bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix
Authors: Tang Chenwei , Sun Quan , Zeng Xinyue , Li Gang , Yang Xiaoyu , Liu Fei , Zhao Jinying , Shen Yin , Liu Boxiang , Wen Jia , Li Yun 
Published: September 2024

Abstract

Cell type-specific (CTS) analysis is crucial for uncovering biological insights hidden in bulk tissue data, yet single-cell (sc) or single-nuclei (sn) approaches are often cost-prohibitive for large samples. We introduce EPIC-unmix, a novel two-step empirical Bayesian method combining reference sc/sn and bulk RNA-seq data to improve CTS inference, accounting for the difference between reference and target datasets. Under comprehensive simulations, EPIC-unmix outperformed alternative methods in accuracy. Applied to Alzheimer's disease (AD) brain RNA-seq data, EPIC-unmix identified multiple differentially expressed genes in a CTS manner, and empowered CTS eQTL analysis.
Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation
Authors: Quinn Robert , Fu Yousi , Guzior Douglas , Okros Maxwell , Bridges Christopher , Rosset Sabrina , Gonzalez Cely , Martin Christian , Karunarathne Hansani , Watson Victoria 
Published: September 2024

Abstract

Conjugated bile acids (BAs) are multi-functional detergents produced in the gastrointestinal (GI) tract by the liver enzyme bile acid:amino acid N-acyltransferase (BAAT) and by the microbiome from acyltransferase activity of the ubiquitous enzyme bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in the dextran sodium sulfate (DSS) model of colitis using a BAAT knockout background. Baat-/- KO mice have severe phenotypes in the DSS model that were rescued by supplementation with taurocholate (TCA). Gene expression and histological analysis showed that this rescue was likely due to an improved epithelial barrier and goblet cell function. TCA supplementation also increased microbiome diversity, particularly the BA metabolizing Lachnospiraceae. Metabolomics showed that TCA supplementation in the DSS model increased all known forms of conjugated BAs including both host and microbial sources, but also their hydrolysis and metabolism to secondary BAs. The ability of TCA to improve pathology under DSS inflammation despite its ready hydrolysis led us to investigate the BSH activity of diverse gut bacteria on a panel of conjugated BAs in vitro and in vivo. Exposure of 17 gut bacterial isolates to a panel of 10 amino acid conjugated BAs showed broad hydrolytic capacity depending on the bacterium. Host-produced TCA and the MCBAs SerCA and AlaCA were readily hydrolyzed, whereas GluCA, AspCA and ThrCA were more resistant. This hydrolytic variability translated in vivo where mice fed the recalcitrant GluCA had less secondary BAs production in the DSS model compared to TCA. The complexity of microbial dysbiosis and conjugated BA metabolism in an inflamed murine gut led to the exploration of BSHs genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in the diseased states including that from Ruminococcus gnavus and Enterocloster clostridioformis in people with Crohn’s disease. Collectively, this study shows that the conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the BSH sequences present.
Polymorphism and whole-molecule disorder of an antitubercular 8- nitrobenzothiazinone
Authors: Seidel Rüdiger W. , Goddard Richard , Schlegel Tom U. , Richter Adrian , Rudolph Ines , Imming Peter 
Published: September 2024

Abstract

8-Nitrobenzo-1,3-thiazin-4-ones (BTZs) are a promising class of antitubercular agents with a novel mechanism of action, viz. suicide inhibition of decaprenylphosphoryl-β-d-ribose 2’-epimerase (DprE1), an enzyme crucial for cell wall synthesis in the pathogen Mycobacterium tuberculosis. 8-Nitro-2-(piperidin-1-yl)-6-(trifluoromethyl)-4H-benzo-1,3-thiazin-4-one (1) is a chemically simplified analogue of the anti-tuberculosis phase 2 clinical drug candidate BTZ-043. Structural elucidation of 1 in the solid-state has been carried out by X-ray crystallography and two polymorphic forms of 1 have been revealed. 1-I crystallizes in the triclinic system (space group P-1, Z = 6) with one molecule exhibiting whole-molecule disorder with a preferred orientation. The crystal structure of 1-II belongs to the tetragonal system (space group P43, Z = 4) and exhibits positional disorder in several parts of the molecule.
Physiologically Based Pharmacokinetic Modelling of the Co-administration of Ritonavir-Boosted Atazanavir and Rifampicin in Children Co-treated for HIV and Tuberculosis
Authors: Atoyebi Shakir , Montanha Maiara Camotti , Nakijoba Ritah , Orrell Catherine , Mugerwa Henry , Siccardi Marco , Denti Paolo , Waitt Catriona 
Published: September 2024

Abstract

Purpose
A dosing strategy for ritonavir-boosted atazanavir (ATV/r) to overcome the drug-drug interaction (DDI) effect with standard doses of rifampicin (10mg/ kg) was investigated in children aged between 7 and 18 years who were divided into 3 weight bands: 25-30 kg, 30-49 kg, and 50-70 kg.
Methods
We developed a paediatric physiologically-based pharmacokinetic (PBPK) model from a validated adult PBPK model with the necessary DDI components. The paediatric PBPK model was validated using relevant clinical data of ATV/r alone and rifampicin alone in children.
Results
Dose escalation to twice-daily dosing of ATV/r was predicted to boost ATV Ctrough adequately. With ATV/r 300/100 mg twice daily dosing in the presence of standard doses of rifampicin, predicted ATV Ctrough was higher than 150 ng/ml in over 90% of the paediatric population.
Conclusions
This model results suggests ATV/r 300/100 mg twice daily could maintain sufficient concentrations for antiviral efficacy when co-administered with standard dose of rifampicin taken once daily in children between 7 and 18 years. However, clinical studies are still warranted to confirm safety and efficacy of the dose escalation in children.
Comparative analysis of EGFR mutations between circulating tumor DNA and tissue samples in non-small cell lung carcinoma patients using BEAMing PCR: results of a single institutional observational study
Authors: Mirikar Duhita , Banerjee Nandini , Prabhash Kumar , Kaushal Rajiv Kumar , Naronha Vanita , Pramesh CS , Karimundackal George , Joshi Amit , Rane Swapnil , Basak Ranjan 
Published: September 2024

Abstract

In this study we measured the human epidermal growth factor receptor (EGFR) mutations in both tissue and circulating tumor DNA (ctDNA) by using beads, emulsion, amplification and magnetics polymerase chain reaction (BEAMing PCR). Noninvasive mutation detection by assessing circulating tumor DNA (ctDNA) offers many advantages over tumor biopsy. One hundred non-small cell lung cancer (NSCLC) patients were enrolled and both preoperative plasma samples and formalin-fixed and paraffin embedded (FFPE) samples were collected for the study. EGFR mutation status was determined by BEAMing PCR in ctDNA. Real-time quantitative PCR (qPCR) data were collected from our hospital database (EMR-qPCR, Electronic Medical Records) for comparative analysis. Additionally, qPCR was also done from FFPE tissues using Diatech EGFR qPCR kit. The positive concordance rate was 98.8%, 100% and 95.5% for exon 19, 20 and 21 respectively when BEAMing data were compared with EMR-qPCR data. Additionally, when BEAMing and Diatech qPCR data were compared we obtained 90%, 100%, 96% and 98% respectively for exon 19, 20, 21 (L858R) and 21 (L861Q). For both the comparisons, the value of Cohen’s kappa agreement showed significant results. The advantage of BEAMing is its ability to identify mutated DNA sequence in the cancer cells in the background of normal cell DNA contamination. This could be useful for disease monitoring and progression.
Associations between the lockdown group, free memory recall, and emotional responses during the COVID-19 lockdown: A global survey of 49 countries
Authors: Oyejide AO , Besharati SN , Alcock S , Schioth HB , Brooks SJ 
Published: September 2024

Abstract

The unprecedented outbreak of the COVID-19 pandemic has altered the course of many lives, resulting in multiple health and social challenges. Due to the speed at which this pandemic spread, various public health ‘lockdown’ measures were introduced to mitigate its spread. The outcome of adherence to these measures has revealed the possible influence on individuals’ varying cognitive abilities. Accordingly, this study aimed to explore the predictive relationships between lockdown responses and COVID-19 restrictions, memory recall performance, and associated emotional responses while examining the sociodemographic influences of age and sex. Participants were drawn from a secondary dataset of an international online survey study of 1634 individuals aged 18–75 years across 49 countries. Participants’ demographic questionnaires, free memory recall, and hospital anxiety and depression scale scores were used to collect the data for analysis. Four-way MANOVA and hierarchical multiple regression were utilised to explore the mean differences and predict relationships between the study variables. Significant differences were found in memory recall performance and anxiety and depression scores across lockdown groups (the comply, sufferer, and defiant). Regression analysis indicated that age and gender were predictive markers of lockdown responses and anxiety (R2 = .14, F4,1625 = 66.15, p < .001, f2 = 0.17), while age was the only predictor of lockdown responses and depression association (b = -0.78, t(1625) = -4.35, p < .001). Lockdown compliance was associated with better free recall (M = 8.51, SD = 6.38, p < .001; 𝜂2 = .01), lockdown suffering was associated with greater anxiety (M = 9.97, SD = 4.36, p < .001; 𝜂2 = .06), and lockdown deviance was associated with greater depression (M = 7.90, SD = 3.12, p < .001; 𝜂2 = .05). The current study provides valuable information on the mechanisms of cognitive interpretations and emotional arousal in individuals’ social isolation responses to recent life stress and potential severe pandemics. This may support the need for robust interventions aimed at improving people’s psychological appraisals associated with anxiety in preparation for any new potential waves or future pandemics.
Buccal Mucosa Glansoplasty as a Salvage Procedure for a Circumcision-Related Glans Amputation in an Infant: A Case Report and Literature Review
Authors: OBENG FRANK , ADAMU AISHAH FADILAH , Whittal •	Karen Michelle A. , Adanu F MPH MD •	Kekeli Kodjo , AYAMBA ALI M. 
Published: September 2024

Abstract

Introduction:
Accidental glans amputation during circumcision is a rare but devastating complication, especially in neonates and infants. Salvage procedures such as buccal mucosa glansoplasty are critical in restoring anatomical and functional integrity.
Case Presentation:
We report a case of an 11-week old infant who sustained a partial glans amputation during circumcision by a retired health personnel. After presenting to us, the patient underwent immediate salvage surgery using buccal mucosa graft for glans reconstruction and meatoplasty. Postoperative recovery was uneventful, with satisfactory cosmetic and functional outcomes.
Conclusion
Buccal mucosa glansoplasty is a viable option for the salvage of glans amputation in neonates, providing both functional and aesthetic restoration.
Anatomic-radiological feasibility of transorbital magnetic resonance imaging-guided laser interstitial thermal therapy (MRIgLITT) for amygdalohippocampectomy in refractory epilepsy
Authors: Valdivia Doriam Perera , Somma Alberto Di , Arboix Jordi Rumià , Manfrelloti Roberto , Gagliano Dario , Mosteiro Alejandra , Canto Santiago Candela , Nora Joaquim Enseñat , Ferrés Abel , López Lorena Gómez , Prats-Galino Alberto , Ramos Pedro Roldán 
Published: September 2024

Abstract

OBJECTIVE: to study the anatomical feasibility of laser fiber insertion for interstitial thermal therapy via transorbital approach to the temporo-mesial structures (amygdala-hippocampus-parahippocampus complex)
METHODS: Anatomical dissections were performed on two human cadaveric heads via a transorbital approach, in which screws and laser fibers were used for magnetic resonance imaging-guided laser interstitial thermal therapy (MRIgLITT) assisted by neuronavigation. In addition, eight transorbital trajectories were simulated using the transorbital entry points obtained from a cadaveric radiological study of four patients previously operated on for mesial temporal lobe epilepsy.
RESULTS: The placement of all four laser fibers was successfully achieved in the anatomical specimens according to the established plan, with an average vectorial error of 1.3 ± 0.2 mm, and a complete coverage of the amygdala-hippocampus-parahippocampus complex. In addition, safe vascular trajectories were confirmed in the simulations of live patient trajectories. We found an ideal transorbital entry area in the inferolateral quadrant of the orbit, on the lateral wall of the orbit, over the greater wing of the sphenoid, between 15 and 20 mm lateral to the superior portion of the inferior orbital fissure, and between 5 and 10 mm superior to the inferior portion of the inferior orbital fissure.
CONCLUSIONS: Placement of a transorbital laser fiber for MRIgLITT of the temporomesial structures for epilepsy is feasible; however, the small size of the laser fiber-anchoring screw currently precludes its use in clinical practice.
Do Demographic Factors Influence Pre-retirement Anxiety Among Civil Servants Near Retirement in Southwest Nigeria?
Authors: Fagbenro Dare A. , Olasupo Mathew O. , Alliu Sadiat I. 
Published: September 2024

Abstract

The study examined the influence of demographic factors (gender, job cadre and educational qualification) on pre-retirement anxiety among civil servants near retirement in Southwest Nigeria. A sample of 413 respondents aged 45 to 60 (Mean = 53.55 years: SD = 3.18) was selected through a multi-stage sampling technique. The participants responded to a bio-data and Pre-Retirement Anxiety Scale (NPAS). The hypotheses postulated were analysed using t-test for independent measure and one-way analysis of variance (ANOVA).
The result showed that gender has no direct influence on pre-retirement anxiety (social alienation, social obligation and financial preparedness). The study found that junior cadre influence pre-retirement anxiety (social alienation and financial preparedness). The result also revealed that respondents who had OND/NCE certificate impacted pre-retirement anxiety (financial preparedness). The study concluded that employees who are junior staff and who had OND/NCE qualification experience higher pre-retirement anxiety. The study recommended that job cadre and educational qualification of prospective retirees must be given adequate attention in a way to reduce the challenge of pre-retirement anxiety (social alienation and financial preparedness).
Assessment of Groundwater quality for drinking water purposes in Sub-Saharan Africa environment: the case study of Ebolowa City Council, Cameroon (Central Africa)
Authors: Mvongo Victor Dang 
Published: September 2024

Abstract

The present study was carried out to evaluate the groundwater quality and its suitability for domestic purposes in the Ebolowa City Council (ECC). The groundwater quality in ECC has been evaluated based on the Water Quality Index (WQI). A total of 15 groundwater samples were collected, and their physical parameters (temperature, pH, EC, TDS, and TSS) and microbial content (fecal coliforms, fecal streptococci, and Total Coliforms) were analyzed using standard methods. The results indicated that the physical characteristics of the water (temperature range from 24°C to 30 °C; pH range from 3.7 to 5.6; EC range from 114 μS/cm to 1,818 μS/cm; TDS range from 54 mg/L to 913 mg/L; TSS range from 0 mg/L to 24 mg/L) were within WHO guidelines for potability except for the temperature, EC, and TSS. The chemical characteristics of groundwater (NO3- range from 0 mg/L to 19.8 mg/L; NH4+ range from 0.2 mg/L to 12.9 mg/L) were also within WHO guidelines for potability, except for NH4+. The fecal Coliforms ranged from 1 to 51 CFU/100 ml, while the fecal streptococci ranged between 0 and 25 CFU/100 ml. The concentration of Total Coliform is between 2.0 and 84.0 CFU/100 ml. The groundwater quality index reveals that ten samples out of fifteen have water unfit for consumption, three are very poor, and one is poor.
Development and validation of experimental induction tasks for worry and rumination: A comparison of scripted and personalized approaches
Authors: Kim Hanjoo , Newman Michelle 
Published: September 2024

Abstract

Worry and rumination are two forms of repetitive negative thoughts. Prior studies have identified similarities and differences between these two states. For a more comprehensive understanding of these thought processes, researchers need reliable methods to induce them experimentally. Traditionally, researchers have used either scripted or personalized approaches to trigger worry and rumination, but it remains unclear which method is more effective. Additionally, the potential impact of preexisting disorders like generalized anxiety disorder (GAD) or major depression (MDD) on these inductions is not well understood. This study aimed to compare scripted and personalized induction methods to identify which was more effective for eliciting worry and rumination, while also considering the potential influence of generalized anxiety and depression. Participants (N = 355) included individuals with GAD, depression, or healthy controls. They were randomly assigned to either scripted or personalized induction tasks designed to induce worry or rumination. Findings revealed that personalized induction methods were consistently more effective than scripted methods for inducing both worry and rumination, regardless of participants' group characteristics. In addition to the general underperformance of scripted induction methods, the scripted rumination induction was notably less successful, failing to induce rumination to a greater extent than the scripted worry induction. Given these findings, personalized approaches are recommended for experimental studies that aim to compare worry and rumination. Limitations of the study and implications for future research are also discussed.
Research on neonatal conditions in Africa: volume, impact, thematic spectrum, and collaboration from a bibliometric perspective
Authors: Vieira Elizabeth 
Published: September 2024

Abstract

The literature has addressed the negative impact of poor neonatal conditions (NC) across regions. This has drawn attention to the need to improve NC, particularly in Africa. NC research can make an important contribution. However, there is no study dedicated to this topic in Africa. Through a bibliometric analysis, we arrive at outputs that can inform scientists in planning ongoing or new NC research and those involved in developing and implementing strategies to combat poor NC. Using bibliometrics, the study identified the scientific knowledge on NC between 2000 and 2019, its visibility in the community, the main topics researched, and collaboration patterns. The results show that knowledge on NC has increased between 2000 and 2019, it is concentrated in a few African countries (Egypt, South Africa, Nigeria, Tanzania and Kenya), its visibility is below the world average, in general, maternal mortality is the most researched topic and collaborative activities are frequently, mainly international research collaboration (IRC), being the United States of America (USA) and the United Kingdom (UK) the main partners (they participated in 57% and 28% of all articles with IRC). The collaboration networks are fragile as 43%-67% of all links represent one article in 20 years. Ongoing or new research on NC in Africa should consider the main African players and their partners. There is a need to implement strategies to increase NC knowledge in other African countries, expand and strengthen the collaboration networks and diversify the sources of knowledge.
Investigating In silico and In vitro Therapeutic Potential of Diosmetin as the Anti-Parkinson Agent
Authors: Varshney Krishna Kumar , Gupta Jeetendra Kumar , Srivastava Rajnish 
Published: September 2024

Aim:
This study aimed to investigate how diosmetin interacts with seven target receptors
associated with oxidative stress (OS) and validate its antioxidant properties for the potential
management of Parkinson’s disease (PD).

Background:
In PD, the degeneration of dopaminergic cells is strongly influenced by OS. This
stressor is intricately connected to various mechanisms involved in neurodegeneration, such as mitochondrial
dysfunction, neuroinflammation, and excitotoxicity induced by nitric oxide.

Objective:
The aim of this research was to establish a molecular connection between diosmetin
and OS-associated target receptors was the goal, and it investigated how this interaction can lessen
PD.

Methods:
Seven molecular targets - Adenosine A2A (AA2A), Peroxisome Proliferator-Activated
Receptor Gamma (PPARγ), Protein Kinase AKT1, Nucleolar Receptor NURR1, Liver - X Receptor
Beta (LXRβ), Monoamine Oxidase - B (MAO-B) and Tropomyosin receptor kinase B (TrkB)
were obtained from RCSB. Molecular docking software was employed to determine molecular interactions,
while antioxidant activity was assessed through in-vitro assays against various free radicals.

Results:
Diosmetin exhibited interactions with all seven target receptors at their binding sites.
Notably, it showed superior interaction with AA2A and NURR1 compared to native ligands, with
binding energies of -7.55, and -6.34 kcal/mol, respectively. Additionally, significant interactions
were observed with PPARγ, AKT1, LXRβ, MAO-B, and TrkB with binding energies of -8.34,
-5.42, -7.66, -8.82, -8.45 kcal/mol, respectively. Diosmetin also demonstrated antioxidant activity
against various free radicals, particularly against hypochlorous acid (HOCl) and nitric oxide (NO)
free radicals.

Conclusion:
Diosmetin possibly acts on several target receptors linked to the pathophysiology of
PD, demonstrating promise as an OS inhibitor and scavenger.