bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel deep learning based method for myocardial strain quantification
Authors: Bernardo Agustín , Mato Germán , Calandrelli Matías , Medus Jorgelina , Curiale Ariel 
Published: November 2024

Abstract

Purpose.
This paper introduces a deep learning method for myocardial strain analysis while also evaluating the efficacy of the method across a public and a private dataset for cardiac pathology discrimination.
Methods.
We measure the global and regional myocardial strain in cSAX CMR images by first identifying a ROI centered in the LV, obtaining the cardiac structures (LV, RV and Myo) and estimating the motion of the myocardium. Finally, we compute the strain for the heart coordinate system and report the global and regional strain.
Results.
We validated our method in two public datasets (ACDC, 80 subjects, and CMAC, 16 subjects) and a private dataset (SSC, 75 subjects), containing healthy and pathological cases (acute myocardial infarction, DCM and HCM). We measured the mean Dice coefficient and Hausdorff distance for segmentation accuracy, and the absolute end point error for motion accuracy, and we conducted a study of the discrimination power of the strain and strain rate between populations of healthy and pathological subjects. The results demonstrated that our method effectively quantifies myocardial strain and strain rate, showing distinct patterns across different cardiac conditions achieving notable statistical significance. Results also show that the method’s accuracy is on par with iterative non-parametric registration methods and is also capable of estimating regional strain values.
Conclusion.
Our method proves to be a powerful tool for cardiac strain analysis, achieving results comparable to other state-of-the-art methods, and computational efficiency over traditional methods.
Paired autoencoders for likelihood-free estimation in inverse problems
Authors: Chung Matthias , Hart Emma , Chung Julianne , Peters Bas , Haber Eldad 
Published: November 2024

Abstract
We consider the solution of nonlinear inverse problems where the forward problem is a discretization of a partial differential equation. Such problems are notoriously difficult to solve in practice and require minimizing a combination of a data-fit term and a regularization term. The main computational bottleneck of typical algorithms is the direct estimation of the data misfit. Therefore, likelihood-free approaches have become appealing alternatives. Nonetheless, difficulties in generalization and limitations in accuracy have hindered their broader utility and applicability. In this work, we use a paired autoencoder framework as a likelihood-free estimator (LFE) for inverse problems. We show that the use of such an architecture allows us to construct a solution efficiently and to overcome some known open problems when using LFEs. In particular, our framework can assess the quality of the solution and improve on it if needed. We demonstrate the viability of our approach using examples from full waveform inversion and inverse electromagnetic imaging.
Boreal summer intraseasonal oscillation-related precipitation in eastern China modulated by Pacific sea surface temperature
Authors: Weng Liyuan , Liang Ping , Lin Yanluan 
Published: November 2024

Abstract
The boreal summer intraseasonal oscillation (BSISO) is a key source of subseasonal to seasonal predictability, significantly enhancing precipitation in eastern China when BSISO convection is over the Indian Ocean. While background sea surface temperature (SST) modulates the strength and propagation of BSISO, how the SST further modulates the BSISO-caused precipitation change in eastern China is not well understood. Based on observations and National Center for the Environmental Prediction-National Center for Atmospheric Research reanalysis, this study shows the enhanced rainband caused by BSISO shifts latitudinally on interannual timescale in eastern China. Composite and correlation analyses reveal that this interannual shift is closely associated with the Pacific meridional mode (PMM) in preceding boreal spring (February–April). Specifically, the rainband in eastern China shifts southward during the positive PMM phase and northward during the negative phase. During the positive PMM phase, an upper-level anticyclonic anomaly forms over the North Pacific, which strengthens the BSISO-triggered Rossby wave train and results in a southward shift of the westerly jet in eastern China. The ascent along the southern flank of the westerly jet also shifts southward. Besides, a lower-level cyclonic anomaly forms over the western North Pacific as a Gill-type response to warm SST anomalies in the eastern Pacific. This response weakens the western North Pacific subtropical high and the background easterly wind over the tropical Pacific, impeding the eastward propagation of BSISO. Both the weakened subtropical high and the impeded BSISO favour a southward shift of moisture convergence in eastern China. During the negative PMM phase, the BSISO-triggered Rossby wave train is weakened and the westerly jet and the ascent in eastern China shift northward. The moisture convergence in eastern China also shifts northward due to the strengthened subtropical high and the eastward extension of BSISO. These results can provide guidance for subseasonal forecast of summer precipitation in eastern China.
Impact of pharmacy involvement on care gap closure in Managed Medicaid patients
Authors: Montgomery Ellen , Sherod-Harris Tiffany , Adkins Marina , Hinely Molly 
Published: November 2024

Abstract

Purpose
A population health pharmacy team was developed to improve health and increase reimbursement for patients with value-based care plans. The purpose of this study was to evaluate the impact of pharmacy involvement on care gap closure in Managed Medicaid patients.

Methods
This was a single-center, retrospective cohort study of Managed Medicaid patients seen at outpatient facilities. Patients had a pharmacy risk score (PRS) of 6 or greater and had not achieved the Medicaid quality measures for both glycated hemoglobin (HbA1c) and blood pressure (BP). The intervention group included patients reviewed by pharmacy, compared to a control group of patients not reviewed by pharmacy. The primary outcome was closure of at least one care gap by the end of 2022. Secondary outcomes were the number of each type of gap closed, the frequency at which recommendations were made by pharmacists, and the frequency at which pharmacist recommendations were implemented by providers.

Results
Data were collected for 80 patients for the period from January through October 2022. The primary outcome occurred in 37 (74%) patients in the intervention group and 15 (50%) patients in the control group (odds ratio, 2.85; P = 0.032). The HbA1c gap was closed in 30 (60%) patients in the intervention group and 8 (27%) patients in the control group. The BP gap was closed in 24 (48%) patients in the intervention group and 11 (37%) patients in the control group. The frequency with which recommendations were made by a pharmacist was associated with gap closure (P = 0.012). No significant difference was found based on the frequency at which recommendations were implemented by providers (P = 0.4).

Conclusion
Pharmacy intervention was associated with an almost 3-fold-higher likelihood of closing at least one care gap in Medicaid patients. HbA1c gap closure was achieved more frequently than BP gap closure due to pharmacy involvement. The frequency with which recommendations were made by pharmacy was associated with increased gap closure regardless of the frequency with which these recommendations were implemented by providers.
Less is more: relative rank is more informative than absolute abundance for compositional NGS data
Authors: Zheng Xubin , Jin Nana , Wu Qiong , Zhang Ning , Wu Haonan , Wang Yuanhao , Luo Rui , Liu Tao , Ding Wanfu , Geng Qingshan , Cheng Lixin 
Published: November 2024

Abstract
High-throughput gene expression data have been extensively generated and utilized in biological mechanism investigations, biomarker detection, disease diagnosis and prognosis. These applications encompass not only bulk transcriptome, but also single cell RNA-seq data. However, extracting reliable biological information from transcriptome data remains challenging due to the constrains of Compositional Data Analysis. Current data preprocessing methods, including dataset normalization and batch effect correction, are insufficient to address these issues and improve data quality for downstream analysis. Alternatively, qualification methods focusing on the relative order of gene expression (ROGER) are more informative than the quantification methods that rely on gene expression abundance. The Pairwise Analysis of Gene expression method is an enhancement of ROGER, designed for data integration in either sample space or feature space. In this review, we summarize the methods applied to transcriptome data analysis and discuss their potentials in predicting clinical outcomes.
FastTENET: an accelerated TENET algorithm based on manycore computing in Python
Authors: Sung Rakbin , Kim Hyeonkyu , Kim Junil , Lee Daewon 
Published: November 2024

Abstract

Summary
TENET reconstructs gene regulatory networks from single-cell RNA sequencing (scRNAseq) data using the transfer entropy (TE), and works successfully on a variety of scRNAseq data. However, TENET is limited by its long computation time for large datasets. To address this limitation, we propose FastTENET, an array-computing version of TENET algorithm optimized for acceleration on manycore processors such as GPUs. FastTENET counts the unique patterns of joint events to compute the TE based on array computing. Compared to TENET, FastTENET achieves up to 973× performance improvement.

Availability and implementation
FastTENET is available on GitHub at https://github.com/cxinsys/fasttenet.
Skin microbiome dynamics in patients with polymorphic light eruption in response to UV radiations
Authors: Amar Yacine , Niedermeier Sebastian , Silva Rafaela , Kublik Susanne , Schloter Michael , Biedermann Tilo , Köberle Martin , Eberlein Bernadette 
Published: November 2024

Abstract

Background
Polymorphic light eruption (PLE) is the most frequent photodermatosis in Europe with an estimated prevalence of 10 to 20%, particularly in temperate climates. Itching or burning lesions appear only in sun-exposed areas, predominantly on the chest, the arms and forearms within a few hours following exposure. The disease’s cause is still unknown, yet studies have suggested that skin microbial elements may play a role in its pathogenesis.

Objectives
We investigated in this cohort the skin microbiome of PLE patients upon exposure to ultraviolet radiation (UVR), to assess its role in the onset of PLE lesions.

Methods
Forty-one skin swabs have been collected from eleven PLE patients at baseline and following a three-day exposure to UVR and from healthy controls. The collected swabs were analyzed for their microbial composition using a 16S amplicon sequencing approach.

Results
The PLE skin showed a dysbalanced microbiome, already at baseline, with significantly reduced microbial diversity and noticeable colonization by bacterial pathogens as Staphylococcus aureus. Upon UVR exposure, the PLE microbiome exhibited a further loss of diversity and decline of beneficial skin commensals. In line with this, we observed that UVR exerted strong antimicrobial effects in vitro against representative skin residents.

Conclusions
Taken together, UVR can lead to profound skin microbiome changes, allowing the proliferation of dysbiotic members that can release a variety of elements able to trigger PLE lesions. This is the first study investigating the cutaneous microbiome changes in PLE patients upon UVR, offering new insights into disease pathogenesis, so far unexplored.
Causal association of physical activity with lymphoma risk: a Mendelian randomization analysis
Authors: Zhao Jin , Wen Xiaolian , Zheng Meijing , Su Liping , Guo Xiaojing 
Published: November 2024

Abstract
Controversial relationship of physical activity with lower lymphoma risk has been reported in observational studies. The purpose of this study was to explore the causal correlation of physical activity with lymphoma risk using two-sample Mendelian randomization (MR). Genetic variants associated with physical activity (moderate-to-vigorous physical activity (MVPA), average acceleration physical activity, number of days/week of moderate physical activity 10+ min, and number of days/week of vigorous physical activity 10+ min) and lymphoma [overall lymphoma, Hodgkin lymphoma, mature T/NK-cell lymphomas, diffuse large B-cell lymphoma (DLBCL), and follicular lymphoma] were obtained from published genome-wide association studies (GWAS) and the FinnGen database and used as instrumental variables. Primary results were based on inverse variance-weighted (IVW) analysis and were described as odds ratio (OR) and 95% confidence interval (CI). Higher levels of genetically predicted MVPA (OR = 0.079, 95% CI: 0.021–0.300, P = 0.0002) and number of days/week of vigorous physical activity 10+ min (OR = 0.237, 95% CI: 0.098–0.573, P = 0.0014) were negatively associated with Hodgkin lymphoma risk. There was a weak negative association between high levels of genetically predicted MVPA (OR = 0.114, 95% CI: 0.015–0.856, P = 0.0348) and average acceleration physical activity (OR = 0.830, 95% CI: 0.705–0.976, P = 0.0243) and risk of DLBCL. No causal relationship was observed between physical activity and the risk of overall lymphoma, mature T/NK-cell lymphomas, and follicular lymphoma (P &gt; 0.05). This study supported the causal relationship between higher physical activity levels and lower risks of Hodgkin lymphoma and DLBCL.
Public health approaches to ‘Leave No One Behind’ in heatwave resilience: insights from the UK
Authors: Nunes Ana Raquel 
Published: November 2024

Abstract
Heatwaves pose significant threats to vulnerable populations, making resilience efforts crucial. This study aims to explore stakeholders' perspectives on heatwave resilience from a public health perspective, with a specific focus on operationalising the commitment to ‘Leave No One Behind’ (LNOB) as outlined in the United Nations 2030 Agenda for Sustainable Development. In-depth qualitative interviews were conducted with key stakeholders from national and local government, industry and business, academia, and civil society organizations. Interviews examined stakeholders' understanding of the progress and challenges associated with fulfilling the commitment of LNOB in the context of heat resilience from a public health perspective, in England, UK. Content analysis of interview transcripts was undertaken. Stakeholders emphasize the importance of equity, inclusivity, and public health priorities in heatwave resilience efforts while specifically addressing the commitment to LNOB. Disparities in vulnerability due to socioeconomic factors, challenges in identifying and supporting vulnerable populations, progress made in addressing heatwave resilience, and the role of government and society in improving resilience efforts were emphasized. Stakeholders highlighted the need for targeted interventions, strengthened community support networks, and policy changes to address systemic inequalities and promote inclusivity in resilience strategies. Stakeholders’ perspectives underscore the importance of aligning heatwave resilience efforts with global goals, particularly in promoting public health equity and inclusivity. By addressing the challenges identified and implementing the recommendations for improvement, policymakers and practitioners should work towards more equitable and inclusive resilience strategies to safeguard public health during heatwaves.
Heritability and age-dependent changes in genetic variation of telomere length in a wild house sparrow population
Authors: Chik Heung Ying Janet , Sibma Aaron , Mannarelli Maria-Elena , dos Remedios Natalie , Simons Mirre J P , Burke Terry , Dugdale Hannah L , Schroeder Julia 
Published: November 2024

Abstract
Telomere length (TL) and/or its rate of change are popular biomarkers of senescence, as telomere dynamics are linked with survival and lifespan. However, the evolutionary potential of telomere dynamics has received mixed support in natural populations. To better understand how telomere dynamics evolve, it is necessary to quantify genetic variation in TL and how such variation changes with age. Here, we analyzed 2,083 longitudinal samples from 1,225 individuals across 16 years, collected from a wild, insular house sparrow (Passer domesticus) population with complete life history and genetic relatedness data. Using a series of “animal” models, we confirmed that TL changes with age, reflecting senescence in this population. We found TL to be repeatable (14.0%, 95% CrI: 9.1%–19.9%) and heritable (12.3%, 95% CrI: 7.5%–18.2%); and detected a genotype-by-age interaction, meaning that genotypes differ in their rate of change of TL, and additive genetic variance increases at older ages. Our findings provide empirical evidence from a wild population that supports hypotheses explaining the evolution of senescence and highlight the importance of telomere dynamics as a key biomarker of body physiology for the evolution of senescence.
Wild yeast isolation by middle-school students reveals features of populations residing on North American oaks
Authors: Yeager Randi , Heasley Lydia R , Baker Nolan , Shrivastava Vatsal , Woodman Julie , McMurray Michael A 
Published: November 2024

Abstract
Features of the natural life cycle of the budding yeast Saccharomyces cerevisiae were crucial to its domestication as a laboratory experimental model, especially the ability to maintain stable haploid clones and cross them at will to combine alleles via meiosis. Stable haploidy results from mutations in HO, which encodes an endonuclease required for haploid-specific mating-type switching. Previous studies found an unexpected diversity of HO alleles among natural isolates within a small geographic area. We developed a hands-on field and laboratory activity for middle-school students in Denver, CO, USA, to isolate wild yeast from oak bark, identify species via DNA sequencing, and sequence HO from S. cerevisiae isolates. We find limited HO diversity in North American oak isolates, pointing to efficient, continuous dispersal across the continent. In contrast, we isolated the “dairy yeast,” Kluyveromyces lactis, from a tree &lt;10 m away and found that it represents a new population distinct from an oak population in an adjacent state. The outreach activity partnered middle-school, high-school, and university students in making scientific discoveries and can be adapted to other locations and natural yeast habitats. Indeed, a pilot sampling activity in southeast Texas yielded S. cerevisiae oak isolates with a new allele of HO and, from a nearby prickly pear cactus, a heat-tolerant isolate of Saccharomyces paradoxus.
A collection of split-Gal4 drivers targeting conserved signaling ligands in Drosophila
Authors: Ewen-Campen Ben , Joshi Neha , Hermon Ashley Suraj , Thakkar Tanuj , Zirin Jonathan , Perrimon Norbert 
Published: November 2024

Abstract
Communication between cells in metazoan organisms is mediated by a remarkably small number of highly conserved signaling pathways. Given this small number of signaling pathways, the existence of multiple related ligands for many of these pathways represents a key evolutionary innovation for encoding complexity into cell–cell signaling. Relatedly, crosstalk between pathways is another critical feature, which allows a modest number of pathways to ultimately generate an enormously diverse range of outcomes. It would thus be useful to have genetic tools to identify and manipulate not only those cells that express a given signaling ligand but also those cells that specifically coexpress pairs of signaling ligands. We present a collection of split-Gal4 knock-in lines targeting many of the ligands for highly conserved signaling pathways in Drosophila (Notch, Hedgehog, fibroblast growth factor (FGF), epidermal growth factor (EGF), transforming growth factor β (TGFβ), Janus kinase/signal transducer and activator of transcription (JAK/STAT), Jun kinase (JNK), and platelet-derived growth factor (PDGF)/vascular endothelial growth factor (VEGF)-related receptor (PVR). We demonstrate that these lines faithfully recapitulate the endogenous expression pattern of their targets and that they can be used to identify cells and tissues that coexpress pairs of ligands. As a proof of principle, we demonstrate that the 4th chromosome TGFβ ligands myoglianin and maverick are broadly coexpressed in muscles and other tissues of both larva and adults and that the JAK/STAT ligands upd2 and upd3 are partially coexpressed from cells of the midgut following gut damage. Together with our previously collection of split-Gal4 lines targeting the 7 Wnt ligands, this resource allows Drosophila researchers to identify and genetically manipulate cells that specifically express pairs of conserved ligands from nearly all the major intercellular signaling pathways.
Transcriptomic Sexual Conflict at Two Evolutionary Timescales Revealed by Experimental Evolution in Caenorhabditis elegans
Authors: Kasimatis Katja R , Willis John H , Sedore Christine A , Phillips Patrick C 
Published: November 2024

Abstract
Sex-specific regulation of gene expression is the most plausible way for generating sexually differentiated phenotypes from an essentially shared genome. However, since genetic material is shared, sex-specific selection in one sex can have an indirect response in the other sex. From a gene expression perspective, this tethered response can move one sex away from their wild-type expression state and potentially impact many gene regulatory networks. Here, using experimental evolution in the model nematode Caenorhabditis elegans, we explore the coupling of direct sexual selection on males with the transcriptomic response in males and females over microevolutionary timescales to uncover the extent to which postinsemination reproductive traits share a genetic basis between the sexes. We find that differential gene expression evolved in a sex-specific manner in males, while in females, indirect selection causes an evolved response. Almost all differentially expressed genes were downregulated in both evolved males and females. Moreover, 97% of significantly differentially expressed genes in males and 69% of significantly differentially expressed genes in females have wild-type female-biased expression profile. Changes in gene expression profiles were likely driven through trans-acting pathways that are shared between the sexes. We found no evidence that the core dosage compensation machinery was impacted by experimental evolution. Together, these data suggest a defeminization of the male transcriptome and masculinization of the female transcriptome driven by direct selection on male sperm competitive ability. Our results indicate that on short evolutionary timescales, sexual selection can generate putative sexual conflict in expression space.