Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Artificial Neural Networks to Model Errors in Biochemical Manipulation of DNA Molecules

In recent years, the non-biological applications of DNA molecules have made considerable progress; most of these applications were performed in vitro, involving biochemical operations such as synthesis, amplification and sequencing. Because errors may occur with specific sequence patterns or experimental instruments, these biochemical operations are not completely reliable. Modeling errors in these biochemical procedures is an interesting research topic. For example, researchers have proposed several methods to avoid the known vulnerable sequence patterns in the study of storing binary information in DNA molecules. However, there are few end-to-end methods to evaluate these biochemical errors with regard to the DNA sequences. In this article, based on the data generated by a DNA storage research, we use artificial neural networks to predict whether a DNA sequence tends to cause errors in biochemical operations. Through comparative experiments and hyperparameter optimization, we analyze the known and potential problems in the research process. As a result, an end-to-end method to model the biochemical errors of DNA molecules in vitro through a computer system is proposed.
Smoking and obesity negatively affect the favourable outcome of varicocelectomy in sub‐fertile men

We assessed the effect of smoking and/or obesity on semen parameters and testosterone/oestradiol (T/E) ratio among sub‐fertile men treated with sub‐inguinal varicocelectomy. In this prospective, controlled, clinical study, 80 sub‐fertile men with clinical varicocele who were subjected to sub‐inguinal varicocelectomy were assigned into four equal groups (n = 20/each), group A: obese and smokers, group B: obese and nonsmokers, group C: smokers and nonobese and group D: nonsmokers and nonobese. Semen parameters, serum testosterone, oestradiol, follicle‐stimulating hormone, luteinising hormone, prolactin and calculation of T/E ratio were assessed at baseline and 6 months post‐varicocelectomy. The mean age ± SD of the study population was 26.1 ± 4.55. No statistical difference was detected among the study groups regarding age, residence, education, marital status and occupation (p > 0.05 for each). Post‐operatively, significant improvements in semen parameters were detected in all groups. There was a significant difference between groups A and B versus C and D (obese versus nonobese groups) and between groups A and C versus B and D (smokers versus nonsmokers; p < 0.05 for each) regarding semen parameters, testosterone level and T/E ratio. Smoking and/or obesity negatively affect(s) the favourable outcome of varicocelectomy, specifically improvement of semen parameters and hormonal pattern in sub‐fertile men with varicocele.
HeLa TI cell-based assay as a new approach to screen for chemicals able to reactivate the expression of epigenetically silenced genes

Chemicals reactivating epigenetically silenced genes target diverse classes of enzymes, including DNMTs, HDACs, HMTs and BET protein family members. They can strongly influence the expression of genes and endogenous retroviral elements with concomitant dsRNA synthesis and massive transcription of LTRs. Chemicals reactivating gene expression may cause both beneficial effects in cancer cells and may be hazardous by promoting carcinogenesis. Among chemicals used in medicine and commerce, only a small fraction has been studied with respect to their influence on epigenetic silencing. Screening of chemicals reactivating silent genes requires adequate systems mimicking whole-genome processes. We used a HeLa TSA-inducible cell population (HeLa TI cells) obtained by retroviral infection of a GFP-containing vector followed by several rounds of cell sorting for screening purposes. Previously, the details of GFP epigenetic silencing in HeLa TI cells were thoroughly described. Herein, we show that the epigenetically repressed gene GFP is reactivated by 15 agents, including HDAC inhibitors–vorinostat, sodium butyrate, valproic acid, depsipeptide, pomiferin, and entinostat; DNMT inhibitors–decitabine, 5-azacytidine, RG108; HMT inhibitors–UNC0638, BIX01294, DZNep; a chromatin remodeler–curaxin CBL0137; and BET inhibitors–JQ-1 and JQ-35. We demonstrate that combinations of epigenetic modulators caused a significant increase in cell number with reactivated GFP compared to the individual effects of each agent. HeLa TI cells are competent to metabolize xenobiotics and possess constitutively expressed and inducible cytochrome P450 mono-oxygenases involved in xenobiotic biotransformation. Thus, HeLa TI cells may be used as an adequate test system for the extensive screening of chemicals, including those that must be metabolically activated. Studying the additional metabolic activation of xenobiotics, we surprisingly found that the rat liver S9 fraction, which has been widely used for xenobiotic activation in genotoxicity tests, reactivated epigenetically silenced genes. Applying the HeLa TI system, we show that N-nitrosodiphenylamine and N-nitrosodimethylamine reactivate epigenetically silenced genes, probably by affecting DNA methylation.
An emotional competence curriculum for young children four to five years old

Abstract The aim of this study is to test the efficacy of the Seeds of Unity curriculum on a Pre-Kindergarten class consisting of four to five-year-old children in Brooklyn New York. The syllabus is a fusion of The Starting Small Program created by the Southern Poverty Law Center and the teaching of emotional competence theory. This study measured fourteen, four to five-year-old children before and after a ten-month exposure to the Seeds of Unity Curriculum. The Social Skills Rating Scale (SSRS) was utilized to measure changes in emotional competence before and after exposure to the curriculum. The results showed a mean score on the Gresham Social Skills index that placed the girls in the 76% before the program and the 97% after, and the boys went from the 64% to the 89% when measured against children their age. Despite the small N, this study showed that using this curriculum, increased social emotional intelligence. The competencies incorporated into this paradigm are vital to improving relations between cultures in the ethnically diverse New York city schools and provides hope that change is possible.
Long-term outcomes of ischemic post-conditioning primary PCI and conventional primary PCI in acute STEMI: a meta-analysis of randomized trials

ABSTRACT Background Data regarding ischemic postconditioning during percutaneous coronary intervention (PCI) as compared conventional PCI alone has yielded conflicting results. Methods Online databases comparing use of ischemic postconditioning percutaneous coronary intervention (ICP-PPCI) in STEMI patients with conventional PPCI were selected. Mortality, heart failure (HF), myocardial infarction (MI), and major adverse cardiac events (MACE) were evaluated. The primary outcome was composite of HF, MI, and mortality. Pooled risk ratio (RR) with 95% confidence interval (CI) were computed using random-effects model. Results Eight studies consisting of 2,566 patients (ICP-PPCI n = 1,228; PPCI n = 1,278) were included. The mean age for PPCI group was 61.38 ± 7.86 years (51% men) and for PCI 59.83 ± 8.94 years (47% men). There were no differences in outcome between ICP-PPCI and PPCI in terms of HF (RR 0.87 95% CI0.51–1.48; p = 0.29), MI (RR 1.28, 95%CI0.74–2.20; p = 0.20), mortality (RR 0.93, 95%CI0.64–1.34; p = 0.58), and MACE (RR 0.89, 95%CI0.74–1.07; p = 0.22). The results for composite event for the ICP-PPCI and PPIC procedures, at ≥1 year follow-up duration, were comparable (RR 1.00 95%CI0.82–1.22; p = 1). Conclusion Ischemic postconditioning post percutaneous coronary intervention in STEMI patients has no long-term benefits over conventional PCI.
A pilot study on automatic 3D quantification of Barrett's esophagus for risk stratification and therapy monitoring.

BACKGROUND AIMS Barrett's epithelium measurement using widely accepted Prague C&M classification is highly operator dependent. We propose a novel methodology for measuring this risk score automatically. The method also enables quantification of the area of Barrett's epithelium (BEA) and islands which was not possible before. Furthermore, it allows 3D reconstruction of the esophageal surface enabling interactive 3D visualization. We aim to assess the accuracy of the proposed AI system both on phantom and endoscopic patient data. METHODS Utilizing advanced deep learning, a depth estimator network is used to predict endoscope camera distance from the gastric folds. By segmenting BEA and gastro-esophageal junction and projecting them to the estimated mm distances, we measure C&M scores including the BEA. The derived endoscopy AI system is tested on a purpose-built 3D printed esophagus phantom with varying BEA and on 194 high-definition videos from 131 patients with C&M values scored by expert endoscopists. RESULTS Endoscopic phantom video data demonstrated a 97.2 % accuracy with a marginal ± 0.9 mm average deviation for C&M and island measurements, while for BEA we achieved 98.4 % accuracy with only ± 0.4 cm2 average deviation compared to ground-truth. On patient data, the C&M measurements provided by our system concord with expert scores with marginal overall relative error (mean difference) of 8 % (3.6 mm) and 7 % (2.8 mm) for C and M scores, respectively. CONCLUSIONS The proposed methodology automatically extracts Prague C&M scores with high accuracy. Quantification and 3D-reconstruction of the entire Barrett's area provides new opportunities for risk stratification and assessment of therapy response.
Regular Resistance Training Enhances Fibrinolytic Potential but Does Not Affect Coagulation

ABSTRACT Elevated coagulation and/or lowered fibrinolytic activity increases the risk of a thrombotic event, which affects more than 2 million people each year. Resistance training (RT) produces various adaptations that are theorized to influence hemostasis, but research in this area is limited. Purpose This study aimed to identify effects of an 8-wk, whole-body RT program on coagulation and fibrinolysis. Methods Sixteen healthy women and men (23 ± 5 yr) completed an RT program three times per week for 8 wk. Exercises included 2–3 sets of 8–12 repetitions performed at approximately 60%–80% of a one repetition maximum. Strength, body composition, and body circumferences were assessed before and after training. Plasma samples were obtained before and after training, and analyzed for active tissue plasminogen activator (tPA activity), total tissue plasminogen activator (tPA antigen), active plasminogen activator inhibitor-1 (PAI-1 activity), total plasminogen activator inhibitor-1 (PAI-1 antigen), fibrinogen, and coagulation factors VII (FVII) and VIII (FVIII). Results Significant increases in lean mass, arm and thigh circumferences, maximal chest press (PRE: 57.8 ± 37.5 kg, POST: 73.3 ± 43.2 kg), and leg press (PRE: 189.5 ± 96.0 kg, POST: 256.7 ± 97.9 kg) were observed (P < 0.05 for all). PAI-1 activity (PRE: 20.3 ± 32.5 IU·mL−1, POST 9.5 ± 20.9 IU·mL−1) and PAI-1 antigen decreased (PRE: 10.2 ± 9.0 ng·dL−1, POST: 7.2 ± 5.7 ng·dL−1; both, P < 0.05). No change in tPA activity or tPA antigen occurred. Fibrinogen, FVII, and FVIII did not change after training. Conclusions Inhibition of fibrinolysis was decreased after training, and coagulation was unaffected. These results suggest that regular RT may beneficially influence the risk of a thrombotic event. More research is warranted to understand the mechanisms through which RT affects hemostasis.
Human tear fluid analysis for clinical applications: progress and prospects

ABSTRACT Introduction: Human blood and saliva are increasingly under investigation for the detection of biomarkers for early diagnosis of non-communicable (e.g.cancers) and communicable diseases like COVID-19. Exploring the potential application of human tears, an easily accessible body fluid, for the diagnosis of various diseases is the need of the hour. Areas covered: This review deals with a comprehensive account of applications of tear analysis using different techniques, their comparison and overall progress achieved till now. The techniques used for tear fluid analysis are HPLC/UPLC/SDS-PAGE, CE, etc., together with ELISA, Mass Spectrometry, etc. But, with advances in instrumentation and data processing methods, it has become easy to couple the various separation methods with highly sensitive optical techniques for the analysis of body fluids. Expert opinion: Tear analysis can provide valuable information about the health condition of the eyes since it contains several molecular constituents, and their relative concentrations may alter under abnormal conditions. Tear analysis has the advantage that it is totally non-invasive. This study recommends tear fluid as a reliable clinical sample to be probed by highly sensitive optical techniques to diagnose different health conditions, with special emphasis on eye diseases.
The p16/ki-67 assay is a safe, effective and rapid approach to triage women with mild cervical lesions

Objective The aim of this study was to evaluate the diagnostic accuracy and efficiency of p16/ki-67 dual stain in the identification of CIN2+ lesions, in Greek women with ASCUS or LSIL cytology. Methods A total of 200 women, 20 to 60 years old, were enrolled in the study. All samples were cytologically evaluated and performed for p16/ki-67 and high-risk HPV (HR-HPV) test. All patients were referred to colposcopy for biopsy and histological evaluation. Three cervical cancer (CC) screening strategies were designed and the total direct medical costs of the procedures during our clinical trial were evaluated, from a healthcare perspective. Results HPV 16 as expected was the most common HR-HPV type followed by HPV 31 and HPV 51. The risk for CIN2+ was significantly higher in HPV 16/18 positive cases. p16/ki-67 demonstrated a high sensitivity for CIN2+ identification in both ASCUS and LSIL groups (90.4% and 95%, respectively). HR-HPV test with sensitivity 52.3% and 65.5%, as well as colposcopy with sensitivity 14.3% and 36% respectively in ASCUS and LSIL group, showed inferior results compared to p16/ki-67. The specificity of p16/ki-67 for ASCUS and LSIL was 97.2% and 95.2% respectively, inferior only to colposcopy: 100% and 100%, lacking however statistical significance. HR-HPV test instead, presented the lowest specificity: 76.4% and 71.4% respectively in comparison to the other two methods. From a healthcare perspective, the costs and benefits of the tests implementation for the annual screening and triaging, in three CC screening strategies, were also calculated and discussed. Conclusions The results of the study indicate that p16/ki-67 is a safe and rapid assay that could be used to detect CIN2+ among women with mild cervical lesions, presenting both high sensitivity and specificity and could minimize the psychological and economic burden of HPV screening.
Microfinance, retention in care, and mortality among patients enrolled in HIV care in East Africa

Supplemental Digital Content is available in the text Objective: To measure associations between participation in community-based microfinance groups, retention in HIV care, and death among people with HIV (PWH) in low-resource settings. Design and methods: We prospectively analyzed data from 3609 patients enrolled in an HIV care program in western Kenya. HIV patients who were eligible and chose to participate in a Group Integrated Savings for Health Empowerment (GISHE) microfinance group were matched 1 : 2 on age, sex, year of enrollment in HIV care, and location of initial HIV clinic visit to patients not participating in GISHE. Follow-up data were abstracted from medical records from January 2018 through February 2020. Logistic regression analysis examined associations between GISHE participation and two outcomes: retention in HIV care (i.e. >1 HIV care visit attended within 6 months prior to the end of follow-up) and death. Socioeconomic factors associated with HIV outcomes were included in adjusted models. Results: The study population was majority women (78.3%) with a median age of 37.4 years. Microfinance group participants were more likely to be retained in care relative to HIV patients not participating in a microfinance group [adjusted odds ratio (aOR) = 1.31, 95% confidence interval (CI) 1.01–1.71; P = 0.046]. Participation in group microfinance was associated with a reduced odds of death during the follow-up period (aOR = 0.57, 95% CI 0.28–1.09; P = 0.105). Conclusion: Participation in group-based microfinance appears to be associated with better HIV treatment outcomes. A randomized trial is needed to assess whether microfinance groups can improve clinical and socioeconomic outcomes among PWH in similar settings.
Psychostimulants and opioids differentially influence the epigenetic modification of histone acetyltransferase and histone deacetylase in astrocytes

Illicit drugs are known to affect central nervous system (CNS). Majorly psychostimulants such as cocaine, methamphetamine (METH) and opioids such as morphine are known to induce epigenetic changes of histone modifications and chromatin remodeling which are mediated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). Aberrant changes in histone acetylation-deacetylation process further exacerbate dysregulation of gene expression and protein modification which has been linked with neuronal impairments including memory formation and synaptic plasticity. In CNS, astrocytes play a pivotal role in cellular homeostasis. However, the impact of psychostimulants and opioid mediated epigenetic changes of HAT/HADCs in astrocytes has not yet been fully elucidated. Therefore, we have investigated the effects of the psychostimulants and opioid on the acetylation-regulating enzymes- HAT and HDACs role in astrocytes. In this study, Class I and II HDACs and HATs gene expression, protein changes and global level changes of acetylation of H3 histones at specific lysines were analyzed. In addition, we have explored the neuroprotective “nootropic” drug piracetam were exposed with or without psychostimulants and opioid in the human primary astrocytes. Results revealed that psychostimulants and opioid upregulated HDAC1, HDAC4 and p300 expression, while HDAC5 and GCN5 expression were downregulated. These effects were reversed by piracetam coexposure. Psychostimulants and opioid exposure upregulated global acetylation levels of all H3Ks, except H3K14. These results suggest that psychostimulants and opioids differentially influence HATs and HDACs.
Neuromorphic Context-Dependent Learning Framework With Fault-Tolerant Spike Routing

Neuromorphic computing is a promising technology that realizes computation based on event-based spiking neural networks (SNNs). However, fault-tolerant on-chip learning remains a challenge in neuromorphic systems. This study presents the first scalable neuromorphic fault-tolerant context-dependent learning (FCL) hardware framework. We show how this system can learn associations between stimulation and response in two context-dependent learning tasks from experimental neuroscience, despite possible faults in the hardware nodes. Furthermore, we demonstrate how our novel fault-tolerant neuromorphic spike routing scheme can avoid multiple fault nodes successfully and can enhance the maximum throughput of the neuromorphic network by 0.9%–16.1% in comparison with previous studies. By utilizing the real-time computational capabilities and multiple-fault-tolerant property of the proposed system, the neuronal mechanisms underlying the spiking activities of neuromorphic networks can be readily explored. In addition, the proposed system can be applied in real-time learning and decision-making applications, brain–machine integration, and the investigation of brain cognition during learning.
No need for secondary Pneumocystis jirovecii pneumonia prophylaxis in adult people living with HIV from Europe on ART with suppressed viraemia and a CD4 cell count greater than 100 cells/µL

Since the beginning of the HIV epidemic in resource‐rich countries, Pneumocystis jirovecii pneumonia (PjP) is one of the most frequent opportunistic AIDS‐defining infections. The Collaboration of Observational HIV Epidemiological Research Europe (COHERE) has shown that primary Pneumocystis jirovecii Pneumonia (PjP) prophylaxis can be safely withdrawn in patients with CD4 counts of 100 to 200 cells/µL if plasma HIV‐RNA is suppressed on combination antiretroviral therapy. Whether this holds true for secondary prophylaxis is not known, and this has proved difficult to determine due to the much lower population at risk.
Automatic classification of medical image modality and anatomical location using convolutional neural network

Modern radiologic images comply with DICOM (digital imaging and communications in medicine) standard, which, upon conversion to other image format, would lose its image detail and information such as patient demographics or type of image modality that DICOM format carries. As there is a growing interest in using large amount of image data for research purpose and acquisition of large amount of medical image is now a standard practice in the clinical setting, efficient handling and storage of large amount of image data is important in both the clinical and research setting. In this study, four classes of images were created, namely, CT (computed tomography) of abdomen, CT of brain, MRI (magnetic resonance imaging) of brain and MRI of spine. After converting these images into JPEG (Joint Photographic Experts Group) format, our proposed CNN architecture could automatically classify these 4 groups of medical images by both their image modality and anatomic location. We achieved excellent overall classification accuracy in both validation and test sets (> 99.5%), specificity and F1 score (> 99%) in each category of this dataset which contained both diseased and normal images. Our study has shown that using CNN for medical image classification is a promising methodology and could work on non-DICOM images, which could potentially save image processing time and storage space.