gebhart/patrepeval huggingface dataset:
Recognition of an Antigenic Peptide Derived from Tyrosinase-Related Protein-2 by CTL in the Context of HLA-A31 and -A33 (1998)

Tumor-infiltrating lymphocytes (TILs) derived from tumor-bearing patients recognize tumor-associated Ags presented by MHC class I molecules. The infusion of TIL586 along with IL-2 into the autologous patient with metastatic melanoma resulted in the objective regression of tumor. Two T cell epitopes derived from tumor Ags, tyrosinase-related protein (TRP)-1 and TRP-2, were shown to be recognized by HLA-A31 restricted TIL586 and its T cell clones. In this study we tested the hypothesis that these two peptides can be recognized by CTL from non-HLA-A31 patients with melanoma. It was found that both peptides were capable of binding to HLA-A3, -A11, -A31, -A33, and -A68 of the HLA-A3 supertype. Importantly, we found that HLA-A33-positive TIL1244 and its T cell clones can recognize TRP197-205 presented by both HLA-A31 and -A33 molecules, suggesting that a single TCR can recognize peptide/A31 and peptide/A33 complexes. However, peptide titration experiments showed that the affinity of TCR receptor to peptide/A33 could be higher than that to the peptide/A31. These studies have important implications for the development of peptide-based cancer vaccines.
hedgehog is required for the proliferation and specification of ovarian somatic cells prior to egg chamber formation in Drosophila (1996)

The hedgehog (hh) gene plays a role in regulating cell proliferation and specifying cell identity in diverse systems. We show that hh is expressed at the extreme apical end of Drosophila ovarioles in terminal filament cells and a newly identified group of associated somatic cells. Reducing or ectopically expressing hh affects somatic cells in region 2 of the germarium, 2-5 cells away from the cells in which Hh protein is detected. hh activity stimulates the proliferation of pre-follicle somatic cells, and promotes the specification of polar follicle cells. hh signaling during egg chamber assembly appears to be closely related to, or part of pathways involving the neurogenic genes.
A Greenhouse-Gas Information System - Monitoring and Validating Emissions Reporting and Mitigation - Chapter 2: Requirements Framework (2011)

The present study on a proposed greenhouse-gas information system (GHGIS) was undertaken without the benefit of requirements and specifications that will ultimately drive its choices and architecture. The discussion in this chapter attempts to develop a requirements framework that can be relied on to make choices between desired accuracy, precision, and confidence, vs. cost, schedule, and other elements. The accuracy or precision of the GHGIS (top-down) components required to validate reporting and international commitments depends on factors determined by the nature of the commitments as well as the goals of the users. The present study focuses on the task of measuring GHG emissions and attributing anthropogenic surface fluxes. This chapter explores possible emissions pathways that depart from targets and makes a number of assumptions about the needs of users to detect and quantify such departures, regardless of whether they are the result of inadvertent or willful reporting errors. Such user needs would be used to set GHGIS requirements.
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data (2012)

Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.
Fetal Oxygen Saturation and Uterine Contractions During Labor (1998)

Oxygen availability to the fetus during uterine contractions has not been widely reported. We examined whether fetal oxygen saturation (FSpO2) values and signal quality (SQ) were affected by uterine contractions. An intrauterine pressure catheter and a Nellcor FS14 fetal oxygen saturation sensor (Nellcor Puritan Bennett Inc., Pleasanton, CA) were placed transvaginally during the first stage of 17 labors. Fetal SPO2 and SQ units were recorded on a beat-to-beat basis and 10 sec averages of the data calculated over 25 contractions per patient. Five epochs were determined: (1) 30 sec prior to a contraction; (2) during a contraction; (3) 50 sec following completion of a contraction; (4) noncontraction periods, excluding epochs 1 or 3; and (5) equivocal, that is, overlap of epochs 1-3. Mean FSpO2 was lowest during epoch 3 (45.0) and highest during epoch 2 (47.3%) (p <0.001). This small difference is unlikely to be of any clinical significance, however. Mean signal quality was lowest in epoch 1 (42.8 units) and highest in epoch 4 (48.0 units) (p <0.05), that is, in noncontraction periods. We conclude that FSpO2 and SQ were unaffected by uterine contractions.
Expression of Invasion-Related Extracellular Matrix Molecules in Human Glioblastoma Versus Intracerebral Lung Adenocarcinoma Metastasis (2010)

Tumor cell invasion into the surrounding brain tissue is mainly responsible for the failure of radical surgical resection, with tumor recurrence in the form of microdisseminated disease. Extracellular matrix (ECM)-related molecules and their receptors predominantly participate in the invasion process, including cell adhesion to the surrounding microenvironment and cell migration. The extent of infiltration of the healthy brain by malignant tumors strongly depends on the tumor cell type. Malignant gliomas show much more intensive peritumoral invasion than do metastatic tumors. In this study, the mRNA expression of 30 invasion-related molecules (twenty-one ECM components, two related receptors, and seven ECM-related enzymes) was investigated by quantitative reverse transcriptase-polymerase chain reaction. Fresh frozen human tissue samples from glioblastoma (GBM), intracerebral lung adenocarcinoma metastasis, and normal brain were evaluated. Significant differences were established for 24 of the 30 molecules. To confirm our results at the protein level, immunohistochemical analysis of seven molecules was performed (agrin, neurocan, syndecan, versican, matrix metalloproteinase 2 [MMP-2], MMP-9, and hyaluronan). Determining the differences in the levels of invasion-related molecules for tumors of different origins can help to identify the exact molecular mechanisms that facilitate peritumoral infiltration by glioblastoma cells. These results should allow the selection of target molecules for potential chemotherapeutic agents directed against highly invasive malignant gliomas.
Scanning fiber-optic nonlinear endomicroscopy with miniature aspherical compound lens and multimode fiber collector (2009)

A flexible scanning fiber-optic endomicroscope using a miniature compound lens and a multimode-fiber (MMF) collector was developed for two-photon fluorescence (TPF) and second-harmonic generation (SHG) imaging. The compound lens consisted of a pair of aspherical lenses and exhibited reduced chromatic aberration compared with gradient-index lenses, thus increasing the TPF/SHG collection efficiency. The introduction of a short MMF collector at the distal end of the double-clad fiber of the endomicroscope further mitigated the adverse influence of chromatic aberration of the lens and enhanced the TPF/SHG collection efficiency. Both ray-tracing simulations and experiments on TPF imaging of fluorescent beads and SHG imaging of rattail tendon demonstrated approximately nine (approximately four) times improved collection efficiency for TPF (SHG) with the new endomicroscope design that utilized a compound lens and an MMF collector.
Number and Adhesive Properties of Circulating Endothelial Progenitor Cells in Patients With In-Stent Restenosis (2003)

Reduced numbers of circulating EPC in patients with diffuse in-stent restenosis and impaired adhesion of EPC from patients with restenosis provides a potential mechanism mediating the exuberant proliferative process. These markers, if further validated, could provide means of risk stratifying patients for likelihood of developing in-stent restenosis.
A new maximum photovoltaic power tracking control scheme based on power equilibrium at DC link (2003)

This paper proposes a new simple MPPT (maximum power point tracking) control scheme for A PV (photovoltaic) array based on the principle of power equilibrium at the DC link. In contrast to the typical conventional MPPT scheme based on the so-called mountain climbing method, the proposed scheme needs no detection or calculation of the power and no decision making logic or look up tables, except for several numbers of operational amplifiers. Its operation principle is explained quantitatively. In order to confirm the availability of the scheme, a simulation study using general purpose circuit simulation software PSIM and an experiment have been carried out. Although the stability study and system design are left for future study, the validity of the proposed new MPPT method has been clarified through the simulation and experimental results.
Norovirus P Particle: A Subviral Nanoparticle for Vaccine Development Against Norovirus, Rotavirus and Influenza Virus (2012)

Noroviruses (NoVs) are important pathogens causing epidemic acute gastroenteritis that affects millions of people worldwide. The protruding (P) domain of the NoV capsid protein, the surface antigen of NoV, forms a 24-mer subviral particle called the P particle that is an excellent candidate vaccine against NoVs. The P particles are easily produced in Escherichia coli, highly stable and highly immunogenic. Each P domain has three surface loops that can be used for foreign antigen presentation, making the P particles a useful platform for vaccine development against other infectious diseases. This article summarizes the discovery, structure, development and applications of the P particles as a vaccine against NoVs, as well as a vaccine platform against rotavirus, influenza virus and possibly other pathogens in the future.
Tubulysins, New Cytostatic Peptides from Myxobacteria Acting on Microtubuli. Production, Isolation, Physico-chemical and Biological Properties. (2000)

New cytostatic compounds, tubulysins, were isolated from the culture broth of strains of the myxobacteria Archangium gephyra and Angiococcus disciformis. The compounds are peptides partly consisting of unusual amino acids and are distantly related to the dolastatins. The tubulysins were not active against bacteria and only little against fungi, but showed high cytostatic activity against mammalian cell lines with IC50 values in the picomolar range. An incubation with 50 ng/ml tubulysin A led to a complete disappearance of the microtubuli network of the cells within 24 hours. The more active tubulysin D induced multipolar spindles: At 0.5 ng/ml all mitotic cells showed more than four spindle poles.
Evaluation of two carrier protein–angiotensin I conjugate vaccines to assess their future potential to control high blood pressure (hypertension) in man (2003)

KLH was shown to be a suitable alternative to TT as a carrier protein for AI, thus supporting continued evaluation of our AI-KLH conjugate vaccine for treatment of hypertension in man.
Practice and Theory of Blendshape Facial Models (2014)

''Blendshapes'', a simple linear model of facial expression, is the prevalent approach to realistic facial animation. It has driven animated characters in Hollywood films, and is a standard feature of commercial animation packages. The blendshape approach originated in industry, and became a subject of academic research relatively recently. This report describes the published state of the art in this area, covering both literature from the graphics research community, and developments published in industry forums. We show that, despite the simplicity of the blendshape approach, there remain open problems associated with this fundamental technique.
Emergence of Drug Resistance during an Influenza Epidemic: Insights from a Mathematical Model (1998)

A model was developed for the emergence of drug-resistant influenza viruses during a closed population influenza epidemic that occurs in a single wave. The model was used to consider several treatment and chemoprophylaxis strategies and to determine their effects on the spread of the infection. The model predicts frequent emergence and transmission of drug-resistant viruses with certain treatment scenarios. According to the model, chemoprophylaxis of susceptible persons (without treatment of those who are symptomatic) may be the best way to reduce the force of an epidemic and to keep development of drug resistance low. The model predictions indicate that the relative transmissibility of resistant variants compared with wild type virus and the choice of the treatment or chemoprophylaxis strategy can be decisive for the spread of drug-resistant viruses, a feature that may be crucial in a pandemic.
A GENETIC ANALYSIS OF PRIMARY PRODUCTS OF BACTERIOPHAGE LAMBDA RECOMBINATION (1986)

Primary products of bacteriophage lambda recombination that display heterozygosity as a consequence of the presence of regions of heteroduplex DNA are rare in standard lambda crosses. Phage manifesting heterozygosity at a given allele are evident when recombinants, emerging from a cross, are selected for an exchange in a neighboring interval. We show that the abundance of such heterozygotes can be increased 10- to 20-fold by selection on an E. coli indicator that is defective in methyl-directed mismatch repair (mutL). Thus, the activity of the methyl-directed mismatch repair system is, at least in part, responsible for the low frequency of detectably heterozygous phage emerging from a standard cross. In a mutL indicator, many primary products of recombination are replicated without the intervention of mismatch repair.--The products of a six-factor phage cross have been plated on a mutL indicator allowing visual detection of those phage products heterozygous for one of the allelic pairs, cI. By genetic analysis, we show that the heteroduplex regions of these primary products of recombination are on the average about 4 kb in length and can include as much as half of the lambda genome.
Barrel-to-Barrel Variation of Volatile Oak Extractives in Barrel-Fermented Chardonnay (1996)

Barrel-to-barrel variation in barrel-fermented wines was measured by determining the concentrations of seven volatile oak extractives — furfural, 5-methylfurfural, furfuryl alcohol, guaiacol, <i>cis</i>-ß-methyl-γ-octalactone, <i>trans</i>-ß-methyl-γ-octalactone, and syringol — in individual barrels of four 10-barrel lots, two French and two American oak — of barrel-fermented Chardonnay after seven months of oak aging. Within individual commercial production lots, the variance of individual compounds averaged 27% and ranged from 15% to 40% as measured by the percentage of standard deviation with respect to the mean. Statistical analysis of the data showed that an experiment with four barrels per lot would yield chemical levels within 30% of the barrel population (a specific barrel type from a specific producer) while a 10-barrel lot would be within 20% and a 39-barrel lot would be within 10%. However, the use of one barrel could yield chemical levels more than 50% different from the population.
(3R,4S)-3-[4-(4-Fluorophenyl)-4-hydroxypiperidin-1-yl]chroman-4,7-diol:  A Conformationally Restricted Analogue of the NR2B Subtype-Selective NMDA Antagonist (1S,2S)-1-(4-Hydroxyphenyl)-2- (4-hydroxy-4-phenylpiperidino)-1-propanol (1998)

(1S,2S)-1-(4-Hydroxyphenyl)-2-(4-hydroxy-4-phenylpiperidino)-1-propanol (CP-101,606, 1) is a recently described antagonist of N-methyl-D-aspartate (NMDA) receptors containing the NR2B subunit. In the present study, the optimal orientation of compounds of this structural type for their receptor was explored. Tethering of the pendent methyl group of 1 to the phenolic aromatic ring via an oxygen atom prevents rotation about the central portion of the molecule. Several of the new chromanol compounds have high affinity for the racemic [3H]CP-101,606 binding site on the NMDA receptor and protect against glutamate toxicity in cultured hippocampal neurons. The new ring caused a change in the stereochemical preference of the receptor-cis (erythro) compounds had better affinity for the receptor than the trans isomers. Computational studies suggest that steric interactions between the pendent methyl group and the phenol ring in the acyclic series determine which structures can best fit the receptor. The chromanol analogue, (3R,4S)-3-[4-(4-fluorophenyl)-4-hydroxypiperidin-1- yl]chroman-4,7-diol (12a, CP-283,097), was found to possess potency and selectivity comparable to CP-101,606. Thus 12a is a new tool to explore the function of the NR2B-containing NMDA receptors.
ShK-Dap22, a Potent Kv1.3-specific Immunosuppressive Polypeptide (1998)

The voltage-gated potassium channel in T lymphocytes, Kv1.3, is an important molecular target for immunosuppressive agents. A structurally defined polypeptide, ShK, from the sea anemone Stichodactyla helianthus inhibited Kv1.3 potently and also blocked Kv1.1, Kv1.4, and Kv1.6 at subnanomolar concentrations. Using mutant cycle analysis in conjunction with complementary mutagenesis of ShK and Kv1.3, and utilizing the structure of ShK, we determined a likely docking configuration for this peptide in the channel. Based upon this topological information, we replaced the critical Lys22 in ShK with the positively charged, non-natural amino acid diaminopropionic acid (ShK-Dap22) and generated a highly selective and potent blocker of the T-lymphocyte channel. ShK-Dap22, at subnanomolar concentrations, suppressed anti-CD3 induced human T-lymphocyte [3H]thymidine incorporation in vitro. Toxicity with this mutant peptide was low in a rodent model, with a median paralytic dose of approximately 200 mg/kg body weight following intravenous administration. The overall structure of ShK-Dap22 in solution, as determined from NMR data, is similar to that of native ShK toxin, but there are some differences in the residues involved in potassium channel binding. Based on these results, we propose that ShK-Dap22 or a structural analogue may have use as an immunosuppressant for the prevention of graft rejection and for the treatment of autoimmune diseases.
Three-Dimensional Attitude Determination with the Ashtech 3DF 24-Channel GPS Measurement System (1991)

A method for real-time, 3 dimensional attitude determination (heading, pitch, roll) has been developed using state-of-the-art GPS technology. This method is based on differential carrier phase measurements between four antennas which are connected to one 24-channel receiver. (The 24 channels are divided into four banks of six channels each.) Key advantages of this method over existing methods include the following: the initial phase ambiguity is determined with one epoch of data, the attitude is updated once per epoch, and cycle-slip detection and repair are achieved instantaneously.

The differential phase measurements are processed using doublc-
differecing techniques, which have already been proven successful in real-time kinematic applications. The attitude angles calculated can be as accurate as one milliradian (3.5 arc-minutes) for antenna spacings on the order of one meter. Since such accurate attitude measurements may be achieved in real time, numerous applications for the Ashtech Three-dimensional Direction Finding (3DF) system will arise. One obvious application is the integration of 3DF with an inertial measurement unit (IMU) for aircraft control and navigation.

In this paper, we describe the basic system architecture of the 3DF
system, the antenna conligurations, as well as accuracy of attitude
as a function of geometry, baseline length, multipath, and number of satellites visible. Also shown are preliminary results from differential kinematic testing.
The effects of interfacial potential on antimicrobial propensity of ZnO nanoparticle (2015)

The work investigates the role of interfacial potential in defining antimicrobial propensity of ZnO nanoparticle (ZnONP) against different Gram positive and Gram negative bacteria. ZnONPs with positive and negative surface potential are tested against different bacteria with varying surface potentials, ranging -14.7 to -23.6 mV. Chemically synthesized ZnONPs with positive surface potential show very high antimicrobial propensity with minimum inhibitory concentration of 50 and 100 μg/mL for Gram negative and positive bacterium, respectively. On other hand, ZnONPs of the same size but with negative surface potential show insignificant antimicrobial propensity against the studied bacteria. Unlike the positively charged nanoparticles, neither Zn(2+) ion nor negatively charged ZnONP shows any significant inhibition in growth or morphology of the bacterium. Potential neutralization and colony forming unit studies together proved adverse effect of the resultant nano-bacterial interfacial potential on bacterial viability. Thus, ZnONP with positive surface potential upon interaction with negative surface potential of bacterial membrane enhances production of the reactive oxygen species and exerts mechanical stress on the membrane, resulting in the membrane depolarization. Our results show that the antimicrobial propensity of metal oxide nanoparticle mainly depends upon the interfacial potential, the potential resulting upon interaction of nanoparticle surface with bacterial membrane.
Network Working Group (2004)

Location-to-URL Mapping Architecture and Framework This document describes an architecture for a global, scalable, resilient, and administratively distributed system for mapping geographic location information to URLs, using the Location-to-Service Translation (LoST) protocol. The architecture generalizes well-known approaches found in hierarchical lookup systems such as DNS. Status of This Memo This memo provides information for the Internet community. It does not specify an Internet standard of any kind. Distribution of this memo is unlimited. Copyright Notice Copyright (c) 2009 IETF Trust and the persons identified as the document authors. All rights reserved. This document is subject to BCP 78 and the IETF Trust’s Legal Provisions Relating to IETF Documents in effect on the date of publication of this document
IMPACT OF THE TECHNOLOGIES WEB 2.0 IN THE SMALL AND MEDIUMCOMPANIES OF SOFTWARE IN VENEZUELA (2009)

In the context of the small and medium companies of the
					industry of the software (called here, pymesoft), the use of the
					resources named generically as Web can represent the access
					to necessary knowledge in order that analysts and programmers
					realize his work. Nevertheless, the Web 2.0 also could turn into a
					distraction of resources or fugue of valuable knowledge from the
					company. Therefore, the managers and project leaders should tackle
					actions and take decisions to balance these electronic flows of
					knowledge based on Web 2.0, in a such way of making them favorable
					to the performance of the company. This work explores the use of
					the applications Web 2.0 to acquire and to share knowledge in the
					small and medium companies that develop software in Venezuela, from
					the perspectives of the managerial and operative positions. This
					one is a work of exploratory character, based on the review of
					trends and emergent patterns of use of technology Web 2.0
					orientated to the access, apprehension and exchange of knowledge
					not structured in the small enterprise of software in Venezuela,
					from the managerial and operative perspectives. For it, using an
					adjustment of the heuristic evaluation as method of evaluation of
					web sites, a survey was formulated and distributed via e-mail to
					180 members of 56 companies, destined to measure the perception of
					the use and management of the Web 2.0. The unit of research were
					members of the pymesoft, belonging to one of two groups: operative
					and managerial. The first one of them is constituted by the
					analysts, designers, analysts - programmers and programmers and
					second, relies on the managers, leaders and project coordinators.