Miracle-dz/UniFAR-FTUs huggingface dataset:
ImageCL: An image processing language for performance portability on heterogeneous systems

Modern computer systems typically conbine multicore CPUs with accelerators like GPUs for inproved performance and energy efficiency. However, these systems suffer from poor performance portability - code tuned for one device must be retuned to achieve high performance on another. Image processing is increasing in importance, with applications ranging from seismology and medicine to Photoshop. Based on our experience with medical image processing, we propose ImageCL, a high-level domain-specific language and source-to-source compiler, targeting heterogeneous hardware. ImageCL resembles OpenCL, but abstracts away performance optimization details, allowing the programmer to focus on algorithm development, rather than performance tuning. The latter is left to our source-to-source compiler and auto-tuner. From high-level ImageCL kernels, our source-to-source compiler can generate multiple OpenCL implementations with different optimizations applied. We rely on auto-tuning rather than machine models or expert programmer knowledge to determine which optimizations to apply, making our tuning procedure highly robust. Furthermore, we can generate high performing implementations for different devices from a single source code, thereby improving performance portability. We evaluate our approach on three image processing benchmarks, on different GPU and CPU devices, and are able to outperform other state of the art solutions in several cases, achieving speedups of up to 4.57x.
Mycoplasma fermentans Lipoprotein M161Ag-Induced Cell Activation Is Mediated by Toll-Like Receptor 2: Role of N-Terminal Hydrophobic Portion in its Multiple Functions1

M161Ag is a 43-kDa surface lipoprotein of Mycoplasma fermentans, serving as a potent cytokine inducer for monocytes/macrophages, maturing dendritic cells (DCs), and activating host complement on affected cells. It possesses a unique N-terminal lipo-amino acid, S-diacylglyceryl cysteine. The 2-kDa macrophage-activating lipopeptide-2 (MALP-2), recently identified as a ligand for Toll-like receptor 2 (TLR2), is derived from M161Ag. In this study, we identified structural motifs sustaining the functions of M161Ag using wild-type and unlipidated rM161Ag with (SP+) or without signal peptides (SP−). Because the SP+ rM161Ag formed dimers via 25Cys, we obtained a monomeric form by mutagenesis (SP+C25S). Only wild type accelerated maturation of human DCs as determined by the CD83/86 criteria, suggesting the importance of the N-terminal fatty acids for this function. Wild-type and the SP+ form of monomer induced secretion of TNF-α and IL-12 p40 by human monocytes and DCs. Either lipid or signal peptide at the N-terminal portion of monomer was required for expression of this function. In contrast, murine macrophages produced TNF-α in response to wild type, but not to any recombinant form of M161Ag, suggesting the species-dependent response to rM161Ag. Wild-type and both monomeric and dimeric SP+ forms possessed the ability to activate complement via the alternative pathway. Again, the hydrophobic portion was associated with this function. These results, together with the finding that macrophages from TLR2-deficient mice did not produce TNF-α in response to M161Ag, infer that the N-terminal hydrophobic structure of M161Ag is important for TLR2-mediated cell activation and complement activation.
Preparation and characterization of biocomposite films from kenaf-derived cellulose fibers and polylactic acid

The aim of this study was to produce kenaf derived cellulose-polylactic acid (KDCPLA) biocomposites and characterize its properties relevant to potential packaging application such as thermal properties and barrier properties against oxygen and water vapor. Other important bicomposite properties in the development of packaging material such as tensile and morphological analysis were also carried out. Kenaf bast fiber is a fiber which was used to derive cellulose via chlorination and mercerization processes. It was then designated as kenaf derived cellulose (KDC). The incorporation of KDC presents an alternative approach to achieve the intended properties. Thus, in this work, KDC loadings ranging from 0-60% were incorporated in the KDC-PLA biocomposite films. The KDC was found to be less thermal stable than the kenaf bast fiber. X-Ray Diffraction (XRD) spectrum revealed that the cellulose has relatively higher crystallinity index as compared to kenaf bast fiber which led to this phenomenon. In the case of biocomposite’s thermal stability, 6% lower degradation temperature was demonstrated when maximum 60% KDC incorporated in PLA matrix. The thermal properties of KDC-PLA biocomposite showed no major changes with KDC addition. This reflected by nearly unmodified crystallization temperature (Tc) of KDC-PLA biocomposite films. The additional loading of cellulose also shifted the melting temperature (Tm) value to the higher temperature. It means that by incorporating KDC into the PLA matrix have increases the melting point of biocomposite while percent of crystallinity (%Xc) showed no particular trend with additional loadings of KDC in biocomposite. With the additional KDC loading, the oxygen gas permeability was significantly reduced by 85% (shown by decrease in permeability value) but the water vapor permeability was increased by 91% for the highest KDC loading (60%). However the water vapor permeability is still acceptable as the value is within moderate water vapor permeability (50-100 g/m2/day). Composite properties on tensile strength and elongation at break were found reduced as compared to the neat PLA while tensile modulus was found increased showing that the stiffer biocomposite is produced with higher KDC loading. Proven with Environmental Scanning Electron Microscope (ESEM) micrograph, the reduced in tensile strength was due to weak interfacial adhesion between PLA matrix and KDC. Significant reduction in elongation at break suggested that a lower interfacial interaction effect and/or lack of optimum dispersion of KDC in biocomposite. This resulted biocomposite possibly has the potential application in the fruits and vegetables packaging field that require low oxygen gas permeability and moderate water vapor permeability.
A Viral Satellite RNA Induces Yellow Symptoms on Tobacco by Targeting a Gene Involved in Chlorophyll Biosynthesis using the RNA Silencing Machinery

Symptoms on virus-infected plants are often very specific to the given virus. The molecular mechanisms involved in viral symptom induction have been extensively studied, but are still poorly understood. Cucumber mosaic virus (CMV) Y satellite RNA (Y-sat) is a non-coding subviral RNA and modifies the typical symptom induced by CMV in specific hosts; Y-sat causes a bright yellow mosaic on its natural host Nicotiana tabacum. The Y-sat-induced yellow mosaic failed to develop in the infected Arabidopsis and tomato plants suggesting a very specific interaction between Y-sat and its host. In this study, we revealed that Y-sat produces specific short interfering RNAs (siRNAs), which interfere with a host gene, thus inducing the specific symptom. We found that the mRNA of tobacco magnesium protoporphyrin chelatase subunit I (ChlI, the key gene involved in chlorophyll synthesis) had a 22-nt sequence that was complementary to the Y-sat sequence, including four G-U pairs, and that the Y-sat-derived siRNAs in the virus-infected plant downregulate the mRNA of ChlI by targeting the complementary sequence. ChlI mRNA was also downregulated in the transgenic lines that express Y-sat inverted repeats. Strikingly, modifying the Y-sat sequence in order to restore the 22-nt complementarity to Arabidopsis and tomato ChlI mRNA resulted in yellowing symptoms in Y-sat-infected Arabidopsis and tomato, respectively. In 5′-RACE experiments, the ChlI transcript was cleaved at the expected middle position of the 22-nt complementary sequence. In GFP sensor experiments using agroinfiltration, we further demonstrated that Y-sat specifically targeted the sensor mRNA containing the 22-nt complementary sequence of ChlI. Our findings provide direct evidence that the identified siRNAs derived from viral satellite RNA directly modulate the viral disease symptom by RNA silencing-based regulation of a host gene.
Control of the Underactuated Inertia Wheel Inverted Pendulum for Stable Limit Cycle Generation

This paper deals with a control approach dedicated to stable limit cycle generation for underactuated mechanical systems. The proposed approach is based on partial nonlinear feedback linearization and dynamic control for optimal periodic reference trajectories tracking. The computation of the reference trajectories is performed in order to optimize the behavior of the whole dynamics of the system and especially its zero dynamics at the end of each cycle. Simulation results as well as experiments show the performance and the efficiency of the proposed control scheme.
Effects of dietary xylanase supplementation on performance and functional digestive parameters in broilers fed wheat‐based diets

&NA; This experiment was conducted to evaluate dietary xylanase supplementation in broilers wheat‐based diets on performance and functional digestive parameters including ileal digesta viscosity, apparent ileal digestibility, intestinal morphology and microflora, digestive enzyme activities, and excreta odor content. A total of 600 1‐day‐old Ross 308 male broilers with an initial average BW of 45 ± 0.6 g were randomly allotted into 4 treatments with 10 replicate pens per treatment and 15 broilers in each pen for 35 d. The 4 dietary treatments were wheat‐based diets and supplemented with 0, 1,875, 3,750, and 5,625 XU/kg xylanase. Xylanase supplementation improved (linear, P < 0.05) the body weight gain and decreased (linear, P < 0.05) the feed conversion ratio during d 1 to 18 and for the duration of the experiment. Dietary supplementation of xylanase led to a decrease (linear, P < 0.01) in ileal digesta viscosity. The apparent ileal digestibility of dry matter (DM), crude protein (CP), gross energy, and most amino acids (with the exception of Ile, Phe, Asp, Glu, and Pro) were increased (linear, P < 0.05) by xylanase supplementation. Increasing the dietary xylanase levels improved (linear, P < 0.05) the villus height and the ratio of villus height to crypt depth of the duodenum, jejunum, and ileum. In addition, inclusion of xylanase increased (linear, P < 0.05) the Lactobacillus numbers in the ileum and cecum, while decreased the ileal E. coli counts (linear, P < 0.01) and cecal E. coli populations (linear, P < 0.01; quadratic, P < 0.05). There were no significant differences (P > 0.05) in trypsin, amylase, and protease activities of small intestine among dietary treatments. Furthermore, xylanase supplementation reduced excreta NH3 (linear, P < 0.05; quadratic, P < 0.05) and total mercaptan (R.SH) (linear, P < 0.01) concentration. Taken together, dietary xylanase supplementation in broilers wheat‐based diets had beneficial effects on growth performance, apparent ileal digestibility of nutrients, intestinal morphology, and microflora balance. Furthermore, the xylanase could reduce the ileal digesta viscosity and excreta odor contents.
Distributed fault tolerance specification through the use of interface definitions

Fault tolerance can no longer be viewed as an exorbitant optional extra, but must be treated as an essential requirement in any distributed system. It is fair to say that if any distributed system is to operate for any contiguous interval of time without failure, a fault tolerant mechanism must be used. This paper reviews and discusses what extensions and functionality may be added to an interface definition language to allow for the description of four different fault tolerant mechanisms.
Sensitivity and Specificity of Procalcitonin to Determine Etiology of Diarrhea in Children Younger Than 5 Years

Aim: The aim of this study is to assess the sensitivity and specificity of procalcitonin to determine bacterial etiology of diarrhea. The examinees and methods: For this purpose we conducted the study comprising 115 children aged 1 to 60 months admitted at the Department of Pediatric Gastroenterology, Pediatric Clinic, divided in three groups based on etiology of the diarrhea that has been confirmed with respective tests during the hospitalization. Each group has equal number of patients – 35. The first group was confirmed to have bacterial diarrhea, the second viral diarrhea and the third extra intestinal diarrhea. The determination of procalcitonin has been established with the ELFA methods of producer B.R. A.H. M.S Diagnostica GmbH, Berlin, (Germany). Results: From the total number of 1130 patient with acute diarrhea procalcitonin was assessed in 105. 67 (63.8%) of these patient were male. More than one third (38.14%) of the children in our study were younger then 12 months. Approximately the same was the number of children 13-24 months (33 patients or 31.43%) and 25-60 months (32 patients or 30.43%). The mean value of PRC in children with viral diarrhea was 0.13±0.5 ng/mL in children with bacterial diarrhea was 5.3±4.9 ng/m Land in children with extra intestinal diarrhea was 1.7±2.8 ng/mL. When measured using ANOVA and Turkey HSD tests, results have shown the statistical significance when comparing viral with bacterial and extra intestinal diarrhea but were statistically insignificant when comparing bacterial and extra intestinal diarrhea. Conclusion: Procalcitonin is an important but not conclusive marker of bacterial etiology of acute diarrhea in children younger than 5 years.
Filter Design With Secrecy Constraints: The MIMO Gaussian Wiretap Channel

This paper considers the problem of filter design with secrecy constraints, where two legitimate parties (Alice and Bob) communicate in the presence of an eavesdropper (Eve) over a Gaussian multiple-input-multiple-output (MIMO) wiretap channel. This problem involves designing, subject to a power constraint, the transmit and the receive filters which minimize the mean-squared error (MSE) between the legitimate parties whilst assuring that the eavesdropper MSE remains above a certain threshold. We consider a general MIMO Gaussian wiretap scenario, where the legitimate receiver uses a linear zero-forcing (ZF) filter and the eavesdropper receiver uses either a ZF or an optimal linear Wiener filter. We provide a characterization of the optimal filter designs by demonstrating the convexity of the optimization problems. We also provide generalizations of the filter designs from the scenario where the channel state is known to all the parties to the scenario where there is uncertainty in the channel state. A set of numerical results illustrates the performance of the novel filter designs, including the robustness to channel modeling errors. In particular, we assess the efficacy of the designs in guaranteeing not only a certain MSE level at the eavesdropper, but also in limiting the error probability at the eavesdropper. We also assess the impact of the filter designs on the achievable secrecy rates. The penalty induced by the fact that the eavesdropper may use the optimal nonlinear receive filter rather than the optimal linear one is also explored in the paper.
Control of Promatrilysin (MMP7) Activation and Substrate-specific Activity by Sulfated Glycosaminoglycans*

Matrix metalloproteinases are maintained in an inactive state by a bond between the thiol of a conserved cysteine in the prodomain and a zinc atom in the catalytic domain. Once this bond is disrupted, MMPs become active proteinases and can act on a variety of extracellular protein substrates. In vivo, matrilysin (MMP7) activates pro-α-defensins (procryptdins), but in vitro, processing of these peptides is slow, with about 50% conversion in 8–12 h. Similarly, autolytic activation of promatrilysin in vitro can take up to 12–24 h for 50% conversion. These inefficient reactions suggest that natural cofactors enhance the activation and activity of matrilysin. We determined that highly sulfated glycosaminoglycans (GAG), such as heparin, chondroitin-4,6-sulfate (CS-E), and dermatan sulfate, markedly enhanced (>50-fold) the intermolecular autolytic activation of promatrilysin and the activity of fully active matrilysin to cleave specific physiologic substrates. In contrast, heparan sulfate and less sulfated forms of chondroitin sulfate did not augment matrilysin activation or activity. Chondroitin-2,6-sulfate (CS-D) also did not enhance matrilysin activity, suggesting that the presentation of sulfates is more important than the overall degree of sulfation. Surface plasmon resonance demonstrated that promatrilysin bound heparin (KD, 400 nm) and CS-E (KD, 630 nm). Active matrilysin bound heparin (KD, 150 nm) but less so to CS-E (KD, 60 μm). Neither form bound heparan sulfate. These observations demonstrate that sulfated GAGs regulate matrilysin activation and its activity against specific substrates.
The influence of social capital on health in eight former Soviet countries: why does it differ?

Background Previous research has identified the role of social capital in explaining variations in health in the countries of the former Soviet Union. This study explores whether the benefits of social capital vary among these countries and why. Methods The impact of micro social capital (trust, membership and social isolation) on individual health was estimated in each of eight former Soviet republics using instrumental variables to overcome methodological hazards such as endogeneity and reverse causality. Interactions with institutional variables (voice and accountability, effectiveness of the legal system, informal economy) and social protection variables (employment protection, old age and disability benefits, sickness and health benefits) were examined. Results Most social capital indicators, in most countries, are associated with better health but the magnitude and significance of the impact differ between countries. Some of this variation can be explained by interacting social capital indicators with measures of institutional quality, with membership of organisations bringing greater benefit for health in countries where civil liberties are stronger, whereas social isolation has more adverse consequences where there is a large informal economy. A lesser amount is explained by the interaction of social capital indicators with selected measures of social protection. Conclusion When considering interventions to improve social capital as a means of improving population health, it seems advisable to take into account the influence of macrocontextual variables, in order not to overstate or understate the likely impact of the intervention.
Ju n 19 98 Turbulent Decay of a Passive Scalar in Batchelor Limit : Exact Results from a Quantum-Mechanical Approach

We show that the decay of a passive scalar θ advected by a random incompressible flow with zero correlation time in Batchelor limit can be mapped exactly to a certain quantum-mechanical system with a finite number of degrees of freedom. The Schrödinger equation is derived and its solution is analyzed for the case when at the beginning the scalar has Gaussian statistics with correlation function of the form e−|x−y| 2 . Any equal-time correlation function of the scalar can be expressed via the solution to the Schrödinger equation in a closed algebraic form. We find that the scalar is intermittent during its decay and the average of |θ|α (assuming zero mean value of θ) falls as e−γαDt at large t, where D is a parameter of the flow, γα = α(6− α)/4 for 0 < α < 3, and γα = 9/4 for α ≥ 3, independent of α. Typeset using REVTEX †Email address: son@ctp.mit. edu ∗This work is supported in part by funds provided by the U.S. Department of Energy (D.O.E.) under cooperative research agreement #DF-FC02-94ER40818. The problem of advection of a passive scalar (e.g., temperature or density of a pollutant) by a random flow has attracted considerable interest recently [1–5]. In many cases, the steady state of the scalar exhibits the phenomenon of intermittency, i.e. violation of Gaussianity, which, while being simpler than the Navier–Stokes intermittency [6], might well be the key for the understanding of the latter. In this paper, we consider the problem of turbulent decay of a passive scalar, i.e. its advection without external injection, in the limit of very large correlation length of the velocity (the Batchelor limit.) We show that the problem can be reduced to the quantum mechanics of a system with a finite number of degrees of freedom, which allows for the exact computation of any equal-time correlation function of the scalar. For a particular, yet physically interesting, choice of the initial condition, the number of relevant degrees of freedom of the effective quantum theory is only three, and one can easily find all intermittency properties of the scalar during the decay. The method does not rely on any phenomenological model or uncontrollable approximation. The problem is to find statistical properties of a scalar θ satisfying the equation [7] ∂tθ + vi∂iθ = κ∆θ (1) where vi is a Gaussian random field which is white in time, 〈vi(t,x)vj(t ,y)〉 = δ(t− t)fij(r) (2) where r = |x − y|. In this paper we will consider only the case of three spatial dimensions. For incompressible flows, ∂ifij = 0. In the Batchelor limit [5,8], which corresponds to the viscous-convective range in real turbulence at high Prandtl numbers, r is much smaller than the correlation length of v, and fij(r) = V δij −D(2δijr 2 − rirj) (3)
9-Genes Reinforce the Phylogeny of Holometabola and Yield Alternate Views on the Phylogenetic Placement of Strepsiptera

Background The extraordinary morphology, reproductive and developmental biology, and behavioral ecology of twisted wing parasites (order Strepsiptera) have puzzled biologists for centuries. Even today, the phylogenetic position of these enigmatic “insects from outer space” [1] remains uncertain and contentious. Recent authors have argued for the placement of Strepsiptera within or as a close relative of beetles (order Coleoptera), as sister group of flies (order Diptera), or even outside of Holometabola. Methodology/Principal Findings Here, we combine data from several recent studies with new data (for a total of 9 nuclear genes and ∼13 kb of aligned data for 34 taxa), to help clarify the phylogenetic placement of Strepsiptera. Our results unequivocally support the monophyly of Neuropteroidea ( = Neuropterida + Coleoptera) + Strepsiptera, but recover Strepsiptera either derived from within polyphagan beetles (order Coleoptera), or in a position sister to Neuropterida. All other supra-ordinal- and ordinal-level relationships recovered with strong nodal support were consistent with most other recent studies. Conclusions/Significance These results, coupled with the recent proposed placement of Strepsiptera sister to Coleoptera, suggest that while the phylogenetic neighborhood of Strepsiptera has been identified, unequivocal placement to a specific branch within Neuropteroidea will require additional study.
Experiences with the PEPA performance modelling

The performance evaluation process algebra (PEPA) language is supported by a suite of modelling tools which assist in the solution and analysis of PEPA models. The design and development of these tools have been influenced by a variety of factors, including the wishes of other users of the tools to use the language for purposes which were not anticipated by the tool designers. In consequence, the suite of PEPA tools has adapted to attempt to serve the needs of these users while continuing to support the language designers themselves. This paper reports on the use of the PEPA tools and gives some advice gained from user experiences.