Miracle-dz/UniFAR-FTUs huggingface dataset:
Circulation EBV Mir-Bart-7 Relating to Clinical Manifestation in Nasopharyngeal Carcinoma

Objective: Nasopharyngeal Carcinoma (NPC) is an endemic head and neck malignancy in Asia Pacific regions that is associated with chronic infection by Epstein-Barr virus (EBV). EBV miR-BART-7 is a microRNA (miRNA) encoded by EBV that regulates malignant behavior of NPC. However, the role and function of miR-BART7 are not clear, particularly the relation of circulating levels and patient’s clinical presentation. Methods: Circulating miR-BART-7 levels were measured by using qRT-PCR and were correlated with clinical and pathological data. Result: Of 52 NPC patients included in this study, 85% were diagnosed in the late stages (Stage III-IV). 73% of tumors were non-keratinizing undifferentiated NPC, 92% of tumors were WHO class III histology and all cases were EBV-IgA positive. Over-expression of miR-BART7-3p was correlated with positive regional lymph nodes in newly diagnosed (4.61 fold changes, p<0.05). Conclusion: Over-expression of circulating EBV miR-BART7 correlated with positive regional lymph nodes reflecting the diagnostic and prognostic values of circulating miR-BART7 for patients with NPC.
A Bipolar-Channel Hybrid Brain-Computer Interface System for Home Automation Control Utilizing Steady-State Visually Evoked Potential and Eye-Blink Signals

The goal of this study was to develop and validate a hybrid brain-computer interface (BCI) system for home automation control. Over the past decade, BCIs represent a promising possibility in the field of medical (e.g., neuronal rehabilitation), educational, mind reading, and remote communication. However, BCI is still difficult to use in daily life because of the challenges of the unfriendly head device, lower classification accuracy, high cost, and complex operation. In this study, we propose a hybrid BCI system for home automation control with two brain signals acquiring electrodes and simple tasks, which only requires the subject to focus on the stimulus and eye blink. The stimulus is utilized to select commands by generating steady-state visually evoked potential (SSVEP). The single eye blinks (i.e., confirm the selection) and double eye blinks (i.e., deny and re-selection) are employed to calibrate the SSVEP command. Besides that, the short-time Fourier transform and convolution neural network algorithms are utilized for feature extraction and classification, respectively. The results show that the proposed system could provide 38 control commands with a 2 s time window and a good accuracy (i.e., 96.92%) using one bipolar electroencephalogram (EEG) channel. This work presents a novel BCI approach for the home automation application based on SSVEP and eye blink signals, which could be useful for the disabled. In addition, the provided strategy of this study—a friendly channel configuration (i.e., one bipolar EEG channel), high accuracy, multiple commands, and short response time—might also offer a reference for the other BCI controlled applications.
Remote Monitoring Empowerment of Patients with IBDs during the SARS-CoV-2 Pandemic

Once the WHO declared the Sars-CoV-2 pandemic, the world had to reprogram numerous clinical activities, particularly those related to highly disabling diseases such as inflammatory bowel diseases (IBDs). In this study, 1083 IBD patients were assessed, affected by Crohn’s Disease (CD) and Ulcerative Colitis (UC), and subdivided into two groups. The first group included patients who needed treatment in person at the outpatients clinic, while the second group could be tele-monitored because they were able to self-administer therapy. The tele-monitoring was based on telecommunication applications via smartphone, driven by a dedicated clinical control room in the IBD Clinic. The aim of this study was to assess the quality of life (using IBDQ32) of UC patients and tele-monitored CD patients (tele-monitoring group) as compared to those patients who underwent assessment in person in the outpatients clinic (control group). Despite observing a lower number of relapses in the control group than the tele-monitoring group, there were no statistically significant differences between the groups in terms of the IBD32Q scores. Tele-monitoring of patients who are able to self-administer the IBD therapy can be an effective vicarious system as compared to the clinical evaluation in person, that could lead to important changes to avoid the overcrowding of the IBD outpatients clinic, especially during public health crises like the present pandemic.
Neurotoxicity and physiological stress in brain of zebrafish chronically exposed to tributyltin

ABSTRACT Tributyltin (TBT), an organotin compound, is hazardous in aquatic ecosystems. However, the mechanisms underlying TBT-induced central nervous system (CNS) toxicity remain to be determined especially in freshwater aquatic vertebrates. The aim of present study was to investigate the effects of chronic exposure to TBT on brain functions in a freshwater teleost the adult wild-type zebrafish (Danio rerio). Fish were exposed to sublethal concentrations of TBT (10, 100 or 300 ng/L) for 6 weeks. The influence of long-term TBT exposure was assessed in the brain of zebrafish with antioxidant related indices including malondialdehyde (MDA) levels and total antioxidant capacity, neurological parameters such as activities of acetylcholinesterase, and monoamine oxidase as well as levels of nitric oxide, dopamine, 5-hydroxytryptamine. In addition indices related to sensitivity of toxic insult such as cytochrome P450 1 regulation and heat shock protein 70 were determined. The regulation of related genes involved in endoplasmic reticulum stress (ERS), apoptosis and Nrf2 pathway were measured. Adverse physiological and biochemical responses were significantly enhanced in a concentration-dependent manner reflecting neurotoxicity attributed to TBT exposure. Our findings provide further insight into TBT-induced toxicity in wild-type zebrafish. and enhance our understanding of the molecular mechanisms underlying TBT-initiated CNS effects.
3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy

Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.
Integrated analysis identifies a long non-coding RNAs-messenger RNAs signature for prediction of prognosis in hepatitis B virus-hepatocellular carcinoma patients

Abstract Hepatitis B virus (HBV) infection is a leading cause of hepatocellular carcinoma (HCC), but HBV-HCC related prognosis signature remains rarely investigated. This study was to identify an integrated long non-coding RNAs-messenger RNAs (lncRNA-mRNA) signature for prediction of overall survival (OS) and explore their underlying functions. One RNA-sequencing dataset (training set, n = 95) and one microarray dataset E-TABM-36 (validation set, n = 44) were collected. Least absolute shrinkage and selection operator analysis was performed to identify an lncRNA-mRNA prognosis signature. The OS difference of patients in the high-risk and low-risk risk groups was evaluated by Kaplan–Meier curve. Area under the receiver operating characteristic curve (AUC), Harrell concordance index (C-index) calculation, and multivariate analyses with clinical characteristics were used to determine the prognostic ability. Furthermore, a coexpression network was constructed to interpret the functions. Nine signature genes (3 lncRNAs and 6 mRNAs) were selected to generate the risk score model. Patients belonging to the high-risk group showed a significantly shorter survival than those of the low-risk group. The prediction accuracy of the risk score for 5-year OS was 0.936 and 0.905 for the training set and validation set, respectively. Also, this risk score was independent of various clinical variables for the prognosis prediction. Incorporation of the risk score remarkably increased the predictive power of the routine clinical prognostic factors (vascular invasion status, tumor recurrence status) (AUC = 0.942 vs 0.628; C-index = 0.7997 vs 0.6908). Furthermore, LncRNA insulin-like growth factor 2 antisense RNA (IGF2-AS) and long intergenic non-protein coding RNA 342 (LINC00342) were predicted to exert tumor suppression effects by regulating homeobox D1 (HOXD1) and secreted frizzled related protein 5 (SFRP5), respectively; while lncRNA rhophilin Rho GTPase binding protein 1 antisense RNA 1 (RHPN1-AS1) may possess carcinogenic potential by promoting the transcription of chromobox 2 (CBX2), cell division cycle 20 (CDC20), matrix metallopeptidase 12 (MMP12), stratifin (SFN), tripartite motif containing 16 (TRIM16), and uroplakin 3A (UPK3A). These mRNAs may be associated with cell proliferation or apoptosis related pathways. This study may provide a novel, effective prognostic biomarker, and some therapeutic targets for HBV-HCC patients.
Network theory of the bacterial ribosome

In the past two decades, research into the biochemical, biophysical and structural properties of the ribosome have revealed many different steps of protein translation. Nevertheless, a complete understanding of how they lead to a rapid and accurate protein synthesis still remains a challenge. Here we consider a coarse network analysis in the bacterial ribosome formed by the connectivity between ribosomal (r) proteins and RNAs at different stages in the elongation cycle. The ribosomal networks are found to be dis-assortative and small world, implying that the structure allows for an efficient exchange of information between distant locations. An analysis of centrality shows that the second and fifth domains of 23S rRNA are the most important elements in all of the networks. Ribosomal protein hubs connect to much fewer nodes but are shown to provide important connectivity within the network (high closeness centrality). A modularity analysis reveals some of the different functional communities, indicating some known and some new possible communication pathways Our mathematical results confirm important communication pathways that have been discussed in previous research, thus verifying the use of this technique for representing the ribosome, and also reveal new insights into the collective function of ribosomal elements.
The hippo kinase STK38 ensures functionality of XPO1

ABSTRACT The proper segregation of basic elements such as the compartmentalization of the genome and the shuttling of macromolecules between the nucleus and the cytoplasm is a crucial mechanism for homeostasis maintenance in eukaryotic cells. XPO1 (Exportin 1) is the major nuclear export receptor and is required for the export of proteins and RNAs out of the nucleus. STK38 (also known as NDR1) is a Hippo pathway serine/threonine kinase with multifarious functions in normal and cancer cells. In this review, we summarize the history of the discovery of the nucleo/cytoplasmic shuttling of proteins and focus on the major actor of nuclear export: XPO1. After describing the molecular events required for XPO1-mediated nuclear export of proteins, we introduce the Hippo pathway STK38 kinase, synthetize its regulation mechanisms as well as its biological functions in both normal and cancer cells, and finally its intersection with XPO1 biology. We discuss the recently identified mechanism of XPO1 activation by phosphorylation of XPO1_S1055 by STK38 and contextualize this finding according to the biological functions previously reported for both XPO1 and STK38, including the second identity of STK38 as an autophagy regulator. Finally, we phrase this newly identified activation mechanism into the general nuclear export machinery and examine the possible outcomes of nuclear export inhibition in cancer treatment.
Application of accelerating energies to the maceration of sherry vinegar with citrus fruits.

BACKGROUND In the present work we propose the use of accelerating energies (microwaves and ultrasounds) to the maceration process of sherry vinegar with citrus fruit peels (orange and lemon). For the application of microwaves, an experimental design has been developed in order to optimize the maceration conditions. To evaluate the effect of these energies on the maceration, the volatile and polyphenolic content of the samples has been analyzed, as well as their sensory characteristics. RESULTS Orange peel provided a higher number of volatile and polyphenolic compounds to the vinegar, while lemon's yielded a greater amount of some of them. The multivariate analysis showed that the samples macerated using microwaves were the most similar to the samples macerated in the traditional way. This aspect was corroborated by the sensory analysis, which was more noticeable when orange peel was used in the macerations. CONCLUSION Therefore, it seems that the use of microwaves to accelerate maceration is a good alternative to the traditional method of making sherry vinegars macerated with citrus peel, since it cuts down the maceration time from 3 days to just a few minutes. This article is protected by copyright. All rights reserved.
Trends in the national food supply of absorbable zinc in Ethiopia: 1990–2017

Abstract Objective: This study analysed trends (1990–2017) in the availability of absorbable Zn in the national food supply of Ethiopia. Design: The supply statistics of ninety-five food groups were obtained from the Ethiopian Food Balance Sheets compiled by FAO. Zn and phytate contents were determined using multiple composition databases and absorbable Zn estimated via the ‘Miller’ equation. Estimated average requirement cut-point method was performed to estimate proportions at risk of inadequate intake. Physiological Zn requirements set by Institute of Medicine (IOM) and International Zinc Nutrition Consultative Group (IZiNCG) were applied. Time trend was tested using Mann–Kendall statistics and Z-score and P-values are provided. Setting: Ethiopia. Participants: NA. Results: Between 1990 and 2017, the supply of total dietary Zn was increased by 33 % from 9·8 to 13·0 mg/person/d (Z = 6·46, P < 0·001). However, that of absorbable Zn remained constant around 2·7 mg/person/d (Z = 1·87, P > 0·05). Over the period, the phytate supply was increased by 48 % from 1415 to 2095 mg/person/d (Z = 6·50, P < 0·001) and fractional Zn absorption declined from 27·0 to 20·9 % (Z = –6·62, P < 0·001). The contribution of animal source foods for bioavailable Zn was reduced by 45 % and the share of cereals raised by 11·3 %. Over the period, prevalence of inadequate Zn intake estimated using IZiNCG and IOM requirements remained constant around 10 and 50 %, respectively. Conclusion: Between 1990 and 2017, Ethiopia considerably increased the total supply of Zn; however, meaningful changes in bioavailable Zn and prevalence of deficiency were not observed due to proportional rise in phytate and concomitant decline in Zn absorption.
Beyond Forensic Evidence: Examining Sexual Assault Medical Forensic Exam Mechanisms that Influence Sexual Assault Case Outcomes

Despite the widespread use of sexual assault medical forensic exams (SAMFEs), practitioners and researchers continue to debate the role of SAMFEs and the evidence they provide in the investigation and prosecution of sexual assault cases. Using data from a review of sexual assault cases reported to police between 2015 and 2017 in two jurisdictions (n = 534), we use logistic regression examine whether the presence of a SAMFE predicts the likelihood of achieving criminal case processing outcomes and whether the relationship of the SAMFE with criminal case processing outcomes is moderated by other legal and extralegal case characteristics. We did not find evidence that the presence of a SAMFE in a case significantly predicts whether a suspect will be identified, arrested, or convicted overall, but we did find evidence of the SAMFE’s injury documentation value for arrest. Researchers and practitioners should account for the multiple ways SAMFEs can influence decision-making in future research and policymaking.
Non-diabetic glycosuria as a diagnostic clue for acute tubulointerstitial nephritis in patients with azotemia

Abstract Background Glycosuria is one of the manifestations of acute tubulointerstitial nephritis (ATIN), but may also be observed in other renal diseases. In this study, we investigated the value of non-diabetic glycosuria as a diagnostic clue for ATIN. Methods We retrospectively reviewed the medical records of adult patients who underwent a kidney biopsy as an evaluation for serum creatinine > 1.4 mg/dL. Patients with proteinuria in the nephrotic range, diabetes mellitus, or transplanted kidney were excluded. The laboratory abnormalities suggestive of tubular injury were compared between 28 patients (14 men and 14 women, mean age 48.5 ± 14.1 years) with ATIN and 116 patients (76 men and 40 women, mean age 53.1 ± 15.0 years) with other diagnoses. Results In ATIN, glycosuria (≥ 1+ on dipstick; 68%) was more frequent than hypophosphatemia (18%), hypouricemia (18%), hypokalemia (18%), and tubular proteinuria (40%). In other diagnoses, glycosuria (≥ 1+) was detected in 7 (6%) patients; 6 of them had the histological diagnosis of antineutrophil cytoplasmic antibody-associated glomerulonephritis. The presence of glycosuria (≥ 1+) had 68% sensitivity and 94% specificity for ATIN, with the positive likelihood ratio of 11.24 and the negative likelihood ratio of 0.34. Pyuria and low total CO2 were equally and more sensitive (68% and 71%, respectively) than glycosuria (≥ 1+), but had no diagnostic value due to low specificities (58% and 60%, respectively). Conclusion In non-diabetic, non-nephrotic patients undergoing a kidney biopsy for azotemia, 1+ or higher glycosuria, if present, was a good predictor of the diagnosis of ATIN.
The Effects of a Brief Motivational Intervention for Alcohol Use through Stages of Change among Non-Treatment Seeking Injured Patients.

BACKGROUND Little is known about the mechanisms of change underlying brief interventions and the patient characteristics that may affect them. The present study tested whether the stages of change mediate the effects of a BMI with and without a telephone booster relative to brief advice (i.e., multiple mediation). Further, the present study tested whether the effects of the BMI conditions on the stages of change were contingent on patients' alcohol use severity (i.e., moderated mediation). METHODS The present study is a secondary analysis using data from injured adult patients at three trauma centers who were screened for inclusion in the study and randomly assigned to brief advice (n = 200), BMI (n = 203), or BMI with a telephone booster (n = 193) (Field et al., 2014). Participants completed a baseline assessment and 3-, 6-, and 12-month follow-up assessments that included self-report measures of the stages of change, alcohol use, and alcohol-related problems, as well as other variables of interest. RESULTS The results demonstrated significant and consistent mediation at p < . 05 wherein BMI with a telephone booster increased action at 3-month follow-up leading to reduced likelihood of at-risk drinking, less alcohol use, and fewer alcohol problems at both 6- and 12-month follow-up. However, moderated mediation analyses suggested that the effects of the BMI conditions on the stages of change were not contingent on patients' alcohol use severity. CONCLUSIONS This study contributes to the understanding of stages of change as potential mechanisms of change of BMI. Directions for future research are discussed.
Leydig stem cells and future therapies for hypogonadism

Purpose of review In this review, we outline the most recent advances in the development of Leydig stem cells (LSCs) and summarize the current and upcoming treatments for hypogonadism. Recent findings In-vitro and in-vivo studies show that inducing stem cells to differentiate into testosterone-producing adult Leydig cells is possible. In addition, LSCs can be grafted with Sertoli cells to increase testosterone levels in vivo. This therapy causes minimal effects on luteinizing hormone and follicle stimulating hormone levels. Novel therapies for hypogonadism include varying methods of testosterone delivery such as intranasal and oral agents, as well as novel selective estrogen and androgen receptor modulators. Summary LSC therapies provide an effective way of increasing testosterone levels without detrimentally affecting gonadotropin levels. Next steps in developing viable Leydig cell grafting options for the treatment of hypogonadism should include the assessment of efficacy and potency of current animal models in human trials. Recently, both intranasal and oral testosterone have been made available and shown promising results in treating hypogonadism while maintaining fertility. Enclomiphene citrate and selective androgen receptor modulators have been suggested as future therapies for hypogonadism; however, further studies assessing efficacy and adverse effects are needed.
Thoracoscopy or Thoracotomy for Esophageal Atresia

Supplemental Digital Content is available in the text Objective: This systematic review with meta-analysis compares health- and provider-based outcomes of thoracoscopic to thoracotomy repair of esophageal atresia. Summary of Background Data: Thoracoscopic surgery has become a routine operation for esophageal atresia repair. However, large studies comparing the safety and efficacy of thoracoscopy to thoracotomy are scarce. Current reviews are obscured with institutional experiences or pool small samples. Methods: PRISMA-compliant search in Medline/PubMed, EMBASE, Web of Science, and Cochrane Library (PROSPERO #CRD42019121862) for original studies comparing thoracoscopy to thoracotomy for esophageal atresia. Quality assessments were performed using the Joanna Briggs Institute Critical Appraisal Tool. Meta-analyses were presented as odds ratios and standardized mean differences. Results: This is the largest published meta-analysis, including 17 studies and 1043 patients. Thoracoscopy produce shorter hospital stay [standardized mean differences (SMD) −11.91; 95% confidence interval (CI) 23.49–6.10; P = 0.0440], time until extubation (SMD −3.22; 95% CI 5.93–0.51; P = 0.0198), time until first oral feeding (SMD −2.84; 95% CI 4.62–1.07; P = 0.0017), and fewer musculoskeletal complications [odds ratio (OR) 0.08; 95% CI 0.01–0.58; P = 0.0133). Thoracoscopy is as safe as thoracotomy regarding leakage (OR −1.92; 95% CI 0.97–3.80; P = 0.0622), stricture formation (OR 2.66; 95% CI 0.86–3.23; P = 0.1339), stricture dilatation (OR 1.90; 95% CI 0.16–3.88; P = 0.0767), and mortality (OR 1.18; 95% CI 0.34–4.16; P = 0.7934). However, thoracoscopy take longer (SMD +27.69; 95% CI 12.06–43.32; P = 0.0005) and necessitate more antireflux surgery (OR 2.12; 95% CI 1.06–4.24; P = 0.0343). Conclusion: Thoracoscopy is effective and safe, with similar or better outcomes than thoracotomy for patients and providers. The only significant drawback is the need for antireflux surgery in the first years of life. Comparative randomized long-term studies are needed.