Miracle-dz/UniFAR-FTUs huggingface dataset:
Reciprocal regulation of eNOS and caveolin-1 functions in endothelial cells

We hypothesized that the maintenance of vascular homeostasis is critically dependent on the expression and reciprocal regulation of caveolin-1 (Cav-1) and endothelial nitric oxide synthase (eNOS) in endothelial cells (ECs). Skeletal muscle biopsies from subjects with type 2 diabetes showed 50% less Cav-1 and eNOS than those from lean healthy controls. The Cav-1:eNOS expression ratio was 200:1 in primary culture human ECs. Cav-1 small interfering RNA (siRNA) reduced eNOS protein and gene expression in association with a twofold increase in eNOS phosphorylation and nitrate production per molecule of eNOS, which was reversed in cells overexpressing Adv-Cav-1-GFP. Upon addition of the Ca2+ ionophore A23187 to activate eNOS, we observed eNOS Ser1177 phosphorylation, its translocation to β-catenin-positive cell–cell junctions, and increased colocalization of eNOS and Cav-1 within 5 min. We also observed Cav-1 S-nitrosylation and destabilization of Cav-1 oligomers in cells treated with A23187 as well as insulin or albumin, and this could be blocked by L-NAME, PP2, or eNOS siRNA. Finally, caveola-mediated endocytosis of albumin or insulin was reduced by Cav-1 or eNOS siRNA, and the effect of Cav-1 siRNA was rescued by Adv-Cav-1-GFP. Thus, Cav-1 stabilizes eNOS expression and regulates its activity, whereas eNOS-derived NO promotes caveola-mediated endocytosis.
Database of transcription factors in lung cancer (DBTFLC): A novel resource for exploring transcription factors associated with lung cancer

Lung cancer is considered as the most prevalent form of cancer and it is found to be frequent cause of cancer related death. Even though, approved molecular targeted therapies other than chemotherapy are currently unavailable, the mechanism of pathogenesis in lung cancer remains still unclear. Transcription factors (TFs) play a critical role in cancer cell processes, such as cell proliferation, apoptosis, migration, and regulate gene expression. Thus, the identification and characterization of transcription factors involved in lung cancer would provide valuable information for further elucidation of the mechanism(s) underlying pathogenesis and the identification of potential therapeutic target types, which are critical for the development of therapeutic strategies. Through an extensive literature survey, we have identified 349 transcription factors noted for their strong involvement in lung cancer. Database of Transcription Factors in Lung Cancer (DBTFLC) was constructed as a data repository and analytical platform for systematic collection, curation of TFs and their interacting partners. The database includes all pertinent information such as lung cancer related TFs, chromosomal location, family, lung cancer type, references, TF‐TF interaction(s), and TF‐target gene interaction(s); thus, it could serve as a valuable resource for therapeutic studies in lung cancer. The database is freely available at http://www.vit. ac.in/files/database/Home.php
Regularization: Convergence of Iterative Half Thresholding Algorithm

— In recent studies on sparse modeling, the nonconvex regularization approaches (particularly, regularization with ) have been demonstrated to possess capability of gaining much bene ﬁ t in sparsity-inducing and ef ﬁ ciency. As compared with the convex regularization approaches (say, regularization), however, the convergence issue of the corresponding algorithms are more dif ﬁ cult to tackle. In this paper, we deal with this dif ﬁ cult issue for a speci ﬁ c but typical nonconvex regularization scheme, the regularization, which has been successfully used to many applications. More speci ﬁ cally, we study the convergence of the iterative half thresholding algorithm (the half algorithm for short), one of the most ef ﬁ cient and important algorithms for solution to the regularization. As the main result, we show that under certain conditions, the half algorithm converges to a local minimizer of the regularization, with an eventually linear convergence rate. The established result provides a theoretical guarantee for a wide range of applications of the half algorithm. We provide also a set of simulations to support the correctness of theoretical assertions and compare the time ef ﬁ ciency of the half algorithm with other known typical algorithms for regularization like the iteratively reweighted least squares (IRLS) algorithm and the iteratively reweighted minimization (IRL1) algorithm.
Cell‐laden composite suture threads for repairing damaged tendons

Tendons have limited regenerative capacity due to their low cellularity and hypovascular nature, which results in poor clinical outcomes of presently used therapies. As tendon injuries are often observed in active adults, it poses an increasing socio‐economic burden on healthcare systems. Currently, suture threads are used during surgical repair to anchor the tissue graft or to connect injured ends. Here, we created composite suture threads coated with a layer of cell‐laden hydrogel that can be used for bridging the injured tissue aiming at tendon regeneration. In addition, the fibres can be used to engineer 3‐dimensional constructs through textile processes mimicking the architecture and mechanical properties of soft tissues, including tendons and ligaments. Encapsulated human tendon‐derived cells migrated within the hydrogel and aligned at the surface of the core thread. An up‐regulation of tendon‐related genes (scleraxis and tenascin C) and genes involved in matrix remodelling (matrix metalloproteinases 1, matrix metalloproteinases 2) was observed. Cells were able to produce a collagen‐rich matrix, remodelling their micro‐environment, which is structurally comparable to native tendon tissue.
Gene Variations of Sixth Complement Component Affecting Tacrolimus Metabolism in Patients with Liver Transplantation for Hepatocellular Carcinoma

Background: Orthotopic liver transplantation (OLT) improves the prognosis of patients with hepatocellular carcinoma (HCC). Moreover, the complement system is a powerful immune effector that can affect liver function and process of liver cirrhosis. However, studies correlating the complement system with tacrolimus metabolism after OLT are scarce. In this study, the role of single nucleotide polymorphisms (SNPs) associated with the sixth complement component (C6) in tacrolimus metabolism was investigated during the early stages of liver transplantation. Methods: The study enrolled 135 adult patients treated with OLT for HCC between August 2011 and October 2013. Ten SNPs in C6 gene and rs776746 in cytochrome P450 3A5 (CYP3A5) gene were investigated. The tacrolimus levels were monitored daily during 4 weeks after transplantation. Results: Both donor and recipient CYP3A5 rs776746 allele A were correlated with decreased concentration/dose (C/D) ratios. Recipient C6 rs9200 allele G and donor C6 rs10052999 homozygotes were correlated with lower C/D ratios. Recipient CYP3A5 rs776746 allele A (yielded median tacrolimus C/D ratios of 225.90 at week 1 and 123.61 at week 2), C6 rs9200 allele G (exhibited median tacrolimus C/D ratios of 211.31 at week 1, 110.23 at week 2, and 99.88 at week 3), and donor CYP3A5 rs776746 allele A (exhibited median C/D ratios of 210.82 at week 1, 111.06 at week 2, 77.49 at week 3, and 85.60 at week 4) and C6 rs10052999 homozygote (exhibited median C/D ratios of 167.59 at week 2, 157.99 at week 3, and 155.36 at week 4) were associated with rapid tacrolimus metabolism. With increasing number of these alleles, patients were found to have lower tacrolimus C/D ratios at various time points during the 4 weeks after transplantation. In multiple linear regression analysis, recipient C6 rs9200 group (AA vs. GG/GA) was found to be related to tacrolimus metabolism at weeks 1, 2, and 3 (P = 0.005, P = 0.045, and P = 0.033, respectively), whereas donor C6 rs10052999 group (CC/TT vs. TC) was demonstrated to be correlated with tacrolimus metabolism only at week 4 (P = 0.001). Conclusions: Recipient C6 gene rs9200 polymorphism and donor C6 gene rs10052999 polymorphism are new genetic loci that affect tacrolimus metabolism in patients with HCC after OLT.
Development of novel surface treatments for corrosion protection of aluminum: self-repairing coatings

Abstract Two types of self-repairing coatings for the protection of Al and its alloys are reviewed: (1) organic coatings with capsules containing repairing agent and (2) porous anodic oxide films with inhibitor solution stored in the pores of the oxide film. First, polyurethane microcapsules containing liquid surface-repairing agents were synthesized and polyurethane coating with the capsules was painted on Al alloy specimens. After mechanical damage to the coating, self-repairing occurred by the reaction of water vapor in the air with the repairing agents released from the capsules. Second, porous-type anodic oxide films were formed on Al alloys, and the pores of the anodic oxide films were filled with inhibitor solutions, followed by application of a covering polyurethane layer. Inhibitors released from the pores efficiently protected the Al alloy substrate from corrosion arising from induced mechanical damage.
Polyp detection rate may predict adenoma detection rate: a meta-analysis

Background Adenoma detection rate (ADR) is defined as the number of colonoscopies with at least one adenoma, expressed as the ratio of the total number of colonoscopies performed. Recently, an application of a conversion factor to estimate the ADR from the polyp detection rate (PDR) was described. Aim In this meta-analysis, we examined the correlation between ADR and PDR in the published studies and assessed the relative ratio of these ratios for a better and more accurate estimation. Methods English Medical literature searches were performed for ‘PDR’ AND ‘ADR’. A meta-analysis was carried out for papers that fulfilled the inclusion criteria using comprehensive meta-analysis software. Results Twenty-five studies and 42 sets of data, including 31 623 patients, from nine countries published till 31 August 2017, were found. Funnel plot did not indicate a significant publication bias. relative ratio for ADR calculated from PDR was 0.688, 95% confidence intervals: 0.680–0.695, P value of less than 0.0001 in the meta-analysis fixed model. Heterogeneity (the proportion of inconsistency in individual studies) between studies was significant, with Q=492.753, d.f. (Q) 41, P<0.0001, and I2 91.679. Conclusion We found the ratio of 0.688 can be used to calculate ADR from PDR for the individual endoscopist or for a group of endoscopists before receiving the formal results from the pathology department.
A Web-Based Knowledge Management System for Scientific Research Team

Scientific research teams have immense valuable knowledge that need to be managed. Organizing scientific contributions of team members constitutes a major challenge for the monitoring of knowledge evolution, team member’s competences discovery, and facilitating information retrieval processes. However, performing manual annotations is often time consuming and labor-intensive task, especially in case of complex annotation schemas. Currently, existing knowledge management systems focus on ensuring the scientific knowledge creation, sharing, organization and evaluation but don’t provide a way for helping researchers in the classification task. In this paper, we introduce a knowledge management system that offers an annotation service for researchers’ contributions by including some natural language processing techniques. The provided service process comprises four phases: (1) the semantic enrichment of domain ontology based on the extraction of background data from Babelnet knowledge base, (2) the automatic generation of candidate categories using the enriched domain ontology, (3) the forwarding of the pre-annotated papers to our web-based system to interact with researchers, and finally (4) the human revision of the generated annotations. Evaluation results show its advantage not only in reducing human effort and time consumption during the annotation task but also in improving annotations quality.
Prognostic models in predicting outcomes in myelodysplastic syndromes after hypomethylating agent failure

Abstract Myelodysplastic syndromes (MDS) are clonal stem cell disorders marked by bone marrow failure with varying degrees of cytopenias. MDS are characterized by the accumulation of complex genetic alterations that influence disease pathogenesis and outcomes. Given the heterogeneity of MDS patients, multiple prognostic scoring systems have been developed to predict patient outcomes. Most focus primarily on untreated patients in whom outcomes are predicted accurately only at diagnosis; their application dynamically, during the disease course and especially after hypomethylating agent (HMA) failure, may not be accurate. In this focused review, we discuss the utility of established MDS prognostic models and a novel tool at the time of HMA failure, along with the strengths and limitations of each.
A Polish Study on the Influence of Food Neophobia in Children (10–12 Years Old) on the Intake of Vegetables and Fruits

Adhering to the recommended intake of fruits and vegetables is an important habit that should be inculcated in children, whereas food neophobia is indicated as one of the most important factors creating food preferences that may interfere. The aim of the presented study was to analyze the association between the food neophobia level and the intake of fruits and vegetables in children aged 10–12 years. The study was conducted among a group of 163 children (78 girls and 85 boys). The assessment of the food neophobia level was based on the Food Neophobia Scale (FNS) questionnaire and the assessment of the fruit and vegetable intake was based on the food frequency questionnaire. A negative correlation between the food neophobia level and the vegetable intake was observed both for girls (p = 0.032; R = −0.2432) and for boys (p = 0.004; R = −0.3071), whereas for girls differences in vegetable intake were observed also between various food neophobia categories (p = 0.0144). It may be concluded that children with higher food neophobia level are characterized by lower vegetable intake than children with lower food neophobia level. For fruits and juices of fruits and vegetables, associations with food neophobia level were not observed.
Design and biological functionality of a novel hybrid Ti‐6Al‐4V/hydrogel system for reconstruction of bone defects

We have designed a unique injectable bioactive hydrogel comprising of alginate, gelatin, and nanocrystalline hydroxyapatite and loaded with osteoblasts, with the ability to infiltrate into three‐dimensional Ti‐6Al‐4V scaffolds with interconnected porous architecture, fabricated by electron beam melting. A two‐step crosslinking process using the EDC/NHS and CaCl2 was adopted and found to be effective in the fabrication of cell‐loaded hydrogel/Ti‐6Al‐4V scaffold system. This hybrid Ti‐6Al‐4V scaffold/hydrogel system was designed for the reconstruction of bone defects, which are difficult to heal in the absence of suitable support materials. The hybrid Ti‐6Al‐4V/hydrogel system favourably modulated the biological functions, namely, adhesion, proliferation, cell‐to‐cell, and cell‐material communication because of the presence of extracellular matrix‐like hydrogel in the interconnected porous structure of 3D printed Ti‐6Al‐4V scaffold. The hydrogel was cytocompatible, which was proven through live/dead assay, the expression level of prominent proteins for cell adhesion and cytoskeleton, including 3‐(4,5‐Dimethylthiazol‐2‐yl)‐2,5‐Diphenyltetrazolium Bromide (MTT) assay. Furthermore, the high bone formation ability of the hydrogel was confirmed using alkaline phosphatase assay. A high equilibrium water content (~97%) in the hydrogel enables the delivery of cells and bioactive molecules, necessary for bone tissue growth. Although not studied, the presence of hydrogel in the pores of the scaffold can provide the space for the cell migration as well as vascularization through it, required for the effective exchange of nutrients. In conclusion, we underscore that the 3D‐printed Ti‐6Al‐4V scaffold‐loaded with bioactive hydrogel to treat the bone defects significantly impacted cellular functions and cell‐material interaction.
The Virtual Trackpad: An Electromyography-Based, Wireless, Real-Time, Low-Power, Embedded Hand-Gesture-Recognition System Using an Event-Driven Artificial Neural Network

This brief presents a wireless, low-power embedded system that recognizes hand gestures by decoding surface electromyography (EMG) signals. Ten hand gestures used on commercial trackpads, including pinch, stretch, swipe left, swipe right, scroll up, scroll down, single click, double click, pat, and ok, can be recognized in real time. Features from four differential EMG channels are extracted in multiple time windows. Unlike traditional data segmentation methods, an event-driven method is proposed, with the gesture event detected in the hardware. Feature extraction is triggered only when an event is detected, minimizing computation, memory, and system power. A time-delayed artificial neural network (ANN) is used to predict the gesture from the transient EMG features instead of traditional steady-state features. The ANN is implemented in the microcontroller with a processing time less than 0.2 ms. The detection results are sent wirelessly to a computer. The device weights 15.2 g. A 4.6 g battery supports up to 40 h continuous operation. To our knowledge, this brief shows the first real-time, embedded hand-gesture-recognition system using only transient EMG signals. Experiments with four subjects show that the device can achieve a recognition of ten gestures with an average accuracy of 94%.
Perceived life stress and anxiety correlate with chronic gastrointestinal symptoms in runners

ABSTRACT Numerous causes of exercise-related gastrointestinal (GI) distress exist but scarce research has evaluated potential psychological causes. Runners (74 men, 76 women) prospectively recorded running duration, intensity (Rating of Perceived Exertion [RPE]), and GI symptoms for 30 days. Six GI symptoms were rated on a 0–10 scale. The percentage of runs over 30 days that participants reported at least one upper, lower, or any GI symptom ≥3 was calculated. After 30 days, participants completed a questionnaire on GI distress triggers (demographics, anthropometrics, experience, analgesic use, antibiotic use, probiotic consumption, fluid/food intake, stress, anxiety). Stress and anxiety were measured via the Perceived Stress Scale (PSS) and Beck Anxiety Inventory (BAI). The median percentage of runs that participants experienced at least one GI symptom ≥3 was 45.6% (interquartile range [IQR], 16.6–67.3%). Age and running experience negatively correlated with GI distress occurrence (rho = −0.17 to −0.34; p < 0.05). Run RPE, probiotic food consumption, PSS scores, and BAI scores positively correlated with GI distress occurrence (rho = 0.18 to 0.36; p < 0.05). Associations between GI distress, stress and anxiety remained significant after adjustment for covariates, except for lower GI symptoms. This study suggests that stress and anxiety contribute to running-related GI distress.
Further delineation of a rare recessive encephalomyopathy linked to mutations in GFER thanks to data sharing of whole exome sequencing data

Alterations in GFER gene have been associated with progressive mitochondrial myopathy, congenital cataracts, hearing loss, developmental delay, lactic acidosis and respiratory chain deficiency in 3 siblings born to consanguineous Moroccan parents by homozygosity mapping and candidate gene approach (OMIM#613076). Next generation sequencing recently confirmed this association by the finding of compound heterozygous variants in 19‐year‐old girl with a strikingly similar phenotype, but this ultra‐rare entity remains however unknown from most of the scientific community.
An efficient decision and planning method for high speed autonomous driving in dynamic environment

This paper describes an improved decision and planning algorithm based on our previously proposed methods for unmanned ground vehicle (UGV). The new method can be applied to UGV driving both in structured environment and unstructured environment. In the improved method, the prospect of planning is extended from 40m to 100m for safe driving at high speed and some piecewise linear speed functions are designed for the new prospect. After this improvement our UGV now can drive at a maximum speed of 60km/h rather than 40km/h while avoiding obstacles safely. Besides, a velocity feedforward control is added to make the UGV overtake other cars driving at about 25km/h on the road. At last, the collision detection algorithm is improved to make the lane changing maneuver safer. The proposed decision and planning algorithm is implemented both on our old Polaris all terrain vehicle (ATV) and new FAW-H7 car, which exhibited good performance on Across Dangers & Obstacles 2016, Tahe, China and Future Challenge 2016, Changshu, China, respectively.
Precise manipulation of GUI on a touch screen with haptic cues

In this work, we designed a haptic stylus interface interacting with a touch screen. The stylus has functions of providing vibration, impact, and sound and it is a stand-alone system including its own battery and wireless communication module. We present a new interaction scheme on the Windows graphical user interface based on haptic feedback events for clicking, drag & drop, moving, scrolling, highlighting, and other things. From conducting experiments, we evaluated its performance that the haptic stylus improved precise control of GUI elements. A simple interactive digital sketchbook has been also implemented, which is providing haptic and auditory feedback while drawing and touching objects.
Increases in core temperature counterbalance effects of haemoconcentration on blood viscosity during prolonged exercise in the heat

What is the central question of this study? The purpose of the present study was to determine the effects of exercise‐induced haemoconcentration and hyperthermia on blood viscosity. What is the main finding and its importance? Exercise‐induced haemoconcentration, increased plasma viscosity and increased blood aggregation, all of which increased blood viscosity, were counterbalanced by increased red blood cell (RBC) deformability (e.g. RBC membrane shear elastic modulus and elongation index) caused by the hyperthermia. Thus, blood viscosity remained unchanged following prolonged moderate‐intensity exercise in the heat.
TagScan: Simultaneous Target Imaging and Material Identification with Commodity RFID Devices

Target imaging and material identification play an important role in many real-life applications. This paper introduces TagScan, a system that can identify the material type and image the horizontal cut of a target simultaneously with cheap commercial off the-shelf (COTS) RFID devices. The key intuition is that different materials and target sizes cause different amounts of phase and RSS (Received Signal Strength) changes when radio frequency (RF) signal penetrates through the target. Multiple challenges need to be addressed before we can turn the idea into a functional system including (i) indoor environments exhibit rich multipath which breaks the linear relationship between the phase change and the propagation distance inside a target; (ii) without knowing either material type or target size, trying to obtain these two information simultaneously is challenging; and (iii) stitching pieces of the propagation distances inside a target for an image estimate is non-trivial. We propose solutions to all the challenges and evaluate the system's performance in three different environments. TagScan is able to achieve higher than 94% material identification accuracies for 10 liquids and differentiate even very similar objects such as Coke and Pepsi. TagScan can accurately estimate the horizontal cut images of more than one target behind a wall.