gebhart/patrepeval huggingface dataset:
Accelerating computing with the cell broadband engine processor (2008)

In this paper, we describe our approach to utilizing the compute power of the Cell Broadband Engine™ (Cell/B.E.)1 processor as an accelerator for computationally intensive portions of high performance computing applications. We call this approach "hybrid programming" because it distributes application execution across heterogeneous processors. IBM developed a hardware implementation and software infrastructure that enables this hybrid computing model as part of the Roadrunner project for Los Alamos National Laboratory (LANL). In the hybrid programming model, a process running on a host processor, such as an x86_64 architecture processor, creates an accelerator process on an accelerator processor, such as the IBM® PowerXCell™8i2. The PowerXCell8i is a new implementation of the Cell Broadband Engine architecture. The host process then schedules compute intensive operations onto the accelerator process. The host and accelerator process can continue execution concurrently and synchronize when needed to transfer results or schedule new accelerator computation. We describe the Data Communication and Synchronization (DaCS) Library and Accelerated Library Framework (ALF) which are designed to allow applications to create new applications and adapt existing applications to exploit hybrid computing platforms. We also describe our experience in using such frameworks to construct hybrid versions of the familiar Linpack benchmark and an implicit Monte Carlo radiation transport application named Milagro. Performance measurements on prototype hardware are presented that show the performance improvements achieved to date, along with projections of the expected performance on the final Roadrunner system.
Soft-Tissue Handling (1995)

Divisions of Orthopaedics, Plastic and Reconstructive Surgery, Department of Surgery, Duke University Medical Center, Durham, North Carolina, U.S.A
A survey of spatial deformation from a user-centered perspective (2008)

The spatial deformation methods are a family of modeling and animation techniques for indirectly reshaping an object by warping the surrounding space, with results that are similar to molding a highly malleable substance. They have the virtue of being computationally efficient (and hence interactive) and applicable to a variety of object representations. In this article we survey the state of the art in spatial deformation. Since manipulating ambient space directly is infeasible, deformations are controlled by tools of varying dimension—points, curves, surfaces and volumes—and it is on this basis that we classify them. Unlike previous surveys that concentrate on providing a single underlying mathematical formalism, we use the user-centered criteria of versatility, ease of use, efficiency and correctness to compare techniques.
The Pd(II) Complex of a Bidentate Di(benzimidazol-2-ylidene) Ligand (2004)

Abstract The pale yellow palladium(II) dicarbene complex cis-[PdI 2 (L)], 2 (L = 1,3-bis-(3-neopentylbenzimidazol- 2-ylidene)-2,2-dimethylpropane) was synthesized by the reaction of PdI 2 with an N1,N1’- 2,2’-dimethylpropane-bridged dibenzotetraazafulvalene 1 in tetrahydrofuran. The X-ray structure analysis revealed a mononuclear complex with a palladium(II) center coordinated in a slightly distorted square-planar fashion by the bidentate carbene ligand and two iodo ligands.
Architecture and implementation of a VLIW supercomputer (1990)

Very-long-instruction-word (VLIW) computers achieve high performance by exploiting the fine-grain parallelism present in sequential or vectorizable code. Multiflow's /200 and /300 VLIW systems yielded near-supercomputer performance by this means despite the relatively slow (65 ns) clocks. With its much faster clock period (15 ns) and architectural improvements, the new /500 system attains approximately 4-9* the performance of its predecessors. The authors describe the /500 architecture and implementation (i.e. TRACE/500), with special attention paid to the tradeoffs involved in designing very-high-speed VLIWs. >
The effective treatment of acne vulgaris by a high-intensity, narrow band 405-420 nm light source (2003)

BACKGROUND: Available topical treatments are slow and frequently irritating. Oral therapies may be associated with increased bacterial resistance (antibiotics) or possible severe side effects (oral isotretinoin). In vitro and in vivo exposure of acne bacteria to 405–420 nm ultraviolet (UV) free blue light results in the photo‐destruction of these bacteria through the effects on the porphyrins produced naturally by Propionibacterium acnes. A novel, high‐intensity, narrow band 420 nm UV free blue light has been shown to decrease inflammatory acne lesions after eight bi‐weekly treatments.OBJECTIVES: To examine the effects of high‐intensity, narrow band 420 nm UV free blue light (ClearLight™) on inflammatory acne lesions.METHODS: Three studies were carried out to examine the clinical effects of high‐intensity, narrow band blue light on papulo‐pustular acne: the split‐face dose–response study, the full‐face open trial and the split‐face, double‐blind controlled study. The studies enrolled 10, 13 and 23 patients respectively.RESULTS: The data show more than an 80% response to 420 nm acne phototherapy with a significant reduction of 59–67% of inflammatory acne lesions after only eight treatments of 8–15 minutes. The reduction in lesions was steady in the follow‐ups at 2, 4 and 8 weeks after the end of therapy. Prolonged remission was evident in the 8 weeks after the end of therapy. No adverse effects or patient discomfort were noted in any of the patients.CONCLUSIONS: Acne phototherapy by high intensity, narrow band 405–420 nm light is proven to be an attractive, fast, effective, non‐invasive alternative to current topical and parenteral anti‐acne remedies.
Molecular cloning of olfactomedin, an extracellular matrix protein specific to olfactory neuroepithelium. (1993)

The extracellular mucous matrix of olfactory neuroepithelium is a highly organized structure in intimate contact with chemosensory cilia that house the olfactory transduction machinery. Here we describe the molecular cloning and primary structure of olfactomedin, which is the major component of this extracellular matrix. Olfactomedin is expressed exclusively in olfactory neuroepithelium and its amino acid sequence shows no homologies to any known protein. This olfactory tissue-specific glycoprotein contains cysteines which form disulfide-linked polymers that constitute the primary architecture of the olfactory extracellular matrix. By analogy to other extracellular matrix proteins of the nervous system, olfactomedin may influence the maintenance, growth, or differentiation of chemosensory cilia on the apical dendrites of olfactory neurons.
A catalogue of splice junction and putative branch point sequences from plant introns (1986)

Splice junction and possible branch point sequences have been collected from 177 plant introns. Consensus sequences for the 5' and 3' splice junctions and for possible branch points have been derived. The splice junction consensus sequences were virtually identical to those of animal introns except that the polypyrimidine stretch at the 3' splice junction was less pronounced in the plant introns. A search for possible branch points with sequences related to the yeast, vertebrate and fungal consensus sequences revealed a similar sequence in plant introns.
The Fibronectin-binding MSCRAMM FnbpA ofStaphylococcus aureus Is a Bifunctional Protein That Also Binds to Fibrinogen (2000)

Staphylococcus aureus is an important pathogen capable of causing a wide spectrum of diseases in humans and animals. This bacterium expresses a variety of virulence factors that participate in the process of infection. These include MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) that mediate the adherence of the bacteria to host extracellular matrix components, such as collagen, fibronectin (Fn), and fibrinogen (Fg). Two Fn-binding MSCRAMMs, FnbpA and FnbpB, have been previously identified. The Fn binding activity has been localized to the approximately 40-amino acid residue D repeats in the C-terminal part of these proteins. However, no biological activity has yet been attributed to the N-terminal A regions of these proteins. These regions exhibit substantial amino acid sequence identity to the A regions of other staphylococcal MSCRAMMs, including ClfA, ClfB, and SdrG (Fbe), all of which bind Fg. This raises the question of whether the Fn-binding MSCRAMMs can also bind specifically to Fg. In this report, we show that a recombinant form of the A region of FnbpA does specifically recognize Fg. We localize the binding site in Fg for recombinant FnbpA to the gamma-chain, in particular to the C-terminal residues of this polypeptide, the site also recognized by ClfA. In addition, we demonstrate that recombinant FnbpA can compete with ClfA for binding to both immobilized and soluble Fg. By the use of surface plasmon resonance spectroscopy and fluorescence polarization, we determine the dissociation equilibrium constant for the interaction of recombinant FnbpA with intact immobilized Fg and with a synthetic C-terminal gamma-chain peptide, respectively. Finally, by overexpressing FnbpA in a mutant strain of S. aureus that lacks the expression of both ClfA and ClfB, we show that native FnbpA can mediate the interaction of S. aureus with soluble Fg.
Childhood leukodystrophies: a clinical perspective (2011)

Leukodystrophies are white matter disorders that are genetic in nature. In the young, they represent an important cause of progressive neurological disability. They are frequently recognized on MRI, but their identification remains a challenge. Their diagnosis is important for prognostication, palliative and experimental treatment, as well as family screening. The diagnostic strategy rests upon clinical clues and MRI patterns, complemented by appropriately selected electrophysiological and laboratory testing. Considerable overlap exists between white and gray matter disease, as neuronal degeneration will result in myelin loss. An understanding of the pathophysiology and natural disease evolution is necessary to understand the risks and benefits of experimental and palliative treatments.
Levodopa for the Treatment of Parkinson's Disease (2008)

A 62-year-old man presents with Parkinson's disease, and treatment with levodopa is recommended. Levodopa, a naturally occurring amino acid that is metabolized to dopamine in the brain, is considered the most effective drug available for Parkinson's disease. However, after several years of therapy, serious side effects, including motor fluctuations and dyskinesias, may occur.
The distribution of points on the sphere and corresponding cubature formulae (1999)

In applications, for instance in optics and astrophysics, there is a need for high-accuracy integration formulae for functions on the sphere. To construct better formulae than previously used, almost equidistantly spaced nodes on the sphere and weights belonging to these nodes are required. This problem is closely related to an optimal dispersion problem on the sphere and to the theories of spherical designs and multivariate Gauss quadrature formulae. We propose a two-stage algorithm to compute optimal point locations on the unit sphere and an appropriate algorithm to calculate the corresponding weights of the cubature formulae. Points as well as weights are computed to high accuracy. These algorithms can be extended to other integration problems. Numerical examples show that the constructed formulae yield impressively small integration errors of up to 10-12.
The electrical properties of polycrystalline silicon films (1975)

Boron doses of 1×1012–5×1015/cm2 were implanted at 60 keV into 1-μm-thick polysilicon films. After annealing at 1100 °C for 30 min, Hall and resistivity measurements were made over a temperature range −50–250 °C. It was found that as a function of doping concentration, the Hall mobility showed a minimum at about 2×1018/cm3 doping. The electrical activation energy was found to be about half the energy gap value of single-crystalline silicon for lightly doped samples and decreased to less than 0.025 eV at a doping of 1×1019/cm3. The carrier concentration was very small at doping levels below 5×1017/cm3 and increased rapidly as the doping concentration was increased. At 1×1019/cm3 doping, the carrier concentration was about 90% of the doping concentration. A grain-boundary model including the trapping states was proposed. Carrier concentration and mobility as a function of doping concentration and the mobility and resistivity as a function of temperature were calculated from the model. The theoretical and experimental results were compared. It was found that the trapping state density at the grain bound was 3.34×1012/cm2 located at 0.37 eV above the valence band edge.
The Vent-Like Homeobox Gene VENTX2 Is Expressed in Human Hematopoietic Progenitor Cells and Promotes Human Myeloid Development In Vitro and In Vivo. (2007)

Abstract Recent data indicate that a variety of regulatory molecules active in early development may also play a role in the maintenance of hematopoietic stem cells with repopulating activity. Since it was shown, that the Xvent-2 homeobox gene is part of the BMP-4 signalling pathway in Xenopus, we sought to define the expression profile and function of the human homologue VENTX2 in hematopoietic development. When VENTX2 expression was assessed by TaqMan qRT-PCR in highly purified human cord blood subpopulations, expression of VENTX2 was detected in CD33 and CD15 positive myeloid cells as well as in B and T cells. In addition VENTX2 expression was observed in the primitive CD34+38- human subset as well as in 34+38+ compartment. Furthermore, VENTX2 expression was recurrently detected in bone marrow samples from AML patients at diagnosis as determined by TaqMan qRT-PCR (n=3). In an attempt to characterize the functional relevance of VENTX2 expression for hematopoietic development we retrovirally engineered murine hematopoietic progenitor cells to constitutively express the gene using a MSCV-based retroviral construct with an IRES-EGFP cassette. Successfully transduced cells were injected into lethally irradiated mice or used for in vitro experiments. At the level of the clonogenic progenitor VENTX2 induced myeloid and blocked erythroid differentiation with a significant 1.5 fold increase in the number of CFU-G (n=10; p&lt;0.01) compared to the GFP control and a 5.4 fold decrease in the number of erythroid colonies (n=10; p&lt;0.005) without a change of the total number of colonies produced indicating that VENTX2 promoted granulocytic differentiation in vitro. Re-plating assays showed an over 2 fold increase in the number of secondary CFU-G. In MS-5 murine assay VENTX2 transduced cord blood cells increase CD15+ cells 10.4 fold compared to the control (n=3)(p&lt;0,01). When the effect of VENTX2 was determined on the frequency of LTC-IC by limiting dilution assay (n=2), no major differences were detected between the homeobox gene and the control arm. In NOD/SCID mice VENTX2 induced a 2.9 fold increase in the proportion of CD15+ mature myeloid cells as compared to the GFP control (VENTX2 mean 4 x 106 + 1 x 106 n=7; GFP mean 2x106 cells + 6 x 105 n=9; p&lt;0.02). Using competitive repopulation unit assay (CRU) in NOD/SCID mice we could demonstrate that VENTX2 is able to increase the frequency of CRU cells by 1.8 over GFP control (n=4). These findings characterize VENTX2 as a novel regulatory protein of early human hematopoiesis and extend our knowledge on the regulatory role of non-clustered homeobox genes in hematopoietic development.
Identification of a GABA A Receptor Anesthetic Binding Site at Subunit Interfaces by Photolabeling with an Etomidate Analog (2006)

General anesthetics, including etomidate, act by binding to and enhancing the function of GABA type A receptors (GABA(A)Rs), which mediate inhibitory neurotransmission in the brain. Here, we used a radiolabeled, photoreactive etomidate analog ([(3)H]azietomidate), which retains anesthetic potency in vivo and enhances GABA(A)R function in vitro, to identify directly, for the first time, amino acids that contribute to a GABA(A)R anesthetic binding site. For GABA(A)Rs purified by affinity chromatography from detergent extracts of bovine cortex, [(3)H]azietomidate photoincorporation was increased by GABA and inhibited by etomidate in a concentration-dependent manner (IC(50) = 30 microm). Protein microsequencing of fragments isolated from proteolytic digests established photolabeling of two residues: one within the alphaM1 transmembrane helix at alpha1Met-236 (and/or the homologous methionines in alpha2,3,5), not previously implicated in etomidate function, and one within the betaM3 transmembrane helix at beta3Met-286 (and/or the homologous methionines in beta1,2), an etomidate sensitivity determinant. The pharmacological specificity of labeling indicates that these methionines contribute to a single binding pocket for etomidate located in the transmembrane domain at the interface between beta and alpha subunits, in what is predicted by structural models based on homology with the nicotinic acetylcholine receptor to be a water-filled pocket approximately 50 A below the GABA binding site. The localization of the etomidate binding site to an intersubunit, not an intrasubunit, binding pocket is a novel conclusion that suggests more generally that the localization of drug binding sites to subunit interfaces may be a feature not only for GABA and benzodiazepines but also for etomidate and other intravenous and volatile anesthetics.
Ribonucleases from T2 Family (2002)

Ribonucleases are ubiquitous in distribution. Ribonucleases that hydrolyse RNA to 3' mononucleotides via 2', 3' cyclic nucleotides are classified into three groups, RNase A, RNase T1, and RNase T2 families. Apart from salvage of cellular or extracellular RNAs, RNases participate in vital cellular functions such as DNA replication, transcription and RNA processing, splicing and editing, and control of translation by determining the turnover of RNA. T2 family RNases have been implicated in nutrition, phosphate remobilization, self-incompatibility, senescence, and defense against pathogens. They are important analytical enzymes and have been exploited for the structural determination of RNAs. Although considerable information is available on RNase A and T1 family RNases, less information is available on RNases from T2 family except RNase Rh from Rhizopus niveus and RNase LE from tomato. However, during the last few years, the primary structure, active site nature based on sequence homology, and probable mechanism of action have been postulated for some of these enzymes. RNases of T2 family, their occurrence, purification, characteristics, biological role, and applications have been reviewed.
Increasing Heterogeneity of the ‘a’ Determinant of HBsAg Found in the Presumed Late Phase of Chronic Hepatitis B Virus Infection (1996)

To investigate if the concomitant presence of hepatitis B virus (HBV) DNA and antibodies to hepatitis B surface antigen (anti-HBs) is associated with mutations in the HBV envelope gene, selected sequences of the HBV genome in 54 patients with chronic liver disease, collected from the Wuhan district of China, were amplified by polymerase chain reaction (PCR) and the DNA sequences of the products were determined. The part of the S gene coding for the 'a' determinant of HBsAg was found to be prone to diversity. A total of 19 aberations occurring at 11 of the 69 nucleotide positions of this part of the genome were found in sera from 15 HBsAg-negative but anti-HBs-positive patients. One of 13 HBsAg/HBeAg-positive and 8 of 17 HBsAg/anti-HBe-positive samples also showed point mutations in this gene sequence. Most prevalent was a point mutation from adenine to guanine at nucleotide 530 resulting in a change from threonine to alanine at amino acid position 126. This study highlights that the long time course of chronic HBV infection could favour a selection of escape mutants. The occurrence of such HBV variants in patients with chronic liver disease are not detected by conventional HBV serology, and the patients can therefore easily by be misdiagnosed. If viral mutants like those described here can be transmitted to other patients, there will be difficulties in identifying these infections, and conventional HBV vaccination will presumably not be protective against them.
Natural Killer Cell–Mediated Lysis of Hepatoma Cells via Specific Induction of NKG2D Ligands by the Histone Deacetylase Inhibitor Sodium Valproate (2005)

Natural killer (NK) cells as components of the innate immunity substantially contribute to antitumor immune responses. However, the tumor-associated ligands engaging activating NK cell receptors are largely unknown. An exception are the MHC class I chain-related molecules MICA and MICB and the UL16-binding proteins (ULBP) which bind to the activating immunoreceptor NKG2D expressed on cytotoxic lymphocytes. A therapeutic induction of NKG2D ligands that primes cancer cells for NK cell lysis has not yet been achieved. By microarray studies, we found evidence that treatment of human hepatocellular carcinoma cells with the histone deacetylase inhibitor (HDAC-I) sodium valproate (VPA) mediates recognition of cancer cells by cytotoxic lymphocytes via NKG2D. VPA induced transcription of MICA and MICB in hepatocellular carcinoma cells, leading to increased cell surface, soluble and total MIC protein expression. No significant changes in the expression of the NKG2D ligands ULBP1-3 were observed. The induction of MIC molecules increased lysis of hepatocellular carcinoma cells by NK cells which was abolished by addition of a blocking NKG2D antibody. Importantly, in primary human hepatocytes, VPA treatment did not induce MIC protein expression. Taken together, our data show that the HDAC-I VPA mediates specific priming of malignant cells for innate immune effector mechanisms. These results suggest the clinical evaluation of HDAC-I in solid tumors such as hepatocellular carcinoma, especially in combination with immunotherapy approaches employing adoptive NK cell transfer.
Principles of Nanoflow Liquid Chromatography and Applications to Proteomics (2005)

The low levels of endogenous proteins in biological samples and the large dynamic range of the proteome complicate global analysis of gene expression at the protein level. The use of liquid chromatography (LC) in analytical chemistry is well established. However, the relatively low sensitivity associated with conventional LC makes it unsuitable for the analysis of certain biological samples. Furthermore, the flow rates at which it is operated are not compatible with the use of specific detectors, such as electrospray ionization mass spectrometers. Therefore, due to the analytical demands of biological samples, miniaturized LC techniques were developed to allow for the analysis of samples with greater sensitivity than that afforded by conventional LC. In nanoflow LC (nanoLC) chromatographic separations are performed using flow rates in the range of low nanoliter per minute, which result in high analytical sensitivity due to the large concentration efficiency afforded by this type of chromatography. NanoLC, in combination to tandem mass spectrometry, was first used to analyze peptides and as an alternative to other mass spectrometric methods to identify gel-separated proteins. More recently, gel-free analytical approaches based on LC and nanoLC separations have been developed, which are allowing proteomics to be performed in faster and more comprehensive manner than by using strategies based on the classical 2D gel electrophoresis approach.