gebhart/patrepeval huggingface dataset:
Target genes and regulatory domains of the GAMYB transcriptional activator in cereal aleurone (1999)

GAMYB is an MYB transcription factor which is expressed in cereal aleurone cells in response to gibberellin (GA). HvGAMYB binds to the TAACAAA box of a high-pl alpha-amylase gene promoter and transcriptionally activates its expression. In this study, we examined the role of HvGAMYB in activating expression of other GA-regulated genes encoding hydrolytic enzymes. In transient expression experiments, HvGAMYB transactivated expression of reporter genes fused to a low-pl alpha-amylase gene promoter, an EII (1-3, 1-4)-beta-glucanase gene promoter and a cathepsin B-like protease promoter. HvGAMYB DNA binding specificity was determined using a PCR-based random site selection using HvGAMYB fusion protein isolated from E. coli. The deduced consensus closely resembled gibberellin response elements in alpha-amylase promoters. Functional analysis of HvGAMYB by transient expression of C terminal HvGAMYB deletions in barley aleurone cells identified two transcriptional activation domains (TADs) which function in transcriptional regulation of both high- and low-pl alpha-amylase promoters. The same TADs were identified using a heterologous yeast expression system. Together, these results indicate that HvGAMYB has two TADs. These domains are C-terminal to its DNA-binding domain.
Homologous transformation of Trichoderma hamatum with an endochitinase encoding gene, resulting in increased levels of chitinase activity (1998)

A 42-kDa endochitinase encoding gene, Tham-ch, was cloned by screening the genomic library of Trichoderma hamatum strain Tam-61 with a PCR-amplified chitinase sequence from the same fungus. Tham-ch with its own regulatory sequences was reintroduced into the host strain. The integration of the transforming construct was stable only in one copy. Homologous integration occurred in nine transformants, while non-homologous integration was detected in one transformant. All but one transformant expressed higher levels of chitinase activity in comparison to the wild-type recipient strain; the maximum level of increase was 5-fold. Duplicating the copy number of the highly conserved ∼42-kDa endochitinase encoding gene appears to be one potential means by which the biocontrol capability of the Trichoderma species might be improved.
Time Trends in Primary HIV-1 Drug Resistance Among Recently Infected Persons (2002)

The frequency of primary resistance to NNRTIs is increasing, although resistance to all available classes of antiretroviral therapy remains rare. Genotypic resistance testing in recently infected persons predicts time to viral suppression during therapy.
Effective API navigation and reuse (2010)

Most reuse libraries come with few source-code examples that demonstrate how the library at hand should be used. We have developed a source-code recommendation approach for constructing and delivering relevant code snippets that programmers can use to complete a certain programming task. Our approach is semantic-based; relying on an explicit ontological representation of source-code. We argue that such representation opens new doors for an improved recommendation mechanism that ensures relevancy and accuracy. Current recommendation systems require an existing repository of relevant code samples. However, for many libraries, such a repository does not exist. Therefore, we instead utilize points-to analysis to infer precise type information of library components. We have backed our approach with a tool that has been tested on multiple libraries. The obtained results are promising and demonstrate the effectiveness of our approach.
Incidence and Prognostic Influence of DNMT3A Mutations in Acute Myeloid Leukemia (2011)

DNMT3A mutations are frequent in younger patients with AML and are associated with an unfavorable prognosis.
DENATURED STATES OF PROTEINS (1991)

The denatured "state" of a protein is a distribution of many different molecular conformations, the averages of which are measured by experiments. The properties of this ensemble depend sensitively on the solution conditions. There is now considerable evidence that even in strong denaturants such as 6M GuHC1 and 9M urea, some structure may remain in protein chains. Under milder or physiological conditions, the denatured states of most proteins appear to be highly compact with extensive secondary structure. Both theoretical and experimental studies suggest that hydrophobic interactions, chain conformational entropies, and electrostatic forces are dominant in determining this structure. The denaturation reaction of many proteins in GuHC1 or urea can be most simply modelled as a two-state transition between the native structure and a relatively compact denatured state, which then undergoes a gradual increase in radius on further addition of denaturant. However, when a protein acquires a large net charge in acids or bases, it can have two stable denatured populations, one compact and the other more highly unfolded. The prediction and elucidation of the structural details of the non-native states of proteins may ultimately prove to be as difficult as predicting the native structures, particularly for D0, the denatured state under physiological conditions. Just as with the native state, the structure of this biologically important denatured state appears to depend on the amino acid sequence. The development of synthetic, peptide and protein fragment models of the denatured state and the recent progress in NMR spectroscopy provide bases for optimism that new insights will be gained into this poorly understood realm of protein biochemistry.
Scale-Space SIFT flow (2014)

The state-of-the-art SIFT flow has been widely adopted for the general image matching task, especially in dealing with image pairs from similar scenes but with different object configurations. However, the way in which the dense SIFT features are computed at a fixed scale in the SIFT flow method limits its capability of dealing with scenes of large scale changes. In this paper, we propose a simple, intuitive, and very effective approach, Scale-Space SIFT flow, to deal with the large scale differences in different image locations. We introduce a scale field to the SIFT flow function to automatically explore the scale deformations. Our approach achieves similar performance as the SIFT flow method on general natural scenes but obtains significant improvement on the images with large scale differences. Compared with a recent method that addresses the similar problem, our approach shows its clear advantage being more effective, and significantly less demanding in memory and time requirement.
Cynanchum wilfordiiameliorates hypertension and endothelial dysfunction in rats fed with high fat/cholesterol diets (2011)

Hypercholesterolemia increases the incidence of atherosclerosis and its pathologic complications. This study was performed to test the effect of an ethanol extract of Cynanchum wilfordii (ECW) on vascular dysfunction in rats fed with high fat/cholesterol diets (HFCD). Male rats were fed a HFCD consisting of 7.5% cocoa butter and 1.25% cholesterol, with or without 100, 200 mg/day/kg ECW. Rats fed with HFCD increased body weight associated with an increase in plasma low-density lipoprotein (LDL) cholesterol level. Chronic ECW treatment in HFCD-fed rats lessened LDL cholesterol and triglyceride levels as well as elevated high-density lipoprotein (HDL) cholesterol. Chronic ECW treatment recovered the HFCD-induced increase in systolic blood pressure, maintained smooth and soft intima endothelial layers by the decrease of intima-media thickness. ECW significantly recovered the diet-induced decrease in vasorelaxation to acetylcholine, high-dose ECW apparently increased vasorelaxation response to sodium nitroprusside in rats fed with HFCD. ECW clearly restored the HFCD-induced reduction in endothelial nitric oxide (NO) synthase expression and Akt expression levels in aortic tissue, leading to improve endothelial function through an increase in endothelium-derived NO production. Furthermore, treatment of ECW significantly recovered the HFCD-induced decrease in aortic cGMP levels in rats. These findings suggest that ECW ameliorates hypertension and endothelial dysfunction via improvement of NO/cGMP signaling pathway in aortic tissue of rats fed with HFCD, suggesting a vascular protective role for this herb in the treatment and prevention of atherosclerotic vascular disease.
Use of naloxone in septic shock. (1989)

Experimental and clinical evidence show that endogenous opiates (endorphins) contribute to the pathophysiology of circulatory shock. The authors evaluated the effectiveness and safety of continuous infusion of naloxone in five septic patients with prolonged hypotension unresponsive to volume replacement and dopamine infusion. Naloxone (2 mg bolus) was intravenously administered and continued at 0.25 mg/hr for 24 to 48 hours. All five patients had significant increase in mean arterial pressure of between 20 and 30 mmHg (P less than 0.0012). Cardiac index, systemic vascular resistance, and pulmonary arterial pressure were not significantly altered; however, there was a significant difference in pulmonary capillary wedge pressure (P less than 0.034) and urinary output (P less than 0.0273). Subjects did not experience side effects with naloxone. We conclude that continuous infusion of naloxone can reverse endorphin-mediated hypotension in septic shock patients.
Protective effect of zinc gluconate on chemically induced gastric ulcer. (1997)

This study was undertaken in rats to ascertain the role of zinc as an antiulcerogenic agent employing its more bioavailable gluconate derivative. Pretreatment with zinc gluconate 10 mg/kg body wt orally for three consecutive days, protected against alcohol induced gastric epithelial damage and also significantly prevented non-steroidal anti-inflammatory drugs (NSAID) induced gastric ulcer in rats. The enhanced levels of mucus, and hexosamine and decreased acid output in the gastric secretion of zinc treated rats, increased the gastric mucosal barrier. Studies on the mechanism of action suggested the involvement of -SH groups in producing gastric antisecretory effect. Thus, zinc gluconate at > > 100 microM concentrations inhibited H(+)-ion transport which could be reversed by incorporating beta-mercaptoethanol in the secretory solution (luminal side). On the other hand, beta-mercaptoethanol added from the nutrient side showed no effect on the inhibition of H(+)-transport indicting that the implication of -SH groups may not be the sole factor. Zinc appeared to play a vital and multifaceted protective role in chemically induced gastric ulcer disorders.
Flexible Solid-State Supercapacitors Based on Three-Dimensional Graphene Hydrogel Films (2013)

Flexible solid-state supercapacitors are of considerable interest as mobile power supply for future flexible electronics. Graphene or carbon nanotubes based thin films have been used to fabricate flexible solid-state supercapacitors with high gravimetric specific capacitances (80-200 F/g), but usually with a rather low overall or areal specific capacitance (3-50 mF/cm(2)) due to the ultrasmall electrode thickness (typically a few micrometers) and ultralow mass loading, which is not desirable for practical applications. Here we report the exploration of a three-dimensional (3D) graphene hydrogel for the fabrication of high-performance solid-state flexible supercapacitors. With a highly interconnected 3D network structure, graphene hydrogel exhibits exceptional electrical conductivity and mechanical robustness to make it an excellent material for flexible energy storage devices. Our studies demonstrate that flexible supercapacitors with a 120 μm thick graphene hydrogel thin film can exhibit excellent capacitive characteristics, including a high gravimetric specific capacitance of 186 F/g (up to 196 F/g for a 42 μm thick electrode), an unprecedented areal specific capacitance of 372 mF/cm(2) (up to 402 mF/cm(2) for a 185 μm thick electrode), low leakage current (10.6 μA), excellent cycling stability, and extraordinary mechanical flexibility. This study demonstrates the exciting potential of 3D graphene macrostructures for high-performance flexible energy storage devices.
Anticipating Information Needs: Everyday Applications as Interfaces to Internet Information Resources. (1998)

This paper outlines work on a class of systems called Personal Information Management Assistants (PIMAs). PIMAs observe user interaction with everyday applications and use these observations to anticipate a user's information needs. They then automatically fulfill these needs by accessing Internet information sources, filtering the results, and presenting them to the user. They allow everyday applications to serve as interfaces for traditional information retrieval systems (e.g., Internet search engines) . The paper presents preliminary work on an architecture for this class of systems and progress in implementing such a system, including finding relevant pages (i.e., query construction and information filtering) and exploiting structural clues. Preliminary results and directions for future work are also discussed. Two tables present output of a query generated from a page on Java standardization and results of clustering responses; three figures show the PIMA architecture and examples of displays suggesting relevant World Wide Web pages and images. (Author/AEF) ******************************************************************************** * Reproductions supplied by EDRS are the best that can be made * * from the original document. * ******************* ***** ********************************************************
A parametric study of the factors affecting the fatigue strength of porous coated Ti‐6A1‐4V implant alloy (1990)

The high cycle fatigue strength of porous coated Ti-6A1-4V is approximately 75% less than the fatigue strength of uncoated Ti-6A1-4V. This study separates the effects of three parameters thought to be responsible for this reduction: interfacial geometry, microstructure, and surface alterations brought about by sintering. To achieve the goal of one parameter variations, hydrogen-alloying treatments, which refined the lamellar microstructure of beta-annealed and porous coated Ti-6A1-4V, were formulated. The fatigue strength of smooth-surfaced Ti-6A1-4V subjected to hydrogen-alloying treatments is 643-669 MPa, significantly greater than the fatigue strength of beta-annealed Ti-6A1-4V (497 MPa) and also greater than the fatigue strength of pre-annealed, equiaxed Ti-6A1-4V (590 MPa). The fatigue strength of porous coated Ti-6A1-4V, however, is independent of microstructure. This leads to the conclusion that the notch effect of the surface porosity does not allow the material to take advantage of the superior fatigue crack initiation resistance of a refined alpha-grain size. Thus, sinternecks acts as initiated microcracks and fatigue of porous coated Ti-6A1-4V is propagation controlled.
Metabolic correction and cross-correction of mucopolysaccharidosis type II (Hunter syndrome) by retroviral-mediated gene transfer and expression of human iduronate-2-sulfatase. (1993)

To explore the possibility of using gene transfer to provide iduronate-2-sulfatase (IDS; EC 3.1.6.13) enzyme activity for treatment of Hunter syndrome, an amphotropic retroviral vector, L2SN, containing the human IDS coding sequence was constructed and studied for gene expression in vitro. Lymphoblastoid cell lines (LCLs) from patients with Hunter syndrome were transduced with L2SN and expressed high levels of IDS enzyme activity, 10- to 70-fold higher than normal human peripheral blood leukocytes or LCLs. Such L2SN-transduced LCLs failed to show accumulation of 35SO4 into glycosaminoglycan (35SO4-GAG), indicating that recombinant IDS enzyme participated in GAG metabolism. Coculture of L2SN-transduced LCLs with fibroblasts from patients with Hunter syndrome reduced the accumulation of 35SO4-GAG. These results demonstrated retroviral-mediated IDS gene transfer into lymphoid cells and the ability of such cells to provide recombinant enzyme for intercellular metabolic cross-correction.
A Double-Blind, Placebo-Controlled Study of Aripiprazole Adjunctive to Antidepressant Therapy among Depressed Outpatients with Inadequate Response to Prior Antidepressant Therapy (ADAPT-A Study) (2012)

This study provides clear support for the tolerability of low-dose aripiprazole as an ADT-augmenting agent, with marginal efficacy.
Affinity Improvement of a Therapeutic Antibody by Structure-Based Computational Design: Generation of Electrostatic Interactions in the Transition State Stabilizes the Antibody-Antigen Complex (2014)

The optimization of antibodies is a desirable goal towards the development of better therapeutic strategies. The antibody 11K2 was previously developed as a therapeutic tool for inflammatory diseases, and displays very high affinity (4.6 pM) for its antigen the chemokine MCP-1 (monocyte chemo-attractant protein-1). We have employed a virtual library of mutations of 11K2 to identify antibody variants of potentially higher affinity, and to establish benchmarks in the engineering of a mature therapeutic antibody. The most promising candidates identified in the virtual screening were examined by surface plasmon resonance to validate the computational predictions, and to characterize their binding affinity and key thermodynamic properties in detail. Only mutations in the light-chain of the antibody are effective at enhancing its affinity for the antigen in vitro, suggesting that the interaction surface of the heavy-chain (dominated by the hot-spot residue Phe101) is not amenable to optimization. The single-mutation with the highest affinity is L-N31R (4.6-fold higher affinity than wild-type antibody). Importantly, all the single-mutations showing increase affinity incorporate a charged residue (Arg, Asp, or Glu). The characterization of the relevant thermodynamic parameters clarifies the energetic mechanism. Essentially, the formation of new electrostatic interactions early in the binding reaction coordinate (transition state or earlier) benefits the durability of the antibody-antigen complex. The combination of in silico calculations and thermodynamic analysis is an effective strategy to improve the affinity of a matured therapeutic antibody.
Ion-sensitive field-effect transistors with inorganic gate oxide for pH sensing (1982)

Ion-sensitive field-effect transistors (ISFET's) have been fabricated by using silicon films on sapphire substrates (SOS). Using this structure SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , ZrO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , and Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> films are examined as hydrogenion-sensitive materials, and Ta <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> film has been found to have the highest pH sensitivity (56 mV/pH) among them. The measured pH sensitivity of this SOS-ISFET's is compared with the theoretical sensitivity based on the site-binding model of proton dissociation reaction on the metal oxide film and good agreement between them is obtained.
Guselkumab for the Treatment of Moderate-to-Severe Plaque Psoriasis During Induction Phase: A Systematic Review and Network Meta-Analysis (2018)

Background: Guselkumab is an interleukin-23 inhibitor indicated for treatment of moderate-to-severe plaque psoriasis. Objective: The objective was to determine the relative efficacy and safety of guselkumab compared to other biologics. Methods: A systematic review was performed to identify randomized controlled trials (RCTs). Bayesian network meta-analyses (NMAs) were conducted using meta-regression analyses that adjusted for cross-trial differences and risk differences. The primary outcome was Psoriasis Area and Severity Index (PASI) 90 response. Other efficacy and safety outcomes were considered. Several meta-regressions were performed to account for variations in patient and study characteristics: baseline risk adjustment (ie, control group response), prior biologic use, duration of psoriasis, weight, age, race, and baseline PASI/dermatology life quality index scores. The best-fitting model using predefined criteria was selected. Results: Forty-five RCTs were identified. Patient and study characteristics differed between RCTs as reflected in variations in control group response. Both the baseline risk-adjusted NMA and the risk-difference NMA fit the data best and suggested guselkumab has one of the highest PASI 90 responses. Pairwise comparisons from the baseline risk-adjusted PASI 90 NMA suggested guselkumab has comparable efficacy with ixekizumab (relative risk [RR]: 0.999, 95% credible intervals [CrIs]: 0.89-1.13) and brodalumab (RR: 1.04, 95% CrIs: 0.91-1.17) and superior efficacy versus all other treatments in the network (RR range, 1.20 to 43.22). Guselkumab was superior or comparable to other therapies for other efficacy outcomes and had a more favorable safety profile than most. Conclusions: Guselkumab has one of the highest PASI 90 responses among psoriasis treatments; similar findings were observed for other efficacy outcomes. Guselkumab has a favorable benefit–risk balance compared to moderate-to-severe psoriasis therapies.
Induction of sterile transcription from the kL chain gene locus in V(D)J recombinasedeficient progenitor B cells (1995)

B cell development in RAG-2-deficient (RAG-2T) mice is impeded at an early stage, due to the inability of these animals to rearrange their endogenous ig gene loci. Expression of an E mu-bcl-2 transgene in these mice did not change this phenotype. However, stromal cell/IL-7-reactive B cell progenitors (pro-B cells) were found in fetal live and bone marrow of RAG-2T and RAG-2T/E mu-bcl-2 transgenic mice in numbers comparable to normal mice. Like cells from normal mice they are c-kit+, surrogate L chain+ and CD25-, and can proliferate in vitro for long periods of time. Upon IL-7 deprivation, they can be induced to differentiate into c-kit-, surrogate L chain- and CD25+ cells that are no longer clonable on stromal cells and IL-7. Furthermore, sterile transcription from the kappa L chain gene loci is induced. The latter was also observed with pro-B cells directly isolated ex vivo from the bone marrow of RAG-2-deficient animals. The results suggest that progenitor B cell differentiation can occur in cells from V(D)J recombinase-deficient mice to the stage where kL chain gene rearrangements would normally be initiated. It further indicates that some molecular programs of early B cell differentiation can take place in the absence of Ig gene rearrangements.
Magnetic Field Sensitivity in Animals (1984)

Mitochondrial fatty acid β-oxidation (FAO) is the major pathway for the degradation of fatty acids and is essential for maintaining energy homeostasis in the human body. Fatty acids are a crucial energy source in the postabsorptive and fasted states when ...Read More
High numerical aperture full-field optical coherence tomography with space-invariant resolution without scanning the focus (2007)

In high-numerical-aperture optical coherence tomography, the depth-of-field is usually quite short and therefore the focus is scanned through the object to form a well-resolved image of the entire volume. However, this may be inconvenient for in vivo scanning when precision placement is not easily achieved between the object and the focusing objective. We show that by scanning the illumination wavelength, and using novel inverse scattering methods on the detected interferograms, features outside of the focus can be resolved and therefore the focus does not need to be scanned.