analysis. This study also built a new framework based on the updated RBV model that was transformed based on the RPA literature review results.Findings By bridging the two bodies of literature on RBV and RPA, this study manages to show the strategic side of the technology. Therefore, this study brought to light the most updated fundamental concepts of complementarity and scale-free fungible resources from RBV theory and AI technologies, applied to the domains of RPA, information systems and information technology (IS/IT) through the development of a new theoretical lens. Also, this study was able to elaborate on a new conceptual framework for AI strategy formulation to help organizations on their journey to AI utilization.Originality/value The authors did not find any research that has shown the strategic side of RPA, nor any that has used a theoretical lens based on the RBV theory to show this side. To the best of the author’s knowledge, this study seems to be the first to make the case for RPA's strategic potential.
ESG performance and firms' innovation efficiency: the moderating role of state-owned firms and regional market development
Authors: Wan He , Fu Jialiang , Zhong Xi 
Published: November 2023

PurposeAlthough the impact of environmental, social and governance (ESG) on firms' innovation has attracted attention, the existing research findings diverge. The authors believe that failure to consider both innovation input and output is an important reason for the divergence of conclusions in the extant literature when discussing the impact of ESG and firm innovation. Thus, based on signaling theory, this study aims to reconcile these divergent findings by examining the impact of ESG performance on firms' innovation efficiency.Design/methodology/approachTo seek empirical evidence to support the authors’ theoretical view, the authors conduct an empirical test based on the Tobit model using 8 years of data from Chinese listed companies.FindingsAlthough ESG performance effectively improves firms' innovation efficiency, the institutional-level signaling environment (including state-owned firms and regional market development) weakens the positive effect of ESG performance on firms' innovation efficiency. Further tests suggest that financing constraints partially mediate the relationship between ESG performance and firms' innovation efficiency.Originality/valueBy systematically revealing whether, how and under what circumstances ESG performance improves firms' innovation advantages, this study bridges the gap in the existing literature and highlights important implications to suggest how firms can better capture the value associated with ESG.
Drivers of disaster planning among African-American households
Authors: Pudlo Jason M. , Ellis William Curtis , McGowen Ernest B. 
Published: November 2023

PurposeThe paper seeks to explore the drivers of disaster planning in African-American households. While the paper is exploratory, the authors attempt to dialogue with substantial theoretical and applied research around vulnerability and disaster. Race, ethnicity and vulnerability are issues deeply entangled with American disaster preparedness and response. In this study, the authors hope to illuminate the threads which bind them together and contribute to a more nuanced understanding of the relationship between race, ethnicity, class and preparedness.Design/methodology/approachData for this project come from a disaster planning question placed on the 2020 Collaborative Multiracial Post-Election Survey (CMPS). The authors analyze a split sample of around 5,000 African-American households descriptively and with multinomial logistic regression.FindingsDisaster planning among African-American households is a product of past experiences, concern about other hazards, social trust and gender identity. These results are similar to other findings within the study of household preparedness and help to advance the understanding of predictors within the African-American community. Key drivers such as income, education level, gender identity, social trust and perceptions of other risks are consistent with previous studies.Originality/valueThis project is the first to examine issues of disaster planning utilizing a national sample of African-American households via the one-of-a-kind 2020 CMPS.