bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism
Authors: Yang Bo , Chen Hailin 
Published: January 2023

Abstract
Recent studies have shown that the expression of circRNAs would affect drug sensitivity of cells and thus significantly influence the efficacy of drugs. Traditional biomedical experiments to validate such relationships are time-consuming and costly. Therefore, developing effective computational methods to predict potential associations between circRNAs and drug sensitivity is an important and urgent task. In this study, we propose a novel method, called MNGACDA, to predict possible circRNA–drug sensitivity associations for further biomedical screening. First, MNGACDA uses multiple sources of information from circRNAs and drugs to construct multimodal networks. It then employs node-level attention graph auto-encoders to obtain low-dimensional embeddings for circRNAs and drugs from the multimodal networks. Finally, an inner product decoder is applied to predict the association scores between circRNAs and drug sensitivity based on the embedding representations of circRNAs and drugs. Extensive experimental results based on cross-validations show that MNGACDA outperforms six other state-of-the-art methods. Furthermore, excellent performance in case studies demonstrates that MNGACDA is an effective tool for predicting circRNA–drug sensitivity associations in real situations. These results confirm the reliable prediction ability of MNGACDA in revealing circRNA–drug sensitivity associations.
Deleterious synonymous mutation identification based on selective ensemble strategy
Authors: Wang Lihua , Zhang Tao , Yu Lihong , Zheng Chun-Hou , Yin Wenguang , Xia Junfeng , Zhang Tiejun 
Published: January 2023

Abstract
Although previous studies have revealed that synonymous mutations contribute to various human diseases, distinguishing deleterious synonymous mutations from benign ones is still a challenge in medical genomics. Recently, computational tools have been introduced to predict the harmfulness of synonymous mutations. However, most of these computational tools rely on balanced training sets without considering abundant negative samples that could result in deficient performance. In this study, we propose a computational model that uses a selective ensemble to predict deleterious synonymous mutations (seDSM). We construct several candidate base classifiers for the ensemble using balanced training subsets randomly sampled from the imbalanced benchmark training sets. The diversity measures of the base classifiers are calculated by the pairwise diversity metrics, and the classifiers with the highest diversities are selected for integration using soft voting for synonymous mutation prediction. We also design two strategies for filling in missing values in the imbalanced dataset and constructing models using different pairwise diversity metrics. The experimental results show that a selective ensemble based on double fault with the ensemble strategy EKNNI for filling in missing values is the most effective scheme. Finally, using 40-dimensional biology features, we propose a novel model based on a selective ensemble for predicting deleterious synonymous mutations (seDSM). seDSM outperformed other state-of-the-art methods on the independent test sets according to multiple evaluation indicators, indicating that it has an outstanding predictive performance for deleterious synonymous mutations. We hope that seDSM will be useful for studying deleterious synonymous mutations and advancing our understanding of synonymous mutations. The source code of seDSM is freely accessible at https://github.com/xialab-ahu/seDSM.git.
From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies?
Authors: Defo Joel , Awany Denis , Ramesar Raj 
Published: January 2023

AbstractGenome-wide association studies (GWAS) have benefited greatly from enhanced high-throughput technology in recent decades. GWAS meta-analysis has become increasingly popular to highlight the genetic architecture of complex traits, informing about the replicability and variability of effect estimations across human ancestries. A wealth of GWAS meta-analysis methodologies have been developed depending on the input data and the outcome information of interest. We present a survey of current approaches from SNP to pathway-based meta-analysis by acknowledging the range of resources and methodologies in the field, and we provide a comprehensive review of different categories of Genome-Wide Meta-analysis methods employed. These methods highlight different levels at which GWAS meta-analysis may be done, including Single Nucleotide Polymorphisms, Genes and Pathways, for which we describe their framework outline. We also discuss the strengths and pitfalls of each approach and make suggestions regarding each of them.
Benchmarking differential abundance analysis methods for correlated microbiome sequencing data
Authors: Yang Lu , Chen Jun 
Published: January 2023

AbstractDifferential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Current microbiome studies frequently generate correlated samples from different microbiome sampling schemes such as spatial and temporal sampling. In the past decade, a number of DAA tools for correlated microbiome data (DAA-c) have been proposed. Disturbingly, different DAA-c tools could sometimes produce quite discordant results. To recommend the best practice to the field, we performed the first comprehensive evaluation of existing DAA-c tools using real data-based simulations. Overall, the linear model-based methods LinDA, MaAsLin2 and LDM are more robust than methods based on generalized linear models. The LinDA method is the only method that maintains reasonable performance in the presence of strong compositional effects.
Benchmarking of computational methods for predicting circRNA-disease associations
Authors: Lan Wei , Dong Yi , Zhang Hongyu , Li Chunling , Chen Qingfeng , Liu Jin , Wang Jianxin , Chen Yi-Ping Phoebe 
Published: January 2023

AbstractAccumulating evidences demonstrate that circular RNA (circRNA) plays an important role in human diseases. Identification of circRNA-disease associations can help for the diagnosis of human diseases, while the traditional method based on biological experiments is time-consuming. In order to address the limitation, a series of computational methods have been proposed in recent years. However, few works have summarized these methods or compared the performance of them. In this paper, we divided the existing methods into three categories: information propagation, traditional machine learning and deep learning. Then, the baseline methods in each category are introduced in detail. Further, 5 different datasets are collected, and 14 representative methods of each category are selected and compared in the 5-fold, 10-fold cross-validation and the de novo experiment. In order to further evaluate the effectiveness of these methods, six common cancers are selected to compare the number of correctly identified circRNA-disease associations in the top-10, top-20, top-50, top-100 and top-200. In addition, according to the results, the observation about the robustness and the character of these methods are concluded. Finally, the future directions and challenges are discussed.
Metadata retrieval from sequence databases with ffq
Authors: Gálvez-Merchán Ángel , Min Kyung Hoi (Joseph) , Pachter Lior , Booeshaghi A Sina 
Published: January 2023

Abstract

Motivation
Several genomic databases host data and metadata for an ever-growing collection of sequence datasets. While these databases have a shared hierarchical structure, there are no tools specifically designed to leverage it for metadata extraction.

Results
We present a command-line tool, called ffq, for querying user-generated data and metadata from sequence databases. Given an accession or a paper’s DOI, ffq efficiently fetches metadata and links to raw data in JSON format. ffq’s modularity and simplicity make it extensible to any genomic database exposing its data for programmatic access.

Availability and implementation
ffq is free and open source, and the code can be found here: https://github.com/pachterlab/ffq.
Vaa3D-x for cross-platform teravoxel-scale immersive exploration of multidimensional image data
Authors: Liang Jiangshan , Deng Luchen , Chen Shize , Wang Yimin , Ruan Zongcai , Zhang Lingli 
Published: January 2023

Abstract

Summary
Vaa3D is a software package that has been widely used to visualize and analyze multidimensional microscopic images in a number of cutting edge bioimage informatics applications. However, due to many recent updates of both software development environments and operating systems, it was highly requested to maintain Vaa3D and disseminate it on latest operating systems. In addition, there has never been a showcase about how to use Vaa3D’s cross-platform visualization and immersive exploration functions for multidimensional and teravoxel-scale images. Here, we introduce a newly developed version of the software, called Vaa3D-x, to address all the above issues.

Availability and implementation
Vaa3D-x is released in both binary and Open-Source available at vaa3d.org and GitHub (https://github.com/Vaa3D).

Supplementary information
Supplementary data are available at Bioinformatics online.
Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers
Authors: Peng Xiyu , Dorman Karin S 
Published: January 2023

Abstract

Motivation
Amplicon sequencing is widely applied to explore heterogeneity and rare variants in genetic populations. Resolving true biological variants and quantifying their abundance is crucial for downstream analyses, but measured abundances are distorted by stochasticity and bias in amplification, plus errors during polymerase chain reaction (PCR) and sequencing. One solution attaches unique molecular identifiers (UMIs) to sample sequences before amplification. Counting UMIs instead of sequences provides unbiased estimates of abundance. While modern methods improve over naïve counting by UMI identity, most do not account for UMI reuse or collision, and they do not adequately model PCR and sequencing errors in the UMIs and sample sequences.

Results
We introduce Deduplication and Abundance estimation with UMIs (DAUMI), a probabilistic framework to detect true biological amplicon sequences and accurately estimate their deduplicated abundance. DAUMI recognizes UMI collision, even on highly similar sequences, and detects and corrects most PCR and sequencing errors in the UMI and sampled sequences. DAUMI performs better on simulated and real data compared to other UMI-aware clustering methods.

Availability and implementation
Source code is available at https://github.com/DormanLab/AmpliCI.

Supplementary information
Supplementary data are available at Bioinformatics online.
Upregulation of FOXA2 in uterine luminal epithelium and vaginal basal epithelium of epiERα−/− (Esr1fl/flWnt7aCre/+) mice
Authors: Hancock Jonathan Matthew , Li Yuehuan , Martin Taylor Elijah , Andersen Christian Lee , Ye Xiaoqin 
Published: January 2023

Abstract
Forkhead box protein A2 (FOXA2) is a pioneer transcription factor important for epithelial budding and morphogenesis in different organs. It has been used as a specific marker for uterine glandular epithelial cells (GE). FOXA2 has close interactions with estrogen receptor α (ERα). ERα binding to Foxa2 gene in the uterus indicates its regulation of Foxa2. The intimate interactions between ERα and FOXA2 and their essential roles in early pregnancy led us to investigate the expression of FOXA2 in the female reproductive tract of pre-implantation epiERα−/− (Esr1fl/flWnt7aCre/+) mice, in which ERα is conditionally deleted in the epithelium of reproductive tract. In the oviduct, FOXA2 is detected in the ciliated epithelial cells of ampulla but absent in the isthmus of day 3.5 post-coitum (D3.5) Esr1fl/fl control and epiERα−/− mice. In the uterus, FOXA2 expression in the GE appears to be comparable between Esr1fl/fl and epiERα−/− mice. However, FOXA2 is upregulated in the D0.5 and D3.5 but not PND25-28 epiERα−/− uterine luminal epithelial cells (LE). In the vagina, FOXA2 expression is low in the basal layer and increases toward the superficial layer of the D3.5 Esr1fl/fl vaginal epithelium, but FOXA2 is detected in the basal, intermediate, and superficial layers, with the strongest FOXA2 expression in the intermediate layers of the D3.5 epiERα−/− vaginal epithelium. This study demonstrates that loss of ERα in LE and vaginal basal layer upregulates FOXA2 expression in these epithelial cells during early pregnancy. The mechanisms for epithelial cell-type specific regulation of FOXA2 by ERα remain to be elucidated.
Inviting, Affording and Translating Harm: Understanding the Role of Technological Mediation in Technology-Facilitated Violence
Authors: Wood Mark A , Mitchell Matthew , Pervan Flynn , Anderson Briony , O’Neill Tully , Wood Jackson , Arpke-Wales Will 
Published: January 2023

Abstract
Technologies not only extend capabilities but also mediate experience and action. To date, however, research on technology-facilitated violence has tended not to focus on the role technological mediation plays in acts of violence facilitated through technology. Building on prior work in the field, this article develops a theoretical framework and typology for understanding the role technological mediation plays in producing technology-facilitated violence. First, drawing on postphenomenological theories of technology, we argue that technology-facilitated violence is best understood as a form of ‘harm translation,’ where a technology’s affordances and other properties ‘invite’ an individual to actualize harmful ends. Then, distinguishing between four modes of harm translation, we construct a typology for analysing the intersections between user intention and technological design that, together, facilitate violence. We argue that by attending to these distinctions our typology may help researchers and designers identify and address the specific causal dynamics involved in producing different kinds of technology-facilitated harm.
Secukinumab long-term efficacy and safety in psoriasis through to year 5 of treatment: results of a randomized extension of the phase III ERASURE and FIXTURE trials
Authors: Langley Richard G , Sofen Howard , Dei-Cas Ignacio , Reich Kristian , Sigurgeirsson Bardur , Warren Richard B , Paul Carle , Szepietowski Jacek C , Tsai Tsen-Fang , Hampele Isabelle , You Ruquan , Charef Pascal , Papavassilis Charis 
Published: January 2023

Abstract

Background
In the long-term extension study of the ERASURE and FIXTURE trials, the efficacy of secukinumab (a fully human anti-interleukin-17A monoclonal antibody) was demonstrated to have been maintained through to year 3 of treatment in moderate-to-severe plaque psoriasis.

Objectives
To assess the efficacy and safety of secukinumab through to year 5 of treatment in moderate-to-severe plaque psoriasis.

Methods
Responders with ≥ 75% improvement in Psoriasis Area and Severity Index (PASI 75) from two core trials – ERASURE and FIXTURE – were randomized 2 : 1 at year 1 (end of core trials) to either the same dose (300 or 150 mg, continuous treatment) or placebo (treatment withdrawal) every 4 weeks, until year 3 or relapse (&gt; 50% reduction in maximal PASI from core study baseline). Partial responders (achieving PASI 50 but not PASI 75) at year 1 continued at the same dose as in the core trials. At year 3, all patients received open-label secukinumab treatment, with those on secukinumab 300 mg continuing on their dose, while those on secukinumab 150 mg or placebo received secukinumab 150 or 300 mg based on the physician’s discretion. The study is registered on ClinicalTrials.gov with the identifier NCT01544595.

Results
Most patients randomized to placebo at year 1 relapsed, but the response was rapidly recaptured upon reinitiation of treatment. PASI responses were sustained with secukinumab through to year 5. The PASI responses for the 300 mg responders + partial responders group at year 1 (PASI 75/90/100: 86.8%/72.8%/45.9%) trended downwards until year 3 (PASI 75/90/100: 82.3%/58.4%/32.7%) and then remained stable through year 4 (PASI 75/90/100: 83.3%/60.1%/32.2%) until year 5 (PASI 75/90/100: 81.1%/62.8%/35.1%). Dermatology Life Quality Index showed sustained benefit up to year 5. Absolute PASI responses were maintained throughout the study. The most common adverse events (AEs) were infections and infestations, nasopharyngitis, and upper respiratory tract infections (URTIs). The overall exposure-adjusted incidence rate (EAIR; with 95% confidence interval) for all AEs was 139.9 (130.3–149.9). EAIRs for Crohn's disease and neutropenia were 0.1 (0.0–0.3) and 0.5 (0.3–0.8), respectively.

Conclusions
The 4-year extension of two pivotal phase III trials demonstrated that secukinumab treatment was effective through to year 5 and improved quality of life in patients with moderate-to-severe plaque psoriasis. The most common AEs were infections and infestations, nasopharyngitis, and URTIs. The safety profile was consistent with that in the secukinumab phase II/III clinical development programme.
Photoprotection for people with skin of colour: needs and strategies
Authors: Krutmann Jean , Piquero-Casals Jaime , Morgado-Carrasco Daniel , Granger Corinne , Trullàs Carles , Passeron Thierry , Lim Henry W 
Published: January 2023

Abstract
Skin of colour or pigmented skin has unique characteristics: it has a higher eumelanin-to-pheomelanin ratio, more mature melanosomes, an increased amount of melanin distributed in the upper layers of the epidermis, and more efficient DNA repair compared with lighter skin. However, individuals with skin of colour are at a significant risk of skin damage caused by ultraviolet radiation, including the development of photodermatoses and photoageing changes such as uneven skin tone, and are predisposed to pigmentary disorders. In fact, one of the most common conditions leading to dermatology consultations by patients with skin of colour is photoexacerbated pigmentary disorders. Unfortunately, individuals with skin of colour may be less prone to engage in photoprotective measures, including the use of sunscreens. Physicians are also less likely to prescribe sunscreens for them. There is thus a clear need for better education on photodamage and for more efficient and suitable photoprotection in populations with skin of colour. However, this need has thus far only partially been met, and the development of sunscreen products designed to provide optimal photoprotection for people with skin of colour remains a challenge. Targeted sunscreens for individuals with skin of colour require optimal cosmetic appeal (leaving no white residue and not disrupting skin tone). They should include broad-spectrum [ultraviolet (UV)B/UVA] protection with high sun protection factor, as well as protection against long-wave UVA (UVA1) and visible light, as these wavelengths are capable of inducing or augmenting pigmentary disorders. They may also contain depigmenting agents for patients with pigmentary disorders.
DO WE USE ANTIBIOTICS CORRECTLY FOR THE TREATMENT OF ACUTE CHOLECYSTITIS?
Authors: Torroella Vallejo A , Carolina Caldera M C , Morales Sevillano X , Turrado Rodríguez V , Vidal O 
Published: January 2023

Abstract

Introduction
Adequate antibiotic therapy is one of the mainstays in treatment of acute cholecystitis. The Tokyo Guidelines 2018 (TG18) offer recommendations for the appropriate use of antimicrobials in clinical practice. This work evaluates whether antibiotic therapy in patients operated on for cholecystitis is in line with current recommendations.

Methods
Retrospective analysis of patients undergoing cholecystectomy for acute cholecystitis between 06/01/2021 and 12/31/2021. Demographic variables were collected, including risk factors (RRFF) for developing infectious complications or presenting multiresistant microorganisms, as well as SIRS criteria. Information was collected on antibiotic prophylaxis, empiric treatment, its duration, and adherence to both the guidelines and the results of the cultures. Finally, hospital stay and postoperative infectious complications were recorded.

Results
64 patients were operated upon. 51.6% had RRFF of presenting infectious complications, 29.7% had SIRS criteria, 17.2% had RRFF of multiresistant bacteria. According to the TG18, 62.5% were grade 2. Antibiotic prophylaxis was administrated in 82.8% of the cases. Empirical treatment was maintained in 76.6% of the patients, with a mean duration of 5.87±4.1 days. The empirical antibiotic was adapted to the antibiogram in 57.9% of the cases. In none of the cases in which it was not adapted was the antibiotic changed. Surgical site infection was 7.8%.

Conclusions
The concordance of the empirical antibiotic treatment and its duration according to the guidelines, as well as the adequacy of the type of antibiotic according to the cultures, is only fulfilled in a little more than half of the cases.
CONTRAST-ENHANCED ULTRASOUND IN PEDIATRIC ABDOMINAL TRAUMA
Authors: Núñez García B , Álvarez García N , Patricia Beltrán V , Romero Novo M I , Jiménez Gómez J , Santiago Martínez S , Esteva Miró C , Betancourth Alvarenga J E 
Published: January 2023

Abstract

Introduction
Evaluation of the use of contrast-enhanced ultrasound (CEUS) in patients with abdominal trauma.

Methods
Retrospective study of patients with grade III or higher abdominal trauma, according to the American Association of Surgical Association (AAST) severity scale. All patients underwent an initial CT scan, mode B ultrasound before discharge and a second-generation contrast-enhanced ultrasound (CEUS) one month after the trauma (contrast dose=0.03 ml/kg).

Results
From January 2017 to December 2021, a total of 36 patients (2–15 years) with abdominal trauma were collected. 18 hepatic, 8 splenic, 8 renal and 2 pancreatic traumas. Of these, 8 patients required urgent embolization due to active bleeding or pseudoaneurysm and 1 patient required urgent surgical intervention.
CEUS at 1 month showed: complete resolution in 22 patients, 2 residual hematomas, 1 patient with urinoma and devascularized area, 3 pseudoaneurysms, 7 with persistence of lacerations resolved at 2 weeks and 1 patient with 2 pancreatic cysts.

Conclusions
CEUS allows evaluation of parenchymal injuries of abdominal organs, as well as the presence of residual hematomas, active bleeding, pseudoaneurysms, urinomas and/or devascularized areas, therefore, it can be a useful tool for follow-up and monitoring of abdominal trauma.
The absence of irradiation and its great accessibility allow it to be repeated as often as desired; and the confirmation of resolution enables an earlier return to daily life.