Miracle-dz/UniFAR-FTUs huggingface dataset:
Herpes Simplex Virus Evasion of Early Host Antiviral Responses

Herpes simplex viruses type 1 (HSV-1) and type 2 (HSV-2) have co-evolved with humans for thousands of years and are present at a high prevalence in the population worldwide. HSV infections are responsible for several illnesses including skin and mucosal lesions, blindness and even life-threatening encephalitis in both, immunocompetent and immunocompromised individuals of all ages. Therefore, diseases caused by HSVs represent significant public health burdens. Similar to other herpesviruses, HSV-1 and HSV-2 produce lifelong infections in the host by establishing latency in neurons and sporadically reactivating from these cells, eliciting recurrences that are accompanied by viral shedding in both, symptomatic and asymptomatic individuals. The ability of HSVs to persist and recur in otherwise healthy individuals is likely given by the numerous virulence factors that these viruses have evolved to evade host antiviral responses. Here, we review and discuss molecular mechanisms used by HSVs to evade early innate antiviral responses, which are the first lines of defense against these viruses. A comprehensive understanding of how HSVs evade host early antiviral responses could contribute to the development of novel therapies and vaccines to counteract these viruses.
Perioperative hematoma with subcutaneous ICD implantation: Impact of anticoagulation and antiplatelet therapies

The safety of perioperative anticoagulation (AC) and antiplatelet (AP) therapy with subcutaneous implantable cardioverter‐defibrillator (S‐ICD) implantation is unknown. The purpose of this study was to identify the risk factors associated with hematoma complicating S‐ICD implantation.
Depth and the Uncertainty of Statistical Knowledge on Musical Creativity Fluctuate Over a Composer's Lifetime

Brain models music as a hierarchy of dynamical systems that encode probability distributions and complexity (i.e., entropy and uncertainty). Through musical experience over lifetime, a human is intrinsically motivated in optimizing the internalized probabilistic model for efficient information processing and the uncertainty resolution, which has been regarded as rewords. Human's behavior, however, appears to be not necessarily directing to efficiency but sometimes act inefficiently in order to explore a maximum rewards of uncertainty resolution. Previous studies suggest that the drive for novelty seeking behavior (high uncertain phenomenon) reflects human's curiosity, and that the curiosity rewards encourage humans to create and learn new regularities. That is to say, although brain generally minimizes uncertainty of music structure, we sometimes derive pleasure from music with uncertain structure due to curiosity for novelty seeking behavior by which we anticipate the resolution of uncertainty. Few studies, however, investigated how curiosity for uncertain and novelty seeking behavior modulates musical creativity. The present study investigated how the probabilistic model and the uncertainty in music fluctuate over a composer's lifetime (all of the 32 piano sonatas by Ludwig van Beethoven). In the late periods of the composer's lifetime, the transitional probabilities (TPs) of sequential patterns that ubiquitously appear in all of his music (familiar phrase) were decreased, whereas the uncertainties of the whole structure were increased. Furthermore, these findings were prominent in higher-, rather than lower-, order models of TP distribution. This may suggest that the higher-order probabilistic model is susceptible to experience and psychological phenomena over the composer's lifetime. The present study first suggested the fluctuation of uncertainty of musical structure over a composer's lifetime. It is suggested that human's curiosity for uncertain and novelty seeking behavior may modulate optimization and creativity in human's brain.
Sex Determination from Fourth Rib by Osteometric Analysis

1 Senior Resident, Forensic Medicine and Toxicology, Lady Hardinge Medical College, New Delhi, India. 2 Junior Resident (PG IInd Year), Forensic Medicine and Toxicology, Lady Hardinge Medical College, New Delhi, India. 3 Junior Resident (PG Ist Year), Forensic Medicine and Toxicology, Lady Hardinge Medical College, New Delhi, India. 4 Professor and Head, Forensic Medicine and Toxicology, Lady Hardinge Medical College, New Delhi, India.
USP7: Novel Drug Target in Cancer Therapy

Ubiquitin specific protease 7 (USP7) is one of the deubiquitinating enzymes (DUB) that erases ubiquitin and protects substrate protein from degradation. Full activity of USP7 requires the C-terminal Ub-like domains fold back onto the catalytic domain, allowing the remodeling of the active site to a catalytically competent state by the C-terminal peptide. Until now, numerous proteins have been identified as substrates of USP7, which play a key role in cell cycle, DNA repair, chromatin remodeling, and epigenetic regulation. Aberrant activation or overexpression of USP7 may promote oncogenesis and viral disease, making it a target for therapeutic intervention. Currently, several synthetic small molecules have been identified as inhibitors of USP7, and applied in the treatment of diverse diseases. Hence, USP7 may be a promising therapeutic target for the treatment of cancer.
Modeling Stroke in Mice: Permanent Coagulation of the Distal Middle Cerebral Artery

Stroke is the third most common cause of death and a main cause of acquired adult disability in developed countries. Only very limited therapeutical options are available for a small proportion of stroke patients in the acute phase. Current research is intensively searching for novel therapeutic strategies and is increasingly focusing on the sub-acute and chronic phase after stroke because more patients might be eligible for therapeutic interventions in a prolonged time window. These delayed mechanisms include important pathophysiological pathways such as post-stroke inflammation, angiogenesis, neuronal plasticity and regeneration. In order to analyze these mechanisms and to subsequently evaluate novel drug targets, experimental stroke models with clinical relevance, low mortality and high reproducibility are sought after. Moreover, mice are the smallest mammals in which a focal stroke lesion can be induced and for which a broad spectrum of transgenic models are available. Therefore, we describe here the mouse model of transcranial, permanent coagulation of the middle cerebral artery via electrocoagulation distal of the lenticulostriatal arteries, the so-called “coagulation model”. The resulting infarct in this model is located mainly in the cortex; the relative infarct volume in relation to brain size corresponds to the majority of human strokes. Moreover, the model fulfills the above-mentioned criteria of reproducibility and low mortality. In this video we demonstrate the surgical methods of stroke induction in the “coagulation model” and report histological and functional analysis tools.
A Direct Demonstration of Functional Differences between Subdivisions of Human V5/MT+

Abstract Two subdivisions of human V5/MT+: one located posteriorly (MT/TO‐1) and the other more anteriorly (MST/TO‐2) were identified in human participants using functional magnetic resonance imaging on the basis of their representations of the ipsilateral versus contralateral visual field. These subdivisions were then targeted for disruption by the application of repetitive transcranial magnetic stimulation (rTMS). The rTMS was delivered to cortical areas while participants performed direction discrimination tasks involving 3 different types of moving stimuli defined by the translational, radial, or rotational motion of dot patterns. For translational motion, performance was significantly reduced relative to baseline when rTMS was applied to both MT/TO‐1 and MST/TO‐2. For radial motion, there was a differential effect between MT/TO‐1 and MST/TO‐2, with only disruption of the latter area affecting performance. The rTMS failed to reveal a complete dissociation between MT/TO‐1 and MST/TO‐2 in terms of their contribution to the perception of rotational motion. On the basis of these results, MT/TO‐1 and MST/TO‐2 appear to be functionally distinct subdivisions of hV5/MT+. While both areas appear to be implicated in the processing of translational motion, only the anterior region (MST/TO‐2) makes a causal contribution to the perception of radial motion.
Influence of betaine and arginine supplementation of reduced protein diets on fatty acid composition and gene expression in the muscle and subcutaneous adipose tissue of cross-bred pigs

Abstract The isolated or combined effects of betaine and arginine supplementation of reduced protein diets (RPD) on fat content, fatty acid composition and mRNA levels of genes controlling lipid metabolism in pig m. longissimus lumborum and subcutaneous adipose tissue (SAT) were assessed. The experiment was performed on forty intact male pigs (Duroc×Large White×Landrace cross-breed) with initial and final live weights of 60 and 93 kg, respectively. Pigs were randomly assigned to one of the following five diets (n 8): 16·0 % of crude protein (control), 13·0 % of crude protein (RPD), RPD supplemented with 0·33 % of betaine, RPD supplemented with 1·5 % of arginine and RPD supplemented with 0·33 % of betaine and 1·5 % of arginine. Data confirmed that RPD increase intramuscular fat (IMF) content and total fat content in SAT. The increased total fat content in SAT was accompanied by higher GLUT type 4, lipoprotein lipase and stearoyl-CoA desaturase mRNA expression levels. In addition, the supplementation of RPD with betaine and/or arginine did not affect either IMF or total fat in SAT. However, dietary betaine supplementation slightly affected fatty acid composition in both muscle and SAT. This effect was associated with an increase of carnitine O-acetyltransferase mRNA levels in SAT but not in muscle, which suggests that betaine might be involved in the differential regulation of some key genes of lipid metabolism in pig muscle and SAT. Although the arginine-supplemented diet decreased the mRNA expression level of PPARG in muscle and SAT, it did not influence fat content or fatty acid composition in any of these pig tissues.
Leveraging Automated Image Analysis Tools to Transform Our Capacity to Assess Status and Trends of Coral Reefs

Digital photography is widely used by coral reef monitoring programs to assess benthic status and trends. In addition to creating a permanent archive, photographic surveys can be rapidly conducted, which is important in environments where bottom-time is frequently limiting. However, substantial effort is required to manually analyze benthic images; which is expensive and leads to lags before data are available. Using previously analyzed imagery from NOAA’s Pacific Reef Assessment and Monitoring Program, we assessed the capacity of a trained and widely used machine-learning image analysis tool – CoralNet (coralnet.ucsd.edu) - to generate fully-automated benthic cover estimates for the main Hawaiian Islands (MHI) and American Samoa. CoralNet was able to generate estimates of site-level coral cover for both regions that were highly comparable to those generated by human analysts (Pearson’s r > 0.97, and with bias of 1% or less). CoralNet was generally effective at estimating cover of common coral genera (Pearson’s r > 0.92 and with bias of 2% or less in 6 of 7 cases), but performance was mixed for other groups including algal categories, although generally better for American Samoa than MHI. CoralNet performance was improved by simplifying the classification scheme from genus to functional group and by training within habitat types, i.e., separately for coral-rich, pavement, boulder, or ‘other’ habitats. The close match between human-generated and CoralNet-generated estimates of coral cover pooled to the scale of island and year demonstrates that CoralNet is capable of generating data suitable for assessing spatial and temporal patterns. The imagery we used was gathered from sites randomly located in <30 m hard-bottom at multiple islands and habitat-types per region, suggesting our results are likely to be widely applicable. As image acquisition is relatively straightforward, the capacity of fully-automated image analysis tools to minimize the need for resource intensive human analysts opens possibilities for enormous increases in the quantity and consistency of coral reef benthic data that could become available to researchers and managers.
A genomic analysis of disease-resistance genes encoding nucleotide binding sites in Sorghum bicolor

A large set of candidate nucleotide-binding site (NBS)-encoding genes related to disease resistance was identified in the sorghum (Sorghum bicolor) genome. These resistance (R) genes were characterized based on their structural diversity, physical chromosomal location and phylogenetic relationships. Based on their N-terminal motifs and leucine-rich repeats (LRR), 50 non-regular NBS genes and 224 regular NBS genes were identified in 274 candidate NBS genes. The regular NBS genes were classified into ten types: CNL, CN, CNLX, CNX, CNXL, CXN, NX, N, NL and NLX. The vast majority (97%) of NBS genes occurred in gene clusters, indicating extensive gene duplication in the evolution of S. bicolor NBS genes. Analysis of the S. bicolor NBS phylogenetic tree revealed two major clades. Most NBS genes were located at the distal tip of the long arms of the ten sorghum chromosomes, a pattern significantly different from rice and Arabidopsis, the NBS genes of which have a random chromosomal distribution.
Preharvest treatments with salicylates enhance nutrient and antioxidant compounds in plum at harvest and after storage.

BACKGROUND Previous reports have addressed the effectiveness of salicylic acid (SA), acetylsalicylic acid (ASA) and methylsalicylate (MeSA) postharvest treatments on maintaining quality properties during storage in several commodities. However, there is no literature regarding the effect of preharvest treatments with salicylates on plum quality attributes (at harvest or after long-term cold storage), which was evaluated in this research. RESULTS At harvest, weight, firmness, individual organic acids, sugars, phenolics, anthocyanins and total carotenoids were found at higher levels in plums from SA-, ASA- and MeSA-treated trees than in those from controls. During storage, softening, colour changes and acidity losses were delayed in treated fruits as compared to controls. In addition, organic acids and antioxidant compounds were still found at higher levels in treated than in control plums after 40 days of storage. Results show a delay in the postharvest ripening process due to salicylate treatments, which could be attributed to their effect in delaying and decreasing ethylene production. CONCLUSION Preharvest treatment with salicylates could be a safety, eco-friendly and new tool to improve (at harvest) and maintain (during storage) plum quality and especially its content of bioactive compounds with antioxidant properties, increasing the health effects of plum consumption. © 2017 Society of Chemical Industry.
An Intelligent Monitoring Network for Detection of Cracks in Anvils of High-Press Apparatus

Due to the endurance of alternating high pressure and temperature, the carbide anvils of the high-press apparatus, which are widely used in the synthetic diamond industry, are prone to crack. In this paper, an acoustic method is used to monitor the crack events, and the intelligent monitoring network is proposed to classify the sound samples. The pulse sound signals produced by such cracking are first extracted based on a short-time energy threshold. Then, the signals are processed with the proposed intelligent monitoring network to identify the operation condition of the anvil of the high-pressure apparatus. The monitoring network is an improved convolutional neural network that solves the problems that may occur in practice. The length of pulse sound excited by the crack growth is variable, so a spatial pyramid pooling layer is adopted to solve the variable-length input problem. An adaptive weighted algorithm for loss function is proposed in this method to handle the class imbalance problem. The good performance regarding the accuracy and balance of the proposed intelligent monitoring network is validated through the experiments finally.
Nonparametric Sharpe Ratio Function Estimation in Heteroscedastic Regression Models via Convex Optimization

We consider maximum likelihood estimation (MLE) of heteroscedastic regression models based on a new “parametrization” of the likelihood in terms of the Sharpe ratio function, or the ratio of the mean and volatility functions. While with a standard parametrization the MLE problem is not convex and hence hard to solve globally, our parametrization leads to a functional that is jointly convex in the Sharpe ratio and inverse volatility functions. The major difficulty with the resulting infinite-dimensional convex program is the shape constraint on the inverse volatility function. We propose to solve the problem by solving a sequence of finite-dimensional convex programs with increasing dimensions, which can be done globally and efficiently. We demonstrate that, when the goal is to estimate the Sharpe ratio function directly, the finite-sample performance of the proposed estimation method is superior to existing methods that estimate the mean and variance functions separately. When applied to a financial dataset, our method captures a well-known covariate-dependent effect on the Shape ratio.
Factors associated with disease self-efficacy in individuals aging with a disability

ABSTRACT Self-management of a disability consists of treatment adherence, obtaining information about the disease and treatment options, caring for oneself, participating in decisions, and maintaining social relationships and emotional balance. Understanding and measuring an individual’s beliefs about their ability to successfully self-manage and live well with a disability allows researchers and clinicians to better target interventions aimed at increasing disability management self-efficacy (DMSE). The purpose of this study was to examine the associations between demographic and clinical indicators, and self-efficacy for DMSE in individuals with chronic physical conditions. Adults (N = 815) with muscular dystrophy, multiple sclerosis, spinal cord injury, or post-polio syndrome completed a self-report mailed survey assessing DMSE, perceived social support, depression symptoms, resilience, fatigue, pain interference, satisfaction with participation in social roles, physical function, and demographics. A cross-sectional regression model was used to examine the associations between the clinical and demographic factors, and DMSE. The model explained 67% of the variance in DMSE. Satisfaction with participation in social roles, resilience, pain interference, social support, and fatigue were statistically significant. Better social functioning, more resilience, and less pain and fatigue were most strongly associated with DMSE. Interventions aimed at increasing DMSE should include strategies for improving social participation.
Microbiome and Metabolome Profiles Associated With Different Types of Short Bowel Syndrome: Implications for Treatment.

BACKGROUND The gut microbiome and metabolome may significantly influence clinical outcomes in patients with short bowel syndrome (SBS). The study aimed to describe specific metagenomic/metabolomics profiles of different SBS types and to identify possible therapeutic targets. METHODS Fecal microbiome (FM), volatile organic compounds (VOCs), and bile acid (BA) spectrum were analyzed in parenteral nutrition (PN)-dependent SBS I, SBS II, and PN-independent (non-PN) SBS patients. RESULTS FM in SBS I, SBS II, and non-PN SBS shared characteristic features (depletion of beneficial anaerobes, high abundance of Lactobacilaceae and Enterobacteriaceae). SBS I patients were characterized by the abundance of oxygen-tolerant microrganisms and depletion of strict anaerobes. Non-PN SBS subjects showed markers of partial FM normalization. FM dysbiosis was translated into VOC and BA profiles characteristic for each SBS cohort. A typical signature of all SBS patients comprised high saturated aldehydes and medium-chain fatty acids and reduced short-chain fatty acid (SCFA) content. Particularly, SBS I and II exhibited low protein metabolism intermediate (indole, p-cresol) content despite the hypothetical presence of relevant metabolism pathways. Distinctive non-PN SBS marker was high phenol content. SBS patients' BA fecal spectrum was enriched by chenodeoxycholic and deoxycholic acids and depleted of lithocholic acid. CONCLUSIONS Environmental conditions in SBS gut significantly affect FM composition and metabolic activity. The common feature of diverse SBS subjects is the altered VOC/BA profile and the lack of important products of microbial metabolism. Strategies oriented on the microbiome/metabolome reconstitution and targeted delivery of key compounds may represent a promising therapeutic strategy in SBS patients.
Guillain–Barré Syndrome Associated With Zika Virus Infection: A Prospective Case Series From Mexico

Background: On May 2016, anticipating the rainy season from June to October in Mexico, we expected an increase in cases of Zika virus (ZIKV) infections. With the goal of identifying cases of GBS associated with ZIKV infection, a prospective joint study was conducted by a reference center for neurological patients and the Secretary of Health in Mexico City from July 2016 to November 2016. Methods: Serum, cerebrospinal fluid, urine, and saliva were tested by RT-PCR for ZIKV, dengue virus, and chikungunya virus in patients referred from states with reported transmissions of ZIKV infection, and with clinical symptoms of GBS according to the Brighton Collaboration criteria. Clinical, electrophysiological, and long-term disability data were collected. Results: In the year 2016 twenty-eight patients with GBS were diagnosed at our institute. In five hospitalized patients with GBS, RT-PCR was positive to ZIKV in any collected specimen. Dengue and chikungunya RT-PCR results were negative. All five patients had areflexic flaccid weakness, and cranial nerves affected in three. Electrophysiological patterns were demyelinating in two patients and axonal in three. Three patients were discharged improved in 10 days or less, and two patients required intensive care unit admission, and completely recovered during follow-up. Conclusion: Our results are similar to those reported from the state of Veracruz, Mexico, in which out of 33 samples of urine of patients with GBS two had a positive RT-PCR for ZIKV. Simultaneous processing of serum, CSF, urine, and saliva by RT-PCR may increase the success of diagnosis of GBS associated to ZIKV.