gebhart/patrepeval huggingface dataset:
Fast Kinetics of Thiolic Self-Assembled Monolayer Adsorption on Gold: Modeling and Confirmation by Protein Binding (2014)

This study presents an improved kinetics for the formation of self-assembled monolayers (SAMs) of thiols on gold substrates. Based on predictions of a computational model developed to study the SAM growth kinetics, SAMs of 11-mercaptoinic acid and 1-octanethiol were successfully formed for the first time within 15 min by incubation of planar gold chips in a 10 mM solution of thiols in pure ethanol. The performance of this new rapid SAM formation protocol is compared to the conventional 24 h incubation protocol by evaluating the binding capacity of a fluorescent-labeled antibody to the SAM samples prepared using both protocols. Tetramethylrhodamine conjugated polyclonal goat γ-globulin (IgG) was bound to all SAMs previously modified with 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC) to improve antibody immobilization. Resulting binding density of the fast SAM was evaluated using epifluorescence and atomic force microscopy (AFM) and found to be comparable with reported values in the literature using conventional 24 h protocols.
Mutations in the gyrA and grlA genes of quinolone-resistant clinica isolates of methicillin-resistant Staphylococcus aureus (1996)

The mutations in the quinolone-resistance determining regions (QRDR) of the gyrA, gyrB and grlA genes and in the norA gene from five clinical isolates of methicillin resistant Staphylococcus aureus (MRSA) were examined by DNA sequencing. The mutation from Ser84 to Leu in GyrA was associated with relatively high-level resistance to quinolones, whereas the mutation from Glu88 to Gly or Lys in GyrA was associated with low-level resistance to quinolones. Mutations of the grlA gene were observed at codon 80 (Ser80) or 84 (Glu84), independent of the mutations of gyrA. No mutations were observed in either the gyrB or norA genes.
The putative glutamate receptor 1.1 (AtGLR1.1) functions as a regulator of carbon and nitrogen metabolism in Arabidopsis thaliana (2003)

The ability to coordinate carbon (C) and nitrogen (N) metabolism enables plants to regulate development and metabolic responses to different environmental conditions. The regulator(s) or sensor(s) that monitor crosstalk between biosynthetic pathways and ultimately control the flow of C or N through them have remained elusive. We used an antisense strategy to demonstrate that the putative glutamate receptor 1.1 (AtGLR1.1) functions as a regulator of C and N metabolism in Arabidopsis. Seeds from AtGLR1.1-deficient Arabidopsis (antiAtGLR1.1) lines did not germinate in the presence of an animal ionotropic glutamate receptor (iGLR) antagonist, but germination was restored upon coincubation with an iGLR agonist or the putative ligand glutamate. In antiAtGLR1.1 lines, endogenous abscisic acid (ABA) concentrations increased with iGLR antagonist treatments and decreased with coincubation with an iGLR agonist, suggesting that germination was controlled by ABA. antiAtGLR1.1 seedlings also exhibited sensitivity to increased levels of Ca2+ compared with wild type, and they exhibited a conditional phenotype that was sensitive to the C:N ratio. In the presence of C, specifically sucrose, but not glucose, mannitol, or sorbitol, antiAtGLR1.1 seeds did not germinate, but germination was restored upon coincubation with NO3-, but not NH4+. Immunoblot, isoenzyme, and RT-PCR analyses indicate that AtGLR1.1 regulates the accumulation of distinct C- and N-metabolic enzymes, hexokinase 1 (HXK1) and zeaxanthin epoxidase (ABA1), by transcriptional control. We provide a model to describe the role of AtGLR1.1 in C/N metabolism and ABA biosynthesis, which in turn controls seed germination.
Homocitric Acid Accumulation by a Lysine-requiring Yeast Mutant (1966)

Abstract The accumulation of β-carboxy-β-hydroxyadipic acid (homocitric acid) in the culture medium of the lysine-requiring yeast mutant, Ly4, grown on limiting amounts of lysine, has been demonstrated. Identity of the biologically formed acid with synthetic homocitric acid was established by comparison of infrared spectra, Rf values from paper chromatograms, optical rotations, and melting points. Radioactively labeled homocitric acid was obtained from the mutant grown on uniformly labeled 14C-glucose, as well as by incubation of a cell-free extract of the organism with 1-14C-acetate and α-ketoglutarate. Radioactive lysine was obtained from the hydrolysate of wild-type yeast grown in the presence of 14C-labeled homocitrate. The excretion of homocitric acid by a lysine-requiring yeast mutant and its conversion into lysine convincingly establish the biosynthesis of lysine in yeast via the previously proposed scheme involving homologues of the citric acid cycle.
Salomé, una pequeña con alma de investigadora (2014)

Salome Trujillo Berrio es sonadora, inspiradora y amante del estudio. En clase se distingue por estar atenta y ser muy comprensiva y carismatica con sus companeros.
Histone Deacetylase 1 Can Repress Transcription by Binding to Sp1 (1999)

The members of the Sp1 transcription factor family can act as both negative and positive regulators of gene expression. Here we show that Sp1 can be a target for histone deacetylase 1 (HDAC1)-mediated transcriptional repression. The histone deacetylase inhibitor trichostatin A activates the chromosomally integrated murine thymidine kinase promoter in an Sp1-dependent manner. Coimmunoprecipitation experiments with Swiss 3T3 fibroblasts and 293 cells demonstrate that Sp1 and HDAC1 can be part of the same complex. The interaction between Sp1 and HDAC1 is direct and requires the carboxy-terminal domain of Sp1. Previously we have shown that the C terminus of Sp1 is necessary for the interaction with the transcription factor E2F1 (J. Karlseder, H. Rotheneder, and E. Wintersberger, Mol. Cell. Biol. 16:1659-1667, 1996). Coexpression of E2F1 interferes with HDAC1 binding to Sp1 and abolishes Sp1-mediated transcriptional repression. Our results indicate that one component of Sp1-dependent gene regulation involves competition between the transcriptional repressor HDAC1 and the transactivating factor E2F1.
The characterization of a rabbit model of inflammatory bowel disease. (1995)

The absence of a simple, clinically relevant, animal model of inflammatory bowel disease (IBD) hampers research into this disease. In this study, colitis was induced in rabbits by intracolonic installation of 2,4,6-trinitrobenzene sulphonic acid (TNB) in 25% ethanol. Rabbits were killed from zero hours to 6 weeks and their colons examined. Rabbits were examined by endoscopy at weekly intervals. A single dose of TNB in ethanol produced dose dependent inflammation and ulceration, which at its optimum (40 mg) resulted in cobblestoning, strictures, and bowel wall thickening. The damage score at endoscopy was consistent with the score on macroscopic examination of the colon. Histopathological features of inflammation and ulceration observed in all animals that received 40 mg TNB included crypt abscesses, ulceration, crypt architectural distortion and, occasionally, granulomas and pseudopolyps. These changes, which are similar to those observed in IBD, persisted for 6 weeks. No lasting abnormalities were observed in control animals treated with TNB in saline, with ethanol alone, or with saline only. Histopathological similarity and the prolonged duration of inflammation, compared to other models, make this a suitable model for investigating inflammation in the colon. Furthermore, the model is accessible to endoscopy which adds to its value in experimental studies.
Proton nuclear magnetic resonance spectroscopy of human transferrin N-terminal half-molecule: titration and hydrogen-deuterium exchange (1987)

The binding of Ga(III) to the proteolytically derived N-terminal half-molecule of human transferrin (HTF/2N) was studied by proton nuclear magnetic resonance spectroscopy. The pH-dependent titration curves of the histidinyl C(2) proton chemical shifts were altered upon formation of the GaIIIHTF/2N(C2O4) ternary complex. Two high-pK'a histidines failed to titrate when the metal and synergistic anion formed a complex with the protein. These results implicated two histidinyl residues as direct ligands to the metal. The rates of hydrogen-deuterium exchange for the C(2) protons of certain histidinyl residues were substantially decreased by metal ion binding. The two ligand histidines were protected from exchange, and a third, low-pK'a, histidinyl residue was protected. We propose that this third histidinyl residue is involved in anion binding and may serve as the base in the putative proton-relay scheme proposed for complex formation.
Diffuse Large B-Cell Lymphoma With Extra Bcl-2 Gene Signals Detected by FISH Analysis Is Associated With a “Non-Germinal Center Phenotype” (2005)

Amplification and translocation of the Bcl-2 gene has been detected in a certain subset of diffuse large B-cell lymphomas (DLBCL). The correlations among Bcl-2 protein expression, gene translocation or amplification, and the molecular signature determined by cDNA array are poorly understood. This study examined 25 cases with de novo nodal DLBCL. Interphase fluorescence in situ hybridization (FISH) analysis was performed to evaluate the Bcl-2 gene using IGH/BCL2 and CEP18 centromere probes (Vysis). When extra Bcl-2 gene signals were observed in each tumor cell and when these signals were in proportion to the extra CEP18 probe signals, we regarded the findings as indicating the presence of an additional chromosome 18; when extra Bcl-2 signals were observed but additional CEP18 signals were not, we regarded the findings as indicating the presence of gene amplification. A panel of 3 antigens (CD10, Bcl-6, and MUM-1) was applied to categorize each case as either a "germinal center B-cell (GCB) phenotype" or a "non-GCB phenotype." Of the 25 cases examined, 8 cases (32%) were classified as "GCB phenotype" and 17 cases (68%) were classified as "non-GCB phenotype." A FISH analysis revealed that t(14;18) was detected in 2 of the 8 cases (25%) with the "GCB phenotype" but in none of the 17 "non-GCB phenotype" cases. Extra Bcl-2 gene signals were detected in 7 of the 25 (28%) cases examined: n = 5 for an additional chromosome 18, n = 1 for gene amplification, and n = 1 for additional chromosome 18 + gene amplification. Extra Bcl-2 gene signals were exclusively detected in DLBCL with the "non-GCB phenotype"; these cases, with the exception of one, stained strongly positive for Bcl-2. The DLBCLs with Bcl-2 protein overexpression were classified into at least two heterogeneous molecular groups, based on the results of the FISH analysis.
Control of Cachectin (Tumor Necrosis Factor) Synthesis: Mechanisms of Endotoxin Resistance (1986)

Cachectin (tumor necrosis factor) is a macrophage hormone strongly implicated in the pathogenesis of endotoxin-induced shock. The availability of a DNA probe complementary to the cachectin messenger RNA (mRNA), as well as a specific antibody capable of recognizing the cachectin gene product, has made it possible to analyze the regulation of cachectin gene expression under a variety of conditions. Thioglycollate-elicited peritoneal macrophages obtained from mice contain a pool of cachectin mRNA that is not expressed as protein. When the cells are stimulated with endotoxin, large quantity of additional cachectin mRNA is produced, and immunoreactive cachectin is secreted. Macrophages from mice of the C3H/HeJ strain do not produce cachectin in response to endotoxin. A dual defect appears to prevent cachectin expression. First, a diminished quantity of cachectin mRNA is expressed in response to low concentrations of endotoxin. Second, a post-transcriptional defect prevents the production of cachectin protein. Macrophages from endotoxin-sensitive mice do not produce cachectin if they are first treated with dexamethasone, apparently for similar reasons. These findings give new insight into the nature of the C3H/HeJ mutation and suggest an important mechanism by which glucocorticoids may act to suppress inflammation.
RNAcentral: a comprehensive database of non-coding RNA sequences (2016)

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.
Blockade of Vascular Smooth Muscle Cell Proliferation and Intimal Thickening After Balloon Injury by the Sulfated Oligosaccharide PI-88 (2003)

Percutaneous transluminal coronary angioplasty is a frequently used interventional technique to reopen arteries that have narrowed because of atherosclerosis. Restenosis, or renarrowing of the artery shortly after angioplasty, is a major limitation to the success of the procedure and is due mainly to smooth muscle cell accumulation in the artery wall at the site of balloon injury. In the present study, we demonstrate that the antiangiogenic sulfated oligosaccharide, PI-88, inhibits primary vascular smooth muscle cell proliferation and reduces intimal thickening 14 days after balloon angioplasty of rat and rabbit arteries. PI-88 reduced heparan sulfate content in the injured artery wall and prevented change in smooth muscle phenotype. However, the mechanism of PI-88 inhibition was not merely confined to the antiheparanase activity of this compound. PI-88 blocked extracellular signal-regulated kinase-1/2 (ERK1/2) activity within minutes of smooth muscle cell injury. It facilitated FGF-2 release from uninjured smooth muscle cells in vitro, and super-released FGF-2 after injury while inhibiting ERK1/2 activation. PI-88 inhibited the decrease in levels of FGF-2 protein in the rat artery wall within 8 minutes of injury. PI-88 also blocked injury-inducible ERK phosphorylation, without altering the clotting time in these animals. Optical biosensor studies revealed that PI-88 potently inhibited (Ki 10.3 nmol/L) the interaction of FGF-2 with heparan sulfate. These findings show for the first time the capacity of this sulfated oligosaccharide to directly bind FGF-2, block cellular signaling and proliferation in vitro, and inhibit injury-induced smooth muscle cell hyperplasia in two animal models. As such, this study demonstrates a new role for PI-88 as an inhibitor of intimal thickening after balloon angioplasty. The full text of this article is available online at http://www.circresaha.org.
A Machine Vision Based System for Guiding Lane-change Maneuvers (1995)

We propose a new approach for vision based longitudinal and lateral ve-hicle control which makes extensive use of binocular stereopsis. Longitudi-nal control - i.e. maintaining a safe, constant distance from the vehicle infront - is supported by detecting and measuring the distances to leadingvehicles using binocular stereo.A known camera geometry with respect tothe locally planar road is used to map the images of the road plane in thetwo camera views into alignment.Any significant residual image disparitythen indicates an object not lying in the road plane and hence a potentialobstacle. This approach allows us to separate image features into those lyingin the road plane, e.g.lane markers, and those due to other objects. Thefeatures which lie on the road are stationary in the scene and appear to moveonly because of the egomotion of the vehicle. Measurements on these featuresare used for dynamic update of (a) the camera parameters in the presenceof camera vibration and changes in road slope (b) the lateral position of thevehicle with respect to the lane markers.In the absence of this separation,image features due to vehicles which happen to lie in the search zone for lanemarkers would corrupt the estimation of the road boundary contours. Thisproblem has not yet been addressed by any lane marker based vehicle guid-ance approach, but has to be taken very seriously, since usually one has tocope with crowded traffic scenes where lane markers are often obstructed byvehicles. Lane markers are detected and used for lateral control, i.e. followingthe road while maintaining a constant lateral distance to the road boundary.For that purpose we model the road and hence the shape of the lane markersas clothoidal curves, the curvatures of which we estimate recursively along theimage sequence. These curvature estimates also provides desirable look-aheadinformation for a smooth ride in the car.
The Thermal Mechanics of Tool Wear (1966)

Empirical evidence is presented to show that the geometry of tool wear, and the presence of built-up-edge, is strongly controlled by the chip curl. Evidence is also given which shows that some free-machining additives affect only the cutting temperature while others may affect the basic wear mechanism. Two simple theories are presented for calculating the rate of tool wear based on diffusion of tool material into the workpiece. While not conclusive, the results show remarkable agreement between predicted and measured wear based on a model wherein tool atoms jump into excess vacancies created in the chip by the plastic deformation of friction.
A structured literature review of treatment for localized prostate cancer. Prostate Disease Patient Outcome Research Team (1993)

Although we were able to compare complications of treatments, we were unable to determine treatment effectiveness for localized prostate cancer because of methodologic inadequacies in the literature we reviewed. Until better scientific evidence is available, patients and their physicians cannot make informed choices based on knowledge of the benefits of radical prostatectomy, radiation, or watchful waiting.
Inhibition of Adipogenesis by Wnt Signaling (2000)

Wnts are secreted signaling proteins that regulate developmental processes. Here we show that Wnt signaling, likely mediated by Wnt-10b, is a molecular switch that governs adipogenesis. Wnt signaling maintains preadipocytes in an undifferentiated state through inhibition of the adipogenic transcription factors CCAAT/enhancer binding protein alpha (C/EBPalpha) and peroxisome proliferator- activated receptor gamma (PPARgamma). When Wnt signaling in preadipocytes is prevented by overexpression of Axin or dominant-negative TCF4, these cells differentiate into adipocytes. Disruption of Wnt signaling also causes transdifferentiation of myoblasts into adipocytes in vitro, highlighting the importance of this pathway not only in adipocyte differentiation but also in mesodermal cell fate determination.
An evaluation of the role of insulin-like growth factors (IGF) and of type-I IGF receptor signalling in hepatocarcinogenesis and in the resistance of hepatocarcinoma cells against drug-induced apoptosis (2004)

Strong evidence emphasizes the role of the insulin-like growth factor (IGF) system and of type-I IGF receptor (IGF-IR) signalling in tumourigenesis. In this connection: (i) changes in the expression pattern of components of the IGF system (autocrine/paracrine expression of IGF-I and -II, overexpression of IGF-IR, decreased expression of IGF-binding proteins (IGFBPs) and of type-II IGF receptor/cation-independent mannose-6-phosphate receptor (IGF-II/M6PR) and (ii) increased serum concentrations of proteases that cleave the IGFBPs (e.g., cathepsin D) were observed in patients with hepatocellular carcinomas (HCC), in human hepatoma cell lines and in their conditioned culture medium, as well as in rodent models of hepatocarcinogenesis. Accordingly, studies carried out with animal models do suggest that the IGF system and IGF-IR signalling may play a role in hepatocarcinogenesis and in deregulated proliferation and apoptosis of HCC cells. Finally the instrumental role of Raf/MEK/ERK, one of the signalling cascades stimulated by IGF-IR, in anthracycline-induced apoptosis of HepG2 and Huh-7 human hepatoma cell lines emphasizes that care must be taken when designing combinations of antitumoural molecules for antineoplastic treatment. This review addresses the putative roles of the IGF system in primary HCC, with a special focus on the underlying molecular mechanisms. In a second part it emphasizes the putative interference of IGF-IR signalling with chemotherapeutic drug-induced apoptosis in human hepatoma cells.
Squalene – biochemistry, molecular biology, process biotechnology, and applications (2011)

Abstract Squalene is a natural triterpene and an important intermediate of sterol and hopanoid biosynthesis in various types of cell from bacteria to human. Synthesis and further conversion of squalene are key steps in the metabolism of sterols and related components. Here we summarize the recent knowledge of squalene biochemistry, its molecular properties, and its physiological effects. We compare squalene biosynthetic pathways in different cell types and describe biotechnological strategies to isolate this lipid. Finally, applications of squalene in nutrition, pharmacy, and medicine are discussed.
Signal Processing Technique to Remove Signature Distortion in ARL Synchronous Impulse Reconstruction (SIRE) Ultra-Wideband (UWB) Radar (2008)

Abstract : ARL has designed and developed the SIRE UWB SAR radar in support of the U.S. Army vision for increased mobility, survivability, and lethality. The radar is based on time-domain wideband impulses. For this radar, ARL designed and implemented a data acquisition technique called Synchronous Impulse Reconstruction (SIRE) that allowed us to employ relatively slow ADC (40 MHz) to digitize wideband signals (>3000 MHz). However, the scheme assumed that the radar and targets are stationary during the data acquisition cycle and in reality the target signatures did suffer the distortions in phase and shape due to the radar motion. The phase error would lead to significant loss in target radar cross section values in resulting SAR imagery. The shape errors would destroy the frequency contents of the targets and thus the ability to discriminate targets from other confuser classes. This report describes a signal processing technique that removes the phase and shape distortions in the radar signal due to the motion of the platform. This technique results in SAR imagery with significant improvement in focus quality and signal-to-noise level. This has been tested and verified with simulated and measured radar data. This technique could be applied for any time-based impulse radar system that experiences the relative motion between the radar and the targets during the data acquisition cycle.
Genetic Modification of T Cells Redirected toward CS1 Enhances Eradication of Myeloma Cells (2014)

CS1 is a promising antigen that can be targeted by CAR-expressing T cells for treatment of MM.