gebhart/patrepeval huggingface dataset:
Identification of New Candidate Therapeutic Target Genes in Triple-Negative Breast Cancer (2012)

Triple-negative breast cancer (TNBC) is a subgroup of breast cancer that is negative for estrogen and progesterone receptor and ERBB2 protein expression. It is characterized by its aggressive behavior and by the lack of targeted therapies. To identify new therapeutic targets in TNBC, we used real-time quantitative RT-PCR to analyze 63 TNBC samples in terms of their mRNA expression of 26 genes coding for the major proteins currently targeted by drugs used to treat other cancers or undergoing clinical trials in breast cancer. Six of the 26 genes tested (VEGFA, SRC, PARP1, PTK2, RAF1, and FGFR3) were significantly upregulated in 13% to 46% of the TNBCs. None of the 6 genes was specifically upregulated in the TNBCs compared with 3 other classical breast tumor subtypes. No association was observed between overexpression of these 6 genes (except for FGFR3) and PIK3CA mutation status. These results confirm the interest of targeting VEGFA and PARP1 in ongoing clinical trials in TNBC patients and also identify new target genes (SRC, PTK2, RAF1, and FGFR3). Clinical trials could be initiated easily with existing drugs. Our results also suggest that these target genes might serve as predictive biomarkers of the TNBC treatment response.
Multimedia storage servers: a tutorial (1995)

Real-time processing of multimedia data is required of those who offer audio and video on-demand. This tutorial highlights the unique issues and data storage characteristics that concern designers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antitumor constituents from Alternanthera philoxeroides (2007)

Two new compounds, alternanthin B (1) and N-trans-feruloyl-3,5-dimethoxytyramine (2), along with four known compounds (3-6) were isolated from the aerial parts of Alternanthera philoxeroides. Their structures were elucidated on the basis of spectroscopic methods. The antitumor activity of the isolated compounds was also evaluated.
Labeling of platelets with oxine complexes of Tc-99m and In-111. Part 1. In vitro studies and survival in the rabbit. (1978)

We have used both Tc-99m oxine and In-111 oxine to study the effects in the rabbit of various parameters on platelet labeling and the in vivo survival of platelets harvested by four different methods. For In-111 oxine, platelet labeling in saline produces much higher efficiencies (90%) than labeling in the presence of plasma (20%), with no significant shortening of in vivo survival (1% survival at 5.9 days). For Tc-99m oxine, labeling efficiencies are considerably lower (30%) and survival is shorter (1% survival at 3.8 days). For both radioagents, a 30-min labeling incubation at room temperature is suggested.
Social Motility in African Trypanosomes (2010)

African trypanosomes are devastating human and animal pathogens that cause significant human mortality and limit economic development in sub-Saharan Africa. Studies of trypanosome biology generally consider these protozoan parasites as individual cells in suspension cultures or in animal models of infection. Here we report that the procyclic form of the African trypanosome Trypanosoma brucei engages in social behavior when cultivated on semisolid agarose surfaces. This behavior is characterized by trypanosomes assembling into multicellular communities that engage in polarized migrations across the agarose surface and cooperate to divert their movements in response to external signals. These cooperative movements are flagellum-mediated, since they do not occur in trypanin knockdown parasites that lack normal flagellum motility. We term this behavior social motility based on features shared with social motility and other types of surface-induced social behavior in bacteria. Social motility represents a novel and unexpected aspect of trypanosome biology and offers new paradigms for considering host-parasite interactions.
Pre beta 1-high-density lipoprotein increases in coronary artery disease (1996)

Pre beta 1-HDL promotes cholesterol efflux from cell membranes. Its plasma concentration is regulated by lecithin: cholesterol acyltransferase (LCAT). To clarify whether the concentration of pre beta 1-HDL changes in coronary artery disease (CAD), we determined the distribution of apolipoprotein A-I (apoA-I) among HDL subfractions in 20 CAD patients and 20 healthy controls, using nondenaturing two-dimensional gel electrophoresis. We found that CAD patients had significantly higher concentrations of pre beta 1-HDL than the controls [7.6% +/- 3.4% vs 4.6% +/- 2.3% of apoA-I (P < 0.01)]. Even after correcting for apoA-I concentrations, this increase remained significant [87 +/- 37 vs 63 +/- 28 mg/L apoA-I (P < 0.05)]. The mean LCAT concentration was significantly lower (P < 0.05) in CAD patients than in controls. These findings, that pre beta 1-HDL concentrations increase in CAD, strongly suggest that the process of reverse cholesterol transport could be altered in CAD.
Cell Interactions with Polyelectrolyte Multilayer Films (2002)

The short-term interactions of chondrosarcoma cells with polyelectrolyte multilayer films built up by the alternate adsorption of poly(L-lysine) (PLL) and poly(L-glutamic acid) (PGA) was studied in the presence and in the absence of serum. The films and their interaction with serum proteins were first characterized by means of optical waveguide lightmode spectroscopy, quartz crystal microbalance, and zeta potential measurements. In a serum-containing medium, the detachment forces measured by the micropipet technique were about eight times smaller on PGA-ending than on PLL-ending films. For these latter ones, the adhesion force decreased when the film thickness increased. In a serum-free medium, the differences between the negative- and positive-ending films were enhanced: adhesion forces on PLL-ending films were 40-100% higher, whereas no cellular adherence was found on PGA-terminating films. PGA-ending films were found to prevent the adsorption of serum proteins, whereas important protein adsorption was always observed on PLL-ending films. These results show how cell interactions with polyelectrolyte films can be tuned by the type of the outermost layer, the presence of proteins, and the number of layers in the film.
Prediction of Myelinated Nerve Fiber Stimulation Thresholds: Limitations of Linear Models (2004)

Computer models of neurons are used to simulate neural behavior, and are important tools for designing neural prostheses. Computation time remains an issue when simulating large numbers of neurons or applying models to real time applications. Warman et al. developed a method to predict excitation thresholds for axons using linear models and a predetermined critical voltage. We calculated threshold prediction error as a function of the location of an extracellular electrode using two different axon models to examine further threshold prediction using linear models. Threshold prediction error was low (<3% error) under the conditions examined by Warman et al., but under more general conditions, threshold prediction error was as high as 23.6%. Linear models were limited as effective tools for single fiber threshold prediction because accuracy was dependent on the nonlinear and linear models used, and any parameter that affected the extracellular potential distribution. Threshold prediction could be improved by appropriately choosing the membrane conductance of the linear model, but determination of an optimal conductance was computationally expensive. Finally, although single fiber threshold prediction error was partially masked when considering the input-output (I/O) properties of populations of axons, relatively large errors still occurred in population I/O curves generated with linear models.
Direct Borylation of Primary CH Bonds in Functionalized Molecules by Palladium Catalysis (2014)

Organoborane compounds are among the most commonly employed intermediates in organic synthesis and serve as crucial precursors to alcohols, amines, and various functionalized molecules. A simple palladium-based system catalyzes the conversion of primary C(sp(3) )H bonds in functionalized complex organic molecules into alkyl boronate esters. Amino acids, amino alcohols, alkyl amines, and a series of bioactive molecules can be functionalized with the use of readily available and removable directing groups in the presence of commercially available additives, simple ligands, and oxygen (O2 ) as the terminal oxidant. This approach represents an economic and environmentally friendly method that could find broad applications.
The Hungarian method for the assignment problem (1955)

Abstract Assuming that numerical scores are available for the performance of each of n persons on each of n jobs, the “assignment problem” is the quest for an assignment of persons to jobs so that the sum of the n scores so obtained is as large as possible. It is shown that ideas latent in the work of two Hungarian mathematicians may be exploited to yield a new method of solving this problem.
Nucleic Acids: Thermal Stability and Denaturation (2002)

Abstract Nucleic acid structures can have different stabilities that depend on a variety of factors that include the nucleic acid sequence, the structure adopted, and the solution environment. Together, these factors influence the thermal stability of the complex.
Quality enhancement of coded transient audio with a post-filter in frequency domain (2010)

This paper proposed a post-filter in frequency domain for enhancing the perceptual quality of the coded transient audio. The post-filter is used to filter the frequency coefficients of the coded transient and consists of a short-term post-filter which is derived from the Linear Predictive Coding (LPC) predictor based on the Discrete Cosine Transform (DCT) coefficients of the transient frame. In order to compensate the overall spectral tilt, a spectral tilt compensation filter is used following the short-term post-filter. As a result, the post-filter in frequency domain shapes the temporal noise in time domain while introducing a little distortion in audio. This kind of post-filter doesn't need side information from the encoder and can be used in any audio decoder.
A large region (approximately equal to 95 kDa) of human factor VIII is dispensable for in vitro procoagulant activity. (1986)

Factor VIII (antihemophilic factor) is a high molecular weight plasma glycoprotein that participates in the blood clotting cascade. The recent cloning and sequence analysis of the cDNA encoding human factor VIII revealed an obvious domain structure for the protein, which can be represented as A1-A2-B-A3-C1-C2. We now report the DNA sequence analysis of porcine exons encoding the entire B domain and part of the A2 and A3 domains. We found an unusually high degree of porcine-human amino acid sequence divergence in the B region compared with the limited sequence available for other regions of the porcine factor VIII molecule. In addition to sequence divergence, there are numerous gaps in the porcine B domain totalling over 200 amino acids. Recombinant DNA techniques were used to effect the removal of large segments of DNA encoding the B domain from the full-length human factor VIII cDNA. These constructs directed the synthesis of biologically active factor VIII when introduced into mammalian cells despite the deletion of up to 38% of the factor VIII molecule.
Deformation of red blood cells using acoustic radiation forces (2014)

Acoustic radiation forces have been used to manipulate cells and bacteria in a number of recent microfluidic applications. The net force on a cell has been subject to careful investigation over a number of decades. We demonstrate that the radiation forces also act to deform cells. An ultrasonic standing wave field is created in a 0.1 mm glass capillary at a frequency of 7.9 MHz. Using osmotically swollen red-blood cells, we show observable deformations up to an aspect ratio of 1.35, comparable to deformations created by optical tweezing. In contrast to optical technologies, ultrasonic devices are potentially capable of deforming thousands of cells simultaneously. We create a finite element model that includes both the acoustic environment of the cell, and a model of the cell membrane subject to forces resulting from the non-linear aspects of the acoustic field. The model is found to give reasonable agreement with the experimental results, and shows that the deformation is the result of variation in an acoustic force that is directed outwards at all points on the cell membrane. We foresee applications in diagnostic devices, and in the possibility of mechanically stimulating cells to promote differentiation and physiological effects.
Chichibabin amination of 1,X-naphthyridines. Nuclear magnetic resonance studies on the .sigma. adducts of heterocyclic systems with nucleophiles (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChichibabin amination of 1,X-naphthyridines. Nuclear magnetic resonance studies on the .sigma. adducts of heterocyclic systems with nucleophilesHenk J. W. Van den Haak, Henk C. Van der Plas, and Beb Van VeldhuizenCite this: J. Org. Chem. 1981, 46, 10, 2134–2137Publication Date (Print):May 1, 1981Publication History Published online1 May 2002Published inissue 1 May 1981https://pubs.acs.org/doi/10.1021/jo00323a031https://doi.org/10.1021/jo00323a031research-articleACS PublicationsRequest reuse permissionsArticle Views507Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Gamma‐Hydroxybutyric Acid in the Treatment of Alcohol Dependence: A Double‐Blind Study (1992)

The effect of gamma-hydroxybutyric acid on alcohol consumption and alcohol craving in alcoholics was investigated in a randomized double-blind study versus placebo. Patients were treated as outpatients during a three month period either with gamma-hydroxybutyric acid (50 mg/kg/day, divided into three daily doses) or with placebo. Of the 82 alcoholics that entered the study, 71 completed it, 36 in the gamma-hydroxybutyric acid and 35 in the placebo group. Alcohol consumption was assessed by the subject's self report. At the 3rd month of treatment, 11 patients in the gamma-hydroxybutyric acid group referred to be abstinent and 15 referred controlled drinking; while in the placebo group only two and six patients referred abstinence and controlled drinking, respectively. Serum-gammaglutamyl-transferase activity correlated with the admitted alcohol consumption. Gamma-hydroxybutyric acid treatment decreased alcohol craving during the 3 months of treatment. Transient side effects were noted by six patients on gamma-hydroxybutyric acid and two on placebo. The results suggest that gamma-hydroxybutyric acid may be useful in the treatment of alcohol dependence.
Small Molecule Modulators of Endogenous and Co-chaperone-stimulated Hsp70 ATPase Activity (2004)

The molecular chaperone and cytoprotective activities of the Hsp70 and Hsp40 chaperones represent therapeutic targets for human diseases such as cancer and those that arise from defects in protein folding; however, very few Hsp70 and no Hsp40 modulators have been described. Using an assay for ATP hydrolysis, we identified and screened small molecules with structural similarity to 15-deoxyspergualin and NSC 630668-R/1 for their effects on endogenous and Hsp40-stimulated Hsp70 ATPase activity. Several of these compounds modulated Hsp70 ATPase activity, consistent with the action of NSC 630668-R/1 observed previously (Fewell, S. W., Day, B. W., and Brodsky, J. L. (2001) J. Biol. Chem. 276, 910-914). In contrast, three compounds inhibited the ability of Hsp40 to stimulate Hsp70 ATPase activity but did not affect the endogenous activity of Hsp70. Two of these agents also compromised the Hsp70/Hsp40-mediated post-translational translocation of a secreted pre-protein in vitro. Together, these data indicate the potential for continued screening of small molecule Hsp70 effectors and that specific modulators of Hsp70-Hsp40 interaction can be obtained, potentially for future therapeutic use.
Simple 'neural' optimization networks: An A/D converter, signal decision circuit, and a linear programming circuit (1986)

We describe how several optimization problems can be rapidly solved by highly interconnected networks of simple analog processors. Analog-to-digital (A/D) conversion was considered as a simple optimization problem, and an A/D converter of novel architecture was designed. A/D conversion is a simple example of a more general class of signal-decision problems which we show could also be solved by appropriately constructed networks. Circuits to solve these problems were designed using general principles which result from an understanding of the basic collective computational properties of a specific class of analog-processor networks. We also show that a network which solves linear programming problems can be understood from the same concepts.
An Update on the Role of Markers of Inflammation in Atherosclerosis (2010)

In recent years, several studies have used the measurement of carotid intima-media thickness (IMT) as a marker of early atherosclerosis: IMT has been shown to correlate significantly with the presence of coronary artery disease (CAD) and to predict fatal and not fatal cerebro- and cardio-vascular events. These findings highlight the importance of recognizing and managing early stages of atherosclerosis for effective cardiovascular prevention. Beyond traditional established cardiovascular risk factors, inflammation has been shown to be crucial throughout atherosclerosis from endothelial dysfunction to plaque rupture and thrombosis. Several studies have shown the existence of a strong relation between CAD and fibrinogen or highly sensitive C-reactive protein (hs-CRP) levels and their predictive role has been examined through stratification or multivariable statistical analyses: levels of these markers of inflammation have been independently associated with the incidence of coronary events after adjusting for traditional cardiovascular risk factors. Recent studies have further addressed the importance of therapeutical modulation of hs-CRP levels in high-risk patients for the prevention of vascular events. The strong relationship between hs-CRP and IMT may potentially account for the complex role of hs-CRP and IMT in the pathogenesis of cardiovascular events. However, beyond the utility of measuring markers of inflammation to assess patients with subclinical carotid atherosclerosis at higher risk of vascular events, further studies are needed to evaluate the therapeutic implications in this category of patients.
Diazepinone Nucleosides as Inhibitors of Cytidine Deaminase. (1996)

Abstract The synthesis of 2′-deoxy and 2′,3′-dideoxy derivatives of 1-ß-D-ribofuranosyl-1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one (2) was undertaken in order to find new cytidine deaminase (CDA) inhibitors and potential adjuvants in anticancer chemotherapy. Replacement of ribose by a 2-deoxyribose moiety led to compound 9 that appeared slightly more potent than 2 (Ki = 2.5 × 10−8 M). Remarkably, the corresponding α-2′-deoxynucleoside 10 acted as a very potent inhibitor of human placenta CDA, with a Ki = 7.5 × 10−8 M. Attempt to synthesize the 2′,3′-dideoxy derivative of 2 led to N-[4,5-dihydroxy-1-(2-oxo-2,3,4,7-tetrahydro[1,3] diazepin-1-yl)-pentyl]-2,2,2-trifluoroacetamide (13), which is devoid of CDA inhibitory activity.
Design requirements for technologies that encourage physical activity (2006)

Overweight and obesity are a global epidemic, with over one billion overweight adults worldwide (300+ million of whom are obese). Obesity is linked to several serious health problems and medical conditions. Medical experts agree that physical activity is critical to maintaining fitness, reducing weight, and improving health, yet many people have difficulty increasing and maintaining physical activity in everyday life. Clinical studies have shown that health benefits can occur from simply increasing the number of steps one takes each day and that social support can motivate people to stay active. In this paper, we describe Houston, a prototype mobile phone application for encouraging activity by sharing step count with friends. We also present four design requirements for technologies that encourage physical activity that we derived from a three-week long in situ pilot study that was conducted with women who wanted to increase their physical activity.
Dinucleotide repeat polymorphisms within the Flt‐1 gene in minimal change nephropathy (1999)

Dysregulation of Flt-1, a major receptor for vascular permeability factor (VPF), may provide a mechanism for the development of proteinuria in minimal change nephropathy (MCN). The gene for Flt-1 has a polymorphic dinucleotide repeat. We have demonstrated an 88% predominance of one allele and an 80% rate of homozygosity for this polymorphism with no association with MCN.
Current Rectification at Quartz Nanopipet Electrodes (1997)

Ag/AgCl reference electrodes fabricated from pulled quartz tubes with orifice radii of 20 nm to 20 μm were characterized in KCl solutions of different concentrations by cyclic voltammetry. Linear current−voltage (i−V) dependence was observed with micropipet electrodes (with micrometer-sized tips) with the same concentration (0.01−1 M) of KCl inside and outside the pipet, but current rectification was found at nanopipet electrodes at KCl concentrations of ≤0.1 M (with nanometer-sized tips). This is attributed to formation of a diffuse electrical double layer within the tip orifice. The effects of electrode size, electrolyte concentration, and solution pH on the nonlinear i−V behavior of these electrodes were investigated. A model for the observed behavior shows the rectification to be caused by the permselectivity in the tip region and the geometric asymmetry of the tip orifice. This phenomenon may be important in studies of ion transport in charged channels and porous membranes.