bluuebunny/crossref_metadata_2025 huggingface dataset:
Update Breast Cancer 2022 Part 4 – Advanced-Stage Breast Cancer
Authors: Aktas Bahriye , Fehm Tanja N. , Welslau Manfred , Müller Volkmar , Lüftner Diana , Schütz Florian , Fasching Peter A. , Janni Wolfgang , Thomssen Christoph , Witzel Isabell , Belleville Erik , Untch Michael , Thill Marc , Tesch Hans , Ditsch Nina , Lux Michael P. , Banys-Paluchowski Maggie , Kolberg-Liedtke Cornelia , Hartkopf Andreas D. , Wöckel Achim , Kolberg Hans-Christian , Stickeler Elmar , Harbeck Nadia , Schneeweiss Andreas
Published: September 2022

For the treatment of patients with advanced HER2-negative hormone receptor-positive breast cancer, several substances have been introduced into practice in recent years. In addition, other
drugs are under development. A number of studies have been published over the past year which have shown either an advantage for progression-free survival or for overall survival. This
review summarizes the latest results, which have been published at current congresses or in specialist journals, and classifies them in the clinical treatment context. In particular, the
importance of therapy with CDK4/6 inhibitors – trastuzumab deruxtecan, sacituzumab govitecan and capivasertib – is discussed. For trastuzumab deruxtecan, an overall survival benefit in
HER2-negative breast cancer with low HER2 expression (HER2-low expression) was reported in the Destiny-Breast-04 study. Similarly, there was an overall survival benefit in the FAKTION study
with capivasertib. The lack of overall survival benefit for palbociclib in the first line of therapy raises the question of clinical classification.
Endoscopic Self-Expanding Metallic Stent Placement in the Management of Post Laparoscopic Sleeve Gastrectomy Complications
Authors: Goudarzi Hamidreza , Obney Jacob R. , Hemmatizadeh Mahsa , Anbara Taha
Published: September 2022

Introduction Endoscopic treatments have become popular by providing the best solution for healing complications while allowing oral nutrition. In this study, we aim to evaluate outcomes of the endoscopic-covered stents for staple line complications following bariatric surgery.

Methods A prospective evaluation was performed for all patients treated for staple line complications after bariatric surgery. Bariatric patients with acute leaks, chronic gastrocutaneous fistulas, and anastomotic strictures refractory to endoscopic dilation after sleeve gastrectomy were included in this survey.

Results From January 2019 to June 2020, 41 patients (12 with acute leaks, 16 with chronic fistulas, and 13 with strictures) were treated with endoscopic silicone-covered stents (polyester or nitinol). The mean follow-up was 3.5 months. Immediate symptomatic improvement occurred in 95.2% (91.7% of acute leaks, 81.2% of fistulas, and 92.3% of strictures). In addition, 87.8% of patients initiated oral feeding immediately after stenting. There was no mortality case in this population.

Conclusion Although stent migration rarely occurs in subjects, the endoscopic silicone-covered stents strategy is one of the best treatments for anastomotic complications after bariatric surgery, providing rapid healing while simultaneously allowing for oral nutrition.
Future of Metabolic Endoscopy
Authors: Ghazi Rabih , Vargas Eric J. , Abboud Donna , Abdul Razak Farah , Mahmoud Tala , Storm Andrew C. , Chandrasekhara Vinay , Abu Dayyeh Barham K.
Published: September 2022

Obesity has been escalating as one of the worst public health epidemics. Conservative therapies including lifestyle modifications and weight loss medications have limited efficacy and long-term sustainability. Bariatric surgeries, although effective, remain underutilized due to their cost, safety concerns, and patient acceptance. In the past two decades, endoscopic bariatric and metabolic therapies (EBMTs) have emerged as safe, effective, and less invasive options for the treatment of obesity and its comorbidities, with recent studies reporting favorable outcomes in terms of weight loss and metabolic parameters. This article reviews the major and newly developed EBMTs, with emphasis on their metabolic effects and potential use in the management of metabolic conditions.
Gastrointestinal Emergencies and the Role of Endoscopy
Authors: Dixit Vinod Kumar , Sahu Manoj Kumar , Venkatesh Vybhav , Bhargav Varanasi Yugandhar , Kumar Vinod , Pateriya Mayank Bhushan , Venkataraman Jayanthi
Published: September 2022

Many gastrointestinal (GI) disorders present to the emergency room with acute clinical presentations, some even life threatening. Common emergencies encountered that require urgent endoscopic interventions include GI hemorrhage (variceal and nonvariceal), foreign body ingestion, obstructive jaundice, postprocedure-related complications such as postpolypectomy bleed or perforation, etc. A major advantage of emergency endoscopy is that it is cost effective and, on many occasions, can be life-saving. The present review will highlight a practical approach on various endoscopic modalities and their use in the GI emergencies.
Associations of digestibility with phenotypic and genetic variation in methane production in Angus cattle
Authors: Smith H. C. , Herd R. M. , Donoghue K. A. , Bird-Gardiner T. , Arthur P. F. , Hegarty R. S.
Published: September 2022

Context Cattle and sheep emit methane, a potent greenhouse gas, as part of the fermentation process of feed digestion in their gut; however, the mechanisms explaining differences among animals in enteric methane production are not fully understood. Aim To investigate whether variation among animals in their ability to digest their test ration was associated with phenotypic and genetic variation in methane production. Methods The experiment used 135 Angus beef cattle measured for their phenotypic and genetic merit for methane production. The extent of digestion of the dry matter (DMD) in the test ration by individual cattle was determined using silica as a naturally present indigestible marker. Its concentration in feed consumed and faeces was determined using rapid portable X-ray fluorescence spectroscopy, from which DMD was calculated. Key results Higher daily methane-production rate (MPR), higher methane produced per unit of feed consumed (methane yield; MY) and higher methane produced than the predicted daily production (residual MPR; RMP) by animals was accompanied by higher DMD. Higher genetic merit for MPR was also accompanied by higher DMD, but DMD had no detectable association with genetic variation in the other two methane emission traits. The regression coefficients for change in MPR (g/day), MY (g/kg DMI), RMP (g/day) with change in DMD (%) were 2.6 ± 1.1 (s.e.; P < 0.05), 0.14 ± 0.07 (P < 0.1) and 0.68 ± 0.38 (P < 0.1) respectively. Conclusions Differences among animals in their DMD were found and were associated with phenotypic variation in the three methane emission traits studied, and with genetic variation in daily methane production. The results support the caution that feeding and breeding interventions seeking to reduce methane emissions can also reduce the extent of digestion of feed by cattle. Implications Feeding and breeding interventions that seek to reduce methane emissions may change rumen physiology and reduce the extent of digestion of feed by cattle, which may be undesirable.
Microbiome engineering to combat antimicrobial resistance and upsurge productivity of food animals: a systematic review
Authors: Johar Al-Reem A. , Abu-Rub Lubna I. , Al Mana Hassan , Yassine Hadi M. , Eltai Nahla O.
Published: September 2022

Extensive antimicrobial usage in animal farming plays a prominent role in the antimicrobial resistance (AMR) crisis and is repeatedly highlighted as an area needing development under the ‘One Health’ approach. Alternative therapies such as microbiome products can be used as prophylaxis to help avoid infectious disease. However, a limited number of studies have focused on AMR-targeted microbiome products. We conducted this systematic review by using PRISMA guidelines to screen for literature that have evaluated food animals’ health when administrated with microbiome products targeting antimicrobial resistance (AMR) or antibiotic-resistant genes (ARGs). We searched and examined studies from SCOPUS, Web of Science, Embase, and Science direct databases for studies published up to November 2021, restricted to the English language. The findings of this review showed that microbiome products have a promising capability to tackle specific AMR/ARGs coupled with animal’s health and productivity improvement. Furthermore, our study showed that probiotics were the most favourable tested microbiome products, with the most targeted resistance being to tetracycline, macrolides, and beta-lactams. While microbiome products are promising alternatives to antibiotic prophylactics, there is a dearth of studies investigating their efficacy in targeting AMR. Thus, it is highly recommended to further investigate, develop, and improve the microbiome, to better understand their utility and circumvent their limitations.
Genotypic variability and physio-morphological efficiency of buckwheat (
Authors: Hajong Subarna , Rangappa Krishnappa , Dasaiah Harish Ganjalagatta , Moirangthem Prabha , Saikia Uday Sankar , Bhattacharjee Bijoya , Ahlawat Sudhir Pal , Kandpal Basant Kumar
Published: September 2022

Context Crop production in Eastern Himalaya is constrained by combined effects of soil acidity and moisture deficit during post monsoon under a changing climate. Aim This study aimed to identify potential buckwheat genotypes and stress mechanisms in hill environments of Meghalaya (India). Method Field and microcosm experiments were conducted to study field performance, genotypic variability and physio-morphological efficiency in buckwheat. Key results Substantial genetic variability for shoot length (30.3–110 cm), crop canopy distribution (3.0–7.5 number of primary branches), leaf area retention (15.7–60.2 cm2/two leaves), 1000 seed weight (16.2–34.7 g) and seed yield (0.088–1.31 metric tonne (MT)/ha) was observed. Mean grain yield of buckwheat genotypes was 0.446 MT/ha whereas IC13411, IC24298 and IC37305 produced significantly higher seed yield (1.31, 1.28 and 1.14 MT/ha, respectively) accounting to 1.93, 1.87 and 1.67 times higher than average yield (0.680 MT/ha). Genotypes like IC42416, EC323730 and EC218784 have lower crop yields (0.8, 1.02, 0.93 MT/ha respectively). Interestingly, few high yielders (IC13411 and IC24298) exhibited higher photosynthetic rate (46.1 and 32.3 μmol/m2.s), increased stomatal conductance (311.0 and 326.2 mmol/m2.s), leaf chlorophyll (2.47 and 2.55 mg/g fresh weight (FW)) and carotenoids (95 and 106.3 μg/g FW). Chlorophyll a and b ratio (3.3 and 3.0) and total chlorophyll to carotenoids (4.2 and 4.0) were higher in high yielders (IC13411 and IC24298) compared to other low yielders. Conclusions Robust root systems, stomatal structure and higher cuticle wax ideally enhanced water use efficiency (WUE) and drought tolerance in high-yielding buckwheat genotypes. Implications IC13411 and IC24298 are promising for enhanced productivity in the mountainous ecosystem of Meghalaya.
Smart Glass with Multi-Functionalities for Assisting Visually Impaired People
Authors: Sudharshan G , Sowdeshwar S , Jagannath M
Published: September 2022

Smart glass is a device that is obliging for visually impaired people. It becomes difficult for impaired people to recognize objects in front of them, study, etc. The objective of the work is to design and develop a device that is obliging for visually impaired people. Though, there are many approaches to help them, the major disadvantage of some of the products that are currently present in the market is that they are very costly and bulky. Also, some of the proposed systems either perform only object recognition or only help in reading the text. Almost all proposed systems did not help the visually impaired people to write or to have a hardcopy in the form of braille code which then helps them to read offline. To overcome the disadvantages mentioned above the paper discusses various techniques- Seeing mode, which can recognize 550 classes of objects along with object’s position (Left, Right or Centre). Moreover, in the reading mode, it recognizes the text in front of the person which is then read out loud to the user along with creating a copy of the braille script. Further, in the writing mode, speech is converted to a file containing braille codes.
Gender Differences in Postural Stability in a Cohort of Adolescent Age
Authors: Varsha S , Anbalagan Deepa , Adalarasu K , Jagannath M , Celestin Jerald A
Published: September 2022

Daily tasks necessitate improved locomotive abilities and movements, which are determined by an individual’s balance control. Body postures allows us to stay in a stable and balanced stance without falling. The present study examines postural stability in males and females using centre of pressure metrics in two planes for the adolescent group. Force data was collected in three directions (Fx, Fy, and Fz) using a standard force platform (SENSIX force plates) under two support and two visual conditions, including eyes-open, stand-up on two limbs (OB), eyes-closed, stand-up on two limbs (CB), eyes-open, stand-up on single limb (OO), eyes-closed, stand-up on single limb (CO). The CoP was determined in both the antero-posterior and medio-lateral planes. Two features were derived from the CoP data: sway and average velocity in both planes. The findings demonstrate that for all experimental conditions in both directions, CoP characteristics (sway and velocity) of male gender were significantly (p<0.05) higher than female gender. This work concludes that males have higher postural stability than females of similar age, indicating that hormonal variables such as thyroid, estrogens, and others reduce postural stability.
Efficient Cardiac Arrhythmia Detection Using Machine Learning Algorithms
Authors: Anandha Praba R , Suganthi L , Selva Priya E S , Jeslin Libisha J
Published: September 2022

The most common type of chronic and life-threatening disease is cardiovascular disease (CVD). For the early prediction of arrhythmia, electrocardiogram (ECG) is recorded from the patients, non-invasively using surface electrode. In this approach, Empirical Mode Decomposition (EMD) is performed for noise removal followed by Pan Tompkins algorithm for feature extraction. To reduce the amount of signal characteristics and computation time, Principal Component Analysis (PCA) is utilized. Finally, two classifiers, The Support Vector Machine (SVM) and the Naive Bayes (NB) classifier is used to determine the cardiac abnormality from the ECG signal. The comparison is made between the two classifiers and their accuracy will be analysed. We obtained 89% accuracy for SVM and 99% for NB classifier. Lakhs of samples will be available in the Physionet. The amplitude of the signal is 0.1 Mv and time period (T) is 10ms and the frequency of 100Hz. The Confusion Matrix can then be used to assess how well an ECG signal is performing. A MATLAB program is used which has the capacity to observe the ECG bio-signal on a computer.
Method for registration of vaccines for covid 19, through nfc technology
Authors: Auccahuasi Wilver , Herrera Lucas , Rojas Karin , Martinez Hernando Campos , Ponce Erick Loja , Sotomayor Daniel Yucra , Herrera Salazar José Luis
Published: September 2022

In these times of pandemic caused by Covid-19, new ways of dealing with the effects of the virus emerge, for this reason multiple measures are being carried out with the intention of mitigating its effects in the event of a possible contagion, which is why vaccinations are being carried out massive in order to be able to defend oneself against potential contagions, in this work an application made using the NFC communication protocol that mobile devices have is shown, as a result the demonstration of the use of the application is presented, where it reflects the data to be entered and can be viewed from any device.
Experimental Analysis of Biometric System using Various Multimodal Fusion Algorithms
Authors: Poornima S , Subramanian S
Published: September 2022

Demand for high end privacy and security in human computer interaction, telecom environment is very high in the era of digital world. Multibiometric system combines information from multiple biometric traits of an individual and has an exceptional ability to address these demands with add-on customer satisfaction. It also overcomes intra class variations, non-universality, noisy data and attacks during authentication process. This paper proposes a multibiometric system suitable for secure access of data, devices and services. A database has been constructed using real time multiple biometric samples acquired from 500 individuals in an unconstrained environment. Existence of noise in the samples captured in an unconstrained environment are removed using filtering techniques, and the contrast is adjusted using dark channel priorities and scattering model. Then, the region of interest and features appropriate to each trait are extracted and fused in various forms like multiple samples, instances and traits in recognizing an individual. The proposed system is analysed by computing genuine and false acceptance rates. With the promising experimental results of various fusion schemes, the authentication is tested using transfer learning process with automatic extraction of essential features using Convolution Neural Network and classifying the target using Support Vector Machine (SVM), which outperforms in identifying an individual through fusion of biometric features acquired even in an unconstrained environment. Hence this authentication process could be modified into an effective one to identify and monitor the user interacting with a security related application in online mode with their unique available unconstrained features.
Detection and optimization of skin cancer using deep learning
Authors: Balambigai S , Elavarasi K , Abarna M , Abinaya R , Arun Vignesh N
Published: September 2022

Convolutional Neural Network (CNN) is a branch of deep learning which has been one of a popular methods in different applications, especially in medical field. In this study, an optimized CNN model is built using the random search optimization to classify seven types of skin cancer, namely, basal cell carcinoma, melanoma, dermatofibroma, vascular lesion, melanocytic nevus, actinic keratosis and benign keratosis. Total of 10,015 images were collected from the Human Against Machine dataset (HAM10000) which is available in Kaggle, Even though CNN has shown best results in many applications, the hyper-parameters that are required to build CNN model is difficult to choose. If the chosen hyper-parameters doesn’t show good results, the model should be trained again with other set of hyper-parameter values. To avoid this circumstance, the hyper-parameter optimization is required and in this study, it is done using random search optimization. A base CNN model is initially created without using any optimization technique, so that the performance of the CNN model which is optimized by the random search method can be compared and analysed. The first model provided an accuracy of 73.34%, whereas the optimized model shown an improvement in accuracy of 77.17%.
Promoting continence in older people
Authors: Schlögl Mathias , Umbehr Martin H , Habib Muhammad Hamza , Wagg Adrian , Gordon Adam L , Harwood Rowan
Published: September 2022

The prevalence of urinary incontinence (UI) is strongly associated with increasing age. Twenty five percent of women over 80 years of age have clinically significant symptoms in population surveys, but prevalence is as high as 70% in older hospital in-patients and residents of care homes with nursing. UI substantially affects quality of life and well-being, and generates significant economic burden for health and social care. Sadly, UI is considered as taboo by society, leading to isolation, depression and reluctance to seek help. As with all aspects of care of older people, a multi-modal approach to assessment and management is needed. Key to effective management of incontinence is recognition. As a minimum, clinicians should actively ask patients about continence, especially in older adults living with frailty. Careful evaluation and establishment of any underpinning diagnosis and aetiological factors requires comprehensive, multimodal, usually multidisciplinary, assessment. A lack of awareness of the problem and what can be done about it exists in both laypeople and clinicians, this needs correcting. An interdisciplinary approach to research and management must be the way into the future.
Low-density lipoprotein cholesterol in oldest old with acute myocardial infarction: Is lower the better?
Authors: Liu Hui-Hui , Zhang Meng , Chen Run-Zhen , Zhou Jin-Ying , Qian Jie , Dou Ke-Fei , Yan Hong-Bing , Li Jian-Jun
Published: September 2022

Background

the relationship between low-density lipoprotein cholesterol (LDL-C) and adverse outcomes among the older people remains controversial.

Objective

to further clarify the association between admission LDL-C levels and cardiovascular mortality (CVM) among oldest old individuals (≥80 years) with acute myocardial infarction (AMI).

Design

a prospective cohort study.

Setting

two-centre.

Subjects

a consecutive sample of 1,224 oldest old individuals with AMI admitted to Beijing FuWai and Shenzhen FuWai hospitals.

Methods

all individuals were subdivided according to baseline LDL-C levels (<1.8, 1.8–2.6 and ≥ 2.6 mmol/l) and further stratified by high-sensitivity C-reactive protein (hsCRP) concentrations (<10 and ≥10 mg/l). The primary outcome was CVM. The time from admission to the occurrence of CVM or the last follow-up was analysed in Kaplan–Meier and Cox analyses.

Results

the median age of the overall population was 82 years. During an average of 24.5 months’ follow-up, 299 cardiovascular deaths occurred. Kaplan–Meier analysis showed that LDL-C < 1.8 mmol/l group had the highest CVM among oldest old individuals with AMI. Multivariate Cox regression analysis further revealed that compared with those with LDL-C levels <1.8 mmol/l, subjects with LDL-C levels ≥2.6 mmol/l (hazard ratio: 0.67, 95% confidence interval: 0.46–0.98) had significantly lower risk of CVM, especially in those with high hsCRP levels. Moreover, when categorising according to LDL-C and hsCRP together, data showed that individuals with low LDL-C and high hsCRP levels had the highest CVM.

Conclusions

LDL-C < 1.8 mmol/l was associated with a high CVM after AMI in oldest old individuals, especially when combined with high hsCRP levels, which may need to be confirmed by randomised controlled trials.
Sarcoidosis in the older person: diagnostic challenges and treatment consideration
Authors: Brennan Michelle , Breen David
Published: September 2022

Background

Sarcoidosis is a multi-system disorder with an increasing propensity to present in older patients. Diagnostic uncertainty is common and understandable given the higher prevalence of co-morbidities in older patients and broad differential for multi-system clinical presentations. Excluding malignancy and infection with a high degree of certainty is challenging and may require repeated confirmatory investigation where the diagnosis remains in doubt.

Summary of main findings

There are a paucity of studies examining late-onset sarcoidosis. Female predominance, pulmonary, ocular, skin and systemic symptoms are common, while more classical presentations such as Lofgren’s syndrome are uncommon. Positivity rates of biopsies vary between studies; however, targeted biopsies of accessible sites with organ involvement are the most successful. Therapeutic management is directed at reducing inflammation, and thereby reducing symptom burden, improving quality of life and avoiding progression of organ damage. While most older patients will require corticosteroid therapy, they are also more prone to developing adverse effects. Most older patients will experience a clinical remission; however, the risk of developing chronic sarcoidosis and organ damage is higher compared with younger counterparts. Patients with evidence of pulmonary fibrosis and pulmonary hypertension are at particular risk.

Impact on clinical practice

Health care providers who care for older adults should be aware of the increasing prevalence of late-onset sarcoidosis and consider the diagnosis in those who present with otherwise unexplained systemic symptoms, thoracic abnormalities on imaging and/or evidence of other organ involvement. Earlier diagnosis and therapeutic intervention to halt the development of pulmonary fibrosis and pulmonary hypertension and monitoring for treatment-related adverse effects will confer a mortality benefit.
The genetic algorithm-aided three-stage ensemble learning method identified a robust survival risk score in patients with glioma
Authors: Zhu Sujie , Kong Weikaixin , Zhu Jie , Huang Liting , Wang Shixin , Bi Suzhen , Xie Zhengwei
Published: September 2022

Ensemble learning is a kind of machine learning method which can integrate multiple basic learners together and achieve higher accuracy. Recently, single machine learning methods have been established to predict survival for patients with cancer. However, it still lacked a robust ensemble learning model with high accuracy to pick out patients with high risks. To achieve this, we proposed a novel genetic algorithm-aided three-stage ensemble learning method (3S score) for survival prediction. During the process of constructing the 3S score, double training sets were used to avoid over-fitting; the gene-pairing method was applied to reduce batch effect; a genetic algorithm was employed to select the best basic learner combination. When used to predict the survival state of glioma patients, this model achieved the highest C-index (0.697) as well as area under the receiver operating characteristic curve (ROC-AUCs) (first year = 0.705, third year = 0.825 and fifth year = 0.839) in the combined test set (n = 1191), compared with 12 other baseline models. Furthermore, the 3S score can distinguish survival significantly in eight cohorts among the total of nine independent test cohorts (P < 0.05), achieving significant improvement of ROC-AUCs. Notably, ablation experiments demonstrated that the gene-pairing method, double training sets and genetic algorithm make sure the robustness and effectiveness of the 3S score. The performance exploration on pan-cancer showed that the 3S score has excellent ability on survival prediction in five kinds of cancers, which was verified by Cox regression, survival curves and ROC curves together. To enable its clinical adoption, we implemented the 3S score and other two clinical factors as an easy-to-use web tool for risk scoring and therapy stratification in glioma patients.
Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments
Authors: Gable Annika L , Szklarczyk Damian , Lyon David , Matias Rodrigues João F , von Mering Christian
Published: September 2022

A knowledge-based grouping of genes into pathways or functional units is essential for describing and understanding cellular complexity. However, it is not always clear a priori how and at what level of specificity functionally interconnected genes should be partitioned into pathways, for a given application. Here, we assess and compare nine existing and two conceptually novel functional classification systems, with respect to their discovery power and generality in gene set enrichment testing. We base our assessment on a collection of nearly 2000 functional genomics datasets provided by users of the STRING database. With these real-life and diverse queries, we assess which systems typically provide the most specific and complete enrichment results. We find many structural and performance differences between classification systems. Overall, the well-established, hierarchically organized pathway annotation systems yield the best enrichment performance, despite covering substantial parts of the human genome in general terms only. On the other hand, the more recent unsupervised annotation systems perform strongest in understudied areas and organisms, and in detecting more specific pathways, albeit with less informative labels.
Learning global dependencies and multi-semantics within heterogeneous graph for predicting disease-related lncRNAs
Authors: Xuan Ping , Wang Shuai , Cui Hui , Zhao Yue , Zhang Tiangang , Wu Peiliang
Published: September 2022

Motivation

Long noncoding RNAs (lncRNAs) play an important role in the occurrence and development of diseases. Predicting disease-related lncRNAs can help to understand the pathogenesis of diseases deeply. The existing methods mainly rely on multi-source data related to lncRNAs and diseases when predicting the associations between lncRNAs and diseases. There are interdependencies among node attributes in a heterogeneous graph composed of all lncRNAs, diseases and micro RNAs. The meta-paths composed of various connections between them also contain rich semantic information. However, the existing methods neglect to integrate attribute information of intermediate nodes in meta-paths.

Results

We propose a novel association prediction model, GSMV, to learn and deeply integrate the global dependencies, semantic information of meta-paths and node-pair multi-view features related to lncRNAs and diseases. We firstly formulate the global representations of the lncRNA and disease nodes by establishing a self-attention mechanism to capture and learn the global dependencies among node attributes. Second, starting from the lncRNA and disease nodes, respectively, multiple meta-pathways are established to reveal different semantic information. Considering that each meta-path contains specific semantics and has multiple meta-path instances which have different contributions to revealing meta-path semantics, we design a graph neural network based module which consists of a meta-path instance encoding strategy and two novel attention mechanisms. The proposed meta-path instance encoding strategy is used to learn the contextual connections between nodes within a meta-path instance. One of the two new attention mechanisms is at the meta-path instance level, which learns rich and informative meta-path instances. The other attention mechanism integrates various semantic information from multiple meta-paths to learn the semantic representation of lncRNA and disease nodes. Finally, a dilated convolution-based learning module with adjustable receptive fields is proposed to learn multi-view features of lncRNA-disease node pairs. The experimental results prove that our method outperforms seven state-of-the-art comparing methods for lncRNA-disease association prediction. Ablation experiments demonstrate the contributions of the proposed global representation learning, semantic information learning, pairwise multi-view feature learning and the meta-path instance encoding strategy. Case studies on three cancers further demonstrate our method’s ability to discover potential disease-related lncRNA candidates.

Contact

zhang@hlju.edu.cn or peiliangwu@ysu.edu.cn

Supplementary information

Supplementary data are available at Briefings in Bioinformatics online.
TSomVar: a tumor-only somatic and germline variant identification method with random forest
Authors: Shi Shuo , Wang Qi , Shang Yunfei , Bu Congfan , Lu Mingming , Jiang Meiye , Zhang Hao , Yu Shuhuan , Zeng Jingyao , Zhang Zaichao , Du Zhenglin , Xiao Jingfa
Published: September 2022

Somatic variants act as critical players during cancer occurrence and development. Thus, an accurate and robust method to identify them is the foundation of cutting-edge cancer genome research. However, due to low accessibility and high individual-/sample-specificity of the somatic variants in tumor samples, the detection is, to date, still crammed with challenges, particularly when lacking paired normal samples as control. To solve this burning issue, we developed a tumor-only somatic and germline variant identification method (TSomVar) using the random forest algorithm established on sample-specific variant datasets derived from genotype imputation, reads-mapping level annotation and functional annotation. We trained TSomVar by using genomic variant datasets of three major cancer types: colorectal cancer, hepatocellular carcinoma and skin cutaneous melanoma. Compared with existing tumor-only somatic variant identification tools, TSomVar shows excellent performances in somatic variant detection with higher accuracy and better capability of recalling for test datasets from colorectal cancer and skin cutaneous melanoma. In addition, TSomVar is equipped with the competence of accurately identifying germline variants in tumor samples. Taken together, TSomVar will undoubtedly facilitate and revolutionize somatic variant explorations in cancer research.
A novel circRNA-miRNA association prediction model based on structural deep neural network embedding
Authors: Guo Lu-Xiang , You Zhu-Hong , Wang Lei , Yu Chang-Qing , Zhao Bo-Wei , Ren Zhong-Hao , Pan Jie
Published: September 2022

A large amount of clinical evidence began to mount, showing that circular ribonucleic acids (RNAs; circRNAs) perform a very important function in complex diseases by participating in transcription and translation regulation of microRNA (miRNA) target genes. However, with strict high-throughput techniques based on traditional biological experiments and the conditions and environment, the association between circRNA and miRNA can be discovered to be labor-intensive, expensive, time-consuming, and inefficient. In this paper, we proposed a novel computational model based on Word2vec, Structural Deep Network Embedding (SDNE), Convolutional Neural Network and Deep Neural Network, which predicts the potential circRNA-miRNA associations, called Word2vec, SDNE, Convolutional Neural Network and Deep Neural Network (WSCD). Specifically, the WSCD model extracts attribute feature and behaviour feature by word embedding and graph embedding algorithm, respectively, and ultimately feed them into a feature fusion model constructed by combining Convolutional Neural Network and Deep Neural Network to deduce potential circRNA-miRNA interactions. The proposed method is proved on dataset and obtained a prediction accuracy and an area under the receiver operating characteristic curve of 81.61% and 0.8898, respectively, which is shown to have much higher accuracy than the state-of-the-art models and classifier models in prediction. In addition, 23 miRNA-related circular RNAs (circRNAs) from the top 30 were confirmed in relevant experiences. In these works, all results represent that WSCD would be a helpful supplementary reliable method for predicting potential miRNA-circRNA associations compared to wet laboratory experiments.
Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data
Authors: Mercatelli Daniele , Cabrelle Chiara , Veltri Pierangelo , Giorgi Federico M , Guzzi Pietro H
Published: September 2022

Cell surface proteins have been used as diagnostic and prognostic markers in cancer research and as targets for the development of anticancer agents. Many of these proteins lie at the top of signaling cascades regulating cell responses and gene expression, therefore acting as ‘signaling hubs’. It has been previously demonstrated that the integrated network analysis on transcriptomic data is able to infer cell surface protein activity in breast cancer. Such an approach has been implemented in a publicly available method called ‘SURFACER’. SURFACER implements a network-based analysis of transcriptomic data focusing on the overall activity of curated surface proteins, with the final aim to identify those proteins driving major phenotypic changes at a network level, named surface signaling hubs. Here, we show the ability of SURFACER to discover relevant knowledge within and across cancer datasets. We also show how different cancers can be stratified in surface-activity-specific groups. Our strategy may identify cancer-wide markers to design targeted therapies and biomarker-based diagnostic approaches.
Prophylactic Medication for the Prevention of Endoscopic Recurrence in Crohn’s Disease: a Prospective Study Based on Clinical Risk Stratification
Authors: Arkenbosch Jeanine H C , Beelen Evelien M J , Dijkstra Gerard , Romberg-Camps Mariëlle , Duijvestein Marjolijn , Hoentjen Frank , van der Marel Sander , Maljaars P W Jeroen , Jansen Sita , de Boer Nanne K H , West Rachel L , Horjus Carmen S , Stassen Laurents P S , van Schaik Fiona D M , van Ruler Oddeke , Jharap Bindia J H , Visschedijk Marijn , Janssen Alfred , Erler Nicole S , Doukas Michail , Ooms Ariadne H A G , Kats-Ugurlu Gursah , van der Woude Christien Janneke , de Vries Annemarie C
Published: September 2022

Background

To prevent recurrence after ileocolonic resection [ICR] in Crohn’s disease [CD], postoperative prophylaxis based on risk stratification is recommended in international guidelines. This study aimed to evaluate postoperative CD recurrence after implementation of a clinical management algorithm and to determine the predictive value of clinical and histological risk factors [RFs].

Methods

In this multicentre, prospective cohort study, CD patients [≥16 years] scheduled for ICR were included. The algorithm advised no postoperative medication for low-risk patients, and treatment with prophylaxis [immunosuppressant/biological] for high-risk patients [≥1 RF: active smoking, penetrating disease, prior ICR]. Clinical and histological RFs [active inflammation, granulomas, plexitis in resection margins] for endoscopic recurrence [Rutgeerts’ score ≥i2b at 6 months] were assessed using logistic regression and ROC curves based on predicted probabilities.

Results

In total, 213 CD patients after ICR were included [age 34.5 years; 65% women] (93 [44%] low-risk; 120 [56%] high-risk: 45 [38%] smoking; 51 [43%] penetrating disease; 51 [43%] prior ICR). Adherence to the algorithm was 82% in low-risk [no prophylaxis] and 51% in high-risk patients [prophylaxis]. Endoscopic recurrence was higher in patients treated without prophylaxis than with prophylaxis in both low [45% vs 16%, p = 0.012] and high-risk patients [49% vs 26%, p = 0.019]. Clinical risk stratification including the prescription of prophylaxis corresponded to an area under the curve [AUC] of 0.70 (95% confidence interval [CI] 0.61–0.79). Clinical RFs combined with histological RFs increased the AUC to 0.73 [95% CI 0.64–0.81].

Conclusion

Adherence to this management algorithm is 65%. Prophylactic medication after ICR prevents endoscopic recurrence in low- and high-risk patients. Clinical risk stratification has an acceptable predictive value, but further refinement is needed.
How to optimize the adherence to a guideline-directed medical therapy in the secondary prevention of cardiovascular diseases: a clinical consensus statement from the European Association of Preventive Cardiology
Authors: Pedretti Roberto F E , Hansen Dominique , Ambrosetti Marco , Back Maria , Berger Thomas , Ferreira Mariana Cordeiro , Cornelissen Véronique , Davos Constantinos H , Doehner Wolfram , de Pablo y Zarzosa Carmen , Frederix Ines , Greco Andrea , Kurpas Donata , Michal Matthias , Osto Elena , Pedersen Susanne S , Salvador Rita Esmeralda , Simonenko Maria , Steca Patrizia , Thompson David R , Wilhelm Matthias , Abreu Ana
Published: September 2022

A key factor to successful secondary prevention of cardiovascular disease (CVD) is optimal patient adherence to treatment. However, unsatisfactory rates of adherence to treatment for CVD risk factors and CVD have been observed consistently over the last few decades. Hence, achieving optimal adherence to lifestyle measures and guideline-directed medical therapy in secondary prevention and rehabilitation is a great challenge to many healthcare professionals. Therefore, in this European Association of Preventive Cardiology clinical consensus document, a modern reappraisal of the adherence to optimal treatment is provided, together with simple, practical, and feasible suggestions to achieve this goal in the clinical setting, focusing on evidence-based concepts.
Slugging in horizontal channel flow
Authors: Giddings Josef Adam , Billingham John , Cox Stephen Michael
Published: September 2022

The stratified flow of gas–liquid mixtures is important in many industries, in particular oil and gas, where the formation of liquid slugs is usually undesirable. In this paper, we analyse the hydraulic model for turbulent, two-layer, gas–liquid flow in a horizontal channel developed by Needham et al. (2008, The development of slugging in two-layer hydraulic flows, IMA J. Appl. Math., 73, 274–322) who considered only the thin layer limit, for liquid layers of arbitrary thickness. This allows us to consider the effect of the prescribed inlet velocity ratio and the interaction of the gas layer with the upper wall of the channel on the formation of slug formation.

We show that there is a critical Froude number above which small-amplitude disturbances to the uniform flow are unstable and grow to form non-linear roll waves. We investigate the existence of periodic travelling wave solutions and find that these are strongly influenced by the existence of two equilibrium solutions that are not present when the liquid layer is thin. The system of ordinary differential equations that describe travelling wave solutions has a complicated phase portrait which we study in some typical cases. We find that periodic solutions that have the channel close to filled with liquid can exist, and we identify them as slugs. We also study an initial value problem driven by noise at the inlet of the channel and find that structures locally similar to these periodic travelling waves are generated. We provide numerical evidence for the formation of slugs in cases where the initial liquid to homogeneous velocity ratio is greater than 0.5.
Utilization of pharmacological labour analgesia: a survey of obstetric care providers in eastern Ethiopia
Authors: Eyeberu Addis , Getachew Tamirat , Debella Adera , Balis Bikila , Eshetu Bajirond , Mesfin Sinetibeb , Bekele Habtamu , Tamiru Dawit , Tiruye Getahun , Degefa Meron , Alemu Addisu , Dheressa Merga , Dessie Yadeta
Published: September 2022

Background

Despite a crucial role played by obstetric care providers (OCPs) in providing pain relief methods during labour, the evidence suggests that there is a large number of women in Ethiopia who did not have access to pain relief methods. Moreover, to the best of the investigators’ knowledge, evidence is scarce regarding the utilization of pharmacological labour pain management methods in the study area. Thus this study was carried out to determine the practice of pharmacological labour pain management methods among OCPs in Harari regional state health facilities in Ethiopia.

Methods

A facility-based cross-sectional study was conducted from 20 May to 10 June 2021 in Harari regional state health facilities. All (n=464) OCPs in Harari regional state health facilities were included in the study. Data were collected using a structured questionnaire adapted from previous studies. The data were entered into Epi-data version 3.1 statistical software. Statistical analysis was carried out using SPSS for Windows version 22. Bivariate and multivariate logistic regression analyses were employed to determine the association between independent variables and the outcome variable. A p-value <0.05 was used to establish statistical significance.

Results

In this study, 464 OCPs participated. The overall utilization of pharmacological labour pain relief methods was 50.9% (95% confidence interval [CI] 45.8 to 55.8). The main barriers to labouring mothers receiving pain relief include high patient flow (54.4%), the limited number of staff (51.9%) and a lack of knowledge and skill (32.9%). Being female (adjusted odds ratio [AOR] 2.07 [95% CI 1.31 to 3.26]), not having training (AOR 1.60 [95% CI 1.02 to 2.53]) and having an unfavourable attitude (AOR 9.1 [95% CI 5.34 to 15.35]) were the predictors of utilization of pharmacological labour pain management methods.

Conclusions

The study revealed that half of the OCPs utilized the pharmacological labour pain management method. In general, this study identified that variables like sex, training and the attitude of OCPs were factors associated with the utilization of pharmacological labour pain management methods. The health facilities should provide training to enhance the skill of OCPs and equip themselves with sufficient analgesic drugs.
Impact of a continuous quality improvement program on contrast-induced nephropathy in outpatients with chronic kidney disease: an interrupted time-series study
Authors: Hirano Keita , Kobayashi Daiki , Shimbo Takuro , Komatsu Yasuhiro
Published: September 2022

Background

Contrast-induced nephropathy (CIN) caused by exposure to radioactive contrast media can cause acute kidney injury in patients with chronic kidney disease (CKD). We developed a multifaceted approach in a CIN-quality improvement (QI) program based on a shorter saline hydration protocol for the prevention of CIN in outpatients and assessed the effect of our CIN-QI program on decreasing both the incidence rate of CIN and overall use of contrast agents in patients undergoing contrast-enhanced computed tomography (CT).

Methods

We conducted a multi-center prospective interrupted time-series study from 2006 to 2018 investigating the efficacy of a CIN-QI program in preventing CIN among outpatients with CKD. An automatic medical record system alert was implemented to instruct physicians to consult a nephrologist and administer prophylactic hydration and follow-up when ordering contrast-enhanced imaging in patients with an estimated glomerular filtration rate (eGFR) <45 mL/min/1.73 m2. The primary outcomes were the rates of prophylactic hydration and follow-up kidney function assessment, and the incidence of CIN for eligible patients. The usage rate of contrast-enhanced CT was also examined.

Results

A total of 95 594 patients who underwent contrast-enhanced CT were included in the study. The annual prophylactic hydration rate before the CIN-QI program ranged from 2.0% to 23.2% but increased to 59.2%–75.2% during the CIN-QI program (P < .001). The annual rate of follow-up kidney function testing also improved from 18.6%–25.8% to 34.1%–42.5% after implementation of the CIN-QI program (P < .001). The rate of CIN significantly declined in level by 10.0% at the start of the CIN-QI program (P = .002) and in trend by 2.9%/year (P < .001). The number of contrast-enhanced CT orders showed a positive level change in patients with advanced CKD, who were the CIN-QI program target group of patients with eGFR <45 mL/min/1.73 m2, at the start of the implementation of the CIN-QI program. After implementing the CIN-QI program, the number of contrast-enhanced CT orders showed a negative trend change across all patients, which decreased from −1.4%/year to −10.0%/year for patients with advanced CKD.

Conclusion

The multifaceted approach in the CIN-QI program may be associated with the decreased incidence of CIN and increased rates of prophylactic hydration and follow-up kidney function testing.