bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Analysis of miRNA-mRNA Regulation Pair in Bladder Cancer
Authors: Fan Xingchen , Zou Xuan , Liu Cheng , Peng Shuang , Zhang Shiyu , Zhou Xin , Wang Tongshan , Zhu Wei 
Published: November 2021

Abstract
Purpose: MicroRNA (miRNA) is a class of short non-coding RNA molecules that functions in RNA silencing and post-transcriptional regulation of gene expression. This study aims to identify critical miRNA-mRNA regulation pairs contributing to bladder cancer (BLCA) pathogenesis. Patients and methods: MiRNA and mRNA microarray and RNA-sequencing datasets were downloaded from gene expression omnibus (GEO) and the cancer genome atlas (TCGA) databases. The tool of GEO2R and R packages were used to screen differential miRNAs (DE-miRNAs) and mRNAs (DE-mRNAs) and DAVID, DIANA, and Hiplot tools were used to perform gene enrichment analysis. The miRNA-mRNA regulation pair were screened from the experimentally validated miRNA-target interactions databases (miRTarBase and TarBase). Twenty-eight pairs of BLCA tissues were used to further verify the screened DE-miRNAs and DE-mRNAs by quantitative reverse transcription and polymerase chain reaction (qRT-PCR). The diagnostic value of the miRNA-mRNA regulation pairs was evaluated by receiver operating characteristic curve (ROC) and decision curve analysis (DCA). The correlation analysis between the selected miRNA-mRNAs regulation pair and clinical, survival and tumor-related phenotypes was performed in this study.Results: After the analysis of 2 miRNA datasets, 6 mRNA datasets and TCGA-BLCA dataset, a total of 13 miRNAs (5 down-regulated and 8 up-regulated in BLCA tissues) and 181 mRNAs (72 up-regulated and 109 down-regulated in BLCA tissues) were screened out. The pairs of miR-17-5p (up-regulated in BLCA tissues) and TGFBR2 (down-regulated in BLCA tissues) were verified in the external validation cohort (28 BLCA vs. 28 NC) using qRT-PCR. Areas under the ROC curve of the miRNA-mRNA regulation pair panel were 0.929 (95% CI: 0.885-0.972, p<0.0001) in TCGA-BLCA and 0.767 (95% CI: 0.643-0.891, p=0.001) in the external validation. The DCA also showed that the miRNA-mRNA regulation pairs had an excellent diagnostic performance distinguishing BLCA from normal controls. Correlation analysis showed that miR-17-5p and TGFBR2 correlated with tumor immunity.Conclusions: The research identified potential miRNA-mRNA regulation pairs, providing a new idea for exploring the genesis and development of BLCA.
Associations of Walking Impairment With Visual Impairment, Depression, And Cognitive Function In US Older Adults: NHANES 2013-2014
Authors: Gao Wei , Dai Pengfei , Wang Yuqian , Zhang Yurong 
Published: November 2021

Abstract
Background: Walking impairment, a common health problem among older adults, has been linked to poor vision and mental health. This study aimed to investigate the associations of walking impairment with visual impairment, depression, and cognitive function in older adults. Methods: A total of 1,489 adults aged 60 years and older who had participated in the National Health and Examination Survey (NHANES) 2013-2014 in the United States were included. Multivariate logistic regression models were used to examine the associations of walking impairment with visual impairment, depression, and four subdomains of cognitive function. Sample weights were used to ensure the generalizability of the results.Results: Among all the participants (median age=68 years; 53.7% women), 17.5% reported walking impairment. Walking impairment was significantly associated with visual impairment (adjusted odds ratio [aOR] =2.76; 95% CI: 1.47-5.20) and depression (aOR=4.66; 95% CI: 3.11-6.99). Walking impairment was only associated with the Digit Symbol Substitution (DSST) subdomain of cognitive function in total participants (aOR=0.97; 95% CI: 0.95-0.99), and in non-Hispanic white adults (aOR=0.96; 95% CI: 0.94-0.98). Participants with more than 1 impairment indicators had higher OR of walking impairment (aOR = 3.64, 95% CI =2.46-5.38) than those with 0-1 (reference group) impairment indicator.Conclusions: Walking impairment was associated with visual impairment, depression, and cognitive impairment in the American older adults and also positively associated with the number of impairment indicators. The association between walking impairment and cognitive impairment varied according to race. Evaluations of vision, cognition, and depression should be conducted among the elderly with walking impairment, and that needs of the older adults with biological aspect of their particular race should be provided in the evaluations.
Is an Endorectal Balloon Beneficial for Rectal Sparing After Spacer Implantation in Prostate Cancer Patients Treated With Hypofractionated Intensity-modulated Proton Beam Therapy? A Dosimetric and Radiobiological Comparison Study
Authors: Khalil Dalia Ahmad , Wulff Jörg , Jazmati Danny , Geismar Dirk , Bäumer Christian , Kramer Paul Heinz , Steinmeier Theresa , Schleithoff Stefanie Schulze , Tschirdewahn Stephan , Hadaschik Boris , Timmermann Beate 
Published: November 2021

Abstract
BackgroundThe aim of this study is to examine the dosimetric influence of endorectal balloons (ERB) in rectal sparing in prostate cancer patients with implanted hydrogel rectum spacers treated with dose escalated/hypofractionated intensity modulated proton beam therapy (IMPT). MethodsTen patients with localised prostate cancer included in the ProRegPros study and treated at our centre were invastigated in this study. All patients underwent a placement of hydrogel rectum spacers before planning. Two planning CTs (with and without 120 cm3 fluid-filled ERB) were acquired for each patient. Dose prescription was set according to the used simultaneous integrated boost strategy with 72 Gray (Gy)/2.4 Gy/5 x weekly to prostate+1 cm of the seminal vesicle, and 60 Gy/2 Gy/5 x weekly to prostate+2 cm of the seminal vesicle. Planning with two lateral-opposed IMPT beams was performed in both CTs. Rectal dosimetry values including dose-volume statistics and normal tissue complication probability (NTCP) in both plans were compared (non-ERB plans vs. ERB plans).ResultsFor ERB plans compared to non-ERB, the reductions were 8.51 ± 5.25 Gy (RBE) (p= 0.000) and 15.76 ± 11.11Gy (P= 0.001) for the mean and the median rectal dose, respectively. No significant reductions in rectal volumes receiving high dose levels were found. The use of ERB resulted in significant reduction in rectal volume receiving 50 Gy (RBE), 40 Gy (RBE), 30 Gy (RBE), 20 Gy (RBE), and 10 Gy (RBE) with P values of 0.034, 0.008, 0.003, 0.001, and 0.001, respectively. For the anterior rectum, no differences between ERB and non-ERB plans were observed. For the posterior rectum, ERB reduced rectal volumes received 30 Gy (RBE), 20 Gy (RBE), and 10 Gy (RBE) with P values of 0.019, 0.003, and 0.001, respectively. No significant reductions in mean or median rectal toxicity (Late rectal bleeding ≥2, necrosis/stenosis, and Late rectal toxicity ≥ 3) were observed when using the ERB according to NTCP models.ConclusionThe ERB reduced rectal volumes exposed to intermediate/low dose levels. However, no significant reduction in rectal volumes receiving high/intermediate doses could be observed. No benefit but also no disadvantage of the ERB for late rectal toxicity was found according to available NTCP models.
Eye Disorders Spectrum: A Tertiary Hospital Pediatric Ophthalmology Clinic Based in Ethiopia
Authors: Kidane Yohannes Tewolde , Teshome Addisu Worku 
Published: November 2021

Abstract
Background: Epidemiological studies to determine the pattern of eye disorders among children are important for proper health care planning and management. This study aimed to document the spectrum and frequency of eye diseases of children who attended the pediatric ophthalmology clinic of a tertiary teaching hospital Addis Ababa, Ethiopia. Methods: A cross sectional and convenient sample of 1237, male and female children (16 years and below) with ocular disorders presenting for the first time and those children with settled diagnosis coming for follow up visit between June 1, 2018 to May 31, 2019 were included in the study. Data on age at presentation, sex and diagnosis were collected and analyzed. Eye disorders were classified into various categories. Children were grouped into four age groups. Ratios, percentages and chi square associations were calculated. P< 0.05 was considered statistically significant.Results: Of the children 60% were male. The mean age (standard deviation) of the children was 4.26 (+4.1) years. Patients aged 0–5 years old were the largest group constituting 70.5%. Ocular motility imbalances were the most common ocular disorders seen (32.8 %), followed by childhood cataract (18.4%) and infection and inflammation of eye and adnexa (8.3%). Ocular motility imbalances were recorded more frequently and statistically significant (p < 0.001) among 1­ 5 years age group. Within the childhood cataract category, congenital cataract was more prominent (7.1%). Within the infection and inflammation category, cornea/ sclera infections were more common (3.7%). Conclusions: The study highlights common eye disorders seen in children in a specialized hospital ophthalmic clinic. Ocular motility imbalance, childhood cataract, and infection and inflammation of the eye and adnexa, were the most common occurring disorders. Early presentation was common, and males were more affected than females.
Mitochondrial matrix protein Letmd1 maintains thermogenic capacity of brown adipose tissue
Authors: Park Anna , Kim Kwang-eun , Park Isaac , Kim Dae-Soo , Kim Jaehoon , Lim Dae-Sik , Woo Euijeon , Lee Eun-Woo , Han Baek-Soo , Oh Kyoung-Jin , Lee Sang Chul , Mun Ji Young , Rhee Hyun-Woo , Kim Won Kon , Bae Kwang-Hee , Suh Jae Myoung 
Published: November 2021

Abstract
Brown adipose tissue (BAT) has abundant mitochondria with the unique capability of generating heat via uncoupled respiration. Mitochondrial uncoupling protein 1 (Ucp1) is activated in BAT during cold stress and dissipates mitochondrial proton motive force generated by the electron transport chain to generate heat. However, other mitochondrial factors required for brown adipocyte respiration and thermogenesis under cold stress are largely unknown. Here we identify LETM1 domain-containing protein 1 (Letmd1) is a BAT-enriched, cold-induced protein that is required for cold-stimulated respiration and thermogenesis of BAT. Proximity labeling studies reveal that Letmd1 is a mitochondrial matrix protein. Letmd1 knockout mice display aberrant BAT mitochondria and fail to carry out adaptive thermogenesis under cold stress. Letmd1 knockout BAT is deficient in oxidative phosphorylation (OXPHOS) complex proteins and has impaired mitochondrial respiration. Taken together, we identify that the BAT-enriched mitochondrial matrix protein Letmd1 is required for cold-stimulated respiration and thermogenic function of BAT.
Construction and Evaluation of Self-Directing Expression System Using Regulatory Elements of Cry Gene of Bacillus Thuringiensis
Authors: Singh Drishtant , . Samiksha , Thayil Seema Madhumal , Sohal Satwinder Kaur , Kesavan Anup Kumar 
Published: November 2021

Abstract
An expression system based on the cry gene regulatory elements was constructed. The Terminator region of cry gene from B. thuringiensis subsp. kurstaki HD-1 was cloned in pSG1151 plasmid downstream to gfpmut1. The promoter region of the cry gene was amplified to give three different reading frames. The Promoter region of cry gene was cloned in pSG1151T plasmid upstream to gfpmut1. The expression of GFP under the promoter/terminator expression system was evaluated by checking the expression of gfpmut1 under the same promoter. The GFP content of pSG1151 and three constructs; pDSA1, pDSA2 and pDSA3 were compared by fluorescence spectroscopy. The fluorescent intensity of pSG1151 and pDSA1 were compared at time interval of 6 hours upto 72 hours. Both the samples showed detectable fluorescence that increased with time up to 12 hours, but the increase in the fluorescence of pDSA1 was 3 times higher as compared to pSG1151. A cold peptidase gene was cloned under the control of the cry promoter. The transformed E.coli DH5α colonies were patched on skim milk agar plates and the clones of pSG1151CP and pDSA1CP were compared on the basis of zone of clearance. The zone of clearance of pDSA1CP was much higher as compared to that of pSG1151CP. The cell-free supernatant of Bacillus sp. S1DI 10 and recombinant pDSA1CP collected at different time points was assayed for the specific activity of the extracellular protease. At 72 hours the protease activity in pDSA1CP was 2.7 fold higher compared to that of wild Bacillus sp. S1DI 10.
Automated Computed Tomography Based Parasitoid Detection in Mason Bee Rearings
Authors: Thomson Bart R. , Hagenbucher Steffen , Zboray Robert , Oesch Michelle Aimée , Richter Henning 
Published: November 2021

Abstract
In recent years, insect husbandry has seen an increased in- terest in order to supply in the production of raw materials, food or as biological/environmental control. Unfortunately, large insect rearings are susceptible to pathogens, pests and parasitoids which can spread rapidly due to the confined nature of a rearing system. Thus, it is of interest to quickly and efficiently monitor the spread of such manifesta- tions and the overall population size. Medical imaging techniques could be used for this purpose, as large volumes can be scanned non-invasively. Due to its 3D acquisition nature, computed tomography seems to be the most suitable for this task. This study presents an automated, computed tomography-based, counting method for bee rearings that performs com- parable/similar to identifying all Osmia cornuta cocoons manually. The proposed methodology achieves this in an average of 7 minutes per sam- ple, compared to 90 minutes per sample for the manual count over a total of 12 samples collected around lake Zurich in 2020. Such an automated bee population evaluation tool is a valuable in combating environmental influences on bee, and potentially other insect, rearings.
Analyses of Key Gene Networks Controlling Carotenoid Metabolism in Xiangfen 1 Banana
Authors: Dong Chen , Wang Jiuxiang , Hu Yulin , Xiao Weijun , Hu Huigang , Xie Jianghui 
Published: November 2021

Abstract
Background: Banana fruits are rich in various high-value metabolites and play a key role in the human diet. Of these components, carotenoids have attracted considerable attention due to their physiological role and human health care functions. However, the accumulation patterns of carotenoids and genome-wide analysis of gene expression during banana fruit development have not been comprehensively evaluated. Results: In the present study, an integrative analysis of metabolome and transcriptome profiles in banana fruit with three different development stages was performed. A total of 11 carotenoid compounds were identified, and most of these compounds showed markedly higher abundances in mature green and/or mature fruit than in young fruit. Results were linked to the high expression of carotenoid synthesis and regulatory genes in the middle and late stages of fruit development. Co-expression network analysis revealed that 79 differentially expressed transcription factor genes may be responsible for the regulation of LCYB, a key enzyme catalyzing the biosynthesis of α- and β-carotene. Conclusions: Collectively, the study provided new insights into the understanding of dynamic changes in carotenoid content and gene expression level during banana fruit development.
Melatonin and its-Remodeled Fecal Microbiota Improve Gut Health Through Inhibiting Oxidative Stress, Autophagy and Inflammation
Authors: Wang Yingqian , Shaoyong Weike , Cai Rui , Yi Xudong , Yong Wenlong , Wang Chenyang , Kou Zhongyun , Gao Lei , Chu Guiyan , Wu Jiangwei , Pang Weijun 
Published: November 2021

Abstract
Background

Gut health is involved in the nutrition absorption, reproduction and lactation in antenatal, perinatal and early weaned mammals. Recent literatures have demonstrated that melatonin functions in aging, cancer and obesity, but to date, few investigations toward exploring whether melatonin-reprogrammed fecal microbiota transplantation (FMT) and foster care (FC) affect gut health have been performed.
Results

Here, compared with the control group, melatonin and FMT increased intestinal villus height/crypt depth (V/C), inhibited gut oxidative stress, autophagy and inflammation in antenatal and perinatal rats. Likewise, not only melatonin and FMT, but also FC enhanced intestinal V/C through above parallel ways with decreasing intestinal permeability in early weaned rats. Mechanically, melatonin directly strengthened antioxidation, attenuated autophagy and apoptosis in H2O2-induced IEC6 intestinal epithelial cells. Furthermore, melatonin, FMT and FC reprogrammed intestinal microbiota in which more beneficial microbiota, including Allobaculum, Bifidobacterium and Faecalibaculum produced more metabolic short-chain fatty acids (SCFAs) including acetic acid and butyric acid to protect gut health. Most interestingly, compared with the control group, early weaned rats may get above probiotics via eating or licking the dung of the co-cage rats treated with melatonin in the FC group.
Conclusions

Overall, melatonin, FMT and FC improved gut health and the potential regulatory mechanism was associated with strengthening antioxidation, suppressing autophagy, inflammatory and apoptosis, as well as producing more SCFAs from reprogrammed gut microbiota. These findings suggest that melatonin, FMT and FC may be novel and effective methods to ameliorate gut health in antenatal, perinatal and weaned mammals.
PerFSeeB: Designing Long High-weight Single Spaced Seeds for Full Sensitivity Alignment with a Given Number of Mismatches
Authors: Titarenko Valeriy , Titarenko Sofya 
Published: November 2021

Abstract
Background: Technical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. A standard procedure is usually based on pre-aligning of short subsequences followed by proper comparison of neighbouring parts. For this purpose index files are created that store all subsequences (or numbers associated with them) and their positions within a reference sequence. Index files designed on subsequences of 32–64 symbols for a human reference genome can now be easily stored without any compression even on a budget computer. The main goal now is to choose a combination of symbols (a spaced seed) that will tolerate various mismatches between reference and given sequences. An ideal spaced seed should allow us to find all such positions (full sensitivity). By increasing the seed’s weight by one we usually reduce the number of candidate positions fourfold. At the same time longer seeds also reduce the number of signatures to be checked. Results: Several algorithms to assist seed generation are presented. The first one allows us to find all permitted spaced seeds iteratively. The results obtained with the algorithm show specific patterns of the seeds of the highest weight. Among the best seeds, there are periodic seeds with a simple relation between the period of a seed, its length and the length of a read. The second algorithm generates blocks for periodic seeds. A list of blocks is found for blocks of up to 50 symbols and up to 9 mismatches. The third algorithm uses those lists to find spaced seeds for reads of an arbitrary length. Conclusions: Lists of long high-weight spaced seeds are found and available in Supplementary Materials. The seeds are best in terms of weights compared to seeds from other papers and can usually be applied to shorter reads. Codes for all algorithms are available at https://github.com/vtman/PerFSeeB.
Breast Conservative Surgery for Breast Cancer: Indian Surgeon’s Preferences and Factors Influencing Them
Authors: Dutta Rohini , Virk Sargun , Patil Priti , Bhandoria Geetu , Sarang Bhakti , Mahajan Anshul , Khajanchi Monty , Jain Samarvir , Bains Lovenish , Bhandarkar Prashant , Chatterjee Shamita , Roy Nobhojit , Gadgil Anita 
Published: November 2021

Abstract
Background: It is well established that disease-free survival and overall survival after breast conservation surgery (BCS) followed by radiotherapy are equivalent to that after mastectomy. However, in Asian countries, the rate of BCS continues to remain low. The cause may be multifactorial including the patient’s choice, availability and accessibility of infrastructure and surgeon’s choice. We aimed to elucidate the Indian surgeons’ perspective while choosing between BCS and mastectomy, in women oncologically eligible for BCS. Methods: We conducted a survey-based cross-sectional study over 3 weeks between January-February 2021. Indian surgeons with general surgical or specialised onco-surgical training, who consented to participate were included in the study. Multinomial logistic regression was performed to assess the effect of study variables on offering mastectomy or BCS to an eligible patient.Results: A total of 347 responses were included. The mean age of the participants was 43(11) years. 63% of the surgeons were in the 25-44 years age group with the majority (80%) being males. 66.4% of surgeons ‘almost always’ offered BCS to oncologically eligible patients. Surgeons who had undergone specialised training in oncosurgery or breast conservation surgery were 35 times more likely to offer BCS (p<0.01). Surgeons working in hospitals with in-house radiation oncology facilities were 9 times more likely to offer BCS (p<0.05). Surgeons’ years of practice, age, sex and hospital setting did not influence the surgery offered.Conclusion: Our study found that two-thirds of Indian surgeons preferred BCS over mastectomy. Lack of radiotherapy facilities and specialised surgical training were deterrents to offering BCS to eligible women.