bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of new, mScarlet-based red fluorescent tags inCaenorhabditis elegans
Authors: Cao Wen Xi , Merritt Daniel , Pe Karinna , Cesar Michael , Hobert Oliver 
Published: June 2024

ABSTRACTOne problem that has hampered the use of red fluorescent proteins in the fast-developing nematodeC. eleganshas been the substantial time delay in maturation of several generations of red fluorophores. The recently described mScarlet-I3 protein has properties that may overcome this limitation. We compare here the brightness and maturation time of CRISPR/Cas9 genome-engineered mScarlet, mScarlet3, mScarlet-I3 and GFP reporter knock-ins. Comparing the onset and brightness of expression of reporter alleles ofC. elegans golg-4, encoding a broadly expressed Golgi resident protein, we found that the onset of detection of mScarlet-I3 in the embryo is several hours earlier than older versions of mScarlet and comparable to GFP. These findings were further supported by comparing mScarlet-I3 and GFP reporter alleles forpks-1, a gene expressed in the CAN neuron and cells of the alimentary system, as well as reporter alleles for the panneuronal, nuclear markerunc-75. Hence, the relative properties of mScarlet-I3 and GFP do not depend on cellular or subcellular context. In all cases, mScarlet-I3 reporters also show improved signal-to-noise ratio compared to GFP.
Frequency of pharmacogenomic variation and medication exposures among All of Us Participants
Authors: Haddad Andrew , Radhakrishnan Aparna , McGee Sean , Smith Joshua D. , Karnes Jason H. , Venner Eric , Wheeler Marsha M. , Patterson Karynne , Walker Kimberly , Kalra Divya , Kalla Sara E. , Wang Qiaoyan , Gibbs Richard A. , Jarvik Gail P. , Sanchez Janeth , Musick Anjene , Ramirez Andrea H. , Denny Joshua C. , Empey Philip E. 
Published: June 2024

AbstractPharmacogenomics promises improved outcomes through individualized prescribing. However, the lack of diversity in studies impedes clinical translation and equitable application of precision medicine. We evaluated the frequencies of PGx variants, predicted phenotypes, and medication exposures using whole genome sequencing and EHR data from nearly 100k diverse All of Us Research Program participants. We report 100% of participants carried at least one pharmacogenomics variant and nearly all (99.13%) had a predicted phenotype with prescribing recommendations. Clinical impact was high with over 20% having both an actionable phenotype and a prior exposure to an impacted medication with pharmacogenomic prescribing guidance. Importantly, we also report hundreds of alleles and predicted phenotypes that deviate from known frequencies and/or were previously unreported, including within admixed American and African ancestry groups.
Association between routinely reported symptoms and 3 month hospital admission and mortality risk: a landmark analysis investigation in 86,000 individuals with heart failure in the UK
Authors: Ali MR , Lam CSP , Stromberg A , Hand SPP , Booth S , Zaccardi F , McCann GP , Khunti K , Lawson CA 
Published: June 2024

ABSTRACTObjectivesIn patients with heart failure (HF), investigate the association between symptoms recorded in routine primary care consultations and short-term (3-month) hospitalisation and mortality.DesignLandmark analysis using Royston-Parmar flexible parametric survival models fitted at three different timepoints (landmarks): baseline (diagnosis date), and 6 and 12 month post-diagnosis.SettingPrimary care database analysis using Clinical Practice Research Datalink (CPRD), linked to hospitalisations and mortality (1998 to 2020).ParticipantsAdults (>40 years) with a first code for HF diagnosis in primary or secondary care records.ExposuresShortness of breath (SOB), ankle swelling, oedema, fatigue, chest pain, depression and anxiety measured in a 3-month time-window prior to HF diagnosis and in survivors at 6 and 12-months.Main outcome measures3-month first all-cause hospitalisation and mortality, separately. Secondary outcomes were hospitalisations for HF and non-cardiovascular disease.ResultsThere were 86,882 patients with a diagnosis of HF, of whom 62,742 and 54,555 survived 6 and 12 months, respectively. There were differential symptom associations among different landmarks and outcomes. The highest risk associations for symptoms recorded just prior to diagnosis (baseline) were for depression for all-cause hospitalisation (adjusted hazard ratio: 1.26; 95% CI 1.15, 1.39), for non-cardiovascular hospitalisation (1.15; 1.10, 1.21) and death (1.22; 1.09, 1.36) and SOB for HF hospitalisation (1.18; 1.12, 1.26). Patients with HF exhibiting symptoms just prior to 6 and 12 month landmarks had increased risk of hospitalisation and mortality: at 6-months, the highest risk associations were with symptoms of depression for all-cause hospitalisation (1.46; 1.25, 1.70) and non-CVD hospitalisation (1.46; 1.23, 1.74), SOB for HF-specific hospitalisation (1.72; 1.50, 1.98); ankle swelling for mortality (1.49; 1.14, 1.94). At the 12-month landmark, classic HF symptoms had the highest risk associations: ankle swelling for all-cause hospitalisation (1.47; 1.21, 1.79) and non-CVD hospitalisation (1.55; 1.24, 1.93); SOB for HF hospitalisation (1.99; 1.68, 2.35); and fatigue for mortality (1.57; 1.22, 2.03).ConclusionsSymptoms reported by patients with HF in routine primary care consultations were associated with short-term risk of hospitalisations and death. These risk associations were more prominent in patients with HF at 6 and 12-months post-diagnosis than at the point of diagnosis.
The effect of coronary revascularization timing on cardiovascular outcomes in patients with ischemic heart disease
Authors: Hardiman Sean , Fradet Guy , Kuramoto Lisa , Law Michael , Robinson Simon , Sobolev Boris 
Published: June 2024

ABSTRACTBackgroundThere is little evidence on whether the timing of revascularization affects cardiovascular disease progression in patients with stable ischemic heart disease. We aimed to determine if disease progression differed between patients who underwent coronary artery bypass graft (CABG) surgery after the time recommended by physicians compared to timely percutaneous coronary intervention (PCI).MethodsWe identified 25,469 British Columbia, Canada residents ages 60 years or older who underwent their first non-emergency revascularization for angiographically proven, stable left main or multi-vessel ischemic heart disease. We estimated the cumulative incidence of a composite cardiovascular outcome (CVO) and death as a competing risk for patients undergoing delayed CABG versus timely PCI.ResultsAfter adjustment, patients who underwent delayed CABG had a statistically significantly lower cumulative CVO incidence at three years compared with those who received timely PCI (9.6% delayed CABG, 23.2% timely PCI; subdistribution hazard ratio for CVO at three years 0.50, 95% CI 0.26–0.99).ConclusionOur results suggest that for patients who wish to wait for CABG, doing so may lead to slower disease progression compared with receiving PCI.
Investigating different factors on the outcome of severe Idiopathic Granulomatous Mastitis in 110 women from 2017 to 2021: A cross-sectional study
Authors: Zarpoosh Mahsa , Asgari Zahra , Amirian Parsa , Mousavi Tahereh Sadat , Golpazir Arash , Pournazari Mehran 
Published: June 2024

AbstractAimIdiopathic Granulomatous Mastitis is a distressing chronic disease without precise etiology and cure. While this disease is rare worldwide, it has been recorded as a prevalent one in Middle Eastern countries; therefore, our aim to investigate the role of different factors on the outcome of the severe form of the disease can shed light on various aspects of the disease.MethodsWe retrospectively identified 110 Iranian women, from 2017 to 2021, with severe Idiopathic Granulomatous Mastitis who met the required histological criteria of this benign disease. All patients had developed severe mastitis according to their signs and required treatment. After gathering the information retrospectively, we analyzed them by using statistical tests.ResultsIn our study, most patients were overweight or obese in their reproductive age with a positive history of pregnancy and breastfeeding. It typically appeared as a painful erythematous mass-like lesion in the upper-outer of the left breast (mean size: 26.75 ± 20.08 mm). Approximately half of the participants experienced extra-mammary manifestations such as arthritis, hair loss, or erythema nodosum. Even though all patients were treated with corticosteroids and Methotrexate or Azathioprine, 32.33% were not completely remitted. Lastly, we realized that there are statistical associations between three variables (family history of Granulomatous Mastitis, the size of the lesions, and the number of recurrences) and the final outcome; all P-values were less than 0.05.ConclusionThe remission rate may decrease when the lesion size exceeds 5 cm, and some hereditary factors may play a role in the response to treatment.
Multispectral live-cell imaging with uncompromised spatiotemporal resolution
Authors: Kumar Akaash , McNally Kerrie E. , Zhang Yuexuan , Haslett-Saunders Alex , Wang Xinru , Guillem-Marti Jordi , Lee David , Huang Buwei , Stallinga Sjoerd , Kay Robert R. , Baker David , Derivery Emmanuel , Manton James D. 
Published: June 2024

AbstractMultispectral imaging is an established method to extend the number of colours usable in fluorescence imaging beyond the typical limit of three or four, but standard approaches are poorly suited to live-cell imaging. We introduce an approach for multispectral imaging in live cells, comprising an iterative spectral unmixing algorithm and eight channel camera-based image acquisition hardware. This enables the accurate unmixing of low signal-to-noise ratio datasets, typical of live-cell imaging, captured at video rates. We use this approach on a commercial spinning disk confocal microscope and a home-built oblique plane light sheet microscope to image 1–7 spectrally distinct fluorophore species simultaneously, using both fluorescent protein fusions and small-molecule dyes. We further use de novo designed protein-binding proteins (minibinders), labelled with organic fluorophores, and use these in combination with our multispectral imaging approach to study the endosomal trafficking of cell-surface receptors at endogenous levels.
Prevalent chromosome fusion inVibrio choleraeO1
Authors: Cuénod Aline , Chac Denise , Khan Ashraful I. , Chowdhury Fahima , Hyppa Randy W. , Markiewicz Susan M. , Calderwood Stephen B. , Ryan Edward T. , Harris Jason B. , LaRocque Regina C. , Bhuiyan Taufiqur R. , Smith Gerald R. , Qadri Firdausi , Lypaczewski Patrick , Weil Ana A. , Shapiro B. Jesse 
Published: June 2024

AbstractTwo circular chromosomes are a defining feature of the familyVibrionaceae, including the pathogenVibrio cholerae, with rare reports of isolates with a single, fused chromosome. Here we report chromosome fusions in clinicalV. choleraeO1 isolates, including several independent fusion events stable enough to be transmitted between patients within a household. Fusion occurs in a 12 kilobase-pair homologous sequence shared between the two chromosomes, which may lead to reversible chromosomal fusion.
PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators
Authors: Wang Yuexi , Chembazhi Ullas Valiya , Yee Danielle , Chen Sijie , Ji Jie , Wang Yujie , Nguyen Ka Lam , Lin PoChing , Ratti Antonia , Hess Rex , Qiao Huanyu , Ko CheMyong , Yang Jing , Kalsotra Auinash , Mei Wenyan 
Published: June 2024

ABSTRACTSpermatogenesis is a biological process within the testis that produces haploid spermatozoa for the continuity of species. Sertoli cells are somatic cells in the seminiferous epithelium that orchestrate spermatogenesis. Cyclic reorganization of Sertoli cell actin cytoskeleton is vital for spermatogenesis, but the underlying mechanism remains largely unclear. Here, we report that RNA-binding protein PTBP1 controls Sertoli cell actin cytoskeleton reorganization by programming alternative splicing of actin cytoskeleton regulators. This splicing control enables ectoplasmic specializations, the actin-based adhesion junctions, to maintain the blood-testis barrier and support spermatid transport and transformation. Particularly, we show that PTBP1 promotes actin bundle formation by repressing the inclusion of exon 14 ofTnik, a kinase present at the ectoplasmic specialization. Our results thus reveal a novel mechanism wherein Sertoli cell actin cytoskeleton dynamics is controlled post-transcriptionally by utilizing functionally distinct isoforms of actin regulatory proteins, and PTBP1 is a critical regulatory factor in generating such isoforms.
Balancing Equity and HLA Matching in Deceased-Donor Kidney Allocation with Eplet Mismatch
Authors: Mankowski Michal A. , Gragert Loren , Segev Dorry L. , Montgomery Robert , Gentry Sommer E. , Mangiola Massimo 
Published: June 2024

ABSTRACTBackgroundPrioritization of HLA antigen-level matching in the US kidney allocation system intends to improve post-transplant survival but causes racial disparities and thus has been substantially de-emphasized. Recently, molecular matching based on eplets has been found to improve risk stratification compared to antigen matching.MethodsTo assign eplets unambiguously, we utilized a cohort of 5193 individuals with high resolution allele-level HLA genotypes from the National Kidney Registry. Using repeated random sampling to simulate donor-recipient genotype pairings based on the ethnic composition of the historical US deceased donor pool, we profiled the percentage of well-matched donors for candidates by ethnicity.ResultsThe percentage of well-matched donors with zero-DR/DQ eplet mismatch was 3-fold less racially disparate for Black and Asian candidates than percentage of donors with zero-ABDR antigen mismatches, and 2-fold less racially disparate for Latino candidates. For other HLA antigen and eplet mismatch thresholds, the percentage of well-matched donors was more similar across candidate ethnic groups.ConclusionsCompared to the current zero-ABDR antigen mismatch, prioritizing a zero-DR/DQ eplet mismatch in allocation would decrease racial disparities and increase the percentage of well-matched donors. High resolution HLA deceased donor genotyping would enable unambiguous assignment of eplets to operationalize molecular mismatch metrics in allocation.Key PointsQuestionWhat is the impact of prioritizing low molecular mismatch transplants on racial and ethnic disparities in US deceased-donor kidney allocation, compared to the current prioritization of antigen-level matching?FindingsThe lowest-risk eplet mismatch approach decreases racial disparities up to 3-fold compared to lowest-risk antigen mismatch and identifies a larger number of the lowest allo-immune risk donors.MeaningPrioritizing eplet matching in kidney transplant allocation could both improve outcomes and reduce racial disparities compared to the current antigen matching.
Simple and Versatile Pharmacokinetic Model for Radioligand Therapy
Authors: Zounek Adrian Jun , Zounek Alexis Nikolai 
Published: June 2024

AbstractIn recent years radioligand therapy has emerged as an effective treatment modality for various solid malignancies, with pharmacokinetic modeling being routinely used for absorbed dose calculation and patient-specific therapy planning. Exemplary time-activity curves of FAP-targeted radioligands in a mouse model are accurately fitted by a sum of right skew biexponential distributions with four adjustable parameters in total. This type of modeling function is versatile and also suitable for conventional drugs. For further insight, an auxiliary equation is derived that relates tumor clearance to FAP expression and the radioligand dissociation constant.
Elevated meningioma risk among individuals who are Non-Hispanic Black is strongest for grade 2-3 tumors and synergistically modified by male sex
Authors: Walsh Kyle M. , Price Mackenzie , Raleigh David R. , Calabrese Evan , Kruchko Carol , Barnholtz-Sloan Jill S. , Ostrom Quinn T. 
Published: June 2024

ABSTRACTBackgroundMeningioma risk factors include older age, female sex, and African-American race. There are limited data exploring how meningioma risk in African-Americans varies across the lifespan, interacts with sex, and differs by tumor grade.MethodsThe Central Brain Tumor Registry of the United States (CBTRUS) is a population-based registry covering the entire U.S. population. Meningioma diagnoses from 2004-2019 were used to calculate incidence rate ratios (IRRs) for non-Hispanic Black individuals (NHB) compared to non-Hispanic white individuals (NHW) across 10-year age intervals, and stratified by sex and by WHO tumor grade.Results53,890 NHB individuals and 322,373 NHW individuals with an intracranial meningioma diagnosis were included in analyses. Beginning in young adulthood, the NHB-to-NHW IRR was elevated for both grade 1 and grade 2/3 tumors. The IRR peaked in the seventh decade of life regardless of grade, and was higher for grade 2/3 tumors (IRR=1.57; 95% CI: 1.46-1.69) than grade 1 tumors (IRR=1.27; 95% CI: 1.25-1.30) in this age group. The NHB-to-NHW IRR was elevated in females (IRR=1.17; 95% CI: 1.16-1.18) and further elevated in males (IRR=1.28; 95% CI: 1.26-1.30), revealing synergistic interaction between NHB race/ethnicity and male sex (PInteraction=0.001).ConclusionsRelative to NHW individuals, NHB individuals are at elevated risk of meningioma from young adulthood through old age. NHB race/ethnicity conferred higher risk of meningioma among men than women, and higher risk of developing WHO grade 2/3 tumors. Results identify meningioma as a significant source of racial disparities in neuro-oncology and may help to improve preoperative predictions of meningioma grade.
Three-dimensional institutional equivalence: how industry, community, and network peers influence corporate innovation quality in China
Authors: Gao Jiaxin , Gu Xin , Yang Xue 
Published: June 2024

PurposeInnovation quality is a critical component of enterprise innovation. Prior research primarily focuses on company-level and external policy-level factors that affect innovation quality, while ignoring social-level factors. Based on institutional isomorphism theory, this study examines how the innovation quality of three-dimensional institutional equivalence, which is an important and unique reference group for firms to follow the “law of imitation of close preference”, affects the likelihood of firms' innovation quality.Design/methodology/approachThis study conducts firm random effects and industry/year fixed effects models using China's listed companies from 2002 to 2021.FindingsThis study finds that compared with the innovation quality of its other industry, community, or network peers, the innovation quality of three-dimensional institutional equivalence has a greater impact on firm innovation quality. Furthermore, technological intensity significantly increases the effect of three-dimensional institutional equivalence on focal company innovation quality, while financing constraints significantly attenuate this effect. Additionally, when there is no institutional equivalent, the innovation quality of network, industry, and community peers has significant positive effects on enterprise innovation quality. Heterogeneity analysis also indicates that, under the conditions of non-state-owned enterprises, a low regional legal environment, or low regional factor market development, three-dimensional institutional equivalence contributes significantly to firm innovation quality.Research limitations/implicationsThis study focuses on the effect of three-dimensional institutional equivalence on Chinese enterprises' innovation quality. Nonetheless, research samples from other countries are not considered in this study.Originality/valueThis study explores the impact of three-dimensional institutional equivalence on firm innovation quality within a systematic theoretical framework and incorporates firm attributes into this framework.
Is eating meat the new smoking? Exploring the dynamics between meat consumption and education in Switzerland
Authors: Loginova Daria , Mann Stefan 
Published: June 2024

PurposeThis study aims to test Singer’s suggestion that ‘over the next 20 years meat could follow smoking into disrepute” using the findings of the recent literature on meat consumption, education and smoking and data from consumers in Switzerland in 1990–2017.Design/methodology/approachWe hypothesise that meat consumption in developed countries has increasingly shifted to people with less education, as has been observed for smoking in previous studies. Using trend analysis by regressions, we describe the consumption dynamics of nine sorts of meat in Switzerland and estimate meat consumption trends for populations with and without university education separately.FindingsOur results partly confirm the hypothesis. Less educated households consume more non-fish meat per person than households with at least one member educating or having finished education at university. For most categories of meat, the relative decline in consumption has been significantly higher for households in which at least one person holds a university education.Originality/valueOur study contributes to the studies on sociology of meat eating and suggests paying more attention to risks related to meat consumption and to awareness of the population about these risks.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-05-2023-0335
ESG and financial performance via uncertain mining technology: do Multilatinas contribute to the sustainability of the region?
Authors: Grajales Carlos Alexander , Albanés Uribe Katherine 
Published: June 2024

PurposeThis paper proposes a methodology based on an uncertain mining technology that identifies the linguistic relationships of ESG and its components with a financial performance metric to help the sustainability diagnosis of a region, specifically Latin America.Design/methodology/approachFirst, based on a relevant dataset of companies in a region, a procedure is formulated whereby an uncertain mining technology extracts the mathematically significant linguistic relationships of ESG and its components with a financial performance metric. Second, a knowledge management process is designed based on the linguistic summaries obtained from the mining process. As a final step and drawing upon the two preceding processes, a diagrammatic system of signals is proposed for diagnosing the sustainability of the region as contributed by its companies.FindingsAfter this methodology is instantiated on a group of Multilatinas, it is observed that their sustainability contributions to the region are limited and that none of the identified linguistic relationships between ESG and the financial performance metric are favorable for the region.Originality/valueThis is the first proposal of its kind and it can be applied to any region of the world to assess the financial performance of its companies regarding their ESG commitments. In addition, it enables the region to comprehensively monitor compliance with the 2030 SDG agenda.