bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies
Authors: Zou Jian , Li Zheqi , Carleton Neil , Oesterreich Steffi , Lee Adrian V , Tseng George C 
Published: November 2024

Abstract

Motivation
Biomarker detection plays a pivotal role in biomedical research. Integrating omics studies from multiple cohorts can enhance statistical power, accuracy, and robustness of the detection results. However, existing methods for horizontally combining omics studies are mostly designed for two-class scenarios (e.g. cases versus controls) and are not directly applicable for studies with multi-class design (e.g. samples from multiple disease subtypes, treatments, tissues, or cell types).

Results
We propose a statistical framework, namely Mutual Information Concordance Analysis (MICA), to detect biomarkers with concordant multi-class expression pattern across multiple omics studies from an information theoretic perspective. Our approach first detects biomarkers with concordant multi-class patterns across partial or all of the omics studies using a global test by mutual information. A post hoc analysis is then performed for each detected biomarkers and identify studies with concordant pattern. Extensive simulations demonstrate improved accuracy and successful false discovery rate control of MICA compared to an existing multi-class correlation method. The method is then applied to two practical scenarios: four tissues of mouse metabolism-related transcriptomic studies, and three sources of estrogen treatment expression profiles. Detected biomarkers by MICA show intriguing biological insights and functional annotations. Additionally, we implemented MICA for single-cell RNA-Seq data for tumor progression biomarkers, highlighting critical roles of ribosomal function in the tumor microenvironment of triple-negative breast cancer and underscoring the potential of MICA for detecting novel therapeutic targets.

Availability and implementation
The source code is available on Figshare at https://doi.org/10.6084/m9.figshare.27635436. Additionally, the R package can be installed directly from GitHub at https://github.com/jianzou75/MICA.
Tailored bioengineering and nanomedicine strategies for sex-specific healing of chronic wounds
Authors: Mahmoudi Negar , Sharifi Shahriar , Leshchiner Dmitry , Horibata Sachi , Lin Zijin , Ghazali Noor , Shahbazi Mohammad-Ali , Priyam Ayushi , Williams Richard J , Pastar Irena , Gould Lisa , Matoori Simon , Nisbet David R , Mahmoudi Morteza 
Published: November 2024

Abstract
Chronic wounds, defined by their prolonged healing process, significantly impair patients’ quality of life and impose a hefty financial burden on healthcare systems worldwide. Sex- and gender-specific mechanisms regulate inflammation and infection, angiogenesis, matrix synthesis and cell recruitment. All of these processes contribute to cutaneous wound healing but remain largely understudied. This review aims to spotlight the innovative realm of bioengineering and nanomedicine, which is at the helm of revolutionizing complex chronic wound care. It underscores the significance of integrating patient sex into the development and (pre)clinical testing of these avant-garde treatment modalities, in order to enhance healing prospects for all patients regardless of sex. Moreover, we explore the representation of male and female patients in clinical trials of bioengineered and nanomedicine products. Finally, we examine the primary reasons for the historical neglect in translating sex-specific wound healing research into clinical practice and propose strategic solutions. By tackling these issues, the article advocates advanced treatment frameworks that could significantly improve healing outcomes for individuals of all sexes, thereby optimizing both efficacy and inclusivity in chronic wound management.
Quality assurance in lung cancer screening
Authors: Taib Adnan G , Au-Yong Iain T H , Nair Arjun , Devaraj Anand , Chen Yan , Baldwin David R 
Published: November 2024

Abstract
The effectiveness of screening programmes is critically dependent on the accuracy of the screening test. Where this relies on clinical expertise, there is an imperative to assure that the level of expertise meets expected standards. In cancer screening involving images, the focus is on the reader. Auditing of results is fraught with difficulty because of the time taken to accumulate enough data with confirmed outcomes to identify underperformance before any harm is done. Late recognition can lead to the need for reanalysis and recall of screening participants with loss of confidence in the programme. External quality assurance (EQA) is a method that enables clinical expertise to be tested rapidly by using test datasets with confirmed clinical outcome. In the UK, the breast cancer screening programme has had EQA in place for over 30 years. This article describes the development of the first EQA process in lung cancer screening, using the experience gained from running the breast cancer EQA, and the proposed future developments.
Social work, personalisation, and the : A Bourdieusian analysis
Authors: Bark Harry 
Published: November 2024

Abstract
This article considers the role of social work in English social care within the context of the Care Act 2014 and related policy agendas. This is achieved through a theoretical analysis of English social care policy and legislation rooted in the work of Pierre Bourdieu. Having been contextualized in the consolidation of neoliberal hegemony in Britain, particular focus is given to social care reforms stemming from the 2010–2015 Coalition Government, including the implementation of the Care Act 2014 and its associated personalisation principles. Utilizing Pierre Bourdieu’s concepts of ‘habitus’, ‘field’, and ‘capital’, social care policy and reform is viewed as embodying an ongoing ideological shift in the ways in which the state, and its social care professions, are envisaged as functioning and interacting with its citizens. From this, the role of social work in English social care is considered in relation to policy agendas underpinning the Care Act 2014 and more recent policy reviews and proposals. This article concludes by drawing on Bourdieu’s notion of ‘hysteresis’ to conceptualize a profession facing a complex negotiation of its skills and values within destabilizing political, economic, and ideological framings of practice.
The emerging field of non-invasive brain stimulation in Alzheimer’s disease
Authors: Koch Giacomo , Altomare Daniele , Benussi Alberto , Bréchet Lucie , Casula Elias P , Dodich Alessandra , Pievani Michela , Santarnecchi Emiliano , Frisoni Giovanni B 
Published: November 2024

Abstract
Treating cognitive impairment is a holy grail of modern clinical neuroscience. In the past few years, non-invasive brain stimulation is increasingly emerging as a therapeutic approach to ameliorate performance in patients with cognitive impairment and as an augmentation approach in persons whose cognitive performance is within normal limits. In patients with Alzheimer’s disease, better understanding of brain connectivity and function has allowed for the development of different non-invasive brain stimulation protocols. Recent studies have shown that transcranial stimulation methods enhancing brain plasticity with several modalities have beneficial effects on cognitive functions. Amelioration has been shown in preclinical studies on behaviour of transgenic mouse models for Alzheimer’s pathology and in clinical studies with variable severity of cognitive impairment. While the field is still grappling with issues related to the standardization of target population, frequency, intensity, treatment duration and stimulated region, positive outcomes have been reported on cognitive functions and on markers of brain pathology. Here we review the most encouraging protocols based on repetitive transcranial magnetic stimulation, transcranial direct current stimulation, transcranial alternating current stimulation, visual-auditory stimulation, photobiomodulation and transcranial focused ultrasound, which have demonstrated efficacy to enhance cognitive functions or slow cognitive decline in patients with Alzheimer’s disease. Beneficial non-invasive brain stimulation effects on cognitive functions are associated with the modulation of specific brain networks. The most promising results have been obtained targeting key hubs of higher-level cognitive networks, such as the frontal-parietal network and the default mode network. The personalization of stimulation parameters according to individual brain features sheds new light on optimizing non-invasive brain stimulation protocols for future applications.
Synaptic and cognitive impairment associated with L444P heterozygous glucocerebrosidase mutation
Authors: Lado Wudu , Ham Ahrom , Li Hongyu , Zhang Hong , Chang Audrey Yuen , Sardi Sergio Pablo , Alcalay Roy N , Arancio Ottavio , Przedborsky Serge , Tang Guomei 
Published: November 2024

Abstract
Cognitive impairment is a common but poorly understood non-motor aspect of Parkinson’s disease, negatively affecting patient’s functional capacity and quality of life. The mechanisms underlying cognitive impairment in Parkinson’s disease are still elusive, limiting treatment and prevention strategies.
This study investigates the molecular and cellular basis of cognitive impairment associated with heterozygous mutations in GBA1, the strongest risk gene for Parkinson’s disease that encodes glucocerebrosidase (GCase), a lysosome enzyme that degrades the glycosphingolipid glucosylceramide into glucose and ceramide. Using a Gba1L444P/+ mouse model, we provide evidence that L444P heterozygous Gba1 mutation (L444P/+) causes hippocampus-dependent spatial and reference memory deficits independently of α-synuclein (αSyn) accumulation, GCase lipid substrate accumulation, dopaminergic dysfunction and motor deficits. The mutation disrupts hippocampal synaptic plasticity and basal synaptic transmission by reducing the density of hippocampal CA3-CA1 synapses, a mechanism that is dissociated from αSyn-mediated presynaptic neurotransmitter release. Using a well-characterized Thy1-αSyn pre-manifest Parkinson’s disease mouse model overexpressing wild type human αSyn, we find that the L444P/+ mutation exacerbates hippocampal synaptic αSyn accumulation, synaptic and cognitive impairment in young Gba1L444P/+:Thy1-αSyn double mutant animals. With age, Thy1-αSyn mice manifest motor symptoms, and the double mutant mice exhibit more exacerbated synaptic and motor impairment than the Thy1-αSyn mice.
Taken together, our results suggest that heterozygous L444P GBA1 mutation alone perturbs hippocampal synaptic structure and function, imposing a subclinical pathological burden for cognitive impairment. When co-existing αSyn overexpression is present, heterozygous L444P GBA1 mutation interacts with αSyn pathology to accelerate Parkinson’s disease-related cognitive impairment and motor symptoms.
Germline alteration analysis reveals EPHB4R91H mutation as a key player in multiple primary lung tumors
Authors: Li Jing , Li Yanan , Wang Xinjuan , Zhou Zhigang , Li Xiangnan , Yue Songwei , Wang Huaqi , Yang Ming , Zhang Guojun 
Published: November 2024

Abstract
Multiple primary lung tumors are garnering attention from clinicians, with adenocarcinoma emerging as the predominant histological type. Because of the heterogeneity and diffuse distribution of lesions in the same patient, the treatment of multiple primary lung adenocarcinoma (MPLA) is a significant challenge. As a kind of variation unaffected by tumor heterogeneity, germline alterations may play a key role in the development of MPLA. Here, whole-exome sequencing of peripheral blood was employed to obtain germline alteration data. Intergroup comparative analyses on rare and deleterious alterations of MPLA, solitary lung adenocarcinoma, and healthy individuals in an MPLA family were performed to clarify the candidate alterations. Whole-exome sequencing and targeted Sanger sequencing were performed in 27 disseminated MPLA patients to detect the mutation site that had been screened. A rare and deleterious germline alteration, EPHB4R91H, was found in all of the patients of an MPLA family and a patient with disseminated MPLA. It was revealed that EPHB4R91H was able to enhance the proliferation, migration, and invasion ability of A549 cells through increased binding affinity to ephrinB2, which in turn activated the EPHB4/ERK/JNK/MAPK pathway. Our findings corroborate that germline alterations are involved in the development of MPLA. And it was found for the first time that the EPHB4R91H mutation promotes the development of MPLA by enhancing its affinity for ephrinB2 and thereby active EPHB4/ERK/JNK/MAPK pathway.
Monitoring of nonspatial information within working memory in the common marmoset (Callithrix jacchus)
Authors: Zlatkina Veronika , Frey Stephen , Petrides Michael 
Published: November 2024

Abstract
The mid-dorsolateral prefrontal cortical region (areas 46 and 9/46) is critical for the monitoring of information in working memory both in the macaque monkey brain and the human brain. The presence of this cytoarchitectonic region in the New World marmoset brain was in debate, but recent anatomical evidence demonstrated a limited area 46. This finding raised the question of the extent to which the marmoset brain can support the cognitive control process of monitoring information within working memory. This cognitive control process was assessed in adult marmosets and was shown to be limited to the monitoring of only two items in contrast to macaque monkeys, who can monitor as many as five items in working memory. The results are consistent with the limited development of the relevant prefrontal region in the marmoset and contribute to understanding the evolution of higher cognitive control processes in the primate brain.
Catalytic construction of stereogenic boron center on BODIPY via enantioselective Suzuki–Miyaura coupling
Authors: Kondo Aiko , Takano Hideaki , Shinokubo Hiroshi 
Published: November 2024

Abstract
Catalytic and enantioselective construction of the boron-stereogenic center is challenging due to the instability of the tetracoordinate boron center. We herein report the enantioselective intermolecular Suzuki–Miyaura coupling of dichloro BODIPY through desymmetrization. The mechanistic study reveals that kinetic resolution plays an important role in the improvement of enantioselectivity.
Association Between Use of a Voluntary Isolation Center and Reduced Household SARS-CoV-2 Transmission: A Matched Cohort Study From Toronto, Canada
Authors: Brown Kevin A , Ulloa Ana Cecilia , Buchan Sarah A , Daneman Nick , Gournis Effie , Laxer Rachel , Schwartz Kevin L , Edwards Jocelyn 
Published: November 2024

Abstract

Background
Throughout the coronavirus disease 2019 (COVID-19) pandemic, many jurisdictions established isolation centers to help reduce household transmission; however, few real-world studies support their effectiveness. We compared transmission among households where first cases used the Toronto Voluntary Isolation Centre (TVIC) with households that received routine self-isolation guidance, prior to widespread vaccine availability.

Methods
Households with a first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) case that had symptom onset between September 2020 and March 2021 and that used TVIC were propensity score matched with up to 10 self-isolation households. Follow-up began for TVIC households on the day after check-in or, for matched self-isolation households, the equivalent delay since first-case symptom onset. The outcome, 28-day secondary attack rate, was analyzed using proportional hazards models.

Results
A total of 303 TVIC households were matched with 2943 self-isolation households. Median duration from first-case symptom onset to TVIC check-in was 3 days (interdecile range [IDR] = 1–6); median check-out date was 11 days after onset (IDR = 10–13). The attack rate among TVIC households was 5.2% (53/1015) compared with 8.4% (787/9408) among self-isolation households (hazard ratio [HR] = 0.50; 95% confidence interval [CI], .28–.90). Greater reductions were observed when first cases isolated sooner after symptom onset (HR = 0.37; 95% CI, .13–1.04) and in larger (HR = 0.30; 95% CI, .14–.67) and more crowded (HR = 0.34; 95% CI, .15–.77) households.

Conclusions
Use of a voluntary isolation center was associated with a 50% reduction in household SARS-CoV-2 prior to the availability of vaccines. Beyond SARS-CoV-2, voluntary isolation centers may help control resurgences of other communicable infections or future pandemic pathogens, particularly for individuals who experience difficulties isolating.
Temporomandibular joint assessment in MRI images using artificial intelligence tools: where are we now? A systematic review
Authors: Manek Mitul , Maita Ibraheem , Bezerra Silva Diego Filipe , Pita de Melo Daniela , Major Paul W , Jaremko Jacob L , Almeida Fabiana T 
Published: November 2024

Abstract

Objectives
To summarize the current evidence on the performance of artificial intelligence (AI) algorithms for the temporomandibular joint (TMJ) disc assessment and TMJ internal derangement diagnosis in magnetic resonance imaging (MRI) images.

Methods
Studies were gathered by searching 5 electronic databases and partial grey literature up to May 27, 2024. Studies in humans using AI algorithms to detect or diagnose internal derangements in MRI images were included. The methodological quality of the studies was evaluated using the Quality Assessment Tool for Diagnostic of Accuracy Studies-2 (QUADAS-2) and a proposed checklist for dental AI studies.

Results
Thirteen studies were included in this systematic review. Most of the studies assessed disc position. One study assessed disc perforation. A high heterogeneity related to the patient selection domain was found between the studies. The studies used a variety of AI approaches and performance metrics with CNN-based models being the most used. A high performance of AI models compared to humans was reported with accuracy ranging from 70% to 99%.

Conclusions
The integration of AI, particularly deep learning, in TMJ MRI, shows promising results as a diagnostic-assistance tool to segment TMJ structures and classify disc position. Further studies exploring more diverse and multicentre data will improve the validity and generalizability of the models before being implemented in clinical practice.
Preparing for downstream tasks in artificial intelligence for dental radiology: a baseline performance comparison of deep learning models
Authors: Fernandes Fara A , Ge Mouzhi , Chaltikyan Georgi , Gerdes Martin W , Omlin Christian W 
Published: November 2024

Abstract

Objectives
To compare the performance of the convolutional neural network (CNN) with the vision transformer (ViT), and the gated multilayer perceptron (gMLP) in the classification of radiographic images of dental structures.

Methods
Retrospectively collected two-dimensional images derived from cone beam computed tomographic volumes were used to train CNN, ViT, and gMLP architectures as classifiers for four different cases. Cases selected for training the architectures were the classification of the radiographic appearance of maxillary sinuses, maxillary and mandibular incisors, the presence or absence of the mental foramen, and the positional relationship of the mandibular third molar to the inferior alveolar nerve canal. The performance metrics (sensitivity, specificity, precision, accuracy, and f1-score) and area under the curve (AUC)—receiver operating characteristic and precision-recall curves were calculated.

Results
The ViT with an accuracy of 0.74-0.98, performed on par with the CNN model (accuracy 0.71-0.99) in all tasks. The gMLP displayed marginally lower performance (accuracy 0.65-0.98) as compared to the CNN and ViT. For certain tasks, the ViT outperformed the CNN. The AUCs ranged from 0.77 to 1.00 (CNN), 0.80 to 1.00 (ViT), and 0.73 to 1.00 (gMLP) for all of the four cases.

Conclusions
The ViT and gMLP exhibited comparable performance with the CNN (the current state-of-the-art). However, for certain tasks, there was a significant difference in the performance of the ViT and gMLP when compared to the CNN. This difference in model performance for various tasks proves that the capabilities of different architectures may be leveraged.
Incidence, Disease Burden, and Clinical Presentation of Patients Newly Diagnosed With Inflammatory Bowel Disease in a Population-Based Inception Cohort
Authors: Attauabi Mohamed , Madsen Gorm Roager , Bendtsen Flemming , Seidelin Jakob Benedict , Burisch Johan 
Published: November 2024

Abstract

Background and Aims
Emerging data indicate a stabilizing incidence of inflammatory bowel diseases (IBD), including ulcerative colitis (UC), Crohn’s disease (CD), and IBD unclassified (IBDU) in Western countries. We aimed to investigate the incidence of IBD, its initial clinical presentation, and patient-reported burden.

Methods
Copenhagen IBD Inception Cohort is a prospective, population-based cohort of patients with newly diagnosed IBD according to the ECCO guidelines in the period between May 2021 and May 2023, within a catchment area covering 20% of the Danish population.

Results
Based on 554 patients (UC: 308, CD: 201, and IBDU: 18), the incidence rates per 100 000 person-years were as follows: IBD: 23.4 (95% confidence interval, 21.5–25.4), UC: 14.0 (12.6–15.6), CD: 8.6 (7.4–9.8), and IBDU: 0.8 (0.5–1.3). The median diagnostic delay was significantly shorter for UC (2.5 months [interquartile range {IQR} 1–6]) than for CD (5 months [IQR 1.5–11], p &lt; 0.01). Moderate-to-severe disability was reported by 34% of CD patients and 22% of UC patients (p = 0.01), severe fatigue by 30% and 26% (p = 0.43), and severely impaired health-related quality of life (HRQoL) by 43% and 30% of patients, respectively (p = 0.01). Hospitalization rates (UC: 20%, CD: 34%, p &lt; 0.01), and need for immunomodulators, biologics, or surgery within 3 months of diagnosis, were high in both UC (3%, 7%, and 37%, respectively) and CD (31%, 18%, and 10%, respectively).

Conclusions
We found a high incidence of IBD in Copenhagen with a substantial disease burden characterized by early and high requirements for advanced therapies and high rates of fatigue, disability, and impaired HRQoL at diagnosis.