Miracle-dz/UniFAR-FTUs huggingface dataset:
Inhibition of neointima hyperplasia of mouse vein grafts by locally applied suramin.

BACKGROUND Saphenous vein grafts are widely used for aortocoronary bypass surgery as treatment for severe atherosclerosis and often are complicated by subsequent occlusion of the graft vessel. METHODS AND RESULTS We described a mouse model of venous bypass graft arteriosclerosis that can be effectively retarded by locally applied suramin, a growth factor receptor antagonist. Mouse isogeneic vessels of the vena cava veins pretreated with suramin were grafted end to end into the carotid arteries and enveloped with a mixture of suramin (1 mmol/L) and pluronic-127 gel. In the untreated group, vessel wall thickening was observed as early as 1 week after surgery and progressed to 4-fold and 10-fold the original thickness in grafted veins at 4 and 8 weeks, respectively. Pluronic-127 gel alone did not influence neointima formation. Suramin treatment reduced the neointima hyperplasia 50% to 70% compared with untreated controls. Immunohistochemical studies demonstrated that a significant proliferation of vascular smooth muscle cells (SMCs) constituted neointimal lesions between 4 and 8 weeks. The majority of SMCs expressed platelet-derived growth factor (PDGF) receptors-alpha and -beta, which were significantly reduced by suramin treatment. In vitro studies indicated that suramin completely blocked PDGF receptor activation or phosphorylation stimulated by PDGF-AB, inhibited activation of mitogen-activated protein kinase (ERK) kinases (MEK1/2) and ERK1/2, and abrogated transcription factor AP-1 DNA-binding activity. CONCLUSIONS Suramin inhibited SMC migration and proliferation in vivo and in vitro by blocking PDGF-initiated PDGF receptor and MAPK-AP-1 signaling. These findings indicate that locally applied suramin is effective in a mouse model of venous bypass graft arteriosclerosis.
Microbial Diversity Across an Oxygen Gradient Using Large-scale Phylogenetic-based Analysis of Marine Metagenomes

iv ACKNOWLEDGMENTS v LIST OF FIGURES vi LIST OF TABLES viii LIST OF EQUATIONS ix INTRODUCTION 1 CHAPTER 1: Completion of the Phylogenetic Analysis Workflow 5 INTRODUCTION 5 METHODS 11 RESULTS 15 CONCLUSIONS 19 CHAPTER 2: PAW/DAP Capabilities & A New Study on Diversity 20 INTRODUCTION 20 METHODS 24 RESULTS & DISSCUSSION 27 CONCLUSIONS 46 FUTURE DIRECTIONS 47 APPENDIX: 54
Inflammatory Stimuli Regulate Caspase Substrate Profiles*

The inflammatory caspases, human caspases-1, -4, and -5, proteolytically modulate diverse physiological outcomes in response to proinflammatory signals. Surprisingly, only a few substrates are known for these enzymes, including other caspases and the interleukin-1 family of cytokines. To more comprehensively characterize inflammatory caspase substrates, we combined an enzymatic N-terminal enrichment method with mass spectrometry-based proteomics to identify newly cleaved proteins. Analysis of THP-1 monocytic cell lysates treated with recombinant purified caspases identified 82 putative caspase-1 substrates, three putative caspase-4 substrates, and no substrates for caspase-5. By contrast, inflammatory caspases activated in THP-1 cells by mimics of gout (monosodium urate), bacterial infection (lipopolysaccharide and ATP), or viral infection (poly(dA·dT)) were found to cleave only 27, 16, and 22 substrates, respectively. Quantitative stable isotope labeling with amino acids in cell culture (SILAC) comparison of these three inflammatory stimuli showed that they induced largely overlapping substrate profiles but different extents of proteolysis. Interestingly, only half of the cleavages found in response to proinflammatory stimuli were contained within our set of 82 in vitro cleavage sites. These data provide the most comprehensive set of caspase-1-cleaved products reported to date and indicate that caspases-4 and -5 have far fewer substrates. Comparisons between the in vitro and in vivo data highlight the importance of localization in regulating inflammatory caspase activity. Finally, our data suggest that inducers of inflammation may subtly alter caspase-1 substrate profiles.
Robust Transceiver Design for MIMO-OFDM Systems Based on Cluster Water-Filling

In this paper, robust transceiver designs for point-to-point MIMO-OFDM systems are investigated. A general performance metric of weighted mean-square-error (MSE) minimization is adopted as the optimization objective function. Exploiting the signal structure of point-to-point MIMO-OFDM systems, a simple and readily comprehensive derivation procedure for the optimal solution is given. It is revealed that for the optimal robust transceiver design the solution is an interesting variant of the famous water-filling solution, which is named as cluster water-filling. This solution is significantly different from that of the robust transceiver design over flat fading channels and its counterpart with perfect channel state information (CSI) as the water-filling bottoms are also variables to be optimized among different subcarriers. Finally, the simulation result demonstrates the performance advantages of the proposed robust design.
Simulation of Facial Muscle Actions Based on Rational Free Form Deformations

This paper describes interactive facilities for simulating abstract muscle actions using Rational Free Form Deformations (RFFD). The particular muscle action is simulated as the displacement of the control points of the control‐unit for an RFFD defined on a region of interest. One or several simulated muscle actions constitute a Minimum Perceptible Action (MPA), which is defined as the atomic action unit, similar to Action Unit (AU) of the Facial Action Coding System (FACS), to build an expression.
Effect of inter-crystal scatter events on coincidence detection in LabPET scanners

Compton scattering of gamma photons can give rise to inter-crystal crosstalk in detector arrays for positron emission tomography (PET). PET systems made of pixelated detectors with individual readout can recover inter-crystal scatter (ICS) events in the list-mode data file, but these events are generally ignored since their inclusion in the image reconstruction process leads to undesirable image noise. For such systems, including lines-of-response (LORs) resulting from triple events increases detection efficiency, but at the expense of degrading image quality. Therefore, it is important to understand the various processes contributing to triple coincidences to underline neglected sources of noise counteracting the benefit of ICS inclusion. It was found that a main source of mispositioned LORs is caused by triple randoms consisting of a true coincidence with a single detection. Limiting the contribution of these triple randoms when recovering ICS events resulted in improvements of image quality.
A Numerical Example on the Principles of Stochastic Discrimination

Studies on ensemble methods for classication suffer from the difculty of modeling the complementary strengths of the components. Kleinberg’s theory of stochastic discrimination (SD) addresses this rigorously via mathematical notions of enrichment, uniformity, and projectability of a model ensemble. We explain these concepts via a very simple numerical example that captures the basic principles of the SD theory and method. We focus on a fundamental symmetry in point set covering that is the key observation leading to the foundation of the theory. We believe a better understanding of the SD method will lead to developments of better tools for analyzing other ensemble methods.
Runtime dependence computation and execution of loops on heterogeneous systems

GPUs have been used for parallel execution of DOALL loops. However, loops with indirect array references can potentially cause cross iteration dependences which are hard to detect using existing compilation techniques. Applications with such loops cannot easily use the GPU and hence do not benefit from the tremendous compute capabilities of GPUs. In this paper, we present an algorithm to compute at runtime the cross iteration dependences in such loops. The algorithm uses both the CPU and the GPU to compute the dependences. Specifically, it effectively uses the compute capabilities of the GPU to quickly collect the memory accesses performed by the iterations by executing the slice functions generated for the indirect array accesses. Using the dependence information, the loop iterations are levelized such that each level contains independent iterations which can be executed in parallel. Another interesting aspect of the proposed solution is that it pipelines the dependence computation of the future level with the actual computation of the current level to effectively utilize the resources available in the GPU. We use NVIDIA Tesla C2070 to evaluate our implementation using benchmarks from Polybench suite and some synthetic benchmarks. Our experiments show that the proposed technique can achieve an average speedup of 6.4x on loops with a reasonable number of cross iteration dependences.
Shear Modulus Estimation on Vastus Intermedius of Elderly and Young Females over the Entire Range of Isometric Contraction

Elderly people often suffer from sarcopenia in their lower extremities, which gives rise to the increased susceptibility of fall. Comparing the mechanical properties of the knee extensor/flexors on elderly and young subjects is helpful in understanding the underlying mechanisms of the muscle aging process. However, although the stiffness of skeletal muscle has been proved to be positively correlated to its non-fatiguing contraction intensity by some existing methods, this conclusion has not been verified above 50% maximum voluntary contraction (MVC) due to the limitation of their measurement range. In this study, a vibro-ultrasound system was set up to achieve a considerably larger measurement range on muscle stiffness estimation. Its feasibility was verified on self-made silicone phantoms by comparing with the mechanical indentation method. The system was then used to assess the stiffness of vastus intermedius (VI), one of the knee extensors, on 10 healthy elderly female subjects (56.7±4.9 yr) and 10 healthy young female subjects (27.6±5.0 yr). The VI stiffness in its action direction was confirmed to be positively correlated to the % MVC level (R2 = 0.999) over the entire range of isometric contraction, i.e. from 0% MVC (relaxed state) to 100% MVC. Furthermore, it was shown that there was no significant difference between the mean VI shear modulus of the elderly and young subjects in a relaxed state (p>0.1). However, when performing step isometric contraction, the VI stiffness of young female subjects was found to be larger than that of elderly participants (p<0.001), especially at the relatively higher contraction levels. The results expanded our knowledge on the mechanical property of the elderly’s skeletal muscle and its relationship with intensity of active contraction. Furthermore, the vibro-ultrasound system has a potential to become a powerful tool for investigating the elderly’s muscle diseases.
Improving the Accuracy and Efficiency of MAP Inference for Markov Logic

In this work we present Cutting Plane Inference (CPI), a Maximum A Posteriori (MAP) inference method for Statistical Relational Learning. Framed in terms of Markov Logic and inspired by the Cutting Plane Method, it can be seen as a meta algorithm that instantiates small parts of a large and complex Markov Network and then solves these using a conventional MAP method. We evaluate CPI on two tasks, Semantic Role Labelling and Joint Entity Resolution, while plugging in two different MAP inference methods: the current method of choice for MAP inference in Markov Logic, MaxWalkSAT, and Integer Linear Programming. We observe that when used with CPI both methods are significantly faster than when used alone. In addition, CPI improves the accuracy of MaxWalkSAT and maintains the exactness of Integer Linear Programming.
Another look at the behaviors of novice programmers

This paper reports on the progress of an NSF funded research project investigating the development practices of students in introductory programming courses. In previous work, we describe our extension of the BlueJ IDE to capture events associated with program development. Here we report on data collected during the Fall 2007 and Spring 2008 semesters on CS 1 students. In particular, we show that our data analysis independently confirms the results obtained in separate studies by Jadud [3, 2]. In addition we use our empirical evidence to discern some higher level "patterns" of beginning student programming behaviors including potential cheating and the impact on success of students starting projects late.
BSS: Blockchain security over software defined network

One of the major concerns on today's Software-Defined Network (SDN) is to enhance its security. Files sharing in SDN can be made much more secured against fraudulent activities by the implementation of blockchain technology. When the privacy of network's users is increased, the reliability of system increases correspondingly. Blockchain Security over SDN (BSS) is proposed which protects privacy and availability of resources against non-trusting members. Mininet emulator is used for simulating custom SDN network topology. OpenDaylight controller is integrated with OpenStack controller. For cloud data storage, OpenStack platform is used. For testing purpose of Blockchain, Pyethereum tester tool under Ethereum platform is implemented. Serpent programming is used for creating contract in the blockchain. BSS facilitates files sharing among SDN users in distributed peer-to-peer basis using OpenStack as a cloud storage platform.
Balanced energy optimization

Summary form only given. Energy efficiency is now the number one issue for many applications, determining weight and cost, and constraining system performance. Many techniques have been developed to minimize the dynamic and static power consumed by digital designs without any impact on functionality. To achieve further savings it is necessary to employ methods that do constrain functionality in some way. The designer must then balance increased energy efficiency with the functional implications of those techniques. In communications systems non-zero error rates are accommodated and corrected in order to reduce power. In digital designs it is also possible to accept and correct errors generated when worst case timing paths exceed the clock interval. This allows the design to be operated beyond the worst case point at a reduced voltage to save energy. The increased energy efficiency must then be balanced against a decrease in determinism and the addition of error detection and correction structures. Processing scalability can also be employed to increase energy efficiency for workloads which vary dynamically. In single processor system this can be achieved using voltage and frequency scaling, and in multi-processor systems this can be supplemented with adaptive shutdown of unused processors. Scalability does imply a loss of system responsiveness when workloads transition from low to high levels, and this must be balanced against the increased energy efficiency achieved. Power efficiency can also be increased by optimising a processor for the application it is intended to run. By analyzing the algorithms to be executed it is possible to create a processor tailored to its workload. This loss of generality and flexibility must be balanced against the increased energy efficiency of a customized implementation. This talk describes work which ARM and its partners are doing to balance energy efficiency with functionality to create optimized designs.
Staying Current Mechanisms in cardiovascular diseases : how useful are medical textbooks , eMedicine , and YouTube ?

Azer SA. Mechanisms in cardiovascular diseases: how useful are medical textbooks, eMedicine, and YouTube? Adv Physiol Educ 38: 124–134, 2014; doi:10.1152/advan.00149. 2013. —The aim of this study was to assess the contents of medical textbooks, eMedicine (Medscape) topics, and YouTube videos on cardiovascular mechanisms. Medical textbooks, eMedicine articles, and YouTube were searched for cardiovascular mechanisms. Using appraisal forms, copies of these resources and videos were evaluated independently by three assessors. Most textbooks were brief in explaining mechanisms. Although the overall average percentage committed to cardiovascular mechanisms in physiology textbooks (n 7) was 16.1% and pathology textbooks (n 4) was 17.5%, there was less emphasis on mechanisms in most internal medicine textbooks (n 6), with a total average of 6.9%. In addition, flow diagrams explaining mechanisms were lacking. However, eMedicine topics (n 48) discussed mechanisms adequately in 22.9% (11 of 48) topics, and the percentage of content allocated to cardiovascular mechanisms was higher (15.8%, 46.2 of 292) compared with that of any internal medicine textbooks. Only 29 YouTube videos fulfilled the inclusion criteria. Of these, 16 YouTube were educationally useful, scoring 14.1 0.5 (mean SD). The remaining 13 videos were not educationally useful, scoring 6.1 1.7. The concordance between the assessors on applying the criteria measured by score was in the range of 0.55– 0.96. In conclusion, despite the importance of mechanisms, most textbooks and YouTube videos were deficient in cardiovascular mechanisms. eMedicine topics discussed cardiovascular mechanisms for some diseases, but there were no flow diagrams or multimedia explaining mechanisms. These deficiencies in learning resources could add to the challenges faced by students in understanding cardiovascular mechanisms.
BEYOND LIFE IN SCHOOLS

This research attempts to explore the possibility of new discursive space, and resistance strategy and tactics in the conflict and gap between the discourse of the school system and the life world of educators. Through sketching their own life stories, educators in this research represent the border situation of their life world and the education process in which they actualize their subjectivity and revive their passion in teaching. It is found that through the process of speaking out and interpretation, a public sphere of intimate dialogues could be created, where hybridity and diversity of citizenry and the meaning of education praxis could be understood. The researchers are also taking part in an illuminating and emancipative education processes in which the researchers and the participants are reconstructing each other into ethical subjects.
Processing flows of information: From data stream to complex event processing

A large number of distributed applications requires continuous and timely processing of information as it flows from the periphery to the center of the system. Examples include intrusion detection systems which analyze network traffic in real-time to identify possible attacks; environmental monitoring applications which process raw data coming from sensor networks to identify critical situations; or applications performing online analysis of stock prices to identify trends and forecast future values. Traditional DBMSs, which need to store and index data before processing it, can hardly fulfill the requirements of timeliness coming from such domains. Accordingly, during the last decade, different research communities developed a number of tools, which we collectively call Information flow processing (IFP) systems, to support these scenarios. They differ in their system architecture, data model, rule model, and rule language. In this article, we survey these systems to help researchers, who often come from different backgrounds, in understanding how the various approaches they adopt may complement each other. In particular, we propose a general, unifying model to capture the different aspects of an IFP system and use it to provide a complete and precise classification of the systems and mechanisms proposed so far.
The effects of groups' variety and disparity on groups' cognitive complexity

This study examined the influence of group diversity conceptualized as disparity and as variety on group cognitive complexity. Data on individual cognitive complexity and group cognitive complexity were collected in 44 groups using a conceptual mapping technique. Also data on the quality of teamwork processes and satisfaction were collected using an individual questionnaire. The results indicate that (a) gender variety has a positive impact on group cognitive complexity, (b) cognitive disparity has a negative impact on group cognitive complexity, and (c) groups with a high average individual cognitive complexity have the highest cognitive complexity as a group only if the quality of their interactions is high.
Immigrant Assimilation, Trust and Social Capital

Trust is a crucial component of social capital. We use an experimental moonlighting game with a representative sample of the U.S. population, oversampling immigrants, to study trust, positive, and negative reciprocity between first-generation immigrants and native-born Americans as a measure of immigrant assimilation. We also survey subjects in order to relate trusting and trustworthy behavior with demographic characteristics and traditional, survey-based measures of social capital. We find that immigrants are as trusting as native-born U.S. citizens when faced with another native-born citizen, but do not trust other immigrants. Immigrants appear to be less trustworthy overall but this finding disappears when we control for demographic variables and the amount sent by the first mover. The length of time an immigrant has been a naturalized U.S. citizen appears to increase trustworthiness but does not affect trusting behavior. Women and older people are less likely to trust, but no more or less trustworthy.
The New Handbook of Methods in Nonverbal Behavior Research

Introduction BASIC RESEARCH METHODS AND PROCEDURES 2. Measuring facial action 3. Vocal expression of affect 4. Proxemics, kinesics, and gaze 5. Conducting judgment studies: some methodological issues RESEARCH APPLICATIONS IN NONVERBAL BEHAVIOR 6. Nonverbal behavior and interpersonal sensitivity 7. Nonverbal behavior in education 8. Nonverbal behavior and psychopathology 9. Research methods in detecting deception research 10. Nonverbal communication coding systems of committed couples 11. Macrovariables in affective expression in women with breast cancer participating in support groups SUPPLEMENTARY MATERIALS 12. Technical issues in recording nonverbal behavior Appendix: Methodological issues in studying nonverbal behavior