gebhart/patrepeval huggingface dataset:
Software challenges in extreme scale systems (2009)

Computer systems anticipated in the 2015 – 2020 timeframe are referred to as Extreme Scale because they will be built using massive multi-core processors with 100's of cores per chip. The largest capability Extreme Scale system is expected to deliver Exascale performance of the order of 1018 operations per second. These systems pose new critical challenges for software in the areas of concurrency, energy efficiency and resiliency. In this paper, we discuss the implications of the concurrency and energy efficiency challenges on future software for Extreme Scale Systems. From an application viewpoint, the concurrency and energy challenges boil down to the ability to express and manage parallelism and locality by exploring a range of strong scaling and new-era weak scaling techniques. For expressing parallelism and locality, the key challenges are the ability to expose all of the intrinsic parallelism and locality in a programming model, while ensuring that this expression of parallelism and locality is portable across a range of systems. For managing parallelism and locality, the OS-related challenges include parallel scalability, spatial partitioning of OS and application functionality, direct hardware access for inter-processor communication, and asynchronous rather than interrupt-driven events, which are accompanied by runtime system challenges for scheduling, synchronization, memory management, communication, performance monitoring, and power management. We conclude by discussing the importance of software-hardware co-design in addressing the fundamental challenges for application enablement on Extreme Scale systems.
TGF-β-Elicited Induction of Tissue Inhibitor of Metalloproteinases (TIMP)-3 Expression in Fibroblasts Involves Complex Interplay between Smad3, p38α, and ERK1/2 (2013)

Transforming growth factor-β (TGF-β) promotes extracellular matrix deposition by down-regulating the expression of matrix degrading proteinases and upregulating their inhibitors. Tissue inhibitor of metalloproteinases (TIMP)-3 is an ECM-associated specific inhibitor of matrix degrading metalloproteinases. Here, we have characterized the signaling pathways mediating TGF-β-induced expression of TIMP-3. Basal and TGF-β-induced TIMP-3 mRNA expression was abolished in Smad4-deficient mouse embryonic fibroblasts and restoring Smad4 expression rescued the response. Inhibition of Smad signaling by expression of Smad7 and dominant negative Smad3 completely abolished TGF-β-elicited expression of TIMP-3 in human fibroblasts, whereas overexpression of Smad3 enhanced it. Inhibition of extracellular signal-regulated kinase 1/2 (ERK1/2) activation with PD98059 and p38 mitogen-activated protein kinase activity by SB203580 resulted in suppression of TGF-β-induced TIMP-3 expression, indicating that ERK1/2 and p38 MAPK mediate the effect of TGF-β on TIMP-3 expression. Specific activation of p38α and ERK1/2 by constitutively active mutants of MKK3b or MEK1, respectively, and simultaneous co-expression of Smad3 resulted in induction of TIMP-3 expression in the absence of TGF-β indicating that Smad3 co-operates with p38 and ERK1/2 in the induction of TIMP-3 expression. These results demonstrate the complex interplay between Smad3, p38α, and ERK1/2 signaling in the regulation of TIMP-3 gene expression in fibroblasts, which may play a role in inflammation, tissue repair, and fibrosis.
The design and implementation of heterogeneous multicore systems for energy-efficient speculative thread execution (2013)

With the emergence of multicore processors, various aggressive execution models have been proposed to exploit fine-grained thread-level parallelism, taking advantage of the fast on-chip interconnection communication. However, the aggressive nature of these execution models often leads to excessive energy consumption incommensurate to execution time reduction. In the context of Thread-Level Speculation, we demonstrated that on a same-ISA heterogeneous multicore system, by dynamically deciding how on-chip resources are utilized, speculative threads can achieve performance gain in an energy-efficient way. Through a systematic design space exploration, we built a multicore architecture that integrates heterogeneous components of processing cores and first-level caches. To cope with processor reconfiguration overheads, we introduced runtime mechanisms to mitigate their impacts. To match program execution with the most energy-efficient processor configuration, the system was equipped with a dynamic resource allocation scheme that characterizes program behaviors using novel processor counters. We evaluated the proposed heterogeneous system with a diverse set of benchmark programs from SPEC CPU2000 and CPU20006 suites. Compared to the most efficient homogeneous TLS implementation, we achieved similar performance but consumed 18% less energy. Compared to the most efficient homogeneous uniprocessor running sequential programs, we improved performance by 29% and reduced energy consumption by 3.6%, which is a 42% improvement in energy-delay-squared product.
Memory efficient acceleration structures and techniques for CPU-based volume raycasting of large data (2005)

Most CPU-based volume raycasting approaches achieve high performance by advanced memory layouts, space subdivision, and excessive pre-computing. Such approaches typically need an enormous amount of memory. They are limited to sizes which do not satisfy the medical data used in daily clinical routine. We present a new volume raycasting approach based on image-ordered raycasting with object-ordered processing, which is able to perform high-quality rendering of very large medical data in real-time on commodity computers. For large medical data such as computed tomographic (CT) angiography run-offs (512 /spl times/ 512 /spl times/ 1202) we achieve rendering times up to 2.5 fps on a commodity notebook. We achieve this by introducing a memory efficient acceleration technique for on-the-fly gradient estimation and a memory efficient hybrid removal and skipping technique of transparent regions. We employ quantized binary histograms, granular resolution octrees, and a cell invisibility cache. These acceleration structures require just a small extra storage of approximately 10%.
Use-Dependent and Error-Based Learning of Motor Behaviors (2010)

Human motor behavior is constantly adapted through the process of error-based learning. When the motor system encounters an error, its estimate about the body and environment will change, and the next movement will be immediately modified to counteract the underlying perturbation. Here, we show that a second mechanism, use-dependent learning, simultaneously changes movements to become more similar to the last movement. In three experiments, participants made reaching movements toward a horizontally elongated target, such that errors in the initial movement direction did not have to be corrected. Along this task-redundant dimension, we were able to induce use-dependent learning by passively guiding movements in a direction angled by 8 degrees from the previous direction. In a second study, we show that error-based and use-dependent learning can change motor behavior simultaneously in opposing directions by physically constraining the direction of active movements. After removal of the constraint, participants briefly exhibit an error-based aftereffect against the direction of the constraint, followed by a longer-lasting use-dependent aftereffect in the direction of the constraint. In the third experiment, we show that these two learning mechanisms together determine the solution the motor system adopts when learning a motor task.
Functions of Plant Secondary Metabolites and Their Exploitation in Biotechnology (1999)

Functions of plant secondary metabolites and their exploitation in biotechnology / , Functions of plant secondary metabolites and their exploitation in biotechnology / , مرکز اسناد، مدارک علمی و کتابخانه دانشگاه گیلان
Model Studies of the Iron-Catalysed Haber-Weiss Cycle and the Ascorbate-Driven Fenton Reaction (1990)

Complementary hydroxylation assays and stopped-flow e.s.r. techniques have been employed in the investigation of the effect of various iron chelators (of chemical, biological and clinical importance) on hydroxyl-radical generation via the Haber-Weiss cycle and the ascorbate-driven Fenton reaction. Chelators have been identified which selectively promote or inhibit various reactions involved in hydroxyl-radical generation (for example, NTA and EDTA promote all the reactions of both the Haber-Weiss cycle and the ascorbate-driven Fenton reaction, whereas DTPA and phytate inhibit the recycling of iron in these reactions). The biological chelators succinate and citrate are shown to be relatively poor catalysts of the Haber-Weiss cycle, whereas they are found to be effective catalysts of .OH generation in the ascorbate-driven Fenton reaction. It is also suggested that continuous redox-cycling reactions between iron, oxygen and ascorbate may represent an important mechanism of cell death in biological systems.
Production of multiply charged ion beams from solid substances with the mVINIS ion source (2006)

The mVINIS ion source has enabled us to obtain multiply charged ion beams from gases as well as from solid materials. The solid substance ion beams were produced by using two techniques: (a) the evaporation of metals by using the inlet system based on a minioven and (b) the metal-ions-from-volatile-compounds method (MIVOC) by using the modified gas inlet system. Great efforts were made in the production of high current stable ion beams of solids with relatively high melting points (over 1000°C). The B3+ ion-beam current of over 300μA was one of the most intensive beams extracted until now. The obtained multiply charged ion-beam spectra of solid substances (B, Fe, and Zn) are presented as well as some of the corresponding experimental results achieved during the modification of polymers, carbon materials, and fullerenes.
Towards Mitigation of Low and Slow Application DDoS Attacks (2014)

Distributed Denial of Service attacks are a growing threat to organizations and, as defense mechanisms are becoming more advanced, hackers are aiming at the application layer. For example, application layer Low and Slow Distributed Denial of Service attacks are becoming a serious issue because, due to low resource consumption, they are hard to detect. In this position paper, we propose a reference architecture that mitigates the Low and Slow Distributed Denial of Service attacks by utilizing Software Defined Infrastructure capabilities. We also propose two concrete architectures based on the reference architecture: a Performance Model-Based and Off-The-Shelf Components based architecture, respectively. We introduce the Shark Tank concept, a cluster under detailed monitoring that has full application capabilities and where suspicious requests are redirected for further filtering.
A Review of Positive Blood Cultures: Identification and Source of Microorganisms and Patterns of Sensitivity to Antibiotics (1980)

All strains of bacteria and fungi isolated from blood cultures of patients hospitalized in a large primary and tertiary care center were studied prospectively for determination of their clinical significance and probable source. In some instances the immediate mortality rate was also determined. The sensitivity patterns of all aerobic organisms to antibiotics were studied in relation to the role of antibiotic therapy. A positive culture was obtained from 6.8% of all blood specimens cultured and these positive cultures represented 639 episodes of bacteremia or fungemia. The organism isolated most of ten was Escherichia coli, and the most common known source was the urinary tract. Anaerobic organisms were isolated from 9.2% of the episodes of bacteremia, with the bowel being the most common probable source of infection. Antibiotic sensitivity testing revealed that all staphylococci were sensitive to methicillin, but only 22% were sensitive to penicillin. No penicillin-resistant pneumococci were encountered. The Enterobacteriaceae exhibited such a high sensitivity to gentamicin that comparison of its activity with that of other, newer aminoglycosides was impossible.
Co-Segmentation of Non-Homogeneous Image Sets (2018)

In this paper, we formulate image co-segmentation as a classification problem in an unsupervised framework with the classes being the common foreground and the remaining regions in the image set. We first find a set of superpixels across all images with high feature similarity such that the constituent superpixels in individual images are spatially compact and label them as seed for the common foreground. Those superpixels with high background probability are labeled as respective seeds for multiple background classes. Seed computation here is unsupervised and automated unlike some semi-supervised methods. Then, we compute discriminative features that separate the initially labeled classes using linear discriminant analysis. We use these features to perform spatially constrained label propagation and obtain labels for the unlabeled regions, and iterate this process till the seed regions grow to the common object. Experimental results demonstrate excellent robustness properties even while processing non-homogeneous image sets where the common object is present only in majority of the images.
Digital computers for distribution systems (1958)

Exactly what is the nature of the “computing revolution” that is now under way and, specifically, what is the future for computers in distribution engineering? These are some of the provocative questions discussed in an attempt to assay the significance of digital computers for power distribution.
An efficient method for dispersing <i>Ds</i> elements in the barley genome as a tool for determining gene function (2000)

To devise a method for function-based gene isolation and characterization in barley, we created a plasmid containing the maize Activator (Ac) transposase (AcTPase) gene and a negative selection gene, codA, and a plasmid containing Dissociation (Ds) inverted-repeat ends surrounding the selectable herbicide resistance gene, bar. These plasmids were used to stably transform barley (Hordeum vulgare). In vitro assays, utilizing a Ds-interrupted uidA reporter gene, were used to demonstrate high-frequency excisions of Ds when the uidA construct was introduced transiently into stably transformed, AcTPase-expressing plant tissue. Crosses were made between stably transformed plants expressing functional transposase under the transcriptional control of either the putative AcTPase promoter or the promoter and first intron from the maize ubiquitin (Ubi1) gene, and plants containing Ds-Ubi-bar. In F(1) plants from these crosses, low somatic and germinal transposition frequencies were observed; however, in F(2) progeny derived from individual selfed F(1) plants, up to 47% of the plants showed evidence of Ds transposition. Further analyses of F(3) plants showed that approximately 75% of the transposed Ds elements reinserted into linked locations and 25% into unlinked locations. Transposed Ds elements in plants lacking the AcTPase transposase gene could be reactivated by reintroducing the transposase gene through classical genetic crossing, making this system functional for targeted gene tagging and studies of gene function. During the analysis of F(3) plants we observed two mutant phenotypes in which the transposed Ds elements co-segregate with the new phenotype, suggesting the additional utility of such a system for tagging genes.
BLOCKADE BY INTRAVENOUS LOSARTAN OF AT<sub>1</sub> ANGIOTENSIN II RECEPTORS IN RAT BRAIN, KIDNEY AND ADRENALS DEMONSTRATED BY <i>IN VITRO</i> AUTORADIOGRAPHY (1994)

1. The in vivo inhibition of angiotensin II (AII) receptor binding in the rat brain, kidney and adrenal was investigated after intravenous administration of the AT1-selective AII receptor antagonist losartan. 2. Male Sprague-Dawley rats were administered intravenously either vehicle, or losartan at doses of 1, 3 or 10 mg/kg. Plasma samples were collected and tissues removed at 1, 2, 8 or 24 h after administration of the antagonist. The effects of losartan on AII receptor binding were assessed by quantitative in vitro autoradiography. 3. Losartan significantly increased plasma renin activity (PRA) by six-fold and nine-fold at doses of 1 and 10 mg/kg, respectively (P < 0.05). Plasma losartan concentrations rose from 0.83 micrograms/mL at 1 mg/kg to 46.5 micrograms/mL at 10 mg/kg 1 h after administration of the drug. Plasma renin activity returned to control, whilst losartan was undetectable 24 h after injection of the antagonist. 4. In the brain, losartan produced a dose-dependent inhibition of AII receptor binding to the brain structures which express exclusively, or predominantly, AT1 receptors both outside and within the blood brain barrier. By contrast, losartan did not affect binding to the nuclei which contain exclusively, or predominantly, AT2 receptors. 5. In the kidney, losartan blocked AII receptor binding to all anatomical sites in a dose-dependent manner. The inhibition peaked at 1 h and persisted beyond 24 h despite the fact that PRA had returned to control, and losartan was not detectable in the circulation. In the adrenal gland, where AT1 and AT2 receptors occur in both the cortex and medulla, losartan caused partial inhibition at both regions. 6. These results indicate that losartan, administered intravenously at these doses, and/or its active metabolites, partially penetrate the blood brain barrier to selectively inhibit central AT1 receptors, and exert selective and prolonged blockade at AT1 receptors in peripheral target tissues.
Gammalt och nytt i det svenska järnets historia: en översikt över fem årtionden (Old and new in the history of Swedish iron: an overview of five decades) (1997)

Gammalt och nytt i det svenska jarnets historia: en oversikt over fem artionden (Old and new in the history of Swedish iron: an overview of five decades)
Cellulose nanocrystals and related nanocomposites: Review of some properties and challenges (2014)

ABSTRACT Cellulosic nanoparticles with high Young's modulus, crystallinity, specific surface area, and aspect ratio can be found in the natural structure of plant fibers. Indeed, lignocellulosic fibers consist of semicrystalline cellulose nanofibrils embedded in an amorphous matrix mainly composed of lignin and hemicelluloses. These nanostructures give the mechanical strength to higher plant cells, and are biodegradable, renewable, resistant, and widely available to produce nanocomposites with low density, and improved and controlled mechanical, optical, and barrier properties. Nanoparticles can be extracted from cellulose using a top‐down mechanically or chemically assisted deconstructing strategy, and owing to their highly reactive surface ensuing nanomaterials can be chemically modified to tailor their properties for a wide range of applications. This review is limited to cellulose chemically extracted nanocrystals and aims to provide an overview about several aspects that involve this material, including sources, properties, challenges, and perspectives. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52 , 791–806
Development of a graphene oxide-based assay for the sequence-specific detection of double-stranded DNA molecules (2017)

Graphene oxide (GO) is a promising material for the development of cost-effective detection systems. In this work, we have devised a simple and rapid GO-based method for the sequence-specific identification of DNA molecules generated by PCR amplification. The csp genes of Escherichia coli, which share a high degree of sequence identity, were selected as paradigm DNA templates. All tested csp genes were amplified with unlabelled primers, which can be rapidly removed at the end of the PCR taking advantage of the preferential binding to GO of single-stranded versus duplex DNA molecules. The amplified DNAs (targets) were heat-denatured and hybridized to a fluorescently-labelled single strand oligonucleotide (probe), which recognizes a region of the target DNAs displaying sequence variability. This interaction is extremely specific, taking place with high efficiency only when target and probe show perfect or near perfect matching. Upon GO addition, the unbound fraction of the probe was captured and its fluorescence quenched by the GO's molecular properties. On the other hand, the probe-target complexes remained in solution and emitted a fluorescent signal whose intensity was related to their degree of complementarity.
HARD Track Overview in TREC 2004: High Accuracy Retrieval from Documents (2004)

The HARD track of TREC 2004 aims to improve the accuracy of information retrieval through the use of three techniques: (1) query metadata that better describes the information need, (2) focused and time-limited interaction with the searcher through "clarification forms", and (3) incorporation of passage-level relevance judgments and retrieval.Participation in all three aspects of the track was excellent this year with about 10 groups trying something in each area.No group was able to achieve huge gains in effectiveness using these techniques, but some improvements were found and enthusiasm for the clarification forms (in particular) remains high.The track will run again in TREC 2005.
Parameter Extractions for a GaAs pHEMT Thermal Model Using a TFR-Heated Test Structure (2015)

The temperature-dependent thermal conductivities of a GaAs pseudomorphic high-electron mobility transistor's (pHEMT) substrate and epilayer regions are extracted to develop a 3-D finite-element-method thermal model. The thermal characterization is based on electrical gate-metal-finger temperature measurements of a customized GaAs pHEMT test structure. Heat flow from an integrated thin-film resistor is shown to be sensitive to the device's substrate thermal conductivity, while heat flow from the device's channel is most significantly affected by the epilayer region thermal conductivity. These observations are used in the formulation of the thermal parameter extraction technique, which serves as a useful and convenient device modeling tool that can be integrated into an engineering design flow. Specific knowledge about the semiconductor material fabrication process, which may be unavailable to the design engineer, is not required for accurate thermal characterization; this is the overriding advantage of the technique presented.
Combinatorial cancer immunotherapy strategies with proapoptotic small-molecule IAP antagonists (2015)

Members of the inhibitor of apoptosis (IAP) family control several critical aspects of innate immunity, cell death, and tumorigenesis. Small molecule antagonists that target specific IAP oncoproteins, primarily cIAP1 and cIAP2, but potentially also XIAP and Livin, modulate distinct immune signal transduction pathways that can lead to an increased sensitivity of tumors cells to cytokine-mediated apoptosis. These antagonists are based on the structure of an endogenous cellular IAP inhibitor called Smac. Smac is normally sequestered within the mitochondria and is released into the cytoplasm upon cell death stimuli, thereby overcoming the anti-apoptotic action of the IAPs. The therapeutic usefulness of recombinant tumoricidal cytokines to treat cancer patients is principally limited due to their unacceptable adverse side effects. Therefore, investigators have sought to develop alternative regimens that do not rely on exogenously delivered death ligands. These approaches include the stimulation of the immune system with oncolytic virus-based agents or Toll-like receptor agonists in combination with Smac mimetics. Similarly, preclinical combination immunotherapy studies reveal that recombinant interferon synergizes with Smac mimetics to kill cancer. This strategy opens up new therapeutic avenues for anti-cancer therapy by modulating specific immune-mediated death pathways employing unique dual-pronged combinatorial approaches.