gebhart/patrepeval huggingface dataset:
Use of high-speed rolling to detect respiratory syncytial virus in cell culture (1989)

We examined the effect of motion on respiratory syncytial virus (RSV) growth in cell culture. Infected cultures were incubated stationary, rolling, or on an orbital shaker. Enzyme immunoassay (EIA) results for cultures infected with high concentrations of a laboratory strain of RSV were similar for all incubation conditions. However, cultures infected with low concentrations of virus and rolled at 96 rpm had a significantly greater mean EIA optical density (1.78 +/- 0.22) than cultures rolled at 2 rpm (1.42 +/- 0.08) (P less than 0.05). The mean EIA optical density of high-speed-rolled cultures was also significantly greater than for cultures on an orbital shaker (1.25 +/- 0.08) or for stationary cultures (0.21 +/- 0.17) (P less than 0.01). The amount of virus measured by EIA from cultures infected with clinical specimens was also found to be significantly greater at 96 rpm than for stationary cultures. Cultures infected with cell culture isolates were detected significantly earlier at 96 rpm than when stationary. We suggest that high-speed-rolling can be used to enhance the detection of RSV in clinical specimens, especially if the virus is present in low concentrations.
Cloning of ATAC, an activation‐induced, chemokine‐related molecule exclusively expressed in CD8+ T lymphocytes (1995)

Abstract A cDNA clone, designated ATAC, was isolated from a collection of human T cell activation genes. Analysis of tissue distribution determined that ATAC mRNA of approxiamtely 0.9 kb is exclusively expressed in activated CD8 + T cells. Induction of the ATAC gene requires stimulation by both phorbol 12‐myristate 13‐acetate and Ca 2+ ionophore A23187 (“two‐signal gene”) and is fully abrogated by the immunosuppressive agent cyclosporin A. Upon stimulation, ATAC mRNA is detectable within 30 min, maximal expression is seen after 4 h. The polypeptide encoded by the open reading frame of ATAC mRNA is 114 amino acids long with a calculated M r of 12.52 kDa. The structural features predict the cleavage and secretion of a mature ATAC protein of approximately 10 kDa from the 12.52‐kDa precursor. ATAC is highly similar to a very recently identified murine molecule designated lymphotactin both at the cDNA (73.8% identity) and the protein (61.4% identity) levels, and related to members of the C‐C and C‐X‐C chemokine families. Two variants of the ATAC protein were expressed and tested for chemotaxis and Ca 2+ release on a variety of target cells. The ATAC gene was located to chromosome 1q23.
Kinetics and Product Studies for Ozonolysis Reactions of Organic Particles Using Aerosol CIMS (2004)

The recently developed technique of aerosol chemical ionization mass spectrometry is used to study the reaction of ozone with particles consisting of unsaturated organic molecules, including oleic acid, linoleic acid, oleyl alcohol, and 1-octadecene. The reactive uptake coefficients, γ, for polydisperse aerosols with mean diameters of 800 nm are determined from the rates of loss of the particle species to be (7.5 ± 1.2) × 10-4 for oleic acid, (1.1 ± 0.2) × 10-3 for linoleic acid, (7.5 ± 1.3) × 10-4 for oleyl alcohol, and (2.4 ± 0.4) × 10-4 for 1-octadecene. The ozonolysis products of oleic acid particles are studied in detail with simultaneous detection of the four primary products: nonanal, nonanoic acid, 9-oxononanoic acid, and azelaic acid. All four products are found to exist in the reacted particles, though nonanal is also detected in the gas phase indicating that it partially evaporates. The yield of azelaic acid is determined to be 0.12 ± 0.04, and the yields of nonanal and 9-oxononanoic acid are found to be larger than the yields of the other products suggesting the existence of secondary reactions involving the Criegee intermediates. A fifth product, 9-oxooctadecanoic acid, is detected with a small yield (∼0.02) and is believed to result from different secondary reactions. Implications of these results for the alteration of chemical and physical properties of aerosols as they are aged in the atmosphere are discussed.
Li2NiO2 as a Novel Cathode Additive for Overdischarge Protection of Li-Ion Batteries (2007)

By employing Li2NiO2 exhibiting the distinctively low coulombic efficiency at the first cycle as a cathode additive, lithium-ion batteries can be tuned to exhibit cathode-limiting configuration that is inherently immune to overdischarge abuse.
Development and Evaluation of a Solid-Phase Microextraction Probe for in Vivo Pharmacokinetic Studies (2003)

Simplified procedures and a reduction in sampling errors are important advantages for performing as many chemical analysis steps as possible at the site where a sample or subject is located. Solid-phase microextraction technology addresses this goal, and for our purposes, it also allows for in vivo monitoring of a dynamic living system with minimal disturbance of the system. Here we report the development of a solid-phase microextraction application for in vivo monitoring of circulating blood concentrations of benzodiazepines. A probe based on a polypyrrole extraction phase was developed and used for extraction of drug molecules directly from a peripheral vein with subsequent instrumental quantification. The probe provides good sensitivity and selectivity for the drugs versus the blood matrix, while eliminating the need to draw blood. After sampling, the extracted drugs are quantified by liquid chromatography−tandem mass spectrometry. The limit of detection of the method is ∼3−7 ng/mL for analysis of the benzodiazepines from whole blood, and the method is linear to 1000 ng/mL. The method was used to monitor the pharmacokinetic profiles of diazepam and its metabolites in dogs, and the results compared favorably with profiles determined by conventional methods. Because no blood and only very small amounts of drugs are removed, minimal disruption to the chemical balance in blood occurs. This approach offers the potential for reduced exposure to blood for analytical personnel, simplified, less disruptive sampling, and lower stress levels on animals for pharmacokinetic studies. It also allows for a significant reduction in animal usage for these studies, which is important both ethically and for improving data quality.
Antiallergic Drug Cromolyn May Inhibit Histamine Secretion by Regulating Phosphorylation of a Mast Cell Protein (1980)

Cromolyn inhibited histamine release from mast cells that was induced by a classic secretagogue and correspondingly increased incorporation of radioactive phosphate into a 78,000-dalton protein. These effects on histamine secretion and on protein phosphorylation were rapid in onset and both showed tachyphylaxis. Cromolyn may therefore act by altering the phosphorylation of a protein involved in the regulation of secretion.
Proteins in cerebrospinal fluid and blood: Barriers, CSF flow rate and source-related dynamics (2003)

Cerebrospinal fluid (CSF) routine analysis for diagnosis of neurological diseases is based on the concepts for discrimination of blood-derived and brain-derived immunoglobulin fractions in CSF. The actual molecular flux/CSF flow theory of the blood/CSF barrier function, which founded the hyperbolic discrimination lines in quotient diagrams, is derived from the laws of molecular diffusion combined with CSF flow rate. It emerged from this theory that the decrease of CSF flow rate is sufficient to explain quantitatively the increase of CSF protein concentrations as observed in many neurological diseases. With this concept of CSF flow rate as the modulator of the normal and pathological blood-CSF barrier function, we got for the first time a theoretical frame work to explain also quantitatively the dynamics of brain-derived proteins and their source related (neurons and glial cells or leptomeningal cells) differences. The review of the anatomical, physiological and biophysical knowledge points to the new interpretations: The changing albumin quotient is an indicator of changing CSF flow rate and not for a morphological "leakage" of the blood-brain barrier. As an application of these concepts the dynamics of brain-derived molecules in blood are discussed with two examples: beta trace protein, flowing with CSF into venous blood, and neuron-specific enolase, passing from tissue into blood the opposite direction of serum proteins, again a gradient-dependent protein diffusion across the intact blood vessel wall.
Antiproliferative and proapoptotic activities of triptolide (PG490), a natural product entering clinical trials, on primary cultures of human prostatic epithelial cells. (2002)

Interest in exploiting traditional medicines for prevention or treatment of cancer is increasing. Extracts from the herb Tripterygium wilfordii hook F have been used in China for centuries to treat immune-related disorders. Recently it was reported that triptolide (PG490), a purified compound from Tripterygium, possessed antitumor properties and induced apoptosis by p53-independent mechanisms in a variety of malignant cell lines. This property of triptolide attracted our attention because we have found that primary cultures of human prostatic epithelial cells derived from normal tissues and adenocarcinomas are in general extremely resistant to apoptosis. Furthermore, the function of wild-type p53 is impaired in these cells such that drugs that require p53 activity to induce cell death are ineffective. Therefore, the properties of triptolide and the recent approval of its water-soluble form (PG490-88) for entry into Phase I clinical trials suggested that this drug was a promising candidate to test for antitumor activity against prostate cells. Experiments presented here demonstrated that triptolide had dose-dependent effects on both normal and cancer-derived primary cultures of human prostatic epithelial cells. Low concentrations of triptolide inhibited cell proliferation and induced a senescence-like phenotype. Higher concentrations of triptolide induced apoptosis that was unexpectedly associated with nuclear accumulation of p53. Paradoxically, levels of the p53 target genes, p21(WAF1/CIP1) and hdm-2, were reduced, as was bcl-2. Our preclinical studies suggest that triptolide might be an effective preventive as well as therapeutic agent against prostate cancer and that triptolide may activate a functional p53 pathway in prostate cells.
Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map (2003)

An international effort is underway to generate a comprehensive haplotype map (HapMap) of the human genome represented by an estimated 300,000 to 1 million 'tag' single nucleotide polymorphisms (SNPs). Our analysis indicates that the current human SNP map is not sufficiently dense to support the HapMap project. For example, 24.6% of the genome currently lacks SNPs at the minimal density and spacing that would be required to construct even a conservative tag SNP map containing 300,000 SNPs. In an effort to improve the human SNP map, we identified 140,696 additional SNP candidates using a new bioinformatics pipeline. Over 51,000 of these SNPs mapped to the largest gaps in the human SNP map, leading to significant improvements in these regions. Our SNPs will be immediately useful for the HapMap project, and will allow for the inclusion of many additional genomic intervals in the final HapMap. Nevertheless, our results also indicate that additional SNP discovery projects will be required both to define the haplotype architecture of the human genome and to construct comprehensive tag SNP maps that will be useful for genetic linkage studies in humans.
Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing (2013)

Olfactory receptors (ORs) provide the molecular basis for the detection of volatile odorant molecules by olfactory sensory neurons. The OR supergene family encodes G-protein coupled proteins that belong to the seven-transmembrane-domain receptor family. It was initially postulated that ORs are exclusively expressed in the olfactory epithelium. However, recent studies have demonstrated ectopic expression of some ORs in a variety of other tissues. In the present study, we conducted a comprehensive expression analysis of ORs using an extended panel of human tissues. This analysis made use of recent dramatic technical developments of the so-called Next Generation Sequencing (NGS) technique, which encouraged us to use open access data for the first comprehensive RNA-Seq expression analysis of ectopically expressed ORs in multiple human tissues. We analyzed mRNA-Seq data obtained by Illumina sequencing of 16 human tissues available from Illumina Body Map project 2.0 and from an additional study of OR expression in testis. At least some ORs were expressed in all the tissues analyzed. In several tissues, we could detect broadly expressed ORs such as OR2W3 and OR51E1. We also identified ORs that showed exclusive expression in one investigated tissue, such as OR4N4 in testis. For some ORs, the coding exon was found to be part of a transcript of upstream genes. In total, 111 of 400 OR genes were expressed with an FPKM (fragments per kilobase of exon per million fragments mapped) higher than 0.1 in at least one tissue. For several ORs, mRNA expression was verified by RT-PCR. Our results support the idea that ORs are broadly expressed in a variety of tissues and provide the basis for further functional studies.
Effects of glucose and glycerol on γ-poly(glutamic acid) formation byBacillus licheniformis ATCC 9945a (1998)

Bacillus licheniformis ATCC 9945a is one of the bacterial strains that produce gamma-poly(glutamic acid) (gamma-PGA). The use of carbohydrate medium components for gamma-PGA production was explored. Cells were grown in shake flasks or in controlled pH fermentors using medium formulations that contain different carbon sources. During the cultivations, aliquots were removed to monitor cell growth, carbon utilization, polymer production, and polymer molecular weight. Glucose was a better carbon source than glycerol for cell growth. Furthermore, glucose was utilized at a faster rate than glycerol, citrate, or glutamate. However, by using mixtures of glucose and glycerol in medium formulations, the efficiency of gamma-PGA production increased. For example, by increasing the glycerol in medium formulations from 0 to 40 g/L, the gamma-PGA broth concentration after 96 h increased from 5.7 to 20.5 g/L. Considering that glycerol utilization was low for the glucose/glycerol mixtures studied, it was unclear as to the mechanism by which glycerol leads to enhanced product formation. Cell growth and concomitant gamma-PGA production (12 g/L) at pH 6.5 was possible using glucose as a carbon source if trace amounts (0.5 g/L each) of citrate and glutamate were present in the medium. We suggested that citrate and glutamate were useful in preventing salt precipitation from the medium. In addition, glutamate may be preferred relative to ammonium chloride as a nitrogen source. The conversion of glucose to gamma-PGA by the strain ATCC 9945a was believed to occur by glycolysis of glucose to acetyl-CoA and tricarboxylic acid (TCA) cycle intermediates that were then metabolized via the TCA cycle to form alpha-ketoglutarate, which is a direct glutamate precursor.
Pesticide Degradation Mechanisms and Environmental Activation (1991)

Pesticides are degraded by many different mechanisms. Physical, chemical, and biological agents play significant roles in the transformation of insecticide, herbicide, and fungicide molecules to various degradation products. Transformation mechanisms include oxidation, hydrolysis, reduction, hydration, conjugation, isomerization, and cyclization. Resultant products are usually less bioactive than the parent psticide molecule, but numerous cases have been documented of metabolites with greater bioactivity. The physical and chemical properties of the degradation products are also different from those of the parent compound, and their fate and significance in the environment also are altered with the structural changes. The concept of "environmental activation" is introduced, to describe the transformation of a pesticide to a degradation product that is of significance in the environment as a result of its environmental toxicology or chemistry.
Hydrogen Blended Natural Gas Operation of a Heavy Duty Turbocharged Lean Burn Spark Ignition Engine (2004)

&lt;div class="htmlview paragraph"&gt;A turbocharged lean burn natural gas engine was upgraded to operate on a blend of hydrogen and natural gas (HCNG). Tests were carried out to determine the most suitable H&lt;sub&gt;2&lt;/sub&gt;/NG blend for H&lt;sub&gt;2&lt;/sub&gt; fractions between 20 and 32 vol%. A 20 vol% H&lt;sub&gt;2&lt;/sub&gt; content was found to provide the desired benefits when taking into consideration the engine and vehicle performance attributes. A full engine map was developed for the chosen mixture, and was verified over the steady-state AVL8 cycle. In general, the HCNG calibration included operation at higher air-fuel ratios and retarded spark timings. The results indicated that the NOx and NMHC emissions were reduced by 50% and 58% respectively, while the CO and CH&lt;sub&gt;4&lt;/sub&gt; emissions were slightly reduced. The HCNG engine torque, power and fuel consumption were maintained the same as for the natural gas fuel. The chassis dynamometer transient testing confirmed large NOx reduction of about 56% for HCNG operation. The buses have successfully completed the 24,000 miles field trials and their performance was found very satisfactory.&lt;/div&gt;
Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens (2004)

Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. The analysis of proteins E6 and E7 showed that ANN models appear to be more accurate for prediction of HLA-A3 hot spots and HMM models for HLA-A2 predictions. For illustration of its utility we applied MULTIPRED for prediction of promiscuous T-cell epitopes in all four SARS coronavirus structural proteins. MULTIPRED predicted HLA-A2 and HLA-A3 hot spots in each of these proteins.
Pulsed near-infrared laser diode excitation system for biomedical photoacoustic imaging (2006)

A pulsed laser diode system operating at 905 nm has been developed for the generation of photoacoustic signals in tissue. It was evaluated by measuring the photoacoustic waveforms generated in a blood vessel phantom comprising three dye-filled (mu(a)=1 mm(-1)) tubes of diameters 120-580 microm immersed to a maximum depth of 9 mm in a turbid liquid (mu'(s)=1 mm(-1)). The system was then combined with a cylindrical scanning system to obtain two-dimensional images of a tissue phantom. The signal-to-noise ratio of the detected signals in both cases and the image contrast in the latter suggest that such a system could provide a compact and inexpensive alternative to current excitation sources for superficial imaging applications.
Ferroelectric-gate thin-film transistors using indium-tin-oxide channel with large charge controllability (2005)

We have fabricated and characterized ferroelectric-gate thin-film transistors (TFTs) using indium-tin-oxide (ITO) as a channel and ferroelectric Bi4−xLaxTi3O12 (BLT) as a gate insulator. We have obtained a typical n-channel transistor property with clear current saturation in drain current and drain voltage (ID–VD) characteristics. The obtained on∕off current ratio is more than 104 and the field-effect mobility is estimated 9.1cm2∕Vs. In particular, we demonstrate a large “on”-current of 2.5 mA in ITO∕BLT structure TFT in spite of the low channel mobility. This is because the ferroelectric film can induce large charge density due to the spontaneous polarization.
Glutaraldehyde: Behavior in Aqueous Solution, Reaction with Proteins, and Application to Enzyme Crosslinking (2004)

Glutaraldehyde possesses unique characteristics that render it one of the most effective protein crosslinking reagents. It can be present in at least 13 different forms depending on solution conditions such as pH, concentration, temperature, etc. Substantial literature is found concerning the use of glutaraldehyde for protein immobilization, yet there is no agreement about the main reactive species that participates in the crosslinking process because monomeric and polymeric forms are in equilibrium. Glutaraldehyde may react with proteins by several means such as aldol condensation or Michael-type addition, and we show here 8 different reactions for various aqueous forms of this reagent. As a result of these discrepancies and the unique characteristics of each enzyme, crosslinking procedures using glutaraldehyde are largely developed through empirical observation. The choice of the enzyme-glutaraldehyde ratio, as well as their final concentration, is critical because insolubilization of the enzyme must result in minimal distortion of its structure in order to retain catalytic activity. The purpose of this paper is to give an overview of glutaraldehyde as a crosslinking reagent by describing its structure and chemical properties in aqueous solution in an attempt to explain its high reactivity toward proteins, particularly as applied to the production of insoluble enzymes.
Directed evolution of a single-chain class II MHC product by yeast display (2003)

Many autoimmune diseases have been linked to the class II region of the major histocompatibility complex (MHC). The linkage is thought to be a result of autoreactive T cells that recognize self-peptides bound to a product of this locus. For example, T cells from non-obese diabetic mice recognize specific 'diabetogenic' peptides bound to a class II MHC allele called I-A(g7). The I-A(g7) molecule is noted for being unstable and difficult to work with, especially in soluble form. In this work, yeast surface display combined with fluorescence-activated cell sorting was used as a means of directed evolution to engineer stabilized variants of a single-chain form of I-A(g7). A library containing mutations at two residues (positions 56 and 57 of the I-A(g7) beta-chain) that are important in the class II disease associations yielded stabilized mutants with preferences for a glutamic acid at residue 56 and a leucine at residue 57. Random mutation of I-A(g7) followed by selection with an anti-I-A(g7) antibody also yielded stabilized variants with mutations in other residues. The methods described here allow the discovery of novel MHC complexes that could facilitate structural studies and provide new opportunities in the development of diagnostics or antagonists of class II MHC-associated diseases.