gebhart/patrepeval huggingface dataset:
X-Ray Structure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil (1991)

The x-ray crystal structure of a peptide corresponding to the leucine zipper of the yeast transcriptional activator GCN4 has been determined at 1.8 angstrom resolution. The peptide forms a parallel, two-stranded coiled coil of alpha helices packed as in the "knobs-into-holes" model proposed by Crick in 1953. Contacts between the helices include ion pairs and an extensive hydrophobic interface that contains a distinctive hydrogen bond. The conserved leucines, like the residues in the alternate hydrophobic repeat, make side-to-side interactions (as in a handshake) in every other layer of the dimer interface. The crystal structure of the GCN4 leucine zipper suggests a key role for the leucine repeat, but also shows how other features of the coiled coil contribute to dimer formation.
Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis (2006)

This report describes a new genotyping method capable of detecting low-abundant point mutations in a homogeneous, separation-free format. The method is based on integration of oligonucleotide ligation with a semiconductor quantum dot (QD)-mediated two-color fluorescence coincidence detection scheme. Surface-functionalized QDs are used to capture fluorophore-labeled ligation products, forming QD-oligonucleotide nanoassemblies. The presence of such nanoassemblies and thereby the genotype of the sample is determined by detecting the simultaneous emissions of QDs and fluorophores that occurs whenever a single nanoassembly flows through the femtoliter measurement volume of a confocal fluorescence detection system. The ability of this method to detect single events enables analysis of target signals with a multiple-parameter (intensities and count rates of the digitized target signals) approach to enhance assay sensitivity and specificity. We demonstrate that this new method is capable of detecting zeptomoles of targets and achieve an allele discrimination selectivity factor >10(5).
Similarity Searching in Files of Three-Dimensional Chemical Structures:  Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors (1999)

This paper compares the effectiveness of similarity measures based on two-dimensional fingerprints and on molecular fields for identifying pairs of bioisosteric molecules in the BIOSTER database. The results suggest that the two types of descriptor are complementary in nature, each finding some bioisosteric pairs that are not found by the other. This conclusion is confirmed by studies of groups of BIOSTER molecules that share the same activity characteristics, and by experiments that involve combining the two types of similarity measure.
T‐Cell Recognition of Antigen (1995)

As recently as ten years ago, the nature of the T-cell receptor for antigen was a mystery, as was the precise role of histocompatibility molecules in antigen-presentation to T cells. Although T-cell receptors have now been cloned and crystal structures of MHC/peptide molecules exist, our understanding of the parameters that characterize this interaction and other interactions relevant to T-cell immunity are still unclear. The engineering of soluble forms of proteins that mediate T-cell recognition of antigen has allowed the first measurements of these parameters. Interestingly, many of these interactions are of a transient nature, with very rapid off-rates. These data suggest a model whereby highly reversible intermolecular interactions mediate the cell-cell association. The association of adhesion molecules is probably the first step in the stabilization of a conjugate, because they are more numerous than any antigen-specific interaction, followed later by TCR-MHC engagements. Diffusion within each lipid bilayer should allow the congregation of MHC/TCR interactions at the cell-cell interface, with peptide-specific TCR interactions outcompeting irrelevant interactions. Rapid off-rates for both the antigen-specific and nonspecific interactions may be necessary to maintain reversibility, yet allow a rapid approach to equilibrium and consequent signaling when a specific antigen is present or disengagement when it is not.
Simulation/evaluation environment for a VLIW processor architecture (1997)

We describe the environment used for the simulation and evaluation of a processor architecture based on very long instruction word (VLIW) principles. In this architecture, a program consists of a set of tree instructions, each one containing multiple branches and operations which can be performed simultaneously. The simulation/evaluation environment comprises • An optimizing compiler, which generates tree instructions in a VLIW assembly language. • A translator from VLIW assembly code into PowerPC® assembly code which emulates the functionality of the VLIW processor for the specific VLIW program. The emulating code also includes instrumentation for collecting execution counts of VLIWs, profiling information, and generation of predecoded execution traces. • A cycle timer, invoked by the emulating code on a VLIW-by-VLIW basis, which processes VLIW execution traces as they are generated. The environment supports the evaluation of alternatives and trade-offs among the VLIW architecture, its compiler, and processor implementations. Emphasis has been placed on providing fast turnaround time for the development of compilation algorithms and an efficient compilation-to-simulation cycle which allows analysis of architecture/compiler trade-offs over complete execution runs of realistic workloads.
Adhesion of Biologically Inspired Vertical and Angled Polymer Microfiber Arrays (2007)

This paper proposes an approximate adhesion model for fibrillar adhesives for developing a fibrillar adhesive design methodology and compares numerical simulation adhesion results with macroscale adhesion data from polymer microfiber array experiments. A technique for fabricating microfibers with a controlled angle is described for the first time. Polyurethane microfibers with different hardnesses, angles, and aspect ratios are fabricated using optical lithography and polymer micromolding techniques and tested with a custom tensile adhesion measurement setup. Macroscale adhesion and overall work of adhesion of the microfiber arrays are measured and compared with the models to observe the effect of fiber geometry and preload. The adhesion strength and work of adhesion behavior of short and long vertical and long angled fiber arrays have similar trends with the numerical simulations. A scheme is also proposed to aid in optimized fiber adhesive design.
Memory CD4 T cells: generation, reactivation and re‐assignment (2010)

Immunological memory is one of the features that define the adaptive immune response: by generating specific memory cells after infection or vaccination, the host provides itself with a set of cells and molecules that can prevent future infections and disease. Despite the obvious importance of memory cells, memory CD4 T cells are incompletely understood. Here we discuss recent progress in understanding which activated T cells surmount the barrier to enter into the memory pool and, once generated, what signals are important for memory cell survival. There is still, however, little understanding of how (or even whether) memory CD4 T cells are useful once they have been created; a surprising thought considering the critical role CD4 T cells play in all adaptive primary immune responses. In light of this, we will discuss how CD4 T memory T cells respond to reactivation in vivo and whether they are malleable to a re-assignment of their effector response.
Application of Rhizobacteria for Plant Growth Promotion Effect and Biocontrol of Anthracnose Caused by Colletotrichum acutatum on Pepper (2012)

In vitro and greenhouse screening of seven rhizobacterial isolates, AB05, AB10, AB11, AB12, AB14, AB15 and AB17, was conducted to investigate the plant growth promoting activities and inhibition against anthracnose caused by Colletotrichum acutatum in pepper. According to identification based on 16S rDNA sequencing, the majority of the isolates are members of Bacillus and a single isolate belongs to the genus Paenibacillus. All seven bacterial isolates were capable of inhibiting C. acutatum to various degrees. The results primarily showed that antibiotic substances produced by the selected bacteria were effective and resulted in strong antifungal activity against the fungi. However, isolate AB15 was the most effective bacterial strain, with the potential to suppress more than 50% mycelial growth of C. acutatumin vitro. Moreover, antibiotics from Paenibacillus polymyxa (AB15) and volatile compounds from Bacillus subtilis (AB14) exerted efficient antagonistic activity against the pathogens in a dual culture assay. In vivo suppression activity of selected bacteria was also analyzed in a greenhouse with the reference to their prominent in vitro antagonism efficacy. Induced systemic resistance in pepper against C. acutatum was also observed under greenhouse conditions. Where, isolate AB15 was found to be the most effective bacterial strain at suppressing pepper anthracnose under greenhouse conditions. Moreover, four isolates, AB10, AB12, AB15, and AB17, were identified as the most effective growth promoting bacteria under greenhouse conditions, with AB17 inducing the greatest enhancement of pepper growth.
Regulation of the acute phase and immune responses in viral disease. Enhanced expression of the beta 2-interferon/hepatocyte-stimulating factor/interleukin 6 gene in virus-infected human fibroblasts. (1988)

We have defined the expression of the mRNA for, and secretion of, IFN-beta 2/hepatocyte-stimulating factor/IL-6 (IFN-beta 2/IL-6) in human diploid fibroblasts (FS-4 strain) infected with different RNA- and DNA-containing viruses. RNA blot-hybridization analyses carried out 6-8 h after the beginning of infection showed that the RNA-containing Sendai virus (paramyxoviridae) enhanced IFN-beta 2/IL-6 mRNA levels 10-fold, followed, in decreasing order, by encephalomyocarditis (EMC, picornaviridae), vesicular stomatitis (VSV, rhabdoviridae), Newcastle disease virus (NDV, paramyxoviridae), and influenza A (Flu, myxoviridae) viruses. The DNA-containing pseudorabies virus (PR, herpesviridae) enhanced IFN-beta 2/IL-6 mRNA levels sixfold, while the effect of adenovirus type 5 (Ad5, adenoviridae) was considerably less and comparable with that of NDV or Flu. A rabbit antiserum raised against E. coli-derived human IFN-beta 2/IL-6 was used in immunoprecipitation experiments to monitor the secretion of 35S-methionine-pulse-labeled IFN-beta 2/IL-6 proteins by fibroblasts up to 7 h after the beginning of infection. Enhanced levels of secretion of IFN-beta 2/IL-6 (2-14-fold) were observed in every instance evaluated (Sendai, EMC, VSV, Flu, PR, Ad5 viruses). A biological consequence of enhanced secretion of IFN-beta 2/IL-6 was the ability of media from infected FS-4 cell cultures to enhance by 8-15-fold the synthesis and secretion of a typical acute phase plasma protein (alpha 1-antichymotrypsin) by human hepatoma Hep3B2 cells. These observations make it likely that IFN-beta 2/IL-6 mediates, in part, the host response to acute virus infections.
A miniaturized GaAs power amplifier for 1.5 GHz digital cellular phones (2002)

An extremely miniaturized GaAs PA has been developed for the application in 1.5-GHz Japanese digital cellular phones. By using MuMIC (i.e. multilayer microwave integrated circuit) technology, the half sized (0.2 cc) PA with 1.1 W output power has successfully been implemented. The 48-% power-added efficiency has been obtained with drain supply voltage of 3.5-V.
TOSO promotes β-cell proliferation and protects from apoptosis (2012)

Decreased β-cell mass reflects a shift from quiescence/proliferation into apoptosis, it plays a crucial role in the pathophysiology of diabetes. A major attempt to restore β-cell mass and normoglycemia is to improve β-cell survival. Here we show that switching off the Fas pathway using Fas apoptotic inhibitory protein (Faim/TOSO), which regulates apoptosis upstream of caspase 8, blocked β-cell apoptosis and increased proliferation in human islets. TOSO was clearly expressed in pancreatic β-cells and down-regulated in T2DM. TOSO expression correlated with β-cell turnover; at conditions of improved survival, TOSO was induced. In contrast, TOSO downregulation induced β-cell apoptosis. Although TOSO overexpression resulted in a 3-fold induction of proliferation, proliferating β-cells showed a very limited capacity to undergo multiple rounds of replication. Our data suggest that TOSO is an important regulator of β-cell turnover and switches β-cell apoptosis into proliferation.
Disrupted Sleep Patterns and Daily Functioning in Patients with Chronic Pain (2002)

Sleep disruption is usually considered to be a consequence of the pain experience. However, the results of the present study reinforce the view that sleep disturbance may have a bidirectional relation with other features of chronic pain. Future studies should confirm that repairing disrupted sleep leads to an improvement in patients' daily activity and a reduction in their suffering.
Flexpoint: An Adaptive Numerical Format for Efficient Training of Deep Neural Networks (2017)

Deep neural networks are commonly developed and trained in 32-bit floating point format. Significant gains in performance and energy efficiency could be realized by training and inference in numerical formats optimized for deep learning. Despite advances in limited precision inference in recent years, training of neural networks in low bit-width remains a challenging problem. Here we present the Flexpoint data format, aiming at a complete replacement of 32-bit floating point format training and inference, designed to support modern deep network topologies without modifications. Flexpoint tensors have a shared exponent that is dynamically adjusted to minimize overflows and maximize available dynamic range. We validate Flexpoint by training AlexNet, a deep residual network and a generative adversarial network, using a simulator implemented with the neon deep learning framework. We demonstrate that 16-bit Flexpoint closely matches 32-bit floating point in training all three models, without any need for tuning of model hyperparameters. Our results suggest Flexpoint as a promising numerical format for future hardware for training and inference.
Structure-Function Analysis of the -Adrenergic Receptor (1988)

A major goal of medicinal chemistry and pharmacology is to understand the molecular basis for the interactions of drugs with their targets. Many drugs act by binding to specific cell-surface receptors, either as agonists, which stimulate receptor function, or as antagonists, which block the action of endogenous agonists. In recent years, it has become clear that cell-surface receptors can be classified into groups on the basis of their ligand-binding characteristics, their mechanisms of signal transduction, and their structural properties (Dixon et al. 1988). One such class of receptors, which binds small molecule or peptide hormones and neurotransmitters, couples through guanine-nucleotide-binding regulatory proteins (G proteins) to modulate the intracellular levels of a variety of second-messenger molecules (Fig. 1). On binding agonists, receptors of this class catalyze the exchange of a bound GDP molecule for GTP on one of several G proteins in the cell membrane. Most receptors appear to associate with...
In-situ Re-Glazing of Structural Sealant Glazing Joints a Case History (1995)

Structural sealant glazing has attracted considerable attention due to its inherent glass retaining method which allows smooth exterior glass walls interrupted only by narrow weatherseal joints. The technique has become increasingly popular with owners and architects since its inception in the early 1970's. In 1990 it was determined that a five story office building nearing completion had structurally glazed insulating glass units in multi-story bay windows that had been incorrectly installed. Verification of the required structural glazing design was performed to compare with the as-built conditions, and re-glazing the structural silicone glazing joints was indicated to be warranted. The construction team desired to perform the re-glazing without removing the installed units for cost and time reasons. In-situ re-glazing of a single insulating glass unit was performed as a test of the proposed remedial technique. The test was deemed successful and the remaining defectively glazed units were re-glazed in-situ. The design and construction circumstances that led to the situation requiring the re-glazing, the lessons learned during their resolution, the in-situ re-glazing techniques utilized, and comments on the need for potential re-glazing of structurally glazed systems are presented.
UWB radars in medicine (2002)

Applied research on biomedical applications of UWB radar is targeted to the identification of the possible new devices made possible by the technology, to the design and development of those devices, and to the clinical testing of the systems obtained. Applications can be divided into two main sectors according to the frequency range used. For the conventional UWB radar microwave region: cardiac biomechanics assessment; chest movements assessment OSA (obstructive sleep apnoea) monitors; soft-tissue biomechanics research; heart imaging ("Holter type" echocardiography); chest imaging. Together with systems for: cardiac monitoring; respiratory monitoring; SIDS (sudden infant death syndrome) monitor; vocal tract studying. If an IR laser diode is used as the antenna, a more common radar is obtained (actually a hybrid between a narrow band and a wide band radar) which emits a short packet of electromagnetic waves whose echoes are sampled using conventional UWB receiver equipped with a PIN photodiode. Possibilities include: non-invasive biochemical study of soft tissues, non-invasive study of metabolic processes, and IR spectral imaging.
Luminescent properties of Pr3+-sensitized LaPO4:Gd3+ ultraviolet-B phosphor under vacuum-ultraviolet light excitation (2009)

Luminescent properties of Pr3+-sensitized LaPO4:Gd3+ under vacuum-ultraviolet (vuv) light excitation have been investigated. The energy transfer probably occurs from the 5d levels in Pr3+ ions to Gd3+ ions under 172nm light excitation. LaPO4:Gd3+,Pr3+ shows efficient ultraviolet-B (uv-B) emission at 312nm, whose peak intensity reaches its maximum at Gd=35mol% and Pr=5mol%. (La0.65Gd0.35)0.95Pr0.05PO4 is about 1.6 times higher than a typical uv-B phosphor for vuv lamp, Y0.75Gd0.25Al3(BO3)4, in Gd3+-emission intensity under 172nm light excitation. This result implies that the Pr3+-sensitized LaPO4:Gd3+ is a candidate of uv-B phosphors for xenon-excimer discharge vuv lamps. In order to evaluate the effect of the narrow-band uv-B emission by LaPO4:Gd3+,Pr3+ phosphor, irradiation test on DNA was performed. The irradiation damage of pUC 18 DNA by the narrow-band uv-B light from the LaPO4:Gd3+,Pr3+ phosphor is in the same magnitude as that by uv-A light from a filtered Hg lamp, even though the uv-B lamp is higher than the uv-A lamp in power density and photon energy.
Association of matrilysin-2 (MMP-26) expression with tumor progression and activation of MMP-9 in esophageal squamous cell carcinoma (2004)

Expression of matrilysin-2, matrix metalloproteinase (MMP)-26, has been implicated in the progression of several types of human cancer. Matrilysin-2 has been reported to be a physiological and pathological activator of pro-MMP-9. The aim of this study was to examine matrilysin-2 expression and determine whether it is correlated with progression of human esophageal squamous cell carcinoma (ESCC). Semi-quantitative reverse transcriptase-polymerase chain reaction, immunohistochemical analysis, zymography and an in vitro invasion assay were performed. Matrilysin-2 mRNA expression was undetectable or only faintly detected in non-tumor tissues, but its overexpression was detected in 24 of the 50 ESCC tissues. Matrilysin-2 overexpression was significantly correlated with depth of invasion, lymph node metastasis and an advance in pathological tumor node metastasis (pTNM) stage. Sections with immunostaining signals in >10% of carcinoma cells at the invasive front, which were observed in 46 of 100 cases, were judged to be positive for matrilysin-2 expression. Matrilysin-2 expression was significantly correlated with depth of invasion, lymph node and distant metastasis, advance in pTNM stage and recurrence. Expression of matrilysin-2 was significantly correlated with nuclear beta-catenin expression and MMP-9 expression. Patients with matrilysin-2-positive cancer had significantly shorter overall and disease-free survival periods than did those with matrilysin-2-negative cancer. Matrilysin-2 expression retained its significant predictive value for overall and disease-free survival in multivariate analysis. Moreover, patients with concomitant expression of matrilysin-2 and MMP-9 had the worst prognosis. Zymography revealed that matrilysin-2 expression was significantly correlated with expression of active MMP-9 in ESCC tissues. Matrilysin-2-transfected TE-1 ESCC cells showed active MMP-9 activity and were more invasive in vitro compared with mock-transfected TE-1 cells. The results of this study suggest that matrilysin-2, the expression of which is closely correlated with nuclear beta-catenin expression and active MMP-9 activity, plays a key role in the progression of ESCC.
Identificação e avaliação de rizobactérias isoladas de raízes de milho (2010)

Estudos sobre a atividade microbiológica que ocorre na rizosfera de diversos vegetais levaram ao descobrimento de grupos de microrganismos importantes para o desenvolvimento vegetal. Dentre eles estão as rizobactérias que são capazes de colonizar as raízes, estimulando-a diretamente ou beneficiando o crescimento e o desenvolvimento de diversas plantas. Estas bactérias são chamadas Rizobactérias Promotoras de Crescimento em Plantas (RPCP). Este trabalho teve o objetivo de isolar, identificar, testar a capacidade da solubilização de fosfato e a produção de ácido indol acético (AIA) de bactérias que habitam a rizosfera de plantas de milho. A análise parcial do gene 16S rRNA dos 58 isolados possibilitou a identificação dos gêneros, Bacillus, Burkholderia e Azospirillum, sendo os mais frequentes totalizando 68% dos isolados, seguidos de Sphingomonas, Pseudomonas, Herbaspirillum, Pantoea , Bosea. Desses, 27 apresentaram a capacidade de solubilização do fosfato e 18 foram positivos no teste colorimétrico para detecção de produção do AIA. A partir destes resultados, selecionou-se um organismo pertencente ao gênero Sphingomonas para ser testado em casa de vegetação como promotor de crescimento com as estirpes de Azospirillum brasilense (AbV5 e AbV6). As plantas foram avaliadas quanto à altura aos vinte e setenta dias após a germinação e a massa seca da parte aérea (MSPA)e parte radicular (MSPR) foi quantificada após setenta dias no encerramento do experimento. Os resultados das análises do isolado pertencente ao gênero Sphingomonas foram estatisticamente semelhantes às estirpes AbV5 e AbV6 na planta de milho indicando que este microrganismo possui potencial para ser utilizado como RPCP