gebhart/patrepeval huggingface dataset:
Visual Animation of Parallel Algorithms for Matrix Computations (2005)

In this talk we show how graphical animation of the behavior of parallel algorithms can facilitate the design and performance enhancement of algorithms for matrix computations on parallel computer architectures. Using a portable instrumented communication library and a graphical animation package developed at Oak Ridge National Laboratory, we illustrate the effects of various strategies in parallel algorithm design, including interconnection topologies, global communication patterns, data mapping schemes, load balancing, and pipelining techniques for overlapping communication with computation. In this talk we focus on distributed-memory parallel architectures in which the processors communicate by passing messages. The linear algebra problems we consider include matrix factorization and the solution of triangular systems.
Apparent Anti-Woodward–Hoffmann Addition to a Nickel Bis(dithiolene) Complex: The Reaction Mechanism Involves Reduced, Dimetallic Intermediates (2013)

Nickel dithiolene complexes have been proposed as electrocatalysts for alkene purification. Recent studies of the ligand-based reactions of Ni(tfd)2 (tfd = S2C2(CF3)2) and its anion [Ni(tfd)2](-) with alkenes (ethylene and 1-hexene) showed that in the absence of the anion, the reaction proceeds most rapidly to form the intraligand adduct, which decomposes by releasing a substituted dihydrodithiin. However, the presence of the anion increases the rate of formation of the stable cis-interligand adduct, and decreases the rate of dihydrodithiin formation and decomposition. In spite of both computational and experimental studies, the mechanism, especially the role of the anion, remained somewhat elusive. We are now providing a combined experimental and computational study that addresses the mechanism and explains the role of the anion. A kinetic study (global analysis) for the reaction of 1-hexene is reported, which supports the following mechanism: (1) reversible intraligand addition, (2) oxidation of the intraligand addition product prior to decomposition, and (3) interligand adduct formation catalyzed by Ni(tfd)2(-). Density functional theory (DFT) calculations were performed on the Ni(tfd)2/Ni(tfd)2(-)/ethylene system to shed light on the selectivity of adduct formation in the absence of anion and on the mechanism in which Ni(tfd)2(-) shifts the reaction from intraligand addition to interligand addition. Computational results show that in the neutral system the free energy of activation for intraligand addition is lower than that for interligand addition, in agreement with the experimental results. The computations predict that the anion enhances the rate of the cis-interligand adduct formation by forming a dimetallic complex with the neutral complex. The [(Ni(tfd)2)2](-) dimetallic complex then coordinates ethylene and isomerizes to form a Ni,S-bound ethylene complex, which then rapidly isomerizes to the stable interligand adduct but not to the intraligand adduct. Thus, the anion catalyzes the formation of the interligand adduct. Significant experimental evidence for dimetallic species derived from nickel bis(dithiolene) complexes has been found. ESI-MS data indicate the presence of a [(Ni(tfd)2)2](-) dimetallic complex as the acetonitrile adduct. A charge-neutral association complex of Ni(tfd)2 with the ethylene adduct of Ni(tfd)2 has been crystallographically characterized. Despite the small driving force for the reversible association, very major structural reorganization (square-planar → octahedral) occurs.
On the Construction of Practical Key Predistribution Schemes for Distributed Sensor Networks Using Combinatorial Designs (2008)

In this paper, we discuss the use of combinatorial set systems (combinatorial designs) in the design of key predistribution schemes (KPSs) for sensor networks. We show that the performance of a KPS can be improved by carefully choosing a certain class of set systems as “key ring spaces”. Especially, we analyze KPSs based on a type of combinatorial design known as a <it>transversal design</it>. We employ two types of transversal designs, which are represented by the set of all linear polynomials and the set of quadratic polynomials (over some finite field), respectively. These KPSs turn out to have significant efficiency in a shared-key discovery phase without degrading connectivity and resiliency.
Resonant infrared pulsed-laser deposition of polymer films using a free-electron laser (2001)

Thin films of polyethylene glycol (MW 1500) have been prepared by pulsed-laser deposition (PLD) using both a tunable infrared (λ=2.9 μm, 3.4 μm) and an ultraviolet laser (λ=193 nm). A comparison of the physicochemical properties of the films by means of Fourier transform infrared spectroscopy, electrospray ionization mass spectrometry, and matrix-assisted laser desorption and ionization shows that when the IR laser is tuned to a resonant absorption in the polymer, the IR PLD thin films are identical to the starting material, whereas the UV PLD show significant structural modification. These results are important for several biomedical applications of organic and polymeric thin films.
Evidence-Based Recommendations for the Diagnosis and Treatment of Pediatric Acne (2013)

These expert recommendations by the American Acne and Rosacea Society as reviewed and endorsed by the American Academy of Pediatrics constitute the first detailed, evidence-based clinical guidelines for the management of pediatric acne including issues of special concern when treating pediatric patients.
Design and fabrication of an all-dielectric grating with top-hat high diffraction efficiency over a broad spectral range (2007)

Between 98% and 100% flat top efficiency –1 st order TE diffraction over a 40 nm wavelength range centered at 800 nm can be obtained by an all-dielectric grating structure where the corrugation is etched in a high index layer unlike in the state of the art. 98% maximum efficiency and a wide-band top-hat diffraction efficiency spectrum are demonstrated experimentally.
Molecular Disorder and Mesoscopic Order in Polydisperse Acrylic Block Copolymers Prepared by Controlled Radical Polymerization (2006)

Self-assembly of high molecular weight polydisperse acrylic block copolymers and their blends is presented under conditions as close as possible to thermodynamic equilibrium. Di- and triblock copolymers comprising a poly(butyl acrylate) (PBA) first or middle block, and poly(methyl methacrylate) (PMMA) second or outer blocks, denoted MBA and MBAM, respectively, are prepared by nitroxide-mediated polymerization (NMP). Their particularity is that the acrylic block is controlled while the methacrylate block is polymerized via an uncontrolled radical process under the synthesis conditions used. Overall composition and molecular weight polydispersities are large. Molecular disorder does not yield macrophase separation, and TEM on solvent cast films reveals lamellar and poorly ordered bicontinuous, cylindrical, or spherical morphologies. Except for the lamellar phase, clear multiple orders of diffraction are not visible in SAXS, and scattering profiles instead indicate a liquidlike order of microdomains. More importantly, morphology boundaries are strongly shifted compared to those commonly accepted for model monodisperse block copolymers. Hence, symmetric copolymers adopt morphologies with highly curved interfaces while lamellae are displaced to PMMA-rich compositions. These results suggest that unbalanced polydispersity between the two blocks can induce interfacial curvature toward to broadest molecular weight distribution, thereby releasing stretching energy of the whole chain. This effect is expected to be encountered in radical or hybrid block copolymer syntheses whenever control cannot be optimized for all blocks.
Protective effect of betaine on survival of<i>Lactobacillus plantarum</i>subjected to drying (1994)

The aim of this study was to investigate the effect of betaine on survival of Lactobacillus plantarum subjected to drying. A defined medium was devised devoid of betaine. Addition of 2 mM betaine to this medium increased the growth rate of cells grown under osmotic stress and also made the organism more tolerant. Cells cultivated under osmotic stress of 0.6 M sodium chloride and in the presence of betaine showed an increased survival after air drying and subsequent vacuum desiccation to a water activity of 0.12.
Turbo Bayesian Compressed Sensing (2011)

Compressed sensing (CS) theory specifies a new signal acquisition approach, po- tentially allowing the acquisition of signals at a much lower data rate than the Nyquist sampling rate. In CS, the signal is not directly acquired but reconstructed from a few measurements. One of the key problems in CS is how to recover the original signal from measurements in the presence of noise. This dissertation addresses signal reconstruction problems in CS. First, a feedback structure and signal recovery algorithm, orthogonal pruning pursuit (OPP), is proposed to exploit the prior knowledge to reconstruct the signal in the noise-free situation. To handle the noise, a noise-aware signal reconstruction algorithm based on Bayesian Compressed Sensing (BCS) is developed. Moreover, a novel Turbo Bayesian Compressed Sensing (TBCS) algorithm is developed for joint signal reconstruction by exploiting both spatial and temporal redundancy. Then, the TBCS algorithm is applied to a UWB positioning system for achieving mm-accuracy with low sampling rate ADCs. Finally, hardware implementation of BCS signal reconstruction on FPGAs and GPUs is investigated. Implementation on GPUs and FPGAs of parallel Cholesky decomposition, which is a key component of BCS, is explored. Simulation results on software and hardware have demonstrated that OPP and TBCS outperform previous approaches, with UWB positioning accuracy improved by 12.8x. The accelerated computation helps enable real-time application of this work.
Evaluation of Head Injury Criteria (1974)

<div class="htmlview paragraph">An impact model of the human head characterized by an elastic spherical shell (skull) containing a low modulus core (brain) is studied using experimentally determined geometric, material, and structural properties. Injury criteria represented by skull fracture, brain cavitation, and brain shear deformation are interpreted and investigated in terms of effective acceleration-time thresholds. Contact stresses and durations are identified for head impacts typical in automobile collisions. In addition, selected comparisons of results with experimental data and head severity indices are given.</div>
Snakes in the Garden: (1995)

The attractions of rural life coupled with the gains of the gay rights movement are encouraging psychotherapists to practice openly in non-urban areas as lesbians and gays, despite the increased stress caused by isolation and homophobic reactions. This article explores the experience of gay and lesbian psychotherapists practicing in Maine. Professional successes and personal satisfaction of these therapists are described, along with their struggles around boundary setting and social and cultural isolation. Suggestions for those contemplating country practice or already doing so are included.
Optical Absorption in HgTe and HgCdTe (1964)

Absorption and reflectivity near the fundamental absorption edge have been measured in the HgTe-CdTe alloy series for CdTe concentrations of up to 28%. In the HgTe rich region, the edge shifts to longer wave-lengths with decreasing temperature. For HgTe, the absorption rises to 2\ifmmode\times\else\texttimes\fi{}${10}^{4}$ ${\mathrm{cm}}^{\ensuremath{-}1}$ at $\ensuremath{\hbar}\ensuremath{\omega}=0.6$ eV. Absorption did not decrease below 1.4\ifmmode\times\else\texttimes\fi{}${10}^{3}$ ${\mathrm{cm}}^{\ensuremath{-}1}$ at room temperature. The theory of optical absorption in zincblende compounds is reviewed. Absorption in this alloy series agrees with theory for direct transitions with an energy-independent matrix element evaluated by Kane for InSb. Analysis of reflectivity in HgTe indicates an electron effective mass of $0.02m$ at 100\ifmmode^\circ\else\textdegree\fi{}C.
A Mobile Application for Running Form Analysis Based On Pose Estimation Technique (2018)

Motion capture systems have been conventionally used for motion analysis. However, deep learning technique has recently made significant progress in human pose estimation in a two-dimensional image. The purpose of this study is to develop a mobile application evaluating running form using deep learning in two-dimensional images. We conducted a biomechanical experiment to investigate the accuracy of the application in comparison to a motion capture system. It showed an excellent consistency between the data. In addition, we collected running form data from 642 runners and developed evaluation standards of running form in six metrics. Thus the application of the pose estimation technique combined with evaluation standards could be an easy and useful tool for running form analysis.
The <i>Arabidopsis</i> Major Intrinsic Protein NIP5;1 Is Essential for Efficient Boron Uptake and Plant Development under Boron Limitation (2006)

Boron (B) is essential in plants but often present at low concentrations in the environment. To investigate how plants survive under conditions of B limitation, we conducted a transcriptome analysis and identified NIP5;1, a member of the major intrinsic protein family, as a gene upregulated in B-deficient roots of Arabidopsis thaliana. Promoter-beta-glucuronidase fusions indicated that NIP5;1 is strongly upregulated in the root elongation zone and the root hair zone under B limitation, and green fluorescent protein-tagged NIP5;1 proteins localized to the plasma membrane. Expression in Xenopus laevis oocytes demonstrated that NIP5;1 facilitated the transport of boric acid in addition to water. Importantly, two T-DNA insertion lines of NIP5;1 displayed lower boric acid uptake into roots, lower biomass production, and increased sensitivity of root and shoot development to B deficiency. These results identify NIP5;1 as a major plasma membrane boric acid channel crucial for the B uptake required for plant growth and development under B limitation.
A framework for search interfaces (1997)

Searching textual databases can be confusing for users. Popular search systems for the World Wide Web and stand alone systems typically provide a simple interface: users type in keywords and receive a relevance ranked list of 10 results. This is appealing in its simplicity, but users are often frustrated because search results are confusing or aspects of the search are out of their control. If we are to improve user performance, reduce mistaken assumptions, and increase successful searches, we need more predictable design. To coordinate design practice, we suggest a four-phase framework that would satisfy first time, intermittent, and frequent users accessing a variety of textual and multimedia libraries.
Assimilation of Formaldehyde in Transgenic Plants Due to the Introduction of the Bacterial Ribulose Monophosphate Pathway Genes (2010)

Formaldehyde (HCHO) is an air pollutant suspected of being carcinogenic and a cause of sick-house syndrome. Microorganisms called methylotrophs, which can utilize reduced C(1) compounds such as methane and methanol, fix and assimilate HCHO, whereas most plants are unable to assimilate HCHO directly. We found that a bacterial formaldehyde-fixing pathway (ribulose monophosphate pathway) can be integrated as a bypass to the Calvin-Benson cycle in transgenic Arabidopsis thaliana and tobacco by genetic engineering. These plants showed enhanced tolerance to HCHO and enhanced capacity to eliminate gaseous HCHO by fixing it as a sugar phosphate. Our results provide a novel strategy for phytoremediation of HCHO pollution, and also represent the first step toward the production of plants that can assimilate natural gas-derived C(1) compounds.
In Vivo Expression of Insulin-Like Growth Factor-Binding Protein-2 in Human Gliomas Increases with the Tumor Grade (2001)

Human central nervous system tumors and glioma cell lines highly express the insulin-like growth factor-binding protein (IGFBP)-2. As IGFBP-2 can affect tumor growth, we studied the relationship between IGFBP-2 expression and the malignancy of brain tumors in vivo. To do so, we investigated by immunohistochemistry the accumulation of IGFBP-1, -2, and -3 in 50 human gliomas classified by the WHO Malignancy Scale. Double labeling using anti-CD68 (monocytes/macrophages), antiglial fibrillary acidic protein, and anti-CD3 (T cells) antibodies was performed to further characterize the IGFBP-1, -2, and -3+ cells. The expression of IGFBP messenger RNAs (mRNAs) was tested by RT-PCR in tumor samples from nine gliomas of different grades and in eight cell lines representing the cellular composition of human glioma. As controls, the accumulation of IGFBP-2 was investigated in normal brain and in the rat C6 glioblastoma model. IGFBP-1 and -3 accumulated in endothelial and macrophage/microglial cells. IGFBP-2+ macrophage/microglial and glioma cells clustered in the immediate vicinity of focal necrosis of the human gliomas as well as of the rat C6 glioblastoma. The labeling score of IGFBP-1 accumulation in endothelial cells correlated negatively (P = 0.0229), and that of IGFBP-2 accumulation in glioma cells correlated positively (P < 0.0006) with the tumor grade of the gliomas. In addition, RT-PCR analysis confirmed mRNA expression of IGFBP-1, -2, and -3 by the gliomas and glial cells. Small amounts of IGFBP-1 and -3 mRNA, but high amounts of IGFBP-2 mRNA, were detectable in macrophage-like and glioma cell lines.
Traffic analysis with low frame rate camera networks (2010)

We propose a new traffic analysis framework using existing traffic camera networks. The framework integrates vehicle detection and image-based matching methods with geographic context to match vehicles across different views and analyze traffic. This is a challenging problem due to the low frame-rate of traffic-cams and the large distance between views. A vehicle may not always appear in a camera due to large inter-frame interval or inter-occlusion. We applied the proposed method to a traffic camera network to detect and track key vehicles to analyze traffic condition. Vehicles are detected using a multi-view approach. By integrating camera calibration information and GIS data, we extract traffic lane information and prior knowledge of expected vehicle orientation and image size at each image location. This improves detection speed and reduces false alarms by discarding unlikely scale and orientation. Subsequently, detected vehicles are matched across cameras using a view-invariant appearance model. For more accurate vehicle matching, traffic patterns observed at two sets of cameras are temporally aligned. Finally, key vehicles are globally tracked across cameras using the max-flow/min-cut network tracking algorithm. Traffic conditions at each camera location are presented on a map.
A rapid method for the preparation of multiple samples of eucaryotic DNA (1987)

Journal Article A rapid method for the preparation of multiple samples of eucaryotic DNA Get access Christophe D. Reymond Christophe D. Reymond Institut suisse de recherches expérimentales sur le cancerCH 1066 Epalinges, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 15, Issue 19, 12 October 1987, Page 8118, https://doi.org/10.1093/nar/15.19.8118 Published: 12 October 1987 Article history Received: 17 July 1987 Published: 12 October 1987
KDC1, a Novel Carrot Root Hair K+Channel (2000)

Potassium is an essential nutrient which plays an important role in many aspects of plant growth and development. Plants have developed a number of highly specific mechanisms to take up potassium from the soil; these include the expression of K(+) transporters and potassium channels in root cells. Despite the fact that root epidermal and hair cells are in direct contact with the soil, the role of these tissues in K(+) uptake is not well understood. Here we report the molecular cloning and functional characterization of a novel potassium channel KDC1 which forms part of a new subfamily of plant K(in) channels. Kdc1 was isolated from carrot root RNA and in situ hybridization experiments show Kdc1 to be highly expressed in root hair cells. Expressing the KDC1 protein in Chinese hamster ovary cells identified it as a voltage and pH-dependent inwardly rectifying potassium channel. An electrophysiological analysis of carrot root hair protoplasts confirmed the biophysical properties of the Kdc1 gene product (KDC1) in the heterologous expression system. KDC1 thus represents a major K(+) uptake channel in carrot root hair cells.
Enhanced activity of adenine-DNA glycosylase (Myh) by apurinic/apyrimidinic endonuclease (Ape1) in mammalian base excision repair of an A/GO mismatch (2001)

Adenine-DNA glycosylase MutY of Escherichia coli catalyzes the cleavage of adenine when mismatched with 7,8-dihydro-8-oxoguanine (GO), an oxidatively damaged base. The biological outcome is the prevention of C/G-->A/T transversions. The molecular mechanism of base excision repair (BER) of A/GO in mammals is not well understood. In this study we report stimulation of mammalian adenine-DNA glycosylase activity by apurinic/apyrimidinic (AP) endonuclease using murine homolog of MutY (Myh) and human AP endonuclease (Ape1), which shares 94% amino acid identity with its murine homolog Apex. After removal of adenine by the Myh glycosylase activity, intact AP DNA remains due to lack of an efficient Myh AP lyase activity. The study of wild-type Ape1 and its catalytic mutant H309N demonstrates that Ape1 catalytic activity is required for formation of cleaved AP DNA. It also appears that Ape1 stimulates Myh glycosylase activity by increasing formation of the Myh-DNA complex. This stimulation is independent of the catalytic activity of Ape1. Consequently, Ape1 preserves the Myh preference for A/GO over A/G and improves overall glycosylase efficiency. Our study suggests that protein-protein interactions may occur in vivo to achieve efficient BER of A/GO.
Cold active hydrolytic enzymes production by psychrotrophic Bacilli isolated from three sub‐glacial lakes of NW Indian Himalayas (2015)

The diversity of culturable, cold-active enzymes producing Bacilli was investigated from three sub-glacial lakes of north western Indian Himalayas. Amplified ribosomal DNA restriction analysis (ARDRA) using three restriction enzymes Alu I, Msp I, and Hae III led to the clustering of 136 Bacilli into 26, 23, and 22 clusters at 75% similarity index from Chandratal Lake, Dashair Lake, and Pangong Lake, respectively. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 35 Bacilli that could be grouped in seven families viz.: Bacillaceae (48%), Staphylococcaceae (14%), Bacillales incertae sedis (13%), Planococcaceae (12%), Paenibacillaceae (9%), Sporolactobacillaceae (3%), and Carnobacteriaceae (1%), which included twelve different genera Bacillus, Desemzia, Exiguobacterium, Jeotgalicoccus, Lysinibacillus, Paenibacillus, Planococcus, Pontibacillus, Sinobaca, Sporosarcina, Staphylococcus, and Virgibacillus. Based on their optimal temperature for growth, 35 Bacilli were grouped as psychrophilic (11 strains), psychrotrophic (17 strains), or psychrotolerant (7 strains), respectively. The representative isolates from each cluster were screened for cold-active enzyme activities. Amylase, β-glucosidase, pectinase, and protease activities at 4 °C were detected in more than 80% of the strains while approximately 40, 31, 23, 14, 11, and 9% of strains possessed cellulase, xylanase, β-galactosidase, laccase, chitinase, and lipase activity, respectively. Among 35 Bacilli, Bacillus amyloliquefaciens, Bacillus marisflavi, Exiguobacterium indicum, Paenibacillus terrae, Pontibacillus sp., Sporosarcina globispora, and Sporosarcina psychrophila were efficient producers of different cold-active enzymes. These cold-adapted Bacilli could play an important role in industrial and agricultural processes.