Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization and comparative analysis of microRNAs in the rice pest Sogatella furcifera

MicroRNAs (miRNAs) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that act as functional regulators of post-transcriptional repression of messenger RNA. We report the identification and characterization of a conserved miRNA and 171 novel miRNAs in the migratory rice pest Sogatella furcifera by deep sequencing, which were observed to be biased towards female adults of the insect, modulating the functionality and targets of the miRNAs in sex differentiation. A switch in arm usage was also observed in 9 miRNA when compared to the insect ancestor during insect evolution. The miRNA loci showed high 5’ fidelity in both miRNA and star species and about 93.4% of WBPH miRNAs conserved within non-planthopper species were homologous with planthopper species. The novel miRNAs identified in this study provide a better understanding of the sRNA and the regulatory role of miRNA in sexual dimorphism and alteration in the expression or function of miRNAs in the rice pest.
Prevalence of Subclinical Hypothyroidism in Acute Coronary Syndrome in Nondiabetics: Detailed Analysis from Consecutive 1100 Patients from Eastern India

Background The association between subclinical thyroid dysfunction (defined by no symptoms or clinical features of hypothyroidism but biochemically TSH level in the range of above 5 miu/ml but below 10 miu/ml with normal FT4 level) and Acute Coronary Syndrome (ACS) is not known so far. This study was done to calculate the prevalence of subclinical thyroid dysfunction in patients with ACS. Methods A retrospective chart review of 1100 consecutive patients was done who presented to Emergency Department with symptoms suggestive of ACS and admitted. They were later classified in 3 categories that includes Acute ST Elevated Myocardial Infarction (STEMI), Unstable Angina (UA), and Acute Non-ST Elevated Myocardial Infarction (NSTEMI). Thyroid function test (FT4, TSH) and antithyroid peroxidase (TPO) were done and evaluated properly. Results Of 1100 consecutive patients 168 (15.27%) patients had the biochemical features of subclinical thyroid dysfunction. These 168 patients include 60 STEMI, 66 NSTEMI, and 42 Unstable Angina patients. There were no statistically significant differences in terms of left ventricular ejection fraction (LVEF) and catheterisation results considering thyroid dysfunction. Conclusions Subclinical thyroid dysfunction is quite prevalent in ACS patients. There are no significant associations between STEMI, Unstable Angina, or NSTEMI patients in terms of thyroid dysfunction neither in single vessel versus multivessel disease involvement. The causative role and outcomes of treatment are still uncertain and need further follow-up.
Pathological upgrading at radical prostatectomy for patients with Grade Group 1 prostate cancer: implications of confirmatory testing for patients considering active surveillance

To examine the association between National Comprehensive Cancer Network (NCCN) risk, number of positive biopsy cores, age, and early confirmatory test results on pathological upgrading at radical prostatectomy (RP), in order to better understand whether early confirmatory testing and better risk stratification are necessary for all men with Grade Group (GG) 1 cancers who are considering active surveillance (AS).
Teleophthalmology Support for Primary Care Diagnosis and Management

This study was performed to evaluate a healthcare strategy based on teleophthalmology for diagnosis and management of primary healthcare users. A descriptive cross-sectional study was conducted to review the medical records of patients from January 2013 to December 2014 from primary care units in the city of São Paulo. The units referred patients, who had diabetes or high blood pressure, and were users of chloroquine compounds, for a fundus examination. The images were sent to a reading center for review, diagnosis, and patient referrals. From 9173 analyzed patients, 570 (6.2%) were excluded because of poor image quality. Of the remaining patients, 4933 (57.3%) had diabetes, 7242 (84,2%) systemic hypertension, and 113 (1.3%) used chloroquine. Of these, 989 (11.5%) patients needed ophthalmologic treatment. The most frequently prescribed treatments were cataract extraction in 692 (70%) of 989 and photocoagulation in 245 (24.8%) of 989 cases. Overall, cataract extraction was indicated in 692 (8%) of 8603 cases and photocoagulation in 245 (2.8%) of 8603 cases. When only patients with diabetes were considered, the indication for photocoagulation increased to 4.5%. The results showed that non-medical professionals could produce good-quality ocular images for screening of ocular diseases in most cases; only 6.2% of ocular images did not meet quality requirements. Most patients referred for fundus examination did not need a specific treatment, indicating that this system could be an inexpensive and reliable tool for use in developing countries.
The role of interleukin-6-STAT3 signalling in glioblastoma

Glioblastoma is the most common type of malignant brain tumor among adults and is currently a non-curable disease due primarily to its highly invasive phenotype, and the lack of successful current therapies. Despite surgical resection and post-surgical treatment patients ultimately develop recurrence of the tumour. Several signalling molecules have been implicated in the development, progression and aggressiveness of glioblastoma. The present study reviewed the role of interleukin (IL)-6, a cytokine known to be important in activating several pro-oncogenic signaling pathways in glioblastoma. The current study particularly focused on the contribution of IL-6 in recurrent glioblastoma, with particular focus on glioblastoma stem cells and resistance to therapy.
Structural Covariance Analysis Reveals Differences Between Dancers and Untrained Controls

Dancers and musicians differ in brain structure from untrained individuals. Structural covariance (SC) analysis can provide further insight into training-associated brain plasticity by evaluating interregional relationships in gray matter (GM) structure. The objectives of the present study were to compare SC of cortical thickness (CT) between expert dancers, expert musicians and untrained controls, as well as to examine the relationship between SC and performance on dance- and music-related tasks. A reduced correlation between CT in the left dorsolateral prefrontal cortex (DLPFC) and mean CT across the whole brain was found in the dancers compared to the controls, and a reduced correlation between these two CT measures was associated with higher performance on a dance video game task. This suggests that the left DLPFC is structurally decoupled in dancers and may be more strongly affected by local training-related factors than global factors in this group. This work provides a better understanding of structural brain connectivity and training-induced brain plasticity, as well as their interaction with behavior in dance and music.
Fundamental Limits of Spectrum Sharing for NOMA-Based Cooperative Relaying

Non-orthogonal multiple access (NOMA) and spectrum sharing (SS) are two emerging multiple access technologies for efficient spectrum utilization in the fifth-generation (5G) wireless communications standard. In this paper, we present a closed-form analysis of the average achievable sum-rate and outage probability for a NOMA-based cooperative relaying system (CRS) in an underlay spectrum sharing scenario. We consider a peak interference constraint, where the interference inflicted by the secondary (unlicensed) network on the primary-user (licensed) receiver (PU-Rx) should be less than a predetermined threshold. We show that the CRS-NOMA outperforms the CRS with conventional orthogonal multiple access (OMA) for large values of peak interference power at the PU-Rx.
Insights into Geographic and Temporal Variation in Fatty Acid Composition of Croton Nuts Using ATR-FTIR

Croton megalocarpus seedcake oils from 30 different locations in south central Kenya were analyzed for their fatty acid composition using ATR-FTIR to determine the efficacy of a simple procedure for measuring initial geographic and subsequent temporal variation during five months of seed storage. To our knowledge, this is the first report showing variation in how oils in untreated nuts from different locations change during storage, and how these differences are correlated with local environments. These variations are important to forensic authentication efforts and they provide insights into ways to optimize Croton oil composition.
Portosplenomesenteric vein thrombosis in patients with early-stage severe acute pancreatitis

AIM To investigate the incidence and risk factors of portosplenomesenteric vein thrombosis (PSMVT) in the early stage of severe acute pancreatitis (SAP). METHODS Patients with SAP in a tertiary care setting from January 2014 to December 2016 were retrospectively reviewed. All contrast-enhanced computed tomography (CT) studies were reassessed and reviewed. Clinical outcome measures were compared between SAP patients with and without PSMVT in the early stage of the disease. Univariate and multivariate logistic regression analyses were sequentially performed to assess potential risk factors for the development of PSMVT in SAP patients. A receiver operating characteristic (ROC) curve was generated for the qualifying independent risk factors. RESULTS Twenty-five of the one hundred and forty (17.86%) SAP patients developed PSMVT 6.19 ± 2.43 d after acute pancreatitis (AP) onset. PSMVT was confirmed by contrast-enhanced CT. Multivariate stepwise logistic regression analyses showed that Balthazar’s CT severity index (CTSI) scores [odds ratio (OR): 2.742; 95% confidence interval (CI): 1.664-4.519; P = 0.000], hypoalbuminemia (serum albumin level < 25 g/L) (OR: 32.573; 95%CI: 2.711-391.353; P = 0.006) and gastrointestinal wall thickening (OR: 4.367, 95%CI: 1.218-15.658; P = 0.024) were independent risk factors for PSMVT developed in patients with SAP. The area under the ROC curve for Balthazar’s CTSI scores was 0.777 (P = 0.000), the sensitivity was 52%, and the specificity was 93% at a cut-off value of 5.5. CONCLUSION High Balthazar’s CTSI scores, hypoalbuminemia and gastrointestinal wall thickening are independent risk factors for PSMVT developed in the early stage of SAP.
Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study

Abstract Age-mixing patterns are of key importance for understanding the dynamics of human immunodeficiency virus (HIV)-epidemics and target public health interventions. We use the densely sampled Swiss HIV Cohort Study (SHCS) resistance database to study the age difference at infection in HIV transmission pairs using phylogenetic methods. In addition, we investigate whether the mean age difference of pairs in the phylogenetic tree is influenced by sampling as well as by additional distance thresholds for including pairs. HIV-1 pol-sequences of 11,922 SHCS patients and approximately 240,000 Los Alamos background sequences were used to build a phylogenetic tree. Using this tree, 100 per cent down to 1 per cent of the tips were sampled repeatedly to generate pruned trees (N = 500 for each sample proportion), of which pairs of SHCS patients were extracted. The mean of the absolute age differences of the pairs, measured as the absolute difference of the birth years, was analyzed with respect to this sample proportion and a distance criterion for inclusion of the pairs. In addition, the transmission groups men having sex with men (MSM), intravenous drug users (IDU), and heterosexuals (HET) were analyzed separately. Considering the tree with all 11,922 SHCS patients, 2,991 pairs could be extracted, with 954 (31.9 per cent) MSM-pairs, 635 (21.2 per cent) HET-pairs, 414 (13.8 per cent) IDU-pairs, and 352 (11.8 per cent) HET/IDU-pairs. For all transmission groups, the age difference at infection was significantly (P < 0.001) smaller for pairs in the tree compared with randomly assigned pairs, meaning that patients of similar age are more likely to be pairs. The mean age difference in the phylogenetic analysis, using a fixed distance of 0.05, was 9.2, 9.0, 7.3 and 5.6 years for MSM-, HET-, HET/IDU-, and IDU-pairs, respectively. Decreasing the cophenetic distance threshold from 0.05 to 0.01 significantly decreased the mean age difference. Similarly, repeated sampling of 100 per cent down to 1 per cent of the tips revealed an increased age difference at lower sample proportions. HIV-transmission is age-assortative, but the age difference of transmission pairs detected by phylogenetic analyses depends on both sampling proportion and distance criterion. The mean age difference decreases when using more conservative distance thresholds, implying an underestimation of age-assortativity when using liberal distance criteria. Similarly, overestimation of the mean age difference occurs for pairs from sparsely sampled trees, as it is often the case in sub-Saharan Africa.
Natural Killer Cells in Liver Disease and Hepatocellular Carcinoma and the NK Cell-Based Immunotherapy

Nature killer (NK) cells play a critical role in host innate and adaptive immune defense against viral infections and tumors. NK cells are enriched in liver hematopoietic cells with unique NK repertories and functions to safeguard liver cells against hepatitis virus infection or malignancy transformation. However, accumulating evidences were found that the NK cells were modulated by liver diseases and liver cancers including hepatocellular carcinoma (HCC) and showed impaired functions failing to activate the elimination of the viral-infected cells or tumor cells and were further involved in the pathogenesis of liver injury and inflammation. The full characterization of circulation and intrahepatic NK cell phenotype and function in liver disease and liver cancer has not only provided new insight into the disease pathogenesis but has also discovered new targets for developing new NK cell-based therapeutic strategies. This review will discuss and summarize the NK cell phenotypic and functional changes in liver disease and HCC, and the NK cell-based immunotherapy approaches and progresses for cancers including HCC will also be reviewed.
Eradicating Suicide at Its Roots: Preclinical Bases and Clinical Evidence of the Efficacy of Ketamine in the Treatment of Suicidal Behaviors

Despite the continuous advancement in neurosciences as well as in the knowledge of human behaviors pathophysiology, currently suicide represents a puzzling challenge. The World Health Organization (WHO) has established that one million people die by suicide every year, with the impressive daily rate of a suicide every 40 s. The weightiest concern about suicidal behavior is how difficult it is for healthcare professionals to predict. However, recent evidence in genomic studies has pointed out the essential role that genetics could play in influencing person’s suicide risk. Combining genomic and clinical risk assessment approaches, some studies have identified a number of biomarkers for suicidal ideation, which are involved in neural connectivity, neural activity, mood, as well as in immune and inflammatory response, such as the mammalian target of rapamycin (mTOR) signaling. This interesting discovery provides the neurobiological bases for the use of drugs that impact these specific signaling pathways in the treatment of suicidality, such as ketamine. Ketamine, an N-methyl-d-aspartate glutamate (NMDA) antagonist agent, has recently hit the headlines because of its rapid antidepressant and concurrent anti-suicidal action. Here we review the preclinical and clinical evidence that lay the foundations of the efficacy of ketamine in the treatment of suicidal ideation in mood disorders, thereby also approaching the essential question of the understanding of neurobiological processes of suicide and the potential therapeutics.
The Unfolded Protein Response in Breast Cancer

In 2018, in the US alone, it is estimated that 268,670 people will be diagnosed with breast cancer, and that 41,400 will die from it. Since breast cancers often become resistant to therapies, and certain breast cancers lack therapeutic targets, new approaches are urgently required. A cell-stress response pathway, the unfolded protein response (UPR), has emerged as a promising target for the development of novel breast cancer treatments. This pathway is activated in response to a disturbance in endoplasmic reticulum (ER) homeostasis but has diverse physiological and disease-specific functions. In breast cancer, UPR signalling promotes a malignant phenotype and can confer tumours with resistance to widely used therapies. Here, we review several roles for UPR signalling in breast cancer, highlighting UPR-mediated therapy resistance and the potential for targeting the UPR alone or in combination with existing therapies.
Incorporating Luminance, Depth and Color Information by a Fusion-Based Network for Semantic Segmentation

Semantic segmentation has made encouraging progress due to the success of deep convolutional networks in recent years. Meanwhile, depth sensors become prevalent nowadays; thus, depth maps can be acquired more easily. However, there are few studies that focus on the RGB-D semantic segmentation task. Exploiting the depth information effectiveness to improve performance is a challenge. In this paper, we propose a novel solution named LDFNet, which incorporates Luminance, Depth and Color information by a fusion-based network. It includes a sub-network to process depth maps and employs luminance images to assist the depth information in processes. LDFNet outperforms the other state-of-art systems on the Cityscapes dataset, and its inference speed is faster than most of the existing networks. The experimental results show the effectiveness of the proposed multi-modal fusion network and its potential for practical applications.
Predicting the Outcomes of New Short-Course Regimens for Multidrug-Resistant Tuberculosis Using Intrahost and Pharmacokinetic-Pharmacodynamic Modeling

Short-course regimens for multidrug-resistant tuberculosis (MDR-TB) are urgently needed. Limited data suggest that the new drug bedaquiline (BDQ) may have the potential to shorten MDR-TB treatment to less than 6 months when used in conjunction with standard anti-TB drugs. ABSTRACT Short-course regimens for multidrug-resistant tuberculosis (MDR-TB) are urgently needed. Limited data suggest that the new drug bedaquiline (BDQ) may have the potential to shorten MDR-TB treatment to less than 6 months when used in conjunction with standard anti-TB drugs. However, the feasibility of BDQ in shortening MDR-TB treatment duration remains to be established. Mathematical modeling provides a platform to investigate different treatment regimens and predict their efficacy. We developed a mathematical model to capture the immune response to TB inside a human host environment. This model was then combined with a pharmacokinetic-pharmacodynamic model to simulate various short-course BDQ-containing regimens. Our modeling suggests that BDQ could reduce MDR-TB treatment duration to just 18 weeks (4 months) while still maintaining a very high treatment success rate (100% for daily BDQ for 2 weeks, or 95% for daily BDQ for 1 week during the intensive phase). The estimated time to bacterial clearance of these regimens ranges from 27 to 33 days. Our findings provide the justification for empirical evaluation of short-course BDQ-containing regimens. If short-course BDQ-containing regimens are found to improve outcomes, then we anticipate clear cost savings and a subsequent improvement in the efficiency of national TB programs.
The Long Pentraxin PTX3 Is an Endogenous Inhibitor of Hyperoxaluria-Related Nephrocalcinosis and Chronic Kidney Disease

The long pentraxin 3 (PTX3) exerts a variety of regulatory functions in acute and chronic tissue inflammation. In particular, PTX3 acts as an opsonin for a variety of pathogens and endogenous particles. We hypothesized that PTX3 would exhibit opsonin-like functions toward calcium oxalate crystals, too, and inhibit crystal growth. This process is fundamental in kidney stone disease as well as in hyperoxaluria-related nephrocalcinosis, the paradigmatic cause of chronic kidney disease (CKD) in children with primary hyperoxaluria type I due to genetic defects in oxalate metabolism. Direct effects of PTX3 on calcium oxalate crystals were investigated in chemico by adding recombinant PTX3 to supersaturated calcium and oxalate solutions. PTX3, but not isomolar concentrations of albumin, dose-dependently inhibited crystal growth. In vivo, the PTX3 protein was undetectable in tubular epithelial cells and urine of wild-type mice under physiological conditions. However, its levels increased within 3 weeks of feeding an oxalate-rich diet, an exposure inducing hyperoxaluria-related nephrocalcinosis and CKD in selected mouse strains (male and female C57BL/6N and male Balb/c mice) but not in others (male and female 129SV and CD-1, male and female Balb/c mice). Genetic ablation of ptx3 in nephrocalcinosis un-susceptible B6;129 mice was sufficient to raise the oxalate nephropathy phenotype observed in susceptible strains. We conclude that PTX3 is an endogenous inhibitor of calcium oxalate crystal growth. This mechanism limits hyperoxaluria-related nephrocalcinosis, e.g., in primary or secondary hyperoxaluria, and potentially also in the more prevalent kidney stone disease.
Towards Green Titration: Downscaling the Sequential Injection Analysis Lab-at-valve Titration System with the Stepwise Addition of a Titrant

A downscaling in true titration based on a simple sequential injection analysis-lab-at-valve (SIA-LAV) has been proposed. A titrant solution was stepwise aspirated into a titration LAV chamber and a titration curve was obtained by monitoring the change in the solution color spectroscopically. This fully-automated SIA-LAV system required less volume of the sample/reagents, only a micro-liter scale, compared to the conventional method. The system was investigated with complexometric titration and acid-base titration. Application of the developed technique to some real samples has been demonstrated.
White matter connectivity reductions in the pre‐clinical continuum of psychosis: A connectome study

Widespread white matter connectivity disruptions have commonly been reported in schizophrenia. However, it is questionable whether structural connectivity decline is specifically associated with schizophrenia or whether it extends along a continuum of psychosis into the healthy population. Elucidating brain structure changes associated with psychotic‐like experiences in healthy individuals is insofar important as it is a necessary first step towards our understanding of brain pathology preceding florid psychosis. High resolution, multishell diffusion‐weighted magnetic resonance images (MRI) were acquired from 89 healthy individuals. Whole‐brain white matter fibre tracking was performed to quantify the strength of white matter connections. Network‐based statistics were applied to white matter connections in a regression model in order to test for a linear relationship between streamline count and psychotic‐like experiences. A significant subnetwork was identified whereby streamline count declined with increasing psychotic‐like experiences. This network of structural connectivity reductions affected all cortical lobes, subcortical structures and the cerebellum and spanned along prominent association and commissural white matter pathways. A widespread network of linearly declining connectivity strength with increasing number of psychotic‐like experiences was identified in healthy individuals. This finding is in line with white matter connectivity reductions reported from early to chronic stages of schizophrenia and might therefore aid the development of tools to identify individuals at risk of transitioning to psychosis.