gebhart/patrepeval huggingface dataset:
Kernel Weaver: Automatically Fusing Database Primitives for Efficient GPU Computation (2012)

Data warehousing applications represent an emerging application arena that requires the processing of relational queries and computations over massive amounts of data. Modern general purpose GPUs are high bandwidth architectures that potentially offer substantial improvements in throughput for these applications. However, there are significant challenges that arise due to the overheads of data movement through the memory hierarchy and between the GPU and host CPU. This paper proposes data movement optimizations to address these challenges. Inspired in part by loop fusion optimizations in the scientific computing community, we propose kernel fusion as a basis for data movement optimizations. Kernel fusion fuses the code bodies of two GPU kernels to i) reduce data footprint to cut down data movement throughout GPU and CPU memory hierarchy, and ii) enlarge compiler optimization scope. We classify producer consumer dependences between compute kernels into three types, i) fine-grained thread-to-thread dependences, ii) medium-grained thread block dependences, and iii) coarse-grained kernel dependences. Based on this classification, we propose a compiler framework, Kernel Weaver, that can automatically fuse relational algebra operators thereby eliminating redundant data movement. The experiments on NVIDIA Fermi platforms demonstrate that kernel fusion achieves 2.89x speedup in GPU computation and a 2.35x speedup in PCIe transfer time on average across the micro-benchmarks tested. We present key insights, lessons learned, measurements from our compiler implementation, and opportunities for further improvements.
Neural Modeling of Human Behavior: A Proposal for A New Type of Modifiable Synapse (1977)

Presently published neural models for the stimulation of human behavior have reached a limit in terms of their ability to account for the complexity and magnitude of such behavior. In this paper, these limitations are explored, and a new model is presented which overcomes them. The model employs a new type of modifiable synapse which allows for the integration of three separate bits of information rather than the conventional two bits.
Live demonstration: A versatile, low-cost platform for testing large ReRAM cross-bar arrays (2014)

We demonstrate a practical application of memristors in a cross-bar memory array. The full set-up consists of only a PC, an mBED microcontroller and a PCB hosting external components and the memristor cross-bar chip. The system can be used for general purpose memory storage, but in this case we use it as a binary image storage device. A MATLAB interface allows the user to load a binary image into the memory and observe the resulting internal memory states of each memristor in the array along with key performance metrics describing the speed and degree of success of the memory `write' operation.
Riluzole — What is its Impact in Our Treatment and Understanding of Amyotrophic Lateral Sclerosis? (1997)

Riluzole marks the beginning of pharmacotherapy for patients with ALS. Our task is to fully identify the impact of riluzole in ALS treatment. The ALS Clinical Assessment Research and Education (ALS CARE) is an ambitious database in North America created to establish the benchmarks for patient care and management. Such a program may allow us to analyze the use and impact of riluzole in the treatment of ALS. In the spring of 1997, just 1 year since the approval of riluzole, several more potential drugs for ALS are on the horizon. If a single medication is not sufficient to alter the disease course significantly, we must investigate drug combinations to determine potential additive or synergistic benefits. Although far from ideal, riluzole is allowing clinicians and researchers to lift a corner of the veil surrounding ALS to glimpse the possibility of effective treatment.
Well-Defined Oligosaccharide-Terminated Polymers from Living Radical Polymerization (2000)

beta-cyclodextrin has been transformed into an initiator for copper(I)-mediated living radical polymerization via successive acetylation, ring opening, and condensation reactions. This glycoinitiator has been successfully used to prepare a range of methacrylate polymers, which show all characteristics of living polymerization. Poly(methyl methacrylate) is prepared with an Mn of 10,100 g/mol (theoretical Mn = 10,900) and polydispersity of 1.09. Excellent first-order kinetics and an evolution of mass with time are presented. Hydrophilic polymers based on poly(ethylene glycol), glucose and tertiary amine monomers are successfully prepared with terminal maltoheptose units. Polymerization of styrene results in a broadening of the polydispersity to 1.48 while maintaining good control over the Mn. The acetyl protecting groups on the maltoheptose terminal unit are easily removed in all cases to give the hydroxylated sugar, as shown by NMR. These results demonstrate the applicability of utilizing glycoinitiators as a new, versatile route to a wide range of glycopolymers. The polymerization chemistry is inert to the sugar functionality allowing glyco units to be precisely placed within a synthetic macromolecule with all the associated advantages of living polymerization.
Dipyrrin based luminescent cyclometallated palladium and platinum complexes (2009)

A series of complexes based on the combination of cyclometallated palladium or platinum moieties with functionalized dipyrrin ligands bearing mesityl- or benzonitrile groups have been prepared and characterized both in the solid state and in solution; these compounds exhibit a characteristic dipyrrin-centered luminescence with an emission intensity modulated by the degree of rotational freedom of the aromatic group attached to the dipyrrin chelate.
EXPERIMENTAL AUTOIMMUNE MYASTHENIA GRAVIS: CELLULAR AND HUMORAL IMMUNE RESPONSES* (1976)

Rats inoculated intradermally with eel acetylcholine receptor protein(AChR) with adjuvants developed autoimmunity to skeletal muscle AChR. This is evidenced clinically as two episodes of experimental autoimmune myasthenia gravis (EAMG), an acute phase that occurs early (8 days) and is transient, and a chronic phase (30 days) that is usually progressive. Positive delayed cutaneous reactivity appeared at day 4 and serum antibody to eel AChR was detectable by day 7 postinoculation. After day 25 the titer of antibody to syngeneic muscle AChR rose abruptly. Antibody to muscle AChR sedimented as 7S. Lymph node cells from rats sensitized to AChR were capable of transferring EAMG to normal recipients. Thymectomy after the onset of EAMG had no effect. Early treatment in vivo with antithymocyte serum suppressed acute but not chronic phase EAMG. Experiments combining thymectomy, x-irradiation and reconstitution with distinct populations of lymphocytes indicated athat thymus-derived lymphocytes are required for induction of EAMG and antibody to AChR. These data suggest that both cellular and humoral responses to AChR, either sequentially or in combination, contribute to the pathogenesis of EAMG.
Gremlin utilizes canonical and non-canonical TGFβ signaling to induce lysyl oxidase (LOX) genes in human trabecular meshwork cells (2013)

The TGFβ/BMP signaling pathways are involved in glaucomatous damage to the trabecular meshwork (TM) leading to elevated intraocular pressure (IOP), which is a major risk factor for the development and progression of glaucoma. The BMP antagonist gremlin is elevated in glaucomatous TM cells and tissues and can directly elevate IOP. Gremlin utilizes the TGFβ2/SMAD pathway to induce TM extracellular matrix (ECM) proteins. The purpose of this study is to determine whether expression of the ECM cross-linking lysyl oxidase (LOX) genes is regulated by gremlin in cultured human TM cells. Human TM cells were treated with recombinant gremlin, and expression of the LOX genes was examined by quantitative RT-PCR and western immunoblotting. TM cells were pretreated with TGFBR inhibitors (LY364947 or SB431542), an inhibitor of the SMAD signaling pathway (SIS3), or with JNK (SP600125) and p38 MAPK (SB203580) inhibitors to identify the signaling pathway(s) involved in gremlin induction of LOX protein expression. All five LOX genes (LOX and LOXL1-4) were induced by gremlin. Gremlin induction of LOX genes and protein expression was blocked by TGFBR inhibitors as well as by inhibitors of the SMAD3, JNK and p38 MAPK signaling pathways. We conclude that gremlin employs both canonical TGFβ/SMAD and the non-canonical JNK and p38 MAPK signaling pathways to induce LOX genes and proteins in cultured human TM cells. Increased LOX levels may be at least partially responsible for gremlin-mediated IOP elevation and increased aqueous humor outflow resistance leading to glaucoma.
New nozzle improves FCC feed atomization, unit yield patterns (1994)

Bordetella pertussis was detected by spectrofluorometry following PCR incorporating a molecular beacon probe in the reaction. A DNA fragment from the tandem repeat sequence region (IS 481) of the genome of B. pertussis was amplified in presence of the probe complementary to an internal segment of the amplified DNA fragment. Fluorescein (FAM) and DABCYL were used as the fluorophore and quencher in the probe. The probe was characterized for its signal to noise ratio by homogeneous solution hybridization with a complementary oligonucleotide. Measurement of fluorescent signal at the emission maxima of FAM, immediately after a PCR was used to detect the B. pertussis target, with no additional steps. Presence of B. pertussis in a sample was also examined by agarose gel electrophoresis of the PCR product. A serial diluted stock of B. pertussis (ATCC strain #9797) and fourteen clinical isolates of B. pertussis were examined. The sensitivity of detection by fluorescent measurement was found to be at least in the range of 0.01-0.1 CFU per 10 microl of the sample and was equal to or better than that detected by agarose gel analysis.
ADVANCED MOBILE TRAFFIC INFORMATION AND COMMUNICATION SYSTEM (1990)

This paper gives an overview of the AMTICS advanced traffic information and navigation system. Through a screen display in each vehicle, the system provides traffic information relating to congestion, regulation, road work, and real-time parking. It also provides information on the vehicle's current position and the intended navigation route.
Organization of the human immunoglobulin lambda light-chain locus on chromosome 22q11.2 (1995)

The maps of the human immunoglobulin heavy-chain and kappa light-chain loci have recently been completed. We have now completed a map of the human lambda locus (IGL) located on chromosome 22q11.2. We mapped 52 V lambda genes from 10 V lambda families and 7 J lambda and C lambda genes on a 1140 kb contig constructed from eight YACs and 129 cosmid clones. The V lambda genes are arranged within 800 kb. Genes of the different V lambda families are organized in three clusters, V lambda II and III families (cluster A); V lambda I, V, VII and IX families (cluster B); V lambda IV, VI, VIII and X families (cluster C), in contrast to the dispersed organization of the different VH and V kappa families within the human VH and V kappa loci. We note that the most frequently used V lambda families (V lambda II and III) are proximal to the J lambda and C lambda genes. The VpreB gene, encoding part of the surrogate light chain, the GGT2 gene and the BCRL4 pseudogene were also mapped within the lambda locus.
Survey of Infections Due toStaphylococcusSpecies: Frequency of Occurrence and Antimicrobial Susceptibility of Isolates Collected in the United States, Canada, Latin America, Europe, and the Western Pacific Region for the SENTRY Antimicrobial Surveillance Program, 1997–1999 (2001)

Between January 1997 and December 1999, bloodstream isolates from 15,439 patients infected with Staphylococcus aureus and 6350 patients infected with coagulase-negative Staphylococcus species (CoNS) were referred by SENTRY-participating hospitals in the United States, Canada, Latin America, Europe, and the Western Pacific region. S. aureus was found to be the most prevalent cause of bloodstream infection, skin and soft-tissue infection, and pneumonia in almost all geographic areas. A notable increase in methicillin (oxacillin) resistance among community-onset and hospital-acquired S. aureus strains was observed in the US centers. The prevalence of methicillin (oxacillin)-resistant S. aureus varied greatly by region, site of infection, and whether the infection was nosocomial or community onset. Rates of methicillin resistance were extremely high among S. aureus isolates from centers in Hong Kong and Japan. Uniformly high levels of methicillin resistance were observed among CoNS isolates. Given the increasing multidrug resistance among staphylococci and the possible emergence of vancomycin-resistant strains, global strategies are needed to control emergence and spread of multiply resistant staphylococci.
Phosphorylation of tau by glycogen synthase kinase 3β affects the ability of tau to promote microtubule self-assembly (1997)

To study the effects of phosphorylation by glycogen synthase kinase-3beta (GSK-3beta) on the ability of the microtubule-associated protein tau to promote microtubule self-assembly, tau isoform 1 (foetal tau) and three mutant forms of this tau isoform were investigated. The three mutant forms of tau had the following serine residues, known to be phosphorylated by GSK-3, replaced with alanine residues so as to preclude their phosphorylation: (1) Ser-199 and Ser-202 (Ser-199/202-->Ala), (2) Ser-235 (Ser-235-->Ala) and (3) Ser-396 and Ser-404 (Ser-396/404-->Ala). Wild-type tau and the mutant forms of tau were phosphorylated with GSK-3beta, and their ability to promote microtubule self-assembly was compared with the corresponding non-phosphorylated tau species. In the non-phosphorylated form, wild-type tau and all of the mutants affected the mean microtubule length and number concentrations of assembled microtubules in a manner consistant with enhanced microtubule nucleation. Phosphorylation of these tau species with GSK-3beta consistently reduced the ability of a given tau species to promote microtubule self-assembly, although the affinity of the tau for the microtubules was not greatly affected by phosphorylation since the tau species remained largely associated with the microtubules. This suggests that the regulation of microtubule assembly can be controlled by phosphorylation of tau at sites accessible to GSK-3beta by a mechanism that does not necessarily involve the dissociation of tau from the microtubules.
LARS: A Location-Aware Recommender System (2012)

This paper proposes LARS, a location-aware recommender system that uses location-based ratings to produce recommendations. Traditional recommender systems do not consider spatial properties of users nor items, LARS, on the other hand, supports a taxonomy of three novel classes of location-based ratings, namely, spatial ratings for non-spatial items, non-spatial ratings for spatial items, and spatial ratings for spatial items. LARS exploits user rating locations through user partitioning, a technique that influences recommendations with ratings spatially close to querying users in a manner that maximizes system scalability while not sacrificing recommendation quality. LARS exploits item locations using travel penalty, a technique that favors recommendation candidates closer in travel distance to querying users in a way that avoids exhaustive access to all spatial items. LARS can apply these techniques separately, or in concert, depending on the type of location-based rating available. Experimental evidence using large-scale real-world data from both the Foursquare location-based social network and the Movie Lens movie recommendation system reveals that LARS is efficient, scalable, and capable of producing recommendations twice as accurate compared to existing recommendation approaches.
Pathways to clinical CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease (2017)

Three-dimensional tissue-structural relationships are not well captured by typical thin-section histology, posing challenges for the study of tissue physiology and pathology. Moreover, while recent progress has been made with intact methods for clearing, labeling, and imaging whole organs such as the mature brain, these approaches are generally unsuitable for soft, irregular, and heterogeneous tissues that account for the vast majority of clinical samples and biopsies. Here we develop a biphasic hydrogel methodology, which along with automated analysis, provides for high-throughput quantitative volumetric interrogation of spatially-irregular and friable tissue structures. We validate and apply this approach in the examination of a variety of developing and diseased tissues, with specific focus on the dynamics of normal and pathological pancreatic innervation and development, including in clinical samples. Quantitative advantages of the intact-tissue approach were demonstrated compared to conventional thin-section histology, pointing to broad applications in both research and clinical settings.
A phase II trial of paclitaxel and cisplatin in patients with advanced carcinoma of the esophagus. (2001)

The combination of paclitaxel and cisplatin has significant activity in esophageal adenocarcinoma. Because of hospitalization for toxicity and deaths resulting from treatment, the combination of paclitaxel and cisplatin used in this trial cannot be recommended. The optimal dose and schedule of paclitaxel/cisplatin combination therapy remain to be established.
Recognition of the influenza hemagglutinin by class II MHC-restricted T lymphocytes and antibodies. I. Site definition and implications for antigen presentation and T lymphocyte recognition (1991)

We have identified the site encompassing residues 126-145 on the A/Japan/57 influenza hemagglutinin molecule that is recognized in association with HLA-DRw11 by a clonal population of human, influenza specific, CD4+ cytolytic T lymphocytes. The critical core sequence of the T cell determinant spans hemagglutinin residues 129-140 and overlaps a putative antibody binding site. Hemagglutinins of influenza field strains that are not recognized by the T cell clones contain sequence alterations within the 129-140 target site of the CD4+ T cells. Functional analyses, with synthetic peptides, of the contribution of each of the residues within the sequence toward the capacity of the antigenic fragment to associate with both the restriction element and the TCR revealed a continuous linear array of residues necessary for MHC binding and/or Ag receptor engagement. At least one residue, the lysine at position 134, was shown to be critical for both DRw11 association and TCR recognition. The significance of these findings for recognition of glycoproteins by human CD4+ T cells is discussed.
Probing the Limits of Genetic Recoding in Essential Genes (2013)

Engineering radically altered genetic codes will allow for genomically recoded organisms that have expanded chemical capabilities and are isolated from nature. We have previously reassigned the translation function of the UAG stop codon; however, reassigning sense codons poses a greater challenge because such codons are more prevalent, and their usage regulates gene expression in ways that are difficult to predict. To assess the feasibility of radically altering the genetic code, we selected a panel of 42 highly expressed essential genes for modification. Across 80 Escherichia coli strains, we removed all instances of 13 rare codons from these genes and attempted to shuffle all remaining codons. Our results suggest that the genome-wide removal of 13 codons is feasible; however, several genome design constraints were apparent, underscoring the importance of a strategy that rapidly prototypes and tests many designs in small pieces.
Antiope and D. R. C. S. (1980)

This paper describes a new technique called D. R. C. S. which is extremely helpful in text oriented communication systems: it provides through a very low cost user's terminal nearly unlimited repertoire of characters to be displayed for alphabetic applications and also fine graphics where they are needed. The integration of the feature to the French Antiope (1) Teletext or Teletel Videotex services is then discussed.
Combining Regulatory T Cell Depletion and Inhibitory Receptor Blockade Improves Reactivation of Exhausted Virus-Specific CD8+ T Cells and Efficiently Reduces Chronic Retroviral Loads (2013)

Chronic infections with human viruses, such as HIV and HCV, or mouse viruses, such as LCMV or Friend Virus (FV), result in functional exhaustion of CD8(+) T cells. Two main mechanisms have been described that mediate this exhaustion: expression of inhibitory receptors on CD8(+) T cells and expansion of regulatory T cells (Tregs) that suppress CD8(+) T cell activity. Several studies show that blockage of one of these pathways results in reactivation of CD8(+) T cells and partial reduction in chronic viral loads. Using blocking antibodies against PD-1 ligand and Tim-3 and transgenic mice in which Tregs can be selectively ablated, we compared these two treatment strategies and combined them for the first time in a model of chronic retrovirus infection. Blocking inhibitory receptors was more efficient than transient depletion of Tregs in reactivating exhausted CD8(+) T cells and reducing viral set points. However, a combination therapy was superior to any single treatment and further augmented CD8(+) T cell responses and resulted in a sustained reduction in chronic viral loads. These results demonstrate that Tregs and inhibitory receptors are non-overlapping factors in the maintenance of chronic viral infections and that immunotherapies targeting both pathways may be a promising strategy to treat chronic infectious diseases.
Chemistry and biochemistry of B12 (1999)

This study underscores the advantage of monitoring the spinal cord motor tracts directly by recording transcranial electric motor evoked potentials in addition to somatosensory evoked potentials. Transcranial electric motor evoked potentials are exquisitely sensitive to altered spinal cord blood flow due to either hypotension or a vascular insult. Moreover, changes in transcranial electric motor evoked potentials are detected earlier than are changes in somatosensory evoked potentials, thereby facilitating more rapid identification of impending spinal cord injury.