Miracle-dz/UniFAR-FTUs huggingface dataset:
Experience from Porting Complex Algorithms on Heterogeneous Multi-Core Systems

Advanced Driving Assistance Systems (ADAS) are intended to improve driving safety, so they have to process large amount of data within real time constraints. To achieve the satisfying execution speed, data processing is scheduled to multiple processing units. Multi-core systems are widely used to increase the execution speed of a set of programs. Besides, some of those programs can be realized as a set of tasks. ADAS algorithms that run on a multi-core system-on-chip (SoC) are decomposed to multiple modules in order to support the parallelism of complex data processing. This paper presents an experience from distributing algorithm modules to processing elements (PEs) with various architectures. Each algorithm module runs as a task on a processor core which has the most appropriate architecture for that kind of work.
PCL–HA microscaffolds for in vitro modular bone tissue engineering

The evolution of microscaffolds and bone‐bioactive surfaces is a pivotal point in modular bone tissue engineering. In this study, the design and fabrication of porous polycaprolactone (PCL) microscaffolds functionalized with hydroxyapatite (HA) nanoparticles by means of a bio‐safe and versatile thermally‐induced phase separation process is reported. The ability of the as‐prepared nanocomposite microscaffolds to support the adhesion, growth and osteogenic differentiation of human mesenchymal stem cells (hMSCs) in standard and osteogenic media and using dynamic seeding/culture conditions was investigated. The obtained results demonstrated that the PCL–HA nanocomposite microparticles had an enhanced interaction with hMSCs and induced their osteogenic differentiation, even without the exogenous addition of osteogenic factors. In particular, calcium deposition, alizarin red assay, histological analysis, osteogenic gene expression and collagen I secretion were assessed. The results of these tests demonstrated the formation of bone microtissue precursors after 28 days of dynamic culture. These findings suggest that PCL–HA nanocomposite microparticles represent an excellent platform for in vitro modular bone tissue engineering. Copyright © 2015 John Wiley & Sons, Ltd.
Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties

We present a new clustering algorithm by proposing a convex relaxation of hierarchical clustering, which results in a family of objective functions with a natural geometric interpretation. We give efficient algorithms for calculating the continuous regularization path of solutions, and discuss relative advantages of the parameters. Our method experimentally gives state-of-the-art results similar to spectral clustering for non-convex clusters, and has the added benefit of learning a tree structure from the data.
The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and Its Functional Metagenome

Multiple environmental factors induce dysbiosis in the gut microbiome and cause a variety of human diseases. Previously, we have first demonstrated that arsenic alters the composition of the gut microbiome. However, the functional impact of arsenic on the gut microbiome has not been adequately assessed, particularly at environmentally relevant concentrations. In this study, we used 16S rRNA sequencing and metagenomics sequencing to investigate how exposure to 100 ppb arsenic for 13 weeks alters the composition and functional capacity of the gut microbiome in mice. Arsenic exposure altered the alpha and beta diversities as well as the composition profile of the gut microbiota. Metagenomics data revealed that the abundances of genes involved in carbohydrate metabolism, especially pyruvate fermentation, short-chain fatty acid synthesis, and starch utilization, and were significantly changed. Moreover, lipopolysaccharide biosynthesis genes, multiple stress response genes, and DNA repair genes were significantly increased in the gut microbiome of arsenic-exposed mice. The genes involved in the production or processing of multiple vitamins, including folic acid and vitamins B6, B12, and K2, were also enriched in arsenic-treated mice. In, addition, genes involved in multidrug resistance and conjugative transposon proteins were highly increased after treatment with arsenic. In conclusion, we demonstrate that arsenic exposure, at an environmentally relevant dose, not only perturbed the communal composition of the gut microbiome but also profoundly altered a variety of important bacterial functional pathways.
VIPER: a web application for rapid expert review of variant calls

Abstract Summary With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure. We developed the Variant InsPector and Expert Rating tool (VIPER) to speed up this process by integrating the Integrative Genomics Viewer into a web application. Analysts can then quickly iterate through variants, apply filters and make decisions based on the generated images and variant metadata. VIPER was successfully employed in analyses with manual inspection of more than 10 000 calls. Availability and implementation VIPER is implemented in Java and Javascript and is freely available at https://github.com/MarWoes/viper. Supplementary information Supplementary data are available at Bioinformatics online.
Bradykinin Potentiation by Angiotensin-(1-7) and ACE Inhibitors Correlates With ACE C- and N-Domain Blockade

Abstract—ACE inhibitors block B2 receptor desensitization, thereby potentiating bradykinin beyond blocking its hydrolysis. Angiotensin (Ang)-(1-7) also acts as an ACE inhibitor and, in addition, may stimulate bradykinin release via angiotensin II type 2 receptors. In this study we compared the bradykinin-potentiating effects of Ang-(1-7), quinaprilat, and captopril. Porcine coronary arteries, obtained from 32 pigs, were mounted in organ baths, preconstricted with prostaglandin F2&agr;, and exposed to quinaprilat, captopril, Ang-(1-7), and/or bradykinin. Bradykinin induced complete relaxation (pEC50=8.11±0.07, mean±SEM), whereas quinaprilat, captopril, and Ang-(1-7) alone were without effect. Quinaprilat shifted the bradykinin curve to the left in a biphasic manner: a 5-fold shift at concentrations that specifically block the C-domain (0.1 to 1 nmol/L) and a 10-fold shift at concentrations that block both domains. Captopril and Ang-(1-7) monophasically shifted the bradykinin curve to the left, by a factor of 10 and 5, respectively. A 5-fold shift was also observed when Ang-(1-7) was combined with 0.1 nmol/L quinaprilat. Repeated exposure of porcine coronary arteries to 0.1 &mgr;mol/L bradykinin induced B2 receptor desensitization. The addition of 10 &mgr;mol/L quinaprilat or Ang-(1-7) to the bath, at a time when bradykinin alone was no longer able to induce relaxation, fully restored the relaxant effects of bradykinin. Angiotensin II type 1 or 2 receptor blockade did not affect any of the observed effects of Ang-(1-7). In conclusion, Ang-(1-7), like quinaprilat and captopril, potentiates bradykinin by acting as an ACE inhibitor. Bradykinin potentiation is maximal when both the ACE C- and N-terminal domains are inhibited. The inhibitory effects of Ang-(1-7) are limited to the ACE C-domain, raising the possibility that Ang-(1-7) synergistically increases the blood pressure-lowering effects of N-domain-specific ACE inhibitors.
Insulin Resistance in Youth Without Diabetes Is Not Related to Muscle Mitochondrial Dysfunction

Context Obesity, insulin resistance (IR), and diabetes are increasing in youth, especially in girls. IR is associated with muscle mitochondrial dysfunction in youth and adults with diabetes. However, it is unknown whether this relationship is present in youth prior to development of diabetes. Objective Assess IR and mitochondrial function, including sex differences, in nondiabetic youth. Design Cross-sectional study of youth in the Exploring Perinatal Outcomes among Children, Resistance to InSulin in Type 1 And Type 2 diabetes, and Androgens and Insulin Resistance Study cohorts. Setting Academic medical university. Participants Two hundred seventy-five youth, 13 to 19 years old [43% males: 17.1 (16.52, 17.63) years, body mass index z-score (BMI-Z) 0.36, 64.7% Tanner 5; 57% females: 17.2 (16.43, 17.67) years, BMI-Z 0.72, 78.9% Tanner 5]. Interventions Fasting laboratories, oral glucose tolerance test, and 31P magnetic resonance spectroscopy. Main Outcome Measures IR [triglyceride:high-density lipoprotein (HDL) ratio, Matsuda index, and homeostasis model for insulin resistance (HOMA-IR)] and muscle mitochondrial function (adenosine 5'-diphosphate time constant and oxidative phosphorylation rate). Results Compared with males, females were more insulin resistant, with higher triglyceride:HDL ratio [1.95 (1.30, 2.79) vs 1.69 (1.21, 2.23), P = 0.042], HOMA-IR [3.18 (2.42, 4.39) vs 2.76 (2.02, 4.08), P = 0.035], and fasting free fatty acids (FFAs) and lower Matsuda score [3.98 (2.71, 5.96) vs 5.39 (3.43, 7.57), P < 0.001]. After adjustment for the higher BMI and Tanner stage and lower physical activity levels seen in females, there were no sex differences in mitochondrial function nor in any IR measure except FFAs. We did not find an association between measures of IR and mitochondrial function. Conclusions The greater IR seen in adolescent girls vs boys is mostly explained by differences in BMI and physical activity. Mitochondrial function does not appear to be related to IR in a large cohort of nondiabetic youth.
Performance Evaluation of the PowerChek MERS (upE & ORF1a) Real-Time PCR Kit for the Detection of Middle East Respiratory Syndrome Coronavirus RNA

Background Molecular detection of Middle East respiratory syndrome coronavirus (MERS-CoV) using real-time reverse transcription (rRT)-PCR assays is the method of choice for diagnosis of MERS. We evaluated the performance of the PowerChek MERS (upE & ORF1a) real-time PCR Kit (PowerChek MERS assay; Kogene Biotech, Korea) a one-step rRT-PCR assay for the qualitative detection of MERS-CoV. Methods We evaluated PowerChek MERS assay performance in comparison with nested RT-PCR and sequencing of the RNA-dependent RNA polymerase (RdRp) and N genes. To evaluate diagnostic sensitivity and specificity, 100 clinical specimens (50 positive and 50 negative for MERS-CoV) were simultaneously tested by using the PowerChek MERS and sequencing assays. Assay performance, including limit of detection and precision, was evaluated in vitro by using MERS-CoV RNA transcripts. Analytical specificity was evaluated with a diverse collection of 16 respiratory virus–positive clinical specimens and 14 respiratory bacterial isolates. Results The 95% limits of detection of the PowerChek MERS assay for the upE and the open rading frame (ORF)1a were 16.2 copies/µL and 8.2 copies/µL, respectively. No cross-reactivity was observed. The diagnostic sensitivity and specificity of the PowerChek MERS assay were both 100% (95% confidence interval, 91.1–100%). Conclusions The PowerChek MERS assay is a straightforward and accurate assay for detecting MERS-CoV RNA. The assay will be a useful tool for the rapid diagnosis of MERS and could prove especially important for MERS outbreak control.
Topology identification of sparse networks of continuous time systems

In this paper, topology identification of dynamic systems in the continuous time (CT) framework is considered. The main objective is to identify the direction of information flow and to estimate the transfer function of each node simultaneously. The output of each node is affected by the outputs of the other nodes along with transportation delay and noise. In contrast to the existing works which are in discrete setting, the current paper uses continuous orthonormal basis to represent the transfer functions. As the network is sparsely connected, the topology identification problem is defined as an estimation of a block-sparse signal from the measurements and a standard lo minimization algorithm known as the block orthogonal matching pursuit (BOMP) is used to identify the topology. The accuracy of the proposed method is demonstrated using data obtained from a system of interconnected tanks. A comparison with discrete time topology identification methods shows that the CT method is more robust and provides the exact topology with higher probability.
Automatic breast density classification using a convolutional neural network architecture search procedure

Breast parenchymal density is considered a strong indicator of breast cancer risk and therefore useful for preventive tasks. Measurement of breast density is often qualitative and requires the subjective judgment of radiologists. Here we explore an automatic breast composition classification workflow based on convolutional neural networks for feature extraction in combination with a support vector machines classifier. This is compared to the assessments of seven experienced radiologists. The experiments yielded an average kappa value of 0.58 when using the mode of the radiologists’ classifications as ground truth. Individual radiologist performance against this ground truth yielded kappa values between 0.56 and 0.79.
Metadata creation system for mobile images

The amount of personal digital media is increasing, and managing it has become a pressing problem. Effective management of media content is not possible without content-related metadata. In this paper we describe a content metadata creation process for images taken with a mobile phone. The design goals were to automate the creation of image content metadata by leveraging automatically available contextual metadata on the mobile phone, to use similarity processing algorithms for reusing shared metadata and images on a remote server, and to interact with the mobile phone user during image capture to confirm and augment the system supplied metadata. We built a prototype system to evaluate the designed metadata creation process. The main findings were that the creation process could be implemented with current technology and it facilitated the creation of semantic metadata at the time of image capture.
Direct Synthesis of Nanofibrous Nonwoven Carbon Components: Initial Observations, Capabilities, and Challenges

Widespread adoption of carbon nanomaterials has been hindered by inefficient production and utilization. A recently developed method has shown possibility to directly synthesize bulk nanostructured nonwoven materials from catalytically deposited carbon nanofibers (CNFs). The basic manufacturing scheme involves constraining carbon nanofiber growth to create three-dimensionally featured, macroscale products. Although previously demonstrated as a proof of concept, the possibilities and pitfalls of the method at a larger scale have not yet been explored. In this work, the basic foundation for using the constrained formation of fibrous nanostructures (CoFFiN) process is established by testing feasibility in larger volumes (as much as 2000% greater than initial experiments) and by noting the macroscale carbon growth characteristics. It has been found that a variety of factors contribute to determining the basic qualities of the macroscale fiber collection (nonwoven material), and there are tunable parameters at the catalytic and constraint levels. The results of this work have established that monolithic structures of nonwoven carbon nanofibers can be created with centimeter dimensions in a variety of crosssectional shapes. The only limit to scale noted is the tendency for nanofibers to entangle with one another during growth and self-restrict outward expansion to the mold walls. This may be addressed by pregrowing carbon before placement or selective placement of the catalyst in the mold. [DOI: 10.1115/1.4034609]
Semantics Guided Regression Test Cost Reduction

Software maintainers are faced with the task of regression testing: retesting a modified program on an often large number of test cases. The cost of regression testing can be reduced if the size of the program is reduced and if old test cases and results can be reused. Two complimentary algorithms for reducing the cost of regression testing are presented. The first produces a program called Differences that captures the semantic change between Certified, a previously tested program, and Modified, a changed version of Certified. It is more efficient to test Differences, because it omits unchanged computations. The program Differences is computed using a combination of program slices. The second algorithm identifies test cases for which Certified and Modified produce the same output and existing test cases that test new components in Modified. The algorithm is based on the notion of common execution patterns. Program components with common execution patterns have the same execution pattern during some call to their procedure. They are computed using a calling context slice. Whereas an interprocedural slice includes the program components necessary to capture all possible executions of a statement, a calling context slice includes only those program components necessary to capture the execution of a statement in a particular calling context. Together with Differences, it is possible to test Modified by running Differences on a smaller number of test cases. This is more efficient than running Modified on a large number of test cases. A prototype implementation has been built to examine and illustrate these algorithms.
Editor’s Highlight: Subvisible Aggregates of Immunogenic Proteins Promote a Th1-Type Response

Protein aggregation is associated with enhanced immunogenicity of biotherapeutics. As a result, regulatory guidelines recommend screening for aggregation during bioprocessing. However, the mechanisms underlying the enhanced immunogenicity of aggregates are poorly understood. In the investigations described herein, the immunogenicity in mice of a humanized single chain variable antibody fragment (scFv) purified after expression in Escherichia coli has been examined. Reproducible scFv aggregates were obtained within the subvisible particle size range (mean diameter 2 µm) using thermal and mechanical stresses. Intraperitoneal immunization of BALB/c strain mice with 1 mg/ml of aggregated or monomeric scFv induced similar IgG and IgG1 antibody responses. In contrast, aggregate preparations stimulated significantly higher levels of anti-scFv IgG2a antibody than did the monomer. In comparative studies, aggregates of ovalbumin (OVA) within the subvisible particle size range were prepared by stir stress, and their immunogenicity compared with that of monomeric OVA in mice. Aggregated and monomeric OVA induced similar anti-OVA IgG and IgG1 antibody responses, whereas IgG2a antibody levels were significantly higher in aggregate-immunized mice. Furthermore, cytokine profiles in supernatants taken from splenocyte-dendritic cell co-cultures were consistent with aggregated preparations inducing a T helper (Th) 1-type response. Aggregated proteins within the subvisible range were therefore shown to induce a preferential Th1 type response, whereas monomeric proteins elicited a selective Th2 response. These data indicate that protein aggregation can impact on both the vigor and quality of immune responses.
Cadaveric cardiosphere-derived cells can maintain regenerative capacity and improve the heart function of cardiomyopathy

ABSTRACT Objective: Cardiosphere-derived cells (CDCs) improve cardiac function and attenuate remodeling in ischemic and non-ischemic cardiomyopathy, and are currently obtained through myocardial biopsy. However, there is not any study on whether functional CDCs may be obtained through cadaveric autopsy with similar benefits in non-ischemic cardiomyopathy. Methods: Cardiac tissues from human or mouse cadavers were harvested, plated at 4°C, and removed at varying time points to culture human CDCs (CLH-EDCs) and mouse CDCs (CM-CDCs). The differentiation and paracrine effects of CDCs were also assessed. Furthermore, intramyocardial injection of cadaveric CM-CDCs was performed in an induced dilated cardiomyopathy (DCM) model. Results: With the extension of post mortem hours, the number of CLH-EDCs and CM-CDCs harvested from autopsy specimens decreased. The expressions of von Willebrand factor (VWF) and smooth muscle actin (SMA) on CDCs were gradually reduced, however, cardiac troponin I (TNI) expression increased in the 24 h group compared to the 0 h group. CLH-EDCs were also found to have similar paracrine function in the 24 h group compared to 0 h group. 8 weeks after CM-CDCs transplantion to the injured heart, mean left ventricular ejection fraction increased in both 0 h (64.99 ± 3.4%) and 24 h (62.99 ± 2.8%) CM-CDCs-treated groups as compared to the PBS treated group (53.64 ± 5.6 cm), with a decrease in left ventricular internal diastolic diameter (0.29 ± 0.08 cm and 0.32 ± 0.04 cm in 0 h and 24 h groups, vs. 0.41 ± 0.05 cm in PBS group). Conclusion: CDCs from cadaveric autopsy are highly proliferative and differentiative, and may be used as a source for allograft transplantation, in order to decrease myocardial fibrosis, attenuate left ventricular remodeling, and improve heart function in doxorubicin-induced non-ischemic cardiomyopathy.
Telephone‐assisted self‐help for parents of children with attention‐deficit/hyperactivity disorder who have residual functional impairment despite methylphenidate treatment: a randomized controlled trial

BACKGROUND Self-help parenting interventions have been shown to be effective in the management of children with attention-deficit/hyperactivity disorder (ADHD) and may be useful when there are barriers to face-to-face therapist-led parent trainings. Previous studies indicate that behavioral interventions might be a useful adjunct to medication in children with residual ADHD symptoms, and regarding comorbid oppositional symptoms and multiple domains of functional impairment. In the present study, we examined whether a telephone-assisted self-help (TASH) parenting behavioral intervention (written materials plus telephone counseling) enhanced the effects of methylphenidate treatment in children with ADHD. METHODS In this randomized controlled trial, parents of 103 school-aged children with ADHD and residual functional impairment despite methylphenidate treatment were randomly assigned to either the enhancement group, which received the TASH intervention as adjunct to routine clinical care (including continued medication), or to the active control group, which received routine clinical care only (including continued medication). Parent-completed outcome measures at baseline and at 12 months (postassessment) included functional impairment, ADHD symptoms, oppositional defiant disorder (ODD) symptoms, parenting behavior, and parental satisfaction with the intervention (ClinicalTrials.gov: NCT01660425; URL: https://clinicaltrials.gov/ct2/show/NCT01660425). RESULTS Intention-to-treat analyses of covariance (ANCOVAs), which controlled for baseline data, revealed significant and moderate intervention effects for ODD symptoms and negative parenting behavior at the postassessment, whereas per-protocol analyses additionally showed significant and moderate effects on functional impairment (primary outcome). Parents expressed high satisfaction with the program. CONCLUSIONS The TASH program enhances effects of methylphenidate treatment in families who complete the intervention. The discontinuation rate of about 30% and comparison between completing and discontinuing families suggest that the program may be more suitable for families with a higher educational level and fewer additional stresses.