Miracle-dz/UniFAR-FTUs huggingface dataset:
Building Encoder and Decoder with Deep Neural Networks: On the Way to Reality

Deep learning has been a groundbreaking technology in various fields as well as in communications systems. In spite of the notable advancements of deep neural network (DNN) based technologies in recent years, the high computational complexity has been a major obstacle to apply DNN in practical communications systems which require real-time operation. In this sense, challenges regarding practical implementation must be addressed before the proliferation of DNN-based intelligent communications becomes a reality. To the best of the authors' knowledge, for the first time, this article presents an efficient learning architecture and design strategies including link level verification through digital circuit implementations using hardware description language (HDL) to mitigate this challenge and to deduce feasibility and potential of DNN for communications systems. In particular, DNN is applied for an encoder and a decoder to enable flexible adaptation with respect to the system environments without needing any domain specific information. Extensive investigations and interdisciplinary design considerations including the DNN-based autoencoder structure, learning framework, and low-complexity digital circuit implementations for real-time operation are taken into account by the authors which ascertains the use of DNN-based communications in practice.
Sex hormone Profile in Human Immunodeficiency Virus-Infected Men and It's Correlation with CD4 Cell Counts

Background: In human immunodeficiency virus (HIV)-infected men, hypogonadism is the most common endocrinological disorder, and most cases of hypogonadism are secondary. The aim of this study was to find out the hormonal abnormalities in HIV-infected males and it's correlation with CD4 cell counts. Materials and Methods: One hundred HIV-infected male patients were evaluated in the Department of Medicine, Postgraduate Institute of Medical Education and Research and Dr. Ram Manohar Lohia Hospital, New Delhi, India, over a period of 12 months from September 2014 to August 2015 using history, physical examination, routine baseline investigations, and CD4 counts. Free testosterone, dehydroepiandrosterone sulfate (DHEAS), luteinizing hormone (LH), follicle-stimulating hormone (FSH), and prolactin were measured using an overnight fasting sample. Patients were divided into three groups on the basis of CD4 counts (Group A: CD4 counts ≥350/mm3, Group B: CD4 counts between 200 and 349/mm3, and Group C: CD4 counts <200/mm3). Data were analyzed using Student's t-test, ANOVA test, Chi-square test, and Pearson's test and P ≤ 0.05 was considered statistically significant. Results: In 100 HIV-infected males, overall prevalence of hypogonadism was found to be 66%, and 30%–35% patients had symptoms of hypoandrogenemia. Hypogonadotropic hypogonadism was found in 42% of patients. A significant association (P = 0.027) was found between prevalence of hypogonadism and the level of immunodeficiency with an increase in the prevalence of hypogonadism as CD4 counts decreased. Lower levels of free testosterone and DHEAS were found in cases of severe immunosuppression with a statistically significant correlation with CD4 counts. Correlation of other sex hormones (LH, FSH, and prolactin) with CD4 counts not statistically significant. Mean free testosterone and FSH were found to be significantly higher in patients on antiretroviral therapy (ART) than in those not on ART (P = 0.028 and P = 0.045, respectively), but no specific ART drug or their drug combination was found to have a significant correlation with levels of any sex hormone. Conclusion: Hypogonadism (hypogonadotropic hypogonadism) was found to be a common endocrinological disorder in HIV-infected male population, seen more commonly in association with low CD4 counts.
Protective effects of Vitis vinifera (grapes) and one of its biologically active constituents, resveratrol, against natural and chemical toxicities: A comprehensive review

Vitis vinifera (grape) is one of the “most‐produced fruit” in the world. Grape seeds are a valuable source of phenolic compounds including resveratrol (RSV). Grape and one of its biologically active constituents, RSV, exert their protective effects against different natural or chemical toxins which could alter physiological homeostasis through a variety of mechanisms. Some of these mechanisms of actions include increase in superoxide dismutase, hemeoxygenase‐1, and glutathione peroxidase activities and reduced glutathione content and decrease in malondialdehyde (MDA) levels and activation of the nuclear erythroid2‐related factor2/ARE pathway. There are also various reports of the potential use of such compounds in preventing different ailments including cardiovascular diseases, cancer, degenerative diseases, and inflammatory disorders. Therefore, in this review, we have investigated the possible protective effects of grape and one of its biologically active constituents, RSV, on different organs' toxicity induced by natural toxins (such as mycotoxins, lipopolysaccharide, and triptolide) and chemical toxins (such as antitumors, metals, and carbon tetrachloride). There are insufficient clinical trials on this subject, so our review only includes in vivo and in vitro studies. To establish the grape beneficial effects in human intoxication, more clinical trials need to be accomplished.
C-terminal kink formation is required for lateral gating in BamA

Significance Nearly all outer-membrane proteins (OMPs) in Gram-negative bacteria are inserted via the β-barrel assembly machinery (BAM) complex. Molecular dynamics simulations have revealed a persistent C-terminal strand kink of the core BAM component, BamA, which permits BamA to open laterally to the membrane. Experiments show that inhibiting kinking makes bacteria more susceptible to antibiotics. Kink-induced lateral gating may catalyze OMP insertion through a local disruption of the membrane, a pathway into the membrane, or both. In Gram-negative bacteria, the outer membrane contains primarily β-barrel transmembrane proteins and lipoproteins. The insertion and assembly of β-barrel outer-membrane proteins (OMPs) is mediated by the β-barrel assembly machinery (BAM) complex, the core component of which is the 16-stranded transmembrane β-barrel BamA. Recent studies have indicated a possible role played by the seam between the first and last β-barrel strands of BamA in the OMP insertion process through lateral gating and a destabilized membrane region. In this study, we have determined the stability and dynamics of the lateral gate through over 12.5 μs of equilibrium simulations and 4 μs of free-energy calculations. From the equilibrium simulations, we have identified a persistent kink in the C-terminal strand and observed spontaneous lateral-gate separation in a mimic of the native bacterial outer membrane. Free-energy calculations of lateral gate opening revealed a significantly lower barrier to opening in the C-terminal kinked conformation; mutagenesis experiments confirm the relevance of C-terminal kinking to BamA structure and function.
Survival and Prognostic Factors in Pediatric Patients with Medulloblastoma in Southern Thailand

Background: The current prognosis of medulloblastoma in children is better because of technological advancements and improvements in treatment strategies and genetic investigations. However, there is a lack of studies that focus on medulloblastoma in Thailand. The aims of our study were to conduct a survival analysis and to identify the prognostic factors of pediatric medulloblastoma. Materials and Methods: Fifty-five children, with medulloblastoma, were eligible for analysis between 1991 and 2015. We retrospectively reviewed both the clinical and the histological data. Survival curves were constructed using the Kaplan–Meier method. For comparisons of dichotomous factors, between groups, the log-rank test was used to determine survival. The Cox proportional hazard regression model was used to identify the univariate and multivariate survival predictors. Results: The mortality rate was 49.1% in this study. The median follow-up time was 68.8 months (range: 1–294 months). The 5-year overall survival rate and median survival time were 53.8% (95% CI 38.7–66.7) and 80 months (95% CI 23–230), respectively. Univariate analysis revealed children <3 years of age, hemispheric tumor location, high risk according to risk stratification, and patients who did not receive radiation therapy affected the prognosis. In multivariable analysis, hemispheric tumors (hazard ratio [HR] 2.54 [95% CI 1.11–5.80]; P = 0.01)and high risk groups (HR 3.86 [95% CI 1.28–11.60]; P = 0.01) influenced death. Finally, using conditional inference trees, the study showed that hemispheric tumor locations are truly aggressive in behavior, whereas risk stratification is associated with the prognosis of midline tumors. Conclusions: Hemispheric medulloblastoma and high-risk groups according to risk stratification were associated with poor prognosis.
Segmental Audio Word2Vec: Representing Utterances as Sequences of Vectors with Applications in Spoken Term Detection

While Word2Vec represents words (in text) as vectors carrying semantic information, audio Word2Vec was shown to be able to represent signal segments of spoken words as vectors carrying phonetic structure information. Audio Word2Vec can be trained in an unsupervised way from an unlabeled corpus, except the word boundaries are needed. In this paper, we extend audio Word2Vec from word-level to utterance-level by proposing a new segmental audio Word2Vec, in which unsupervised spoken word boundary segmentation and audio Word2Vec are jointly learned and mutually enhanced, so an utterance can be directly represented as a sequence of vectors carrying phonetic structure information. This is achieved by a segmental sequence-to-sequence autoencoder (SSAE), in which a segmentation gate trained with reinforcement learning is inserted in the encoder. Experiments on English, Czech, French and German show very good performance in both unsupervised spoken word segmentation and spoken term detection applications (significantly better than frame-based DTW).
Optical Coherence Tomography Angiography in Eyes with Retinal Vein Occlusion

Optical coherence angiography (OCTA) is a noninvasive technique that has been introduced in recent years to detect ophthalmological pathology. The growing usage of OCTA to detect retinal abnormalities can be attributed to its advantages over the reference-standard fluorescein angiography (FA), although both of these techniques can be used in association. OCTA's advantages include its dye independency, its ability to produce depth-resolved images of retinal and choroidal vessels that yield images of different vascular layers of the retina, and the better delineation of the foveal avascular zone. OCTA's disadvantages include the lack of normalized patient data, artefactual projection issues, and its inability to detect low-flow lesions or pathologic conditions. Different OCTA platforms use unique algorithms to detect microvasculature, which are implemented in both spectral-domain (SD) and swept-source (SS) OCT machines. Microvascular changes in retinal vein occlusions (RVOs) are visible in both the superficial and deep capillary networks of the retina in OCTA. These visualizations include a decrease in foveal and parafoveal vascular densities, non-perfusion areas, capillary engorgement and telangiectasias, vascular tortuosity, microaneurysms, disruption of the foveal perivascular plexus, and formation of collateral vessels. The restricted field of view and inability to show leakage are important limitations associated with the use of OCTA in RVO cases. In this article, we present a brief overview of OCTA and a review of the changes detectable in different slabs by OCTA in RVO cases published in PubMed and Embase.
Identification and characterization of prescription drugs that change levels of 7-dehydrocholesterol and desmosterol[S]

Regulating blood cholesterol (Chol) levels by pharmacotherapy has successfully improved cardiovascular health. There is growing interest in the role of Chol precursors in the treatment of diseases. One sterol precursor, desmosterol (Des), is a potential pharmacological target for inflammatory and neurodegenerative disorders. However, elevating levels of the precursor 7-dehydrocholesterol (7-DHC) by inhibiting the enzyme 7-dehydrocholesterol reductase is linked to teratogenic outcomes. Thus, altering the sterol profile may either increase risk toward an adverse outcome or confer therapeutic benefit depending on the metabolite affected by the pharmacophore. In order to characterize any unknown activity of drugs on Chol biosynthesis, a chemical library of Food and Drug Administration-approved drugs was screened for the potential to modulate 7-DHC or Des levels in a neural cell line. Over 20% of the collection was shown to impact Chol biosynthesis, including 75 compounds that alter 7-DHC levels and 49 that modulate Des levels. Evidence is provided that three tyrosine kinase inhibitors, imatinib, ponatinib, and masitinib, elevate Des levels as well as other substrates of 24-dehydrocholesterol reductase, the enzyme responsible for converting Des to Chol. Additionally, the mechanism of action for ponatinib and masitinib was explored, demonstrating that protein levels are decreased as a result of treatment with these drugs.
Frontal lobe executive dysfunction and cerebral perfusion study in alcohol dependence syndrome

Background: Long-term alcohol use leading to frontal lobe impairment has been a cause of concern for many decades. However, there are very few studies from India of evaluation of frontal lobe executive dysfunction among alcoholics. Hence, this study was undertaken to evaluate the frontal executive dysfunction using Wisconsin Card Sorting Test (WCST) and perfusion deficits by Single-Photon Emission Computerized Tomography (SPECT) among alcohol-dependent patients. Aim: The aim of this study is to evaluate the frontal executive dysfunction using WCST and frontal lobe perfusion deficits by SPECT among alcohol-dependent patients. Materials and Methods: This was a cross-sectional study involving 20 alcohol dependence syndrome patients in a tertiary care center. After ethical clearance and informed consent, all were evaluated using WCST and SPECT. Results: About 45% patients had impairment on WCST, and it was related to the duration of drinking. About 55% showed reduced frontal lobe perfusion on SPECT scan and they had a long duration of drinking compared to controls. Among the patients showing impairment on WCST subscores, more than 50% had reduced frontal lobe perfusion on SPECT. Conclusion: This study not only confirmed the executive function impairment and frontal lobe perfusion deficits in alcohol-dependent patients but also showed a concomitant presence of both in patients with chronic alcohol abuse.
Digital Blues: An Investigation Into the Use of Bluetooth Protocols

The proliferation of Bluetooth mobile device communications into all aspects of modern society raises security questions by both academicians and practitioners. This environment prompted an investigation into the real-world use of Bluetooth protocols along with an analysis of documented security attacks. The experiment discussed in this paper collected data for one week in a local coffee shop. The data collection took about an hour each day and identified 478 distinct devices. The contribution of this research is two-fold. First, it provides insight into real-world Bluetooth protocols that are being utilized by the general public. Second, it provides foundational research that is necessary for future Bluetooth penetration testing research.
The volume-outcome relationship in severely injured patients: A systematic review and meta-analysis

BACKGROUND The volume-outcome relationship in severely injured patients remains under debate and this has consequences for the designation of trauma centers. OBJECTIVES The aim of this study was to evaluate the relationship between hospital or surgeon volume and health outcomes in severely injured patients. METHODS Six electronic databases were searched from 1980 up to January 30, 2018, to identify studies that describe the relationship between hospital or surgeon volume and health outcomes in severely injured patients (preferably Injury Severity Score above 15). Selection of relevant studies, data extraction, and critical appraisal of the methodological quality were performed by two independent reviewers. Pooled adjusted and unadjusted estimates of the effect of volume on in-hospital mortality, only in study populations with Injury Severity Score greater than 15, were calculated with a random-effects meta-analysis. A mixed effects linear regression model was used to assess hospital volume as continuous parameter. RESULTS Eighteen observational cohort studies were included. The majority (13 [72%] of 18) reported an association between higher hospital or surgeon volume and lower mortality rate. Overall, the quality of the included studies was reasonable, with insufficient adjustment as one of the most common limitations. Eight studies were included in the meta-analysis with a total of 222,418 patients. High hospital volume (>240 admitted severely injured patients per year) was associated with a lower risk of mortality (adjusted odds ratio, 0.85; 95% confidence interval, 0.76–0.94). Four studies were included in the regression model, providing a beta of −0.17 per 10 patients (95% CI, −0.27 to −0.07). There was no clear association between surgeon volume and mortality rates based on three available studies. CONCLUSION Our systematic overview of the literature reveals a modest association between high-volume centers and lower mortality in severely injured patients, suggesting that designation of high-volume centers might improve outcomes among severely injured patients. LEVEL OF EVIDENCE Systematic review and meta-analysis, level III. Systematic review registration number: PROSPERO registration ID CRD42017056729
Parallel Distribution of an Inner Hair Cell and Auditory Nerve Model for Real-Time Application

This paper summarizes recent efforts in implementing a model of the ear's inner hair cell and auditory nerve on a neuromorphic hardware platform, the SpiNNaker machine. This exploits the massive parallelism of the target architecture to obtain real-time modeling of a biologically realistic number of human auditory nerve fibres. We show how this model can be integrated with additional modules that simulate previous stages of the early auditory pathway running on the same hardware architecture, thus producing a full-scale spiking auditory nerve output from a single sound stimulus. The results of the SpiNNaker implementation are shown to be comparable with a MATLAB version of the same model algorithms, while removing the inherent performance limitations associated with an increase in auditory model scale that are seen in the conventional computer simulations. Finally, we outline the potential for using this system as part of a full-scale, real-time digital model of the complete human auditory pathway on the SpiNNaker platform.
PUX10 Is a Lipid Droplet-Localized Scaffold Protein That Interacts with CELL DIVISION CYCLE48 and Is Involved in the Degradation of Lipid Droplet Proteins

PUX10 is a lipid droplet-localized scaffold protein that recruits CDC48 and is involved in the degradation of proteins associated with lipid droplets. The number of known proteins associated with plant lipid droplets (LDs) is small compared with other organelles. Many aspects of LD biosynthesis and degradation are unknown, and identifying and characterizing candidate LD proteins could help elucidate these processes. Here, we analyzed the proteome of LD-enriched fractions isolated from tobacco (Nicotiana tabacum) pollen tubes. Proteins that were highly enriched in comparison with the total or cytosolic fraction were further tested for LD localization via transient expression in pollen tubes. One of these proteins, PLANT UBX DOMAIN-CONTAINING PROTEIN10 (PUX10), is a member of the plant UBX domain-containing (PUX) protein family. This protein localizes to LDs via a unique hydrophobic polypeptide sequence and can recruit the AAA-type ATPase CELL DIVISION CYCLE48 (CDC48) protein via its UBX domain. PUX10 is conserved in Arabidopsis thaliana and expressed in embryos, pollen tubes, and seedlings. In pux10 knockout mutants in Arabidopsis, LD size is significantly increased. Proteomic analysis of pux10 mutants revealed a delayed degradation of known LD proteins, some of which possessed ubiquitination sites. We propose that PUX10 is involved in a protein degradation pathway at LDs, mediating an interaction between polyubiquitinated proteins targeted for degradation and downstream effectors such as CDC48.
Programmable activation of Bombyx gene expression using CRISPR/dCas9 fusion systems

The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)‐based techniques have made it possible to reprogram target gene expression without cloning complementary DNA or disturbing genomic sequence in mammalian cells and several multicellular organisms. We previously showed that CRISPR‐associated protein 9 (Cas9) and CRISPR from Prevotella and Francisella 1 (Cpf1) could induce target mutations, deletions, inversions, and duplications both singly and multiplex in silkworm, Bombyx mori. However, it remains unknown whether the CRISPR activation (CRISPRa) system can be used in B. mori. In this study, we investigated the CRISPRa system, in which a nuclease dead Streptococcus pyogenes Cas9 (SpCas9) is fused to two transcription activation domains, including VP64 (a tetramer of the herpes simplex VP16 transcriptional activator domain), and VPR (a tripartite activator, composed of VP64, p65, and Rta). The results showed that both dCas9‐VP64 and dCas9‐VPR systems could be used in B. mori cells, of which the latter showed significantly higher activity. The dCas9‐VPR system showed considerable activity on all five tested target genes, and further analysis revealed that the up‐regulation of genes was negatively correlated to their basal expression level. We also observed that this system could be used to upregulate a range of target genes. Taken together, our findings demonstrate that CRISPRa can be a powerful tool to study gene functions in B. mori and perhaps other non‐drosophila insects.