gebhart/patrepeval huggingface dataset:
Covalent Conjugation of a Peptide Triazole to HIV-1 gp120 Enables Intramolecular Binding Site Occupancy (2014)

The HIV-1 gp120 glycoprotein is the main viral surface protein responsible for initiation of the entry process and, as such, can be targeted for the development of entry inhibitors. We previously identified a class of broadly active peptide triazole (PT) dual antagonists that inhibit gp120 interactions at both its target receptor and coreceptor binding sites, induce shedding of gp120 from virus particles prior to host-cell encounter, and consequently can prevent viral entry and infection. However, our understanding of the conformational alterations in gp120 by which PT elicits its dual receptor antagonism and virus inactivation functions is limited. Here, we used a recently developed computational model of the PT-gp120 complex as a blueprint to design a covalently conjugated PT-gp120 recombinant protein. Initially, a single-cysteine gp120 mutant, E275CYU-2, was expressed and characterized. This variant retains excellent binding affinity for peptide triazoles, for sCD4 and other CD4 binding site (CD4bs) ligands, and for a CD4-induced (CD4i) ligand that binds the coreceptor recognition site. In parallel, we synthesized a PEGylated and biotinylated peptide triazole variant that retained gp120 binding activity. An N-terminally maleimido variant of this PEGylated PT, denoted AE21, was conjugated to E275C gp120 to produce the AE21-E275C covalent conjugate. Surface plasmon resonance interaction analysis revealed that the PT-gp120 conjugate exhibited suppressed binding of sCD4 and 17b to gp120, signatures of a PT-bound state of envelope protein. Similar to the noncovalent PT-gp120 complex, the covalent conjugate was able to bind the conformationally dependent mAb 2G12. The results argue that the PT-gp120 conjugate is structurally organized, with an intramolecular interaction between the PT and gp120 domains, and that this structured state embodies a conformationally entrapped gp120 with an altered bridging sheet but intact 2G12 epitope. The similarities of the PT-gp120 conjugate to the noncovalent PT-gp120 complex support the orientation of binding of PT to gp120 predicted in the molecular dynamics simulation model of the PT-gp120 noncovalent complex. The conformationally stabilized covalent conjugate can be used to expand the structural definition of the PT-induced "off" state of gp120, for example, by high-resolution structural analysis. Such structures could provide a guide for improving the subsequent structure-based design of inhibitors with the peptide triazole mode of action.
High levels of the BCR/ABL oncoprotein are required for the MAPK-hnRNP-E2–dependent suppression of C/EBPα-driven myeloid differentiation (2007)

The inability of myeloid chronic myelogenous leukemia blast crisis (CML-BC) progenitors to undergo neutrophil differentiation depends on suppression of C/EBPalpha expression through the translation inhibitory activity of the RNA-binding protein hnRNP-E2. Here we show that "oncogene dosage" is a determinant factor for suppression of differentiation in CML-BC. In fact, high levels of p210-BCR/ABL are required for enhanced hnRNP-E2 expression, which depends on phosphorylation of hnRNP-E2 serines 173, 189, and 272 and threonine 213 by the BCR/ABL-activated MAPK(ERK1/2). Serine/threonine to alanine substitution abolishes hnRNP-E2 phosphorylation and markedly decreases its stability in BCR/ABL-expressing myeloid precursors. Similarly, pharmacologic inhibition of MAPK(ERK1/2) activity decreases hnRNP-E2 binding to the 5'UTR of C/EBPalpha mRNA by impairing hnRNP-E2 phosphorylation and stability. This, in turn, restores in vitro and/or in vivo C/EBPalpha expression and G-CSF-driven neutrophilic maturation of differentiation-arrested BCR/ABL(+) cell lines, primary CML-BC(CD34+) patient cells and lineage-negative mouse bone marrow cells expressing high levels of p210-BCR/ABL. Thus, increased BCR/ABL oncogenic tyrosine kinase activity is essential for suppression of myeloid differentiation of CML-BC progenitors as it is required for sustained activation of the MAPK(ERK1/2)-hnRNP-E2-C/EBPalpha differentiation-inhibitory pathway. Furthermore, these findings suggest the inclusion of clinically relevant MAPK inhibitors in the therapy of CML-BC.
The synthesis and high optical birefringence of nematogens incorporating 2,6-disubstituted naphthalenes and terminal cyano-substituent (1993)

Abstract A range of nematogenic materials which incorporate a 2,6-disubstituted naphthyl moiety and a terminal cyano-substituent have been synthesized by using palladium-catalysed cross-coupling procedures involving arylboronic acids and alkynylzinc reagents with aryl iodides, bromides and trifluoromethanesulphonates (triflates). The compounds have very high nematic phase stability, but their melting points are also quite high. The birefringences were measured using an extrapolation technique and the values were found to be between 0·26 and 0·42.
Synthesis of Hexagonal‐Phase NaYF<sub>4</sub>:Yb,Er and NaYF<sub>4</sub>:Yb,Tm Nanocrystals with Efficient Up‐Conversion Fluorescence (2006)

Abstract IR‐to‐visible up‐conversion fluorescent nanocrystals of hexagonal‐phase NaYF 4 :20 %Yb,2 %Er and NaYF 4 :20 %Yb,2 %Tm have been synthesized by decomposition of multiprecursors of CF 3 COONa, (CF 3 COO) 3 Y, (CF 3 COO) 3 Yb, and (CF 3 COO) 3 Er/(CF 3 COO) 3 Tm in oleylamine at 330 °C. The average particle size is 10.5 ± 0.7 nm (from random measurements of 200 particles from five transmission electron microscopy images) and 11.1 ± 1.3 nm (from dynamic‐light‐scattering measurements). The up‐conversion fluorescence intensity of the hexagonal nanocrystals in this work is much higher than that of other cubic‐phase NaYF 4 :Yb,Er nanocrystals, including the ones in this work (by a factor of 7.5). Mechanisms for nucleation and growth of the hexagonal‐phase nanoparticles are proposed. These nanocrystals are easily dispersed in organic solvents, producing a transparent colloidal solution. The hydrophobic surfaces of the particles are made hydrophilic using a bipolar surfactant. These nanoparticles and their dispersions in various media have potential applications in optical nanodevices and bioprobes.
New biomarkers of Maillard reaction damage to proteins (1996)

The amount of advanced glycation end-products (AGE) in tissue proteins increases in diabetes mellitus, and the concentration of a subclass of AGEs, known as glycoxidation products, also increases with chronological age in proteins. The rate of accumulation of glycoxidation products is accelerated in diabetes and age-adjusted concentrations of two glycoxidation products, N epsilon-(carboxymethyl)lysine (CML) and pentosidine, correlate with the severity of complication in diabetic patients. Although AGEs and glycoxidation products are implicated in the development of diabetic complications, these compounds are present at only trace concentrations in tissue proteins and account for only a fraction of the chemical modifications in AGE proteins prepared in vitro. The future of the AGE hypothesis depends on the chemical characterization of a significant fraction of the total AGEs in tissue proteins, a quantitative assessment of their effects on protein structure and function, and an assessment of their role as mediators of biological responses. In this manuscript we describe recent work leading to characterization of new AGEs and glycoxidation products. These compounds include: (1) the imidazolone adduct formed by reaction of 3-deoxyglucosone with arginine residues in protein; (2) N epsilon-(carboxyethyl)lysine, an analogue of CML formed on reaction of methylglyoxal with lysine; (3) glyoxal-lysine dimer; and (4) methyl-glyoxal-lysine dimer, which are imidazolium crosslinks formed by reaction of glyoxal or methylglyoxal with lysine residues in protein. The presence of 3-deoxyglucosone, methylglyoxal and glyoxal in vivo and the formation of the above AGEs in model carbonyl-amine reaction systems suggests that these AGEs are also formed in vivo and contribute to tissue damage resulting from the Maillard reaction.
Some Options for Improving the Governance of State-Owned Electricity Utilities (2004)

Most government-owned utilities in\n developing countries perform poorly when judged as providers\n of electricity, in part because politicians and officials\n use their power, not to encourage the utilities to increase\n sales, improve the collection of bills, and cut costs, but\n to transfer resources to politically influential groups and,\n sometimes, extract bribes. To improve the performance of\n government-owned electricity utilities as electricity\n utilities, rules and practices must be changed in a way that\n reduces politicians' willingness or ability to use the\n utilities for political purposes and subjects the utilities\n to new sources of pressure to perform well. This paper\n considers ways in which a government might seek to achieve\n this goal without privatizing. It focuses on changes in\n corporate governance-that is, changes in the rules that\n structure the relationship between the company and the\n government as its owner. It concludes that governments\n should be cautious about the prospects for improvement\n without privatization-since, among other things, creating a\n truly arms-length relationship between the government and\n the utility will always be difficult as long as the\n government remains the utility's owner-but that\n improvements in corporate governance are still worth pursuing.
Local and Systemic Responses of Antioxidants to Tobacco Mosaic Virus Infection and to Salicylic Acid in Tobacco (Role in Systemic Acquired Resistance) (1997)

Changes in ascorbate and glutathione levels and in activities of ascorbate peroxidase, catalase, dehydroascorbate reductase (DHAR), glutathione reductase (GR), glutathione S-transferase (GST), and superoxide dismutase (SOD) were investigated in tobacco mosaic virus (TMV)-inoculated lower leaves and in non-inoculated upper leaves of Nicotiana tabacum L. cv Xanthi-nc. In separate experiments the effects of exogenous salicylic acid (SA) were also studied. Symptom appearance after TMV inoculation was preceded by a slight, transient decline of ascorbate peroxidase, GR, GST, and SOD activities in the inoculated lower leaves, but after the onset of necrosis these activities and the glutathione level substantially increased. Ascorbic acid level and DHAR activity declined and dehydroascorbate accumulated in the inoculated leaves. In upper leaves, the glutathione level and the activities of GR, GST, and SOD increased 10 to 14 d after TMV inoculation of the lower leaves, concomitantly with the development of systemic acquired resistance. From the six distinct SOD isoenzymes found in tobacco leaves, only the activities of Cu,Zn-SOD isoenzymes were affected by TMV. SA injection induced DHAR, GR, GST, and SOD activities. Catalase activities were not modified by TMV infection or SA treatment. It is supposed that stimulated antioxidative processes contribute to the suppression of necrotic symptom development in leaves with systemic acquired resistance.
CAMBIOS EN LA FRECUENCIA CARDIACA DE ADULTOS CON SOBREPESO PRACTICANTES DE EJERCICIO AEROBIO (2012)

El objetivo de este trabajo fue evaluar el efecto de un programa de ejercicio fisico aerobio de baja a moderada intensidad sobre la frecuencia cardiaca de reposo (FCrep), frecuencia cardiaca de recuperacion (FCrec), en adultos con sobrepeso. Metodo: 12 sujetos con sobrepeso participaron por seis meses en un programa de actividad fisica aerobia en la modalidad de caminata a una intensidad del 50% al 70% de la frecuencia cardiaca de reserva, antes durante y despues del estudio se midieron variables de peso y estatura para determinar el indice de masa corporal (IMC), la frecuencia cardiaca en reposo y la frecuencia cardiaca de recuperacion. Resultados: se encontraron diferencias en la FCrep (78.13 ppm), FCrec (97.64 ppm) e IMC (28.65) disminuyendo a (68.00 ppm), (75.07 ppm) y (27.13 de IMC) respectivamente posterior al programa. Conclusiones: La perdida de peso y adaptaciones fisiologicas cronicas en el sistema circulatorio resultado del ejercicio aerobio coadyuvando a disminuir los riesgos de presentar enfermedades cronico no trasmisibles.
Cone angles for amine ligands. X-ray crystal structures and equilibrium measurements for ammonia, ethylamine, diethylamine, and triethylamine complexes with the [bis(dimethylphosphino)ethane]methylpalladium(II) cation (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCone angles for amine ligands. X-ray crystal structures and equilibrium measurements for ammonia, ethylamine, diethylamine, and triethylamine complexes with the [bis(dimethylphosphino)ethane]methylpalladium(II) cationAllen L. Seligson and William C. TroglerCite this: J. Am. Chem. Soc. 1991, 113, 7, 2520–2527Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/ja00007a028https://doi.org/10.1021/ja00007a028research-articleACS PublicationsRequest reuse permissionsArticle Views1317Altmetric-Citations128LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Epidemiology of Human Anthrax in China, 1955−2014 (2016)

Using national surveillance data for 120,111 human anthrax cases recorded during 1955-2014, we analyzed the temporal, seasonal, geographic, and demographic distribution of this disease in China. After 1978, incidence decreased until 2013, when it reached a low of 0.014 cases/100,000 population. The case-fatality rate, cumulatively 3.6% during the study period, has also decreased since 1990. Cases occurred throughout the year, peaking in August. Geographic distribution decreased overall from west to east, but the cumulative number of affected counties increased during 2005-2014. The disease has shifted from industrial to agricultural workers; 86.7% of cases occurred in farmers and herdsmen. Most (97.7%) reported cases were the cutaneous form. Although progress has been made in reducing incidence, this study highlights areas that need improvement. Adequate laboratory diagnosis is lacking; only 7.6% of cases received laboratory confirmation. Geographic expansion of the disease indicates that livestock control programs will be essential in eradicating anthrax.
DDD17: End-To-End DAVIS Driving Dataset (2017)

Event cameras, such as dynamic vision sensors (DVS), and dynamic and active-pixel vision sensors (DAVIS) can supplement other autonomous driving sensors by providing a concurrent stream of standard active pixel sensor (APS) images and DVS temporal contrast events. The APS stream is a sequence of standard grayscale global-shutter image sensor frames. The DVS events represent brightness changes occurring at a particular moment, with a jitter of about a millisecond under most lighting conditions. They have a dynamic range of >120 dB and effective frame rates >1 kHz at data rates comparable to 30 fps (frames/second) image sensors. To overcome some of the limitations of current image acquisition technology, we investigate in this work the use of the combined DVS and APS streams in end-to-end driving applications. The dataset DDD17 accompanying this paper is the first open dataset of annotated DAVIS driving recordings. DDD17 has over 12 h of a 346x260 pixel DAVIS sensor recording highway and city driving in daytime, evening, night, dry and wet weather conditions, along with vehicle speed, GPS position, driver steering, throttle, and brake captured from the car's on-board diagnostics interface. As an example application, we performed a preliminary end-to-end learning study of using a convolutional neural network that is trained to predict the instantaneous steering angle from DVS and APS visual data.
Efficient modeling of complex Analog integrated circuits using neural networks (2016)

This paper introduces a black-box method for automatically learning an approximate but simulation-time efficient high-level abstraction of given analog integrated circuit (IC). The learned abstraction consists of a non-linear auto-regressive neural network with exogenous input (NARX), which is trained and validated from the input-output traces of the IC stimulated with particular inputs. We show the effectiveness of our approach on the power-up behavior and supply dependency of a CMOS band-gap reference (BGR) circuit. We discuss in detail the precision of the NARX abstraction, and show how this model can be used and implemented in testing of Analog ICs within the Cadence environment. By using our method one can automatically learn high-level abstractions of all the components of an Analog IC. This dramatically speeds up the transient simulation time of the Analog ICs.
Synthesis and characterization of multiarm star polybutadienes (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of multiarm star polybutadienesJacques Roovers, Paul Toporowski, and James MartinCite this: Macromolecules 1989, 22, 4, 1897–1903Publication Date (Print):April 1, 1989Publication History Published online1 May 2002Published inissue 1 April 1989https://pubs.acs.org/doi/10.1021/ma00194a064https://doi.org/10.1021/ma00194a064research-articleACS PublicationsRequest reuse permissionsArticle Views419Altmetric-Citations105LEARN 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
Microfluidic device for capture and isolation of single cells (2010)

We describe a microfluidic device capable of trapping, isolating, and lysing individual cells in parallel using dielectrophoretic forces and a system of PDMS channels and valves. The device consists of a glass substrate patterned with electrodes and two PDMS layers comprising of the microfluidic channels and valve control channels. Individual cells are captured by positive dielectrophoresis using the microfabricated electrode pairs. The cells are then isolated into nanoliter compartments using pneumatically actuated PDMS valves. Following isolation, the cells are lysed open by applying an electric field using the same electrode pairs. With the ability to capture and compartmentalize single cells our device may be combined with analytical methods for in situ molecular analysis of cellular components from single cells in a highly parallel manner.
Development of a microfluidic capture device for the manipulation and concentration of waterborne pathogens (2013)

Severe epidemics in North America due to consumption of polluted water containing pathogens such as Cryptosporidium parvum and Giardia led to the development of standard detection methods like USEPA 1623 (by US Environmental Protection Agency). USEPA 1623 method, although fairly practical, is still at its infancy. There are still questions and ambiguity about the precision and accuracy of this method for the separation and detection of pathogens. USEPA 1623 includes a series of lengthy unreliable procedures that are highly prone to failure. The main purpose of this study is to examine the feasibility of developing alternative methods to improve pathogen recovery. The proposed method includes a microfluidic flow cell which implements physical properties of the pathogens (e.g., mass and electric charge) to manipulate, separate and concentrate them for future detection step. In general, the proposed device includes a flow path with an arbitrary shape through which water sample is flushed. The device then separates and concentrates the pathogens at the proximity of the “capture sites” where they are trapped by complementary antibody molecules. In order to design such a device, first, continuum numerical simulation is used to determine the optimum device geometry from among the many possible configurations. In addition to the device geometry, the effect of two mechanisms, sedimentation and electrophoresis, related to the physical properties of the pathogen is numerically studied using continuum simulation to enhance the pathogen separation process. Discrete numerical simulation is implemented afterwards to achieve a clear understanding of physical phenomena occurring at the molecular level close to the capture sites. The results obtained from the numerical modeling are used to fabricate a microfluidic test cell. The test cell is then examined in terms of pathogen separation and capture performance, and the experimental results are compared with those obtained by the modeling. It is shown that the proposed capture method has a better recovery with a higher precision when used along with the sedimentation process. Electrophoresis, however, introduces new challenges to the problem which necessitates further investigation of the method. Some of the most important challenges are discussed, and the potential remedies are suggested.
Spatial enhancement for immersive stereo audio applications (2011)

In this work, we propose a stereo recording spatial enhancement technique which retains the original panning/source location, proportionally mapped into the perceived expanded sound stage. The technique uses a time-frequency domain metric for retrieving the panning coefficients applied during the initial stereo mixing. Panning information is also used for separating the original single channel audio streams and finally for synthesizing the expanded sound field using binaural processing. The technique is mainly intended for playback applications over short-distant loudspeaker setups or headphones and, in the context of this work, it is subjectively evaluated in terms of the perceived sound field expansion and the sound-source spatial distribution accuracy.