gebhart/patrepeval huggingface dataset:
Performance driven multi-objective distributed scheduling for parallel computations (2011)

With the advent of many-core architectures and strong need for Petascale (and Exascale) performance in scientific domains and industry analytics, efficient scheduling of parallel computations for higher productivity and performance has become very important. Further, movement of massive amounts (Terabytes to Petabytes) of data is very expensive, which necessitates affinity driven computations. Therefore, distributed scheduling of parallel computations on multiple places 1 needs to optimize multiple performance objectives: follow affinity maximally and ensure efficient space, time and message complexity. Simultaneous consideration of these objectives makes distributed scheduling a particularly challenging problem. In addition, parallel computations have data dependent execution patterns which requires online scheduling to effectively optimize the computation orchestration as it unfolds. This paper presents an online algorithm for affinity driven distributed scheduling of multi-place 2 parallel computations. To optimize multiple performance objectives simultaneously, our algorithm uses a low time and message complexity mechanism for ensuring affinity and a randomized work-stealing mechanism within places for load balancing. Theoretical analysis of the expected and probabilistic lower and upper bounds on time and message complexity of this algorithm has been provided. On multi-core clusters such as Blue Gene/P (MPP architecture) and Intel multicore cluster, we demonstrate performance close to the custom MPI+Pthreads code. Further, strong, weak and data (increasing input data size) scalability have been demonstrated on multi-core clusters. Using well known benchmarks, we demonstrate 16% to 30% performance gain as compared to Cilk [6] on multi-core Intel Xeon 5570 (NUMA) architecture. Detailed experimental analysis illustrates efficient space (main memory) utilization as well. To the best of our knowledge, this is the first time multi-objective affinity driven distributed scheduling algorithm has been designed, theoretically analyzed and experimentally evaluated in a multi-place setup for multi-core cluster architectures.
High fidelity adaptive vector quantization at very low bit rates for progressive transmission of radiographic images (1999)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
Electrical properties of nanoceramics reinforced with ropes of single-walled carbon nanotubes (2003)

Single-walled carbon nanotubes (SWCNTs) were used to convert insulating nanoceramics to metallically conductive composites. Dense SWCNT/Al2O3 nanocomposites with CNT contents ranging from 5.7 to 15 vol % and with nanocrystalline alumina matrices have been fabricated by spark-plasma-sintering that retains the integrity of SWCNT in the matrix. The conductivity of these composites increases with increasing content of CNTs. The conductivity has been increased to 3345 S/m in the 15 vol % SWCNT/Al2O3 nanocomposite at room temperature. This is an increase of 13 orders of magnitude over pure alumina and of more than 735% over previously reported results in CNT–ceramic composites.
Predicted proteins of Neisseria meningitidis as potential vaccine candidates: from in silico analyses to experimental corroboration (2012)

Neisseria meningitidis serogroup B infections are a serious health threat to the world that cannot be prevented by vaccination. Here, we report an analysis of the MC58 Neisseria meningitidis genome aimed at the identification of new potential vaccine candidates. 'Hypothetical' and 'conserved hypothetical' annotated genes, together with those with putative functions related to the cell envelope, were subjected to extensive sequence similarity searches, as well as motif, cellular location, and domain analyses complemented with manual curation. As a result, a set of 35 uncharacterized ORFs, predicted to encode for surface exposed or virulence related proteins, was identified. The candidates were subdivided in three categories: 1) predicted outer membrane proteins (OMPs) unique of the Neisseria genus; 2) conserved OMPs from various genus and 3) proteins homologous to known OMPs or to proteins previously found to be immunogenic in animal models. Two of the final candidates, nmb1126 and nmb0181, were cloned and expressed in Escherichia coli. The resulting products were purified by Metal Chelating Chromatography and used to immunize mice. The recombinant proteins were capable of inducing antibodies against the native antigen in preparations of a panel of three strains and displayed bactericidal activity against the homologous strains.
Image Oversampling for Holographic Data Storage (2005)

A method is presented for reading holographic data pages with a non-pixel matched detector array. The method employs sub-Nyquist oversampling and a system of alignment fiducials that can compensate for slowly varying image distortions.
Development of Prolactin Receptor Antagonists: Same Goal, Different Ways (2007)

Hyperprolactinemia is an endocrine pathology resulting from over-production of prolactin (PRL) by pituitary adenomas, and leading to various reproductive disorders. In addition, there is increasing evidence that PRL acts as a growth-promoter of breast and prostate tumors. Classical drugs blocking pituitary PRL production are not necessarily efficient in these pathological situations, which has encouraged the search for alternative ways of inhibiting the undesirable actions of PRL. Prolactin receptor (PRLR) antagonists, acting at the level of receptor activation rather than PRL production, are the most promising strategy. Based on the protein core of human (h)PRL or growth hormone (hGH), the other natural hPRLR ligand, a series of new variants have been engineered within the past couple of years, leading to various patent applications. Modifications of amino acid sequences involve single/multiple substitutions, truncations, or generation of fusion proteins. Three mechanisms of action have been reported for these PRLR antagonists: 1) inhibition of PRLR signaling by competition with endogenous PRL for receptor binding, 2) activation of specific PRLR signalling pathways resulting in actions opposite to those of wild-type hPRL, and 3) engineering of chimeric ligands targeting more than one receptor/cell type, in order to improve tumor-growth inhibition. Since none of these patented molecules is yet in clinical trials, their efficacy to treat PRL-dependent pathologies remains to be demonstrated in humans. Keywords: Breast cancer, prostate cancer, hyperprolactinemia, growth hormone, G129R-hPRL, Δ1-9-G129R-hPRL, G129RhPRL, S179D-hPRL, induced-fit
MeToo: Stochastic Modeling of Memory Traffic Timing Behavior (2015)

The memory subsystem (memory controller, bus, andDRAM) is becoming a bottleneck in computer system performance. Optimizing the design of the multicore memory subsystem requires good understanding of the representative workload. A common practice in designing the memory subsystem is to rely on trace simulation. However, the conventional method of relying on traditional traces faces two major challenges. First, many software users are apprehensive about sharing their code (source or binaries) due to the proprietary nature of the code or secrecy of data, so representative traces are sometimes not available. Second, there is a feedback loop where memory performance affects processor performance, which in turnalters the timing of memory requests that reach the bus. Such feedback loop is difficult to capture with traces. In this paper, we present MeToo, a framework for generating synthetic memory traffic for memory subsystem design exploration. MeToo uses a small set of statistics that summarizes the performance behavior of the original applications, and generates synthetic traces or executables stochastically, allowing applications to remain proprietary. MeToo uses novel methods for mimicking the memory feedback loop. We validate MeToo clones, and show very good fit with the original applications' behavior, with an average error of only 4.2%, which is a small fraction of the errors obtained using geometric inter-arrival(commonly used in queueing models) and uniform inter-arrival.
Ultrathin “Bed-of-Nails” Membranes of Single-Wall Carbon Nanotubes (2004)

Single-wall carbon nanotubes (SWNTs) were arranged in a membrane similar to a "bed-of-nails", in which a single layer of parallel SWNTs was densely packed and aligned along the normal to the membrane. The planar, free-standing, ultrathin SWNT membranes were prepared by milling a neat SWNT fiber with a gallium focused ion beam. The approach is readily applicable to cutting nanotubes to a desirable and precise length and enables further fabrication of devices using the "bed-of-nails" membranes to test the transport properties of SWNTs.
Impedance Flow Cytometry: A Novel Technique in Pollen Analysis (2016)

The presented data demonstrate that IFC is an efficient, label-free, reliable and non-destructive technique to analyse pollen quality in a species-independent manner.
High Strength, Corrosion Resistant Magnesium Alloys for Automotive and Aerospace (1990)

"High Strength, Corrosion Resistant Magnesium Alloys for Automotive and Aerospace." Materials and Processing Report, 4(12), pp. 2–3
Adaptation of compressed HMM parameters for resource-constrained speech recognition (2008)

Recently, we successfully developed and reported a new unsupervised online adaptation technique, which jointly compensates for additive and convolutive distortions with vector Taylor series (JAC/VTS), to adjust (uncompressed) HMMs under acoustically distorted environments [1]. In this paper, we extend that technique to adapt compressed HMMs using JAC/VTS where limited computation and/or memory resources are available for speech recognition (e.g., on mobile devices). Subspace coding (SSC) is developed and used to quantize each dimension of the multivariate Gaussians in the compressed HMMs. Three algorithmic design options are proposed and evaluated that combine SSC with JAC/VTS, where three different types of tradeoffs are made between recognition accuracy and the required computation/memory/storage resources. The strengths and weaknesses of these three options are discussed and shown on the Aurora2 task of noise-robust speech recognition. The first option greatly reduces the storage space and gives 93.2% accuracy, which is the same as the baseline accuracy but with little reduction in the run-time computation/memory cost. The second option reduces about 79.9% of the computation cost and about 33.5% of the memory requirement at a very small price of 0.5% decrease of accuracy (to 92.7%). The third option cuts about 89.2% of the computation cost and about 65.5% of the memory requirement while reducing recognition accuracy by 2.7% (to 90.5%).
[A common antigenic epitope in influenza A virus (H1, H2, H5, H6) hemagglutinin]. (1999)

Avian influenza A viruses belonging to hemagglutinin (HA) subtypes H5 and H6 were studied in the infectivity neutralization test and radioimmunoprecipitation assay (RIPA) with monoclonal antibody MAb C179. This MAb recognizes a conformational antigenic epitope in the stem region of HA formed by two regions (amino acid positions 318-322 in HA1 subunit and 47-58 in HA2), conserved in all H1 and H2 influenza viruses. MAb C179 reacts with HA of H5 viruses in RIPA and neutralizes these strains as efficiently as H2 viruses. C179 precipitates H6 subtype HA but does not neutralize the infectivity of these viruses. Comparison of amino acid sequences of H2, H5, and H6 strains showed identical epitope recognized by MAb C179 in H5 and H6 HAs, which differs from epitopes of H1 and H2 by two amino acids in the HA2 subunit. Causes of disagreement between immunoprecipitation of H6 HA by MAb C179 and neutralization of this serosubtype by this MAb are discussed.
Experimental Investigation of Newly Synthesized Gemini Surfactants as Shale Inhibitors in Drilling Fluids (2019)

Abstract Environmental concerns and the economic aspects curtail usage of oil-based drilling fluids (OBDF) during the drilling operations through shale formations. The OBDF is highly effective in controlling the swelling potential of the clay-rich shale formations in oil/gas wells. Hydration of shale formation by water-based drilling fluids (WBDF) leads to several problems such as collapse of boreholes, tight holes and stuck pipe which may preclude further drilling and time loss in rectifying the problems, leading to heavy economic losses. Designing the drilling fluid that reduces the interaction with shale, is important for safe and efficient drilling. This study investigates the new gemini surfactants as shale swelling inhibitors in the field of drilling. To assess the performance of new cationic Gemini surfactants two reliable clay sources were considered. The first clay (Kaolinite) is from an unconventional formation and the second is sodium bentonite. The inhibition characteristics of gemini surfactants were tested using a dynamic swelling tester. Different formulations based on commercially available solutions for shale swelling inhibitors were applied and compared with cationic shale inhibitor. It was observed that the new gemini surfactants reduced the shale swelling by different percentages for various gemini surfactants based on their spacer length. It also showed acceptable performance compare with common shale inhibitors used in the industry.
Mitochondrial DNA Heteroplasmy Associations With Neurosensory and Mobility Function in Elderly Adults (2015)

These results indicate that increased mtDNA heteroplasmy at disease-causing sites is associated with neurosensory and mobility function in older persons. We propose the novel use of mtDNA heteroplasmy as a simple, noninvasive predictor of age-related neurologic, sensory, and movement impairments.
Advanced thermionic energy conversion (1974)

Basic analytical and experimental exploration was conducted on several types of advanced thermionic energy converters, and preliminary analysis was performed on systems utilizing advanced converter performance. The Pt--Nb cylindrical diode which exhibited a suppressed arc drop, as described in the preceding report, was reassembled and the existence of the postulated hydrid mode of operation was tentatively confirmed. Initial data obtained on ignited and unignited triode operation in the demountable cesium vapor system essentially confirmed the design principles developed in earlier work, with a few exceptions. Three specific advanced converter concepts were selected as candidates for concentrated basic study and for practical evaluation in fixed-configuration converters. Test vehicles and test stands for these converters and a unique controlled-atmosphere station for converter assembly and processing were designed, and procurement was initiated.
Production of sound deep-penetration hybrid weld in aluminum alloy with YAG laser and MIG arc (2006)

Hybrid welding is receiving considerable attention and is used in practical lines. And so YAG laser and MIG arc hybrid welding was performed on A5052 aluminum alloy plate to understand the mechanism of penetration and reduced welding defects as well as to investigate the effect of welding direction on the weld penetration and porosity formation level. In the case of YAG-MIG (laser-head-leading) hybrid welding, the surfaces of weld beads were by far prettier than MIG-YAG hybrid welding. The optimum distances between the laser-focused point and the MIG wire target for deeper penetration were about 2 to 4 mm, and the reason was interpreted in terms of the interaction of a laser beam to droplet, molten pool or solid plate. The penetration increased but porosity was reduced with the increase in MIG arc current. These reasons were attributed to the formation of a concave molten pool surface due to high arc pressure at a high current. In the case of MIG-YAG (MIG-nozzle-leading) hybrid welding, deeper welds were formed especially at high laser power than those made by YAG-MIG hybrid welding. However, a large amount of porosity was formed in the case of the laser beam shot perpendicularly. Such porosity was reduced by declining a laser beam just like the forehand welding, and sound deep weld beads could be produced in MIG-YAG hybrid welding. According to X-ray transmission in-situ observation, these results were interpreted by considering the formation of the wider top inlet of a keyhole produced with a YAG laser to consequently suppress the generation of bubbles. The surface of a MIG-YAG hybrid weld could be cleaned by cleaning action with DCEP-TIG heat source.
Cloning and Expression of a Proteoglycan UDP-Galactose:β-Xylose β1,4-Galactosyltransferase I (1999)

A seventh member of the human beta4-galactosyltransferase family, beta4Gal-T7, was identified by BLAST analysis of expressed sequence tags. The coding region of beta4Gal-T7 depicts a type II transmembrane protein with sequence similarity to beta4-galactosyltransferases, but the sequence was distinct in known motifs and did not contain the cysteine residues conserved in the other six members of the beta4Gal-T family. The genomic organization of beta4Gal-T7 was different from previous beta4Gal-Ts. Expression of beta4Gal-T7 in insect cells showed that the gene product had beta1,4-galactosyltransferase activity with beta-xylosides, and the linkage formed was Galbeta1-4Xyl. Thus, beta4Gal-T7 represents galactosyltransferase I enzyme (xylosylprotein beta1, 4-galactosyltransferase; EC 2.4.1.133), which attaches the first galactose in the proteoglycan linkage region GlcAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser. Sequence analysis of beta4Gal-T7 from a fibroblast cell line of a patient with a progeroid syndrome and signs of the Ehlers-Danlos syndrome, previously shown to exhibit reduced galactosyltransferase I activity (Quentin, E., Gladen, A., Rodén, L., and Kresse, H. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 1342-1346), revealed two inherited allelic variants, beta4Gal-T7(186D) and beta4Gal-T7(206P), each with a single missense substitution in the putative catalytic domain of the enzyme. beta4Gal-T7(186D) exhibited a 4-fold elevated K(m) for the donor substrate, whereas essentially no activity was demonstrated with beta4Gal-T7(206P). Molecular cloning of beta4Gal-T7 should facilitate general studies of its pathogenic role in progeroid syndromes and connective tissue disorders with affected proteoglycan biosynthesis.
[Prediction of WT1/MUC1 peptide dendritic cell therapy responders by quantification of ex vivo induced mRNA in whole blood]. (2012)

Cancer immunotherapy has shown much potential, but is not yet beneficial for all patients. Acquired immunity after immunotherapy can be assessed by a variety of methods; however, the methods for the prediction of such responses before treatment are quite limited. To challenge this classic problem, we quantified 17 different leukocyte function-associated mRNAs( IFN-γ,TNFSF1, TNFSF2, TNFSF5, IL-10, TGF β,CTLA4, PD1, FOXP3, GMCSF, VEGF, IL-8, CCL8, CXCL3, and IL-2) in whole blood after ex vivo stimulation with 7 different agents(PHA, HAG, zymosan, IFN-γ,rIL-2, aTCR, and picibanil) to activate various subsets of leukocytes. The mRNAs were quantified by the Hitachi Chemical Research Center, Inc. Irvine, CA. The clinical outcomes for WT1 peptide-and/or MUC1 peptide-pulsed dendritic cell therapy for advanced cancer (n=26) were CR+PR, 4 cases; SD, 9 cases; and PD, 13 cases. The accuracy of prediction was found to be 100% using the formula developed by multivariate discriminant analysis of the values for ex vivo induced mRNAs. Because the volume of blood needed for this test is less than 1.5 mL, and because cell isolation and culture are not necessary, this method will become a model of personalized medicine diagnostics for cancer immunotherapy.
Blind Estimation of Timing and Amplitude Offsets in Parallel A/D Converters (2000)

Parallel AD converter structures is one way to increase the sampling rate. Instead of increasing the sample rate in one AD converter, several AD converters with lower sampling rate can be used instead. A problem in these structures is that the time between samples is usually not equal because there are errors in the delays between the AD converters. There are also differences in the ground level in the different AD converters. We will here present a method to estimate the timing and amplitude offsets. The estimation algorithm works without any calibration signal, instead the usual input signal is used. The only assumption that is made about the signal is that most of the energy lies in a low frequency band. The AD converter structure will also be simulated to show that the method works.
Optical properties and formation of oxygen-perturbed<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi>F</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow><mml:mi mathvariant="normal"/></mml:mrow><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>color center in NaCl (1987)

The optical properties of a recently discovered laser-active color center in oxygen-doped NaCl are reported. The color center is produced through a two-step photoaggregation process in additively colored crystals. Optical spectroscopy indicates that the point defect is a perturbed ${F}_{2}$${\mathrm{}}^{+}$ center. The center has very broad absorption and emission bands peaking at 1.09 and 1.55 \ensuremath{\mu}m, respectively, with a dipole moment oriented along the 〈110〉 directions of the crystal. The center population can be fully aligned along any 〈110〉 direction by using two-photon pumping. Ground- and excited-state absorption spectra compare well with the dielectrically embedded ${\mathrm{H}}_{2}$${\mathrm{}}^{+}$ model for the eight transitions observed. uv spectroscopy has identified the substitutional ${\mathrm{O}}^{2\mathrm{\ensuremath{-}}}$ ion as being the necessary impurity for the center formation. The proposed model for the color center is an ${\mathrm{O}}^{2\mathrm{\ensuremath{-}}}$-perturbed ${F}_{2}$${\mathrm{}}^{+}$ defect. The perturbing ${\mathrm{O}}^{2\mathrm{\ensuremath{-}}}$ ion serves both as a stable electron trap as well as a spatial trap for the ${F}_{2}$${\mathrm{}}^{+}$ center.
Passive antibody protection of cats against feline immunodeficiency virus infection (1993)

All six cats passively immunized with sera from either feline immunodeficiency virus (FIV)-vaccinated cats or cats infected with FIV (Petaluma strain) were protected from homologous FIV infection at a challenge dose that infected all six control cats. Passive immunization with sera from cats vaccinated with uninfected allogeneic T cells used to grow the vaccine virus did not protect either of two cats against the same FIV challenge. These results suggest that antiviral humoral immunity, perhaps in synergy with anticellular antibodies, may be responsible for previously reported vaccine protection.
An Engraftable Human Embryonic Stem Cell Neuronal Lineage-Specific Derivative Retains Embryonic Chromatin Plasticity for Scale-Up CNS Regeneration (2012)

These observations suggest that, unlike the prototypical neuroepithelial-like nestin-positive hNSCs, these in vitro neuroectoderm-derived Nurr1-positive hESC-I hNuPs are a more neuronal lineage-specific and plastic human stem cell derivative, providing an engraftable human embryonic neuronal progenitor in high purity and large supply with adequate neurogenic potential for scale-up CNS regeneration as stem cell therapy to be translated to patients in clinical trials.