Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer

To better understand prostate function and disease, it is important to define and explore the molecular constituents that signify the prostate gland. The aim of this study was to define the prostate specific transcriptome and proteome, in comparison to 26 other human tissues. Deep sequencing of mRNA (RNA-seq) and immunohistochemistry-based protein profiling were combined to identify prostate specific gene expression patterns and to explore tissue biomarkers for potential clinical use in prostate cancer diagnostics. We identified 203 genes with elevated expression in the prostate, 22 of which showed more than five-fold higher expression levels compared to all other tissue types. In addition to previously well-known proteins we identified two poorly characterized proteins, TMEM79 and ACOXL, with potential to differentiate between benign and cancerous prostatic glands in tissue biopsies. In conclusion, we have applied a genome-wide analysis to identify the prostate specific proteome using transcriptomics and antibody-based protein profiling to identify genes with elevated expression in the prostate. Our data provides a starting point for further functional studies to explore the molecular repertoire of normal and diseased prostate including potential prostate cancer markers such as TMEM79 and ACOXL.
Trial of a Paclitaxel-Coated Balloon for Femoropopliteal Artery Disease.

BACKGROUND The treatment of peripheral artery disease with percutaneous transluminal angioplasty is limited by the occurrence of vessel recoil and restenosis. Drug-coated angioplasty balloons deliver antiproliferative agents directly to the artery, potentially improving vessel patency by reducing restenosis. METHODS In this single-blind, randomized trial conducted at 54 sites, we assigned, in a 2:1 ratio, 476 patients with symptomatic intermittent claudication or ischemic pain while at rest and angiographically significant atherosclerotic lesions to angioplasty with a paclitaxel-coated balloon or to standard angioplasty. The primary efficacy end point was primary patency of the target lesion at 12 months (defined as freedom from binary restenosis or from the need for target-lesion revascularization). The primary safety end point was a composite of freedom from perioperative death from any cause and freedom at 12 months from limb-related death (i.e., death from a medical complication related to a limb), amputation, and reintervention. RESULTS The two groups were well matched at baseline; 42.9% of the patients had diabetes, and 34.7% were current smokers. At 12 months, the rate of primary patency among patients who had undergone angioplasty with the drug-coated balloon was superior to that among patients who had undergone conventional angioplasty (65.2% vs. 52.6%, P=0.02). The proportion of patients free from primary safety events was 83.9% with the drug-coated balloon and 79.0% with standard angioplasty (P=0.005 for noninferiority). There were no significant between-group differences in functional outcomes or in the rates of death, amputation, thrombosis, or reintervention. CONCLUSIONS Among patients with symptomatic femoropopliteal peripheral artery disease, percutaneous transluminal angioplasty with a paclitaxel-coated balloon resulted in a rate of primary patency at 12 months that was higher than the rate with angioplasty with a standard balloon. The drug-coated balloon was noninferior to the standard balloon with respect to safety. (Funded by Lutonix-Bard; LEVANT 2 ClinicalTrials.gov number, NCT01412541.).
Geocaching with a Beam: Shared Outdoor Activities through a Telepresence Robot with 360 Degree Viewing

People often enjoy sharing outdoor activities together such as walking and hiking. However, when family and friends are separated by distance it can be difficult if not impossible to share such activities. We explore this design space by investigating the benefits and challenges of using a telepresence robot to support outdoor leisure activities. In our study, participants participated in the outdoor activity of geocaching where one person geocached with the help of a remote partner via a telepresence robot. We compared a wide field of view (WFOV) camera to a 360° camera. Results show the benefits of having a physical embodiment and a sense of immersion with the 360° view. Yet challenges related to a lack of environmental awareness, safety issues, and privacy concerns resulting from bystander interactions. These findings illustrate the need to design telepresence robots with the environment and public in mind to provide an enhanced sensory experience while balancing safety and privacy issues resulting from being amongst the general public.
On the limits of provable anonymity

We study provably secure anonymity. We begin with rigorous definition of anonymity against wide range of computationally bounded attackers, including eavesdroppers, malicious peers, malicious destinations, and their combinations. Following [hevia2008indistinguishability], our definition is generic, and captures different notions of anonymity (e.g., unobservability and sender anonymity). We then study the feasibility of ultimate anonymity: the strongest-possible anonymity requirements and adversaries. We show there is a protocol satisfying this requirement, but with absurd (although polynomial) inefficiency and overhead. We show that such inefficiency and overhead are unavoidable for 'ultimate anonymity'. We then present a slightly-relaxed requirement and present feasible protocols for it.
Adaptive workflow processing and execution in Pegasus

Workflows are widely used in applications that require coordinated use of computational resources. Workflow definition languages typically abstract over some aspects of the way in which a workflow is to be executed, such as the level of parallelism to be used or the physical resources to be deployed. As a result, a workflow management system has the responsibility of establishing how best to execute a workflow given the available resources. The Pegasus workflow management system compiles abstract workflows into concrete execution plans, and has been widely used in large-scale e-Science applications. This paper describes an extension to Pegasus whereby resource allocation decisions are revised during workflow evaluation, in the light of feedback on the performance of jobs at runtime. The contributions of this paper include: (i) a description of how adaptive processing has been retrofitted to an existing workflow management system; (ii) a scheduling algorithm that allocates resources based on runtime performance; and (iii) an experimental evaluation of the resulting infrastructure using grid middleware over clusters. Copyright © 2009 John Wiley & Sons, Ltd.
Design and Rationale of the Mechanical Retrieval and Recanalization of Stroke Clots Using Embolectomy (MR RESCUE) Trial

Rationale Multimodal imaging has the potential to identify acute ischaemic stroke patients most likely to benefit from late recanalization therapies. Aims The general aim of the Mechanical Retrieval and Recanalization of Stroke Clots Using Embolectomy Trial is to investigate whether multimodal imaging can identify patients who will benefit substantially from mechanical embolectomy for the treatment of acute ischaemic stroke up to eight-hours from symptom onset. Design Mechanical Retrieval and Recanalization of Stroke Clots Using Embolectomy is a randomized, controlled, blinded-outcome clinical trial. Population studied Acute ischaemic stroke patients with large vessel intracranial internal carotid artery or middle cerebral artery M1 or M2 occlusion enrolled within eight-hours of symptom onset are eligible. The study sample size is 120 patients. Study intervention Patients are randomized to endovascular embolectomy employing the Merci Retriever (Concentric Medical, Mountain View, CA) or the Penumbra System (Penumbra, Alameda, CA) vs. standard medical care, with randomization stratified by penumbral pattern. Outcomes The primary aim of the trial is to test the hypothesis that the presence of substantial ischaemic penumbral tissue visualized on multimodal imaging (magnetic resonance imaging or computed tomography) predicts patients most likely to respond to mechanical embolectomy for treatment of acute ischaemic stroke due to a large vessel, intracranial occlusion up to eight-hours from symptom onset. This hypothesis will be tested by analysing whether pretreatment imaging pattern has a significant interaction with treatment as a determinant of functional outcome based on the distribution of scores on the modified Rankin Scale measure of global disability assessed 90 days poststroke. Nested hypotheses test for (1) treatment efficacy in patients with a penumbral pattern pretreatment, and (2) absence of treatment benefit (equivalency) in patients without a penumbral pattern pretreatment. An additional aim will only be tested if the primary hypothesis of an interaction is negative: that patients treated with mechanical embolectomy have improved functional outcome vs. standard medical management.
YIFEI RAO : BIG DATA ALGORITHM APPLIED TO CREDIT RISK ASSESSMENT MODEL

In order to improve the accuracy and computational efficiency of the credit risk assessment model in an environment of large data, a parallel convolution neural network (CNN) model for credit risk assessment based on Mapreduce framework is proposed. First, the framework of Mapreduce parallel system and its composition module are given; secondly, the convolution neural network is introduced, and the parallel computing model of credit risk assessment is built based on the Mapreduce parallel system framework. Finally, by comparing the experimental results on the credit risk assessment test set of ICBC, the proposed algorithm is shown to have: i) higher assessment accuracy, ii) lower assessment error and iii) less computational time. The effectiveness of the proposed algorithm is thus verified.
A Weighted Voting Mechanism for Action Selection Problem in Self-Adaptive Software

Self-adaptive software is a closed-loop system which aims at adjusting itself in response to changes at runtime. Such a system is required to monitor domain events, detect significant changes, decide how to react, and act in order to execute the decisions. This paper focuses on the deciding process particularly for application-level adaptation actions. For this purpose, a weighted voting mechanism has been proposed which makes decisions based on a Goal-Action- Attribute Model (GAAM). The decision-making algorithm traverses GAAM, determines activated goals and feasible actions for voting, and ultimately selects an action as the social choice. The proposed mechanism and GAAM are evaluated within a simulated model of a news web site.
Looking Up Information in Email: Feedback on Visit Durations Discourages Distractions

Data entry often involves looking up information from email. Task switching to email can be disruptive, and people can get distracted and forget to return to their primary task. In this paper, we investigate whether giving people feedback on how long they are away from their task has any effect on the duration and number of their switches. An online experiment was conducted in which participants had to enter numeric codes into an online spreadsheet. They had to look up these codes in an email sent to their personal email address upon starting the experiment. People who were shown how long they were away for made shorter switches, were faster to complete the task and made fewer data entry errors. This suggests feedback on switching duration may make people more aware of their switching behaviour, and assist users in maintaining focus on their main task.
CareNet: Building Regulation-Compliant Home-Based Healthcare Services with Software-Defined Infrastructure

Healthcare network and computing infrastructure is rapidly changing from closed environments to open environments that incorporate new devices and new application scenarios. Home-based healthcare is such an example of leveraging pervasive sensors and analyzing sensor data (often in real-time) to guide therapy or intervene. In this paper, we address the challenges in regulatory compliance when designing and deploying healthcare applications on a heterogeneous cloud environment. We propose the CareNet framework, consisting of a set of APIs and secure data transmission mechanisms, to facilitate the specification of home-based healthcare services running on the software-defined infrastructure (SDI). This work is a collaboration among computer scientists, medical researchers, healthcare IT and healthcare providers, and its goal is to reduce the gap between the availability of SDI and meeting regulatory compliance in healthcare applications. Our prototype demonstrates the feasibility of the framework and serves as testbed for novel experimental studies of emerging healthcare applications.
Electrochemical gas sensor

It describes an electrochemical gas sensor, comprising: (a) located in the cap (2) detecting the lower electrode; (b) a counter electrode (10); (c) a reference electrode (14); (d) a separator ( 11), comprising an electrolyte positioned therebetween, and the counter electrode and a reference electrode in contact with the detection electrode, the separator is made of a material having a capillary action, the electrolyte can be pumped into the separator in contact with the separator; ( e) a reservoir containing an electrolyte and a liquid-absorbent material (12) having a capillary action, the electrolyte can be taken out from the tank and transferred to the separator (11). Capillary action separator (11) is larger than the capillary action of liquid absorbent material, such that the absorption of the electrolyte in the separator is in preference to liquid absorbent material in the absorbent, to separate holding sufficient concentration of ions between the electrodes for operation of the sensor.
A versatile autonomous navigation algorithm for smart indoor environment using FPGA based robot

The Robotic Assistive System (RAS) is playing a vital role in assisting human needs. In robotics, navigation system is mostly preferred to solve Travelling Salesman Problem (TSP) to serve in an indoor environment. The proposed versatile navigation algorithm is hardware efficient to perform in a smart environment which is confined with different static and dynamic (human movement) objects. This proposed approach is novel in terms of serving for multi node scenario by using the triangulation techniques for efficient navigation in an indoor environment without landmarks. This navigation algorithm digital hardware scheme is coded in Verilog 2001 and implemented on FPGA based robots in the real time scenario.
Using roving STARs for on-line testing and diagnosis of FPGAs in fault-tolerant applications

In this paper we present a novel integrated approach to on-line FPGA testing, diagnosis, and fault-tolerance, to be used in high-reliability and high-availability hardware. The test process takes place in self-testing areas (STARs) of the FPGA, without disturbing the normal system operation. The entire chip is eventually tested by having (STARs) gradually rove across the FPGA. Our approach guarantees complete testing of programmable logic blocks and interconnect, and provides maximum diagnostic resolution. A new fault-tolerant (FT) technique allows using partially defective FPGA resources for normal operation, providing longer mission life-span in the presence of faults. We also introduce the basic concepts of a new dynamic FT method, spare resources needed to bypass a fault are always in the neighborhood of the located fault, thus simplifying fault-bypassing.
A screening method to assess biological effects of microRNA overexpression in Chinese hamster ovary cells

MicroRNAs (miRNAs) are a novel class of short non‐coding RNAs, which negatively regulate target gene expression at post‐transcriptional level. They mediate an important layer of control in the global regulation of gene networks, controlling a broad range of physiological as well as patho‐physiological pathways including development, cancer, metabolism, proliferation, and stress resistance. So far, more than 365 miRNA genes have been identified in CHO cells. The functional analysis of the physiological effect of such large numbers of miRNAs, however, requires an efficient functional screening method. In the current study, we therefore established and evaluated a protocol to perform miRNA overexpression and to screen their effect on bio‐industrially relevant phenotypes, such as growth, viability and productivity, using a recombinant, Epo‐Fc producing CHO cell line. For protocol optimization, four CHO miRNAs (cgr‐miR‐17, cgr‐miR‐221, cgr‐miR‐21, and cgr‐miR‐210) were cloned into small hairpin vectors including a GFP cassette and transfected. After transfection cells were analyzed for growth and productivity over a 4‐day period. Even from this small set of four miRNAs, the overexpression of miR‐17, one of the members of the oncogenic miR‐17‐92 cluster, gave proof of principle that this method enables the identification of miRNA engineering candidates as its overexpression increased the speed of cell proliferation without negatively impacting specific productivity. The here presented method is applicable for medium‐throughput screening for microRNA, miR‐sponge, siRNA, or mRNA overexpression along with detailed functional characterization using the same experimental set up. As the same procedure can be applied to different production cell lines, the protocol can also be used to test for individual, cell line specific responses to microRNAs. Thus our system represents a general platform to functionally screen candidates for rational cell factory design. Biotechnol. Bioeng. 2012; 109:1376–1385. © 2012 Wiley Periodicals, Inc.
Escaping High Viral Load Exhaustion

Deletion, anergy, and a spectrum of functional impairments can affect virus-specific CD8 cells in chronic viral infections. Here we characterize a low frequency population of CD8 cells present in chronic hepatitis B virus (HBV) infection which survive in the face of a high quantity of viral antigen. Although they do not appear to exert immunological pressure in vivo, these CD8 cells are not classically “tolerant” since they proliferate, lyse, and produce antiviral cytokines in vitro. They are characterized by altered HLA/peptide tetramer reactivity, which is not explained by TCR down-regulation or reduced functional avidity and which can be reversed with repetitive stimulation. CD8 cells with altered tetramer binding appear to have a specificity restricted to envelope antigen and not to other HBV antigens, suggesting that mechanisms of CD8 cell dysfunction are differentially regulated according to the antigenic form and presentation of individual viral antigens.
This App Would Like to Use Your Current Location to Better Serve You: Importance of User Assent and System Transparency in Personalized Mobile Services

Modern mobile apps aim to provide personalized services without appearing intrusive. A common strategy is to let the user initiate the service request (e.g., "click here to receive coupons for your favorite products"), a practice known as ? overt personalization. " Another strategy is to assuage users' privacy concerns by being transparent about how their data would be collected, utilized and stored. To test these two strategies, we conducted a 2 (Personalization: Overt vs. Covert) x 2 (Transparency: High vs. Low) factorial experiment, with a fifth control condition. Participants (N=302) interacted with GreenByMe, a prototype of an eco-friendly mobile application. Data show that overt personalization affects perceived control. Significant three-way interactions between power usage, perceived overt personalization and perceived information transparency was seen on perceived ease of use, trust in the app, user engagement and behavioral intention to use the app in the future. In addition, results reveal that perceived information transparency also promotes trust, which is negatively linked with privacy concerns and positively correlated with user engagement and product involvement.
On the asymptotic performance of hierarchical transforms

Explicit formulas are derived for the coding gain of hierarchical transforms for a given number of stages, and the asymptotic gain as this number goes to infinity. The intuitive result that hierarchical transforms are not asymptotically optimal, that is, their coding gains do not approach the inverse of the spectral flatness measure as the number of stages goes to infinity, is confirmed. Examples comparing the limits for hierarchical transforms and M-band parallel systems (filter banks) for AR(1) signals are presented. >
Protein subnuclear location based on KLDA with fused kernel and effective fusion representation

Discriminated dimensionality reduction algorithm and informative feature representation are equal importance for improving prediction accuracy of protein subnuclear. Based on this thought, this paper simultaneously proposed an effective fused kernel function and an integrated feature expression for predicting protein subnuclear location. To obtain their optimal fusion parameter respectively, the particle swarm optimization (PSO) algorithm was employed to search them during the fusing processes. To verify the feasibility of our proposed approach, a standard public dataset was adopted to carry out the numerical experiment with k-nearest neighbors (KNN) as the classifier. The last results of Jackknife test method can be as high as 94.6779% with our fused kernel and representation, which undoubtedly reveals that our proposed integration method is of efficiency in protein subnuclear localization to a large extent.
Tempura: Temporal Dimension for IDEs

Modern integrated development environments (IDEs) make many software engineering tasks easier by providing automated programming support such as code completion and navigation. However, such support -- and therefore IDEs as awhole -- operate on one revision of the code at a time, and leave handling of code history to external tools or plugins, such asEGit for Eclipse. For example, when a method is removed froma class, developers can no longer find the method through code completion. This forces developers to manually switch across different revisions or resort to using external tools when they need to learn about previous code revisions.We propose a novel approach of adding a temporal dimensionto IDEs, enabling code completion and navigation to operate on multiple revisions of code at a time. We previously introduced the idea of temporal code completion and navigation,and presented a vision for how that idea may be realized.This paper realizes that vision by implementing and evaluatinga prototype tool called Tempura. We describe our algorithmfor processing and indexing historical code information from repositories for Tempura, and demonstrate Tempura's scalability with three large Eclipse projects. We also evaluate Tempura's usability through a controlled user study. The study participantslearned about the code history with more accuracy when usingTempura compared to EGit. Although the sample size was notlarge enough to provide strong statistical significance, the resultsshow a promising outlook for our approach.