gebhart/patrepeval huggingface dataset:
Gene cluster of Pseudomonas syringae pv. "phaseolicola" controls pathogenicity of bean plants and hypersensitivity of nonhost plants (1986)

Loss of the ability of Pseudomonas syringae pv. "phaseolicola" NPS3121 to elicit a hypersensitive response on tobacco and other nonhost plants was associated with loss of pathogenicity on the susceptible host bean. Eight independent, prototrophic transposon Tn5 insertion mutants which had lost the ability to elicit a hypersensitive response on tobacco plants were identified. Six of these mutants no longer produced disease lesions on primary leaves of the susceptible bean cultivar Red Kidney and failed to elicit a hypersensitive response on the resistant bean cultivar Red Mexican and on the nonhost plants tomato, cowpea, and soybean. The two remaining mutants had reduced pathogenicity on Red Kidney bean and elicited variable hypersensitive responses on the other plants tested. Southern blot analysis indicated that each mutant carried a single independent Tn5 insertion in one of three EcoRI fragments of about 17, 7, and 5 kilobases. Marker exchange mutagenesis further supported the conclusion that the pleiotropic mutant phenotype was not associated with multiple Tn5 insertions. A genomic library of the wild-type strain was constructed in the cosmid vector pLAFR3. A recombinant plasmid, designated pPL6, that carried P. syringae pv. "phaseolicola" genomic sequences was identified by colony hybridization. This plasmid restored the wild-type phenotype to all but one mutant, suggesting that genes affected by the insertions were clustered. Structural analysis of pPL6 and the wild-type genome indicated that the 17- and 5-kilobase EcoRI fragments were contiguous in the strain NPS3121 genome.
Vasopressin antagonism: A future treatment option in heart failure (2005)

Arginine vasopressin plays an important role in volume homeostasis. Patients with heart failure have chronically elevated plasma vasopressin concentrations which may contribute to their clinical syndrome of fluid retention. Recently, a number of agents have been developed to antagonize the effects of vasopressin by targeting its V1a and V2 receptors, which are involved in vascular tone and free water regulation, respectively. Two vasopressin antagonists, in particular, tolvaptan and conivaptan, have shown promise in animal studies and small-scale human trials. The following is a review of current experimental and clinical studies using vasopressin antagonists and their potential role in the treatment of heart failure.
Cell density and estradiol modulation of procollagen type III in cultured calf smooth muscle cells. (1982)

We have reported previously that 17 beta-estradiol reduces the amount of procollagen type III produced in cultured bovine aortic smooth muscle cells. The effect of cell density and estradiol on the production of collagen in second passage cultures has been further evaluated. In agreement with our previous findings, at day 14, significant differences in [14C]hydroxyproline production were detected between hormone-treated and control cultures. To further relate this observation to cell culture density and estradiol treatment, collagen production was evaluated after a 1-h pulse period. Quantities of assembled procollagen molecules and the individual collagenous polypeptides were determined by DEAE-cellulose chromatography or by immunoprecipitation. As cell numbers increased with time in culture, an augmented production of both procollagen types I and III was observed. The increased production of total type III collagen and procollagen molecules lagged behind type I production. Thus, it was found that the ratio of procollagen type I to type III decreased with days in culture from 2.7 to 1.0, and the ratio of the total of each type decreased from 7.5 to 3.4. In the presence of 1.0 x 10(-8) M estradiol, the level of type III collagen was reduced by approximately 50% at all culture times. The production of procollagen type I was not affected and remained equivalent in both hormone-treated and control cultures. The different ratios obtained by the two methods indicates that procollagen type I is processed more rapidly than procollagen type III in the 1-hour pulse period.
Stripe boundary codes for real-time structured-light range scanning of moving objects (2002)

We present a novel approach to real-time structured light range scanning. After an analysis of the underlying assumptions of existing structured light techniques, we derive a new set of illumination patterns based on coding the boundaries between projected stripes. These stripe boundary codes allow range scanning of moving objects, with only modest assumptions about scene continuity and reflectance. We describe an implementation that integrates these new codes with real-time algorithms for tracking stripe boundaries and determining depths. Our system uses a standard video camera and DLP projector, and produces dense range images at 60 Hz with 100 /spl mu/m accuracy over a 10 cm working volume. As an application, we demonstrate the creation of complete models of rigid objects: the objects are rotated in front of the scanner by hand, and successive range images are automatically aligned.
Light trapping in ultrathin silicon photonic crystal superlattices with randomly-textured dielectric incouplers (2013)

We report here several different superlattice photonic crystal based designs for 200nm thick c-Si solar cells, demonstrating that these structures have the ability to increase broadband absorption from λ = 300nm to 1100nm by more than 100% compared to a planar cell with an optimized anti-reflection coating. We show that adding superlattices into photonic crystals introduces new optical modes that contribute to enhanced absorption. The greatest improvements are obtained when combining a superlattice photonic crystal with a randomly textured dielectric coating that improves incoupling into the modes of the absorbing region. Finally, we show that our design methodology is also applicable to layers 1 to 4 microns in thickness, where absorbed currents competitive with conventional thick Si solar cells may be achieved.
Expression of Hepatitis B Virus X Protein Does Not Alter the Accumulation of Spontaneous Mutations in Transgenic Mice (2000)

Chronic infection with hepatitis B virus (HBV) is one of the major etiological factors in the development of human hepatocellular carcinoma. Transgenic mice that express the HBV X protein (HBx) have previously been shown to be more sensitive to the effects of hepatocarcinogens, although the mechanism for this cofactor role remains unknown. The ability of HBx to inhibit DNA repair in transiently transfected cell lines suggests one possible pathway. In the present study, primary hepatocytes isolated from transgenic mice that possess the HBV X gene under the control of the human alpha-1-antitrypsin regulatory region (ATX mice) were found to be deficient in their ability to conduct unscheduled DNA synthesis in response to UV-induced DNA damage. In order to measure the impact of HBx expression on DNA repair in vivo, double-transgenic mice that express HBx and possess a bacteriophage lambda transgene were sacrificed at 30, 90, and 240 days of age. Mutation frequency was determined for high-molecular-weight liver DNA of ATX and control mice by functional analysis of the lambda transgene. Expression of HBx did not significantly increase the accumulation of spontaneous mutations. These results are consistent with previous studies of HBx transgenic mice in which no effect of HBx on liver histology was apparent. This new animal model provides a powerful system in which to investigate the in vivo cooperation between HBx expression and environmental carcinogens.
Anti-Angiogenesis (1972)

From the Department of Surgery, Children's Hospital Medical Center and Harvard Medical School, Boston, Massachusetts Julia Dyckman Andrus Professor of Pediatric Surgery, Harvard Medical School and Surgeon-in-Chief at The Children's Hospital Medical Center.
Noncovalent‐wrapped sidewall functionalization of multiwalled carbon nanotubes with polyimide (2007)

Abstract Multiwalled carbon nanotubes (MWNTs) purified by sulfuric acid and nitric acid were functionalized with polyimide (PI) via an in situ polymerization in N , N ‐diemethyformamide. The transmission electron microscopic and scan electron microscopic images showed that the functionalized MWNTs were wrapped by PI. The results of infrared, Raman, and UV–vis display that there was π‐π‐stacking interaction between imide and benzene ring in PI and the graphitic sidewalls of the MWNTs. The thermogravimetric analysis and differential scanning calorimetry results indicate that the thermal stability of the functionalized MWNTs with PI was improved. POLYM. COMPOS., 28:36–41, 2007. © 2007 Society of Plastics Engineers
Transcriptional repression by YY1 is mediated by interaction with a mammalian homolog of the yeast global regulator RPD3 (1996)

YY1 is a mammalian zinc-finger transcription factor with unusual structural and functional features. It has been implicated as a positive and a negative regulatory factor that binds to the CCATNTT consensus DNA element located in promoters of many cellular and viral genes. A mammalian cDNA that encodes a YY1-binding protein and possesses sequence homology with the yeast transcriptional factor RPD3 has been identified. A Gal4 DNA binding domain-mammalian RPD3 fusion protein strongly represses transcription from a promoter containing Gal4 binding sites. Association between YY1 and mammalian RPD3 requires a glycine-rich region on YY1. Mutations in this region abolish the interaction with mammalian RPD3 and eliminate transcriptional repression by YY1. These data suggest that YY1 negatively regulates transcription by tethering RPD3 to DNA as a cofactor and that this transcriptional mechanism is highly conserved from yeast to human.
Long-Term Gene Transfer in Porcine Myocardium After Coronary Infusion of an Adeno-Associated Virus Vector (1996)

We report the use of adeno-associated virus vectors in the cardiovascular system as well as successful myocardial gene transfer after percutaneous coronary artery infusion of viral vectors in a large, clinically relevant mammalian model. These results suggest that safe and stable gene transfer can be achieved in the heart using standard outpatient cardiac catheterization techniques.
Partial AUC Estimation and Regression (2003)

Accurate diagnosis of disease is a critical part of health care. New diagnostic and screening tests must be evaluated based on their abilities to discriminate diseased from nondiseased states. The partial area under the receiver operating characteristic (ROC) curve is a measure of diagnostic test accuracy. We present an interpretation of the partial area under the curve (AUC), which gives rise to a nonparametric estimator. This estimator is more robust than existing estimators, which make parametric assumptions. We show that the robustness is gained with only a moderate loss in efficiency. We describe a regression modeling framework for making inference about covariate effects on the partial AUC. Such models can refine knowledge about test accuracy. Model parameters can be estimated using binary regression methods. We use the regression framework to compare two prostate-specific antigen biomarkers and to evaluate the dependence of biomarker accuracy on the time prior to clinical diagnosis of prostate cancer.
Setting up meshes of interferometers – reversed local light interference method (2017)

Many interesting linear optical networks, such as lattice filters and some interferometer meshes, are difficult to fabricate precisely and cannot be configured progressively even using recent algorithms. Our approach allows a broad category of optical networks to be set up progressively and automatically, including correcting for fabrication imprecision. We null interference locally in the network based on inputs calculated by considering the network operated in reverse. Calibration is only required for the network inputs, not for individual components (though this method can also calibrate those). We illustrate specific cases of lattice filters and rectangular meshes of interferometers, and we expect the approach can be applied broadly to networks in which the light only propagates forward in the network.
Ubiquitin-Activating/Conjugating Activity of TAF II 250, a Mediator of Activation of Gene Expression in Drosophila (2000)

Ubiquitination of histones has been linked to the complex processes that regulate the activation of eukaryotic transcription. However, the cellular factors that interpose this histone modification during the processes of transcriptional activation are not well characterized. A biochemical approach identified the Drosophila coactivator TAFII250, the central subunit within the general transcription factor TFIID, as a histone-specific ubiquitin-activating/conjugating enzyme (ubac). TAFII250 mediates monoubiquitination of histone H1 in vitro. Point mutations within the putative ubac domain of TAFII250 abolished H1-specific ubiquitination in vitro. In the Drosophila embryo, inactivation of the TAFII250 ubac activity reduces the cellular level of monoubiquitinated histone H1 and the expression of genes targeted by the maternal activator Dorsal. Thus, coactivator-mediated ubiquitination of proteins within the transactivation pathway may contribute to the processes directing activation of eukaryotic transcription.
A framework for join pattern indexing in intelligent database systems (1995)

In intelligent database systems, knowledge directed inference often derives large amounts of data, and the efficiency of query processing in these systems depends upon how the derived data is maintained. This paper focuses on situations where the rule is conditional on a join of multiple data objects (relations) and the rule-derived data are materialized to reduce the overall query processing costs. We develop an indexing technique based on a unique construct called join pattern relation. Several pattern redundancy reduction methods are also introduced to minimize the overhead cost of join indexing.
Biochemical markers of liver fibrosis in patients infected by hepatitis C virus: longitudinal validation in a randomized trial (2002)

A liver fibrosis index was recently prospectively validated in a cross-sectional study where patients infected by hepatitis C virus (HCV) had only one biopsy and no longitudinal follow-up. The aim of this study was to retrospectively assess the diagnostic value of this index in patients included in a randomized trial of interferon (IFN) using repeated measurements, two biopsies and hyaluronic acid as a comparative reference. One-hundred and sixty-five patients who had had two interpretable liver biopsies and at least one stored serum sample before IFN treatment were selected. Seventy-eight patients received 3 MU of IFN-alpha thrice weekly for 24 weeks and 87 followed a reinforced regimen for 48 weeks. A fibrosis index combining five biochemical markers (alpha2-macroglobulin, haptoglobin, apolipoprotein A1, gamma-glutamyl transpeptidase (GGT) and total bilirubin adjusted for gender and age) as well as hyaluronic acid was assessed on 461 samples available at baseline, at the end of treatment and at the end of follow-up (72 weeks). There was a significant decrease of the fibrosis index score among the 17 sustained virologic responders, from 0.33 +/- 0.06 (mean +/- SE) at baseline to 0.18 +/- 0.06 at 72 weeks in comparison with 92 nonresponders (from 0.41 +/- 0.03 at baseline to 0.44 +/- 0.03 at 72 weeks; P < 0.001) and in comparison with 56 relapsers (from 0.36 +/- 0.03 at baseline to 0.32 +/- 0.03 at 72 weeks; P=0.05). No significant differences were observed for hyaluronic acid.Hence, this fibrosis index could be used as a surrogate marker of the antifibrotic effect of treatments in patients with chronic hepatitis C.
T Follicular Helper Cells Express a Distinctive Transcriptional Profile, Reflecting Their Role as Non-Th1/Th2 Effector Cells That Provide Help for B Cells (2004)

Effector T cell responses have long been viewed in the context of the Th1/Th2 paradigm. Recently, a third major subset of nonpolarized effector T cells that provides help to B cells has been identified. These T cells, termed T follicular helper (T(FH)) cells, home to the B cell areas of secondary lymphoid tissue, through interactions mediated via the chemokine receptor CXCR5 and its ligand CXCL13. Affymetrix microarrays were used to identify transcription factors, cytokines, and cell surface molecules that underlie the differentiation pathways and functional properties of the T(FH) subset. The transcriptional profile of human CXCR5(+) T(FH) cells was compared with that of Th1 and Th2 cells, which enabled the identification of numerous genes expressed preferentially by T(FH) cells, over the other effector subsets. Certain T(FH) genes were also expressed by B cells and thus appear to be particularly relevant for humoral immunity. Abs were used to confirm the expression of several factors. In particular, CD84 and CD200, the cytokine IL-21, and the transcription factor BCL6 were all strongly associated with T(FH) cells. Gene microarrays reveal a highly distinctive transcriptional profile for a third subset of effector T cells that differs markedly from Th1 and Th2 cells.
Herpes Simplex Virus Type 1 Latency-Associated Transcript Gene Promotes Neuronal Survival (2001)

A complex interaction has evolved between the host's peripheral nervous system (PNS) and herpes simplex virus type 1 (HSV-1). Sensory neurons are permissive for viral replication, yet the virus can also enter a latent state in these cells. The interplay of viral and neuronal signals that regulate the switch between the viral lytic and latent states is not understood. The latency-associated transcript (LAT) regulates the establishment of the latent state and is required for >65% of the latent infections established by HSV-1 (R. L. Thompson and N. M. Sawtell, J. Virol. 71:5432-5440, 1997). To further investigate how LAT functions, a 1.9-kb deletion that includes the entire LAT promoter and 827 bp of the 5' end of the primary LAT mRNA was introduced into strain 17syn+. The wild-type parent, three independently derived deletion mutants, and two independently derived genomically rescued variants of the mutants were analyzed in a mouse ocular model. The number of latent sites established in trigeminal ganglion (TG) neurons was determined using a single-cell quantitative PCR assay for the viral genome on purified TG neurons. It was found that the LAT null mutants established ~75% fewer latent infections than the number established by the parental strain or rescued variant. The reduced establishment phenotype of LAT null mutants was due at least in part to a dramatic increase in the loss of TG neurons in animals infected with the LAT mutants. Over half of the neurons in the TG were destroyed following infection with the LAT mutants, and this was significantly more than were lost following infection with wild type. This is the first demonstration that the HSV LAT locus prevents the destruction of sensory neurons. The death of these neurons did not appear to be the result of increased apoptosis as measured by a terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling assay. Animals latently infected with the LAT null mutants reactivated less frequently in vivo and this was consistent with the reduction in the number of neurons in which latency was established. Thus, one function of the LAT gene is to protect sensory neurons and enhance the establishment of latency in the PNS.
Histone modifications and methyl-CpG-binding domain protein levels at the TNFSF7 (CD70) promoter in SLE CD4+ T cells (2011)

In systemic lupus erythematosus (SLE), T lymphocytes overexpress CD70 (TNFSF7 gene), leading to the synthesis of autoreactive IgGs. CD70 upregulation in SLE CD4(+) T cells is associated with hypomethylation of TNFSF7 promoter. In this study, we explored histone modifications in the TNFSF7 promoter region in SLE CD4(+) T cells, and characterized the effects of a DNA methyltransferase inhibitor (5-azaC) and a histone deacetylase inhibitor (TSA) on CD70 expression. We found that CD70 mRNA was significantly increased in active lupus CD4(+) T cells, and in control cells treated with 5-azaC, TSA, or both. Histone H3 acetylation and dimethylated H3 lysine 4 (H3K4me2) levels were significantly elevated in patients with lupus, and both factors correlated positively with disease activity. MeCP2 protein levels within the TNFSF7 promoter decreased in patients with active lupus. Treatment of CD4+ T cells with 5-azaC alone significantly raised H3K4 dimethyl levels at the TNFSF7 locus. TSA treatment significantly increased H3 and H4 acetylation levels, as well as levels of H3K4 dimethylation at the TNFSF7 locus. Treatment with 5-azaC plus TSA enhanced H3 acetylation levels. These findings indicate that aberrant histone modifications within the TNFSF7 promoter may contribute to the development of lupus by increasing CD70 expression in CD4(+) T cells.
The purification and characterization of an extremely thermostable alpha-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. (1993)

The alpha-amylase from Pyrococcus furiosus, a hyperthermophilic archaebacterium, has been purified to homogeneity. The enzyme is a homodimer with a subunit molecular mass of 66 kDa. The isoelectric point is 4.3. The enzyme displays optimal activity, with substantial thermal stability, at 100 degrees C, with the onset of activity at approximately 40 degrees C. Unlike mesophilic alpha-amylases there is no dependence on Ca2+ for activity or thermostability. The enzyme displays a broad range of substrate specificity, with the capacity to hydrolyze carbohydrates as simple as maltotriose. No subtrate binding occurs below the temperature threshold of activity, and a decrease in Km accompanies an increase in temperature. Except for a decrease in Asp and an increase in Glu, the amino acid composition does not confirm previously defined trends in thermal adaption. Fourth derivative UV spectroscopy and intrinsic fluorescence measurements detected no temperature-dependent structural reorganization. Hydrogen exchange results indicate that the molecule is rigid, with only a slight increase in conformational flexibility at elevated temperature. Scanning microcalorimetry detected no considerable change in the heat capacity function, at the pH of optimal activity, within the temperature range in which activity is induced. The heat absorption peak due to denaturation, under these conditions, occurred within the temperature range of 90-120 degrees C. When the pH was increased, a change in the shape of the heat absorption peak was observed, which when analyzed thermodynamically shows that the process of heat denaturation is complex, and includes at least three stages, indicating that the protein structure consists of three domains. At temperatures below 90 degrees C no excess heat absorption or change in the CD spectra were observed which could be associated with the cooperative conformational transition of the protein. According to the thermodynamic characteristics of the heat denaturation, the cold denaturation of this protein can be expected only at -3 degrees C. Therefore, the observed inactivation of this enzyme is not caused by the cooperative change of its tertiary structure. It can be associated only with the gradual changes of protein domain interaction.