bluuebunny/crossref_metadata_2025_split huggingface dataset:
GradHC: highly reliable gradual hash-based clustering for DNA storage systems
Authors: Ben Shabat Dvir , Hadad Adar , Boruchovsky Avital , Yaakobi Eitan 
Published: April 2024

Abstract

Motivation
As data storage challenges grow and existing technologies approach their limits, synthetic DNA emerges as a promising storage solution due to its remarkable density and durability advantages. While cost remains a concern, emerging sequencing and synthetic technologies aim to mitigate it, yet introduce challenges such as errors in the storage and retrieval process. One crucial task in a DNA storage system is clustering numerous DNA reads into groups that represent the original input strands.

Results
In this paper, we review different methods for evaluating clustering algorithms and introduce a novel clustering algorithm for DNA storage systems, named Gradual Hash-based clustering (GradHC). The primary strength of GradHC lies in its capability to cluster with excellent accuracy various types of designs, including varying strand lengths, cluster sizes (including extremely small clusters), and different error ranges. Benchmark analysis demonstrates that GradHC is significantly more stable and robust than other clustering algorithms previously proposed for DNA storage, while also producing highly reliable clustering results.

Availability and implementation
https://github.com/bensdvir/GradHC.
Single proxy control
Authors: Park Chan , Richardson David B , Tchetgen Tchetgen Eric J 
Published: April 2024

ABSTRACTNegative control variables are sometimes used in nonexperimental studies to detect the presence of confounding by hidden factors. A negative control outcome (NCO) is an outcome that is influenced by unobserved confounders of the exposure effects on the outcome in view, but is not causally impacted by the exposure. Tchetgen Tchetgen (2013) introduced the Control Outcome Calibration Approach (COCA) as a formal NCO counterfactual method to detect and correct for residual confounding bias. For identification, COCA treats the NCO as an error-prone proxy of the treatment-free counterfactual outcome of interest, and involves regressing the NCO on the treatment-free counterfactual, together with a rank-preserving structural model, which assumes a constant individual-level causal effect. In this work, we establish nonparametric COCA identification for the average causal effect for the treated, without requiring rank-preservation, therefore accommodating unrestricted effect heterogeneity across units. This nonparametric identification result has important practical implications, as it provides single-proxy confounding control, in contrast to recently proposed proximal causal inference, which relies for identification on a pair of confounding proxies. For COCA estimation we propose 3 separate strategies: (i) an extended propensity score approach, (ii) an outcome bridge function approach, and (iii) a doubly-robust approach. Finally, we illustrate the proposed methods in an application evaluating the causal impact of a Zika virus outbreak on birth rate in Brazil.
Addressing age measurement errors in fish growth estimation from length-stratified samples
Authors: Zheng Nan , Kheirollahi Atefeh , Yilmaz Yildiz 
Published: April 2024

ABSTRACT
Fish growth models are crucial for fisheries stock assessments and are commonly estimated using fish length-at-age data. This data is widely collected using length-stratified age sampling (LSAS), a cost-effective two-phase response-selective sampling method. The data may contain age measurement errors (MEs). We propose a methodology that accounts for both LSAS and age MEs to accurately estimate fish growth. The proposed methods use empirical proportion likelihood methodology for LSAS and the structural errors in variables methodology for age MEs. We provide a measure of uncertainty for parameter estimates and standardized residuals for model validation. To model the age distribution, we employ a continuation ratio-logit model that is consistent with the random nature of the true age distribution. We also apply a discretization approach for age and length distributions, which significantly improves computational efficiency and is consistent with the discrete age and length data typically encountered in practice. Our simulation study shows that neglecting age MEs can lead to significant bias in growth estimation, even with small but non-negligible age MEs. However, our new approach performs well regardless of the magnitude of age MEs and accurately estimates SEs of parameter estimators. Real data analysis demonstrates the effectiveness of the proposed model validation device. Computer codes to implement the methodology are provided.
Targeting T-bet expressing B cells for therapeutic interventions in autoimmunity
Authors: Sachinidis Athanasios , Lamprinou Malamatenia , Dimitroulas Theodoros , Garyfallos Alexandros 
Published: April 2024

Summary
Apart from serving as a Th1 lineage commitment regulator, transcription factor T-bet is also expressed in other immune cell types and thus orchestrates their functions. In case of B cells, more specifically, T-bet is responsible for their isotype switching to specific IgG sub-classes (IgG2a/c in mice and IgG1/3 in humans). In various autoimmune disorders, such as systemic lupus erythematosus and/or rheumatoid arthritis, subsets of T-bet expressing B cells, known as age-associated B cells (CD19+CD11c+CD21−T-bet+) and/or double-negative B cells (CD19+IgD−CD27−T-bet+), display an expansion and seem to drive disease pathogenesis. According to data, mostly derived from mice models of autoimmunity, the targeting of these specific B-cell populations is capable of ameliorating the general health status of the autoimmune subjects. Here, in this review article, we present a variety of therapeutic approaches for both mice and humans, suffering from an autoimmune disease, and we discuss the effects of each approach on T-bet+ B cells. In general, we highlight the importance of specifically targeting T-bet+ B cells for therapeutic interventions in autoimmunity.
The Subcortical Atlas of the Marmoset (“SAM”) monkey based on high-resolution MRI and histology
Authors: Saleem Kadharbatcha S , Avram Alexandru V , Glen Daniel , Schram Vincent , Basser Peter J 
Published: April 2024

Abstract
A comprehensive three-dimensional digital brain atlas of cortical and subcortical regions based on MRI and histology has a broad array of applications in anatomical, functional, and clinical studies. We first generated a Subcortical Atlas of the Marmoset, called the “SAM,” from 251 delineated subcortical regions (e.g. thalamic subregions, etc.) derived from high-resolution Mean Apparent Propagator-MRI, T2W, and magnetization transfer ratio images ex vivo. We then confirmed the location and borders of these segmented regions in the MRI data using matched histological sections with multiple stains obtained from the same specimen. Finally, we estimated and confirmed the atlas-based areal boundaries of subcortical regions by registering this ex vivo atlas template to in vivo T1- or T2W MRI datasets of different age groups (single vs. multisubject population-based marmoset control adults) using a novel pipeline developed within Analysis of Functional NeuroImages software. Tracing and validating these important deep brain structures in 3D will improve neurosurgical planning, anatomical tract tracer injections, navigation of deep brain stimulation probes, functional MRI and brain connectivity studies, and our understanding of brain structure–function relationships. This new ex vivo template and atlas are available as volumes in standard NIFTI and GIFTI file formats and are intended for use as a reference standard for marmoset brain research.
Changes in the Appropriateness of US Outpatient Antibiotic Prescribing After the COVID-19 Outbreak: An Interrupted Time Series Analysis of 2017–2021 Data
Authors: Chua Kao-Ping , Fischer Michael A , Rahman Moshiur , Linder Jeffrey A 
Published: April 2024

Abstract

Background
No national study has evaluated changes in the appropriateness of US outpatient antibiotic prescribing across all conditions and age groups after the coronavirus disease 2019 (COVID-19) outbreak in March 2020.

Methods
This was an interrupted time series analysis of Optum's de-identified Clinformatics Data Mart Database, a national commercial and Medicare Advantage claims database. Analyses included prescriptions for antibiotics dispensed to children and adults enrolled during each month during 2017–2021. For each prescription, we applied our previously developed antibiotic appropriateness classification scheme to International Classification of Diseases, Tenth Revision, Clinical Modification diagnosis codes on medical claims occurring on or during the 3 days prior to dispensing. Outcomes included the monthly proportion of antibiotic prescriptions that were inappropriate and the monthly proportion of enrollees with ≥1 inappropriate prescription. Using segmented regression models, we assessed for level and slope changes in outcomes in March 2020.

Results
Analyses included 37 566 581 enrollees, of whom 19 154 059 (51.0%) were female. The proportion of enrollees with ≥1 inappropriate prescription decreased in March 2020 (level decrease: −0.80 percentage points [95% confidence interval {CI}, −1.09% to −.51%]) and subsequently increased (slope increase: 0.02 percentage points per month [95% CI, .01%–.03%]), partly because overall antibiotic dispensing rebounded and partly because the proportion of antibiotic prescriptions that were inappropriate increased (slope increase: 0.11 percentage points per month [95% CI, .04%–.18%]). In December 2021, the proportion of enrollees with ≥1 inappropriate prescription equaled the corresponding proportion in December 2019.

Conclusions
Despite an initial decline, the proportion of enrollees exposed to inappropriate antibiotics returned to baseline levels by December 2021. Findings underscore the continued importance of outpatient antibiotic stewardship initiatives.
Make Modern Microbiology Matter More in the 2023 European Society of Cardiology Guidelines for the Management of Infective Endocarditis
Authors: Oldberg Karl , Rasmussen Magnus 
Published: April 2024

Abstract
The European Society of Cardiology (ESC) 2023 guidelines for the management of infective endocarditis (IE) stress that a multidisciplinary approach is needed to manage patients with IE. In our view, the guidelines do not include the relevant perspectives from modern microbiology. The diagnostic criteria for IE were changed in the ESC 2023 guidelines, and many IE-causing pathogens are either not clearly defined. Moreover, an improved understanding of the relationship between bacterial species and the risk for IE has not been implemented. The guidelines give detailed and, in our view, incorrect instructions about diagnostic testing in blood culture–negative IE without presenting proper evidence. Other important diagnostic aspects, such as the value of repeated blood cultures and incubation time for blood cultures, are not discussed. We believe that a multidisciplinary collaboration that include microbiologists would have improved these guidelines, and we hope for a future harmonization of diagnostic criteria for IE.
Comprehensive atrial fibrillation burden and symptom reduction post-ablation: insights from DECAAF II
Authors: Noujaim Charbel , Assaf Ala , Lim Chanho , Feng Han , Younes Hadi , Mekhael Mario , Chouman Nour , Shamaileh Ghaith , El Hajjar Abdel Hadi , Ayoub Tarek , Isakadze Nino , Chelu Mihail G , Marrouche Nassir , Donnellan Eoin 
Published: April 2024

Abstract

Aims
Traditional atrial fibrillation (AF) recurrence after catheter ablation is reported as a binary outcome. However, a paradigm shift towards a more granular definition, considering arrhythmic or symptomatic burden, is emerging. We hypothesize that ablation reduces AF burden independently of conventional recurrence status in patients with persistent AF, correlating with symptom burden reduction.

Methods and results
Ninety-eight patients with persistent AF from the DECAAF II trial with pre-ablation follow-up were included. Patients recorded daily single-lead electrocardiogram (ECG) strips, defining AF burden as the proportion of AF days among total submitted ECG days. The primary outcome was atrial arrhythmia recurrence. The AF severity scale was administered pre-ablation and at 12 months post-ablation. At follow-up, 69 patients had atrial arrhythmia recurrence and 29 remained in sinus rhythm. These patients were categorized into a recurrence (n = 69) and a no-recurrence group (n = 29). Both groups had similar baseline characteristics, but recurrence patients were older (P = 0.005), had a higher prevalence of hyperlipidaemia (P = 0.007), and had a larger left atrial (LA) volume (P = 0.01). There was a reduction in AF burden in the recurrence group when compared with their pre-ablation burden (65 vs. 15%, P &lt; 0.0001). Utah Stage 4 fibrosis and diabetes predicted less improvement in AF burden. The symptom severity score at 12 months post-ablation was significantly reduced compared with the pre-ablation score in the recurrence group, and there was a significant correlation between the reduction in symptom severity score and the reduction in AF burden (R = 0.39, P = 0.001).

Conclusion
Catheter ablation reduces AF burden, irrespective of arrhythmia recurrence post-procedure. There is a strong correlation between AF burden reduction and symptom improvement post-ablation. Notably, elevated LA fibrosis impedes AF burden decrease following catheter ablation.
Pelagic zone is an evolutionary catalyst, but an ecological dead end, for North American minnows
Authors: Burress Edward D , Hart Pamela B 
Published: April 2024

Abstract
The colonization of a novel geographic area is a classic source of ecological opportunity. Likewise, complex microhabitats are thought to promote biodiversity. We sought to reconcile these two predictions when they are naturally opposing outcomes. We assess the macroevolutionary consequences of an ancestral shift from benthic to pelagic microhabitat zones on rates of speciation and phenotypic evolution in North American minnows. Pelagic species have more similar phenotypes and slower rates of phenotypic evolution, but faster speciation rates, than benthic species. These are likely two independent, opposing responses to specialization along the benthic-pelagic axis, as rates of phenotypic evolution and speciation are not directly correlated. The pelagic zone is more structurally homogenous and offers less ecological opportunity, acting as an ecological dead end for minnows. In contrast, pelagic species may be more mobile and prone to dispersal and subsequent geographic isolation and, consequently, experience elevated instances of allopatric speciation. Microhabitat shifts can have decoupled effects on different dimensions of biodiversity, highlighting the need for nuance when interpreting the macroevolutionary consequences of ecological opportunity.
Building physician wellness into the culture: evaluating a family physician well-being programme using the physician wellness inventory
Authors: Clay Tarin L , Mabachi Natabhona M , Callen Elisabeth F 
Published: April 2024

Abstract

Purpose
Family physicians have a higher incidence of burnout, dissatisfaction, and disengagement compared to other medical specialties. Addressing burnout on the individual and systemic level is important to promoting wellness and preventing deleterious effects on physicians and patients. We used the Physician Wellness Inventory (PWI) to assess the effects of a wellness programme designed to equip family physicians with skills to address burnout.

Methods
The PWI is a fourteen-item 5-point Likert scale broken down into 3 scores; (i) career purpose, (ii) cognitive flexibility, and (iii) distress. The PWI was distributed to a cohort of n = 111 family physician scholars at 3 time points: January 2021, May–June 2021, and October 2021. The response rate was 96.4% at baseline, and 72.1% overall. Demographic information was collected to assess differences. The survey was distributed online through Qualtrics (Provo, UT).

Results
Cognitive Flexibility scores at the endpoint were higher for POC scholars than white scholars (P = 0.024). Distress scores for all groups decreased over time. Female scholars were more nervous, and anxious at the start than male scholars (P = 0.012), which decreased over time (P = 0.022). New career scholars were more likely than later career scholars to be distressed (P = 0.007), but both groups’ distress decreased over time (P = 0.003). Later career scholars’ feelings of being bothered by little interest or pleasure in doing things decreased more than new career scholars (endpoint: P = 0.022; overall: P = 0.023).

Conclusions
The wellness programme shows improvement in PWI scores, indicating the programme content should be evaluated further for system level improvements.
Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution
Authors: Iliopoulou Elisavet , Papadogiannis Vasileios , Tsigenopoulos Costas S , Manousaki Tereza 
Published: April 2024

Abstract
Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts.
On the ∂—-Equation with L2 Estimates on Singular Complex Spaces
Authors: Li Zhenqian , Li Zhi , Zhou Xiangyu 
Published: April 2024

Abstract
In this paper, we present the unsolvability of $\overline \partial $-equation with weighted $L^{2}$ estimates involved curvature terms on any singular normal complex space in general. Moreover, in the non-normal case, we also give a complete description on $L^{2}$-solvability of the $\overline \partial $-equation with weighted $L^{2}$ estimates for plane curve singularities and their variants in the higher dimension.
Rational Points in the Noether-Lefschetz Locus of Moduli Spaces of K3 Surfaces
Authors: Valloni Domenico 
Published: April 2024

Abstract
We give a characterization of rational points lying on the Noether-Lefschetz locus of moduli spaces of K3 surfaces by studying their lifting properties under some natural coverings of the ambient space. We then prove that the Bombieri-Lang conjecture implies non-density statements for the rational points in the Noether-Lefschetz locus, as predicted by a conjecture of Shafarevich.
Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates
Authors: Alvarez-Aponte Zoila I , Govindaraju Alekhya M , Hallberg Zachary F , Nicolas Alexa M , Green Myka A , Mok Kenny C , Fonseca-García Citlali , Coleman-Derr Devin , Brodie Eoin L , Carlson Hans K , Taga Michiko E 
Published: April 2024

Abstract
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12 family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
Extracorporeal Life Support Use in Mixed Distributive–Obstructive Shock Following an Electrical Injury: A Case Report
Authors: Blake Eva , Maqsood Hannan A , Dougherty Jacob M , Vercruysse Gary , Wang Stewart C , Hemmila Mark R , Sangji Naveen F 
Published: April 2024

Abstract
Electrical burn injuries can be catastrophic, threatening severe disability or mortality. We present a patient who suffered from electrical shock, requiring bilateral above-knee amputations, right trans-radial amputation, renal replacement therapy, and veno-arterial extracorporeal life support (VA ECLS) therapy. While there exist reports of cases that have demonstrated the potential use of ECLS in burn patients with cardiogenic shock or acute respiratory distress syndrome, this is a unique case of VA ECLS use for an electrical injury patient who developed mixed distributive–obstructive shock secondary to pulmonary embolism and sepsis. Given the wide variety of morbidities that can result from electrical burns, VA ECLS is a promising tool for those who require cardiopulmonary support refractory to traditional measures.