gebhart/patrepeval huggingface dataset:
Enhanced Immune Presentation of a Single-chain Major Histocompatibility Complex Class I Molecule Engineered to Optimize Linkage of a C-terminally Extended Peptide (2003)

Major histocompatibility complex class I molecules can be expressed as single polypeptides wherein the antigenic peptide, beta2-microglobulin, and heavy chain are attached by flexible linkers. These molecules, single-chain trimers (SCTs), are remarkably stable at the cell surface compared with native (noncovalently attached) class I molecules. In this study, we used a structure-based approach to engineer an F pocket variant SCT of the murine class I molecule Kb that presents the SIINFEKL epitope of ovalbumin. Mutation of heavy chain residue Tyr84 (Y84A) in the SCT resulted in enhanced serological and cytolytic CD8 T cell recognition of the covalently linked peptide due to better accommodation of the linker extending from the C terminus of the peptide. These SCTs exhibit significant cell-surface stability, which we hypothesize is rendered by their ability to continuously and efficiently rebind the covalently attached peptide. In addition, we demonstrate that SCT technology can be applied to tetramer construction using recombinant SCTs expressed in Escherichia coli. SCT-based tetramers could have applications for the enumeration of T and natural killer cells that recognize peptide.class I complexes prone to dissociation.
Avaliação e adaptação do Índice de Severidade de Seca de Palmer (PDSI) e do Índice Padronizado de Precipitação (SPI) às condições climáticas do Estado de São Paulo (2005)

O Índice de Severidade de Seca de Palmer (PDSI) acusa o início de uma seca quando a precipitação pluvial de uma região diminui consideravelmente em relação a que seria climatologicamente esperada. Tal déficit é ponderado por um fator K de caracterização climática. Com base no ajuste de séries de precipitação à distribuição gama, o Índice Padronizado de Precipitação (SPI) quantifica o excesso ou o déficit de chuva, acumulados em diferentes escalas de tempo, em um determinado local. O presente trabalho avaliou e adaptou a metodologia do PDSI e do SPI às condições climáticas do Estado de São Paulo e comparou seus valores a parâmetros do balanço hídrico climático de treze localidades. De maneira geral, essa comparação foi realizada entre os quantificadores e o desvio (anomalia) que se observava nos parâmetros do balanço hídrico climático de um determinado período, em relação aos valores climatologicamente esperados para o intervalo de tempo em questão. O SPI teve seus resultados analisados em diversas escalas de tempo. O ajuste do PDSI (PDSIadap) teve como foco principal o fator K e a equação final do índice. As análises permitiram concluir que, o PDSI adap é uma ferramenta consistente para o monitoramento, da seca meteorológica, na escala mensal no Estado de São Paulo. Constatou-se também que o SPI é um método apropriado para a quantificação do déficit de precipitação pluvial, em diversas escalas de tempo. Ambos os índices devem, portanto, ser utilizados em decisões governamentais de planos de combates aos efeitos do fenômeno natural seca.
Dynamic Cellular Uptake of Mixed-Monolayer Protected Nanoparticles (2012)

Nanoparticles (NPs) are gaining increasing attention for potential application in medicine; consequently, studying their interaction with cells is of central importance. We found that both ligand arrangement and composition on gold nanoparticles play a crucial role in their cellular internalization. In our previous investigation, we showed that 66-34OT nanoparticles coated with stripe-like domains of hydrophobic (octanethiol, OT, 34%) and hydrophilic (11-mercaptoundecane sulfonate, MUS, 66%) ligands permeated through the cellular lipid bilayer via passive diffusion, in addition to endo-/pino-cytosis. Here, we show an analysis of NP internalization by DC2.4, 3T3, and HeLa cells at two temperatures and multiple time points. We study four NPs that differ in their surface structures and ligand compositions and report on their cellular internalization by intracellular fluorescence quantification. Using confocal laser scanning microscopy we have found that all three cell types internalize the 66-34OT NPs more than particles coated only with MUS, or particles coated with a very similar coating but lacking any detectable ligand shell structure, or 'striped' particles but with a different composition (34-66OT) at multiple data points.
Dual-technology optical sensor head for 3D surface shape measurements on the micro- and nanoscales (2004)

New material applications and novel manufacturing processes are driving a systematic rise in market demands concerning surface inspection methods and the performance of non-contact profilers. However, analysis of the specifications and application notes of commercial optical profilers shows that no single system is able to offer all the features a general purpose user would like simultaneously. Whereas white light interferometers can achieve very fast measurements on the micro and nano-scale without any range limitation, they can not easily deal with steep smooth surfaces or structured samples containing dissimilar materials. PSI techniques allow the user to perform shape and texture measurements even below the 0.1 nm scale, but they have an extremely short measurement range. Imaging confocal profilers overcome most of these difficulties. They provide the best lateral resolution achievable with an optical profiler, but they have a resolution limit, which is dependent on the NA and cannot achieve the 0.1 nm vertical resolution. In this paper we introduce a new dual-technology (confocal & interferometer) illumination hardware setup. With this new sensor head it is possible to choose between standard microscope imaging, confocal imaging, confocal profiling, PSI and white light interferometry, by simply placing the right objective on the revolving nosepiece.
Optical Matrix-Vector Processors: Basic Concepts (1986)

During the past decade or so, numerous schemes have been proposed and developed for performing vector-matrix-based algebraic operations optically. This paper reviews the major methods, providing the basis for an understanding of more complicated opto-electronic architectures and algorithms.
Prevalence of overweight and obesity in youth with diabetes in USA: the SEARCH for Diabetes in Youth Study (2009)

As expected, most of the youth with T2DM were obese. Youth with T1DM had a higher prevalence of overweight, but not of obesity, than nondiabetic youth. Future studies of obesity among youth with diabetes of all types will further our understanding of the impact of obesity on diabetes both as a risk factor and a comorbidity.
Wind Instruments (2002)

Abstract In mouth-blown wind instruments, the energy provided by the respiratory system is converted directly into sound. In all cases a primary vibrating element, generically called a reed, controls the airstream. The reed may be a piece of bamboo, the lips, a metallic tongue, or even the air jet (in flutes and recorders). Players control loudness, attack, intonation, and timbre by means of embouchure settings, blowing pressure, airflow, and length of the air column. The respiratory muscles perform complex and systematic movements, generating wide ranges of pressures, and coordinated oscillations that produce the vibrato effect. Intonation may be affected by the characteristics of the lung air. This chapter addresses the associated sensory, physiological, and acoustical phenomena. Common controversial or misleading concepts among wind players are discussed and some simple experiments are proposed for pedagogical applications.
Expression of the HGF/SF Receptor, c-met, and Its Ligand in Human Colorectal Cancers (1997)

The c-met proto-oncogene product is a receptor tyrosine kinase that mediates the effects of the multifunctional cytokine hepatocyte growth factor/scatter factor (HGF/SF). We have studied the expression of both the c-met receptor and HGF/SF at both the protein and message level in colorectal cancer tissues of varying disease stage. All of the tumors displayed an overexpression of the c-met mRNA compared to their normal tissue counterparts while 16 of 21 tissues (75%) displayed up-regulation of c-met protein. No HGF/SF mRNA or protein could be detected in either tissue type. Viable tumor cells extracted from cancer tissue exhibited increased motility in response to HGF/SF stimulation demonstrating that c-met was functionally active. No correlation between expression of c-met and tumor stage or degree of differentiation was observed. HGF/SF is known to be a potent stimulator of tumor cell motility and invasion, two cellular properties essential for the metastatic development of cancers. The overexpression of the HGF/SF receptor in colorectal cancers may result in an increased sensitivity to HGF/SF, which may confer an enhanced metastatic potential to the cancer cells within the tumor body.
Enzymatic Synthesis of Carbon−Fluorine Bonds (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTEnzymatic Synthesis of Carbon−Fluorine BondsDavid L. Zechel, Stephen P. Reid, Oyekanmi Nashiru, Christoph Mayer, Dominik Stoll, David L. Jakeman, R. Antony J. Warren, and Stephen G. WithersView Author Information Protein Engineering Network of Centres of Excellence and Departments of Chemistry and Microbiology University of British Columbia Vancouver, B.C., Canada V6T 1Z1 Cite this: J. Am. Chem. Soc. 2001, 123, 18, 4350–4351Publication Date (Web):April 13, 2001Publication History Received6 December 2000Published online13 April 2001Published inissue 1 May 2001https://pubs.acs.org/doi/10.1021/ja005855qhttps://doi.org/10.1021/ja005855qrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1601Altmetric-Citations57LEARN 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 SUBJECTS:Anions,Halogenation,Halogens,Noncovalent interactions,Peptides and proteins Get e-Alerts
Thiol‐isocyanate‐acrylate ternary networks by selective thiol‐click chemistry (2010)

Abstract Thiol‐isocyanate‐acrylate ternary networks were formed by the combination of thiol‐isocyanate coupling, thiol‐acrylate Michael addition, and acrylate homopolymerization. This hybrid polymerization reaction sequence was preferentially controlled by using phosphine catalyst systems in combination with photolysis. The reaction kinetics of the phosphine/acrylate thiol‐isocyanate coupling reactions were systematically investigated by evaluating model, small molecule reactions. The thiol‐isocyanate reaction was completed within 1 min while the thiol‐acrylate Michael addition reaction required ∼10 min. Both thiol‐isocyanate coupling and thiol‐acrylate Michael addition reactions involving two‐step anionic processes were found to be both quantitative and efficient. However, the thiol‐isocyanate coupling reaction was much more rapid than the thiol‐acrylate Michael addition, promoting initial selectivity of the thiol‐isocyanate reaction in a medium containing thiol, isocyanate, and acrylate functional groups. Films were prepared from thiol‐isocyanate‐acrylate ternary mixtures using 2‐acryloyloxyethylisocyanate and di‐, tri‐, and tetra‐functional thiols. The sequential thiol‐isocyanate, thiol‐acrylate, and acrylate homopolymerization reactions were monitored by infrared spectroscopy during film formation, whereas thermal and mechanical properties of the films were evaluated as a function of the chemical composition following polymerization. The results indicate that the network structures and material properties are tunable over a wide range of properties ( T g ∼ 14–100 °C, FWHM ∼ 8–46 °C), while maintaining nearly quantitative reactions, simply by controlling the component compositions. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3255–3264, 2010
Channelrhodopsin-1 Initiates Phototaxis and Photophobic Responses in<i>Chlamydomonas</i>by Immediate Light-Induced Depolarization (2008)

Channelrhodopsins (CHR1 and CHR2) are light-gated ion channels acting as sensory photoreceptors in Chlamydomonas reinhardtii. In neuroscience, they are used to trigger action potentials by light in neuronal cells, tissues, or living animals. Here, we demonstrate that Chlamydomonas cells with low CHR2 content exhibit photophobic and phototactic responses that strictly depend on the availability of CHR1. Since CHR1 was described as a H+-channel, the ion specificity of CHR1 was reinvestigated in Xenopus laevis oocytes. Our experiments show that, in addition to H+, CHR1 also conducts Na+, K+, and Ca2+. The kinetic selectivity analysis demonstrates that H+ selectivity is not due to specific translocation but due to selective ion binding. Purified recombinant CHR1 consists of two isoforms with different absorption maxima, CHR1505 and CHR1463, that are in pH-dependent equilibrium. Thus, CHR1 is a photochromic and protochromic sensory photoreceptor that functions as a light-activated cation channel mediating phototactic and photophobic responses via depolarizing currents in a wide range of ionic conditions.
Study of the Volatile Fraction of Parmesan Cheese (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudy of the Volatile Fraction of Parmesan CheeseGermana Barbieri, Luciana Bolzoni, Maria Careri, Alessandro Mangia, Giovanni Parolari, Silvia Spagnoli, and Roberta VirgiliCite this: J. Agric. Food Chem. 1994, 42, 5, 1170–1176Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/jf00041a023https://doi.org/10.1021/jf00041a023research-articleACS PublicationsRequest reuse permissionsArticle Views908Altmetric-Citations172LEARN 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
Using proteomics in perinatal and neonatal sepsis: hopes and challenges for the future (2009)

Presence of amniotic fluid proteomic biomarkers of inflammation is associated with increased inflammatory status of the fetus at birth. Future challenges are to find biomarkers that provide insight into molecular mechanisms of chronic fetal and neonatal cellular damage and to identify candidates for early neuroprotection strategies.
A Reactive Poly(ethylene glycol) Layer To Achieve Specific Surface Plasmon Resonance Sensing with a High S/N Ratio:  The Substantial Role of a Short Underbrushed PEG Layer in Minimizing Nonspecific Adsorption (2005)

A reactive poly(ethylene glycol) (PEG)-brushed layer was constructed on a surface plasmon resonance (SPR) sensor chip using a heterobifunctional PEG possessing an acetal group at one end and a mercapto group at the other end (alpha-acetal-omega-mercapto-PEG). The density of the PEG brushed layer substantially increased with repetitive adsorption/rinse cycles of the PEG on the sensor chip, allowing dramatic reduction of nonspecific protein adsorption. Notably, formation of a short, filler layer of PEG (2 kDa) in the preconstructed longer PEG brushed layer (5 kDa) achieved almost complete prevention of nonspecific protein adsorption. The acetal group located at the distal end of the tethered PEG was converted to an aldehyde group by the acid treatment, followed by the installation of biocytin hydrazide through Schiff base formation. SPR sensing of streptavidin was done with a very high S/N ratio even in a proteinous medium using the biotinylated PEG (5 kDa) tethered chip with an inert filler layer of short PEG (2 kDa). Furthermore, the specific affinity of streptavidin for the biotinylated PEG was highly influenced by the length of the filler PEG and was significantly reduced when the length of the filler PEG was longer than that of the biotinylated PEG. This result clearly revealed the substantial importance of the steric factor on biospecific interaction at the distal end of tethered PEG on the sensor surface.
The impact of the automotive environment on power semiconductors (2003)

The authors discuss: (1) the increased use of power semiconductors (specifically power MOSFETs) in automotive applications; (2) environmental factors that have an impact on device cost; (3) changes that should be made to vehicles to reduce component and system cost; and (4) recent power semiconductor developments that increase the chances of survival in the harsh automotive environment. Basic power FET design, and system voltage variations and their impact on power FETs are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Context-Relational Approach for the Internet of Things (2012)

Context-centric applications and services are premised on the ability to readily respond to changes in context. Centralized approaches to enabling this are undermined by their dependencies on DNS n ...
Pressure Buildup Analysis of Geothermal Steam Wells With a Parallelepiped Model (1982)

Summary Geothermal well testing, a discipline that evolved from conventional oil and gas well testing, often requires special considerations. The geometry of the reservoir and those characteristics frequently found in geothermal systems engendered the idea of a parallelepiped model with interpenetrating fractures. Such geometry can be described mathematically using Green's and source functions. Equations of reservoir pressure behavior then can be developed for both drawdown and buildup tests. Graphs describing dimensionless pressure as a function of time and various reservoir parameters are provided in this paper. The general method used is type-curve matching. Introduction There are three major types of geothermal resources:(vapor-dominated (dry-steam) such as in The Geysers (CA) or in Tuscany of central Italy,two-phase such as in New Zealand, andhot-water, found in several locations. The most useful, in terms of power production, are the vapor-dominated reservoirs. They are also the most rare. A number of geothermal reservoirs exhibit transient pressure behavior that indicates large, highly conductive fractures. The size of these reservoirs is controlled by faults and overlying impermeable rocks. A constant-pressure boundary, presumably boiling water, often is observed. A parallelepiped model conceptually could approximate such a configuration. A model with closed, no-flow boundaries on five sides and a constant-pressure boundary on the bottom was described by Cinco-Ley et al. The fracture system was simulated as a rectangular-shaped source. The concept is limited to vapor-dominated reservoirs. Both geologic evidence and production histories have precluded the use of radial models in both The Geysers and Larderello, Italy. Hence, the parallelepiped model, with the included fracture and subformation boiling front, is intended to analyze pressure transient behavior in dry-steam geothermal wells. Model Description The model assumes constant-flow-rate production in an anisotropic, homogeneous reservoir. If the flow rate vases, an influence function such as that described by Economides et al. can be used in the subsequent type-curve matching. The reservoir described by the model contains a slightly compressible fluid of constant viscosity and compressibility c. an assumption totally inadequate in the case of geothermal steam. Yet the shortcomings can be overcome if the pseudopressure function m(p) is used. The real-gas pseudopressure was discussed by Al-Hussainy and Ramey. All of these assumptions normally are used in geothermal well testing, irrespective of the model. Although the solution can be modified to incorporate fracture(s) anywhere in the reservoir, a vertical, partially penetrating fracture has been used. The fracture is in the center of a parallelepiped reservoir of square horizontal cross section. JPT P. 925^
A PBPK Modeling-Based Approach to Account for Interactions in the Health Risk Assessment of Chemical Mixtures (2001)

The objectives of the present study were: (1) to develop a risk assessment methodology for chemical mixtures that accounts for pharmacokinetic interactions among components, and (2) to apply this methodology to assess the health risk associated with occupational inhalation exposure to airborne mixtures of dichloromethane, benzene, toluene, ethylbenzene, and m-xylene. The basis of the proposed risk assessment methodology relates to the characterization of the change in tissue dose metrics (e.g., area under the concentration-time curve for parent chemical in tissues [AUCtissue], maximal concentration of parent chemical or metabolite [Cmax], quantity metabolized over a period of time) in humans, during mixed exposures using PBPK models. For systemic toxicants, an interaction-based hazard index was calculated using data on tissue dose of mixture constituents. Initially, the AUCtarget tissue (AUCtt) corresponding to guideline values (e.g., threshold limit value [TLV]) of individual chemicals were obtained. Then, the AUCtt for each chemical during mixed exposure was obtained using a mixture PBPK model that accounted for the binary and higher order interactions occurring within the mixture. An interaction-based hazard index was then calculated for each toxic effect by summing the ratio of AUCtt obtained during mixed exposure (predefined mixture) and single exposure (TLV). For the carcinogenic constituents of the mixture, an interaction-based response additivity approach was applied. This method consisted of adding the cancer risk for each constituent, calculated as the product of q*tissue dose and AUCtt. The AUCtt during mixture exposures was obtained using an interaction-based PBPK model. The approaches developed in the present study permit, for the first time, the consideration of the impact of multichemical pharmacokinetic interactions at a quantitative level in mixture risk assessments.