bluuebunny/crossref_metadata_2025_split huggingface dataset:
GEEES: inferring cell-specific gene–enhancer interactions from multi-modal single-cell data
Authors: Chen Shuyang , Keleş Sündüz 
Published: October 2024

Abstract

Motivation
Gene–enhancer interactions are central to transcriptional regulation. Current multi-modal single-cell datasets that profile transcriptome and chromatin accessibility simultaneously in a single cell are yielding opportunities to infer gene–enhancer associations in a cell type specific manner. Computational efforts for such multi-modal single-cell datasets thus far focused on methods for identification and refinement of cell types and trajectory construction. While initial attempts for inferring gene–enhancer interactions have emerged, these have not been evaluated against benchmark datasets that materialized from bulk genomic experiments. Furthermore, existing approaches are limited to inferring gene–enhancer associations at the level of grouped cells as opposed to individual cells, thereby ignoring regulatory heterogeneity among the cells.

Results
We present a new approach, GEEES for “Gene EnhancEr IntEractions from Multi-modal Single Cell Data,” for inferring gene–enhancer associations at the single-cell level using multi-modal single-cell transcriptome and chromatin accessibility data. We evaluated GEEES alongside several multivariate regression-based alternatives we devised and state-of-the-art methods using a large number of benchmark datasets, providing a comprehensive assessment of current approaches. This analysis revealed significant discrepancies between gold-standard interactions and gene–enhancer associations derived from multi-modal single-cell data. Notably, incorporating gene–enhancer distance into the analysis markedly improved performance across all methods, positioning GEEES as a leading approach in this domain. While the overall improvement in performance metrics by GEEES is modest, it provides enhanced cell representation learning which can be leveraged for more effective downstream analysis. Furthermore, our review of existing experimentally driven benchmark datasets uncovers their limited concordance, underscoring the necessity for new high-throughput experiments to validate gene–enhancer interactions inferred from single-cell data.

Availability and implementation
https://github.com/keleslab/GEEES.
Bayesian inference for group-level cortical surface image-on-scalar regression with Gaussian process priors
Authors: Whiteman Andrew S , Johnson Timothy D , Kang Jian 
Published: October 2024

ABSTRACT
In regression-based analyses of group-level neuroimage data, researchers typically fit a series of marginal general linear models to image outcomes at each spatially referenced pixel. Spatial regularization of effects of interest is usually induced indirectly by applying spatial smoothing to the data during preprocessing. While this procedure often works well, the resulting inference can be poorly calibrated. Spatial modeling of effects of interest leads to more powerful analyses; however, the number of locations in a typical neuroimage can preclude standard computing methods in this setting. Here, we contribute a Bayesian spatial regression model for group-level neuroimaging analyses. We induce regularization of spatially varying regression coefficient functions through Gaussian process priors. When combined with a simple non-stationary model for the error process, our prior hierarchy can lead to more data-adaptive smoothing than standard methods. We achieve computational tractability through a Vecchia-type approximation of our prior that retains full spatial rank and can be constructed for a wide class of spatial correlation functions. We outline several ways to work with our model in practice and compare performance against standard vertex-wise analyses and several alternatives. Finally, we illustrate our methods in an analysis of cortical surface functional magnetic resonance imaging task contrast data from a large cohort of children enrolled in the adolescent brain cognitive development study.
Derivation of outcome-dependent dietary patterns for low-income women obtained from survey data using a supervised weighted overfitted latent class analysis
Authors: Wu Stephanie M , Williams Matthew R , Savitsky Terrance D , Stephenson Briana J K 
Published: October 2024

ABSTRACT
Poor diet quality is a key modifiable risk factor for hypertension and disproportionately impacts low-income women. Analyzing diet-driven hypertensive outcomes in this demographic is challenging due to the complexity of dietary data and selection bias when the data come from surveys, a main data source for understanding diet-disease relationships in understudied populations. Supervised Bayesian model-based clustering methods summarize dietary data into latent patterns that holistically capture relationships among foods and a known health outcome but do not sufficiently account for complex survey design. This leads to biased estimation and inference and lack of generalizability of the patterns. To address this, we propose a supervised weighted overfitted latent class analysis (SWOLCA) based on a Bayesian pseudo-likelihood approach that integrates sampling weights into an exposure-outcome model for discrete data. Our model adjusts for stratification, clustering, and informative sampling, and handles modifying effects via interaction terms within a Markov chain Monte Carlo Gibbs sampling algorithm. Simulation studies confirm that the SWOLCA model exhibits good performance in terms of bias, precision, and coverage. Using data from the National Health and Nutrition Examination Survey (2015–2018), we demonstrate the utility of our model by characterizing dietary patterns associated with hypertensive outcomes among low-income women in the United States.
A new robust approach for the polytomous logistic regression model based on Rényi’s pseudodistances
Authors: Castilla Elena 
Published: October 2024

ABSTRACT
This paper presents a robust alternative to the maximum likelihood estimator (MLE) for the polytomous logistic regression model, known as the family of minimum Rènyi Pseudodistance (RP) estimators. The proposed minimum RP estimators are parametrized by a tuning parameter $\alpha \ge 0$, and include the MLE as a special case when $\alpha =0$. These estimators, along with a family of RP-based Wald-type tests, are shown to exhibit superior performance in the presence of misclassification errors. The paper includes an extensive simulation study and a real data example to illustrate the robustness of these proposed statistics.
Biologics in congenital ichthyosis: are they effective?
Authors: Mazereeuw-Hautier Juliette , Granier Tournier Céline , Hernandez-Martin Angela , Milesi Sarah , Texier Hélène , Severino-Freire Maëlla , Bellon Nathalia , Bodemer Christine , Gruber Robert , Mahé Emmanuel , Morice Picard Fanny , Hannula-Jouppi Katariina , Murase Jenny E , Barbarot Sébastien , Cohen-Barak Eran , Torres-Pradilla Maurico , Bruckner Anna , Levy Moise , Koh Mark J A , Masson Regnault Marie , Rossel Vanya , Chiaverini Christine , Arkin Lisa M , Ott Hagen , Has Cristina , Süβmuth Kira , Gostynski Antoni , Shourick Jason , Paller Amy S 
Published: October 2024

Abstract

Background
Congenital ichthyoses comprise a heterogeneous group of genetic diseases that require lifelong treatment and have a major impact on patients’ quality of life. Conventional treatments reduce scaling and skin discomfort; however, they usually have little or no effect on erythema and pruritus. The identification of cytokine alterations in congenital ichthyoses has raised the possibility of repurposing currently available biologics. Several case reports have reported success with different biologics.

Objectives
To report the real-life effects of biologics on congenital ichthyoses.

Methods
This was a retrospective observational international multicentric study of patients with congenital ichthyoses treated with at least one biologic for a minimum of 3 months. The effect of the biologics was evaluated using an Investigator Global Assessment for change (IGA-C) scale. A comprehensive literature search was performed in parallel.

Results
Ninety-eight patients were included [mean (SD) age of 19.7 years, 50 female patients]. Patients with Netherton syndrome (NS) or congenital ichthyosiform erythroderma (CIE) represented the majority of patients (30% and 21%, respectively). Most patients (85%) had a severe or very severe form of congenital ichthyoses. The most frequently used biologics were inhibitors targeting interleukin (IL)-17, IL-12/IL-23 or the IL-4 receptor (IL-4R). The mean (SD) duration of treatment was 22.1 (20.1) months. There were 45 responders (46%), including 18 (18%) who were good responders; all had a subset of erythrodermic congenital ichthyoses and received one of the three main biologics. In patients with NS and CIE, IL-12/IL-23 and IL-4R inhibitors tended to be most effective. The literature review revealed a shorter mean (SD) duration of biologic treatment [11.5 (8.5) months] and higher percentage of responders (86%), suggesting reporter bias.

Conclusions
This series identified subsets of congenital ichthyoses that may respond to biologics and will help with the design of future clinical trials of biologics for congenital ichthyoses.
Post-mortem CT service structures in non-suspicious death investigations
Authors: Davendralingam Natasha , Brookes Amy-Lee , Shah Mohammad Ali , Shelmerdine Susan C 
Published: October 2024

Abstract
Post-mortem CT (PMCT) is increasingly used in adult post-mortem investigations as a non-invasive alternative to traditional autopsies. Using PMCT supports death investigations in the face of severe pathologist workforce shortages and the less invasive nature maintains respect for cultural sensitivities. This article reviews the diverse service structures of PMCT, highlighting the importance of customizing these structures to meet the specific needs of various coronial jurisdictions. These jurisdictions often face challenges such as limited access to imaging facilities and logistical issues with geographically dispersed mortuaries. We outline options for leading and operating PMCT services, including models led by pathologists, radiologist, or a hybrid of the two; use of static, relocatable, or mobile CT scanning units; as well as making the most of existing resources such as NHS or private scanning facility scanners already in place. We also explore different PMCT reporting structures through in-house NHS radiologists, combined in-house and teleradiology, or fully outsourced teleradiology services. Each of these offerings provides different levels of efficiency, cost-effectiveness, data security and challenges to set-up. Where applicable, we present and describe real-world examples as case studies for readers interested in replicating existing models.
Parathyroid gland identification and angiography classification using simple machine learning methods
Authors: McEntee Philip D , Greevy Joseph E , Triponez Frédéric , Demarchi Marco S , Cahill Ronan A 
Published: October 2024

Abstract

Background
Near-infrared indocyanine green angiography allows experienced surgeons to reliably evaluate parathyroid gland vitality during thyroid and parathyroid operations in order to predict postoperative function. To facilitate equal performance between surgeons, we developed an automatic computational quantification method using computer vision that portrays expert interpretation of visualized parathyroid gland near-infrared indocyanine green angiographic fluorescence signals.

Methods
Near-infrared indocyanine green-parathyroid gland angiography video recordings (Fluobeam® LX, Fluoptics, Grenoble—part of Getinge—Göteborg) from patients undergoing endocrine cervical surgery in a high-volume unit were used for model development. Computation (MATLAB, Mathworks, Ireland) included segmentation-identification of the parathyroid gland (by autofluorescence), image stabilization (by linear translation) and adjusted time-fluorescence intensity profile generation. Relative upslope and maximum intensity ratios then trained a simple logistic regression model based on expert interpretation and outcome (including hypoparathyroidism), with subsequent unseen testing for validation.

Results
The model was trained on 37 patient videos (45 glands, 29 judged well perfused by parathyroid gland angiography experts), achieving feature data separation with 100% accuracy, and tested on 22 unseen videos (27 glands, 15 judged well perfused), including four in real time. Segmentation-guided parathyroid gland detection correctly identified all parathyroid glands during unseen testing along with three additional non-parathyroid gland regions (90% positive predictive value). Subsequent time-fluorescence intensity profile extraction with vitality prediction was shown feasible in all cases within 5 min, with a 96.3% model accuracy (sensitivity and specificity were 93.3 and 100% respectively) when compared with expert judgement.

Conclusion
Automatic parathyroid gland perfusion quantification using simple machine learning computational methods discriminates parathyroid gland perfusion in concordance with expert surgeon interpretation, providing a means for near-infrared indocyanine green-parathyroid gland signal evaluation.
AAV-based TCAP delivery rescues mitochondria dislocation in limb-girdle muscular dystrophy R7
Authors: Lv Xiaoqing , Liu Shuangwu , Li Xi , Lv He , Shao Kai , Luo Sushan , Zhao Dandan , Yan Chuanzhu , Lin Pengfei 
Published: October 2024

Abstract
Limb-girdle muscular dystrophy R7 is a rare genetic disease caused by homozygous or compound heterozygous variants in the titin-cap (TCAP) gene that results in the absence of the protein telethonin. The primary pathological features of limb-girdle muscular dystrophy R7 are fibre size variation, nuclear centralization and abnormal mitochondrial distribution. The mechanisms underlying this disease are unclear and there is currently no specific treatment for limb-girdle muscular dystrophy R7.
This study established a Tcap-deficient mouse model to explore the disease mechanism of mitochondria dislocation and potential therapeutic strategies. We used methods such as proteomics, immunofluorescence, histopathological staining and western blotting to explore the mechanism of mitochondrial dislocation. Moreover, in the quest for a prospective therapeutic intervention for this disorder, the adeno-associated virus (AAV) serotype 2/9 was employed to deliver the Tcap gene into the muscles of these mice, facilitating preclinical experimentation. After 2 months and 7 months, the muscular phenotype was evaluated and selected mice were humanely euthanized for subsequent molecular and histological analysis.
The phenotype of Tcap−/− mice mimicked that observed in individuals diagnosed with limb-girdle muscular dystrophy R7. This study elucidated the mechanism of mitochondrial dislocation in limb-girdle muscular dystrophy R7. Through our in vitro experiments, we discovered that telethonin aids in preserving the integrity of desmin by preventing truncation at the N-terminus. Additionally, telethonin combined with desmin and co-localized at the Z-disc. Research has shown that the Tcap gene plays a crucial role in controlling the desmin cytoskeleton organization. The absence of telethonin leads to a collapsed desmin cytoskeleton. This causes disorganization of the mitochondrial network, leading to mitochondrial dysfunction. In addition, the study investigated the efficacy of AAV-mediated Tcap replacement in Tcap−/− mice. By intramuscular delivery of AAV, we observed dramatic improvements in muscle phenotype, muscle pathology, CK levels, muscle MRI, mitochondrial network organization and mitochondrial function.
The results of this study demonstrated that telethonin deficiency led to desmin cytoskeleton collapse that caused mitochondrial dislocation. AAV-mediated replacement therapy could be a promising safe and efficient treatment option for limb-girdle muscular dystrophy R7. The study highlights the potential of AAV-mediated replacement therapy for specific types of limb-girdle muscular dystrophy.
CO2 methanation: a bibliometric analysis and review of activated carbon-based materials (2014–24)
Authors: Akpasi Stephen Okiemute , Isa Yusuf Makarfi , Monama Thembisile Patience , Kiambi Sammy Lewis , Ngema Peterson Thokozani 
Published: October 2024

Abstract
This study highlights the significant potential of activated carbon (AC)-based materials in environmental remediation and energy production, particularly in converting carbon dioxide (CO2) and hydrogen (H2) into methane (CH4) and water (H2O) using transition metal-based catalysts. It emphasizes the role of porous AC in waste reduction and resource utilization, examining various applications of CO2 and evaluating environmental impacts. The research explores commercialization opportunities and specifically investigates CO2 methanation using AC-based materials. Using bibliometric analyses of 4196 articles from the Web of Science database, the study identifies a growing research interest in porous AC-related CO2 methanation from 2014 to 2024. The top three journals in this field are Environment Development and Sustainability, Biomass Conversion and Biorefinery, and Journal of Environment Science and Pollution. However, there is limited inter-institutional collaboration in this field, suggesting room for development towards commercializing sustainable CH4 production pathways. CH4 is highlighted as a crucial intermediate in industrial processes, and research directions are identified through co-occurring author keywords analysis. The study suggests the need for a comprehensive approach integrating AC materials into carbon-neutral energy processes while addressing the potential adverse effects of AC nanoparticles on biological and environmental factors. Ultimately, it clarifies the potential uses and commercialization prospects for porous AC materials, especially in conjunction with carbon capture and utilization technologies, promoting sustainable practices in energy production and environmental management.
Tarnish tattoos: localized cutaneous argyria from sterling silver in fresh piercings. A case series
Authors: Madan Vishal 
Published: October 2024

Abstract
Tarnish tattoo is a form of localized cutaneous argyria resulting from the deposition of silver into the skin following exposure to silver jewellery in fresh piercings. This report presents the clinical presentation, diagnosis and management of four female patients with tarnish tattoos on the nose and ear from wearing silver jewellery. All four patients wore silver studs or rings immediately following the piercing. Two of the four patients underwent treatment with nanosecond Q-switched 1064-nm Nd:YAG laser and Q-switched alexandrite 755-nm lasers, with minimal improvement. Tarnish tattoos are an under-recognized side-effect of wearing silver jewellery in fresh piercings. The blue–grey discoloration from tarnish tattoos can be challenging to treat with nanosecond Q-switched lasers.
2024 Clinical Practice Guideline Update by the Infectious Diseases Society of America on the Management of COVID-19: Anti-SARS-CoV-2 Neutralizing Antibody Pemivibart for Pre-exposure Prophylaxis
Authors: Bhimraj Adarsh , Falck-Ytter Yngve , Kim Arthur Y , Li Jonathan Z , Baden Lindsey R , Johnson Steven , Shafer Robert W , Shoham Shmuel , Tebas Pablo , Bedimo Roger , Cheng Vincent Chi-Chung , Chew Kara W , Chiotos Kathleen , Daar Eric S , Dzierba Amy L , Glidden David V , Hardy Erica J , Martin Greg S , MacBrayne Christine , Nadig Nandita , Nakamura Mari M , Shumaker Amy Hirsch , Tien Phyllis , Loveless Jennifer , Morgan Rebecca L , Gandhi Rajesh T 
Published: October 2024

Abstract
This article provides a focused update to the clinical practice guideline on the treatment and management of patients with coronavirus disease 2019, developed by the Infectious Diseases Society of America. The guideline panel presents a recommendation on the use of the anti–severe acute respiratory syndrome coronavirus 2 neutralizing antibody pemivibart as pre-exposure prophylaxis. The recommendation is based on evidence derived from a systematic review and adheres to a standardized methodology for rating the certainty of evidence and strength of recommendation according to the GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) approach. Information on pemivibart is included in the U.S. Food and Drug Administration Emergency Use Authorization for this agent.
Repeatability of swimming activity of the Patagonian grouper Acanthistius patachonicus based on accelerometry
Authors: Venerus Leonardo A , Domenici Paolo , Marras Stefano , Beltramino Lucas E , Ciancio Javier E 
Published: October 2024

Abstract
The study of repeatability in behaviour and activity level can be used to evaluate inter-individual differences, which are fundamental to assess the resilience of populations to environmental variation. Previous work on repeatability in wild fish populations has largely been based on acoustic telemetry or mark-and-recapture and has revealed repeatable activity patterns over relatively long periods in a number of species. Although accelerometry is a promising tool for investigating the swimming activity of fish in the wild, little is known about the repeatability of accelerometry-based traits in wild fish. Here, we used external accelerometers to investigate the swimming activity of the Patagonian grouper Acanthistius patachonicus, a rocky-reef fish with high site fidelity, which ensures a high recapture rate of accelerometer tags. Accelerometry was used to investigate the short-term repeatability of a number of activity traits, including swimming, hovering, daily median tailbeat frequency, percentage of high tailbeat frequency and total number of tailbeats at different times of the year. We found that all of the variables are repeatable over the daily scale and four out of five variables are repeatable over weekly periods. Overall, our work suggests that these traits are individual-specific for the short time period investigated. In addition, the percentage of time spent in swimming and hovering was greater in the warm season compared to the cold season, suggesting higher activity levels related to higher temperatures. These results suggest that activity traits related to swimming are repeatable and likely related to the physiological state of each individual. Finally, our work shows that accelerometry can be considered a valuable tool to explore inter-individual differences with potential applications for assessing the resilience of wild populations.