Miracle-dz/UniFAR-FTUs huggingface dataset:
Exposure of Human CD4 T Cells to IL-12 Results in Enhanced TCR-Induced Cytokine Production, Altered TCR Signaling, and Increased Oxidative Metabolism

Human CD4 T cells are constantly exposed to IL-12 during infections and certain autoimmune disorders. The current paradigm is that IL-12 promotes the differentiation of naïve CD4 T cells into Th1 cells, but recent studies suggest IL-12 may play a more complex role in T cell biology. We examined if exposure to IL-12 alters human CD4 T cell responses to subsequent TCR stimulation. We found that IL-12 pretreatment increased TCR-induced IFN-γ, TNF-α, IL-13, IL-4 and IL-10 production. This suggests that prior exposure to IL-12 potentiates the TCR-induced release of a range of cytokines. We observed that IL-12 mediated its effects through both transcriptional and post-transcriptional mechanisms. IL-12 pretreatment increased the phosphorylation of AKT, p38 and LCK following TCR stimulation without altering other TCR signaling molecules, potentially mediating the increase in transcription of cytokines. In addition, the IL-12-mediated enhancement of cytokines that are not transcriptionally regulated was partially driven by increased oxidative metabolism. Our data uncover a novel function of IL-12 in human CD4 T cells; specifically, it enhances the release of a range of cytokines potentially by altering TCR signaling pathways and by enhancing oxidative metabolism.
PGMPI: Automatically Verifying Self-Consistent MPI Performance Guidelines

The Message Passing Interface (MPI) is the most commonly used application programming interface for process communication on current large-scale parallel systems. Due to the scale and complexity of modern parallel architectures, it is becoming increasingly difficult to optimize MPI libraries, as many factors can influence the communication performance. To assist MPI developers and users, we propose an automatic way to check whether MPI libraries respect self-consistent performance guidelines for collective communication operations. We introduce the PGMPI framework to detect violations of performance guidelines through benchmarking. Our experimental results show that PGMPI can pinpoint undesired and often unexpected performance degradations of collective MPI operations. We demonstrate how to overcome performance issues of several libraries by adapting the algorithmic implementations of their respective collective MPI calls.
Bioenergetic Profiling of Zebrafish Embryonic Development

Many debilitating conditions are linked to bioenergetic defects. Developing screens to probe the genetic and/or chemical basis for such links has proved intractable. Furthermore, there is a need for a physiologically relevant assay of bioenergetics in whole organisms, especially for early stages in life where perturbations could increase disease susceptibility with aging. Thus, we asked whether we could screen bioenergetics and mitochondrial function in the developing zebrafish embryo. We present a multiplexed method to assay bioenergetics in zebrafish embryos from the blastula period (3 hours post-fertilization, hpf) through to hatching (48 hpf). In proof of principle experiments, we measured respiration and acid extrusion of developing zebrafish embryos. We quantified respiratory coupling to various bioenergetic functions by using specific pharmacological inhibitors of bioenergetic pathways. We demonstrate that changes in the coupling to ATP turnover and proton leak are correlated with developmental stage. The multiwell format of this assay enables the user to screen for the effects of drugs and environmental agents on bioenergetics in the zebrafish embryo with high sensitivity and reproducibility.
Generating String Test Data for Code Coverage

String data has traditionally been difficult for test data generation tools to generate. Of particular concern are strings that conform to a given grammar, since coverage of grammar productions does not guarantee high code coverage or fault-finding ability. We address this problem by deriving Java classes from the grammatical categories in the grammar, and then using a collection of deterministic and met heuristic techniques to generate strings from them. We compare the code coverage of these techniques and the standard conformance test suites for the grammars. We conclude that the various techniques have complementary strengths, and that they can be usefully used in combination.
Automated GUI Testing for J2ME Software Based on FSM

J2ME (Java 2 Micro Edition) software is playing a more and more significant role in embedded systems. However, with the growing complexity and function enhancement of J2ME software, its GUI (Graphical User Interface) testing is facing with great challenges. This paper proposes a new automated GUI testing method for J2ME software, which adopts an automated test case generation means based on FSM model and uses a unique program instrumentation scheme. Test cases are translated to the test script, which drives the J2ME program under test, and generates test report. In our experiments the automated testing system is implemented. Example Results show this testing method can automatically generate test cases for GUI based on the specification of the J2ME program and can also drive the running of the tests in the automated way. The testing method is more effective than the traditional ones; it has advantages, such as higher automation level, full fault-detection capability and general applicability. So, this method can see its applicable prospect in J2ME software testing.
The Visual Inspection of Surgical Tasks Using Machine Vision: Applications to Robotic Surgery

— In this paper, the feasibility of using machine vision to assess task completion in a surgical intervention is investigated, with the aim of incorporating vision based inspection in robotic surgery systems. The visually rich operative field presents a good environment for the development of automated visual inspection techniques in these systems, for a more comprehensive approach when performing a surgical task. As a proof of concept, machine vision techniques were used to distinguish the two possible outcomes i.e. satisfactory or unsatisfactory, of three primary surgical tasks involved in creating a burr hole in the skull, namely incision, retraction, and drilling. Encouraging results were obtained for the three tasks under consideration, which has been demonstrated by experiments on cadaveric pig heads. These findings are suggestive for the potential use of machine vision to validate successful task completion in robotic surgery systems. Finally, the potential of using machine vision in the operating theatre, and the challenges that must be addressed, are identified and discussed.
Remotely sensed evidence of tropical peatland conversion to oil palm

Rising global demands for food and biofuels are driving forest clearance in the tropics. Oil-palm expansion contributes to biodiversity declines and carbon emissions in Southeast Asia. However, the magnitudes of these impacts remain largely unquantified until now. We produce a 250-m spatial resolution map of closed canopy oil-palm plantations in the lowlands of Peninsular Malaysia (2 million ha), Borneo (2.4 million ha), and Sumatra (3.9 million ha). We demonstrate that 6% (or ≈880,000 ha) of tropical peatlands in the region had been converted to oil-palm plantations by the early 2000s. Conversion of peatswamp forests to oil palm led to biodiversity declines of 1% in Borneo (equivalent to four species of forest-dwelling birds), 3.4% in Sumatra (16 species), and 12.1% in Peninsular Malaysia (46 species). This land-use change also contributed to the loss of ≈140 million Mg of aboveground biomass carbon, and annual emissions of ≈4.6 million Mg of belowground carbon from peat oxidation. Additionally, the loss of peatswamp forests implies the loss of carbon sequestration service through peat accumulation, which amounts to ≈660,000 Mg of carbon annually. By 2010, 2.3 million ha of peatswamp forests were clear-felled, and currently occur as degraded lands. Reforestation of these clearings could enhance biodiversity by up to ≈20%, whereas oil-palm establishment would exacerbate species losses by up to ≈12%. To safeguard the region's biodiversity and carbon stocks, conservation and reforestation efforts should target Central Kalimantan, Riau, and West Kalimantan, which retain three-quarters (3.9 million ha) of the remaining peatswamp forests in Southeast Asia.
Energy-Efficient Power Loading for OFDM-Based Cognitive Radio Systems With Channel Uncertainties

In this paper, we propose a novel algorithm to optimize the energy efficiency (EE) of orthogonal frequency-division multiplexing (OFDM)-based cognitive radio systems under channel uncertainties. We formulate an optimization problem that guarantees a minimum required rate and a specified power budget for the secondary user (SU) while restricting the interference to primary users (PUs) in a statistical manner. The optimization problem is nonconvex, and it is transformed to an equivalent problem using the concept of fractional programming. Unlike all related works in the literature, we consider the effect of imperfect channel-state information (CSI) on the links between the SU transmitter and receiver pairs, and we additionally consider the effect of limited sensing capabilities of the SU. Since the interference constraints are met statistically, the SU transmitter does not require perfect CSI feedback from the PUs' receivers. Simulation results show that the EE deteriorates as the channel estimation error increases. Comparisons with relevant works from the literature show that the interference thresholds at the PUs' receivers can be severely exceeded and that the EE is slightly deteriorated if the SU does not account for spectrum sensing errors.
Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: A novel superfamily with a two‐layer sandwich architecture

TA0095 is a 96‐residue hypothetical protein from Thermoplasma acidophilum that exhibits no sequence similarity to any protein of known structure. Also, TA0095 is a member of the COG4004 orthologous group of unknown function found in Archaea bacteria. We determined its three‐dimensional structure by NMR methods. The structure displays an α/β two‐layer sandwich architecture formed by three α‐helices and five β‐strands following the order β1‐α1‐β2‐β3‐β4‐β5‐α2‐α3. Searches for structural homologs indicate that the TA0095 structure belongs to the TBP‐like fold, constituting a novel superfamily characterized by an additional C‐terminal helix. The TA0095 structure provides a fold common to the COG4004 proteins that will obviously belong to this new superfamily. Most hydrophobic residues conserved in the COG4004 proteins are buried in the structure determined herein, thus underlying their importance for structure stability. Considering that the TA0095 surface shows a large positively charged patch with a high degree of residue conservation within the COG4004 domain, the biological function of TA0095 and the rest of COG4004 proteins might occur through binding a negatively charged molecule. Like other TBP‐like fold proteins, the COG4004 proteins might be DNA‐binding proteins. The fact that TA0095 is shown to interact with large DNA fragments is in favor of this hypothesis, although nonspecific DNA binding cannot be ruled out.
Extracting action knowledge in security informatics

Actions are the primary way an entity interacts with other entities and acts on the external world. Action knowledge is of vital importance for behavior modeling, analysis and prediction in security informatics. In this paper, we present our approach to action knowledge extraction from Web textual data. Our approach is based on mutual bootstrapping with knowledge reasoning, which can acquire more action knowledge types and require less human participation compared with the related work. We evaluate the performance of our method and demonstrate its effectiveness through experiment.
Ultra-wideband (UWB) communications channel measurements - a tutorial review

This paper presents a comprehensive overview of ultra-wideband (UWB) measurements of all empirical data available on various fading properties of indoor radiowave communication channels. Our focus is on the essential propagation channel parameters mostly used in the physics-based models. This overview is based on more than 50 measurement campaigns from 24 working groups in different countries including North-American, European and Asian, and more than 100 references (in total) mostly books and journals articles on the UWB propagation channels. The measurement campaigns utilise different multipath propagation measurement techniques in various environments office, laboratory, corridor, open areas (classroom, reading room, auditorium) and residential building to measure the propagation channel metrics including power-loss, temporal and spatial characteristics and frequency characteristics. This tutorial overview is supported by an integrated summary on measurement results on each category. These analytic summaries lead to insights on UWB fading channel characterisation and modelling.
Interleukin-12 induction of Th1 cytokines is important for viral clearance in chronic hepatitis B.

Interleukin-12, a cytokine with an important role against intracellular pathogens, promotes Th1 cell development, cellmediated cytotoxicity, and interferon-gamma production. We investigated the immunoregulatory role of IL-12 in 72 chronic hepatitis B virus (HBV) carriers, 33 of whom were monitored longitudinally during interferon-alpha treatment. Serum levels of IL-12 heterodimer, IL-12 p40 subunit, IL-4, and Th1 cytokines were determined by specific ELISAs, and hepatitis B core antigen-specific T cell response by a proliferation assay. Chronic HBV carriers had higher serum levels of IL-12 and IL-12 p40 in comparison with controls (P < 0.01), suggesting that IL-12 production is not impaired. The longitudinal analysis revealed a further substantial increase (> 2.5x baseline level) of bioactive IL-12 and Th1 cytokines in patients who cleared HBV and seroconverted to anti- hepatitis B e, unlike the 23 nonresponders with persistent HBV replication (P < 0.01). The IL-12 peak followed the peak of hepatocytolysis by 9.8+/-2.8 wk and occurred either before or simultaneously with hepatitis B e seroconversion. Hepatitis B core antigen-specific T cell proliferation closely correlated with hepatocytolysis and increased significantly in all patients (8 responders and 15 nonresponders) who developed hepatitis flare, irrespective of the virological outcome. These results provide in vivo evidence that IL-12 may have an important role for viral clearance in chronic HBV infection.
Design and Analysis of Virtual MIMO-Based Low-Power Control Algorithm for WSN

In order to fully reduce network energy consumption, an improved virtual MIMO technique applied to small and medium scale isomorphism WSN is proposed. The life of WSN is prolonged by combining the energy- efficient virtual MIMO communication technology with the method that cluster heads are selected randomly and cyclically and the network energy load is balanced. Influencing factors on the virtual MIMO WSN energy-saving performance are analyzed carefully in this study, including the network size, node density and path loss factor. And the longest life of the network is used as optimization objective, the ratio of cluster head (the ratio of the number of cluster head required and the total number of nodes) which is a key parameter of WSN are optimized by genetic algorithm. Simulation results show that compared with LEACH this novel algorithm is more efficient to save energy of consumption and prolong the living time of the whole network when the parameters of network structure are properly selected.
Reduced NO-cGMP Signaling Contributes to Vascular Inflammation and Insulin Resistance Induced by High-Fat Feeding

Objective—Diet-induced obesity (DIO) in mice causes vascular inflammation and insulin resistance that are accompanied by decreased endothelial-derived NO production. We sought to determine whether reduced NO-cGMP signaling contributes to the deleterious effects of DIO on the vasculature and, if so, whether these effects can be blocked by increased vascular NO-cGMP signaling. Methods and Results—By using an established endothelial cell culture model of insulin resistance, exposure to palmitate, 100 &mgr;mol/L, for 3 hours induced both cellular inflammation (activation of IKK&bgr;–nuclear factor-&kgr;B) and impaired insulin signaling via the insulin receptor substrate–phosphatidylinositol 3-kinase pathway. Sensitivity to palmitate-induced endothelial inflammation and insulin resistance was increased when NO signaling was reduced using an endothelial NO synthase inhibitor, whereas endothelial responses to palmitate were blocked by pretreatment with either an NO donor or a cGMP analogue. To investigate whether endogenous NO-cGMP signaling protects against vascular responses to nutrient excess in vivo, adult male mice lacking endothelial NO synthase were studied. As predicted, both vascular inflammation (phosphorylated I&kgr;B&agr; and intercellular adhesion molecule levels) and insulin resistance (phosphorylated Akt [pAkt] and phosphorylated eNOS [peNOS] levels) were increased in endothelial NO synthase−/− (eNOS−/−) mice, reminiscent of the effect of DIO in wild-type controls. Next, we asked whether the vascular response to DIO in wild-type mice can be reversed by a pharmacological increase of cGMP signaling. C57BL6 mice were either fed a high-fat diet or remained on a low-fat diet for 8 weeks. During the final 2 weeks of the study, mice on each diet received either placebo or the phosphodiesterase-5 inhibitor sildenafil, 10 mg/kg per day orally. In high-fat diet–fed mice, vascular inflammation and insulin resistance were completely prevented by sildenafil administration at a dose that had no effect in mice fed the low-fat diet. Conclusion—Reduced signaling via the NO-cGMP pathway is a mediator of vascular inflammation and insulin resistance during overnutrition induced by high-fat feeding. Therefore, phosphodiesterase-5, soluble guanylyl cyclase, and other molecules in the NO-cGMP pathway (eg, protein kinase G) constitute potential targets for the treatment of vascular dysfunction in the setting of obesity.
An Architecture Approach for 3D Render Distribution using Mobile Devices in Real Time

Nowadays, video games such as Massively Multiplayer Online Game (MMOG) have become cultural mediators. Mobile games contribute to a large number of downloads and potential benefits in the applications market. Although processing power of mobile devices increases the bandwidth transmission, a poor network connectivity may bottleneck Gaming as a Service (GaaS). In order to enhance performance in digital ecosystem, processing tasks are distributed among thin client devices and robust servers. This research is based on the method �divide and rule�, that is, volumetric surfaces are subdivided using a tree-KD of sequence of scenes in a game, so reducing the surface into small sets of points. Reconstruction efficiency is improved, because the search of data is performed in local and small regions. Processes are modeled through a finite set of states that are built using Hidden Markov Models with domains configured by heuristics. Six test that control the states of each heuristic, including the number of intervals are carried out to validate the proposed model. This validation concludes that the proposed model optimizes response frames per second, in a sequence of interactions.
Reliability , fairness and predictive validity of committee peer review Evaluation of the selection of post-graduate fellowship holders by the Boehringer Ingelheim Fonds

In science, peer review is the oldest and best established method of assessing manuscripts, applications for research fellowships and research grants. However, the fairness of peer review, its reliability and whether it achieves its aim to select the best science and scientists has often been questioned. Here we present the first comprehensive study on committee peer review for the selection of doctoral (Ph.D.) and post-doctoral research fellowships. We analysed the selection process of the Boehringer Ingelheim Fonds, a foundation for the promotion of basic research in biomedicine, with regard to its reliability, fairness and predictive validity – the three quality criteria for professional evaluations. We analysed a total of 2,697 applications, 1,954 for doctoral and 743 for post-doctoral fellowships. In 76% of the cases, the decision whether to award a scholarship or not was characterized by agreement between reviewers. Similar figures for reliability were reported for the grant selection processes of other major funding agencies. With regard to fairness, we analysed whether potential sources of bias, i.e. gender, nationality, discipline and institutional affiliation, could have influenced the decisions. For post-doctoral fellowships, no statistically significant influence of any of these variables could be observed. In applications for a doctoral fellowship, evidence of a gender, discipline and institutional bias, but not of a nationality bias, was found. We therefore present some proposals for optimizing committee peer review. The most important aspect of our study was to investigate the predictive validity of the process, i.e. whether the Foundation achieves its aim to select the best young scientists. Our bibliometric analysis showed that this is indeed the case and that the selection process is thus highly valid: research articles from Boehringer Ingelheim Fonds fellows are cited considerably more often than the »average« publication in the Institute for Scientific Information (ISI, Philadelphia, PA, USA) journal sets »Multidisciplinary«, »Molecular Biology & Genetics«, and »Biology & Biochemistry«. These sets include journals covering the research fields in which most of the fellows publish.
Test cost reduction for multiple-voltage designs with bridge defects through Gate-Sizing

Multiple-voltage is an effective dynamic power reduction design technique. Recent research has shown that testing for resistive bridging faults in such designs requires more than one voltage setting for 100% defect coverage; however switching between several supply voltage settings has a detrimental impact on the overall cost of test. This paper proposes an effective Gate Sizing technique for reducing test cost of multi-Vdd designs with bridge defects. Using synthesized ISCAS benchmarks and a parametric fault model, experimental results show that for all the circuits, the proposed technique achieves 100% defect coverage at a single Vdd setting; in addition it has a lower overhead than the recently proposed test point insertion technique in terms of timing, area and power.
DLDR: Deep Linear Discriminative Retrieval for Cultural Event Classification from a Single Image

In this paper we tackle the classification of cultural events from a single image with a deep learning based method. We use convolutional neural networks (CNNs) with VGG-16 architecture [17], pretrained on ImageNet or the Places205 dataset for image classification, and fine-tuned on cultural events data. CNN features are robustly extracted at 4 different layers in each image. At each layer Linear Discriminant Analysis (LDA) is employed for discriminative dimensionality reduction. An image is represented by the concatenated LDA-projected features from all layers or by the concatenation of CNN pooled features at each layer. The classification is then performed through the Iterative Nearest Neighbors-based Classifier (INNC) [20]. Classification scores are obtained for different image representation setups at train and test. The average of the scores is the output of our deep linear discriminative retrieval (DLDR) system. With 0.80 mean average precision (mAP) DLDR is a top entry for the ChaLearn LAP 2015 cultural event recognition challenge.