bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of mortality-risk-related missense variant for renal clear cell carcinoma using deep learning
Authors: Chen Jin-Bor , Yang Huai-Shuo , Moi Sin-Hua , Chuang Li-Yeh , Yang Cheng-Hong 
Published: February 2021

Introduction: Kidney renal clear cell carcinoma (KIRCC) is a highly heterogeneous and lethal cancer that can arise in patients with renal disease. DeepSurv combines a deep feed-forward neural network with a Cox proportional hazards function and could provide optimized survival results compared with convenient survival analysis. Methods: This study used an improved DeepSurv algorithm to identify the candidate genes to be targeted for treatment on the basis of the overall mortality status of KIRCC subjects. All the somatic mutation missense variants of KIRCC subjects were abstracted from TCGA-KIRC database. Results: The improved DeepSurv model (95.1%) achieved greater balanced accuracy compared with the DeepSurv model (75%), and identified 610 high-risk variants associated with overall mortality. The results of gene differential expression analysis also indicated nine KIRCC mortality-risk-related pathways, namely the tRNA charging pathway, the D-myo-inositol-5-phosphate metabolism pathway, the DNA double-strand break repair by nonhomologous end-joining pathway, the superpathway of inositol phosphate compounds, the 3-phosphoinositide degradation pathway, the production of nitric oxide and reactive oxygen species in macrophages pathway, the synaptic long-term depression pathway, the sperm motility pathway, and the role of JAK2 in hormone-like cytokine signaling pathway. The biological findings in this study indicate the KIRCC mortality-risk-related pathways were more likely to be associated with cancer cell growth, cancer cell differentiation, and immune response inhibition. Conclusion: The results proved that the improved DeepSurv model effectively classified mortality-related high-risk variants and identified the candidate genes. In the context of KIRCC overall mortality, the proposed model effectively recognized mortality-related high-risk variants for KIRCC.
Is There Value in Early Postoperative Visits Following Hip Fracture Surgery?
Authors: Ganta Abhishek , Dedhia Nicket , Ranson Rachel A. , Robitsek Jonathan , Hsu Joseph R. , Konda Sanjit R. , Egol Kenneth A. 
Published: February 2021

Introduction: Despite the recommendation for postoperative orthopedic follow-up after a hip fracture in elderly patients, many patients do not return for these visits. In this study, we attempt to determine if early follow-up (<4 weeks post-discharge) changes orthopedic post-operative management. Materials and. Methods: 1232 patients aged > 55 years old who underwent operative fixation for hip fractures were enrolled into an orthopedic trauma registry and followed from hospitalization through one year. Demographics, comorbidities, injury severity, and hospital course data were collected. Need for readmission and orthopedic follow-up were ascertained through chart review. Results: 417 patients (33.8%) patients did not return for any follow-up and 30 (2.4%) patients died <30 days from discharge. 370 (45.5%) patients had early orthopedic follow-up ≤28 days after discharge. 317 (38.9%) patients were seen ≥29 days after discharge (late follow-up). 127 (15.6%) patients returned for isolated non-orthopedic care. There were 23 (6.2%) readmissions in the early group, 17 (5.4%) in the late group, and 24 (18.9%) in the no follow-up group (p < 0.001). Patients discharged home were more likely to present for early follow-up compared to those with late and non-orthopedic follow-up (p = 0.002), however there was no difference in readmission rates between those discharged home vs. SNFs/SARs. Discussion: Patients who received isolated non-orthopedic follow-up within 4 weeks of surgery experienced more hospital readmissions than those with follow-up in that time period; however, these readmissions were primarily due to medical issues. There was no difference in orthopedic-related readmissions and changes in orthopedic management between groups. Patients discharged to SNFs/SARs did not present for early orthopedic as often as those discharged home. Conclusion: Early orthopedic follow up after hip fracture care does not change post-operative management in these patients and has implications for value-based care. Level of Evidence: Prognostic Level III.
Acid tolerance in early colonizers of oral biofilms
Authors: Boisen Gabriella , Davies Julia R. , Neilands Jessica 
Published: February 2021

Abstract
Background
In caries, low pH drives selection and enrichment of acidogenic and aciduric bacteria in oral biofilms, and development of acid tolerance in early colonizers is thought to play a key role in this shift. Since previous studies have focussed on planktonic cells, the effect of biofilm growth as well as the role of a salivary pellicle on this process is largely unknown. We explored acid tolerance and acid tolerance response (ATR) induction in biofilm cells of both clinical and laboratory strains of three oral streptococcal species (Streptococcus gordonii, Streptococcus oralis and Streptococcus mutans) as well as two oral species of Actinomyces (A. naeslundii and A. odontolyticus) and examined the role of salivary proteins in acid tolerance development.

Methods
Biofilms were formed on surfaces in Ibidi® mini flow cells with or without a coating of salivary proteins and acid tolerance assessed by exposing them to a challenge known to kill non-acid tolerant cells (pH 3.5 for 30 min) followed by staining with LIVE/DEAD BacLight and confocal scanning laser microscopy. The ability to induce an ATR was assessed by exposing the biofilms to an adaptation pH (pH 5.5) for 2 hours prior to the low pH challenge.

Results
Biofilm formation significantly increased acid tolerance in all the clinical streptococcal strains (P < 0.05) whereas the laboratory strains varied in their response. In biofilms, S. oralis was much more acid tolerant than S. gordonii or S. mutans. A. naeslundii showed a significant increase in acid tolerance in biofilms compared to planktonic cells (P < 0.001) which was not seen for A. odontolyticus. All strains except S. oralis induced an ATR after pre-exposure to pH 5.5 (P < 0.05). The presence of a salivary pellicle enhanced both acid tolerance development and ATR induction in S. gordonii biofilms (P < 0.05) but did not affect the other bacteria to the same extent.

Conclusions
These findings suggest that factors such as surface contact, the presence of a salivary pellicle and sensing of environmental pH can contribute to the development of high levels of acid tolerance amongst early colonizers in oral biofilms which may be important in the initiation of caries.
Baseline monitoring of volcanic regions with little recent activity: application of Sentinel-1 InSAR to Turkish volcanoes
Authors: Biggs Juliet , Dogru Fikret , Dagliyar Ayse , Albino Fabien , Yip Stanley , Brown Sarah , Anantrasirichai Nantheera , Atıcı Gökhan 
Published: February 2021

AbstractVolcanoes have dormancy periods that may last decades to centuries meaning that eruptions at volcanoes with no historical records of eruptions are common. Baseline monitoring to detect the early stages of reawakening is therefore important even in regions with little recent volcanic activity. Satellite techniques, such as InSAR, are ideally suited for routinely surveying large and inaccessible regions, but the large datasets typically require expert interpretation. Here we focus on Turkey where there are 10 Holocene volcanic systems, but no eruptions since 1855 and consequently little ground-based monitoring. We analyse data from the first five years of the European Space Agency Sentinel-1 mission which collects data over Turkey every 6 days on both ascending and descending passes. The high relief edifices of Turkey’s volcanoes cause two challenges: 1) snow cover during the winter months causes a loss of coherence and 2) topographically-correlated atmospheric artefacts could be misinterpreted as deformation. We propose mitigation strategies for both. The raw time series at Hasan Dag volcano shows uplift of ~ 10 cm between September 2017 and July 2018, but atmospheric corrections based on global weather models demonstrate that this is an artefact and reduce the scatter in the data to < 1 cm. We develop two image classification schemes for dealing with the large datasets: one is an easy to follow flowchart designed for non-specialist monitoring staff, and the other is an automated flagging system using a deep learning approach. We apply the deep learning scheme to a dataset of ~ 5000 images over the 10 Turkish volcanoes and find 4 possible signals, all of which are false positives. We conclude that there has been no cm-scale volcano deformation in Turkey in 2015–2020, but further analysis would be required to rule out slower rates of deformation (< 1 cm/yr). This study has demonstrated that InSAR techniques can be used for baseline monitoring in regions with few historical eruptions or little reported deformation.
Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes
Authors: Raimundo I. , Silva R. , Meunier L. , Valente S. M. , Lago-Lestón A. , Keller-Costa T. , Costa R. 
Published: February 2021

AbstractBackgroundChitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.ResultsWe found that cultivatable host-associated bacteria in the generaAquimarina,Enterovibrio,Microbulbifer,Pseudoalteromonas,Shewanella, andVibriowere able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed thatVibrioandAquimarinaspecies, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely,Alphaproteobacteriaspecies were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes forAquimarinaandVibriostrains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium ofSpongia officinalisis enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated—and biotechnologically versatile—form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivatedGammaproteobacteriaandChloroflexisymbionts in chitin processing within sessile marine invertebrates.ConclusionsOur findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genusAquimarinathat may find applications in the blue biotechnology sector.
Effects of low-level laser therapy on the orthodontic mini-implants stability: a systematic review and meta-analysis
Authors: Costa Ana Carolina de Figueiredo , Maia Thays Allane Cordeiro , de Barros Silva Paulo Goberlânio , Abreu Lucas Guimarães , Gondim Delane Viana , Santos Pedro César Fernandes 
Published: February 2021

Abstract
Objectives
The aim of this systematic review and meta-analysis was to assess the effects of low-level laser therapy (LLLT) on the orthodontic mini-implants (OMI) stability.

Materials and methods
An unrestricted electronic database search in PubMed, Science Direct, Embase, Scopus, Web of Science, Cochrane Library, LILACS, Google Scholar, and ClinicalTrials.gov and a hand search were performed up to December 2020. Randomized clinical trials (RCTs) or non-randomized clinical trials (Non-RCTs) that assessed the effects of LLLT on the OMI stability were included. Data regarding the general information, LLLT characteristics, and outcomes were extracted. The authors performed risk of bias assessment with Cochrane Collaboration’s or ROBINS-I tool. Meta-analysis was also conducted.

Results
Five RCTs and one Non-RCT were included and 108 patients were evaluated. The LLLT characteristics presented different wavelength, power, energy density, irradiation time, and protocol duration. Five RCTs had a low risk of selection bias. Two RCTs had a low risk of performance and detection bias. All RCTs had a low risk of attrition bias, reporting bias and other bias. The Non-RCT presented a low risk of bias for all criteria, except for the bias in selection of participants. The meta-analysis revealed that LLLT significantly increased the OMI stability (p < 0.001, Cohen’s d = 0.67) and the highest clinical benefit was showed after 1 (p < 0.001, Cohen’s d = 0.75), 2 (p < 0.001, Cohen’s d = 1.21), and 3 (p < 0.001, Cohen’s d = 1.51) months of OMI placement.

Conclusions
LLLT shows positive effects on the OMI stability.
Inventory management performance for family planning, maternal and child health medicines in public health facilities of West Wollega zone, Ethiopia
Authors: Kebede Oliyad , Tilahun Gizachew 
Published: February 2021

Abstract
Background
Inventory management is the heart of the supply system in improving availability of medicines, reducing the cost, and improving patient care quality. However, in the government facilities’ supply system, inventory management is poor. So, the purpose of this research is to assess inventory management performance for family planning, maternal and child health medicines in public health facilities of West Wollega zone, Oromia region, Ethiopia.

Method
Facility-based descriptive cross-sectional quantitative study was conducted using checklist, structured and semi-structured questionnaire, and triangulated with qualitative method. Quantitative data were coded and analyzed using SPSS Version 20 and Microsoft excel spreadsheet. Qualitative data were analyzed manually, using thematic analysis technique. Different indicators were used to measure variables.

Results
Among 23 health facilities assessed, availability of family planning/maternal and child health medicines ranged from 0 to 100%. Average availability of medicines was 14 (61.30%) with mean stock-out duration of 70.71 days. Bin cards were available for 559 (78.40%) of medicines, and 374 (52.45%) bin cards were accurate. Report submission rate was 116 (84.06%), with 47 (40.52%) report and resupply forms reported on time, 73 (62.93%) of them were complete and 69 (59.48%) were accurate. Supplier-related problem, lack of human resource, administrative problem, and lack of computer infrastructure were inventory management challenges identified.

Conclusion
Inventory management performance for Family planning/maternal and child health medicines was poor as indicated by low availability, high stock-out duration, and poor LMIS performance. Efforts should be undertaken by concerned bodies to improve it.
Study of motor load regulation training with visual feedback in patients with diabetic polyneuropathy
Authors: Babanov N. D. , Frolov D. V. , Krukov E. V. , Panova E. N. , Kubryak O. V. 
Published: February 2021

BACKGRAUND: Violation of gait and body balance in patients with diabetic polyneuropathy actualizes the development of new effective measures of motor rehabilitation. In this regard, an observation was carried out in which biofeedback training was used for the reference reaction in the conditions of variable feedback parameters.AIMS: To investigate the effect of a stepwise change in the depth of feedback (sensitivity) in a motor-cognitive task with visual feedback on the reference response to the result of its execution.METHODS: Single-sample observational observation with controlled conditions. 27 patients with diabetic polyneuropathy. All patients were treated according to modern standards. The observation was performed in one series at the beginning of the course of inpatient treatment. Estimation of body balance on a power platform — stabiloplatform) — stabilometry. The procedure included 5 stages of management, in which the patient followed the instructions (training) in which there was a stepwise increase in the depth of feedback («sensitivity») at each stage from 10 to 50% of the conditional «normal», with a step of 10%. A quantitative assessment of the external result (execution of instructions) and parameters of regulation of the vertical posture was carried out.RESULTS: All patients included in the follow-up showed that the implementation of instructions with increasing depth of feedback decreased sharply when the conditionally «normal» value was exceeded by 30–35%. At the same time, the initial parameters of vertical posture control in the sample patients did not affect the dynamics of results when performing the task with visual feedback. Factor analysis indicates the presence of the only significant factor associated with the effectiveness of performing a motor-cognitive task here — changes in the depth of feedback. The accepted significance level α = 0.05.CONCLUSIONS: The depth of feedback in motor-cognitive tasks with visual feedback is a key characteristic that affects performance. The ability to increase the depth of feedback in the range of about 35; from conditionally «normal», can be useful for ensuring differentiation of loads during motor rehabilitation of patients in order to increase the effectiveness of training. In addition, in theoretical terms, the proposed model of the motor-cognitive problem can be relevant in the study of «dual» problems, where the relationship of motor and cognitive components is studied.
Long-term Follow-up of treatment of chronic foot wounds with recombinant human epidermal growth factor in patients with different complications of diabetes mellitus
Authors: Zaitseva E. L. , Zhilyaev V. M. , Galstyan G. R. 
Published: February 2021

BACKGROUND: Diabetic foot ulcer (DFU) is a dangerous complication of diabetes mellitus (DM), which can lead to the development of chronic wounds and amputations. Recombinant human epidermal growth factor (rhEGF) can be used as an adjuvant treatment for chronic wounds resistant to standard treatment. Studies have demonstrated its clinical efficacy, however, there is insufficient information on the long-term results of treatment, its safety and the effect on the progression of diabetes complications, adverse cardiovascular events and the development of cancer.AIM: To assess the long-term results of rhEGF therapy for trophic foot ulcers in individuals with multiple complications of diabetes.METHODS: The study included 20 patients with type 1 and type 2 diabetes and various forms of DFS without critical ischemia, who had previously been treated with DFS using rhEGF in order to assess the general condition, progression of microand macrovascular complications of diabetes, adverse cardiovascular events, the development of cancer and the quality of life.RESULTS: There was a statistically significant difference between the area of wound defects, the percentage of granulation tissue that filled the wound defect, before the start of rhEGF treatment and at the time of discharge from the hospital (p <0.05). During treatment with rhEGF, mild adverse events were observed in 35%. Complete epithelialization of wounds in most patients occurred in 3 [2; 4] months. In 11.76%, the wound was not completely epithelialized. Relapse occurred in 5.8% due to non-compliance with limb unloading. Minor amputation was performed in 1 patient. Progression of diabetic retinoand nephropathy was revealed in 23.5%. 11.76% suffered myocardial infarction of unknown age, 1 patient (5.88%) suffered acute cerebrovascular accident. Serious adverse events in the form of PE with a fatal outcome and critical ischemia of the lower limb were recorded in 5.8%.CONCLUSIONS: As a result of the study of long-term results of rhEGF treatment of chronic foot wounds, a low percentage of relapses and small amputations, the absence of high amputations and oncological diseases, the development of serious adverse events in 2 patients, the progression of diabetic retinoand nephropathy in 4 patients, the development of IM of unknown age in 2 patients was recorded. and stroke in 1 patient after rhEGF therapy.
Analysis of melatonin concentration and its correlation with ovarian disfunction among obese women of reproductive age
Authors: Mikheev R. K. , Andreeva E. N. , Sheremetyeva E. V. , Absatarova Yu. S. , Ponomareva T. A. , Grigoryan O. R. 
Published: February 2021

One of the new directions in the study of reproductive disorders in obese women is the effect and receptor sensitivity of melatonin on the gonadotropic function of the pituitary gland and ovariogenesis, taking into account the chronology of «light pollution». At the present stage, there is very little literature on the influence of the aspects of «light pollution» on the problem of obesity and reproductive disorders in the literature. This review is an attempt to combine the above problem in terms of the impact of «light pollution» and the level of receptor sensitivity of melatonin in women of reproductive age with obesity. The literature search was carried out in Russian (eLibrary, CyberLeninka.ru) and international (PubMed, Cochrane Library) databases in Russian and English. Free access to the full text of the articles was a priority. The selection of sources was prioritized for the period from 2015 to 2019. However, given the insufficient knowledge of the chosen topic, the choice of sources was dated from 1992. The work was carried out as part of the study «Central and peripheral pathophysiological mechanisms of development of adipose tissue diseases, taking into account clinical and hormonal characteristics» 2020–2022.
MEDICAL PROBLEM, CONCEQUENCES TO ORAL CARE IN GERIATRIC PATIENT
Authors: Hardini Nadia , Santoso Oedijani 
Published: February 2021

Introduction: Oral and maxillofacial tissue status has a significant impact on the systemic health of elderly patients. Elderly patients without oral diseases are rare to find by dentists. Literature Review: Prevention and treatment for caries and periodontal diseases should be done for elderly patients, except in particular conditions when its not worth the risks treatments. Although the relationship between oral diseases and systemic diseases is still controversial and unresolved, it can be assumed that elderly patients have a greater risk of acute and chronic oral infections due to the use of various drugs and medical disorders, impaired immune function, age related impaired kidney, liver and cardiovascular dysfunction. Conclusion: While on duty, dentists who provides care to elderly patients, must know the medical history and systemic review, and understands general medical problems that affects oral care of the elderly.Keyword : medical problem, elderly, oral treatment