bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA hypomethylation promotes the expression of CASPASE-4 which exacerbates inflammation and amyloid-β deposition in Alzheimer’s disease
Authors: Daily Kylene P. , Badr Asmaa , Eltobgy Mostafa , Estfanous Shady , Whitham Owen , Tan Michelle H. , Carafice Cierra , Krause Kathrin , McNamara Andrew , Hamilton Kaitlin , Houle Samuel , Gupta Spandan , Gupta Gauruv A. , Madhu Shruthi , Fitzgerald Julie , Saadey Abbey A. , Laster Brooke , Yan Pearlly , Webb Amy , Zhang Xiaoli , Pietrzak Maciej , Kokiko-Cochran Olga N. , Ghoneim Hazem E. , Amer Amal O. 
Published: February 2024

AbstractAlzheimer’s disease (AD) is the sixth leading cause of death in the USA. It is established that neuroinflammation contributes to the synaptic loss, neuronal death, and symptomatic decline of AD patients. Accumulating evidence suggests a critical role for microglia, innate immune phagocytes of the brain. For instance, microglia release pro-inflammatory products such as IL-1β which is highly implicated in AD pathobiology. The mechanisms underlying the transition of microglia to proinflammatory promoters of AD remain largely unknown. To address this gap, we performed reduced representation bisulfite sequencing (RRBS) to profile global DNA methylation changes in human AD brains compared to no disease controls. We identified differential DNA methylation of CASPASE-4 (CASP4), which when expressed promotes the generation of IL-1β and is predominantly expressed in immune cells. DNA upstream of the CASP4 transcription start site was hypomethylated in human AD brains, which was correlated with increased expression of CASP4. Furthermore, microglia from a mouse model of AD (5xFAD) express increased levels of CASP4 compared to wild-type (WT) mice. To study the role of CASP4 in AD, we developed a novel mouse model of AD lacking the mouse ortholog of CASP4 and CASP11, which is encoded by mouse Caspase-4 (5xFAD/Casp4−/−). The expression of CASP11 was associated with increased accumulation of pathologic protein aggregate amyloid-β (Aβ) and increased microglial production of IL-1β in 5xFAD mice. Utilizing RNA-sequencing, we determined that CASP11 promotes unique transcriptomic phenotypes in 5xFAD mouse brains, including alterations of neuroinflammatory and chemokine signaling pathways. Notably, in vitro, CASP11 promoted generation of IL-1β from macrophages in response to cytosolic Aβ through cleavage of downstream effector Gasdermin D (GSDMD). Therefore, here we unravel the role for CASP11 and GSDMD in the generation of IL-1β in response to Aβ and the progression of pathologic inflammation in AD. Overall, our results demonstrate that overexpression of CASP4 due to differential DNA methylation in AD microglia contributes to the progression of AD pathobiology. Thus, we identify CASP4 as a potential target for immunotherapies for the treatment and prevention of AD.
Prevalence of asthma in people with type 1 diabetes mellitus: a scoping review
Authors: Kamei Júlia Marchatto , Maués Raissa Dias , de Oliveira Silva Gabriel , Machado Alessandra Helena , Hoshino Erika Megumi , Bacchiega Fabiana Menezes , Sena Laís Mota Furtado , Negrato Carlos Antonio 
Published: February 2024

Abstract
Background
According to the Th1/Th2 paradigm, the expansion of Th1-type clones in individuals with type 1 diabetes results in reduced Th2-type clones, preventing the development of atopic diseases and vice versa. However, there is no consensus regarding the direct or inverse relationship between autoimmune and atopic diseases.

Objective
The aim of this scoping review was to examine the knowledge gap about the possibility of coexistence of asthma and type 1 diabetes and determine the prevalence of this association.

Methods
A scoping review was conducted, following the proposal of the Joanna Briggs Institute. The Population, Concept, and Context strategy was used to formulate the guiding question. The proposed question was: “What is the prevalence of asthma in people with T1DM?” After excluding duplicate articles, analyzing titles and abstracts, and excluding articles that did not answer the guiding question, 17 articles remained and were included in this review.

Results
Most of the articles selected conformed to the Th1/Th2 hypothesis, as the prevalence of asthma was lower in individuals with T1DM. However, similar or higher prevalence of asthma was found between cases and controls in few articles.

Conclusion
The prevalence of asthma in people with T1DM ranged from 1.7% to 23.1%. Maybe the mechanisms that characterizes the Th1/Th2 paradigm aren’t as simple as just the interaction of certain cytokines, since Th1-mediated autoimmune diseases and Th2- mediated atopy can coexist.
Contrast-enhanced mammography BI-RADS: a case-based approach to radiology reporting
Authors: Nicosia Luca , Battaglia Ottavia , Venturini Massimo , Fontana Federico , Minenna Manuela , Pesenti Aurora , Budascu Diana , Pesapane Filippo , Bozzini Anna Carla , Pizzamiglio Maria , Meneghetti Lorenza , Latronico Antuono , Signorelli Giulia , Mariano Luciano , Cassano Enrico 
Published: February 2024

AbstractContrast-enhanced mammography (CEM) is a relatively recent diagnostic technique increasingly being utilized in clinical practice. Until recently, there was a lack of standardized reporting for CEM findings. However, this has changed with the publication of a supplement in the Breast Imaging Reporting and Data System (BI-RADS). A comprehensive understanding of CEM is essential for further enhancing its role in both screening and managing patients with breast malignancies. CEM can also be beneficial for problem-solving, improving the management of uncertain breast findings. Practitioners in this field should become more cognizant of how and when to employ this technique and interpret the various CEM findings. This paper aims to outline the key findings in the updated version of the BI-RADS specifically dedicated to CEM. Additionally, it will present some clinical cases commonly encountered in clinical practice.Critical relevance statement Standardized reporting and a thorough understanding of CEM findings are pivotal for advancing the role of CEM in screening and managing breast cancer patients. This standardization contributes significantly to integrating CEM as an essential component of daily clinical practice.Key points • A complete knowledge and understanding of the findings outlined in the new BI-RADS CEM are necessary for accurate reporting.• BI-RADS CEM supplement is intuitive and practical to use.• Standardization of the CEM findings enables more accurate patient management.
Graphical Abstract
Understanding how therapeutic exercise prescription changes outcomes important to patients with persistent non-specific low back pain: a realist review protocol
Authors: Wood Lianne , Booth Vicky , Dean Sarah , Foster Nadine E. , Hayden Jill A. , Booth Andrew 
Published: February 2024

Abstract
Introduction
Persistent low back pain (LBP) is the leading cause of disability worldwide, and therapeutic exercise is recommended as a first-line treatment in international guidelines. The effects of exercise on clinical outcomes of pain and physical function are small to moderate, despite broader impacts on cardiovascular systems, biological health, mood, and emotional well-being. Therapeutic exercise prescription is defined as exercise that is prescribed by a clinician for a health-related treatment. It is unknown how therapeutic exercise prescription creates effects on outcomes of importance. Realist reviews explore how underlying mechanisms (M) may be active in the context (C) of certain situations, settings, or populations to create an intended or unintended outcome (O). Our objective is to explore and understand the mechanisms by which therapeutic exercise prescription changes outcomes for people with persistent LBP.

Methods
We will develop initial programme theories based on preliminary data from a previous systematic review and consensus workshop. These theories will be modified with input from a steering group (experts), a stakeholder group (people with lived experience of exercise for persistent LBP and clinicians), and a scoping search of the published literature. An information specialist will design and undertake an iterative search strategy. These will be used to create CMO configurations, which will be refined and tested using the literature. The realist review will be reported following RAMESES guidance.

Discussion
Realist reviews are uncommon in LBP research to date, yet those offer an opportunity to contrast with traditional methods of randomised controlled trials and systematic reviews and provide additional information regarding the contexts and mechanisms that may trigger certain outcomes. This can aid our understanding of the contextual features that may influence exercise prescription, such as for whom they are most effective, in what setting, how they are implemented and why. This realist synthesis will enhance our understanding of therapeutic exercise prescription to improve adherence and engagement and ultimately will provide clinically relevant recommendations regarding exercise prescription for those with persistent LBP.

Systematic review registration
The review has been registered with PROSPERO (CRD42017072023).
Protein–protein interaction network-based integration of GWAS and functional data for blood pressure regulation analysis
Authors: Tsare Evridiki-Pandora G. , Klapa Maria I. , Moschonas Nicholas K. 
Published: February 2024

Abstract
Background
It is valuable to analyze the genome-wide association studies (GWAS) data for a complex disease phenotype in the context of the protein–protein interaction (PPI) network, as the related pathophysiology results from the function of interacting polyprotein pathways. The analysis may include the design and curation of a phenotype-specific GWAS meta-database incorporating genotypic and eQTL data linking to PPI and other biological datasets, and the development of systematic workflows for PPI network-based data integration toward protein and pathway prioritization. Here, we pursued this analysis for blood pressure (BP) regulation.

Methods
The relational scheme of the implemented in Microsoft SQL Server BP-GWAS meta-database enabled the combined storage of: GWAS data and attributes mined from GWAS Catalog and the literature, Ensembl-defined SNP-transcript associations, and GTEx eQTL data. The BP-protein interactome was reconstructed from the PICKLE PPI meta-database, extending the GWAS-deduced network with the shortest paths connecting all GWAS-proteins into one component. The shortest-path intermediates were considered as BP-related. For protein prioritization, we combined a new integrated GWAS-based scoring scheme with two network-based criteria: one considering the protein role in the reconstructed by shortest-path (RbSP) interactome and one novel promoting the common neighbors of GWAS-prioritized proteins. Prioritized proteins were ranked by the number of satisfied criteria.

Results
The meta-database includes 6687 variants linked with 1167 BP-associated protein-coding genes. The GWAS-deduced PPI network includes 1065 proteins, with 672 forming a connected component. The RbSP interactome contains 1443 additional, network-deduced proteins and indicated that essentially all BP-GWAS proteins are at most second neighbors. The prioritized BP-protein set was derived from the union of the most BP-significant by any of the GWAS-based or the network-based criteria. It included 335 proteins, with ~ 2/3 deduced from the BP PPI network extension and 126 prioritized by at least two criteria. ESR1 was the only protein satisfying all three criteria, followed in the top-10 by INSR, PTN11, CDK6, CSK, NOS3, SH2B3, ATP2B1, FES and FINC, satisfying two. Pathway analysis of the RbSP interactome revealed numerous bioprocesses, which are indeed functionally supported as BP-associated, extending our understanding about BP regulation.

Conclusions
The implemented workflow could be used for other multifactorial diseases.
Rayleigh step-selection functions and connections to continuous-time mechanistic movement models
Authors: Eisaguirre Joseph M. , Williams Perry J. , Hooten Mevin B. 
Published: February 2024

Abstract
Background
The process known as ecological diffusion emerges from a first principles view of animal movement, but ecological diffusion and other partial differential equation models can be difficult to fit to data. Step-selection functions (SSFs), on the other hand, have emerged as powerful practical tools for ecologists studying the movement and habitat selection of animals.

Methods
SSFs typically involve comparing resources between a set of used and available points at each step in a sequence of observed positions. We use change of variables to show that ecological diffusion implies certain distributions for available steps that are more flexible than others commonly used. We then demonstrate advantages of these distributions with SSF models fit to data collected for a mountain lion in Colorado, USA.

Results
We show that connections between ecological diffusion and SSFs imply a Rayleigh step-length distribution and uniform turning angle distribution, which can accommodate data collected at irregular time intervals. The results of fitting an SSF model with these distributions compared to a set of commonly used distributions revealed how precision and inference can vary between the two approaches.

Conclusions
Our new continuous-time step-length distribution can be integrated into various forms of SSFs, making them applicable to data sets with irregular time intervals between successive animal locations.
Polymeric DNase-I nanozymes targeting neutrophil extracellular traps for the treatment of bowel inflammation
Authors: Wang Chi-Pin James , Ko Ga Ryang , Lee Yun Young , Park Juwon , Park Wooram , Park Tae-Eun , Jin Yoonhee , Kim Se-Na , Lee Jung Seung , Park Chun Gwon 
Published: February 2024

AbstractInflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is a family of chronic disorders along the gastrointestinal tract. Because of its idiopathic nature, IBD does not have a fundamental cure; current available therapies for IBD are limited to prolonged doses of immunomodulatory agents. While these treatments may reduce inflammation, limited therapeutic efficacy, inconsistency across patients, and adverse side effects from aggressive medications remain as major drawbacks. Recently, excessive production and accumulation of neutrophil extracellular traps (NETs) also known as NETosis have been identified to exacerbate inflammatory responses and induce further tissue damage in IBD. Such discovery invited many researchers to investigate NETs as a potential therapeutic target. DNase-I is a natural agent that can effectively destroy NETs and, therefore, potentially reduce NETs-induced inflammations even without the use of aggressive drugs. However, low stability and rapid clearance of DNase-I remain as major limitations for further therapeutic applications. In this research, polymeric nanozymes were fabricated to increase the delivery and therapeutic efficacy of DNase-I. DNase-I was immobilized on the surface of polymeric nanoparticles to maintain its enzymatic properties while extending its activity in the colon. Delivery of DNase-I using this platform allowed enhanced stability and prolonged activity of DNase-I with minimal toxicity. When administered to animal models of IBD, DNase-I nanozymes successfully alleviated various pathophysiological symptoms of IBD. More importantly, DNase-I nanozyme administration successfully attenuated neutrophil infiltration and NETosis in the colon compared to free DNase-I or mesalamine.
Transcutaneous auricular vagus nerve stimulation for the treatment of myoarthropatic symptoms in patients with craniomandibular dysfunction – a protocol for a randomized and controlled pilot trial
Authors: Prott Lea S. , Spitznagel Frank A. , Hugger Alfons , Langner Robert , Gierthmühlen Petra C. , Gierthmühlen Mortimer 
Published: February 2024

Abstract
Background
Temporomandibular disorders (TMD) are a collective term for pain and dysfunction of the masticatory muscles and the temporomandibular joints. The most common types of TMD are pain-related, which may impact the psychological behavior and quality of life. Currently, the most popular methods for the treatment of TMD patients are occlusal splint therapy, often in combination with physical- and/or pharmacotherapy. However, due to the complexity of etiology, the treatment of chronic TMD remains a challenge. Recently, CE-certified systems for non-invasive VNS (transcutaneous auricular vagus nerve stimulation, taVNS) have become available and show positive effects in the treatment of chronic pain conditions, like migraine or fibromyalgia, with which TMD shares similarities. Therefore, it is the main purpose of the study to evaluate the feasibility of daily taVNS against chronic TMD and to assess whether there is an improvement in pain severity, quality of life, and kinetic parameters.

Methods
This study is designed as a single-blinded, double-arm randomized controlled trial (RCT) in a 1:1 allocation ratio. Twenty adult patients with chronical TMD symptoms will be enrolled and randomized to stimulation or sham group. In the stimulation group, taVNS is performed on the left tragus (25 Hz, pulse width 250 µs, 28 s on/32 s off, 4 h/day). The sham group will receive no stimulation via a non-functional identical-looking electrode. Validated questionnaire data and clinical parameters will be collected at the beginning of the study and after 4 and 8 weeks. The compliance of a daily taVNS of patients with chronical TMD will be evaluated via a smartphone app recording daily stimulation time and average intensity. Additionally, the treatment impact on pain severity and quality of life will be assessed with different questionnaires, and the effect on the mandibular mobility and muscle activity will be analyzed.

Discussion
This is the first clinical trial to assess the feasibility of taVNS in patients with chronic TMD symptoms. If taVNS improves the symptoms of TMD, it will be a significant gain in quality of life for these chronic pain patients. The results of this pilot study will help to determine the feasibility of a large-scale RCT.

Trial registration
This study has been registered in the DRKS database (DRKS00029724).
Understanding exposomes and its relation with cancer risk in Malaysia based on epidemiological evidence: a narrative review
Authors: Sharif Razinah , Ooi Theng Choon 
Published: February 2024

AbstractThe prevalence of cancer is increasing globally, and Malaysia is no exception. The exposome represents a paradigm shift in cancer research, emphasizing the importance of a holistic approach that considers the cumulative effect of diverse exposures encountered throughout life. The exposures include dietary factors, air and water pollutants, occupational hazards, lifestyle choices, infectious agents and social determinants of health. The exposome concept acknowledges that each individual’s cancer risk is shaped by not only their genetic makeup but also their unique life experiences and environmental interactions. This comprehensive review was conducted by systematically searching scientific databases such as PubMed, Scopus and Google Scholar, by using the keywords “exposomes (environmental exposures AND/OR physical exposures AND/OR chemical exposures) AND cancer risk AND Malaysia”, for relevant articles published between 2010 and 2023. Articles addressing the relationship between exposomes and cancer risk in the Malaysian population were critically evaluated and summarized. This review aims to provide an update on the epidemiological evidence linking exposomes with cancer risk in Malaysia. This review will provide an update for current findings and research in Malaysia related to identified exposomes-omics interaction and gap in research area related to the subject matter. Understanding the interplay between complex exposomes and carcinogenesis holds the potential to unveil novel preventive strategies that may be beneficial for public health.
Terasi, exploring the Indonesian ethnic fermented shrimp paste
Authors: Herlina Vika Tresnadiana , Setiarto R. Haryo Bimo 
Published: February 2024

AbstractTerasi is an Indonesian traditional fermented shrimp paste commonly used as a condiment to enhance flavor in Indonesian cuisines. This product has distinctive sensory characteristics and is known by various names in Asian countries. The primary reaction that occurs during terasi fermentation is proteolysis by endogenous enzymes generated by microorganisms to produce taste and aroma compounds. This review elaborates on various aspects of terasi, including history, microbiology, fermentation process, nutritional properties, bioactivities, potential hazards, and the future, challenges, and prospects of terasi. Apart from limiting its nutritional value, the long-duration process and high salt content of terasi appear to prevent the formation of toxic biogenic amines. Therefore, this review article also discussed innovative bioprocesses such as low-salt fermentation and the use of novel starter cultures to speed up fermentation and produce terasi with better quality and safety for human consumption.
A novel Cosine-Cosine chaotic map-based video encryption scheme
Authors: Kumari Sweta , Dua Mohit , Dua Shelza , Dhingra Deepti 
Published: February 2024

AbstractThe surge in online activities has led to the increasing popularity of sharing video data across diverse applications, including online education tutorials, social networking, video calling, and OTT platforms. Encryption prevents unauthorized access to the transmitted data over unreliable channels. The well-known features of chaos theory such as random behaviour, unpredictability, and initial parameters dependency facilitate its use in cryptography. Many security issues are faced by chaos-based cryptosystems because of their less complexity. Hence, a new Cosine-Cosine chaotic map characterized by intricate chaotic behaviour is designed in the current study. Additionally, we formulate an original video encryption scheme employing this Cosine-Cosine chaotic map. The encryption process involves five steps, beginning with the segmentation of the original video into frames based on its frame rate. In the second phase, a 384 bits pseudorandom key is generated that is further divided into three subkeys of 128 bits each. The novel Cosine-Cosine chaotic map-based sequence is generated. In the fourth step, red, green, and blue components are encrypted using the pseudorandom key and the chaotic sequence. In the last step, we combine encrypted frames to get cipher video. The security analysis validates that the proposed encryption protects against eavesdropping.