bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pilonidal Disease Management in Young Adults: A Retrospective Analysis of Practices in a single tertiary centre in Bahrain
Authors: Isa Ahmed J. , Alqatari Ali , Daoud Rabbani Mahmoud , Althawadi Reem , Ali Noora Fuad , Salman Esra 
Published: November 2024

Abstract

Background
Pilonidal disease is a prevalent skin condition that predominantly affects young males. This study, conducted at Salmaniya Medical Complex in Bahrain, aimed to analyze the demographics, treatment methodologies, and complications associated with pilonidal disease.

Materials and Methods
We analyzed the medical records of 56 patients, comparing our practices to the American Society of Colon and Rectal Surgeons (ASCRS) guidelines. Variables collected included patient demographics (age and gender), details on preoperative and postoperative antibiotics, the type of surgical intervention performed, the closure technique used, and follow-up results at 2 months post-discharge,

Results
Our findings confirmed the high prevalence of the disease in young males (75%), with a median age at presentation being 20.5 years. Our practices showed minimal compliance (≤69%) to key recommendations. We found no documented practices for hair removal, phenol application, fibrin glue, or minimally invasive approaches. The most common surgical approach was primary closure (60%), followed by flap reconstruction (16%) and leaving wounds open (7%). The commonest complications were wound dehiscence and surgical site infection (27% each). Post-operative complications were significant, with 67.6% in patients who received pre- operative antibiotics and 63.6% in those who received post-operative antibiotics. However, no statistical link to closure type was found, likely due to our small sample size.

Conclusion
We recommend reassessing our management protocols to align with ASCRS guidelines and considering non-operative treatments to reduce morbidity. This study underscores the need for guideline adherence and the potential benefits of non-operative treatments in managing pilonidal disease.
Perspectives on the potential application of microRNAs in the diagnosis and treatment of triple-negative breast cancer
Authors: Wu Yeqin , Song Haitao , Shi Huifang , Wang Gangping 
Published: November 2024

Abstract
Triple-negative breast cancer (TNBC) is currently the most heterogeneous and aggressive breast cancer type. It has a high recurrence rate, poor clinical prospects, and lack of predictive markers and potential treatment options. Dysregulated microRNAs (miRNAs) are involved in various cellular processes in TNBC. Moreover, variations in the miRNA levels in TNBC may act as a dependable indicator for predicting the effectiveness and specificity of treatments. Currently, the application of miRNAs for breast cancer therapy is primarily in the preclinical stage, with a focus on identifying highly specific and sensitive miRNAs that could offer new possibilities for early diagnosis, clinical treatment, and prognostic monitoring of TNBC.
Uncovering causal gene-tissue pairs and variants: A multivariable TWAS method controlling for infinitesimal effects
Authors: Yang Yihe , Lorincz-Comi Noah , Zhu Xiaofeng 
Published: November 2024

AbstractTranscriptome-wide association studies (TWAS) are commonly used to prioritize causal genes underlying associations found in genome-wide association studies (GWAS) and have been extended to identify causal genes through multivariable TWAS methods. However, recent studies have shown that widespread infinitesimal effects due to polygenicity can impair the performance of these methods. In this report, we introduce a multivariable TWAS method named Tissue-Gene pairs, direct causal Variants, and Infinitesimal effects selector (TGVIS) to identify tissue-specific causal genes and direct causal variants while accounting for infinitesimal effects. In simulations, TGVIS maintains an accurate prioritization of causal gene-tissue pairs and variants and demonstrates comparable or superior power to existing approaches, regardless of the presence of infinitesimal effects. In the real data analysis of GWAS summary data of 45 cardiometabolic traits and expression/splicing quantitative trait loci (eQTL/sQTL) from 31 tissues, TGVIS is able to improve causal gene prioritization and identifies novel genes that were missed by conventional TWAS.
NERVE 2.0: boosting the New Enhanced Reverse Vaccinology Environment via artificial intelligence and a user-friendly web interface
Authors: Conte Andrea , Gulmini Nicola , Costa Francesco , Cartura Matteo , Bröhl Felix , Patanè Francesco , Filippini Francesco 
Published: November 2024

AbstractBackgroundVaccines development in this millennium started by the milestone work onNeisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. However, the problem-solving potential of most, if not all, RV programs is still largely unexploited by experimental vaccinologists that impaired by somehow difficult interfaces, requiring bioinformatic skills.ResultsWe report here on the development and release of NERVE 2.0 (available at:https://nerve-bio.org) which keeps the original integrative and modular approach of NERVE, while showing higher predictive performance than its previous version and other web-RV programs (Vaxign and Vaxijen). We renewed some of its modules and added innovative ones, such asLoop Razor, to recover fragments of promising vaccine candidates orepitopepredictfor the epitope prediction binding affinities and population coverage. Along with two newly built AI (Artificial Intelligence)-based models: ESPAAN and Virulent. To improve user-friendliness, NERVE was shifted to a tutored, web-based interface, with a noSQL-database to consent the user to submit, obtain and retrieve analysis results at any moment.ConclusionsWith its redesigned and updated environment, NERVE 2.0 allows customisable and refinable bacterial protein vaccine analyses to all different kinds of users.
OPN5 and TRPV4 subserve intrinsic photosensitivity in mouse corneal epithelium
Authors: Lapajne Luka , Lakk Monika , Rudzitis Christopher N. , Vemaraju Shruti , Lang Richard A. , Hawlina Marko , Križaj David 
Published: November 2024

AbstractThe ocular surface protects the eye from pathogens, mechanical impact and harmful radiation. Excessive exposure of corneal epithelial (CE) layers to ultraviolet B (UVB) photons compromises these protective functions and may be associated with inflammation, pain, vision loss and cancer. We investigated the mechanisms that translate corneal epithelial (CE) transduction of UVB photons into intracellular and inflammatory signaling. Optical imaging in dissociated CECs and intact CE sheets showed rapid, UVB-induced increases in intracellular calcium concentration [Ca2+]ithat were partially reduced by the TRPV4 antagonist HC067047, removal of extracellular Ca2+and knockdown of the Trpv4 gene, and obliterated by depletion of internal calcium stores. Knockdown of neuropsin and inhibition of phospholipase C signaling markedly reduced the amplitude of the evoked calcium signal. UVB photons promoted release of cytokines and chemokines that included interleukins, metalloproteinases and thymic stromal lymphopoietin (TSLP). CECs are thus intrinsically photosensitive, utilizing a rhabdomeric-like phototransduction pathway cou0led to cytokine release to alert trigeminal afferents and stromal keratocytes about the presence of harmful irradiation and protect the visual system from snow blindness, injury, vision loss and cancer.
From Fear to Feast: Rattlesnakes Navigate the Landscape of Fear to Optimize Foraging
Authors: Da Cunha Oceane , Dominguez Rio P , Horne L. Miles , Mead Joshua J. , Fournier Corentin , Johnson Jerry D , Seymoure Brett M 
Published: November 2024

AbstractAccording to optimal foraging theory, mesopredators should forage in areas where their prey is abundant while avoiding high predation risk. Here, we investigate how environmental factors influence mesopredators’ abilities to minimize spatiotemporal overlap with predators while increasing spatiotemporal overlap with prey. We paired thirty western diamond-backed rattlesnake (Crotalus atrox) 3D-printed replicas with game cameras in West Texas for two years to quantify several spatiotemporal factors affecting prey availability and predation risk. Concurrently, 25Crotalus atroxwere radiotracked at the same site to gather activity and microhabitat selection data regarding free-ranging individuals. Random forest algorithms were trained using data obtained from the game camera and applied to predict the probability of predation and the probability of prey encounter for each radiotracking event. Time of day, month, vegetation structure, and concealment percentage, all had a significant association with the probability of predation and the probability of prey encounter. Our results suggest that rattlesnakes choose to be active when and where the probability of prey encounter was significantly higher than the probability of detection by predators, thus following optimal foraging theory. Our results demonstrate that mesopredators increase chances of prey capture while reducing predator detection in natural setting.
The mitochondrial methylation potential gates mitoribosome assembly
Authors: Glasgow Ruth I.C. , Singh Vivek , Peña-Pérez Lucía , Wilhalm Alissa , Moedas Marco F. , Moore David , Rosenberger Florian A. , Li Xinping , Atanassov Ilian , Saba Mira , Cipullo Miriam , Rorbach Joanna , Wedell Anna , Freyer Christoph , Amunts Alexey , Wredenberg Anna 
Published: November 2024

AbstractS-adenosylmethionine (SAM) is crucial for cellular processes, primarily serving as the principal methyl group donor of the cell and playing a key role in gene regulation and translation on the ribosome. Inside mitochondria, SAM-dependent methylations occur at several steps of gene expression, but their role and significance remain unclear. Using direct long-read RNA sequencing on mouse tissue and mouse embryonic fibroblasts, we demonstrate that the mitochondrial ribosomal gene cluster is not efficiently processed without mitochondrial SAM. This results in the accumulation of unprocessed ribosomal RNA precursors. Protein profiling of ribosome fractions revealed that these precursors are associated with processing and ribosome assembly factors, indicating stalling at an early stage. Structural analysis of the mitochondrial ribosome by cryogenic electron microscopy revealed that mitochondrial SAM is required during peptidyl transferase centre formation and mitochondrial ribosome assembly. Our data thus identify a critical role for methylation at two steps during mitochondrial gene expression.
A novel rhodopsin-based voltage indicator for simultaneous two-photon optical recording with GCaMP in vivo
Authors: Villette Vincent , Yang Shang , Valenti Rosario , Macklin John J. , Bradley Jonathan , Mathieu Benjamin , Lombardini Alberto , Podgorski Kaspar , Dieudonné Stéphane , Schreiter Eric R. , Abdelfattah Ahmed S. 
Published: November 2024

AbstractGenetically encoded voltage indicators (GEVIs) allow optical recording of membrane potential from targeted cellsin vivo. However, red GEVIs that are compatible with two-photon microscopy and that can be multiplexedin vivowith green reporters like GCaMP, are currently lacking. To address this gap, we explored diverse rhodopsin proteins as GEVIs and engineered a novel GEVI, 2Photron, based on a rhodopsin from the green algaeKlebsormidium nitens. 2Photron, combined with two photon ultrafast local volume excitation (ULoVE), enabled multiplexed readout of spiking and subthreshold voltage simultaneously with GCaMP calcium signals in visual cortical neurons of awake, behaving mice. These recordings revealed the cell-specific relationship of spiking and subthreshold voltage dynamics with GCaMP responses, highlighting the challenges of extracting underlying spike trains from calcium imaging.
Immunization with Plant-based Vaccine ExpressingToxoplasma gondiiSAG1 Fused to Plant HSP90 Elicits Protective Immune Response in Lambs
Authors: Campero Lucía M. , Gual Ignacio , Sander Valeria A. , Mendoza Morales Luisa F. , Ramos Duarte Victor A. , Formigo Paula M. , Sosa Emiliano , Lázaro Fermín , Scioli María Valeria , Atela Agustín , Legarralde Ariel , Hozbor Federico A. , Cantón Germán J. , Angel Sergio O. , Moore Dadín P. , Clemente Marina 
Published: November 2024

AbstractToxoplasma gondiiis a protozoan parasite causing toxoplasmosis, a principal concern for public health and livestock industries. Effective vaccination strategies are crucial for controlling toxoplasmosis, particularly in the lamb, which are significant reservoirs ofT. gondii. In addition, ovine toxoplasmosis also causes economic losses due to abortions and reproductive complications. In this study, we evaluated two immunization strategies to elucidate the immune protective potential of SAG1 fused to the plant Hsp90 adjuvant against experimental toxoplasmosis in lambs. We performed an oral administration of AtHsp81.2–SAG1HC-infiltrated fresh leaves homogenate (Plant Vaccine) and a subcutaneous administration of recombinant NbHsp90.3-SAG1HC produced inEscherichia coli(Recombinant Vaccine). Our results showed that only the Recombinant Vaccine significantly increased anti-rSAG1 total IgG values. In addition, only lambs immunized with the Plant Vaccine showed a significant increase in IFN-γ serum levels after the experimental infection (evaluated 8 days post-challenge). On the other hand, we also observed a statistically significant decrease in histopathological lesions (injury score) in challenged vaccinated lambs compared to challenged but not vaccinated animals (vehicle and control groups). Finally, to evaluateT. gondiiinfection, we choose the chimera rGra4-Gra7 as an acute phase protein marker. All lambs from the control and vehicle groups showed higher rates of serological reactivity than lambs from the vaccinated groups, concurrently with increased severity of lesions. These results suggest that both the plant-based and recombinant vaccines are promising candidates for controllingT. gondiiinfection in lambs, with potential benefits for enhancing public health and animal welfare.
Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome
Authors: Borodovich Tatiana , Wilson Jason S. , Bardy Pavol , Smith Muireann , Hill Conor , Khokhlova Ekaterina V. , Govi Bianca , Fogg Paul C.M. , Hill Colin , Shkoporov Andrey N. 
Published: November 2024

AbstractTransducing bacteriophages and gene transfer agents (GTA) are constrained by their capsids’ structural properties in the length of host DNA they can package. Nanopore sequencing of intact capsid-packaged DNA molecules with full-sized reads can be used to establish the precise lengths and identity of individual packaged DNA molecules and their association with specific bacterial hosts. This approach was validated using a few well-characterised transducing systems, and then applied to study bacterial DNA encapsidation in the faecal microbiomes from three healthy human donors. Bacterial DNA encapsidation appears to be widespread in the microbiome with up to 5.4% of capsid-packaged DNA in the gut virome being of bacterial (non-prophage) origin. Generalised transduction and GTA activity are especially prevalent in the families Oscillospiraceae and Ruminococcaceae, whereas an example of lateral transduction was observed in genus Bacteroides. In addition to that, induction of prophages in a variety of highly prevalent gut bacteria was observed.
BREASTFEEDING SUPPORT BASED ON SELF-CARE FORM PERSPECTIVE PHILOSOPHY OF SCIENCE: A LITERATURE REVIEW
Authors: Pertami Sumirah Budi , Pandin Moses Glorino Rumambo , Yunitasari Esti , Triharini Mira 
Published: November 2024

AbstractIntroductionFailure of the lactation process leads to decreased milk production, which is a serious problem especially regarding the health of the mother and child. Reduced milk production and failure to provide exclusive breastfeeding directly contribute to high infant morbidity.. Infants who are not breastfed can deteriorate their health and increase the risk of malnutrition and stunting. Breastfeeding mothers need the support of those closest to them, such as family members, friends, relatives and coworkers. The family, in this case the husband or parents, is considered the most capable party to influence the mother to maximize exclusive breastfeeding. Support from others or those closest to them plays a significant role in the success or failure of breastfeeding. The purpose of this study is to examine the philosophy of breastfeeding support from the perspective of the Self Care model theory.MethodsThis study used a literature review using the PICOS framework. Articles were searched from 3 databases namely Sciencedirect, Scopus, Sage. The keywords used in the literature search were breastfeeding AND support, AND self AND care AND theory AND model, AND postpartum. The search was limited to 2020-2024 publications, full articles, not review articles. The strategy used to search for articles using the PICOS framework. Then selected using the PRISMA diagram and obtained eleven articles. Quality assessment of eleven articles using the JBI Critical Appraisal tool.ResultsEleven articles describing the theoretical application of the Dhorothy Orem Self Care Model can be used as guidelines in providing self-care to improve breastfeeding support.Conclusiona more efficient strategy to increase breast milk production can be developed by understanding the self-care model. In addition, the self-care model can be applied in breasfeeding support by providing self-care to improve breastfeeding practices.
Autoimmune responses to myelin-associated proteins as diagnostic and prognostic biomarkers of relapsing-remitting multiple sclerosis: associations with human herpesvirus-6 and Epstein-Barr Virus reactivation
Authors: Vojdani Aristo , Almulla Abbas F. , Vojdani Elroy , Li Jing , Zhang Yingqian , Maes Michael 
Published: November 2024

AbstractBackgroundThe pathogenesis of relapsing-remitting multiple sclerosis (RRMS) is linked to autoimmune attacks against myelin proteins, and reactivation of Epstein-Barr virus (EBV) and human herpesvirus 6 (HHV-6). However, the connection between viral reactivation and autoimmune biomarkers has remained unclear.ObjectivesTo investigate immunoglobulin (Ig)G/IgA/IgM responses targeting myelin-related proteins in association with EBV and HHV-6 replication markers in RRMS.MethodsWe recruited 55 patients with RRMS and 63 healthy controls and assessed IgG/IgA/IgM responses against seven myelin-related components, as well as EBV nuclear antigen 1 (EBNA-1) and deoxyuridine-triphosphate nucleotidohydrolase (dUTPases). Disability was evaluated using the Expanded Disability Status Scale (EDSS) and disease progression using the Multiple Sclerosis Severity Score (MSSS).ResultsIgG/IgA/IgM levels targeting seven myelin-related proteins were significantly higher in RRMS than in controls. IgG against myelin basic protein (MBP) (IgG-MBP), IgM-myelin-associated glycoprotein (IgM-MAG)-37-60, IgA-MBP, and IgA-myelin-oligodendrocyte-glycoprotein (IgA-MOG-31-55) distinguished RRMS from controls with a predictive accuracy of 96.6% (sensitivity = 95.7%, specificity = 95.2%) and an area under the ROC curve of 0.991. A large part of the variance in the EDSS (around 75%) and MSSS score (62.8%) was explained by IgG-MBP, IgM-MBP, IgA-MOG-31-55, and IgM-MAG. Part of the variance (47.4%) in the IgG/IgA/IgM responses to myelin-related proteins was explained by immune responses to EBNA and deoxyuridine-triphosphate nucleotidohydrolases of EBV and HHV-6.ConclusionsAutoimmune reactivities targeting myelin-related proteins are valuable biomarkers of RRMS and the severity and progression of RRMS. Reactivation of EBV and HHV-6 may trigger or maintain these autoimmune responses thereby impacting disease progression.
Quantitative guiding of developmental cell fate transitions using gene-free modelling
Authors: Hajji Ismail , Siggia Eric D. , Corson Francis , Keil Wolfgang 
Published: November 2024

AbstractDuring development, cells gradually assume specialized fates via changes of transcriptional dynamics in thousands of genes. Terminal cell identities are then stabilized through the convergence of gene regulatory network dynamics and the accumulation of epigenetic DNA modifications. “Gene-free” (or geometric) modeling approaches for cell fate acquisition, which abstract from the underlying gene regulatory landscape and reason in phenotypic space, have been remarkably successful in explaining terminal fate outcomes. However, their implications for cellular dynamics during fate acquisition processes have so far not been testedin vivo. To do so, here we combine gene-free mathematical modeling of cell fate acquisition duringC. elegansvulval development with temporally controlled perturbations ofin vivosignaling dynamics using temperature sensitive (ts) mutant alleles of the EGF/Ras/MAPK and Notch signaling pathways. We show that gene-free modeling can quantitatively predict non-intuitive fate outcomes in a variety of ts genetic backgrounds, including pathway epistasis effects. In addition, we use gene-free modeling to infer how cell fate transitions can be guided towards specific outcomes through timed pulses of signaling activity and verify these model predictions quantitatively with temporally controlled signaling perturbations via temperature shifts in ts backgrounds. Our results highlight the predictive power of gene-free models beyond terminal fate outcomes and illustrate a new approach to quantitatively guide cell fate acquisition in a developmental context.
A nucleic acid prodrug activates mitochondrial respiration and extends lifespan
Authors: Anada Takahisa , Kawahara Michiharu , Shimada Taisei , Kuroda Ryotaro , Kage-Nakadai Eriko , Kobayashi Shingo , Tanaka Masaru 
Published: November 2024

AbstractMitochondrial dysfunction caused by aging leads to decreased energy metabolism, resulting in functional decline and increased frailty in multiple tissues. Strategies for protecting and activating mitochondria under stressful conditions are required to suppress aging and age-related diseases. However, it is challenging to develop drugs capable of boosting mitochondrial respiration and compensating for the reduced intracellular adenosine triphosphate (ATP) levels. In this study, we developed a prodrug that stimulates the metabolism of intracellular adenine nucleotides (AXP: adenosine monophosphate (AMP), adenosine diphosphate (ADP), and ATP). It enhances AMP-activated protein kinase activity, fatty acid oxidation, oxidative stress resistance, and mitochondrial respiration, thereby increasing the intracellular ATP levels. Furthermore, this prodrug markedly extended the lifespan ofCaenorhabditis elegans. The stimulation of the AXP energy metabolism (AXP stimulation) proposed in this study is expected to offer a new strategy against aging and pave the way for a novel approach in the bioenergetic molecules drug discovery.