bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allelic hierarchy for USH2A influences auditory and visual phenotypes in South Korean patients
Authors: Nam Dong Woo , Song Yong Keun , Kim Jeong Hun , Lee Eun Kyoung , Park Kyu Hyung , Cha JuHyuen , Choi Byung Yoon , Lee Jun Ho , Oh Seung Ha , Jo Dong Hyun , Lee Sang-Yeon 
Published: November 2023

AbstractWhen medical genetic syndromes are influenced by allelic hierarchies, mutant alleles have distinct effects on clinical phenotypes. Genotype–phenotype correlations for Usher syndrome type 2 (USH2) suggest that the USH2A gene exhibits an allelic hierarchy. Here, we analyzed the phenotypes and genotypes of 16 South Korean patients with USH2A biallelic variants to investigate an allelic hierarchy from audiological and ophthalmological perspectives. Using whole exome and genome sequencing, 18 mutant alleles, including 4 novel alleles, were identified and implicated in USH2A-related disorders. Truncated alleles were linked to earlier onset of subjective hearing loss and more severe thresholds; biallelic truncated alleles had more severe effects. Truncated alleles were also associated with retinal structure degeneration and severe functional deterioration. However, younger patients (aged < 16 years) did not exhibit overt retinitis pigmentosa even when they had biallelic truncated alleles, suggesting that USH2A-related USH2 can mimic nonsyndromic hearing loss. For truncated alleles, there was a clear correlation between mean hearing threshold and 30-Hz flicker electroretinography implicit time. This study provides the first evidence of an USH2A-related allelic hierarchy among South Korean patients; our data yield valuable insights concerning the natural courses of clinical phenotypes and how genotype-based therapies may be used.
Sparse convolutional neural network for high-resolution skull shape completion and shape super-resolution
Authors: Li Jianning , Gsaxner Christina , Pepe Antonio , Schmalstieg Dieter , Kleesiek Jens , Egger Jan 
Published: November 2023

AbstractTraditional convolutional neural network (CNN) methods rely on dense tensors, which makes them suboptimal for spatially sparse data. In this paper, we propose a CNN model based on sparse tensors for efficient processing of high-resolution shapes represented as binary voxel occupancy grids. In contrast to a dense CNN that takes the entire voxel grid as input, a sparse CNN processes only on the non-empty voxels, thus reducing the memory and computation overhead caused by the sparse input data. We evaluate our method on two clinically relevant skull reconstruction tasks: (1) given a defective skull, reconstruct the complete skull (i.e., skull shape completion), and (2) given a coarse skull, reconstruct a high-resolution skull with fine geometric details (shape super-resolution). Our method outperforms its dense CNN-based counterparts in the skull reconstruction task quantitatively and qualitatively, while requiring substantially less memory for training and inference. We observed that, on the 3D skull data, the overall memory consumption of the sparse CNN grows approximately linearly during inference with respect to the image resolutions. During training, the memory usage remains clearly below increases in image resolution—an $$\times 8$$

×
8

increase in voxel number leads to less than $$\times 4$$

×
4

increase in memory requirements. Our study demonstrates the effectiveness of using a sparse CNN for skull reconstruction tasks, and our findings can be applied to other spatially sparse problems. We prove this by additional experimental results on other sparse medical datasets, like the aorta and the heart. Project page at https://github.com/Jianningli/SparseCNN.
Simultaneous quantification of lead, cadmium and zinc in superficial marine sediments using a carbon-fiber microelectrode modified with bismuth film
Authors: Fernández Lenys , Espinoza-Montero Patricio , Sánchez-Sarango Mireya , Bolaños-Méndez Diego , Álvarez-Paguay Jocelyne , Domínguez-Granda Luis , Rodríguez Augusto , Romero Hugo , Debut Alexis , Ortiz Vladimir 
Published: November 2023

AbstractMarine sediments are a useful environmental assessment matrix as they naturally trap toxic substances of anthropogenic origin and thus have higher concentrations of these than the surrounding water. Therefore, developing methods for the sensitive, accurate, and inexpensive quantification of these substances is important, as the traditional techniques have various disadvantages. The current study evaluated the effectiveness of an in situ bismuth-modified carbon-fiber microelectrode (voltamperometric sensor) to simultaneously detect Pb, Cd, and Zn in marine sediments from Puerto Jeli in El Oro Province, Ecuador. This site is representative of the contamination levels present along the coast in this province. Differential pulse anodic stripping voltammetry was applied, and the resulting linear regression for the metal quantification ranged from 12 to 50 μg mL−1, with quantification limits for Pb(II), Cd(II), and Zn(II) of 18.69, 12.55, and 19.29 μg mL−1, respectively. Thus, the quantification with the sensor was successful. According to the preliminary results, Cd and Pb values exceeded the permissible limits established by Ecuador (Texto Unificado de la Legislación Secundaria del Ministerio del Ambiente) and the US Environmental Protection Agency, respectively.
Health-related quality of life and its influencing factors among people with heart failure in Ethiopia: using the revised Wilson and Cleary model
Authors: Mulugeta Henok , Sinclair Peter M. , Wilson Amanda 
Published: November 2023

AbstractHeart failure is a challenging public health problem associated with poor health-related quality of life (HRQoL). Data on the quality of life of people with heart failure are limited in Ethiopia. This study aimed to assess the HRQoL and its influencing factors in people with heart failure in Ethiopia. A hospital-based, cross-sectional study design was conducted in the cardiac outpatient clinics of two tertiary-level hospitals in Addis Ababa, Ethiopia. Data were collected from people with heart failure who met the inclusion criteria using an interviewer-administered questionnaire. The HRQoL was measured using the Minnesota Living with Heart Failure Questionnaire (MLHFQ). A multiple linear regression model was fitted to identify factors that influenced HRQoL. All statistical analyses were conducted using STATA version 17 software. A total of 383 people with heart failure participated in the study. The mean age of the participants was 55 years. The MLHFQ score was 48.03±19.73, and 54% of participants had poor HRQoL. Multiple linear regression analysis revealed that age (β= 0.12, 95% CI 0.11, 0.28), diabetes mellitus comorbidity (β= 4.47, 95% CI 1.41, 7.54), social support score (β= − 1.48, 95% CI − 1.93, − 1.03), and depression score (β = 1.74, 95% CI 1.52, 1.96) were significant factors influencing overall HRQoL (p < 0.05). This study found that people in Ethiopia with heart failure had poor HRQoL, influenced by several factors. The findings can help health professionals identify appropriate interventions to improve the HRQoL of people with heart failure.
Seroprevalence and risk factors for Neospora spp. infection in equine in Egypt
Authors: Alshammari Ayed , Gattan Hattan S. , Marzok Mohamed , Selim Abdelfattah 
Published: November 2023

AbstractNeospora infections in equine are associated with reproductive disorders and neurological diseases. Nevertheless, Egypt has no epidemiological information on this parasite in equine. This study determined the prevalence of Neospora spp. infection in 325 equines from three Egyptian governorates located at Northern Egypt using cELISA. The prevalence of antibodies against Neospora spp. was 19% (95% CI: 14.09–25.05) in horse, 34.1% (95%CI: 24.92–44.69) in donkey and 26.7% (95% CI: 15.97–41.04) in mule. In comparison to horse, donkey had a considerably higher chance of contracting Neospora spp. infection (OR = 1.80, 95% CI: 0.78–4.13; P = 0.016). The risk was also higher in freely grazing animals (OR = 3.49, 95% CI: 0.95–12.78; P = 0.059). Moreover, yearling animals (12–24 months) (OR = 5.03, 95% CI: 1.51–16.80; P = 0.009) and those with natural breeding (OR = 11.80, 95% CI: 3.24–42.99, P < 0.0001) and a history of early abortion (OR = 7.04, 95% CI: 3.01–16.47; P < 0.0001) also showed a greater risk of seropositivity. The risk of Neospora infection increased significantly in equines contacted with dogs (OR = 5.16, 95% CI: 1.76–15.10; P = 0.003). This the first serological study to determine the seroprevalence of Neospora spp. in equine in Egypt. Further studies are necessary to identify the species of Neospora and to understand the role of above-mentioned risk factors in spreading of infection.
Influenza vaccination and major cardiovascular risk: a systematic review and meta-analysis of clinical trials studies
Authors: Omidi Fatemeh , Zangiabadian Moein , Shahidi Bonjar Amir Hashem , Nasiri Mohammad Javad , Sarmastzadeh Tala 
Published: November 2023

AbstractCardiovascular events remain a substantial global health concern, necessitating innovative strategies for prevention. This study aims to assess the potential impact of influenza vaccination on major cardiovascular events. A search of the medical English literature was conducted using PubMed/MEDLINE, EMBASE, and the Cochrane CENTRAL up to 1 August 2023. Meta-analysis and stratified analyses were performed to investigate specific outcomes, including myocardial infarction (MI), cardiovascular death, and stroke. Pooled relative risks (RR) along with their 95% confidence intervals (CI) were calculated to evaluate the associations. A comprehensive analysis was conducted on a total of 9059 patients, with 4529 patients receiving the influenza vaccine and 4530 patients receiving a placebo. Among patients who received the influenza vaccine, a notable reduction in the occurrence of major cardiovascular events was observed, with 517 cases compared to 621 cases in the placebo group (RR 0.70; 95% CI 0.55–0.91). The stratified analysis revealed a decreased risk of MI in vaccinated patients (RR 0.74; 95% CI 0.56–0.97) and a significant reduction in cardiovascular death events (RR 0.67; 95% CI 0.45–0.98). This study provides compelling evidence that influenza vaccination is associated with a decreased risk of major cardiovascular events, particularly myocardial infarction, and cardiovascular death. These findings highlight the potential of influenza vaccination as an adjunctive strategy in cardiovascular disease prevention. Further research and exploration of underlying mechanisms are warranted to elucidate the observed beneficial effects.
Improving nanochemoimmunotherapy efficacy by boosting “eat-me” signaling and downregulating “don't-eat-me” signaling with Ganoderma lucidum polysaccharide-based drug delivery
Authors: Pang Guibin , Wei Siqi , Zhao Jian , Wang Fu-Jun 
Published: November 2023

Prophagocytic mixed nanodrugs are developed to enhance macrophage phagocytosis by encapsulating ICD inducer doxorubicin and CD47 inhibitor gefitinib with immunostimulatory polysaccharides from Ganoderma lucidum.
Elasticity-integrated pricing and allocation heuristic for airline revenue management
Authors: Jayaram Aparna , Amit R. K. , Agarwal Amit , Luo Xiaodong 
Published: November 2023

AbstractSetting the right fares is a key lever for increasing operating profitability in the airline industry. It is crucial to design fares that are both appealing to passengers and contribute to an increase in airline revenue. Although airline revenue management techniques have evolved to capture customer-choice behavior, the pricing and allocation decisions continue to be taken independently. However, since they are linked, a single optimization model can address this shortcoming. This paper presents a joint optimization model (JOM) that considers product prices and their allocation quantities as decision variables. A sequential optimization technique that divides the model into two decision problems is adopted to cope with JOM’s complexity. The problem is divided into a master problem and a sub-problem, wherein product price changes are made in the master problem and, with these fixed prices, optimization is performed in the sub-problem. The sub-problem is solved by simplifying the non-linear JOM into a linear programming problem. The direction of product price changes in the master problem is identified using price elasticity of demand. A heuristic based on this concept is proposed and tested. The Elasticity-integrated Pricing and Allocation Heuristic (EPAH) is observed to produce a consistent increase in existing revenues.
GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level
Authors: Spiegl Benjamin , Kapidzic Faruk , Röner Sebastian , Kircher Martin , Speicher Michael R 
Published: November 2023

Abstract
Analyses of cell-free DNA (cfDNA) are increasingly being employed for various diagnostic and research applications. Many technologies aim to increase resolution, e.g. for detecting early-stage cancer or minimal residual disease. However, these efforts may be confounded by inherent base composition biases of cfDNA, specifically the over - and underrepresentation of guanine (G) and cytosine (C) sequences. Currently, there is no universally applicable tool to correct these effects on sequencing read-level data. Here, we present GCparagon, a two-stage algorithm for computing and correcting GC biases in cfDNA samples. In the initial step, length and GC base count parameters are determined. Here, our algorithm minimizes the inclusion of known problematic genomic regions, such as low-mappability regions, in its calculations. In the second step, GCparagon computes weights counterbalancing the distortion of cfDNA attributes (correction matrix). These fragment weights are added to a binary alignment map (BAM) file as alignment tags for individual reads. The GC correction matrix or the tagged BAM file can be used for downstream analyses. Parallel computing allows for a GC bias estimation below 1 min. We demonstrate that GCparagon vastly improves the analysis of regulatory regions, which frequently show specific GC composition patterns and will contribute to standardized cfDNA applications.
Four new species of dragonfish genus Eustomias (Stomiiformes: Stomiidae: Melanostomiinae) from the western tropical Atlantic, with remarks on Eustomias minimus Clarke, 1999
Authors: Villarins Bárbara T , Fischer Luciano G , Prokofiev Artem M , Mincarone Michael M 
Published: November 2023

Abstract
Four new species of the scaleless black dragonfish genus Eustomias are described based on specimens collected during the ABRACOS (Acoustics along the BRAzilian COaSt) expeditions along the Fernando de Noronha Ridge, off northeastern Brazil, western tropical Atlantic. Eustomias (Haploclonus) antea sp. nov. differs from its congeners by having a long chin barbel without appendages, ending in a very small terminal bulb without terminal filaments. Eustomias (Haploclonus) lucenae sp. nov. has the lowest count of photophores in the lateral series (56) and a simple, short barbel, ending in a small and asymmetrical terminal bulb. Eustomias (Nominostomias) ophioglossa sp. nov. differs from its congeners by the long chin barbel with two terminal bulbs and long terminal filament with bifurcated axis along its length and with bulblets of different sizes and arrangements inside. Eustomias (Nominostomias) bertrandi sp. nov. can be distinguished by the long chin barbel with two terminal bulbs, the distal bulb more than twice as long as the proximal one, and a short terminal filament. Morphological description of a specimen identified as Eustomias (Dinematochirus) cf. minimus is provided, and an overview of the species of Eustomias reported in Brazilian waters is presented and discussed.
Facile Filtration-Based Workflow for Facilitating Sensitive Detection of Pathogenic Bacteria from Blood
Authors: Park Dong Jin , Chen Liben , Wu Tianqi , Lee Pei-Wei , Hsieh Kuangwen , Wang Tza-Huei 
Published: November 2023

AbstractBloodstream infections (BSIs) are a global health concern, contributing to high mortality rates and increased healthcare costs. Current diagnostic methods, such as blood culture, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), immunoassays, and nucleic acid amplification tests (NAATs), have lengthy workflow bottlenecked by the need of culture based method This study introduces an innovative blood processing method that overcomes this limitation, enabling rapid and culture-free isolation of pathogenic bacteria from whole blood. The method combines osmolysis, blood separation membrane filtration, detergent and enzymatic lysis, and bacterial capture, requiring minimal specialized equipment. Notably, it uses a small blood sample volume (0.5 mL or below), making it suitable for pediatric patients. The workflow involves four simple steps and can be completed in approximately 30 minutes, providing rapid pathogen isolation. The protocol was successfully tested with two most common causative bacteria, S. aureus and E. coli, achieving sensitive detection down to approximately 10 CFU using benchtop PCR. The culture-free approach accelerates the diagnosis process and minimizes the risk of bacterial population alterations during culturing. While further optimization and testing with a broader range of pathogens are needed, this method holds promise in advancing the diagnosis of life-threatening bacterial infections. Future applications may include rapid point-of-care testing in resource-limited settings.
Development of a prediction model for 30-day COVID-19 hospitalization and death in a national cohort of Veterans Health Administration patients – March 2022 - April 2023
Authors: Bui David P. , Bajema Kristina L. , Huang Yuan , Yan Lei , Li Yuli , Nallakkandi Rajeevan , Berry Kristin , Rowneki Mazhgan , Argraves Stephanie , Hynes Denise , Huang Grant , Aslan Mihaela , Ioannou George N. 
Published: November 2023

ABSTRACTObjectiveDevelop models to predict 30-day COVID-19 hospitalization and death in the Omicron era for clinical and research applications.Material and MethodsWe used comprehensive electronic health records from a national cohort of patients in the Veterans Health Administration (VHA) who tested positive for SARS-CoV-2 between March 1, 2022, and March 31, 2023. Full models incorporated 84 predictors, including demographics, comorbidities, and receipt of COVID-19 vaccinations and anti-SARS-CoV-2 treatments. Parsimonious models included 19 predictors. We created models for 30-day hospitalization or death, 30-day hospitalization, and 30-day all-cause mortality. We used the Super Learner ensemble machine learning algorithm to fit prediction models. Model performance was assessed with the area under the receiver operating characteristic curve (AUC), Brier scores, and calibration intercepts and slopes in a 20% holdout dataset.ResultsModels were trained and tested on 198,174 patients, of whom 8% were hospitalized or died within 30 days of testing positive. AUCs for the full models ranged from 0.80 (hospitalization) to 0.91 (death). Brier scores were close to 0, with the lowest error in the mortality model (Brier score: 0.01). All three models were well calibrated with calibration intercepts <0.23 and slopes <1.05. Parsimonious models performed comparably to full models.DiscussionThese models may be used for risk stratification to inform COVID-19 treatment and to identify high-risk patients for inclusion in clinical trials.ConclusionsWe developed prediction models that accurately estimate COVID-19 hospitalization and mortality risk following emergence of the Omicron variant and in the setting of COVID-19 vaccinations and antiviral treatments.
Microbiological and Clinical Characteristics of HypervirulentKlebsiella pneumoniaeisolated from Patients in Tertiary Centers
Authors: Khairuddin Aimi , Nik Zuraina Nik Mohd Noor , Mohamad Nasir Nur Syafiqah , Chuan Chua Wei , Abdul Halim Hamimi Salihah , Yusof Wardah , Husin Azura , Yean Chan Yean , Hassan Siti Asma’ 
Published: November 2023

AbstractHypervirulentKlebsiella pneumoniae(hvKp) has emerged as a significant pathogen capable of causing severe community-acquired infections in otherwise healthy people. This cross-sectional, retrospective study aimed to investigate the prevalence of hvKp, its virulence-associated genes, and the clinical manifestations of hvKp infections. HvKp was defined in this study asK. pneumoniaewith a positive string test and harbouring the serotype K1 or K2 gene. A total of 180 isolates from various clinical specimens were collected from June 2020 to June 2021 in four main hospitals in Kelantan. All isolates were examined for hypermucoviscous phenotype by string test, while the presence of capsular serotype and other virulence genes (rmpA, rmpA2, iucA, magA, peg-344) was done by PCR. Patients’ clinical data was collected and analyzed. String test positive isolates (23.8%, n = 43) were identified as hypermucoviscousK. pneumoniae(hmKp). Capsular serotypes K1 and K2 were detected in 11.1% (n = 20) and 6.1% (n = 11), respectively. The prevalence of hvKp was found to be 9.4% (n = 17). All the hvKp isolates were positive forrmpA, rmpA2, iucA,andpeg-344genes, while all ten hvKp-K1 serotypes were positive formagA, the K1serotype-specific gene. The associations of all the corresponding virulence genes with both serotypes K1 and K2 were statistically significant (p<0.05). HvKp infections were more prevalent in men and individuals with hypertension. Pneumonia was the leading clinical diagnosis in hvKp infected patients, with the mortality rate was 12%. The presence of all biomarkers (rmpA, rmpA2, magA(for K1 serotype),iucA,andpeg-344in hmKp, in combination with clinical manifestations, might be reliable for hvKp diagnosis and epidemiological surveillance.