bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D bioprinted chondrogenic gelatin methacrylate-poly(ethylene glycol) diacrylate composite scaffolds for intervertebral disc restoration
Authors: Astudillo Potes Maria D , Tilton Maryam , Mitra Indranath , Liu Xifeng , Dashtdar Babak , Camilleri Emily T , Elder Benjamin D , Lu Lichun 
Published: October 2024

Abstract
Degenerative spine pathologies, including intervertebral disc (IVD) degeneration, present a significant healthcare challenge due to their association with chronic pain and disability. This study explores an innovative approach to IVD regeneration utilizing 3D bioprinting technology, specifically visible light-based digital light processing, to fabricate tissue scaffolds that closely mimic the native architecture of the IVD. Utilizing a hybrid bioink composed of gelatin methacrylate (GelMA) and poly (ethylene glycol) diacrylate (PEGDA) at a 10% concentration, we achieved enhanced printing fidelity and mechanical properties suitable for load-bearing applications such as the IVD. Preconditioning rat bone marrow-derived mesenchymal stem cell spheroids with chondrogenic media before incorporating them into the GelMA-PEGDA scaffold further promoted the regenerative capabilities of this system. Our findings demonstrate that this bioprinted scaffold not only supports cell viability and integration but also contributes to the restoration of disc height in a rat caudal disc model without inducing adverse inflammatory responses. The study underscores the potential of combining advanced bioprinting techniques and cell preconditioning strategies to develop effective treatments for IVD degeneration and other musculoskeletal disorders, highlighting the need for further research into the dynamic interplay between cellular migration and the hydrogel matrix.
Materials, processes, devices and applications of magnetoresistive random access memory
Authors: Yang Meiyin , Cui Yan , Chen Jingsheng , Luo Jun 
Published: October 2024

Abstract
Magnetoresistive random access memory (MRAM) is a promising non-volatile memory technology that can be utilized as an energy and space-efficient storage and computing solution, particularly in cache functions within circuits. Although MRAM has achieved mass production, its manufacturing process still remains challenging, resulting in only a few semiconductor companies dominating its production. In this review, we delve into the materials, processes, and devices used in MRAM, focusing on both the widely adopted spin transfer torque MRAM and the next-generation spin-orbit torque MRAM. We provide an overview of their operational mechanisms and manufacturing technologies. Furthermore, we outline the major hurdles faced in MRAM manufacturing and propose potential solutions in detail. Then, the applications of MRAM in artificial intelligent hardware are introduced. Finally, we present an outlook on the future development and applications of MRAM.
Fabrication, compact & device modeling of 4H–21DNTT organic thin film transistor
Authors: Dadhich Shubham , Upadhyaya Vivek , Mathur Garima , Dwivedi A D D 
Published: October 2024

Abstract
In this study, we explored a novel organic semiconductor (OSC), 6,6 bis-(trans4-butylcyclohexyl) dinaphtho[2,1-b:2,1-f]thieno[3,2-b]thiophene (4H–21DNTT). The work also includes a TCAD device model for optimizing and improving the device performance. Both the experimental and simulated results have demonstrated sufficient mobility to realize complex circuits. To validate its potential, a compact model was developed and employed in the SPICE simulator for complex-circuit simulations. Both models accurately capture the below-threshold, linear, and saturation operating conditions through a unified approach, removing the necessity for explicitly defining the threshold and saturation voltages.
Bearing fault diagnosis based on novel hierarchical multiscale dispersion entropy in corresponding color block images
Authors: Wang Zihan , Peng Jigang , Sun Yongjian 
Published: October 2024

Abstract
The rolling bearing is a critical component of mechanical equipment, and its failure can lead to serious consequences. In order to effectively extract fault features of rolling bearings and improve fault diagnosis performance, a fault diagnosis framework based on hierarchical multiscale dispersion entropy (HMDE) and improved histogram of oriented gradient (HOG) is proposed by combining entropy method with image recognition method. Firstly, the original vibration signal is subjected to moving average filtering to eliminate sudden noise and outliers. Then, HMDE is used for the extraction of fault features. HMDE can evaluate the complexity of the signal at different levels and scales, thereby extracting more comprehensive information. Based on HMDE, entropy color block (ECB) images are generated and the improved HOG of the images are extracted. Finally, K-nearest neighbor (KNN) is used to classify the improved HOG features, completing the recognition of different working states of rolling bearings. The validity and robustness of the proposed fault diagnosis framework are proved by the verification experiments on the public bearing datasets of Case Western Reserve University and Southeast University.
Bonding performance and construction parameters of low-rebound shotcrete
Authors: Liu Xiangyang , Wei Liangwen , Lu Dewang , Sun Liang , Huang Yaoming , Liu Shiyang 
Published: October 2024

Abstract
Shotcrete has the advantages of short setting time, high early strength, simple process and flexible operation methods. It is mainly used as temporary support in domestic highway tunnels. This study investigates the development of low-rebound shotcrete for tunnel construction by adding silica fume and fly ash into the mixture. Sandstone and limestone were employed to simulate the surrounding rock. The workability and mechanical properties of the shotcrete were evaluated based on slump tests, rebound rates, compressive strength measurements, and bonding strength tests between the surrounding rock and the shotcrete. Furthermore, the research investigated construction techniques, with an emphasis on spraying distance, shrinkage angle, and wind pressure, and optimized these parameters for practical engineering uses. The outcomes demonstrate that the addition of silica fume enhances the mechanical properties of the shotcrete and reduces rebound. It was discovered that optimal spraying distance was between 1.2 m and 1.5 m, with the optimal wind pressure at 0.5 m, and the ideal shrinkage angle at 6°. Research on low rebound shotcrete is of great significance for improving construction quality, construction efficiency and engineering structural performance, and also meets the requirements of sustainable development.
Evaluation of a pathology resident wellness initiative: Initial establishment and subsequent expansion through a time of high stress, the COVID-19 pandemic
Authors: Davis Katelynn , Bailey Gabrielle , Butcher Monica R , Dombrowski Katya , Fomchenko Katherine M , Schendzielos Rachel , Boyd Kristy , Nath Nancy , Hanyok Laura A , Hruban Ralph H , Wake Laura M , White Marissa J , Ware Alisha D 
Published: October 2024

Abstract

Objectives
Recent studies have shown that the pathology workforce is at risk of decreased workplace well-being, which may lead to decreased job satisfaction, increased attrition, burnout, depression, anxiety, and suicidality, but there has been relatively little research on well-being initiatives designed for pathologists, pathology trainees, and laboratory professionals. Some studies have suggested that well-being initiatives may decrease burnout and increase workplace satisfaction and engagement.

Methods
Here we describe the creation of a Pathology Wellness Committee in a large residency program. Interventions included emotional, social, and physical well-being interventions as well as system-based improvements. Additional initiatives were introduced in response to the increased stress, isolation, and social distancing guidelines during the height of the COVID-19 pandemic. The program’s impact was measured by an annual House Staff Council Resident Wellness Survey over 4 years.

Results
The annual surveys showed improvements in workplace and residency program satisfaction and emotional well-being following system-based improvements and well-being initiatives. Physical and social well-being showed slight but not statistically significant decreases over the 4-year period. Results from the annual Accreditation Council for Graduate Medical Education Survey were also evaluated.

Conclusions
We found that dedicated well-being initiatives in conjunction with system-based interventions may help improve overall well-being in pathology residents.
Physicochemical and microbiological stability of 40 mg/mL amiodarone hydrochloride oral suspension
Authors: Cavelier Marine , Gondé Henri , Costa Damien , Lamoureux Fabien , Pereira Tony , Varin Rémi , Hervouët Charles 
Published: October 2024

Abstract

Purpose
Amiodarone hydrochloride is an antiarrhythmic drug used to treat supraventricular tachycardia. However, there are currently no commercial pediatric forms available to treat young patients. Various oral formulations were previously reported in the literature, but the concentration was lower than the doses prescribed in clinical practice (a loading dose of 500 mg/m2/day for 7-10 days followed by a maintenance dose of 250 mg/m2/day). The objective of this study was to develop an oral liquid formulation of amiodarone hydrochloride at an optimal concentration for use in children and to evaluate its physicochemical and microbiological stability.

Methods
No commercial suspension vehicle was used, allowing the choice of excipients. Compounding was performed using hydroxypropylmethylcellulose as thickener, potassium sorbate preservative, citric acid/sodium citrate buffer, sodium saccharin as sweetener, and a strawberry flavoring agent. A concentration of 40 mg/mL was selected based on a 5-year compilation of prescribed doses. Analyses performed were the following: visual and microscopic inspection, testing for antimicrobial preservation, osmolality and pH measurements, quantification of amiodarone hydrochloride by a stability-indicating liquid chromatography method, and a microbiological count.

Results
At least 95% of the initial amiodarone hydrochloride remained stable during the 60-day study period under refrigeration. All other tested parameters remained stable at 5 °C. A targeted log reduction of the microorganism inoculum by day 14 and no microbial growth by day 28 were demonstrated in the test for antimicrobial preservation.

Conclusion
The stability of 40 mg/mL amiodarone hydrochloride oral suspension was maintained under refrigeration for 60 days before opening bottles and for 1 month after opening bottles.
Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition
Authors: Nourani Esmaeil , Koutrouli Mikaela , Xie Yijia , Vagiaki Danai , Pyysalo Sampo , Nastou Katerina , Brunak Søren , Jensen Lars Juhl 
Published: October 2024

Abstract

Motivation
Despite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly in chronic diseases, they have still not been systematically described in the biomedical literature. This is in part because no named entity recognition (NER) system exists, which can comprehensively detect all types of LSFs in text. The task is challenging due to their inherent diversity, lack of a comprehensive LSF classification for dictionary-based NER, and lack of a corpus for deep learning-based NER.

Results
We present a novel lifestyle factor ontology (LSFO), which we used to develop a dictionary-based system for recognition and normalization of LSFs. Additionally, we introduce a manually annotated corpus for LSFs (LSF200) suitable for training and evaluation of NER systems, and use it to train a transformer-based system. Evaluating the performance of both NER systems on the corpus revealed an F-score of 64% for the dictionary-based system and 76% for the transformer-based system. Large-scale application of these systems on PubMed abstracts and PMC Open Access articles identified over 300 million mentions of LSF in the biomedical literature.

Availability and implementation
LSFO, the annotated LSF200 corpus, and the detected LSFs in PubMed and PMC-OA articles using both NER systems, are available under open licenses via the following GitHub repository: https://github.com/EsmaeilNourani/LSFO-expansion. This repository contains links to two associated GitHub repositories and a Zenodo project related to the study. LSFO is also available at BioPortal: https://bioportal.bioontology.org/ontologies/LSFO.
DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs
Authors: Sherman Brad T , Panzade Ganesh , Imamichi Tomozumi , Chang Weizhong 
Published: October 2024

Abstract

Motivation
The Database for Annotation, Visualization, and Integrated Discovery (DAVID) is a web-based bioinformatics system for the functional interpretation of large lists of genes/proteins generated from high-throughput assays. It has been cited in 72 287 papers since its debut in 2003 as of 23 July 2024. The analysis is usually limited to the species of study. However, the knowledge of genes may be incomplete or unavailable for some species. Model organisms have been studied more extensively and analyzing gene lists in the context of these species can offer valuable insights, helping users better understand the genes and biological themes in their species of interest.

Results
We developed DAVID Ortholog for the conversion of gene lists between species. We utilized the ortholog data downloaded from Orthologous MAtrix (OMA) and Ensembl Compara as the base for the conversion. The OMA ortholog IDs and Ensembl gene IDs were converted to DAVID gene IDs and the pairing information of these IDs from these two sources was integrated into the DAVID Knowledgebase. DAVID Ortholog can convert the user’s source gene list to an ortholog list of a desired species and the downstream DAVID analysis, in the context of that species, can be continued seamlessly, allowing users to further understand the biological meaning of their gene list based on the functional annotation found for the orthologs.

Availability and implementation
https://davidbioinformatics.nih.gov/ortholog.jsp.
AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software
Authors: Lisi Alessandro , Campbell Michael C 
Published: October 2024

Abstract

Summary
Admixture is a fundamental process that has shaped levels and patterns of genetic variation in human populations. RFMIX version 2 (RFMIX2) utilizes a robust modeling approach to identify the genetic ancestries in admixed populations. However, this software does not have a built-in method to visually summarize the results of analyses. Here, we introduce the AncestryGrapher toolkit, which converts the numerical output of RFMIX2 into graphical representations of global and local ancestry (i.e. the per-individual ancestry components and the genetic ancestry along chromosomes, respectively).

Results
To demonstrate the utility of our methods, we applied the AncestryGrapher toolkit to visualize the global and local ancestry of individuals in the North African Mozabite Berber population from the Human Genome Diversity Panel. Our results showed that the Mozabite Berbers derived their ancestry from the Middle East, Europe, and sub-Saharan Africa (global ancestry). We also found that the population origin of ancestry varied considerably along chromosomes (local ancestry). For example, we observed variance in local ancestry in the genomic region on Chromosome 2 containing the regulatory sequence in the MCM6 gene associated with lactase persistence, a human trait tied to the cultural development of adult milk consumption. Overall, the AncestryGrapher toolkit facilitates the exploration, interpretation, and reporting of ancestry patterns in human populations.

Availability and implementation
The AncestryGrapher toolkit is free and open source on https://github.com/alisi1989/RFmix2-Pipeline-to-plot.
Effect of peritoneal and wound lavage with super-oxidized solution on surgical-site infection after open appendicectomy in perforated appendicitis (PLaSSo): randomized clinical trial
Authors: Sellappan Harivinthan , Alagoo Dinesh , Loo Christina , Vijian Kaesarina , Sibin Rohamini , Chuah Jitt Aun 
Published: October 2024

Abstract

Background
Surgical-site infection following open appendicectomy for perforated appendicitis increases length of hospital stay and treatment costs while compromising patients’ quality of life. Data from randomized clinical trials (RCTs) evaluating the role of super-oxidized solution in perforated appendicitis are lacking. The study objective was to determine the effect of peritoneal and wound lavage with super-oxidized solution in reducing risk of surgical-site infection following open appendicectomy for perforated appendicitis.

Methods
In this multicentre RCT conducted between September 2020 and March 2022, patients aged 13 years and older with perforated appendicitis undergoing open appendicectomy were randomly assigned to receive peritoneal and wound lavage with either super-oxidized solution or normal saline. The primary outcome was surgical-site infection within 30 days after surgery. Randomization was computer-generated, with allocation concealment by opaque, sequentially numbered, sealed envelope. The patients, surgeons, outcome assessors and statisticians performing the analysis were blinded to treatment assigned.

Results
A total of 102 consecutive patients (51 in the super-oxidized solution group and 51 in the normal saline group) were randomized and included in the intention-to-treat analysis. The super-oxidized solution group showed a significant reduction in overall surgical-site infection (8 (15.6%) versus 19 (37.2%); relative risk (RR) 0.42; 95% c.i. 0.20 to 0.87; P = 0.014), and superficial surgical-site infection (5 (9.8%) versus 18 (35.3%); RR 0.28; 95% c.i. 0.11 to 0.69; P = 0.002), with a number-needed-to-treat of four patients. There were no adverse events in either group.

Conclusions
Peritoneal and wound lavage with super-oxidized solution is superior to normal saline in preventing surgical-site infection after open appendicectomy for perforated appendicitis.

Trial Registration
ClinicalTrial.gov Identifier: NCT04512196
Direct quotations in social work writing: multi-functionality and double voicing
Authors: Leedham Maria , Lillis Theresa , Twiner Alison 
Published: October 2024

Abstract
Writing comprises a core area of social work as a substantial amount of time is spent on producing case notes, assessment reports, and other required documentation in order to progress cases; however, little research has been carried out on social workers’ writing and, in particular, the specific discursive and rhetorical devices employed to create effective texts. One rhetorical device often employed in order to include the voices of service users and their families is the use of quotations. This article explores the extent to which quotations are used across social work domains and text types, the different voices represented through quotations, and the perceived functions of the quotations. The study draws on three different data types: (1) a 1-million-word corpus of social workers’ writing; (2) social worker interviews (n = 81); (3) two case studies comprising texts, interviews with the social worker writer, and researcher observations. All data were collected within the WiSP project and were interrogated through a mix of computational and qualitative analysis to develop a taxonomy of functions of quotations. In addition to furthering our understanding of how quotations are employed in professional writing, the study has implications for social worker training and practice.
The clinical and genetic spectrum of paediatric speech and language disorders
Authors: Magielski Jan H , Ruggiero Sarah M , Xian Julie , Parthasarathy Shridhar , Galer Peter D , Ganesan Shiva , Back Amanda , McKee Jillian L , McSalley Ian , Gonzalez Alexander K , Morgan Angela , Donaher Joseph , Helbig Ingo 
Published: October 2024

Abstract
Speech and language disorders are known to have a substantial genetic contribution. Although frequently examined as components of other conditions, research on the genetic basis of linguistic differences as separate phenotypic subgroups has been limited so far.
Here, we performed an in-depth characterization of speech and language disorders in 52 143 individuals, reconstructing clinical histories using a large-scale data-mining approach of the electronic medical records from an entire large paediatric healthcare network.
The reported frequency of these disorders was the highest between 2 and 5 years old and spanned a spectrum of 26 broad speech and language diagnoses. We used natural language processing to assess the degree to which clinical diagnoses in full-text notes were reflected in ICD-10 diagnosis codes. We found that aphasia and speech apraxia could be retrieved easily through ICD-10 diagnosis codes, whereas stuttering as a speech phenotype was coded in only 12% of individuals through appropriate ICD-10 codes. We found significant comorbidity of speech and language disorders in neurodevelopmental conditions (30.31%) and, to a lesser degree, with epilepsies (6.07%) and movement disorders (2.05%). The most common genetic disorders retrievable in our analysis of electronic medical records were STXBP1 (n = 21), PTEN (n = 20) and CACNA1A (n = 18). When assessing associations of genetic diagnoses with specific linguistic phenotypes, we observed associations of STXBP1 and aphasia (P = 8.57 × 10−7, 95% confidence interval = 18.62–130.39) and MYO7A with speech and language development delay attributable to hearing loss (P = 1.24 × 10−5, 95% confidence interval = 17.46–infinity). Finally, in a sub-cohort of 726 individuals with whole-exome sequencing data, we identified an enrichment of rare variants in neuronal receptor pathways, in addition to associations of UQCRC1 and KIF17 with expressive aphasia, MROH8 and BCHE with poor speech, and USP37, SLC22A9 and UMODL1 with aphasia.
In summary, our study outlines the landscape of paediatric speech and language disorders, confirming the phenotypic complexity of linguistic traits and novel genotype–phenotype associations. Subgroups of paediatric speech and language disorders differ significantly with respect to the composition of monogenic aetiologies.