bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate Plane Fat Grafting in Gluteal Augmentation: An Anatomic Study
Authors: Kelishadi S Sean , Chiemi Julia A , Chowdhry Saeed , Colorado Avery , Herring Nicole R , Kinney Brian , Wilhelmi Bradon J 
Published: September 2023

Abstract

Background
The safety of gluteal fat grafting is a global concern in plastic surgery.

Objective
The goal of this study was to test whether fat grafting to the buttocks with Auto Stop Reach (ASR) technology prevents penetration from the subcutaneous space into the fascia and muscle layers of the buttocks.

Methods
Fat transfer simulation was performed with blue dye on 8 fresh tissue cadaver buttocks by 3 board-certified plastic surgeons (S.S.K., S.C., B.W.). An open control was utilized to visualize the process in the different anatomic layers, and all of the other procedures were performed blindly, akin to live surgery. After blue dye transfer reached maximum capacity (ranging from 400-800 mL per buttock), dissection of the anatomical layers of the buttocks was performed to determine the plane(s) of injection.

Results
Blue dye fat transfer injection to the buttocks did not penetrate the gluteal fascia or muscle layers from the subcutaneous space while using ASR.

Conclusions
Auto Stop Reach technology supports the safety of gluteal fat transfer in the subcutaneous space by board-certified plastic surgeons.

Level of Evidence: 4
Interleukin-21 knockout reduces bone loss in ovariectomized mice by inhibiting osteoclastogenesis
Authors: Hou Junlong , Xu Ping , Zhong Yanheng , Zhou Zhigang , Zhang Wencai 
Published: September 2023

ABSTRACT
Estrogen deficiency accelerates osteoporosis in elderly women. However, the role of IL-21 in postmenopausal osteoporosis remains unclear. Female wild-type (WT) C57BL/6 and IL-21 knockout (KO) mice were used for ovariectomy (OVX). Here, IL-21 levels were significantly increased in the serum and bone tissues of WT-OVX mice. The trabecular bone space of the femur was significantly increased, and the bone mass was reduced in OVX mice, accompanied by a significant decrease in the maximum load, energy absorption, and elastic modulus indices. In contrast, IL-21 knockout effectively alleviated the effects of OVX on bone mass. Serum TRACP-5b and receptor activator of nuclear factor kappa B ligand (RANKL) levels and osteoclastogenesis were significantly higher in OVX mice than in sham mice, while serum TRACP-5b and RANKL levels and osteoclastogenesis were significantly decreased in IL-21 KO + OVX mice compared to WT + OVX mice. IL-21 knockdown reduces TRACP-5b, RANKL, and osteoclastogenesis, effectively preventing bone resorption and alleviating the progression of OVX-induced osteoporosis.
Enhanced intestinal barrier function as the mechanism of antibiotic growth promoters in feed additives
Authors: Uehara Akinori , Maekawa Mayumi , Nakagawa Kazuki 
Published: September 2023

ABSTRACT
Antibiotic growth promoters (AGPs) are a cost-effective tool for improving livestock productivity. However, antimicrobial-resistant bacteria have emerged, and the search for alternatives to AGPs has consequently intensified. To identify these alternatives without the risk of the emergence of antimicrobial resistance, it is important to determine the mechanism of action of AGPs and, subsequently, search for compounds with similar properties. We investigated the antimicrobial and anti-inflammatory activities and intestinal barrier function of several AGPs using epithelial and immune cells. At the minimum administered dose of antibiotics, which effectively function as a growth promoter, the mechanism of action is to enhance the intestinal barrier function, but not the antimicrobial activity as determined using Dunnett's test (n = 3, P &lt; .05). Inflammatory response was dependent on the combination of antibiotics (100 µmol/L) and immune cells. The results suggest that future studies should screen for nonantibiotic compounds that ameliorate intestinal barrier function.
Detecting biased validation of predictive models in the positive-unlabeled setting: disease gene prioritization case study
Authors: Molotkov Ivan , Artomov Mykyta 
Published: September 2023

Abstract

Motivation
Positive-unlabeled data consists of points with either positive or unknown labels. It is widespread in medical, genetic, and biological settings, creating a high demand for predictive positive-unlabeled models. The performance of such models is usually estimated using validation sets, assumed to be selected completely at random (SCAR) from known positive examples. For certain metrics, this assumption enables unbiased performance estimation when treating positive-unlabeled data as positive/negative. However, the SCAR assumption is often adopted without proper justifications, simply for the sake of convenience.

Results
We provide an algorithm that under the weak assumptions of a lower bound on the number of positive examples can test for the violation of the SCAR assumption. Applying it to the problem of gene prioritization for complex genetic traits, we illustrate that the SCAR assumption is often violated there, causing the inflation of performance estimates, which we refer to as validation bias. We estimate the potential impact of validation bias on performance estimation. Our analysis reveals that validation bias is widespread in gene prioritization data and can significantly overestimate the performance of models. This finding elucidates the discrepancy between the reported good performance of models and their limited practical applications.

Availability and implementation
Python code with examples of application of the validation bias detection algorithm is available at github.com/ArtomovLab/ValidationBias.
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Authors: Movassagh Mercedeh , Schiff Steven J , Paulson Joseph N 
Published: September 2023

Abstract

Motivation
In recent years, significant strides have been made in the field of genomics, with the commencement of large-scale studies aimed at collecting host mutational profiles and microbiome data. The amalgamation of host gene mutational profiles in both healthy and diseased subjects with microbial abundance data holds immense promise in providing insights into several crucial research questions, including the development and progression of diseases, as well as individual responses to therapeutic interventions. With the advent of sequencing methods such as 16s ribosomal RNA (rRNA) sequencing and whole genome sequencing, there is increasing evidence of interplay of human genetics and microbial communities. Quantitative trait loci associated with microbial abundance (mbQTLs), are genetic variants that influence the abundance of microbial populations within the host.

Results
Here, we introduce mbQTL, the first R package integrating 16S ribosomal RNA (rRNA) sequencing and single-nucleotide variation (SNV) and single-nucleotide polymorphism (SNP) data. We describe various statistical methods implemented for the identification of microbe–SNV pairs, relevant statistical measures, and plot functionality for interpretation.

Availability and implementation
mbQTL is available on bioconductor at https://bioconductor.org/packages/mbQTL/.
BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs
Authors: Callaghan Jackson , Xu Colleen H , Xin Jiwen , Cano Marco Alvarado , Riutta Anders , Zhou Eric , Juneja Rohan , Yao Yao , Narayan Madhumita , Hanspers Kristina , Agrawal Ayushi , Pico Alexander R , Wu Chunlei , Su Andrew I 
Published: September 2023

Abstract

Summary
Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and analyzing graphs. Biomedical knowledge graphs have been used in a variety of applications, including drug repurposing, identification of drug targets, prediction of drug side effects, and clinical decision support. Typically, knowledge graphs are constructed by centralization and integration of data from multiple disparate sources. Here, we describe BioThings Explorer, an application that can query a virtual, federated knowledge graph derived from the aggregated information in a network of biomedical web services. BioThings Explorer leverages semantically precise annotations of the inputs and outputs for each resource, and automates the chaining of web service calls to execute multi-step graph queries. Because there is no large, centralized knowledge graph to maintain, BioThings Explorer is distributed as a lightweight application that dynamically retrieves information at query time.

Availability and implementation
More information can be found at https://explorer.biothings.io and code is available at https://github.com/biothings/biothings_explorer.
SCORPIO: a utility for defining and classifying mutation constellations of virus genomes
Authors: Colquhoun Rachel , Jackson Ben , O’Toole Áine , Rambaut Andrew 
Published: September 2023

Abstract

Summary
Scorpio provides a set of command line utilities for classifying, haplotyping, and defining constellations of mutations for an aligned set of genome sequences. It was developed to enable exploration and classification of variants of concern within the SARS-CoV-2 pandemic, but can be applied more generally to other species.

Availability and implementation
Scorpio is an open-source project distributed under the GNU GPL version 3 license. Source code and binaries are available at https://github.com/cov-lineages/scorpio, and binaries are also available from Bioconda. SARS-CoV-2 specific definitions can be installed as a separate dependency from https://github.com/cov-lineages/constellations.
A machine learning-based quantitative model (LogBB_Pred) to predict the blood–brain barrier permeability (logBB value) of drug compounds
Authors: Shaker Bilal , Lee Jingyu , Lee Yunhyeok , Yu Myeong-Sang , Lee Hyang-Mi , Lee Eunee , Kang Hoon-Chul , Oh Kwang-Seok , Kim Hyung Wook , Na Dokyun 
Published: September 2023

Abstract

Motivation
Efficient assessment of the blood–brain barrier (BBB) penetration ability of a drug compound is one of the major hurdles in central nervous system drug discovery since experimental methods are costly and time-consuming. To advance and elevate the success rate of neurotherapeutic drug discovery, it is essential to develop an accurate computational quantitative model to determine the absolute logBB value (a logarithmic ratio of the concentration of a drug in the brain to its concentration in the blood) of a drug candidate.

Results
Here, we developed a quantitative model (LogBB_Pred) capable of predicting a logBB value of a query compound. The model achieved an R2 of 0.61 on an independent test dataset and outperformed other publicly available quantitative models. When compared with the available qualitative (classification) models that only classified whether a compound is BBB-permeable or not, our model achieved the same accuracy (0.85) with the best qualitative model and far-outperformed other qualitative models (accuracies between 0.64 and 0.70). For further evaluation, our model, quantitative models, and the qualitative models were evaluated on a real-world central nervous system drug screening library. Our model showed an accuracy of 0.97 while the other models showed an accuracy in the range of 0.29–0.83. Consequently, our model can accurately classify BBB-permeable compounds as well as predict the absolute logBB values of drug candidates.

Availability and implementation
Web server is freely available on the web at http://ssbio.cau.ac.kr/software/logbb_pred/. The data used in this study are available to download at http://ssbio.cau.ac.kr/software/logbb_pred/dataset.zip.
Association between new plasma inflammatory markers and risk of colorectal neoplasms in individuals over 50 years old
Authors: Su Jia-Yi , Wang Yun , Wu Shang-Shang , Li Wen-Kun , Wang Cheng-Yao , Ma Jiu-Yue , Qiu Yu-Ting , Zhou Min-Si , Wang Zhan , Li Peng , Liu Chun-Tao , Wu Jing 
Published: September 2023

Abstract

Objective(s)
The prognostic value of systemic cytokine profiles and inflammatory markers in colorectal cancer were explored by several studies. We want to know more about inflammatory biomarkers in colorectal adenoma and early cancer.

Method
The level of 38 inflammatory markers in the plasma of 112 adenoma patients, 72 Tis-T1 staging of colorectal carcinoma patients, 34 T2–T4 staging of colorectal carcinoma patients and 53 normal subjects were detected and compared.

Result(s)
Eight inflammatory biomarkers (Eotaxin, GCSF, IL-4, IL-5, IL-17E, MCP-1, TNF-α and VEGF-A) have higher plasma concentrations in colorectal adenoma and cancer patients compared with normal participants over 50 years old.

Conclusion(s)
Inflammatory markers may have the prognostic value for colorectal adenoma and early-stage carcinoma.
Air pollution and out-of-hospital cardiac arrest risk: a 7-year study from a highly polluted area
Authors: Moderato Luca , Aschieri Daniela , Lazzeroni Davide , Rossi Luca , Biagi Andrea , Binno Simone Maurizio , Monello Alberto , Pelizzoni Valentina , Sticozzi Concetta , Zanni Alessia , Capucci Alessandro , Nani Stefano , Ardissino Diego , Nicolini Francesco , Niccoli Giampaolo 
Published: September 2023

Abstract

Aims
Globally, nearly 20% of cardiovascular disease deaths were attributable to air pollution. Out-of-hospital cardiac arrest (OHCA) represents a major public health problem; therefore, the identification of novel OHCA triggers is of crucial relevance. The aim of the study was to evaluate the association between air pollution (short-, mid-, and long-term exposures) and OHCA risk, during a 7-year period in a highly polluted urban area in northern Italy, with a high density of automated external defibrillators (AEDs).

Methods and results
Out-of-hospital cardiac arrests were prospectively collected from the ‘Progetto Vita Database’ between 1 January 2010 and 31 December 2017; day-by-day air pollution levels were extracted from the Environmental Protection Agency stations. Electrocardiograms of OHCA interventions were collected from the AED data cards. Day-by-day particulate matter (PM) 2.5 and 10, ozone (O3), carbon monoxide (CO), and nitrogen dioxide (NO2) levels were measured. A total of 880 OHCAs occurred in 748 days. A significant increase in OHCA risk with a progressive increase in PM2.5, PM10, CO, and NO2 levels was found. After adjustment for temperature and seasons, a 9% and 12% increase in OHCA risk for each 10 μg/m3 increase in PM10 (P &lt; 0.0001) and PM2.5 (P &lt; 0.0001) levels was found. Air pollutant levels were associated with both asystole and shockable rhythm risk, while no correlation was found with pulseless electrical activity.

Conclusion
Short- and mid-term exposures to PM2.5 and PM10 are independently associated with the risk of OHCA due to asystole or shockable rhythm.
Case report—right atrial mass: a very rare presentation of endometrial cancer metastasis
Authors: Erturk Emre , Soyler Onur , Pehlivan Fatma Seher , Arslan Cagatay 
Published: September 2023

Abstract

Background
We report a case of a 47-year-old woman with right atrial metastasis of endometrioid adenocarcinoma, which is an uncommon clinical presentation for patients with endometrial cancer (EC). The principal aim of this case is to demonstrate the possibility of distant metastasis, something rarely encountered among this group of patients.

Case summary
Our patient, diagnosed with EC and receiving chemotherapy and radiotherapy after surgery, was found to have enhanced 18-fluorodeoxyglucose uptake inside the right atrium on the repeat positron emission tomography–computed tomography scan at the ninth month after initial diagnosis. Following trans-oesophageal echocardiography, cardiac magnetic resonance imaging showed a hyper-vascular mass with right atrial lateral wall involvement likely to be malignant in nature. A right atrial tumour was successfully removed by cardiovascular surgeons, and a pericardial patch was placed at the site of the excised atrium. The pathological examination showed EC metastasis. Following surgery, systemic treatment was planned for recurrent EC. The patient had an uneventful recovery after the surgery.

Discussion
Endometrial cancer is the most common gynaecologic malignancy and the fourth most common cancer in women. The lymphatic pathway is the main metastatic behaviour of EC; however, haematogenous metastases are not uncommon, especially in patients with higher stages of the disease. Our patient did not show any signs and symptoms of cardiac involvement. Nevertheless, clinicians should be alert for symptoms of cardiac involvement like new-onset murmur, embolism, or dyspnoea. Having known the behavioural pattern of the primary tumour, timely utilization of diagnostic imaging methods in accordance with clinical suspicions in patients with rapidly growing tumours can be lifesaving.
Mid- and long-term outcomes after surgical correction of subaortic stenosis: a 27-year experience
Authors: Bandara Dushan , Salve Gananjay G , Marathe Supreet P , Betts Kim S , Cole Andrew D , Ayer Julian G , Nicholson Ian A , Orr Yishay 
Published: September 2023

Abstract

OBJECTIVES
We reviewed the mid- and long-term surgical outcomes of patients with subaortic stenosis (SAS).

METHODS
Patients operated for SAS from April 1990 to August 2016 were reviewed retrospectively. Patients with major associations such as aortic arch obstruction were excluded. Time to reintervention and predictors of recurrence were assessed using Kaplan–Meier analysis, log-rank test and uni/multivariable Cox regression.

RESULTS
120 patients at a median age of 4.7 years (interquartile range 2.9, 8.1) underwent primary operation (median peak preoperative left ventricular outflow tract gradient 52.5 mmHg, interquartile range 40, 70) involving fibrous tissue excision (n = 120) with septal myectomy (93%; n = 112) as the procedure of choice.
At median follow-up of 13 years (interquartile range 7, 18), freedom from reintervention at 1, 3, 5 and 10 years was 99% (95% confidence interval 94%, 99%), 94% (87%, 97%), 93% (86%, 96%) and 90% (82%, 94%), respectively. Recurrence occurred in 18% (n = 20) with 15 patients undergoing reinterventions, 13 of whom required radical reoperation. Multivariable analysis revealed higher preoperative peak left ventricular outflow tract gradient (hazard risk 1.06, confidence interval 1.03, 1.09, P &lt; 0.001), and presence of bicuspid aortic valve (hazard risk 14.13, confidence interval 3.32, 60.1, P &lt; 0.001) as predictors for reintervention. Mild/moderate aortic regurgitation occurred in 49% (n = 55) of patients at the most recent follow-up.

CONCLUSIONS
Reintervention for recurrent SAS is common, predicted by higher preoperative peak left ventricular outflow tract gradient, and presence of bicuspid aortic valve, and frequently involves a radical procedure. Aortic regurgitation is a major consequence of SAS, but its severity usually remains low.

Clinical Registration Number
SCHN HREC reference number 2019/ETH02729, approved on 09 July 2019.
Mechanical atrioventricular valve replacement in patients with single ventricle palliation
Authors: Morgan Conall T , Chetan Devin , Varenbut Jaymie , Haller Christoph , Seed Mike , Mertens Luc L , Honjo Osami 
Published: September 2023

Abstract

OBJECTIVES
Atrioventricular valve (AVV) replacements in patients with single-ventricle circulations pose significant surgical risks and are associated with high morbidity and mortality.

METHODS
From 1997 to 2021, 16 consecutive patients with functionally single-ventricle physiology underwent mechanical AVV replacement. Primary outcome was transplant-free survival. Secondary outcomes included major postoperative morbidity.

RESULTS
The median age of AVV replacement was 2 years old (interquartile range 0.6–3.8 years). All AVV replacements were performed with a St. Jude Medical mechanical valve, median 24 mm (range, 19–31mm). Extracorporeal membrane oxygenation (ECMO) was required in 4 patients. Operative mortality was 38% (6/16). There were 2 late deaths and 3 transplants. Transplant-free survival was 50% at 1 year, 37.5% at 5 years, and 22% at 10 years. Transplant-free survival was higher for patients with preserved ventricular function (P = 0.01). Difference in transplant-free survival at 1 year was 75% vs 25%, at 5 years was 62.5% vs 12.5% and at 10 years was 57% vs 0%. Three (19%) patients had complete heart block requiring permanent pacemaker insertion. 6 of 13 patients (46%) patients reached Fontan completion (3 patients operated at/after Fontan). Significant bleeding events occurred in 8 patients (50%) with 3 patients suffering major cerebrovascular accidents. There were 6 events of valve thrombosis in 5 patients, resulting in 2 deaths and 2 heart transplants.

CONCLUSIONS
Mechanical valve replacement carries significant morbidity and mortality risk. While it successfully salvages about half of patients with preserved ventricular function, careful consideration of alternative options should be made before embarking upon mechanical valve replacement.
Asymptomatic atrial fibrillation among hospitalized patients: clinical correlates and in-hospital outcomes in Improving Care for Cardiovascular Disease in China-Atrial Fibrillation
Authors: Lin Jing , Wu Xue-Ying , Long De-Yong , Jiang Chen-Xi , Sang Cai-Hua , Tang Ri-Bo , Li Song-Nan , Wang Wei , Guo Xue-Yuan , Ning Man , Sun Zhao-Qing , Yang Na , Hao Yong-Chen , Liu Jun , Liu Jing , Du Xin , Fonarow Gregg C , Smith Sidney C , Lip Gregory Y H , Zhao Dong , Dong Jian-Zeng , Ma Chang-Sheng 
Published: September 2023

Abstract

Aims
The clinical correlates and outcomes of asymptomatic atrial fibrillation (AF) in hospitalized patients are largely unknown. We aimed to investigate the clinical correlates and in-hospital outcomes of asymptomatic AF in hospitalized Chinese patients.

Methods and results
We conducted a cross-sectional registry study of inpatients with AF enrolled in the Improving Care for Cardiovascular Disease in China-Atrial Fibrillation Project between February 2015 and December 2019. We investigated the clinical characteristics of asymptomatic AF and the association between the clinical correlates and the in-hospital outcomes of asymptomatic AF. Asymptomatic and symptomatic AF were defined according to the European Heart Rhythm Association score. Asymptomatic patients were more commonly males (56.3%) and had more comorbidities such as hypertension (57.4%), diabetes mellitus (18.6%), peripheral artery disease (PAD; 2.3%), coronary artery disease (55.5%), previous history of stroke/transient ischaemic attack (TIA; 17.9%), and myocardial infarction (MI; 5.4%); however, they had less prevalent heart failure (9.6%) or left ventricular ejection fractions ≤40% (7.3%). Asymptomatic patients were more often hospitalized with a non-AF diagnosis as the main diagnosis and were more commonly first diagnosed with AF (23.9%) and long-standing persistent/permanent AF (17.0%). The independent determinants of asymptomatic presentation were male sex, long-standing persistent AF/permanent AF, previous history of stroke/TIA, MI, PAD, and previous treatment with anti-platelet drugs. The incidence of in-hospital clinical events such as all-cause death, ischaemic stroke/TIA, and acute coronary syndrome (ACS) was higher in asymptomatic patients than in symptomatic patients, and asymptomatic clinical status was an independent risk factor for in-hospital all-cause death, ischaemic stroke/TIA, and ACS.

Conclusion
Asymptomatic AF is common among hospitalized patients with AF. Asymptomatic clinical status is associated with male sex, comorbidities, and a higher risk of in-hospital outcomes. The adoption of effective management strategies for patients with AF should not be solely based on clinical symptoms.