gebhart/patrepeval huggingface dataset:
The amino terminus of human cytomegalovirus glycoprotein B contains epitopes that vary among strains (1992)

We mapped three antigenic domains of continuous epitopes on human cytomegalovirus (CMV) glycoprotein B (gB) by reacting a panel of independently derived monoclonal antibodies with deletion mutants expressed transiently in COS-1 cells. One of these antigenic domains, DC2, maps in the last 75 amino acids of the carboxy terminus. These epitopes are conserved in strains Towne and AD169, as well as in 19 clinical CMV isolates. ELISAs of DC2-reactive antibodies with a set of overlapping synthetic oligopeptides from the carboxy terminus showed that the epitopes of antibodies CH405-1 and CH421-5 map between amino acids 833 and 852 and that the epitope of antibody CH28-2 maps between amino acids 878 and 898. These linear epitopes were grouped into domain DC3. The third antigenic domain, DC1v, maps at the amino-terminal end of CMV strain AD169 gB but is not contained in strain Towne or in 17 of 19 clinical isolates. Epitopes in this domain are likely to map between amino acids 28 and 67, an area where differences occur in the nucleotide sequence of the gB genes from AD169 and Towne. Analysis of CMV-infected cells by flow cytometry with antibodies to the amino- and carboxy-terminal domains revealed that the amino terminus of gB is extracellular and that the carboxy terminus is not exposed on the cell surface.
Asymptotic Cones and Ultrapowers of Lie Groups (2004)

§1. Introduction . Asymptotic cones of metric spaces were first invented by Gromov. They are metric spaces which capture the ‘large-scale structure’ of the underlying metric space. Later, van den Dries and Wilkie gave a more general construction of asymptotic cones using ultrapowers. Certain facts about asymptotic cones, like the completeness of the metric space, now follow rather easily from saturation properties of ultrapowers, and in this survey, we want to present two applications of the van den Dries-Wilkie approach. Using ultrapowers we obtain an explicit description of the asymptotic cone of a semisimple Lie group. From this description, using semi-algebraic groups and non-standard methods, we can give a short proof of the Margulis Conjecture. In a second application, we use set theory to answer a question of Gromov. §2. Definitions . The intuitive idea behind Gromov's concept of an asymptotic cone was to look at a given metric space from an ‘infinite distance’, so that large-scale patterns should become visible. In his original definition this was done by gradually scaling down the metric by factors 1/ n for n ϵ ℕ. In the approach by van den Dries and Wilkie, this idea was captured by ultrapowers. Their construction is more general in the sense that the asymptotic cone exists for any metric space, whereas in Gromov's original definition, the asymptotic cone existed only for a rather restricted class of spaces.
Periostin identified as a potential biomarker of prostate cancer by iTRAQ-proteomics analysis of prostate biopsy (2011)

Our study indicates that the iTRAQ technology is a new strategy for global proteomics analysis of the tissues of PCa. A significant up-regulation of periostin in PCa compared to BPH may provide clues for not only a promising biomarker for the prognosis of PCa but also a potential target for therapeutical intervention.
Risk of Microbiological Contamination when Preparing Total Parenteral Nutrition for Pediatric Patients: A Pilot Study at a Regional Hospital in Southern Vietnam (2020)

Background: Total parenteral nutrition (TPN) presents a risk of contamination because it is a mixture of multiple additives and an excellent growth medium for microbes. In Vietnam, no official standard for TPN preparation has been established, thereby causing inconsistencies in implementation in healthcare facilities. We investigated the risk of microbiological contamination during the preparation of TPN for pediatric patients at a regional hospital in southern Vietnam.
Methods: This cross-sectional study was conducted from July to September 2019 at Children Hospital No. 2 in Ho Chi Minh City, southern Vietnam. Vaminolact 6.5% was the chosen TPN product for analysis. Collected bacterial samples were isolated in petri dishes containing nutrient agar as a solid growth medium. Each colony grown in the dish was subjected to Gram staining, after which species-specific identification was conducted on the basis of 16S ribosomal deoxyribonucleotide acid sequences.
Results: The results showed that after TPN preparation, ambient air in the laboratory contained contaminative agents. The bacteria isolated from medical devices and medical employees hands corresponded to colonies grown in two petri dishes. The bacterial species found included Moraxella osloensis, Micrococcus endophyticus, Micrococcus luteus, Macrococcus canis, Staphylococcus epidermidis, Brachybacterium muris, Micrococcus yunnanensis, Rothia amarae, Bacillus jeotgali, and Staphylococcus haemolyticus.
Conclusion: Disease-causing bacteria were found to proliferate during TPN preparation, highlighting the necessity of considering the risk of external contamination from sampling and testing.
Essential Requirement for Sphingosine Kinase 2 in a Sphingolipid Apoptosis Pathway Activated by FTY720 Analogues (2007)

The clinical immunosuppressant FTY720 is a sphingosine analogue that, once phosphorylated by sphingosine kinase 2 (Sphk2), is an agonist of multiple receptor subtypes for sphingosine 1-phosphate. Short exposures to FTY720 afford long term protection in lymphoproliferative and autoimmune disease models, presumably by inducing apoptosis in subsets of cells essential for pathogenesis. Sphingosine itself is pro-apoptotic, and apoptosis induced with FTY720 or sphingosine is thought to proceed independently of their phosphorylation. Following chemical mutagenesis of Jurkat cells we isolated mutants that are selectively resistant to FTY720 analogue AAL(R), as well as natural sphingolipid bases, including sphingosine. Cells lacking functional Sphk2 were resistant to apoptosis induced with AAL(R), indicating that apoptosis proceeds through AAL(R) phosphorylation. Phosphorylation of AAL(R) was also required for induction of lymphocyte apoptosis in mice, as apoptosis was not induced with the non-phosphorylatable chiral analogue, AAL(S). Apoptosis was induced in the spleen but not the thymus of mice administered 1 mg/kg AAL(R), correlating with levels of AAL(R)-phosphate (AFD(R)) in organ extracts. AFD(R) did not induce apoptosis when added to the cell culture medium, indicating that it induces apoptosis through an intracellular target. NBD-labeled AAL(R) localized to the endoplasmic reticulum, and AAL(R) treatment resulted in elevated cytosolic calcium, Bax redistribution from cytosol to mitochondrial and endoplasmic reticulum membranes, and caspase-independent mitochondrial permeabilization in Jurkat cells. We therefore describe an apoptotic pathway triggered by intracellular accumulation of sphingolipid base phosphates and suggest that sphingoid base substrates for Sphk2 acting intracellularly could be useful in the treatment of lymphoproliferative diseases.
Selective cleavage of the C<sub>α</sub>–C<sub>β</sub> linkage in lignin model compounds via Baeyer–Villiger oxidation (2015)

Lignin is an amorphous aromatic polymer derived from plants and is a potential source of fuels and bulk chemicals. Herein, we present a survey of reagents for selective stepwise oxidation of lignin model compounds. Specifically, we have targeted the oxidative cleavage of Cα-Cβ bonds as a means to depolymerize lignin and obtain useful aromatic compounds. In this work, we prepared several lignin model compounds that possess structures, characteristic reactivity, and linkages closely related to the parent lignin polymer. We observed that selective oxidation of benzylic hydroxyl groups, followed by Baeyer-Villiger oxidation of the resulting ketones, successfully cleaves the Cα-Cβ linkage in these model compounds.
MAXIMIZAR COSTOS Y MAXIMIZAR EL EMPLEO DE INSUMOS PRODUCTIVOS: OBJETIVO PARA 1990 (1979)

DENTRO DEL MARCO DEL SEMINARIO PROSPECTIVA DE LA ADMINISTRACION EN MEXICO HACIA 1990 SE ANALIZO EL DESARROLLO TECNOLOGICO CAMBIANTE Y LAS COMPLEJIDADES DE LAS RELACIONES HUMANAS CON EL FIN DE DEFINIR EL CAMPO DE TRABAJO DE LA ADMINISTRACION PARA LA DECADA DE LOS NOVENTA. EN EL TEXTO DE ADAM SMITH SE ANALIZAN IMPORTANTES CONCEPTOS ECONOMICOS QUE SE RETOMAN PARA EL TRABAJO CORRESPONDIENTE. PARA LLEVAR A CABO EL PLAN EN IMPORTANTE TOMAR EN CUENTA EL PAPEL QUE LAS TRASNACIONALES JUEGAN EN MEXICO, YA QUE SU TRABAJO NO DISMINUIRA EN LOS PROXIMOS ANOS. EL EVENTO TUVO LUGAR EN LA FACULTAD DE CONTADURIA Y ADMINISTRACION (FCYA).
Solubility of Rofecoxib in the Presence of Aqueous Solutions of Glycerol, Propylene Glycol, Ethanol, Span 20, Tween 80, and Sodium Lauryl Sulfate at (298.15, 303.15, and 308.15) K (2005)

The solubility data of rofecoxib in various mass fraction compositions of cosolvents (glycerol, propylene glycol, and ethanol) + water and surfactants (Span 20, Tween 80, and sodium lauryl sulfate) + water at (298.15, 303.15, and 308.15) K are presented. The analysis of rofecoxib was done by high-performance liquid chromatography. The solubility of rofecoxib increased with increasing mass fraction of cosolvents and surfactants at (298.15, 303.15, and 308.15) K. For ethanol + water mixtures, the solubility of rofecoxib was higher when compared to the glycerol + water and propylene glycol + water mixtures. The solubilization power of glycerol, propylene glycol, and ethanol at (298.15, 303.15, and 308.15) K was 0.81, 0.87, and 0.88; 2.2, 2.3, and 2.4; and 3.4, 3.6, and 3.8, respectively. In case of surfactants, sodium lauryl sulfate exhibited higher solubilizing efficiency at (298.15, 303.15, and 308.15) K than Span 20 and Tween 80.
The influence of viral coding sequences on pestivirus IRES activity reveals further parallels with translation initiation in prokaryotes (2002)

Classical swine fever virus (CSFV) is a member of the pestivirus family, which shares many features in common with hepatitis C virus (HCV). It is shown here that CSFV has an exceptionally efficient cis-acting internal ribosome entry segment (IRES), which, like that of HCV, is strongly influenced by the sequences immediately downstream of the initiation codon, and is optimal with viral coding sequences in this position. Constructs that retained 17 or more codons of viral coding sequence exhibited full IRES activity, but with only 12 codons, activity was approximately 66% of maximum in vitro (though close to maximum in transfected BHK cells), whereas with just 3 codons or fewer, the activity was only approximately 15% of maximum. The minimal coding region elements required for high activity were exchanged between HCV and CSFV. Although maximum activity was observed in each case with the homologous combination of coding region and 5' UTR, the heterologous combinations were sufficiently active to rule out a highly specific functional interplay between the 5' UTR and coding sequences. On the other hand, inversion of the coding sequences resulted in low IRES activity, particularly with the HCV coding sequences. RNA structure probing showed that the efficiency of internal initiation of these chimeric constructs correlated most closely with the degree of single-strandedness of the region around and immediately downstream of the initiation codon. The low activity IRESs could not be rescued by addition of supplementary eIF4A (the initiation factor with ATP-dependent RNA helicase activity). The extreme sensitivity to secondary structure around the initiation codon is likely to be due to the fact that the eIF4F complex (which has eIF4A as one of its subunits) is not required for and does not participate in initiation on these IRESs.
Characterization of CD8+ Effector T Cell Responses in Volunteers Immunized with <i>Salmonella enterica</i> Serovar Typhi Strain Ty21a Typhoid Vaccine (2002)

Salmonella enterica serovar Typhi (S. typhi) strain Ty21a remains the only licensed attenuated typhoid vaccine. Despite years of research, the identity of the protective immunological mechanisms elicited by immunization with the Ty21a typhoid vaccine remains elusive. The present study was designed to characterize effector T cell responses in volunteers immunized with S. typhi strain Ty21a typhoid vaccine. We determined whether immunization with Ty21a induced specific CTL able to lyse S. typhi-infected cells and secrete IFN-gamma, a key effector molecule against intracellular pathogens. We measured the functional activity of these CTL by a (51)Cr-release assay using 8-day restimulated PBMC from Ty21a vaccinees as effector cells and S. Typhi-infected autologous PHA-activated PBMC as target cells. Most vaccinees exhibited consistently increased CD8-mediated lysis of targets by postimmunization PBMC when compared with preimmunization levels. We also developed an IFN-gamma ELISPOT assay to quantify the frequency of IFN-gamma spot-forming cells (SFC) in PBMC from Ty21a vaccinees using an ex vivo system. Significant increases in the frequency of IFN-gamma SFC following immunization (mean +/- SD, 393 +/- 172; range 185-548 SFC/10(6) PBMC; p = 0.010), as compared with preimmunization levels, were observed. IFN-gamma was secreted predominantly by CD8(+) T cells. A strong correlation was recorded between the cytolytic activity of CTL lines and the frequency of IFN-gamma SFC (r(2) = 0.910, p < 0.001). In conclusion, this work constitutes the first evidence that immunization of volunteers with Ty21a elicits specific CD8(+) CTL and provides an estimate of the frequency of CD8(+) IFN-gamma-secreting cells induced by vaccination.
Contextual Parameter Generation for Universal Neural Machine Translation (2018)

We propose a simple modification to existing neural machine translation (NMT) models that enables using a single universal model to translate between multiple languages while allowing for language specific parameterization, and that can also be used for domain adaptation. Our approach requires no changes to the model architecture of a standard NMT system, but instead introduces a new component, the contextual parameter generator (CPG), that generates the parameters of the system (e.g., weights in a neural network). This parameter generator accepts source and target language embeddings as input, and generates the parameters for the encoder and the decoder, respectively. The rest of the model remains unchanged and is shared across all languages. We show how this simple modification enables the system to use monolingual data for training and also perform zero-shot translation. We further show it is able to surpass state-of-theart performance for both the IWSLT-15 and IWSLT-17 datasets and that the learned language embeddings are able to uncover interesting relationships between languages.
Supramolecular Complex Formation: A Study of the Interactions between β‐Cyclodextrin and Some Different Classes of Organic Compounds by ESI‐MS, Surface Tension Measurements, and UV/Vis and <sup>1</sup>H NMR Spectroscopy (2003)

Abstract The ability of several organic compounds [alcohols 1 and 2 , the corresponding phosphate esters 3 and 4 and their sodium salts 5 and 6 as well as some commercial surfactants such as C 14 DMAO ( 7 , zwitterionic), SDS ( 8 , anionic) and CTABr ( 9 , cationic)] to produce supramolecular complexes with β‐cyclodextrin has been investigated by four different techniques (ESI‐MS, surface tension measurements, UV/Vis and 1 H NMR spectroscopy). The data collected have allowed information about the formation of complexes and the location of the guest in the host to be gained. Comparison of the results obtained for phosphate esters and their salts, for both saturated and unsaturated derivatives, has made it possible to evaluate the factors that affect the stability of the supramolecular complexes under the different experimental conditions used. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Vagus Nerve Stimulation for Symptomatic Generalized Epilepsy: A Pilot Study (1998)

We conclude that VNS may be useful add-on therapy for SGE. A larger, controlled, and blinded trial may be warranted.
The Slug Suppression System in Operation (2003)

Abstract In a flowline/riser system large liquid slugs and surges can be formed by operational changes or due to the flow conditions and physical characteristics of the flowline. These liquid slugs and gas surges may result in large oil and gas production losses when they arrive at a production platform. Slugging may cause high-level trips in separators and lead to unstable operation of topside facilities. The S3® Slug Suppression System provides a reliable solution to the slugging problem. In 2002 Dril-Quip (Europe) Ltd delivered the first two commercial S3 units to Shell UK Exploration and Production (Shell Expro). The first unit was designed for the Otter development (TotalFinaElf) in the North Sea and installed on the North Cormorant platform (13 km flowline, 12" riser diameter, 18 bara separator pressure). In October 2002 the unit was successfully commissioned and is presently operating. The second system has been installed on the Brent Charlie platform in the North Sea, and is used for the Penguins development (64 km flowline, 14" riser diameter, 35 bara separator pressure). The unit was commissioned in January 2003. The commissioning results prove that the S3 can control liquid slugs and gas surges. The operational data shows that the control strategy is robust, flexible and capable of operating within all flow regimes encountered in the flowline. The S3 system consists of a small separator with dynamically controlled valves at the gas and liquid outlets. The system is placed just upstream of the production separator. Shell Global Solutions developed the system with advanced control algorithms over the past years. The new technology was successfully tested at a test rig in Amsterdam and during field trials at the Shell Expro Gannet Alpha platform [1]. Operation of the S3 system was also extensively simulated with the dynamic numerical tools Traflow and Olga2000 and compared to other slug mitigation methods. An exclusive license was granted to Dril-Quip (Europe) Ltd to manufacture and supply the S3. Based on the field experience with the system, the S3 has proven to control/mitigate slugging.
Apriori Rate Allocation in Wavelet-Based Image Compression (2006)

We present a rate allocation scheme that pre-computes optimal quantisation bucket sizes based on a mathematical model of wavelet transformed natural images prior entropy encoding. We combine the proposed scheme with the JPEG2000 embedded rate-allocator and find in our experiments that it is able to increase JPEG2000 encoding speed by a factor of two without loosing image quality
Automated hot-spot fixing system applied for metal layers of 65 nm logic devices (2006)

Hot spot clearance using process simulation is indispensable under low-k1 lithography process for logic devices of 65 nm and below. Hot spots such as pinching, bridging, line-end shortening will occur, mainly depending on local pattern context. Appropriate calibration of design rule (DR), mask data preparation (MDP), resolution enhancement technique (RET) and optical proximity effect correction (OPC) will reduce potential hot spots. However, pattern layout variety is so enormous that, even with the most careful calibration of every process, an unexpected potential hot spot is occasionally left in the design layout. Manual modification of design at hot spot will be effective, but it takes too much time to determine how to modify layout to be consistent with DR, MDP/OPC rule, and the process often needs to be iterative. Therefore, there is a need for an automated hot spot fixing system is capable of fixing design layout so as to avoid fatal hot spot occurrence, with sufficient process margin and short turn around time (TAT). We developed an automated hot-spot fixing system, Hot Spot Fixer (HSF). The basic system flow in the developed system is as follows; Design data is processed with the conventional mask data preparation process. Then, process simulation is performed to extract hot spots. The hot spots are categorized by lithography error mode, critical level, and surrounding context. An intelligent hot-spot modification instructor, taking the surrounding situation into consideration, generates modification guide for the every hot spot. Design data is automatically modified according to the instruction at every hot spot, complying with the design rule. If necessary, several modification candidates are indicated and the user can choose the most adequate one from them. The design modification process is verified from every aspect, using Design Rule Checker (DRC) and process simulation. The modified design data, with reduced potential hot spot compared with pre-modification design, is processed under the conventional mask data preparation process again, and then makes mask data, which will reduce the number of potential hot spot. We applied the HSF system to metal layer of logic devices of 65 nm and then the hot spots are almost diminished throughout a full chip within twelve hours. Thus HSF feasibility has been proved for metal layers in 65 nm node and below with full chip data volume.
Use of non-absorbable markers in studies of human nutrient absorption. (1986)

Neutron activation analysis signifies a new era in the methodology of studies on nutrient utilization in humans. Yet the classical metabolic balance technique incorporating inert, non-absorbable markers will continue to be an invaluable tool for such studies. This review describes the use and abuse of a number of 'classical' inert markers, and describes the potential use of radioactive and naturally-occurring isotopes, and of heavy metals. The paucity of data critically appraising markers in infant balance trials is apparent. The comparative merits of conventional markers--carmine, polyethylene glycol 4000, chromium oxide--should be assessed. Indeed, it might be argued that the advancing knowledge on the use of naturally occurring isotopes in adults should make similar studies on infants a priority.
Development of theoretical oxygen saturation calibration curve based on optical density ratio and optical simulation approach (2017)

The implementation of surface-based Monte Carlo simulation technique for oxygen saturation (SaO2) calibration curve estimation is demonstrated in this paper. Generally, the calibration curve is estimated either from the empirical study using animals as the subject of experiment or is derived from mathematical equations. However, the determination of calibration curve using animal is time consuming and requires expertise to conduct the experiment. Alternatively, an optical simulation technique has been used widely in the biomedical optics field due to its capability to exhibit the real tissue behavior. The mathematical relationship between optical density (OD) and optical density ratios (ODR) associated with SaO2 during systole and diastole is used as the basis of obtaining the theoretical calibration curve. The optical properties correspond to systolic and diastolic behaviors were applied to the tissue model to mimic the optical properties of the tissues. Based on the absorbed ray flux at detectors, the OD and ODR were successfully calculated. The simulation results of optical density ratio occurred at every 20 % interval of SaO2 is presented with maximum error of 2.17 % when comparing it with previous numerical simulation technique (MC model). The findings reveal the potential of the proposed method to be used for extended calibration curve study using other wavelength pair.