bluuebunny/crossref_metadata_2025_split huggingface dataset:
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
Authors: Santos João Dourado , Sobral Daniel , Pinheiro Miguel , Isidro Joana , Bogaardt Carlijn , Pinto Miguel , Eusébio Rodrigo , Santos André , Mamede Rafael , Horton Daniel L , Gomes João Paulo , consortium* TELEVIR , Borges Vítor 
Published: November 2023

Abstract

Background
Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU (https://insaflu.insa.pt/), a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification.
Results
The routine genomic surveillance component was strengthened with new workflows and functionalities, including: i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; ii) automated SARS-CoV-2 lineage classification; iii) Nextclade analysis; iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a “generic” build for other viruses); and, v) algn2pheno (https://github.com/insapathogenomics/algn2pheno) for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer) and databases (RefSeq viral genome, Virosaurus, etc), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime (https://github.com/INSaFLU/findONTime), a tool aimed at reducing costs and the time between sample reception and diagnosis.
Conclusion
The accessibility, versatility and functionality of INSaFLU-TELEVIR is expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
Experimental Investigation of Biogas Injera Baking Stove Using Circular Ring Pipe Burner
Authors: Abdella Taha 
Published: November 2023

Abstract
Baking and cooking are day-to-day human activities that demand energy from different sources. Injera is stapled food in Ethiopia mainly baked by traditional biomass injera baking stoves. In order to minimize the environmental and social impact of traditional non-clean energy sources of energy, different research has studied replacing traditional stoves with clean and renewable energy sources. However, the developed injera baking stove has low performance and heat distribution problems. The purpose of this study is to solve this problem by developing injera baking biogas stove with better performance. The experimental investigation was conducted using a biogas plant in Addis Ababa University 4 Kilo Campus. A detailed energy analysis of energy demand, energy output, and baking performance has been performed. Baking time is 3 minutes, Idle time is 2 minutes and efficiency is 68%. Thus, this injera baking biogas stove has achieved uniform heat distribution and improved efficiency and hence can be used for injera biogas injera baking stove.
An Improved Toolkit of Gateway- and Gibson Assembly-Compatible Vectors for Protoplast Transfection and Agrobacterium-Mediated Plant Transformation
Authors: Allen Jeffrey , Flanagan Michael , Pathak Sunita , Emenecker Samantha , Emenecker Ryan , Strader Lucia 
Published: November 2023

Abstract

Objective Understanding the regulation and function of plant genes is essential for addressing the challenges faced by modern agriculture. Plant transformation, in conjunction with fluorescence microscopy, offers a powerful approach to investigate the dynamic behavior of plant genes and the proteins they encode. We previously developed a set of Gateway-compatible tissue-specific plant transformation vectors. In this paper we aim to expand the toolkit of vectors available for Agrobacterium-mediated plant transformation and protoplast transfection.Results Here, we introduce new Agrobacterium-mediated plant transformation vectors by introducing additional fluorophores to create the pJRA vector series. Additionally, we introduce the pLCS series of vectors, a new set of modular Gateway- and Gibson assembly-compatible vectors designed for protoplast transfection. All described vectors are available from Addgene to serve as a resource for the plant research community.
High and Low Pitch Sound Stimuli Effects on HRV-EEG Coupling
Authors: vonJakitsch Camila Bomfim , Neto Osmar Pinto , Pinho Tatiana Okubo Rocha , Ribeiro Wellington , Pereira Rafael , Baltatu Ovidiu Constantin , Osório Rodrigo Aléxis Lazo 
Published: November 2023

Abstract
Purpose: This study aimed to explore the influence of sound stimulation on the autonomic nervous system and the potential coupling between cardiac and cerebral activities.
Methods: Thirty-one participants underwent exposure to periods of silence and two distinct continuous, non-repetitive pure tone stimuli: low pitch (110 Hz) and high pitch (880 Hz). Electroencephalography (EEG) data from electrodes F3, F4, F7, F8, Fp1, Fp2, T3, T4, T5, and T6, along with R-R interval data for heart rate, were recorded. Heart-brain connectivity was assessed using wavelet coherence between heart rate variability (HRV) and EEG envelopes (EEGE).
Results: We observed that heart rates were notably higher during silence compared to both high and low-pitch sound periods. The high-frequency (HF) band of HRV was significantly elevated across all tested conditions. However, an interaction between HRV bands and conditions emerged when examining normalized power. The low-pitch stimulus resulted in markedly reduced normalized power in the HF band compared to silence. Notably, HRV-EEGE coherence was considerably enhanced during silence and low-pitch sound intervals compared to high-pitch intervals, especially between the beta band and the low-frequency HRV range. This implies a differential involvement of the frontal and temporal brain regions, in response to varying auditory stimuli.
Conclusion: Our findings highlight the essential nature of discerning the complex interrelations between sound frequencies and their implications for heart-brain connectivity. Such insights could have ramifications for conditions like seizures and sleep disturbances. A deeper exploration is warranted to decipher the potential advantages or drawbacks of specific sound stimuli in diverse clinical scenarios.
Analysis of the transmission rate of SARS-CoV-2 Omicron subvariants BA.5.2 and BF.7 based on COVID-19 surveillance data.
Authors: Ke-Wei  , Qian-Qian  
Published: November 2023

Abstract

Background
The Chinese government, announced new 10 measures for COVID-19 response on December 7, 2022, which meant the thorough abolishment of the dynamic zero-COVID-19 policy. The actual number of SARS-CoV-2-infected residents was much larger than the official data due to the cancellation of large-scale nucleic acid testing.
Methods
This work is a re-analysis of published COVID-19 data. The COVID-19 surveillance data were derived from Human-Society Communication, which is a public service agency for employment. The information of the main endemic strains of SARS-CoV-2 in the Chinese mainland during the Omicron wave obtained from the Chinese Center for Disease Control and Prevention. Human-Society Communication issued online questionnaires of COVID-19 to all Chinese residents via the WeChat Public Account during December 20–21, 2022. Thereafter, Human-Society Communication issued online questionnaires of COVID-19 for the second time on December 26, 2022.
Results
A total of 122,806 residents participated in the first online questionnaire survey during the two days. The results showed that 74,689 participants (60.8%) were infected with SARS-CoV-2 Omicron variants. For the second online questionnaire survey, a total of 47,897 residents participated in the survey in a day. The results showed that the infection rate of COVID-19 in the Chinese mainland was increased from 60.8–73.5% during December 21–26, 2022. The main endemic strains of SARS-CoV-2 were BA.5.2 and BF.7 according to the analysis results of SARS-CoV-2 genome sequences.
Conclusions
Both SARS-CoV-2 Omicron subvariants BA.5.2 and BF.7 had extremely strong transmissibility, and large-scale COVID-19 infections posed unprecedented challenges on the Chinese mainland.
Modern aspects of managing patients with non-erosive reflux disease
Authors: Tsukanov V. V. , Vasyutin A. V. , Tonkikh Ju. L. 
Published: November 2023

A review of current data on the management of patients with non-erosive reflux disease (NERD) was made. Diagnosis of gastroesophageal reflux disease (GERD) is based on symptom analysis, endoscopic evaluation of the esophageal mucosa, objective evidence of gastric contents reflux into the esophagus during pH-impedancemetry, and response to therapeutic intervention. Treatment for GERD should include weight loss if overweight, lifestyle modification, and dietary modification. Current consensus recommends starting NERD treatment with once-daily proton pump inhibitors (PPIs), but only 50% of patients with this pathology respond to such therapy. Incomplete response to PPIs is a reason to increase the dose of PPI and add Gaviscon to treatment to neutralize the post-prandial “acid pocket”. Gaviscon is especially effective in patients with postprandial or nocturnal symptoms and in those with hiatal hernia. The mechanism of action of Gaviscon is based on the formation of an alginate “raft” on the surface of the gastric contents, which neutralizes the acid and blocks its pathological effect to esophageal mucosa. A modern meta-analysis on the NERD treatment, which included 23 studies and 10,735 patients, showed the efficacy of Gaviscon monotherapy comparable to PPIs in treatment for 4 weeks. The combination of a PPI with Gaviscon offers the opportunity to optimize response to treatment in NERD patients with an incomplete response to PPIs monotherapy. The Russian Gastroenterological Association thinks that alginates can be used both as monotherapy for mild clinical variants of NERD and in complex treatment regimens for various GERD variants.
A clinical case of aortic coarctation in combination with a septal defect in a newborn child
Authors: Sagitova G. R. , Tkachev I. V. , Antonova O. V. , Davydova O. V. 
Published: November 2023

Coarctation of the aorta is a congenital malformation characterized by the presence of narrowing of the aorta, which can be localized in any part of it. In this publication, we present a clinical case of coarctation of the aorta before and after surgical correction in a newborn. The child was admitted to the cardiosurgical hospital at the age of 6 days. Congenital heart disease of a low category of complexity was diagnosed prenatally. After birth, the condition is satisfactory. After 3 hours, the negative dynamics due to the clinic of respiratory failure. According to echocardiography – hypoplasia of the aortic arch, coarctation of the aorta? Open ductus arteriosus, ventricular septal defect. On the 3rd day of life, a diagnosis of congenital pneumonia was made and the child was transferred to a cardiosurgical hospital. Upon admission to the FCSSH in Astrakhan, the condition was regarded as severe, due to heart and respiratory failure. The child is examined. On echocardiography – Pronounced preductal form of coarctation of the aorta. Hypoplasia of the proximal arch and isthmus. Open ductus arteriosus. Ventricular septal defect. biventricular hypertrophy. Severe dilatation of the right chambers of the heart. Relative hypoplasia of the left ventricle. Tricuspid regurgitation. On the 7th day of life, surgical correction of the defect was performed plasty of the arch and isthmus of the aorta, plasty of the VSD. The early postoperative period proceeded with a clinic of moderate respiratory and heart failure. Against the background of the expansion of the volume of feeding, chylothorax was detected, drainage of the right pleural cavity was prescribed. Enteral feeding has been replaced by parenteral nutrition. The child was extubated on the 4th postoperative day. However, oxygen dependence was noted. The pleural drainage was removed on the 11th day after the operation. On the 12th day, the newborn was transferred from the intensive care unit. Discharged from the hospital on the 20th day after surgical treatment. After 4 months the child was examined in the hospital. The general condition was regarded as satisfactory. This clinical example shows the complexity of prenatal diagnosis of obstructive pathology of the aortic arch and the rapid manifestation of clinical manifestations after birth against the background of an unfavorable combination with a large septal defect.
Еndoscopic and histological features of the gastroduodenal zone in children with the CagA Helicobacter pylori infection
Authors: Shubina M. V. , Tereshchenko S. Yu. , Gorbacheva N. N. , Anisimova E. N. 
Published: November 2023

Introduction. It is known that the presence of the CagA gene in Helicobacter pylori is associated with its increased pathogenicity. However, in children, studies on the effects of this strain on the gastric mucosa are insufficient.Aim. To compare effects of different Helicobacter pylori (HP) strains on the gastric and duodenum mucosa in children to optimize indications for eradication.Materials and methods. 397 adolescents (169 boys and 227 girls) aged 11–18 were examined on the basis of the hospital gastroenterological department: the content of antibodies to the CagA strain of HP was determined by ELISA, esophagogastroduodenoscopy (EFGDS) was performedwith a biopsy of the gastric mucosa and determination of the HP contamination degree, and also HP gene was detected in the feces.According to the results obtained, all children were divided into 3 groups: 131 children (57 boys and 74 girls) infected with CagA by negative HP strains (CagA “-”); 119 children (52 boys and 67 girls) infected with CagA positive HP strains (CagA “+”); 94 children (36 boys and 57 girls) who are not infected with HP (HP “-”).Results. When we analyzed the endoscopic-histological picture of the gastric mucosa in the CagA “+” group, in contrast to the CagA “-” group, it was found that the chances of developing highbacteria contamination of the mucosa increased 4.7 times, II and III degree of gastritis activity – 6.6 times, chronic inflammation – 2.6 times, hyperplastic gastritis – 2.8 times, erosive gastritis or duodenitis – 2.7 times, peptic ulcer – 3.6 times, andalso signs of concomitant candidiasis (the presence of structural elements of the Candida fungus) – 4.1 times.Conclusion. Thus, it is advisable for all children with gastroduodenal pathology to recommend an examination for the detection of the CagA HP antigen with subsequent eradication.
A clinical case of early multifocal atherosclerosis complicated by acute coronary syndrome in a young man with ulcerative colitis
Authors: Tarasova L. V. , Kucherova N. Yu. , Tsyganova Yu. V. 
Published: November 2023

Inflammatory bowel disease (IBD) is a chronic, relapsing, systemic and immune-mediated conditiondis that frequently involve extraintestinal manifestations. Latest studies showed increased risk of cardiovascular complications, which is the main cause of death in developed countries, in chronic inflammatory disorders, especially during IBD relapses. IBD patients are at increased risk of conditions such as early atherosclerosis, ischaemic heart disease, myocardial infarction, stroke, venous thrombosis, heart failure, аtrial fibrillation. Hypotheses for the mechanism underlying the association of IBD and atherosclerotic cardiovascular diseases include adverse effects of both the IBD itself (chronic inflammation, еndothelium dysfunction, dyslipidemia, thrombocytosis, gut microbiome dysfunction) and its treatment. The predominant role in atherogenesis is currently assigned to disruption of the endothelium. Endothelium plays an important role in physiologic regulation of vascular tone, cell adhesion, migration and resistance to thrombosis. Also, its dysfunction is associated with increased risk of atherosclerosis development. Early multifocal atherosclerosis is a serious complication of ulcerative colitis and can occur in young people without traditional cardiovascular risk factors. Untimely diagnosis, lack of pathogenetic treatment, correction of basic anti-inflammatory therapy and comprehensive consideration of a problem of high cardiovascular risk can lead to acute myocardial infarction and stroke and disability of a patient of working age. The authors present a case report of multifocal atherosclerosis complicated by acute coronary syndrome in a young man with ulcerative colitis, who required a radical revision of the therapy.
Prenatal nursing care is essential! Breastfeeding: focus on maternal health
Authors: Zakharova I. N. , Kuchina A. E. , Kholodova I. N. , Pupykina V. V. 
Published: November 2023

This article deals with the importance and necessity of breastfeeding for both mother and baby. The timeliness of this topic has been brought about by technological advances, which imposes its own rules and offers alternatives in which it seems much easier to neglect the main maternal responsibility – the role of the breastfeeding mother. One gets the feeling that scientific research into breast milk is limited to finding evidence of the benefits of breastfeeding to convince novice mothers to breastfeed. The article mentions the evolutionary significance of breastfeeding, explains the reasons for the mammary glands “suffering” if the only “evolutionarily assigned” function for this female organ is not implemented, which makes us look at the need for natural breastfeeding from a different angle. Evidence of the need for breastfeeding to prevent the development of breast cancer that has high mortality rates in the female population is presented. At the same time, the issue of malignant tumours is not limited only to the mammary glands. The role of the breast milk microbiota disorders in the formation of the above processes is discussed. The preventive role of breastfeeding in the development of metabolic disorders, cardiovascular and endocrine diseases in women has been shown. The article presents data on this issue from numerous clinical studies, reviews and meta-analyses. The emphasis was placed on the prenatal discussions with pregnant women about the importance and necessity of breastfeeding, which should be carried out at the stage of preparing women for childbirth. The question has been raised about the role of the local paediatrician in the prenatal nursing care for women. It explains why “early” acquaintance with the mother is far from being an additional needless burden for the local paediatrician, as it might seem at first glance, but rather, on the contrary, additional opportunities.
Acute sore throat in frequently ill children: potential of topical therapy
Authors: Kirichenko I. M. , Popadyuk V. I. , Kozlova N. S. , Chernolev A. I. 
Published: November 2023

Sore throat is the most common reason for visiting primary care doctors, pediatricians, and ENT doctors. Acute sore throat, as a rule, is not an independent disease and most often accompanies tonsillopharyngitis caused by respiratory viral infections. In childhood, the share of acute respiratory viral infections among other infectious diseases can reach up to 90%, and the proportion of frequently ill children ranges from 30 to 50%. A feature of frequently ill children is a high incidence of illness, regardless of seasonality, and a tendency to a protracted course of the inflammatory process. Uncontrolled systemic antibiotic therapy for acute sore throat in frequently ill children leads to the development of dysbacteriosis and a decrease in mucosal immunity. The use of the topical antibacterial drug Faringazon for sore throat in children reduces inflammation in both viral and bacterial infections and reduces the need for systemic antibiotic therapy. The active substance of Ambazon has a bacteriostatic effect when is kept in the mouth until it resorbs and is effective against Streptococcus haemolyticus, Streptococcus pneumoniae, Streptococcus viridans, and also has antifungal effects against Candida albicans yeast fungus, which is a saprophyte, but exhibits pathogenic properties in decreased body’s immune defence and dysbiosis. The use of topical antimicrobial therapy helps reduce inflammation and speed up the recovery of patients without prescription of systemic antibiotics, and also ensures the preservation of microbiome, reducing the probability of emergence of antibiotic resistant strains to the minimum.
Non-alcoholic fatty liver disease and the risk of malignant tumors
Authors: Livzan M. A. , Syrovenko M. I. , Krolevets T. S. 
Published: November 2023

The prevalence of non-alcoholic fatty liver disease (NAFLD) and metabolic associated liver disease (MAFLD) is growing world-wide. A new terminology (MAFLD) allows us not only to focus on the “metabolic” genesis of this pathology, but also to take into account other factors affecting damage to hepatocytes, such as alcohol consumption in low doses, viral and toxic hepatitis. Currently, obesity is a pathology, that is growing with MAFLD and causes of various non-communicable diseases. Most deaths in patients with NAFLD/MAFLD are caused, firstly, by adverse cardiovascular events, secondly, by malignant tumors of both the digestive organs (liver, intestine, esophagus, stomach and pancreas) and other localizations (kidney cancer in men, breast cancer in women) and, thirdly, by development of hepatic complications (cirrhosis, hepatocellular carcinoma – HCC). Because of the pandemic growth of MAFLD and its association with cardiovascular diseases and obesity, the question about properly clinical management of patients suffered from comorbid pathology to reduce the risks of deaths is timely and very relevant. This review has been prepared to systematize the available literature dates about association of NAFLD/MAFLD with the malignant tumors. A literature searches were conducted, modern epidemiological dates about the prevalence of NAFLD/MAFLD in the population and their complicated forms were presented. The risk of HCC formation both with and without cirrhosis in NAFLD was assessed. It was found that the severity of liver fibrosis can be useful predictor of the future risk of not only the adverse cardiovascular events, but also the malignant tumors in patients with NAFLD/MAFLD. Possible targets for treatment were discussed, the impact on which is useful for the treatment and prevention of progressive forms of the disease. One of the possible therapeutic molecules is essential phospholipids, which are currently included in the consent documents for the managment of patients with NAFLD.