bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital Anal Rectal Examination Usage Among Individuals at Increased Risk for Anal Cancer
Authors: Nyitray Alan G. , Ridolfi Timothy J. , Nitkowski Jenna , McAuliffe Timothy L. , Deshmukh Ashish A. , Giuliano Anna R. , Chiao Elizabeth Y. ,   The Prevent Anal Cancer Self-Swab Study Team
Published: June 2023

Objective
Multiple organizations recommend an annual digital anal rectal examination (DARE) for people at highest risk for anal cancer. The authors assessed DARE usage among sexual minority men and transgender women.

Methods
Community-recruited and asymptomatic individuals from a mid-sized US city were enrolled into the Prevent Anal Cancer Self-Swab Study, a longitudinal clinical trial of anal cancer screening. Self-reported data from the baseline survey were used to assess usage of DARE in the last year and during the lifetime. Adjusted odds ratios (aORs) and CIs for factors associated with each outcome were determined using multivariable logistic regression.

Results
Among 241 participants, median age was 46 years (interquartile range, 33–57 years), 27.0% were living with HIV, and 24.5% reported a previous diagnosis of anal warts. A total of 13.7% (95% CI = 9.4%–18.0%) of individuals reported a DARE in the previous year, whereas 53.9% (95% CI = 47.7%–60.2%) reported a DARE during the lifetime. The following were associated with a DARE in the previous year: increasing age (aOR = 1.04; 95% CI = 1.01–1.08 for each additional year), any previous anal cytology (aOR = 2.62; 95% CI = 1.19–5.80, compared with no previous test or no knowledge of a test), and preferred receptive position during anal sex (aOR = 4.93; 95% CI = 1.17–20.86 compared with insertive)

Conclusions
Despite guidelines recommending an annual DARE, it was uncommonly reported. There is an urgent need to understand barriers to conducting DARE among individuals most vulnerable to anal cancer and their health care providers.
Does the New National Cervical Screening Programme Guideline Detect Cases of High-Grade Squamous Intraepithelial Lesions That Previously Would Have Been Missed?
Authors: Pontré Jennifer C. , Nathan Elizabeth , Goldsmith Hilary , McElhinney Bernadette 
Published: June 2023

Objective
The aim of this study was to determine the number of patients undergoing large loop excision of the transformation zone (LLETZ), for biopsy-confirmed high-grade squamous intraepithelial lesions (HSIL), where the original cervical screening test (CST) reported oncogenic human papillomavirus (HPV) and negative liquid-based cytology (LBC). This reflects the number of patients where a LLETZ procedure would not have occurred under the previous guideline.

Methods
Retrospective observational chart review of all patients (n = 477) who underwent LLETZ procedure in a single tertiary unit over a 36-month period. Prevalence of negative histopathology, positive margins, incidental cervical cancer, and accuracy of HSIL identification at colposcopy were measured. Diagnostic accuracy of HSIL diagnosis from initial colposcopic impression was calculated; factors influencing accuracy were evaluated using multivariable logistic regression analysis. There were no comparators.

Results
Of 477 LLETZs, 5.9% (n = 28) were for oncogenic HPV and normal LBC on referral CST. Demographics between the “study” (oncogenic HPV and normal LBC on referral CST) and the “standard” group were similar, except the study group was less likely to be using contraception (25% vs 47%, p = .023). In the study group, initial colposcopic cervical biopsy confirmed HSIL in 91.6% (n = 27) and low-grade squamous intraepithelial lesions in 3.6% (n = 1). Histopathological analysis of LLETZ specimens confirmed HSIL in 20 patients (71.4%) and low-grade squamous intraepithelial lesions in 2 (7.1%). No microinvasion was detected.

Conclusions
The renewed National Cervical Screening Programme (NCSP), is detecting more “at risk” patients, predicted to lead to a further reduction in incidence of cervical cancer in adequately screened patients.
MARCH9 Mediates NOX2 Ubiquitination to Alleviate NLRP3 Inflammasome-Dependent Pancreatic Cell Pyroptosis in Acute Pancreatitis
Authors: Lin Min , Jin Yuzhou , Wang Fushuang , Meng Yao , Huang Jin , Qin Xihu , Fan Zhining 
Published: June 2023

Objective
The pathogenesis of acute pancreatitis mainly involves NLRP3 inflammasome-mediated pancreatic cell injury, although regulators of this inflammasome machinery are still not fully identified. Membrane-associated RING-CH 9 (MARCH9) is a member of MARCH-type finger proteins, which regulates innate immunity through catalyzing polyubiquitination of critical immune factors. The aim of present research is to examine the function of MARCH9 in acute pancreatitis.

Methods
Cerulein-induced acute pancreatitis was established on pancreatic cell line AR42J and rat model. Reactive oxygen species (ROS) accumulation and NLRP3 inflammasome-dependent cell pyroptosis in pancreas were examined by flow cytometry.

Results
MARCH9 was downregulated by cerulein, but overexpressing MARCH9 could inhibit NLRP3 inflammasome activation and ROS accumulation, thus suppressing pancreatic cell pyroptosis and mitigating pancreatic injury. We further uncovered that the mechanism underlying such an effect of MARCH9 is through mediating the ubiquitination of NADPH oxidase-2, whose deficiency reduces cellular ROS accumulation and inflammasome formation.

Conclusions
Our results suggested that MARCH9 suppresses NLRP3 inflammasome-mediated pancreatic cell injury through mediating the ubiquitination and degradation of NADPH oxidase-2, which compromises ROS generation and NLRP3 inflammasomal activation.
Impact of Scoliosis Severity on Gastrostomy-Related Complications in Children
Authors: Toker Kurtmen Bade , Nalli Aslihan , Oztan Mustafa Onur , Koyluoglu Gokhan 
Published: June 2023

Objectives:
This study aimed to determine the relationship between scoliosis and risk of developing complications in patients who underwent gastrostomy.

Methods:
Patients who underwent percutaneous endoscopic gastrostomy (PEG) or surgical gastrostomy (SG) between 2012 and 2022 were included. Leakage, discharge, granuloma, and hyperemia were considered minor complications, while visceral injury, ileus, and re-do surgery were considered major complications. The degree of scoliosis was calculated using the Cobb angle. The SG and PEG groups were compared by evaluating the complications and their correlation with scoliosis.

Results:
A total of 104 patients with a mean age of 5.0 ± 5.3 were included; 58% of patients were treated with SG. Patients in the SG group were younger (P < 0.001). Minor complications were significantly more common in the PEG group (P = 0.018). There was no difference between the groups in terms of major complications (P = 1.000). Scoliosis was observed in 32.7% of the patients (n = 34). In the SG group, no correlation was found between the Cobb angle and the frequency of minor (P = 0.173) or major complications (P = 0.305). There was no significant difference between the Cobb angles of patients with and without minor complications in the PEG group (P = 0.478); the Cobb angles of patients with major complications (75°) were significantly higher than those without (36°) (P = 0.030).

Conclusion:
Gastrostomy is important for weight gain and nutritional needs of children. This study showed that the risk of complications in SGs did not correlate with the degree of scoliosis and that the risk of major complications in PEGs increased in patients with a high degree of scoliosis.
Pain sensation and gut microbiota profiles in older adults with heart failure
Authors: Chen Jie , Wang Zequan , Starkweather Angela , Chen Ming-Hui , McCauley Paula , Miao Hongyu , Ahn Hyochol , Cong Xiaomei 
Published: June 2023

Abstract

Objectives:
Heart failure (HF) patients experience severe pain and may have altered pain sensation, however, the underlying mechanisms of these symptoms are not yet fully understood. Identifying pain sensation and genomic biomarkers of pain in older adults with HF is a critical step toward developing personalized interventions to improve pain management and outcomes. This study aimed to investigate the differences in pain sensation, gut microbiota, and self-reported pain and symptoms in older adults with and without HF.

Methods:
Twenty older adults with HF and age-matched healthy controls (HCs) were recruited in Northeastern U.S. Quantitative sensory testing (QST) and conditioned pain modulation (CPM) were performed on the non-dominant upper arm to detect the mechanical, thermal, and pressure pain thresholds and pain modulations. Stool samples were collected and the 16S rRNA V4 gene region of stool samples was sequenced and processed using the Mothur 1.42.3 pipeline. Self-reported pain and symptoms were measured by the brief pain inventory (BPI) and the NIH Patient-Reported Outcomes Measurement Information System (PROMIS). The associations between pain sensation, gut microbiota α-diversity indices, and pain and symptoms were explored using Spearman correlations.

Results:
The HF and HC subjects’ mean ages were 73.50 (SD=8.33) and 67.10 (SD=7.64), respectively. The HF participants reported significantly higher pain intensity and interference, sleep disturbance, fatigue, anxiety, and depression than the HCs. The HF subjects also had a significantly lower level of physical function and participation in social roles and activities. Compared to the HCs, the HF subjects had significantly altered conditioned pain modulation heat effect and gut microbiota compositions and predicted metabolic functions. The Statistical Analysis of Metagenomic Profiles (STAMP) indicated that the HF subjects had a significantly decreased cardiac muscle contraction pathway compared with the HCs. The correlation analysis showed that the QST profiles and gut microbiota diversity index were significantly associated with pain and symptoms in older adults with HF.

Conclusions:
Older adults with HF had more severe self-reported pain and symptoms, altered pain sensation, and different gut microbiota composition and function compared to age-matched HCs. Pain sensation and gut microbiota may contribute to pain and symptoms in older adults with HF and could serve as biomarkers of pain and symptoms of HF. Further research with a larger sample size is warranted to confirm these findings.
DQA1 Eplet Mismatch Load As an Independent Risk Factor of CLAD After Lung Transplantation
Authors: González-López Elena , Mora-Cuesta Víctor M. , Roa-Bautista Adriel , Comins-Boo Alejandra , Renaldo André , Irure-Ventura Juan , Iturbe-Fernández David , Tello-Mena Sandra , San Segundo David , Cifrián-Martínez José , López-Hoyos Marcos 
Published: June 2023

Background.
Lung transplantation remains the treatment of choice for end-stage lung diseases, and recipient selection is currently based on clinical urgency, ABO compatibility, and donor size. The risk of allosensitization is classically based on HLA mismatch, but eplet mismatch load is increasingly seen to be important in long-term outcomes in solid organ transplantation. Chronic lung allograft dysfunction (CLAD) is relatively common and relevant, affecting almost 50% of patients 5 y after transplantation and being the first cause of death from the first year after transplantation. The overall class-II eplet mismatch load has been associated with CLAD development.

Methods.
Based on clinical data, 240 lung transplant recipients were eligible for CLAD, and HLA and eplet mismatch was analyzed using the HLAMatchmaker 3.1 software.

Results.
A total of 92 (38.3%) lung transplant recipients developed CLAD. The time free-of-CLAD was significantly decreased in patients with presence of DQA1 eplet mismatches (P = 0.015). Furthermore, when other previously described CLAD risk factors were studied in a multivariate analysis, the presence of DQA1 eplet mismatches was found to be independently associated with the early onset of CLAD.

Conclusions.
The concept of epitope load has arisen as a new tool to better define donor–recipient immunologic compatibility. The presence of DQA1 eplet mismatches potentially would increase the likelihood of developing CLAD.
Normal Blood Pressure in Healthy Adult Eritreans
Authors: Noury Ahmed O , Bakhit Barakat M , Osman Montasir A , Musa Omer A. 
Published: June 2023

AbstractBackground and objectivesBlood pressure levels may vary because of genetic, ethnic, and socioeconomic factors. To date, there have been no large national studies in Eritrea on blood pressure. Therefore, we sought to establish a representative blood pressure reference interval for Health adult EritreansMethodsThe study included a sample of 942 healthy Eritrean individuals aged between 18 and 60 years, comprising 331 males and 611 females. The participants were selected from households located in the cities of Asmara, Keren, and Mandafara. Anthropometric measurements and clinical data were collected from each participant. Blood pressure was measured twice using a standardized procedure.Results942 healthy adults were included, 331 (35.1 %) were males with an average age of 40, and 611 (64.9%) were females, with an average age of 41, with an age range of 18-60 years. Median blood pressure for males was 120/78 mmHg, while the Median blood pressure for female was 118/78 mmHg for femaleConclusionThe values of blood pressure were similar to international values of blood pressure and there was significantly higher blood pressure in males than in females.
Prestimulus neural variability affects behavioral performances mediated by poststimulus-evoked responses at the intraindividual and interindividual levels
Authors: Jiang Zeliang , An Xingwei , Liu Shuang , Yin Erwei , Yan Ye , Ming Dong 
Published: June 2023

AbstractThere are significant intra-individual and inter-individual variabilities in audiovisual temporal perception. Previous studies have shown that prestimulus neural variability could reflect behavioral variabilities. We aimed to investigate whether prestimulus neural variability can predict behavioral variability in audiovisual temporal perception. Furthermore, We also explored whether prestimulus neural variability directly influences behavioral responses or indirectly impacts perceptual decisions through post-stimulus-evoked responses. We analyzed the electroencephalography (EEG) data from a paradigm where the twenty-eight human subjects performed a simultaneity judgment (SJ) task in the beep-flash stimulus. The prestimulus weighted permutation entropy (WPE) was the indicator of neural variability in this study. We found that prestimulus frontal WPE could predict the individual’s TBW in auditory- and visual-leading conditions. In addition, increased prestimulus parietal WPE was associated with more asynchronous responses. Prestimulus frontal WPE may be associated with top-down cognitive control, while parietal WPE may be related to bottom-up cortical excitability. Furthermore, poststimulus evoked responses could mediate the relation between prestimulus WPE and the individual’s TBW or perceptual responses. These results suggested that prestimulus WPE was a marker in reflecting intra-individual and inter-individual variabilities in audiovisual temporal perception. Significantly, prestimulus WPE might influence perceptual responses by affecting poststimulus sensory representations.
A Deep Learning Approach for Modelling the Complex Relationship between Environmental Factors and Biological Features
Authors: Tripathi Devashish , Basu Analabha 
Published: June 2023

AbstractEnvironmental factors play a pivotal role in shaping the genetic and phenotypic diversity among organisms. Understanding the influence of the environment on a biological phenomenon is essential for deciphering the mechanisms resulting in trait differences among organisms. In this study, we present a novel approach utilizing an Artificial Neural Network (ANN) model to investigate the impact of environmental factors on a wide range of biological phenomena. Our proposed workflow includes hyperparameter optimization using model-based methods such as Bayesian and direct-search methods such as Random Search, and a new approach combining random search and linear models (RandomSearch+lm) to ensure a robust ANN architecture. Moreover, we employed a generalized version of the variable importance method to generate the feature importance metric using estimated weights from ANN. By applying this comprehensive ANN-based approach to functional genomics, we can gain valuable insights into the mechanisms underlying trait differentiation in organisms, while simultaneously enabling prediction and feature selection tasks. This methodology provides a robust and efficient framework for studying the complex relationships between environmental factors and biological features in biological systems.
Design, Synthesis, Molecular Docking and Biological Activity of Pyrazolo[3,4-b]pyridines as Promising Lead Candidates AgainstMycobacterium tuberculosis
Authors: Rao H. Surya Prakash , Gunasundari R. , Adigopula Lakshmi Narayana , Muthukumaran Jayaraman 
Published: June 2023

AbstractPyrazolo[3,4-b]pyridine is a medicinally privileged structure. We have achieved a new and facile synthesis of a combinatorial library of its tetra- and persubstituted derivatives by trifluoracetic acid catalysed condensation of a group of 5-aminopyrazoles and a group of α-oxoketene dithioacetals. Furthermore, we demonstrated structural modification of the products via reductive desulfurization, hydrolysis of the ester and Suzuki coupling of the bromo derivative with aryl bornoic acids. Some of the products were subjected toin vitroMABA assay againstM. tuberclulosisH37Rv strain andin silicoanalysis by binding to pantothenate synthetase fromM. tuberclulosis(MTBPS). The results indicated that the pyazolo[3,4-b]pyridine with N(1)CH3, C(3)C6H5, C(4)pCH3C6H5, C(5)CO2Et, C(6)SMe substitutions exhibits promising antituberculotic activity.
Generation of Super-resolution Images from Barcode-based Spatial Transcriptomics Using Deep Image Prior
Authors: Park Jeongbin , Cook Seungho , Lee Dongjoo , Choi Jinyeong , Yoo Seongjin , Im Hyung-Jun , Lee Daeseung , Choi Hongyoon 
Published: June 2023

AbstractSpatial transcriptomics (ST) has revolutionized the field of biology by providing a powerful tool for analyzing gene expressionin situ. However, current ST methods, particularly barcode-based methods, have limitations in reconstructing high-resolution images from barcodes sparsely distributed in slides. Here, we present SuperST, a novel algorithm that enables the reconstruction of dense matrices from low-resolution ST libraries. SuperST based on deep image prior reconstructs spatial gene expression patterns as image matrices. SuperST allows gene expression mapping to better reflect immunofluorescence (IF) images. Compared with previous methods, SuperST generated output images that more closely resembled IF images for given gene expression maps. Additionally, SuperST overcomes the limitations inherent in IF images, highlighting its potential applications in the realm of spatial biology. By providing a more detailed understanding of gene expressionin situ, SuperST has the potential to contribute to comprehensively understanding biology from various tissues.
A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and asymptomatic bacteria
Authors: Flores Carlos , Ling Jefferson , Loh Amanda , Maset Ramón Garcia , Aw Angeline , White Ian J. , Fernando Raymond , Rohn Jennifer L. 
Published: June 2023

AbstractUrinary tract infection is among the most common infections worldwide, and is typically studied in animals and cell lines with limited uropathogenic strains. Here, we assessed diverse bacterial pathogens and asymptomatic bacteria (ASB) in a human urothelial microtissue model including full stratification/differentiation and urine tolerance. Several uropathogens and ASB-likeE. coliinvaded intracellularly, suggesting invasion is a shared survival strategy, instead of a virulence hallmark. TheE. coliadhesin FimH was required for intracellular community formation, but not for invasion. Other shared lifestyles included filamentation (Gram-negatives), chaining (Gram-positives) and hijacking of exfoliating cells, while biofilm-like aggregates formed mainly withPseudomonasandProteus. Urothelial cells expelled invasive bacteria in Rab-/LC3-decorated structures, while highly cytotoxic/invasive uropathogens, but not ASB, disrupted host barrier function and strongly induced exfoliation and cytokine production. Overall, this work highlights diverse species-/strain-specific infection strategies and corresponding host responses in a human urothelial microenvironment, providing insights at the tissue, cell and molecular level.One-Sentence SummaryA human urothelial model revealed shared colonization strategies between uropathogens and asymptomatic bacteria, and pathogen-specific innate immune responses
Variations in Homoeologous Dosage and Epigenomics Mark the Early Evolution of SyntheticBrassicaTetraploids
Authors: Zhang Kang , Yang Yinqing , Zhang Lei , Cui Yinan , Wu Jian , Liang Jianli , Li Xing , Zhang Lingkui , Zhang Xin , Zhang Yiyue , Guo Zhongwei , Chen Shumin , Freeling Michael , Wang Xiaowu , Cheng Feng 
Published: June 2023

ABSTRACTPolyploidization is important in plant evolution and is becoming increasingly important in crop breeding and material creation. Studies have provided evidence for structural variations and epigenomic repatterning in synthetic polyploidizations, but the relationships between structural and epigenomic variations, as well as their effects on gene expression and phenotypic variations are unknown. Here, we investigated the genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics, in the leaf organ as a representative, of progenies from eight generations that derived from the synthetic tetraploidization betweenBrassica rapaandBrassica oleracea. We found that half or complete deletion/duplication of fragments ranging in size from 400 kb to 65.85 Mb, with a mean size of 5.70 Mb, occurred frequently from the first generation of selfing and thereafter. The genes located in these DelDups expressed at levels expected for a positive dosage effect, as indicated by the positive association between expression and the copy number of these genes. Plants containing these DelDups also showed distinct phenotypic variations. The whole genome methylation level experienced significant fluctuations in different generations and eventually decreased in the latter generations. Moreover, the DelDups did not show methylation changes from other individuals of the same generation, and the local regions with methylation alterations did not affect gene expression. Our findings provide new insights into the early evolution of polyploid genomes and guide the use of synthetic polyploidizations in breeding.
Metabolic-Pathway-Presence-Heatmap (MPPH): Constructing phylogenetic trees based on metabolic pathways
Authors: Du Yi-Heng , Mu Jing-Hua 
Published: June 2023

AbstractGenome sequencing has revolutionized the study of biological systems, enabling exploration of species origins, evolution, and identification. However, traditional methods for constructing phylogenetic trees based on raw sequence data require substantial computational resources and may be challenging for biologists with limited computer knowledge. To address this, a lightweight tree-building tool was developed, Metabolic-Pathway-Presence-Heatmap (MPPH), leveraging Python programming and the KEGG metabolomics database to construct phylogenetic trees based on metabolic pathway information. This approach reduces computational and time requirements while focusing the analysis on metabolic pathways. The tool provides a rapid and reliable option for biologists to investigate the evolutionary and taxonomic aspects of species. Additionally, the tool incorporates a heatmap feature, allowing users to visualize the presence or absence of metabolic pathways across multiple species. The code is available athttp://github.com/DeweyYihengDu/Metabolic-Pathway-Presence-Heatmap.