gebhart/patrepeval huggingface dataset:
Porting a vector library: a comparison of MPI, Paris, CMMD and PVM (2002)

The paper describes the design and implementation in MPI of the parallel vector library CVL, which is used as the basis for implementing nested data-parallel languages such as NESL and Proteus. We outline the features of CVL, and compare the ease of writing and debugging the portable MPI implementation with our experiences writing previous versions in CM-2 Paris, CM-5 CMMD, and PVM 3.0. We give initial performance results for MPI CVL running on the SP-1, Paragon, and CM-5, and compare them with previous versions of CVL running on the CM-2, CM-5, and Cray C90. We discuss the features of MPI that helped and hindered the effort, and make a plea for better support for certain primitives. Finally, we discuss the design limitations of CVL when implemented on current RISC based MPP architectures, and outline our plans to overcome this by using MPI as a compiler target.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Viscosupplementation: Therapeutic Mechanisms and Clinical Potential in Osteoarthritis of the Knee (2000)

Viscosupplementation by means of intra-articular injections of hyaluronic acid has been used to treat osteoarthritis of the knee. The proposed mechanisms of action result from the physical properties of hyaluronic acid, as well as from its anti-inflammatory, anabolic, local analgesic, and chrondroprotective effects. Adverse reactions from hyaluronic acid injections into the knee occurred in 8.3% of the 336 patients treated in one study, but at a rate of less than 3% per injection. Reactions were almost always local and generally resolved over 1 to 2 days. Hyaluronic acid injections were approved by the US Food and Drug Administration as a medical device; thus, the level of efficacy demonstrated is less than might have been required for approval as a drug. Several studies have failed to show statistically significant benefit compared with placebo. Furthermore, the treatment is relatively expensive; the cost of the drug for a series of injections is more than $500 per knee. Therefore, widespread use of these agents should be limited until more convincing data on their efficacy are available from well-designed clinical trials.
Why Aren't Operating Systems Getting Faster As Fast as Hardware? (1990)

research relevant to the design and application of high performance scientific computers. We test our ideas by designing, building, and using real systems. The systems we build are research prototypes; they are not intended to become products. There is a second research laboratory located in Palo Alto, the Systems Research Center (SRC). Other Digital research groups are located in Paris (PRL) and in Cambridge,
The movements and innervation of the small intestine (1899)

Physiological Laboratory, Guy's Ilospital
Enhanced UV photosensitivity in boron codoped germanosilicate fibres (1993)

Boron codoped germanosilcate fibres are shown to be highly photosensitive. A UV written 1.53 μm Bragg grating with 95% reflectivity and a 1.1nm bandwidth is formed with a UV intensity as low as 1W/cm2 in only 10 min.
Multiwall carbon nanotubes (2000)

In 1991 Sumio Iijima used a high-resolunon transmission electron microscope to study the soot created in an electrical discharge between two carbon electrodes at the NEC Fundamental Research Laboratory in Tsukuba, Japan. He found that the soot contained structures that consisted of several concentric tubes of carbon, nested inside each other like Russian dolls.
A novel immunosuppressive agent FTY720 induced Akt dephosphorylation in leukemia cells (2003)

1. Our previous studies revealed that the immunosuppressive agent, FTY720, mainly induces mitochondria-involved apoptosis in some types of cancer cells, since Bcl-2 overexpression prevents the FTY720-induction of apoptotic stimuli. Furthermore, FTY720 induces G0/G1 cell cycle arrest. The present study further examines the correlation between intracellular signaling kinases with FTY720-induced mitochondria-involved apoptosis. 2. Human T cell leukemia Jurkat was exposed to FTY720. Dephosphorylation of Akt occurred in a time- and concentration-dependent manner. FTY720 also induced Bad (Ser(136)) and ribosomal p70S6 kinase (p70(S6k)) (Thr(389)) dephosphorylation. 3. FTY720-induced Akt dephosphorylation was not because of Akt upstream phosphatidylinositol 3'-kinase (PI 3-kinase) pathway inhibition. 4. FTY720 also induced Akt dephosphorylation in human B cell leukemia BALL-1. BALL-1 cells were resistant to FTY720-induced apoptosis. 5. Okadaic acid (OA) inhibited the FTY720-induced dephosphorylation of Akt and p70(S6k), suggesting that FTY720 promotes Ser/Thr protein phosphatase (PP) activity. 6. OA partially inhibited FTY720-induced caspase-3 activation. 7. PP2A or PP2A-like phosphatase was temporarily activated in cells exposed to FTY720. In addition, FTY720 activated purified PP2A (ABC). 8. Overall, the results suggest that FTY720 activated PP2A or PP2A-like phosphatase and dephosphorylated Akt pathway factors resulting in the enhancement of apoptosis via mitochondria.
Comparison of biosensor platforms in the evaluation of high affinity antibody-antigen binding kinetics (2016)

The acquisition of reliable kinetic parameters for the characterization of biomolecular interactions is an important component of the drug discovery and development process. While several benchmark studies have explored the variability of kinetic rate constants obtained from multiple laboratories and biosensors, a direct comparison of these instruments' performance has not been undertaken, and systematic factors contributing to data variability from these systems have not been discussed. To address these questions, a panel of ten high-affinity monoclonal antibodies was simultaneously evaluated for their binding kinetics against the same antigen on four biosensor platforms: GE Healthcare's Biacore T100, Bio-Rad's ProteOn XPR36, ForteBio's Octet RED384, and Wasatch Microfluidics's IBIS MX96. We compared the strengths and weaknesses of these systems and found that despite certain inherent systematic limitations in instrumentation, the rank orders of both the association and dissociation rate constants were highly correlated between these instruments. Our results also revealed a trade-off between data reliability and sample throughput. Biacore T100, followed by ProteOn XPR36, exhibited excellent data quality and consistency, whereas Octet RED384 and IBIS MX96 demonstrated high flexibility and throughput with compromises in data accuracy and reproducibility. Our results support the need for a "fit-for-purpose" approach in instrument selection for biosensor studies.
Simultaneous Activation of Viral Antigen-specific Memory CD4+ and CD8+ T-cells Using mRNA-electroporated CD40-activated Autologous B-cells (2006)

Recently, it has become obvious that not only CD8 T-cells, but also CD4 T-helper cells are required for the induction of an effective, long-lasting cellular immune response. In view of the clinical importance of cytomegalovirus (CMV) and human immunodeficiency virus (HIV) infection, we developed 2 strategies to simultaneously reactivate viral antigen-specific memory CD4 and CD8 T-cells of CMV-seropositive and HIV-seropositive subjects using mRNA-electroporated autologous CD40-activated B cells. In the setting of HIV, we provide evidence that CD40-activated B cells can be cultured from HAART-naive HIV-1 seropositive patients. These cells not only express and secrete the HIV p24 antigen after electroporation with codon-optimized HIV-1 gag mRNA, but can also be used to in vitro reactivate Gag antigen-specific interferon-gamma-producing CD4 and CD8 autologous T-cells. For the CMV-specific approach, we applied mRNA coding for the pp65 protein coupled to the lysosomal-associated membrane protein-1 to transfect CD40-activated B cells to induce CMV antigen-specific CD4 and CD8 T-cells. More detailed analysis of the activated interferon-gamma-producing CMV pp65 tetramer positive CD8 T-cells revealed an effector memory phenotype with the capacity to produce interleukin-2. Our findings clearly show that the concomitant activation of both CD4 and CD8 (memory) T-cells using mRNA-electroporated CD40-B cells is feasible in CMV and HIV-1-seropositive persons, which indicates the potential value of this approach for application in cellular immunotherapy of infectious diseases.
Abstract 154: Vaccination Using Advanced Glycation End Product of Low-Density Lipoprotein Pulsed Dendritic Cells Reduces Atherosclerosis in Diabetic Apoe -/- Mice (2012)

Rationale and Objective Accumulation of advanced glycation end-product of low density lipoprotein (AGE-LDL) attributable to hyperglycemia in diabetes contributes to the progression of atherosclerosis (AS). Previous studies showed that immunization against modified LDL reduce AS in animal models. Due to their potent capacity to stimulate T cells, dendritic cells (DCs) are being investigated in immunotherapy approaches. In this study, we immunized AGE-LDL pulsed DCs to diabetic apoE -/- mice and examined the effects on AS. Methods and results The present study explored AS in streptozotocin-induced diabetic apoE -/- mice that were randomized (n=36) to receive no treatment, AGE-LDL pulsed DCs immunization, or ovalbumin (AS-irrelevant antigen) pulsed DCs immunization. Bone marrow-derived DCs were cultured for 10 days in the presence of granulocyte-macrophage colony-stimulating factor. Immature DCs were matured by lipopolysaccharide and pulsed with AGE-LDL or ovalbumin. These DCs were transferred five times to diabetic apoE -/- mice before the induction of AS by western-type diet feeding. Vaccination using AGE-LDL pulsed DCs resulted in a marked reduction in aortic root and carotid artery lesion size, and an increase in plaque stability which was independent of hypercholesterolemia in mice. Transfer of ovalbumin pulsed DCs did not influence lesion size or stability. Vaccination using AGE-LDL pulsed DCs resulted in AGE-LDL-specific Th1 cell activation, and induction of AGE-LDL-specific IgG. Furthermore, AGE-LDL pulsed DCs transfer resulted in impressed function of macrophages with a marked inhibition of TLR4-mediated signaling pathway. Conclusion These findings demonstrate for the first time that vaccination with AGE-LDL-pulsed DCs provides a novel strategy for the immunomodulation of atherosclerosis in diabetes.
Polyhistidine Affinity Chromatography for Purification and Biochemical Analysis of Fungal Cell Wall-Degrading Enzymes (2012)

Polyhistidine Affinity Chromatography for Purification and Biochemical Analysis of Fungal Cell Wall-Degrading Enzymes
Pointing the Unknown Words (2016)

The problem of rare and unknown words is an important issue that can potentially influence the performance of many NLP systems, including both the traditional count-based and the deep learning models. We propose a novel way to deal with the rare and unseen words for the neural network models using attention. Our model uses two softmax layers in order to predict the next word in conditional language models: one predicts the location of a word in the source sentence, and the other predicts a word in the shortlist vocabulary. At each time-step, the decision of which softmax layer to use choose adaptively made by an MLP which is conditioned on the context.~We motivate our work from a psychological evidence that humans naturally have a tendency to point towards objects in the context or the environment when the name of an object is not known.~We observe improvements on two tasks, neural machine translation on the Europarl English to French parallel corpora and text summarization on the Gigaword dataset using our proposed model.
Anisotropic elasticity of jarosite: A high-P synchrotron XRD study (2009)

The elastic properties of jarosite were investigated using synchrotron X-ray diffraction coupled with a multi-anvil apparatus at pressures up to 8.1 GPa. With increasing pressure, the c dimension contracts much more rapidly than a, resulting in a large anisotropy in compression. This behavior is consistent with the layered nature of the jarosite structure, in which the (001) [Fe(O,OH)6]/[SO4] sheets are held together via relatively weak K-O and hydrogen bonds. Fitting of the measured unit-cell parameters to the second-order Birch-Murnaghan equation of state yielded a bulk modulus of 55.7 ± 1.4 GPa and zero-pressure linear compressibilities of 3.2 × 10-3 GPa-1 for the a axis and 13.6 × 10-3 GPa-1 for the c axis. These parameters represent the first experimental determination of the elastic properties of jarosite.
Single depth image super resolution and denoising via coupled dictionary learning with local constraints and shock filtering (2014)

Recently, consumer depth cameras have gained significant popularity due to their affordable cost. However, the limited resolution and quality of the depth map generated by these cameras are still problems for several applications. In this paper, we propose a new algorithm for depth image super resolution using a single depth image as input. We reconstruct the corresponding high resolution depth map through a robust coupled dictionary learning algorithm with local coordinate constraints. The local constraints remove the prediction uncertainty and prevent the dictionary from over-fitting. We also incorporate an adaptively regularized Shock filter to simultaneously reduce the noise and sharpen the edges. Experimental results demonstrate the effectiveness of our proposed algorithm compared to previously reported methods.
Synthesis of Bivalent Lactosides Based on Terephthalamide,N,N′-Diglucosylterephthalamide, and Glycophane Scaffolds and Assessment of Their Inhibitory Capacity on Medically Relevant Lectins (2009)

Glycan recognition by lectins initiates clinically relevant processes such as toxin binding or tumor spread. Thus, the development of potent inhibitors has a medical perspective. Toward this goal, we report the synthesis of both rigid and flexible bivalent lactosides on scaffolds that include secondary and tertiary terephthalamides and N,N'-diglucosylterephthalamides. Construction of these compounds involved Schmidt-Michel glycosidation, and amide coupling or Ugi reactions of relevant glycosyl amines in key steps. A glycocluster based on a rigid glycophane was also prepared from coupling of a glucuronic acid derivative and p-xylylenediamine with subsequent ring-closing metathesis. Finally, a more flexible bivalent lactoside was produced from lactosyl azide with use of the copper-catalyzed azide-alkyne cycloaddition. Distances between lactose residues were analyzed computationally as were their orientations for the relatively rigid subset of compounds. Distinct spacing properties were revealed by varying the structure of the scaffold or by varying the location of the lactose residue on the scaffold. To relate these features to bioactivity a plant toxin and human adhesion/growth-regulatory galectins were used as sensors in three types of assay, i.e. measuring agglutination of erythrocytes, binding to glycans of a surface-immobilized glycoprotein, or binding to human cells. Methodologically, the common hemeagglutination assay was found to be considerably less sensitive than both solid-phase and cell assays. The bivalent compounds were less effective at interfering with glycoprotein binding to the plant toxin than to human lectins. Significantly, a constrained compound was identified that displayed selectivity in its inhibitory potency between galectin-3 and its proteolytically processed form. Conversely, compounds with a high degree of flexibility showed notable ability to protect human cells from plant toxin binding. The applied conjugation chemistry thus is compatible with the long-term aim to produce potent and selective lectin inhibitors.
A new mass spectrometric approach to detect modifications in DNA (1994)

A new approach is described for the enzymatic digestion of DNA yielding oligonucleotides ranging from dinucleoside monophosphates to octanucleoside heptaphosphates. DNA was digested by means of the benzon nuclease, an unspecific nuclease, and alkaline phosphatase to remove the terminal phosphate. The mixture of oligonucleotides was separated using capillary-zone electrophoresis with a buffer system, yielding a rather strong electro-osmotic flow. The oligomers are separated into groups with nucleotides of the same chain length. The separation capillary was used as the innermost capillary of an electrospray spraying system. Negative molecular ions of the nucleotides were recorded using a home-built interface and ion source for a sector-field mass spectrometer. This approach allows the facile detection of DNA modifications since they lead not only to differences in mass, but also can possess altered electrophoretic mobility. For modifying reactions which exhibit sequence specificity, the information is retained in the oligomers. Thus, reactions of DNA with electrophiles can be evaluated at different levels, since in longer chains, even complex sequence specificity may be apparent. Results from calf thymus DNA digests and preliminary experiments with DNA adducts with styrene oxide are discussed.
In vivo detection of intervertebral disk injury using a radiolabeled monoclonal antibody against keratan sulfate. (2001)

Our data suggest that antibodies against nucleus pulposus components, such as proteoglycans, can be used for in vivo detection of intervertebral disk injury. This finding is in spite of the minimal circulation present in intervertebral disks.
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection (2009)

Identification of the transmitted/founder virus makes possible, for the first time, a genome-wide analysis of host immune responses against the infecting HIV-1 proteome. A complete dissection was made of the primary HIV-1-specific T cell response induced in three acutely infected patients. Cellular assays, together with new algorithms which identify sites of positive selection in the virus genome, showed that primary HIV-1-specific T cells rapidly select escape mutations concurrent with falling virus load in acute infection. Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell-mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection. After virus escape, these first T cell responses often rapidly waned, leaving or being succeeded by T cell responses to epitopes which escaped more slowly or were invariant. These latter responses are likely to be important in maintaining the already established virus set point. In addition to mutations selected by T cells, there were other selected regions that accrued mutations more gradually but were not associated with a T cell response. These included clusters of mutations in envelope that were targeted by NAbs, a few isolated sites that reverted to the consensus sequence, and bystander mutations in linkage with T cell-driven escape.
Abstract 5510: Arginine Methylation Index as Integrated Quantification of Arginine Methylation Provides Stronger Independent Risk Prediction of Long-term Cardiovascular Events than Individual Methylated Arginine Metabolites (2008)

Background: The prognostic value of asymmetric dimethylarginine (ADMA) is attributed to its role as an endogenous inhibitor of nitric oxide synthases (NOS). The relationship of related post-translational modification products of arginine methylation and cardiovascular disease (CVD) risks is uncertain. Methods: Plasma was isolated from 1,011 subjects undergoing diagnostic cardiac catheterization, and future major adverse cardiac events (MACE, including myocardial infarction, stroke, and death) were investigated. Levels of ADMA, symmetric dimethylarginine (SDMA), and N-mono-methylarginine (MMA) were quantified by mass spectrometry, and their ratios [(ADMA+SDMA)/MMA], the arginine methylation index (Methy-I Arg ), were determined. Results: After adjusting for Framingham risk factors, CRP, and creatinine clearance, elevated (4th vs. 1st quartile) plasma levels of both SDMA [2.0-fold (95%CI, 1.3–3.1)] and ADMA [1.5-fold (95%CI, 1.00–2.4)] remained associated with higher prevalence of CVD, whereas elevated levels of MMA [0.56-fold (95%CI, 0.36–0.87)] were paradoxically associated with lower CVD. While elevated ADMA and SDMA levels remained significant predictors, MethyI Arg was the strongest independent predictor of incident MACE[2.4-fold (95%CI, 1.3 to 4.5)]. Conclusions: An integrated quantification of arginine methylation in the form of an “Arginine Methylation Index” provided the strongest independent risk prediction for incident major adverse cardiac events in stable patients undergoing elective cardiac evaluation, and significantly added to the prognostic utility of traditional risk factors.
Synthesis of Multiarm Star Poly(glycerol)-block-Poly(2-hydroxyethyl methacrylate) (2006)

Well-defined multiarm star block copolymers poly(glycerol)-b-poly(2-hydroxyethyl methacrylate) (PG-b-PHEMA) with an average of 56, 66, and 90 PHEMA arms, respectively, have been prepared by atom transfer radical polymerization (ATRP) of HEMA in methanol by a core-first strategy. The hyperbranched macroinitiators employed were prepared on the basis of well-defined hyperbranched polyglycerol by esterification with 2-bromoisobutyryl bromide. Polydispersites M(w)/M(n) of the new multiarm stars were in the range of 1.11-1.82. Unexpectedly, with the combination of CuCl/CuBr(2)/2,2'-bipyridyl as catalyst, the polymerization conversion can be driven to maximum values of 79%. The control of CuCl catalyst concentration is also very important to achieve high conversion and narrow polydispersity. The absolute M(n) values of the obtained multiarm star polymers were in good agreement with the calculated ones, and the highest M(n) values of the multiarm star copolymer is around 10(6) g/mol. Kinetic analysis shows that an induction period exists in the polymerization of HEMA. After this induction period, a linear dependence of ln ([M](0)/[M](t)()) on time was observed. Due to the star architecture, the viscosity of the obtained multiarm star PHEMA is much lower than that of linear PHEMA.
Sparsesense: Application of compressed sensing in parallel MRI (2008)

Compressed sensing (CS) has recently drawn great attentions in the MRI research community. The most desirable property of CS in MRI application is that it allows sampling of k-space well below Nyquist sampling rate, while still being able to reconstruct the image if certain conditions are satisfied. Recent work has successfully applied CS to reduce scanning time in conventional Fourier imaging. In this paper, the application of CS to parallel imaging, a fast imaging technique, is investigated to achieve an even higher imaging speed. The sampling scheme for incoherence is discussed and reconstruction method using Begman iteration is proposed. Our experiments show that the combined method, named SparseSENSE, can achieve a reduction factor higher than the number of channels.
Clinical Experience With the Prevention of Rh‐lsoimmunization: A Historical Comparative Analysis (1984)

Clinical experience with prevention of Rh-immunization is reviewed. The pathogenesis of hemolytic disease and the chemistry of prophylaxis is explained. The factors which effect antigenic expression are delineated. The clinical indications for prevention of AMIS are reviewed. International data pertaining to Rhesonativ are presented from postpartum trials and antepartum trials. A protocol for antepartum administration of anti-Rh immunoglobulin is given.