gebhart/patrepeval huggingface dataset:
Ecological analysis of antigen-specific CTL repertoires defines the relationship between naïve and immune T-cell populations (2013)

Ecology is typically thought of as the study of interactions organisms have with each other and their environment and is focused on the distribution and abundance of organisms both within and between environments. On a molecular level, the capacity to probe analogous questions in the field of T-cell immunology is imperative as we acquire substantial datasets both on epitope-specific T-cell populations through high-resolution analyses of T-cell receptor (TCR) use and on global T-cell populations analyzed via high-throughput DNA sequencing. Here, we present the innovative application of existing statistical measures (used typically in the field of ecology), together with unique statistical analyses, to comprehensively assess how the naïve epitope-specific CD8(+) cytotoxic T lymphocyte (CTL) repertoire translates to that found following an influenza-virus-specific immune response. Such interrogation of our extensive, cumulated TCR CDR3β sequence datasets, derived from both naïve and immune CD8(+) T-cell populations specific for four different influenza-derived epitopes (D(b)NP(366), influenza nucleoprotein amino acid residues 366-374; D(b)PA(224), influenza acid polymerase amino acid residues 224-233; D(b)PB1-F2(62), influenza polymerase B 1 reading frame 2 amino acid residues 62-70; K(b)NS2(114), and influenza nonstructural protein 2 amino acid residues 114-121), demonstrates that epitope-specific TCR use in an antiviral immune response is the consequence of a complex interplay between the intrinsic characteristics of the naïve cytotoxic T lymphocyte precursor pool and extrinsic (likely antigen driven) influences, the contribution of which varies in an epitope-specific fashion.
Activation of inflammasome signaling mediates pathology of acute P. aeruginosa pneumonia (2013)

The respiratory tract is exceptionally well defended against infection from inhaled bacteria, with multiple proinflammatory signaling cascades recruiting phagocytes to clear airway pathogens. However, organisms that efficiently activate damaging innate immune responses, such as those mediated by the inflammasome and caspase-1, may cause pulmonary damage and interfere with bacterial clearance. The extracellular, opportunistic pathogen Pseudomonas aeruginosa expresses not only pathogen-associated molecular patterns that activate NF-ÎºB signaling in epithelial and immune cells, but also flagella that activate the NLRC4 inflammasome. We demonstrate that induction of inflammasome signaling, ascribed primarily to the alveolar macrophage, impaired P. aeruginosa clearance and was associated with increased apoptosis/pyroptosis and mortality in a murine model of acute pneumonia. Strategies that limited inflammasome activation, including infection by fliC mutants, depletion of macrophages, deletion of NLRC4, reduction of IL-1Î² and IL-18 production, inhibition of caspase-1, and inhibition of downstream signaling in IL-1Râ or IL-18Rânull mice, all resulted in enhanced bacterial clearance and diminished pathology. These results demonstrate that the inflammasome provides a potential target to limit the pathological consequences of acute P. aeruginosa pulmonary infection.\n
Surface composition of siloxane‐containing polymers (1991)

Abstract X‐ray photoelectron spectroscopy was used to study relationships between the surface and bulk composition in block copolymers and blends of poly(dimethyl‐siloxane), poly(bisphenol A sulfone) and poly(bisphenol A carbonate). In all cases the polymer surfaces were highly enriched in siloxane. At a fixed siloxane concentration in the bulk the highest enrichment was observed in the blends of homopolymers and the lowest in the copolymers. It was found that the addition of small quantities of a siloxane‐rich copolymer to another copolymer having a lower siloxane content may reduce the surface siloxane concentration of the latter. This unusual surface behavior was explained by the formation of an over‐layer in which the macromolecules of the siloxane‐rich copolymer are oriented nearly parallel to the sample surface.
Capacity of intelligent underlay and overlay network (1996)

This paper suggests a method of dimensioning the cell configuration of radio sites in a cellular network using the intelligent overlay and underlay (IOU) technique. The traffic capacity has been analysed by means of a teletraffic model, which is developed based on the classical theory of overflow traffic. The formulas of the model have been implemented with the use of MatLab. To verify the model, measurement methods have been developed to collect the teletraffic information in a real-live GSM network. The measured data indicates that the teletraffic model describes the capacity with high accuracy and therefore can be used to dimension the network. The model shows that the increase of capacity for a GSM network with 34 frequencies is about 30%. Further capacity enhancement can be achieved by intelligent frequency planning method which is currently being developed
3-Hydroxypropionyl-Coenzyme A Synthetase from <i>Metallosphaera sedula</i> , an Enzyme Involved in Autotrophic CO <sub>2</sub> Fixation (2007)

A modified 3-hydroxypropionate cycle has been proposed as the autotrophic CO2 fixation pathway for the thermoacidophilic crenarchaeon Metallosphaera sedula. The cycle requires the reductive conversion of 3-hydroxypropionate to propionyl-coenzyme A (propionyl-CoA). The specific activity of the 3-hydroxypropionate-, CoA-, and MgATP-dependent oxidation of NADPH in autotrophically grown cells was 0.023 micromol min(-1) mg protein(-1). The reaction sequence is catalyzed by at least two enzymes. The first enzyme, 3-hydroxypropionyl-CoA synthetase, catalyzes the following reaction: 3-hydroxypropionate + ATP + CoA --> 3-hydroxypropionyl-CoA + AMP + PP(i). The enzyme was purified 95-fold to a specific activity of 18 micromol min(-1) mg protein(-1) from autotrophically grown M. sedula cells. An internal peptide sequence was determined and a gene encoding a homologous protein identified in the genome of Sulfolobus tokodaii; similar genes were found in S. solfataricus and S. acidocaldarius. The gene was heterologously expressed in Escherichia coli, and the His-tagged protein was purified. Both the native enzyme from M. sedula and the recombinant enzyme from S. tokodaii not only activated 3-hydroxypropionate to its CoA ester but also activated propionate, acrylate, acetate, and butyrate; however, with the exception of propionate, the affinities for these substrates were reduced. 3-Hydroxypropionyl-CoA synthetase is up-regulated eightfold in autotrophically versus heterotrophically grown M. sedula, supporting its proposed role during CO2 fixation in this archaeon and possibly other members of the Sulfolobaceae family.
Megabase deletions of gene deserts result in viable mice - eScholarship (2004)

The functional importance of the approximately 98 percent of mammalian genomes not corresponding to protein coding sequences remain largely un-scrutinized 1. To test experimentally whether some extensive regions of non-coding DNA, referred to as gene deserts 2-4, contain critical functions essential for the viability of the organism, we deleted two large non-coding intervals, 1,511 kb and 845 kb in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regards to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further in-depth analysis of the expression of genes bracketing the deletions revealed similar expression characteristics in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (>100bp, 70 percent identity). These studies demonstrate that some large-scale deletions of non-coding DNA can be well tolerated by an organism, bringing into question the role of many human-mouse conserved sequences 5,6, and further supports the existence of potentially disposable DNAi in the genomes of mammals.
Guanidine Methods for Total <scp>RNA</scp> Preparation (1996)

Three different methods for RNA preparation using guanidine are presented in this unit--a single-step isolation method employing liquid-phase separation to selectively extract total RNA from tissues and cultured cells and two methods that rely on a CsCl step gradient to isolate total RNA.
New kind of humidity sensitive ceramic with linear property (2002)

Using the solid phase reaction method, La/sub 1-x/Sr/sub x/FeO/sub 3/ (0<or=x<or=1) ceramic was synthesized in an oxygen structure. Its resistance vs. relative humidity (RH) characteristics as well as the dielectric and complex impedance spectral characteristics were investigated. These results indicate that the resistance of LaFeO/sub 3/ decreases with RH, while the resistance of La/sub 1-x/Sr/sub x/FeO/sub 3/ (0.1<or=x<or=0.4) increases with increasing RH, and its sensitivity increases with the increasing x value. The equivalent circuit model of La/sub 1-x/Sr/sub x/FeO/sub 3/ has been established by complex impedance analysis, from which the conclusion can be drawn that the linear positive humidity sensitivity of the material is caused by the change in grain boundary resistance.<<ETX>>
Recombinant gamma interferon is a potent adjuvant for a malaria vaccine in mice. (1987)

Mice were protected against lethal Plasmodium yoelii malaria by vaccination with a Triton X-100 lysate of whole parasitized erythrocytes. For full effectiveness this vaccine required an adjuvant, and we have found that recombinant gamma-interferon has strong adjuvanticity in this model when given either intraperitoneally or subcutaneously. Specific immune responses that were enhanced included antibody, T cell help, and delayed hypersensitivity.
Yin and Yang (1995)

A fter watching her father put up with allergy shots for 20 years, Ann Bergeron resolved to treat her own allergies another way. On the recommendation of a friend, she sought the help of a Chinese doctor in San Francisco. During her first visit, instead of the usual scratch tests, the doctor spoke to her for about half an hour, asking about her lifestyle and medical history. At the end of the session, the doctor wrote out a prescription. Bergeron took the piece of notebook paper, filled with cryptic Chinese characters, to a pharmacy deep in the heart of Chinatown. There, the pharmacist carefully measured out the ingredients, which Bergeron says looked like the components of a witch's brew: beetles with hairy legs, lichen, toadstools, and colored powders. Every other night for several months, she boiled this concoction into a tea from hell and drank it. Bit by bit, her allergies went away. Increasingly, people are putting aside their understandable squeamishness in order to sample the touted benefits of Chinese herbal medicines. Skeptics might attribute Bergeron's recovery to a placebo effect and not to any specific biochemical benefit. But many swear by herbal medicine, taking it as a supplement toor even substitute for-conventional drugs. Herbs provide a gentler way to treat ailments as well as to boost the body's own defenses, enthusiasts say. Many medical researchers in the United States and Europe suspect ancient remedies may also harbor new drugs. Government, industry, and academic research groups are zealously mining this potential source of pharmaceuticals, probing Chinese herbs for the chemical constituents that might one day yield new treatments for everything from asthma to AIDS. But proponents of traditional Chinese medicine say this fervor to isolate single compounds is misplaced. To them, the real benefits come from whole herbs and herbal extracts, since the chemicals in them purportedly work in conjunction with one another. The United States, however, supports very little research into whole herbs-in part because its drug approval process doesn't accommodate undifferentiated mixtures of natural chemicals whose collective function is uncertain, notes Mark Blumenthal of the American Botanical Council in Austin, Texas. A dearth of research in this area stems from a clash between two medical cultures-one representing a modern society searching for magic bullets, the other belonging to an ancient society steeped in history and tradition. But the public demand for remedies, no matter what they might be, is challenging scientists and policy makers to find common ground.
Physiological Properties of <i>Saccharomyces cerevisiae</i> from Which Hexokinase II Has Been Deleted (2001)

Hexokinase II is an enzyme central to glucose metabolism and glucose repression in the yeast Saccharomyces cerevisiae. Deletion of HXK2, the gene which encodes hexokinase II, dramatically changed the physiology of S. cerevisiae. The hxk2-null mutant strain displayed fully oxidative growth at high glucose concentrations in early exponential batch cultures, resulting in an initial absence of fermentative products such as ethanol, a postponed and shortened diauxic shift, and higher biomass yields. Several intracellular changes were associated with the deletion of hexokinase II. The hxk2 mutant had a higher mitochondrial H(+)-ATPase activity and a lower pyruvate decarboxylase activity, which coincided with an intracellular accumulation of pyruvate in the hxk2 mutant. The concentrations of adenine nucleotides, glucose-6-phosphate, and fructose-6-phosphate are comparable in the wild type and the hxk2 mutant. In contrast, the concentration of fructose-1,6-bisphosphate, an allosteric activator of pyruvate kinase, is clearly lower in the hxk2 mutant than in the wild type. The results suggest a redirection of carbon flux in the hxk2 mutant to the production of biomass as a consequence of reduced glucose repression.
Piperazinomycin, a new antifungal antibiotic. I. Fermentation, isolation, characterization and biological properties. (1982)

A new antifungal antibiotic, named piperazinomycin, was isolated from the cultured broth of Streptoverticillium olivoreticuli subsp. neoenacticus. The antibiotic was obtained from the mycelial cake by extraction with methanol and also from the broth filtrate by adsorption on Amberlite XAD-2 and subsequent elution with aqueous acetone. The antibitoic is of basic and lipophilic nature and can be extracted with methyl isobutyl ketone at alkaline pH. Its purification was carried out by column chromatography on Sephadex LH-20 and then on Sephadex G-15 followed by preparative thin-layer chromatography on silica gel. The molecular formula of piperazinomycin was determined to be C125H20NsO2 by high resolution mass spectrum and the spectroscopic and chemical properties were examined. Piperazinomycin showed inhibitory activity against fungi and yeasts, especially against Trichophyton.
Selective cation binding with cis,cis-1,3,5-trioxycyclohexyl based ligands: application to ion transport and electrochemical detection and assessment of complexation by electrospray mass spectrometry (1997)

The synthesis is reported of two sets of oxa-amide ionophores based on 2-phenylglycerol and cis,cis-cyclohexane-1,3,5-triol, with ligand coordination numbers of four, five and six. Ionophores based on the hexadentate cyclohexyl triamide 9 show excellent Na+/K+ selectivity (-log KpotNa,K = 3.1), and the pentadentate analogue 10 shows good Li+/Na+ selectivity (-log KpotLi,Na = 2.2). Solution NMR and liquid–liquid extraction studies confirmed the formation of 1∶1 complexes and IR studies pinpointed the presence of amide binding. Ligands based on 2-phenylglycerol exhibited good Ca2+ selectivity which was highest for the hexadentate triamide, 6. Detailed ESMS studies revealed similar trends in ion-binding, performed under controlled conditions.
Mathematical studies in rigorous grating theory (1995)

We consider the diffraction of a time-harmonic wave incident upon a grating (or periodic) structure. We study mathematical issues that arise in the direct modeling, inverse, and optimal design problems. Particular attention is paid to the variational approach and to finite-element methods. For the direct problem various results on existence, uniqueness, and numerical approximations of solutions are presented. Convergence properties of the variational method and sensitivity to TM polarization are examined. Our recent research on inverse diffraction problems and optimal design problems is also discussed.
Multi-agent systems in production planning and control: an overview (2004)

The ever fast changes of customers’ needs and demands ask for reconfigurable and adaptive production systems, which can provide companies with the proper level of agility and effectiveness, without disregarding at the same time cost factors. In the last decade, a large amount of research works on the adoption of multi-agent systems (MAS) in several industrial environments has flourished. This approach, unlike traditional centralized or multilevel hierarchical approaches, assumes the presence of several decision-making entities, distributed inside the manufacturing system, interacting and cooperating each other in order to achieve optimal global performance. Aim of this paper is at first to provide readers, which are not experienced with the multi-agent approach, with some definitions and categorizations of this paradigm. Secondarily, by making use of an extensive database of more than 100 contributions on this field, authors intend to evaluate how multi-agents systems have really impacted on the industrial practices at an enterprise and at a broader supply chain level. Finally, driven by the past research experiences of the authors and by the extensive literature search, considerations and remarks on the real potential benefits and on the major issues currently inhibiting the spread out of this paradigm are reported.
Neutrophil Migration under Agarose: Quantitation and Variables (1979)

Several variables have been evaluated for the in-vitro measurement of neutrophil migration under agarose. Commonly used anticoagulants do not alter migration. Cells may be collected in heparin, sodium citrate, or EDTA. Neither hypotonic or ammonium chloride lysis of erythrocytes affects chemotactic activity. Saponin, however, decreased both leukocytic viability and migration. Passage of neutrophils through a Hypaque-Ficoll density gradient improved migration scores, presumably by removing contaminating material and cells. Both lymphocyte and erythrocyte contamination decreased test scores. Platelets did not have a detrimental effect on neutrophil migration. Fresh serum was the most potent chemotactic agent. This was followed, in order, by zymosan-activated serum, N-formyl-L-methionyl-L-phenylalanine, casein, and Escherichia coli supernatant. A scoring method that combines features of both counting leukocytes and measuring the migration distance has been devised. The technic has a coefficient of variation of 9.2%. Scores for the normal adult population show a gaussian distribution.
SalivaryAntibodies Directed against Outer Membrane Proteins of <i>Moraxella catarrhalis</i> in HealthyAdults (2003)

ABSTRACT Moraxella catarrhalis is a major mucosal pathogen of the human respiratory tract, but the mucosal immune response directed against surface components of this organism has not been characterized in detail. The aim of this study was to investigate the salivary immunoglobulin A (IgA) response toward outer membrane proteins (OMP) of M. catarrhalis in healthy adults, the group of individuals least likely to be colonized and thus most likely to display mucosal immunity. Unstimulated saliva samples collected from 14 healthy adult volunteers were subjected to IgA immunoblot analysis with OMP preparations of M. catarrhalis strain O35E. Immunoblot analysis revealed a consistent pattern of IgA reactivity, with the appearance of five major bands located at >250, 200, 120, 80, and 60 kDa. Eleven (79%) of 14 saliva samples elicited reactivity to all five bands. Immunoblot analysis with a set of isogenic knockout mutants lacking the expression of individual OMP was used to determine the identities of OMP giving rise to IgA bands. Human saliva was shown consistently to exhibit IgA-binding activity for oligomeric UspA2 (>250 kDa), hemagglutinin (200 kDa), monomeric UspA1 (120 kDa), transferrin-binding protein B (TbpB), monomeric UspA2, CopB, and presumably OMP CD. TbpB, oligomeric UspA2, and CopB formed a cluster of bands at about 80 kDa. These data indicate that the human salivary IgA response is directed consistently against a small number of major OMP, some of which are presently considered vaccine candidates. The functional properties of these mucosal antibodies remain to be elucidated.
Performance regression testing of concurrent classes (2014)

Developers of thread-safe classes struggle with two opposing goals. The class must be correct, which requires synchronizing concurrent accesses, and the class should provide reasonable performance, which is difficult to realize in the presence of unnecessary synchronization. Validating the performance of a thread-safe class is challenging because it requires diverse workloads that use the class, because existing performance analysis techniques focus on individual bottleneck methods, and because reliably measuring the performance of concurrent executions is difficult. This paper presents SpeedGun, an automatic performance regression testing technique for thread-safe classes. The key idea is to generate multi-threaded performance tests and to compare two versions of a class with each other. The analysis notifies developers when changing a thread-safe class significantly influences the performance of clients of this class. An evaluation with 113 pairs of classes from popular Java projects shows that the analysis effectively identifies 13 performance differences, including performance regressions that the respective developers were not aware of.
음성출력 의사소통 기구(VOCA)사용 중재가 통합된 자폐 범주성 장애 유아의 또래와의 사회적 상호작용에 미치는 영향 (2008)

본 연구는 통합된 자폐 범주성 장애 유아에게 음성출력 의사소통 기구 (VOCA)사용 중재를 사용했을 때 또래와의 사회적 상호작용이 증가하는지를 살펴보고자 실행되었다.