bluuebunny/crossref_metadata_2025_split huggingface dataset:
StabJGL: a stability approach to sparsity and similarity selection in multiple-network reconstruction
Authors: Lingjærde Camilla , Richardson Sylvia 
Published: December 2023

Abstract

Motivation
In recent years, network models have gained prominence for their ability to capture complex associations. In statistical omics, networks can be used to model and study the functional relationships between genes, proteins, and other types of omics data. If a Gaussian graphical model is assumed, a gene association network can be determined from the non-zero entries of the inverse covariance matrix of the data. Due to the high-dimensional nature of such problems, integrative methods that leverage similarities between multiple graphical structures have become increasingly popular. The joint graphical lasso is a powerful tool for this purpose, however, the current AIC-based selection criterion used to tune the network sparsities and similarities leads to poor performance in high-dimensional settings.

Results
We propose stabJGL, which equips the joint graphical lasso with a stable and well-performing penalty parameter selection approach that combines the notion of model stability with likelihood-based similarity selection. The resulting method makes the powerful joint graphical lasso available for use in omics settings, and outperforms the standard joint graphical lasso, as well as state-of-the-art joint methods, in terms of all performance measures we consider. Applying stabJGL to proteomic data from a pan-cancer study, we demonstrate the potential for novel discoveries the method brings.

Availability and implementation
A user-friendly R package for stabJGL with tutorials is available on Github https://github.com/Camiling/stabJGL.
ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor–ligand interactions that specify cell fate
Authors: Kyaw Wunna , Chai Ryan C , Khoo Weng Hua , Goldstein Leonard D , Croucher Peter I , Murray John M , Phan Tri Giang 
Published: December 2023

Abstract

Motivation
Cell fate is commonly studied by profiling the gene expression of single cells to infer developmental trajectories based on expression similarity, RNA velocity, or statistical mechanical properties. However, current approaches do not recover microenvironmental signals from the cellular niche that drive a differentiation trajectory.

Results
We resolve this with environment-aware trajectory inference (ENTRAIN), a computational method that integrates trajectory inference methods with ligand-receptor pair gene regulatory networks to identify extracellular signals and evaluate their relative contribution towards a differentiation trajectory. The output from ENTRAIN can be superimposed on spatial data to co-localize cells and molecules in space and time to map cell fate potentials to cell-cell interactions. We validate and benchmark our approach on single-cell bone marrow and spatially resolved embryonic neurogenesis datasets to identify known and novel environmental drivers of cellular differentiation.

Availability and implementation
ENTRAIN is available as a public package at https://github.com/theimagelab/entrain and can be used on both single-cell and spatially resolved datasets.
Shipwreck ecology: Understanding the function and processes from microbes to megafauna
Authors: Paxton Avery B , McGonigle Christopher , Damour Melanie , Holly Georgia , Caporaso Alicia , Campbell Peter B , Meyer-Kaiser Kirstin S , Hamdan Leila J , Mires Calvin H , Taylor J Christopher 
Published: December 2023

Abstract
An estimated three million shipwrecks exist worldwide and are recognized as cultural resources and foci of archaeological investigations. Shipwrecks also support ecological resources by providing underwater habitats that can be colonized by diverse organisms ranging from microbes to megafauna. In the present article, we review the emerging ecological subdiscipline of shipwreck ecology, which aims to understand ecological functions and processes that occur on shipwrecks. We synthesize how shipwrecks create habitat for biota across multiple trophic levels and then describe how fundamental ecological functions and processes, including succession, zonation, connectivity, energy flow, disturbance, and habitat degradation, manifest on shipwrecks. We highlight future directions in shipwreck ecology that are ripe for exploration, placing a particular emphasis on how shipwrecks may serve as experimental networks to address long-standing ecological questions.
Cortical myelin and thickness mapping provide insights into whole-brain tumor burden in diffuse midline glioma
Authors: Zhang Simin , Yang Xibiao , Tan Qiaoyue , Sun Huaiqiang , Chen Di , Chen Yinying , Zhang Hongjing , Yang Yuan , Gong Qiyong , Yue Qiang 
Published: December 2023

Abstract
Systemic infiltration is a hallmark of diffuse midline glioma pathogenesis, which can trigger distant disturbances in cortical structure. However, the existence and effects of these changes have been underexamined. This study aimed to investigate whole-brain cortical myelin and thickness alternations induced by diffuse midline glioma. High-resolution T1- and T2-weighted images were acquired from 90 patients with diffuse midline glioma with H3 K27-altered and 64 patients with wild-type and 86 healthy controls. Cortical thickness and myelin content was calculated using Human Connectome Project pipeline. Significant differences in cortical thickness and myelin content were detected among groups. Short-term survival prediction model was constructed using automated machine learning. Compared with healthy controls, diffuse midline glioma with H3 K27-altered patients showed significantly reduced cortical myelin in bilateral precentral gyrus, postcentral gyrus, insular, parahippocampal gyrus, fusiform gyrus, and cingulate gyrus, whereas diffuse midline glioma with H3 K27 wild-type patients exhibited well-preserved myelin content. Furtherly, when comparing diffuse midline glioma with H3 K27-altered and diffuse midline glioma with H3 K27 wild-type, the decreased cortical thickness in parietal and occipital regions along with demyelination in medial orbitofrontal cortex was observed in diffuse midline glioma with H3 K27-altered. Notably, a combination of cortical features and tumor radiomics allowed short-term survival prediction with accuracy 0.80 and AUC 0.84. These findings may aid clinicians in tailoring therapeutic approaches based on cortical characteristics, potentially enhancing the efficacy of current and future treatment modalities.
Genetic analyses identify brain imaging-derived phenotypes associated with the risk of amyotrophic lateral sclerosis
Authors: Wang Yinan , Shen Ouxi , Xu Qingyun , Sun Lulu , Jia Yiming , Liu Yi , He Yu , Chang Xinyue , Guo Daoxia , Shi Mengyao , Chen Guo-Chong , Zheng Jin , Zhu Zhengbao 
Published: December 2023

Abstract
Brain imaging-derived phenotypes have been suggested to be associated with amyotrophic lateral sclerosis in observational studies, but whether these associations are causal remains unclear. We aimed to assess the potential bidirectional causal associations between imaging-derived phenotypes and amyotrophic lateral sclerosis using bidirectional 2-sample Mendelian randomization analyses. Summary statistics for 469 imaging-derived phenotypes (33,224 individuals) and amyotrophic lateral sclerosis (20,806 cases and 59,804 controls) were obtained from 2 large-scale genome-wide association studies of European ancestry. We used the inverse-variance weighted Mendelian randomization method in the main analysis to assess the bidirectional associations between imaging-derived phenotypes and amyotrophic lateral sclerosis, followed by several sensitivity analyses for robustness validation. In the forward Mendelian randomization analyses, we found that genetically determined high orientation dispersion index in the right cerebral peduncle was associated with the increased risk of amyotrophic lateral sclerosis (odds ratio = 1.30, 95% confidence interval = 1.16–1.45, P = 2.26 × 10−6). In addition, the reverse Mendelian randomization analysis indicated that amyotrophic lateral sclerosis had no effect on 469 imaging-derived phenotypes. Mendelian randomization-Egger regression analysis showed no directional pleiotropy for the association between high orientation dispersion index in the right cerebral peduncle and amyotrophic lateral sclerosis, and sensitivity analyses with different Mendelian randomization models further confirmed these findings. The present systematic bidirectional Mendelian randomization analysis showed that high orientation dispersion index in the right cerebral peduncle might be the potential causal mediator of amyotrophic lateral sclerosis, which may provide predictive guidance for the prevention of amyotrophic lateral sclerosis. Further studies are warranted to replicate our findings and clarify the underlying mechanisms.
The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing (December 2023)
Authors: Hayden Mary K , Hanson Kimberly E , Englund Janet A , Lee Mark J , Loeb Mark , Lee Francesca , Morgan Daniel J , Patel Robin , El Mikati Ibrahim K , Iqneibi Shahad , Alabed Farouk , Amarin Justin Z , Mansour Razan , Patel Payal , Falck-Ytter Yngve , Morgan Rebecca L , Murad M Hassan , Sultan Shahnaz , Bhimraj Adarsh , Mustafa Reem A 
Published: December 2023

AbstractAccurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19) and for identifying asymptomatic carriage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The number of available SARS-CoV-2 nucleic acid detection tests continues to increase as does the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) developed an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients, and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss nuances of test result interpretation in a variety of practice settings, and highlight important unmet research needs related to COVID-19 diagnostic testing. IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. The panel agreed on 12 diagnostic recommendations. Access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention, and the public health response to COVID-19 infection. Information on the clinical performance of available tests continues to grow, but the quality of evidence of the current literature to support this updated molecular diagnostic guideline remains moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is suggested for asymptomatic individuals with known or suspected contact with a COVID-19 case when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions. Evidence in support of rapid testing and testing of upper respiratory specimens other than nasopharyngeal swabs, which offer logistical advantages, is sufficient to warrant conditional recommendations in favor of these approaches.
Artificial intelligence-based identification of left ventricular systolic dysfunction from 12-lead electrocardiograms: external validation and advanced application of an existing model
Authors: König Sebastian , Hohenstein Sven , Nitsche Anne , Pellissier Vincent , Leiner Johannes , Stellmacher Lars , Hindricks Gerhard , Bollmann Andreas 
Published: December 2023

Abstract

Aims
The diagnostic application of artificial intelligence (AI)-based models to detect cardiovascular diseases from electrocardiograms (ECGs) evolves, and promising results were reported. However, external validation is not available for all published algorithms. The aim of this study was to validate an existing algorithm for the detection of left ventricular systolic dysfunction (LVSD) from 12-lead ECGs.

Methods and results
Patients with digitalized data pairs of 12-lead ECGs and echocardiography (at intervals of ≤7 days) were retrospectively selected from the Heart Center Leipzig ECG and electronic medical records databases. A previously developed AI-based model was applied to ECGs and calculated probabilities for LVSD. The area under the receiver operating characteristic curve (AUROC) was computed overall and in cohorts stratified for baseline and ECG characteristics. Repeated echocardiography studies recorded ≥3 months after index diagnostics were used for follow-up (FU) analysis. At baseline, 42 291 ECG-echocardiography pairs were analysed, and AUROC for LVSD detection was 0.88. Sensitivity and specificity were 82% and 77% for the optimal LVSD probability cut-off based on Youden’s J. AUROCs were lower in ECG subgroups with tachycardia, atrial fibrillation, and wide QRS complexes. In patients without LVSD at baseline and available FU, model-generated high probability for LVSD was associated with a four-fold increased risk of developing LVSD during FU.

Conclusion
We provide the external validation of an existing AI-based ECG-analysing model for the detection of LVSD with robust performance metrics. The association of false positive LVSD screenings at baseline with a deterioration of ventricular function during FU deserves a further evaluation in prospective trials.
Surveillance and Self-Control
Authors: Cobb-Clark Deborah A , Dahmann Sarah C , Kamhöfer Daniel A , Schildberg-Hörisch Hannah 
Published: December 2023

Abstract
This paper studies important determinants of adult self-control using population-representative data and exploiting Germany’s division as quasi-experimental variation. We find that former East Germans have substantially more self-control than West Germans and provide evidence for government surveillance as a possible underlying mechanism. We thereby demonstrate that institutional factors can shape people’s self-control. Moreover, we find that self-control increases linearly with age. In contrast to previous findings for children, there is no gender gap in adult self-control and family background does not predict self-control.
Digest: Understanding the evolution of sexual dichromatism also requires a female perspective
Authors: Ottenburghs Jente 
Published: December 2023

Abstract
The study of sexual dichromatism has generally focused on sexual selection for conspicuous males, ignoring the potential role played by selection in females. To address this problem, Price et al. took into account evolutionary changes in both males and females when investigating the evolution of plumage dichromatism across the New World blackbirds (Icteridae). They found that sexual dichromatism was repeatedly and rapidly lost as females evolved male-like plumage traits. The evolutionary dynamics in plumage coloration were drastically different in males and females, highlighting the importance of considering both perspectives in trait evolution.
Including stress relaxation in point-process model for seismic occurrence
Authors: Petrillo Giuseppe , Lippiello Eugenio , Zhuang Jiancang 
Published: December 2023

SUMMARY
Physics-based and statistic-based models for describing seismic occurrence are two sides of the same coin. In this paper, we compare the temporal organization of events obtained in a spring-block model for the seismic fault with the one predicted by probabilistic models for seismic occurrence. Thanks to the optimization of the parameters, by means of a Maximum Likelihood Estimation, it is possible to identify the statistical model which fits better the physical one. The results show that the best statistical model must take into account the non-trivial interplay between temporal clustering, related to aftershock occurrence, and the stress discharge following the occurrence of high magnitude main shocks. The two mechanisms contribute in different ways according to the minimum magnitude considered in the data fitting catalogue.
Postoperative cardiac biomarker release is not associated with myocardial mass in computer tomography scans
Authors: Pölzl Leo , Sterzinger Philipp , Lohmann Ronja , Nägele Felix , Hirsch Jakob , Graber Michael , Engler Clemens , Eder Jonas , Abfalterer Hannes , Holfeld Johannes , Maier Sarah , Ulmer Hanno , Ruttmann-Ulmer Elfriede , Griesmacher Andrea , Grimm Michael , Bonaros Nikolaos , Feuchtner Gudrun , Gollmann-Tepeköylü Can 
Published: December 2023

Abstract

OBJECTIVES
Myocardial hypertrophy results in increased levels of cardiac biomarkers in healthy individuals and in patients suffering from acute myocardial infarction. The influence of cardiac mass on postoperative cardiac biomarkers release remains unclear. This study investigated the correlation between myocardial mass and the release of high-sensitivity cardiac Troponin T (hs-cTnT) and creatine kinase-myocardial band (CK-MB) after isolated aortic valve replacement (AVR) or bypass surgery.

METHODS
Myocardial mass of a consecutive retrospective series of patients was measured automatically using preoperative computer tomography scans (636 patients, AVR = 251; bypass surgery = 385). Levels of cardiac biomarkers were measured before and serially after surgery. Spearman and Pearson correlation and a multivariate regression model was performed to measure the degree of association between myocardial mass and the release of hs-cTnT and CK-MB.

RESULTS
Patients were divided into 3 tertiles according to their myocardial mass index. Higher biomarker levels were measured preoperatively in the upper tertile of patients undergoing AVR (P = 0.004) or bypass surgery (P &lt; 0.001). Patients with different heart sizes showed no differences in postoperative biomarker release neither after AVR nor bypass surgery. No statistical significant correlation was observed between myocardial mass index and postoperative release of hs-cTnT or CK-MB in any subgroup (ρ maximum 0.106).

CONCLUSIONS
Postoperative biomarker release is not correlated with myocardial mass. Patient factors leading to increased postoperative biomarker levels need to be elucidated in future studies.
Prasad’s Conjecture About Dualizing Involutions
Authors: Arote Prashant , Mishra Manish 
Published: December 2023

Abstract
Let $G$ be a connected reductive group defined over a finite field ${\mathbb{F}}_{q}$ with corresponding Frobenius $F$. Let $\iota _{G}$ denote the duality involution defined by D. Prasad under the hypothesis $2\textrm{H}^{1}(F,Z(G))=0$, where $Z(G)$ denotes the center of $G$. We show that for each irreducible character $\rho $ of $G^{F}$, the involution $\iota _{G}$ takes $\rho $ to its dual $\rho ^{\vee }$ if and only if for a suitable Jordan decomposition of characters, an associated unipotent character $u_{\rho }$ has Frobenius eigenvalues $\pm $ 1. As a corollary, we obtain that if $G$ has no exceptional factors and satisfies $2\textrm{H}^{1}(F,Z(G))=0$, then the duality involution $\iota _{G}$ takes $\rho $ to its dual $\rho ^{\vee }$ for each irreducible character $\rho $ of $G^{F}$. Our results resolve a finite group counterpart of a conjecture of D. Prasad.
Making Political Science: Material-Aesthetic Approaches to Knowledge Production
Authors: Weitzel Michelle D 
Published: December 2023

Abstract
Making represents an important practice in political science research, but the relative unfamiliarity of “making” within the discipline often pushes discussion of it to the margins. This article helps theorize the value of making in political science and questions the idea that moves away from writerly research modes undermine or otherwise erode standards of scholarship. It argues that making processes generate unique opportunities for intellectual discovery; for data collection; for analytic practices of reflexivity, associative thinking, and the adaptation of multiple positionalities; and finally, for argumentation. As such, it suggests that boundary-pushing research that incorporates hands-on praxis to make aesthetic products may in fact augment systematicity and rigor according to established disciplinary norms.
General media over enrichment media supports growth of Campylobacter jejuni and maintains poultry cecal microbiota enabling translatable in vitro microbial interaction experiments
Authors: Olson Elena G , Dittoe Dana K , Chatman Chamia C , Majumder Erica L-W , Ricke Steven C 
Published: December 2023

Abstract

Aim
This study aimed to assess the suitability of two media types, Bolton enrichment broth (BEB) and anaerobic dilution solution (ADS), in replicating the poultry cecal environment to investigate metabolic interactions and Campylobacter presence within poultry ceca.

Methods
Using an anaerobic in vitro poultry cecal model, cecal contents (free of culturable Campylobacter) were diluted in BEB and ADS, inoculated with 105 CFU of Campylobacter jejuni, and incubated for 48 h at 42°C under microaerophilic conditions. Samples were collected at 0, 24, and 48 h. Genomic DNA was extracted, amplified, and sequenced on Illumina MiSeq platform. Data underwent analysis within QIIME2-2021.11, including alpha and beta diversity assessments, ANOVA, ADONIS, ANCOM, and Bradford assay for protein concentration.

Results
ADS supported a more diverse microbial population than BEB, influencing C. jejuni presence. ANCOM highlighted dominant genera in BEB (Lactobacillus and Campylobacter) and affirmed C. jejuni growth in ADS. Core microbiota analysis revealed unique associations with each media type, while the Bradford assay indicated ADS consistently yielded more uniform microbial growth.

Conclusions
ADS was identified as a preferred diluent for faithfully replicating cecal microbial changes in the presence of Campylobacter.