bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating lncRNAs HIF1A-AS2 and LINLK-A: Role and Relation to Hypoxia-Inducible Factor-1α in Cerebral Stroke Patients
Authors: Ewida Heba A. , Zayed Rana K. , Darwish Hebatallah , Shaheen Amira A. 
Published: March 2021

Abstract
Long noncoding RNAs (lncRNAs) have been recently recognized as key players of gene expression in cerebral pathogenesis. Thus, their potential use in stroke diagnosis, prognosis and therapy is actively pursued. Due to the complexity of the disease, identifying stroke- specific lncRNAs remains a challenge. This study investigated the expression of lncRNAs; HIF1A-AS2 and LINK-A and their target gene Hypoxia-inducible factor-1 (HIF-1) in Egyptian stroke patients. It also aimed to determine the molecular mechanism implicated in the disease. A total of 75 stroke patients were divided into three clinical subgroups, beside 25 healthy controls of matched age and sex. Remarkable upregulation of lncRNA HIF1A-AS2 and HIF1-α along with a downregulation of lncRNA LINK-A were noticed in all stroke groups relative to controls. Serum levels of phosphatidylinositol 3- kinase (PI3K), phosphorylated-Akt (p-Akt), vascular endothelial growth factor (VEGF) and angiopoietin-1 (ANG1) as well as their receptors, malondialdehyde (MDA) and total antioxidant capacity (TAC) were significantly increased, whereas brain-derived neurotrophic factor (BDNF) levels were significantly decreased particularly in hemorrhagic stroke versus ischemic groups. Eventually, these findings support the role of lncRNAs; HIF1A-AS2 and LINK-A as well as HIF1-α in activation of angiogenesis, neovascularization, and better prognosis of stroke, especially the hemorrhagic type.
Monitoring disease and antibiotic treatment in the skin microbiota of farmed seabass fingerlings
Authors: Rosado Daniela , Pérez-Losada Marcos , Severino Ricardo , Xavier Raquel 
Published: March 2021

Abstract
The microbiota of fish skin is the primary barrier against disease; however, it is highly dynamic being modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages with high associated losses. Antibiotic treatments sometimes remain as the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We used a 16S rRNA metataxonomic approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass Dicentrarchus labrax fingerlings. Both disease and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbial structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to disease and antibiotics is not easily predicted.
Prognostic Implications of Autophagy-Related Gene Signatures in Ewing’s Sarcoma
Authors: Zhou Yangfan , Wu Shusheng , Liu Yulian , Xu Bin 
Published: March 2021

Abstract
Backgrand：Ewing's sarcoma (ES) is a highly aggressive malignant bone tumor with a high incidence among children and adolescents. While autophagy often plays an important role in tumor development species, we developed an autophagy-related prognostic signature based on the GEO dataset.Methods: Using the GEO database with the online website Human Autophagy Database(HADb), we screened for autophagy-related differential genes and we performed enrichment analysis and PPI analysis for autophagy-related differential genes, and then, constructed our autophagy-related prognostic gene signature by univariate Cox regression, lasso regression, and multivariate Cox regression .Results: We screened a total of 72 autophagy-related differential genes, and a total of 8 autophagy-related prognostic genes were screened by machine learning algorithms. ROC curves and survival curves also showed good predictive power of the 8 gene signatures. In addition, univariate and multivariate cox regression also showed that the 8 gene signatures were independent prognostic factors. And the results of GSEA enrichment analysis also revealed the correlation between autophagy and metabolic pathways.Conlusion：In summary, we developed an autophagy-related mRNA signature consisting of 8 mRNAs that effectively classified ES patients into low- and high-risk groups. The application of the signature in clinical treatment needs further observation to validate the validity of our findings.
Clinical Feature-Related Single-Base Substitution Sequence Signatures Identified with an Unsupervised Machine Learning Approach
Authors: Hongchen Ji , Junjie Li , Qiong Zhang , Jingyue Yang , Juanli Duan , Xiaowen Wang , Ben Ma , Zhuochao Zhang , Wei Pan , Hongmei Zhang 
Published: March 2021

Abstract
Background: Mutation processes leave different signatures in genes. For single-base substitutions, previous studies have suggested that mutation signatures are not only reflected in mutation bases but also in neighboring bases. However, because of the lack of a method to identify features of long sequences next to mutation bases, the understanding of how flanking sequences influence mutation signatures is limited.Methods: We constructed a long short-term memory – self organizing map (LSTM-SOM) unsupervised neural network. By extracting mutated sequence features via LSTM and clustering similar features with the SOM, single-base substitutions in The Cancer Genome Atlas database were clustered according to both their mutation site and flanking sequences. The relationship between mutation sequence signatures and clinical features was then analyzed. Finally, we clustered patients into different classes according to the composition of the mutation sequence signatures by the K-means method and then studied the differences in clinical features and survival between classes.Results: Ten classes of mutant sequence signatures (mutation blots, MBs) were obtained from 2,141,527 single-base substitutions via LSTM-SOM machine learning approach. Different features in mutation bases and flanking sequences were revealed among MBs. MBs reflect both the site and pathological features of cancers. MBs were related to clinical features, including age, gender, and cancer stage. The class of an MB in a given gene was associated with survival. Finally, patients were clustered into 7 classes according to the MB composition. Significant differences in survival and clinical features were observed among different patient classes.Conclusions: We provided a method for analyzing the characteristics of mutant sequences. Result of this study showed that flanking sequences, together with mutation bases, shape the signatures of SBSs. MBs were shown related to clinical features and survival of cancer patients. Composition of MBs is a feasible predictive factor of clinical prognosis. Further study of the mechanism of MBs related to cancer characteristics is suggested.
Dhaka City Water logging Hazards: Area Identification and Vulnerability Assessment through GIS-Remote Sensing Techniques
Authors: Alam Rafiul , Quayyum Zahidul , Moulds Simon , Radia Marzuka Ahmad , Sara Hasna Hena , Hasan Md Tanvir , Butler Adrian 
Published: March 2021

Abstract
Water logging is one of the most detrimental phenomena continuing to burden Dhaka dwellers. This study aims to spatio-temporarily identify the water logging hazard zones within Dhaka Metropolitan area and assess the extent of their water logging susceptibility based on informal settlements, built-up areas and demographical characteristics. The study utilizes integrated Geographic Information System (GIS)-Remote sensing (RS) methods, using Normalized Difference Vegetation Water and Moisture Index, distance buffer zone from drainage streams and built-up distributions to identify waterlogged zones with a temporal extent, incorporating social and infrastructural attributes to evaluate water logging effects. All the indicators were integrated into an overlay GIS method to measure the vulnerability level across Dhaka city areas. The findings reveal that south and south-western parts of Dhaka were more susceptible to water logging hazards. Almost 30–40% of Dhaka belongs to the high/very highly vulnerable zone. Greater number of slum households were observed within high to very high water logging vulnerable zones with approximately 70% of poorly structured households. The built-up areas increased around the northern part of Dhaka across time and exposed to severe water logging issues. A holistic and integrated approach is necessary in future development plans to mitigate the risk of water logging.
Silylation and characterization of of piroxicam with some silylating reagents
Authors: Galehassadi Mohammad , Jodeiri Somayeh 
Published: March 2021

Abstract
In this work, we synthesized some organosilicon derivatives of piroxicam. Due to the some properties of organosilicon compounds, including increased lipophilicity and thermal stabilization and prodrug for drugs, some silyl ethers of this drug were synthesized and characterized..Increasing of the lipophilic properties of this drug can be very important in the rate of absorption and its effectiveness.
Robust Optimization of SWATH-MS workflow for human blood serum proteome analysis using a Quality by Design approach
Authors: Serrano-Blesa Edith , Porter Andrew , Lendrem Dennis William , Pitzalis Costantino , Barton Anne , Treumann Achim , Isaacs John D. 
Published: March 2021

Abstract
Background: It is not enough to optimize proteomics assays. It is critical those assays are robust to operating conditions. Without robust assays, proteomic biomarkers are unlikely to translate readily into the clinic. This study outlines a structured approach to the identification of a robust operating window for proteomics assays and applies that method to Sequential Window Acquisition of all Theoretical Spectra Mass Spectroscopy (SWATH-MS). Methods: We used a sequential Quality by Design approach exploiting a fractional screening design to first identify critical SWATH-MS parameters, then using response surface methods to identify a robust operating window with good reproducibility, before validating those settings in a separate validation study. Results: The screening experiment identified two critical SWATH-MS parameters. We modelled the number of proteins and reproducibility as a function of those parameters identifying an operating window permitting robust maximization of the number of proteins quantified in human serum. In a separate validation study, these settings were shown to give good proteome-wide coverage and high quantification reproducibility. Conclusions: Using design of experiments permits identification of a robust operating window for SWATH-MS. The method gives a good understanding of proteomics assays and greater data-driven confidence in SWATH-MS performance.
Residency training in family medicine and its impact on coordination and continuity of care: an analysis of referrals to secondary care in Rio de Janeiro
Authors: Jantsch Adelson Guaraci , Burström Bo , Nilsson Gunnar , de Leon Antônio Ponce 
Published: March 2021

Abstract
Objective: To measure the effect that Residency Training in Family Medicine (RTFM) has on continuity and coordination of care. Design: Observational cohort study using electronic health records.Setting: Rio de Janeiro, Brazil, public primary care system.Participants: 504940 patients, 633 generalists (physicians without RTFM) and 204 Family physicians (FP – doctors with two years of RTFM) from one health district between January 2015 and December 2018.Intervention: Two years of Residency Training in Family Medicine (RTFM)Main outcome measures: risk of patients being referred to secondary care for outpatient consultations and diagnostics tests; and having a follow-up medical consultation in primary care within three and six months after being referred.Results: We examined 2414508 medical consultations and 284754 referrals to secondary care. Family physicians (FPs) were less likely to request ambulatory care services (including surgical specialties), but were more likely to request Ophthalmology, Physiotherapy, Rehabilitation, and Surgical evaluations for their patients. Patients referred to secondary care by FPs were at a higher risk of having a follow-up visit in primary care for almost every service requested. If all medical consultations were performed by FPs, a 37.6% (95% CI 32.4% - 42.4%) increased demand for Rehabilitation services would be noticed. Oppositely, 1532 (95%CI 1458; 1602) fewer requests for Dermatology would happen every year. Conclusions: RTFM improves coordination and continuity of care by making FPs more competent to retain those health conditions that can be properly managed in primary care and making FPs more competent to detect health conditions that require specific biomedical technologies and skills, increasing the demand for those services. Besides, it increases the chances of patients having follow-up visits in primary care. Policymakers in low- and middle-income countries must consider investing in RTFM to make primary care systems more comprehensive, with better coordination and continuity of care.
Effect of Dietary Patterns and, or Nutrition Strategies Reducing Risk in Adverse Maternal Health Occurrences during Pregnancy: A Systematic Review
Authors: Larbi Josephine Ansaa 
Published: March 2021

Abstract
Dietary patterns and nutrition strategies are essential to maintain optimal maternal health during pregnancy to prevent and minimize conditions that lead to complications. Previous studies found nutrition education and counseling effect on food habit modification, beneficial during pregnancy. In promoting health and reducing adverse maternal conditions during pregnancy, need increasing knowledge on diversities of dietary pattern consumption, modify attitude and practice. The present review conducted on the effect of dietary patterns and/or nutrition interventions on health risks such as hypertension disorders in pregnancy or gestational hypertension or high blood pressure related to obesity or overweight, low haemoglobin, undernutrition, and anaemia. Eighteen eligible studies identified. Studies on dietary patterns: Mediterranean or DASH diets, DASH diet vs Western diet with dietary counseling, combined nutrition counseling, advice, and healthy diet. Healthy diet vs Western, Traditional or high-energy-foo; 2 healthy diets rich in fruit and vegetables. Two healthy diets combined with dietary counseling, nutrition messages compared with high-energy-food. The remaining 5 studies were nutrition education and health promotion model, dietary counseling and knowledge, attitude and practice with a healthy diet, nutrition education with or without diet plan, then guided counseling with planned behaviour model. The studies reported a positive impact on the reduction of maternal adverse conditions, improved anthropometric, haemoglobin, undernutrition or malnutrition status. Study designs were 5 randomized controlled interventions, 11 prospective or longitudinal cohort studies, and 2 systematic reviews.
Using a dark logic model to explore adverse effects in audit and feedback: a qualitative study of gaming in colonoscopy.
Authors: Catlow Jamie , Bhardwaj-Gosling Rashmi , Sharp Linda , Rutter M D , Sniehotta Falko 
Published: March 2021

Abstract
Background
Audit and feedback (A&F) interventions improve patient care but may result in negative effects. To evaluate plausible harms and maximise benefits, a-priori theorisation using dark logic models can be useful. We aimed to assess the unintended adverse effects of A&F in colonoscopy using Feedback Intervention Theory (FIT) based dark logic model.
Methods
As part of the National Endoscopy Database Automated Performance Reports to Improve Quality Outcomes Trial we undertook a qualitative study exploring current A&F practices in colonoscopy. Interviews were undertaken with endoscopists from six NHS endoscopy centres across England, purposively sampled for clinical background and professional experience. A framework method analysis of A&F in endoscopy was performed, mapping themes of paradoxical outcomes and patient harm to FIT and the theory of planned behaviour (TPB).
Results
Data saturation was achieved on 19th participant, with endoscopists from nursing, surgical and medical professional backgrounds and a median of 7 years’ endoscopy experience (range 2–29 years).
Restoring Shank3 in a rostral sensorimotor brainstem nucleus rescues reduced light-evoked behaviors in shank3ab-/- zebrafish.
Authors: Kozol Robert , James David , Varela Ivan , Sumathipala Sureni , Züchner Stephan , Dallman Julia 
Published: March 2021

Abstract
People with Phelan-McDermid Syndrome, caused by mutations in the SHANK3 gene, commonly present with symptoms of sensory hyporeactivity. To investigate how shank3 mutations impact brain circuits and contribute to sensory hyporeactivity, we generated two shank3 zebrafish mutant models. These shank3 mutant models both exhibit hyporeactivity to visual stimuli. Using whole-brain activity mapping, we show that light receptive brain nuclei show normal levels of activity while sensorimotor integration and motor regions are less active in shank3-/- mutants. Specifically rescuing Shank3 in a sensorimotor nucleus of the rostral brainstem is sufficient to rescue shank3-/- mutant hyporeactivity. In summary, reduced sensory responsiveness in shank3-/- mutant is associated with reduced activity across the brain and can be rescued by restoring Shank3 function in the rostral brainstem.
Eye hydrodynamics indicators in children with congenital cataract, aphakia and pseudophakia
Authors: Khamraeva L. S. , Bobokha L. Yu. , Katargina L. A. 
Published: March 2021

Purpose. To determine the specificity of functional and tonographic parameters of the eyeball in children with cataract, aphakia and pseudophakia. Material and methods. A comparative analysis of eye hydrodynamics indices was made according to a simplified procedure, using the Friedenwald nomogram, on 75 children aged 2 to 17 years with cataract (24 eyes), aphakia (21 eyes), pseudophakia (15 eyes), and IOL dislocation (15 eyes), as well as 12 healthy children.Results. In pseudophakia, true IOP was found to fall to 10.00 ± 0.01 mm Hg due to a decrease in aqueous humor production (to 0.10±0.01 mm3 / min) and increase of its outflow (to 0.75 ± 0.02 mm3/min / mm). IOL dislocation led to an increase in true IOP (24.40±1.0 mm Hg) due to an increase in aqueous humor production (4.09±0.05 mm3/min) and a decrease in its outflow (0.010 ± 0.002 mm3/min/mm). In these eyes, clinical manifestations of secondary pseudophakic glaucoma were noted, which are explained by factors obstructing aqueous humor outflow (vitreous prolapse and partial vitreous block) and considered an indication for re-operation.Conclusion. Statistically significant changes of hydrodynamic eye parameters in children with pseudophakia have been detected: increased true IOP in IOL dislocation, and, conversely, reduced true IOP in case of the normal IOL location. The authors believe that eye “hypotension” in case of pseudophakia requires further study.
The variability of the microbial profile of corneal ulcers
Authors: Maharramov P. M. , Guliyeva M. H. 
Published: March 2021

Purpose. To study the microbiological profile of corneal ulcers depending on demographic and clinical characteristics of patients.Materials and methods. 97 patients (114 eyes) (65 men and 32 women) diagnosed with corneal ulcer were tested. 80 patients had unilateral and 17 bilateral ulcers. The patients’ age varied from 15 to 87 years (24.7 % aged 50–59, 27.8 % aged 60–69, and 19.7 % aged 70 or older). All patients were examined for the microbiological profile of corneal scrapings to determine the microbial flora of the corneal ulcer. The significance of gender, age and clinical differences found in the structure of the microbiological profile was evaluated by the the χ² criterion.Results. Gram-positive microorganisms were among the most frequently detected: Staphylococcus epidermidis in 25.3 % of cases, Streptococcus pneumoniae in 21.7 % of cases, Streptococcus viridians in 16.3 % of cases, and Staphylococcus aureus in 7,8 % of cases. Gram-negative microbial flora (Pseudomonas aeruginosa) was revealed in 22.3 % of cases, while fungi were identified in 6.6 % of cases.Conclusion. The microbiological profile of corneal ulcer depends on the patient’s age, localization, size and depth of the lesion, as well as the presence of complication. Severe and complicated forms of corneal ulcer (sized ˃5 mm, depth of the lesion exceeding two thirds of corneal thickness) are often associated with the detection of more than one type of microorganism.
Modern approaches to the treatment of rhinopharyngitis in the practice of a district pediatrician
Authors: Koltuntceva Inna V. , Bairova Svetlana V. , Sakhno Larisa V. 
Published: March 2021

Introduction. In outpatient practice, acute nasopharyngitis in children is one of the most common reasons for seeking medical attention. The local pediatrician, as a rule, is the first to examine the child and determine the tactics of treatment. A competent approach to the choice of drugs avoids polypharmacy.The article presents the published scientific evidence on the modern approach to the treatment, as well as the author’s own clinical observation.Objective. To study the effectiveness of modern methods for the treatment of rhinopharyngitis, including the use of silver proteinate to treat acute respiratory infections in a group of frequently ill children.Materials and methods. The study involved 38 children aged 3 to 4 years, included in the group of frequent illnesses. The children were divided into 3 groups. In the first group (12 people), for four months (October-December 2019), children received symptomatic treatment of an acute respiratory infection; between episodes of acute respiratory infection, daily prophylactic irrigation of the child’s nose and throat with saline was used. In the second group (13 people), symptomatic treatment and nasal instillation of a preparation of silver proteinate were used at each episode of acute respiratory infection. In the third group (13 people), children received only symptomatic treatment for acute respiratory infection.In the first and third groups, children received symptomatic treatment of an acute respiratory infection without the use of silver proteinate.Results. The chosen approach to the ARVI treatment such as nasal instillation of silver proteinate into the bilateral nasal cavities has shown its effectiveness without having to carry out preventive measures between episodes of the disease.Conclusion. The application of elimination and antiseptic therapy with the use of Sialor for each episode of ARVI in the group of frequently ill children can reduce polypharmacy and incidence of morbidity.