Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Modeling of Hepatitis C Virus Envelope Glycoprotein Structure and Recognition

Hepatitis C virus (HCV) is a major global health concern, and though therapeutic options have improved, no vaccine is available despite decades of research. As HCV can rapidly mutate to evade the immune response, an effective HCV vaccine must rely on identification and characterization of sites critical for broad immune protection and viral neutralization. This knowledge depends on structural and mechanistic insights of the E1 and E2 envelope glycoproteins, which assemble as a heterodimer on the surface of the virion, engage coreceptors during host cell entry, and are the primary targets of antibodies. Due to the challenges in determining experimental structures, structural information on E1 and E2 and their interaction is relatively limited, providing opportunities to model the structures, interactions, and dynamics of these proteins. This review highlights efforts to model the E2 glycoprotein structure, the assembly of the functional E1E2 heterodimer, the structure and binding of human coreceptors, and recognition by key neutralizing antibodies. We also discuss a comparison of recently described models of full E1E2 heterodimer structures, a simulation of the dynamics of key epitope sites, and modeling glycosylation. These modeling efforts provide useful mechanistic hypotheses for further experimental studies of HCV envelope assembly, recognition, and viral fitness, and underscore the benefit of combining experimental and computational modeling approaches to reveal new insights. Additionally, computational design approaches have produced promising candidates for epitope-based vaccine immunogens that specifically target key epitopes, providing a possible avenue to optimize HCV vaccines versus using native glycoproteins. Advancing knowledge of HCV envelope structure and immune recognition is highly applicable toward the development of an effective vaccine for HCV and can provide lessons and insights relevant to modeling and characterizing other viruses.
Scientific and Regulatory Policy Committee Points to Consider: Data Visualization for Clinical and Anatomic Pathologists

Assessment and communication of toxicology data are fundamental components of the work performed by veterinary anatomic and clinical pathologists involved in toxicology research. In recent years, there has been an evolution in the number and variety of software tools designed to facilitate the evaluation and presentation of toxicity study data. A working group of the Society of Toxicologic Pathology Scientific and Regulatory Policy Committee reviewed existing and emerging visualization technologies. This Points to Consider article reviews some of the currently available data visualization options, describes the utility of different types of graphical displays, and explores potential areas of controversy and ambiguity encountered with the use of these tools.
PickleTeam! at SemEval-2018 Task 2: English and Spanish Emoji Prediction from Tweets

We present a system for emoji prediction on English and Spanish tweets, prepared for the SemEval-2018 task on Multilingual Emoji Prediction. We compared the performance of an SVM, LSTM and an ensemble of these two. We found the SVM performed best on our development set with an accuracy of 61.3% for English and 83% for Spanish. The features used for the SVM are lowercased word n-grams in the range of 1 to 20, tokenised by a TweetTokenizer and stripped of stop words. On the test set, our model achieved an accuracy of 34% on English, with a slightly lower score of 29.7% accuracy on Spanish.
Antidiabetic Activity and Chemical Composition of Sanbai Melon Seed Oil

Objectives Many fruits and herbs had been used in Traditional Chinese Medicines for treating diabetes mellitus (DM); however, scientific and accurate evidences regarding their efficacy and possible mechanisms were largely unknown. Sanbai melon seed oil (SMSO) was used in folk medicine in treating DM, but there is no literature about these effects. The present study was aimed at confirming the treatment effects of SMSO in type 1 DM. Methods Diabetes was induced by single intraperitoneal injection of streptozotocin (STZ) at a dose of 65 mg/kg body weight. After diabetes induction, mice were treated with SMSO at dose of 1 g/kg, 2 g/kg, and 4 g/kg. Drugs were given by gavage administration once a day continuously for 28 days. At the end of treatment, several biochemical parameters and molecular mechanisms were determined by biochemical assays, ELISA, and Western blotting. The chemical compositions of SMSO were also tested. Results SMSO treatment significantly improved the symptoms of weight loss, polydipsia, reduced FBG level, increased plasma insulin levels, reduced plasma lipids levels, and protected islet injury. The results also showed that SMSO mitigated oxidative stress and alleviated the liver and renal injury in diabetes mice. SMSO also protected islet cells from apoptotic damage by suppressing ER mediated and mitochondrial dependent apoptotic pathways. Further constituent analysis results showed that SMSO had rich natural resources which had beneficial effects on DM. Conclusions This study showed that SMSO had excellent antidiabetes effect and provided scientific basis for the use of SMSO as the functional ingredients production and dietary supplements production in the food and pharmaceutical industries.
Energy Efficient Subchannel and Power Allocation for Software-defined Heterogeneous VLC and RF Networks

Visible light communication (VLC) is considered as a promising candidate to improve the performance of indoor communication as the complement of wireless radio frequency (RF) communications due to the scarcity of RF resources. Combining the VLC with software-defined small-cell networks will substantially improve the user data rates in indoor heterogeneous networks. In this paper, we introduce the software-defined philosophy into orthogonal frequency-division multiple access-based heterogeneous software-defined and twinned VLC and RF small-cell networks. The pivotal issues of energy efficient (EE) subchannel and power allocation are investigated in the context of software-defined VLC and RF small-cell networks. We formulate the EE resource allocation problem as a non-convex optimization problem, and then, transform it into a convex one using Dinkelbach’s method. In addition, distributed subchannel and power allocation algorithms for both VLC and RF are proposed for solving the problem based on the powerful alternative direction method of multipliers. Simulation results verify the effectiveness of resource allocation algorithms conceived for the heterogeneous software-defined twinned VLC and RF small-cell networks in terms of its good convergence and overall performance.
Systematic evolution of a learning setting for requirements engineering education based on competence-oriented didactics

Requirements engineering is widely accepted as a top success factor for IT (and non-IT) projects. Qualified requirements engineers need to possess not just factual knowledge, but also many skills. Yet, it is unclear which competences requirements engineers actually need, and how these competences may be addressed appropriately in education. As a methodological framework, we devised an approach, Competence-Oriented Didactics, which rests on a sound pedagogical underpinning. This paper shows how Competence-Oriented Didactics is applied to a requirements engineering course in several iterations. In contrast to more traditional teaching approaches, students shall not only acquire technical requirements engineering knowledge, but, at the same time, develop non-technical competences that are necessary for requirements engineering. In particular, students shall better understand why requirements engineering and its core methods, techniques, and skills are needed. Moreover, students shall develop and expand the necessary skills for requirements engineering. Consequently, learning shifted from an instructive to an active and inductive style, which makes students actively discover relevant requirements engineering issues and gain hands-on experiences through carefully devised exercises. Systematic evaluations indicate that the described didactical settings works well. This paper has two main contributions: first, a systematic, competence-driven approach to develop learning settings, and second, a learning setting that is equally directed towards technical and non-technical competences of requirements engineers and demonstrably achieves its goals.
Successful Transfer of a Model T-DNA Plasmid to E. coli Revealed Its Dependence on Recipient RecA and the Preference of VirD2 Relaxase for Eukaryotes Rather Than Bacteria as Recipients

In Agrobacterium-mediated transformation (AMT) of plants, a single-strand (ss) T-DNA covalently linked with a VirD2 protein moves through a bacterial type IV secretion channel called VirB/D4. This transport system originates from conjugal plasmid transfer systems of bacteria. The relaxase VirD2 and its equivalent protein Mob play essential roles in T-DNA transfer and mobilizable plasmid transfer, respectively. In this study, we attempted to transfer a model T-DNA plasmid, which contained no left border but had a right border sequence as an origin of transfer, and a mobilizable plasmid through the VirB/D4 apparatus to Escherichia coli, Agrobacterium and yeast to compare VirD2-driven transfer with Mob-driven one. AMT was successfully achieved by both types of transfer to the three recipient organisms. VirD2-driven AMT of the two bacteria was less efficient than Mob-driven AMT. In contrast, AMT of yeast guided by VirD2 was more efficient than that by Mob. Plasmid DNAs recovered from the VirD2-driven AMT colonies showed the original plasmid structure. These data indicate that VirD2 retains most of its important functions in recipient bacterial cells, but has largely adapted to eukaryotes rather than bacteria. The high AMT efficiency of yeast suggests that VirD2 can also efficiently bring ssDNA to recipient bacterial cells but is inferior to Mob in some process leading to the formation of double-stranded circular DNA in bacteria. This study also revealed that the recipient recA gene was significantly involved in VirD2-dependent AMT, but only partially involved in Mob-dependent AMT. The apparent difference in the recA gene requirement between the two types of AMT suggests that VirD2 is worse at re-circularization to complete complementary DNA synthesis than Mob in bacteria.
MOD: Multi-camera Based Local Position Estimation for Moving Objects Detection

MOD (Moving Object Detection) technology is combined by using recognition, ID tracking, detection and classification by using sensor fusion to get information that local & global position estimation, pose estimation, velocity from around objects in real time over 15 fps. To get more exact information, the object detection and classification should be simultaneously processed. Additionally, this object detection results must have high speed processing time performance in restrict HW platform environment for autonomous vehicle. To solve this problem, we use Darknet based deep learning method and modified detector to obtain local position estimation [1]. And we use UDACITY self-driving [2] and our additional road environment dataset to learn network. Our main purpose is to get moving object local position information from multi cameras fusion. So, we made the fusion server to synchronize and converse multi objects information from four cameras on our autonomous vehicle. In this paper, we introduce the method to solve the local position estimation from four camera using by detection and our fusion server. Additionally, we implement the method to solve the problem caused by steep slope and curve road environment while driving.
Subcutaneous Fat Fibrosis Links Obesity to Insulin Resistance in Chinese Americans

Objective Type 2 diabetes presents at a lower body mass index (BMI) in Chinese individuals than in white individuals. We sought to determine the role of subcutaneous adipose tissue (SCAT)-intrinsic factors, vs BMI or adiposity per se, in the vulnerability of Chinese individuals to obesity-associated impairment of insulin sensitivity. Research Design and Methods Thirty-two Chinese and 30 white men and women from a cohort in the San Francisco Bay Area underwent anthropometric measurements, body composition (dual-energy X-ray absorptiometry) analyses, and measurement of fasting plasma glucose and insulin. Forty-eight also provided abdominal SCAT samples for transcriptional and biochemical analyses of tissue fibrosis. Results BMI correlated with total body fat in white (r = 0.74, P < 0.001) but not Chinese individuals, whereas BMI correlated with visceral adipose tissue (VAT) accrual in both ethnicities (r = 0.88 and 0.81, respectively; P < 0.01). Insulin resistance (homeostatic model assessment of insulin resistance) worsened with VAT mass, but not total body fat, in Chinese subjects (r = 0.63, P < 0.01), whereas it worsened with both in white individuals. By contrast, SCAT mRNA levels of genes encoding profibrotic proteins rose remarkably along with both BMI and VAT mass in Chinese but not white subjects. Similarly, SCAT levels of hydroxyproline, an indicator of tissue collagen content that correlated with increasing VAT mass, were higher in Chinese vs white subjects, particularly in the setting of relative insulin resistance. Conclusions Our findings dissociate BMI from adiposity in Chinese individuals and instead highlight SCAT fibrosis as a process linked to visceral adiposity and insulin resistance in this group.
TGF b Signaling Induces Expression of Gadd45b in Retinal Ganglion Cells

P URPOSE . Growth arrest and DNA damage protein 45b (Gadd45b) functions as an intrinsic neuroprotective molecule protecting retinal ganglion cells (RGCs) from injury. This study was performed to elucidate further the induction pathway of Gadd45b expression in RGCs. M ETHODS . The induction of Gadd45b expression in response to TGF b NF j B signaling was investigated in RGC5 cultures in vitro and murine retina in vivo. Gadd45b mRNA and protein expression were detected by quantitative real-time RT-PCR, immunoblot assay, immunohistochemistry, and immunocytochemistry. Activation of NF j B and TGF b /Gadd45b signaling were assessed by measuring phosphorylation of NF j B and using speciﬁc inhibitors. Gadd45b siRNA was transfected into RGC5 to silence Gadd45b mRNA expression. R ESULTS . Expression of TGF b receptors I and II was detected in RGC5 in vitro and RGCs in vivo. TGF b induced abundant Gadd45b mRNA and protein expression, exhibiting a dose-dependent response in vitro. Exogenous TGF b 1 induced upregulation of Gadd45b expression in RGCs in murine retina in vivo. TGF b stimulated phosphorylation of NF j B, and inhibition of NF j B phosphorylation blocked induction of Gadd45b by TGF b in RGC5 cells. Induction of Gadd45b by TGF b increased the resistance of RGC5 cells against TNF a cytotoxicity and paraquat oxidative stress. C ONCLUSIONS . TGF b signaling induced Gadd45b expression in RGCs. Modulation of the TGF b /NF j B/Gadd45b signaling pathway may provide a means to enhance the neuroprotective
VLSI design of energy efficient computational centric smart objects for IoT

Traditional standalone embedded system and its computational elements firmly connect with physical entities such as Input-Output devices and sensor networks in IoT applications such as medical monitoring, smart grids, smart cities, environmental monitoring systems which are gaining attraction among institutions and industries. A huge quantity of sensors are added to the IoT, and the processing of a large amount of data coming from Input-Output devices and sensor networks increases the energy consumption. To have more efficiency, the mobility of IoT based system requires low energy consumption. Smart devices perform the data offloading to external devices with increased communication effort, and this effort contribute to the overall power consumption of the smart devices. This power hungry nature of the communication infrastructure and computational resources using cloud computing is not very much suitable to design the future computational system. This nature changed the trend to shift the smartness of the things more adjacent to the things themselves and network edge (FoG) instead of towards the cloud. This shift can improve the computing capacity of the smart objects and limit energy consumption. This paper aims at exploring emerging approaches, ideas, and contributions to address the challenges in the design of energy efficient computational centric smart objects for IoT. A proposed energy-efficient Network on Chip (NoC) architecture for embedded high-performance computing is provided.
Classification of device behaviour in internet of things infrastructures: towards distinguishing the abnormal from security threats

Increasingly Internet of Things (IoT) devices are being woven into the fabric of our physical world. With this rapidly expanding pervasive deployment of IoT devices, and supporting infrastructure, we are fast approaching the point where the problem of IoT based cyber-security attacks is a serious threat to industrial operations, business activity and social interactions that leverage IoT technologies. The number of threats and successful attacks against connected systems using IoT devices and services are increasing. The Internet of Things has several characteristics that present technological challenges to traditional cyber-security techniques. The Internet of Things requires a novel and dynamic security paradigm. This paper describes the challenges of securing the Internet of Things. A discussion detailing the state-of-the-art of IoT security is presented. A novel approach to security detection using streaming data analytics to classify and detect security threats in their early stages is proposed. Implementation methodologies and results of ongoing work to realise this new IoT cyber-security technique for threat detection are presented.
Heterologous Expression of Mycobacterium Alkene Monooxygenases in Gram-Positive and Gram-Negative Bacterial Hosts

Alkene MOs are of interest for their potential roles in industrial biocatalysis, most notably for the stereoselective synthesis of epoxides. Wild-type bacteria that grow on alkenes have high activities for alkene oxidation but are problematic for biocatalysis, since they tend to consume the epoxide products. Using recombinant biocatalysts is the obvious alternative, but a major bottleneck is the low activities of recombinant alkene MOs. Here, we provide new high-activity recombinant biocatalysts for alkene oxidation, and we provide insights into how to further improve these systems. ABSTRACT Alkene monooxygenases (MOs) are soluble di-iron-containing enzymes found in bacteria that grow on alkenes. Here, we report improved heterologous expression systems for the propene MO (PmoABCD) and ethene MO (EtnABCD) from Mycobacterium chubuense strain NBB4. Strong functional expression of PmoABCD and EtnABCD was achieved in Mycobacterium smegmatis mc2155, yielding epoxidation activities (62 and 27 nmol/min/mg protein, respectively) higher than any reported to date for heterologous expression of a di-iron MO system. Both PmoABCD and EtnABCD were specialized for the oxidation of gaseous alkenes (C2 to C4), and their activity was much lower on liquid alkenes (C5 to C8). Despite intensive efforts to express the complete EtnABCD enzyme in Escherichia coli, this was not achieved, although recombinant EtnB and EtnD proteins could be purified individually in soluble form. The biochemical function of EtnD as an oxidoreductase was confirmed (1.36 μmol cytochrome c reduced/min/mg protein). Cloning the EtnABCD gene cluster into Pseudomonas putida KT2440 yielded detectable epoxidation of ethene (0.5 nmol/min/mg protein), and this could be stimulated (up to 1.1 nmol/min/mg protein) by the coexpression of cpn60 chaperonins from either Mycobacterium spp. or E. coli. Successful expression of the ethene MO in a Gram-negative host was validated by both whole-cell activity assays and peptide mass spectrometry of induced proteins seen on SDS-PAGE gels. IMPORTANCE Alkene MOs are of interest for their potential roles in industrial biocatalysis, most notably for the stereoselective synthesis of epoxides. Wild-type bacteria that grow on alkenes have high activities for alkene oxidation but are problematic for biocatalysis, since they tend to consume the epoxide products. Using recombinant biocatalysts is the obvious alternative, but a major bottleneck is the low activities of recombinant alkene MOs. Here, we provide new high-activity recombinant biocatalysts for alkene oxidation, and we provide insights into how to further improve these systems.
McMYB10 Modulates the Expression of a Ubiquitin Ligase, McCOP1 During Leaf Coloration in Crabapple

In higher plants, anthocyanins are protective secondary metabolites, which contribute to the color of leaves, stems, flowers, and fruits, and have been found to have an antioxidant role in human health. In this study, we determined the expression of McMYB10 and its specific E3 ubiquitin ligase, McCOP1, in crabapple leaves during the course of a day and in five leaf development stages. Interestingly, the results showed that the transcription level of McCOP1 genes was higher in daylight than at night, and the transcripts of McMYB10 presented a positive correlation with the transcription of McCOP1-1 and McCOP1-2 and anthocyanin accumulation in a crabapple cultivar with red-colored leaves. Several MYB transcription factor (TF) binding sites of the MYBCORE type were found in the McCOP1-1 and McCOP1-2 promoters, and we deduced that there may be a relationship between McMYB10 and McCOP1-1 and McCOP1-2 at the transcriptional level. Yeast one hybrid (Y1H) and electrophoretic mobility shift assays (EMSA) demonstrated that the McMYB10 TF binds specifically to the promoter of McCOP1-1 and McCOP1-2. Furthermore, increased levels of McMYB10 promoted anthocyanin biosynthesis and the expression level of McCOP1-1 and McCOP1-2 in crabapple leaves during continuous light treatments, and overexpression or silencing of McMYB10 in crabapple leaves and apple fruits also result in an increase or decrease, respectively, in the expression of McCOP1-1 and McCOP1-2 and in anthocyanin biosynthesis. Our results reveal a new self-regulation mechanism in where McMYB10 modulates its own expression by activating McCOP1-1 and McCOP1-2 expression to promote ubiquitination of the McMYB10 protein by McCOP1.