Miracle-dz/UniFAR-FTUs huggingface dataset:
Computing Coastal Ocean Surface Currents from MODIS and VIIRS Satellite Imagery

We explore the potential of computing coastal ocean surface currents from Moderate-Resolution Imaging Spectroradiometer (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) satellite imagery using the maximum cross-correlation (MCC) method. To improve on past versions of this method, we evaluate combining MODIS and VIIRS thermal infrared (IR) and ocean color (OC) imagery to map the coastal surface currents and discuss the benefits of this combination of sensors and optical channels. By combining these two sensors, the total number of vectors increases by 58.3 % . In addition, we also make use of the different surface patterns of IR and OC imagery to improve the tracking performance of the MCC method. By merging the MCC velocity fields inferred from IR and OC products, the spatial coverage of each individual MCC field is increased by 65.8 % relative to the vectors derived from OC images. The root mean square (RMS) error of the merged currents is 18 cm · s − 1 compared with coincident HF radar surface currents. A 5-year long time serious of merged MCC computed currents was used to investigate the current structure of the California Current (CC). Weekly, seasonal, and 5-year mean flows provide a unique space-time picture of the oceanographic variability of the CC.
Assessment of machine-learning techniques on large pathology data sets to address assay redundancy in routine liver function test profiles

Abstract Background: Routine liver function tests (LFTs) are central to serum testing profiles, particularly in community medicine. However there is concern about the redundancy of information provided to requesting clinicians. Large quantities of clinical laboratory data and advances in computational knowledge discovery methods provide opportunities to re-examine the value of individual routine laboratory results that combine for LFT profiles. Methods: The machine learning methods recursive partitioning (decision trees) and support vector machines (SVMs) were applied to aggregate clinical chemistry data that included elevated LFT profiles. Response categories for γ-glutamyl transferase (GGT) were established based on whether the patient results were within or above the sex-specific reference interval. Single decision tree and SVMs were applied to test the accuracy of GGT prediction by the highest ranked predictors of GGT response, alkaline phosphatase (ALP) and alanine amino-transaminase (ALT). Results: Through interrogating more than 20,000 individual cases comprising both sexes and all ages, decision trees predicted GGT category at 90% accuracy using only ALP and ALT, with a SVM prediction accuracy of 82.6% after 10-fold training and testing. Bilirubin, lactate dehydrogenase (LD) and albumin did not enhance prediction, or reduced accuracy. Comparison of abnormal (elevated) GGT categories also supported the primacy of ALP and ALT as screening markers, with serum urate and cholesterol also useful. Conclusions: Machine-learning interrogation of massive clinical chemistry data sets demonstrated a strategy to address redundancy in routine LFT screening by identifying ALT and ALP in tandem as able to accurately predict GGT elevation, suggesting that GGT can be removed from routine LFT screening.
Multiview semi-supervised ranking for automatic image annotation

Most photo sharing sites give their users the opportunity to manually label images. The labels collected that way are usually very incomplete due to the size of the image collections: most images are not labeled according to all the categories they belong to, and, conversely, many class have relatively few representative examples. Automated image systems that can deal with small amounts of labeled examples and unbalanced classes are thus necessary to better organize and annotate images. In this work, we propose a multiview semi-supervised bipartite ranking model which allows to leverage the information contained in unlabeled sets of images in order to improve the prediction performance, using multiple descriptions, or views of images. For each topic class, our approach first learns as many view-specific rankers as available views using the labeled data only. These rankers are then improved iteratively by adding pseudo-labeled pairs of examples on which all view-specific rankers agree over the ranking of examples within these pairs. We report on experiments carried out on the NUS-WIDE dataset, which show that the multiview ranking process improves predictive performances when a small number of labeled examples is available specially for unbalanced classes. We show also that our approach achieves significant improvements over a state-of-the art semi-supervised multiview classification model.
PTK6 Localized at the Plasma Membrane Promotes Cell Proliferation and MigratiOn Through Phosphorylation of Eps8

Protein tyrosine kinase 6 (PTK6; also known as Brk) is closely related to the Src family kinases, but lacks a membrane‐targeting myristoylation signal. Sublocalization of PTK6 at the plasma membrane enhances its oncogenic potential. To understand the mechanism(s) underlying the oncogenic property of plasma–membrane‐associated PTK6, proteins phosphorylated by membrane‐targeted myristoylated PTK6 (Myr‐PTK6) were enriched and analyzed using a proteomics approach. Eps8 which was identified by this method is phosphorylated by Myr‐PTK6 in HEK293 cells. Mouse Eps8 expressed in HEK293 cells is phosphorylated by Myr‐PTK6 at residues Tyr497, Tyr524, and Tyr534. Compared to wild‐type Eps8 (Eps8 WT), the phosphorylation‐defective 3YF mutant (Eps8 3YF) reverts the increased proliferation, migration, and phosphorylation of ERK and FAK mediated by Eps8 WT in HEK293 cells overexpressing PTK6. PTK6 knockdown in T‐47D breast cancer cells decreased EGF‐induced phosphorylation of Eps8. Endogenous PTK6 phosphorylates ectopically expressed Eps8 WT, but not Eps8 3YF mutant, in EGF‐stimulated T‐47D cells. The EGF‐induced Eps8 phosphorylation enhances activation of ERK and FAK, cell adhesion, and anchorage‐independent colony formation in T‐47D cells, but not in the PTK6‐knokdown T‐47D cells. These results indicate that plasma–membrane‐associated PTK6 phosphorylates Eps8, which promotes cell proliferation, adhesion, and migration and, thus, tumorigenesis. J. Cell. Biochem. 118: 2887–2895, 2017. © 2017 Wiley Periodicals, Inc.
Long-Term Disease Management Needs of Southern African Americans With Diabetes

PURPOSE this qualitative study explored the issues, concerns, and needs of low-income, southern African Americans in managing type 2 diabetes over time. METHODS Two focus groups (N=22) were conducted with the target population to collect data. Group sessions were audiotaped and transcribed verbatim. Content analysis was used to analyze the data. RESULTS The data revealed an overall theme of learning to live with diabetes, which consisted of 3 processes: (1) symptom management, (2) making healthy choices, and (3) emotional adjustment. This article focuses on the processes of symptom management and making healthy choices. Findings suggest that the sequential processes of symptom management and making healthy choices occurred over time primarily through experiential learning in this population and were influenced by social support, caring and collaborative provider-client relationships, and access to resources and culturally sensitive supportive services. CONCLUSIONS Experiential educational methods that incorporate social support and access to resources may be more appropriate than the traditional didactic method of teaching diabetes self-care.
Breastfeeding and swallowing in a neonate with mild hypoxic-ischaemic encephalopathy

Background Specific breastfeeding and swallowing characteristics in neonates with hypoxic-ischaemic encephalopathy (HIE) have not yet been well described in the literature. Considering the relatively high incidence of HIE in resource-poor settings, speech-language therapists should be cognisant of the feeding difficulties in this population during breastfeeding. Objective To systematically describe the breastfeeding and swallowing of a single case of a neonate diagnosed with mild HIE from admission to discharge. Method A case study of a 2-day old neonate with mild HIE in a neonatal intensive care unit at an urban teaching hospital, is presented. Data were prospectively collected during four sessions in a 12-day period until the participant’s discharge. Feeding and swallowing were assessed clinically, as well as instrumentally using a video-fluoroscopic swallow study. Results After parenteral feeding, nasogastric tube feeding commenced. Breastfeeding was introduced on Day 6, as it was considered a safe option, and revealed problematic rooting, shallow latching, short sucking bursts, infrequent swallowing, and a drowsy state of arousal, with coughing and choking. No penetration or aspiration was identified instrumentally. After 13 days, the neonate was breastfeeding safely. Conclusion Although the pharyngeal stage of swallowing was intact, symptoms of oral stage dysphagia were revealed using a combination of clinical and instrumental measures. Breastfeeding difficulties were identified, exacerbated by poor state regulation, which lead to prolonged hospitalisation. The case study highlights the unexpected long duration of feeding difficulties in an infant with mild HIE and indicates further research.
Vitamin K-Antagonists Accelerate Atherosclerotic Calcification and Induce a Vulnerable Plaque Phenotype

Background Vitamin K-antagonists (VKA) are treatment of choice and standard care for patients with venous thrombosis and thromboembolic risk. In experimental animal models as well as humans, VKA have been shown to promote medial elastocalcinosis. As vascular calcification is considered an independent risk factor for plaque instability, we here investigated the effect of VKA on coronary calcification in patients and on calcification of atherosclerotic plaques in the ApoE−/− model of atherosclerosis. Methodology/Principal Findings A total of 266 patients (133 VKA users and 133 gender and Framingham Risk Score matched non-VKA users) underwent 64-slice MDCT to assess the degree of coronary artery disease (CAD). VKA-users developed significantly more calcified coronary plaques as compared to non-VKA users. ApoE−/− mice (10 weeks) received a Western type diet (WTD) for 12 weeks, after which mice were fed a WTD supplemented with vitamin K1 (VK1, 1.5 mg/g) or vitamin K1 and warfarin (VK1&W; 1.5 mg/g & 3.0 mg/g) for 1 or 4 weeks, after which mice were sacrificed. Warfarin significantly increased frequency and extent of vascular calcification. Also, plaque calcification comprised microcalcification of the intimal layer. Furthermore, warfarin treatment decreased plaque expression of calcification regulatory protein carboxylated matrix Gla-protein, increased apoptosis and, surprisingly outward plaque remodeling, without affecting overall plaque burden. Conclusions/Significance VKA use is associated with coronary artery plaque calcification in patients with suspected CAD and causes changes in plaque morphology with features of plaque vulnerability in ApoE−/− mice. Our findings underscore the need for alternative anticoagulants that do not interfere with the vitamin K cycle.
AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes

Objectives Next-generation sequencing (NGS) data in the identification of disease-causing genes provides a promising opportunity in the diagnosis of disease. Beyond the previous efforts for NGS data alignment, variant detection, and visualization, developing a comprehensive annotation system supported by multiple layers of disease phenotype-related databases is essential for deciphering the human genome. To satisfy the impending need to decipher the human genome, it is essential to develop a comprehensive annotation system supported by multiple layers of disease phenotype-related databases. Methods AnsNGS (Annotation system of sequence variations for next-generation sequencing data) is a tool for contextualizing variants related to diseases and examining their functional consequences. The AnsNGS integrates a variety of annotation databases to attain multiple levels of annotation. Results The AnsNGS assigns biological functions to variants, and provides gene (or disease)-centric queries for finding disease-causing variants. The AnsNGS also connects those genes harbouring variants and the corresponding expression probes for downstream analysis using expression microarrays. Here, we demonstrate its ability to identify disease-related variants in the human genome. Conclusions The AnsNGS can give a key insight into which of these variants is already known to be involved in a disease-related phenotype or located in or near a known regulatory site. The AnsNGS is available free of charge to academic users and can be obtained from http://snubi.org/software/AnsNGS/.
An ID and Address Protection Unit for NoC based Communication Architectures

Security is becoming the primary concern in today's embedded systems. Network-on-Chip (NoC) based communication architectures have emerged as an alternative to shared bus mechanism in Multiprocessor System-on-Chip (MPSoC) devices, and the increasing number and functionality of processing cores has made such systems vulnerable to security attacks. In this paper an id and address verification (IAV) security module is presented, which is embedded in each router at the communication level. IAV verifies the identity and address range to be accessed by incoming and outgoing data packets in a NoC-based many-core shared memory architecture. Our IAV architecture is implemented on a FPGA device for functional verification and evaluated in terms of its area and power consumption overhead. For FPGA-based systems, the IAV module can be reconfigured at run-time through partial reconfiguration. In addition, a cycle-accurate simulation is carried out to analyse the performance overhead for different network configurations. The proposed IAV module has reduced area and power consumption overhead when compared with similar existing solutions.
Adaptive Resource Management and Provisioning in the Cloud Computing: A Survey of Definitions, Standards and Research Roadmaps

The fact that cloud computing services have been proposed in recent years, organizations and individuals face with various challenges and problems such as how to migrate applications and software platforms into cloud or how to ensure security of migrated applications. This study reviews the current challenges and open issues in cloud computing, with the focus on autonomic resource management especially in federated clouds. In addition, this study provides recommendations and research roadmaps for scientific activities, as well as potential improvements in federated cloud computing. This survey study covers results achieved through 190 literatures including books, journal and conference papers, industrial reports, forums, and project reports. A solution is proposed for autonomic resource management in the federated clouds, using machine learning and statistical analysis in order to provide better and efficient resource management.
Role of the E2 Hypervariable Region (HVR1) in the Immunogenicity of a Recombinant Hepatitis C Virus Vaccine

ABSTRACT Current evidence supports a protective role for virus-neutralizing antibodies in immunity against hepatitis C virus (HCV) infection. Many cross-neutralizing monoclonal antibodies have been identified. These antibodies have been shown to provide protection or to clear infection in animal models. Previous clinical trials have shown that a gpE1/gpE2 vaccine can induce antibodies that neutralize the in vitro infectivity of all the major cell culture-derived HCV (HCVcc) genotypes around the world. However, cross-neutralization appeared to favor certain genotypes, with significant but lower neutralization against others. HCV may employ epitope masking to avoid antibody-mediated neutralization. Hypervariable region 1 (HVR1) at the amino terminus of glycoprotein E2 has been shown to restrict access to many neutralizing antibodies. Consistent with this, other groups have reported that recombinant viruses lacking HVR1 are hypersensitive to neutralization. It has been proposed that gpE1/gpE2 lacking this domain could be a better vaccine antigen to induce broadly neutralizing antibodies. In this study, we examined the immunogenicity of recombinant gpE1/gpE2 lacking HVR1 (ΔHVR1). Our results indicate that wild-type (WT) and ΔHVR1 gpE1/gpE2 antigens induced antibodies targeting many well-characterized cross-genotype-neutralizing epitopes. However, while the WT gpE1/gpE2 vaccine can induce cross-genotype protection against various genotypes of HCVcc and/or HCV-pseudotyped virus (HCVpp), antisera from ΔHVR1 gpE1/gpE2-immunized animals exhibited either reduced homologous neutralization activity compared to that of the WT or heterologous neutralization activity similar to that of the WT. These data suggest that ΔHVR1 gpE1/gpE2 is not a superior vaccine antigen. Based on previously reported chimpanzee protection data using WT gpE1/gpE2 and our current findings, we are preparing a combination vaccine including wild-type recombinant gpE1/gpE2 for clinical testing in the future. IMPORTANCE An HCV vaccine is an unmet medical need. Current evidence suggests that neutralizing antibodies play an important role in virus clearance, along with cellular immune responses. Previous clinical data showed that gpE1/gpE2 can effectively induce cross-neutralizing antibodies, although they favor certain genotypes. HCV employs HVR1 within gpE2 to evade host immune control. It has been hypothesized that the removal of this domain would improve the production of cross-neutralizing antibodies. In this study, we compared the immunogenicities of WT and ΔHVR1 gpE1/gpE2 antigens as vaccine candidates. Our results indicate that the ΔHVR1 gpE1/gpE2 antigen confers no advantages in the neutralization of HCV compared with the WT antigen. Previously, we showed that this WT antigen remains the only vaccine candidate to protect chimpanzees from chronic infection, contains multiple cross-neutralizing epitopes, and is well tolerated and immunogenic in humans. The current data support the further clinical development of this vaccine antigen component.
Game-Based Approach for QoS Provisioning and Interference Management in Heterogeneous Networks

For the current 5G era, the deployment of small cells in residential and commercial areas plays an imperious preamble in improving network coverage and the quality of service (QoS). Major technical problems associated with the mass deployment of small cells, such as femtocells are interference management and QoS provisioning. These are important for service-providing operators because the system capacity and achievable data rates mainly depend on interference. Future generation wireless networks will use autonomous and distributed architecture for ameliorating the efficacy and flexibility of communication systems. In this paper, we propose a game theory-based model along with dynamic channel allocation and self-optimizing power control scheme for resolving priority-based access exposure by applying the concept of primary and secondary users. It is expected that the consumers will experience better QoS with reduced interference levels, and the service-providing operators will be able to increase their revenue, while ensuring optimal price for the consumers. We assimilated extensive numerical results to demonstrate the efficacy of our proposed model.
Real-Time Eye Tracking Using IR Stereo Camera for Indoor and Outdoor Environments

We propose a novel eye tracking method that can estimate 3D world coordinates using an infrared (IR) stereo camera for indoor and outdoor environments. This method first detects dark evidences such as eyes, eyebrows and mouths by fast multi-level thresholding. Among these evidences, eye pair evidences are detected by evidential reasoning and geometrical rules. For robust accuracy, two classifiers based on multiple layer perceptron (MLP) using gradient local binary patterns (GLBPs) verify whether the detected evidences are real eye pairs or not. Finally, the 3D world coordinates of detected eyes are calculated by region-based stereo matching. Compared with other eye detection methods, the proposed method can detect the eyes of people wearing sunglasses due to the use of the IR spectrum. Especially, when people are in dark environments such as driving at nighttime, driving in an indoor carpark, or passing through a tunnel, human eyes can be robustly detected because we use active IR illuminators. In the experimental results, it is shown that the proposed method can detect eye pairs with high performance in real-time under variable illumination conditions. Therefore, the proposed method can contribute to human-computer interactions (HCIs) and intelligent transportation systems (ITSs) applications such as gaze tracking, windshield head-up display and drowsiness detection.
Adrenomedullin blockade suppresses sunitinib-resistant renal cell carcinoma growth by targeting the ERK/MAPK pathway

Purpose To evaluate the mechanisms underlying sunitinib resistance in RCC and to identify targets that may be used to overcome this resistance. Results Reanalysis of transcriptome microarray datasets (GSE64052 and GSE76068) showed that adrenomedullin expression was increased in sunitinib-resistant tumors. And adrenomedullin expression was increased in sunitinib-resistant tumor xenografts, accompanied by upregulation of phospho-ERK levels. However, blocking adrenomedullin inhibited sunitinib-resistant tumor growth. Treatment of RCC cells with sunitinib and ADM22-52 was superior to monotherapy with either agent. Additionally, adrenomedullin upregulated cAMP and activated the ERK/MAPK pathway, promoting cell proliferation, while knockdown of adrenomedullin inhibited RCC cell growth and invasion in vitro. Materials and methods We searched the Gene Expression Omnibus (GEO) database to find data regarding sunitinib-resistant RCC. These data were subsequently reanalyzed to identify targets that contribute to sunitinib resistance, and adrenomedullin upregulation was found to mediate sunitinib resistance in RCC. Then, we created an RCC mouse xenograft model. Mice were treated with sunitinib, an adrenomedullin receptor antagonist (ADM22-52), a MEK inhibitor (PD98059) and different combinations of these three drugs to investigate their effects on tumor growth. RCC cells (786-0) were cultured in vitro and treated with an ADM22-52 or PD98059 to determine whether adrenomedullin activates the ERK/MAPK pathway. Adrenomedullin was knocked down in 786-0 cells via siRNA, and the effects of this knockdown on cell were subsequently investigated. Conclusions Adrenomedullin plays an important role in RCC resistance to sunitinib treatment. The combination of sunitinib and an adrenomedullin receptor antagonist may result in better outcomes in advanced RCC patients.