gebhart/patrepeval huggingface dataset:
Characterization of adsorbed protein films by time of flight secondary ion mass spectrometry (2001)

Time of flight secondary ion mass spectrometry (ToF-SIMS) is a useful technique in the study of adsorbed protein films because of its high surface sensitivity and chemical selectivity. However, the protein mass spectra generated by ToF-SIMS are complex fragmentation patterns of a polymer consisting of 20 different monomers (i.e., amino acids). Principal component analysis (PCA) was implemented to classify several reference positive ion protein spectra according to protein and substrate type. Furthermore, the positive ion 74/102 and 120/130 SIMS intensity ratios, radiolabeled experiments, and PCA were used to track the relative surface concentrations of bovine serum albumin and bovine fibronectin in a binary adsorption experiment. In all cases, the combination of ToF-SIMS and PCA proved capable in classifying proteins by their type (in the case of pure protein spectra) and relative surface concentration (in the case of the binary protein spectra). © 2001 John Wiley & Sons, Inc. J Biomed Mater Res 57: 432–440, 2001
Processing and properties of high aspect ratio ferroelectric structures (2005)

High aspect ratio (/spl ges/50:1) ferroelectric structures are potentially applicable in areas such as tunable photonic devices, sensors and actuators. In this work high aspect ratio structures of Pb(Zr/sub x/, Ti/sub 1-x/)O/sub 3/, and LaNiO/sub 3//Pb(Zr/sub x/,Ti/sub 1-x/)O/sub 3//LaNiO/sub 3/ tri-layers were prepared by vacuum infiltration of meso-porous Si templates. Pyrolysis was done at 300/spl deg/C for 2 min. Reactive ion etching followed by XeF/sub 2/ isotropic Si etching was utilized to release the embedded PZT structures from the Si template. The released structures were annealed at 700/spl deg/C for 1 min. in order to induce crystallization. These 2D ferroelectric photonic structures exhibited a TE-mode band gap in the infrared region between 4.0 - 4.4 microns in wavelength, which was found to be consistent with the theoretical photonic band gap calculations.
Subsite Specificity of Memapsin 2 (β-Secretase):  Implications for Inhibitor Design (2001)

Memapsin 2 is the protease known as beta-secretase whose action on beta-amyloid precursor protein leads to the production of the beta-amyloid (Abeta) peptide. Since the accumulation of Abeta in the brain is a key event in the pathogenesis of Alzheimer's disease, memapsin 2 is an important target for the design of inhibitory drugs. Here we describe the residue preference for the subsites of memapsin 2. The relative k(cat)/K(M) values of residues in each of the eight subsites were determined by the relative initial cleavage rates of substrate mixtures as quantified by MALDI-TOF mass spectrometry. We found that each subsite can accommodate multiple residues. The S(1) subsite is the most stringent, preferring residues in the order of Leu > Phe > Met > Tyr. The preferences of other subsites are the following: S(2), Asp > Asn > Met; S(3), Ile > Val > Leu; S(4), Glu > Gln > Asp; S(1)', Met > Glu > Gln > Ala; S(2)', Val > Ile > Ala; S(3)', Leu > Trp > Ala; S(4)', Asp > Glu > Trp. In general, S subsites are more specific than the S' subsites. A peptide comprising the eight most favored residues (Glu-Ile-Asp-Leu-Met-Val-Leu-Asp) was found to be hydrolyzed with the highest k(cat)/K(M) value so far observed for memapsin 2. Residue preferences at four subsites were also studied by binding of memapsin 2 to a combinatorial inhibitor library. From 10 tight binding inhibitors, the consensus preferences were as follows: S(2), Asp and Glu; S(3), Leu and Ile; S(2)', Val; and S(3)', Glu and Gln. An inhibitor, OM00-3, Glu-Leu-Asp-LeuAla-Val-Glu-Phe (where the asterisk represents the hydroxyethylene tansition-state isostere), designed from the consensus residues, was found to be the most potent inhibitor of memapsin 2 so far reported (K(i) of 3.1 x 10(-10) M). A molecular model of OM00-3 binding to memapsin 2 revealed critical improvement of the interactions between inhibitor side chains with enzyme over a previous inhibitor, OM99-2 [Ghosh, A. K., et al. (2000) J. Am. Chem. Soc. 14, 3522-3523].
Sequence of the gene encoding type F neurotoxin ofClostridium botulinum (1992)

Primers designed to conserved regions of botulinum and tetanus clostridial toxins were used to amplify DNA fragments from non-proteolytic Clostridium botulinum type F (202F) DNA using polymerase chain reaction technology. The fragments were cloned and the complete nucleotide sequence of the gene encoding type F toxin determined. Analysis of the nucleotide sequence demonstrated the presence of an open frame encoding a protein of 1274 amino acids, similar to other botulinum neurotoxins. Upstream of the toxin gene is the end of an open reading frame which encodes the C-terminus of a protein with homology to non-toxic-non-hemagglutinin component of type C progenitor toxin.
Endophyte Survival during Seed Storage: Endophyte–Host Interactions and Heritability (2009)

Use of nontoxic endophytes in forage tall fescue [ Schedonorus phoenix (Scop.) Holub.] is a preferred strategy to overcome fescue toxicosis. Endophytes are transmitted through the seed, but suffer mortality preferentially to the embryo during storage. Loss of viable endophyte reduces the value of the seed, so increasing storage life would be a benefit. The objectives of this study were to examine (i) viability of an endophyte AR542 in different tall fescue cultivars and endophytes AR542 and AR584 in a Jesup tall fescue seed when stored for extended periods of time, and (ii) heritability of endophyte persistence during seed storage. Seed from each population were stored at room temperatures for 18 mo. Jesup plants containing endophyte after 18 mo of seed storage were placed into polycross blocks. Seed from the selected and parent populations, Jesup with toxic endophyte, and Grasslands Flecha with AR542, were stored at 30°C for 22 mo and tested for endophyte monthly. Pairwise t tests and regression analysis were performed to describe the population responses to storage conditions. Heritability of endophyte viability during storage was calculated. Endophyte AR542 viability during storage was greatest in Flecha followed by Jesup and least in Advance, a third tall fescue cultivar studied in addition to Jesup and Flecha. Endophyte AR584 had greater viability during storage than did AR542 when in Jesup. Selection for endophyte survival increased endophyte viability in stored seed and had heritabilities of 38 and 63% for AR542 and AR584, respectively.
Canakinumab relieves symptoms of acute flares and improves health-related quality of life in patients with difficult-to-treat Gouty Arthritis by suppressing inflammation: results of a randomized, dose-ranging study (2011)

clinicaltrials.gov: NCT00798369.
Increased frequency of rheumatoid factor precursor B lymphocytes after immunization of normal adults with tetanus toxoid. (1983)

Vaccination of normal adults with tetanus toxoid induced a two-three-fold rise in the frequency of IgM anti-IgG (rheumatoid factor, RF) B lymphocytes inducible by the polyclonal B cell activator, Epstein-Barr virus. The increase in IgM-RF precursors occurred earlier, was greater in magnitude, and was more sustained than the change in plasma IgM-RF. It was associated with a rise in total IgM levels, and correlated positively with the magnitude of the IgG anti-tetanus antibody response, but not with levels of circulating immune complexes. The ability of apparently innocuous infections and immunizations to increase the frequency of IgM-RF precursor B lymphocytes may be the reason for the previously noted expansion in this autoreactive B cell pool between birth and adulthood.
Monitoring Shifts in the Conformation Equilibrium of the Membrane Protein Cytochrome P450 Reductase (POR) in Nanodiscs (2012)

Nanodiscs are self-assembled ∼50-nm(2) patches of lipid bilayers stabilized by amphipathic belt proteins. We demonstrate that a well ordered dense film of nanodiscs serves for non-destructive, label-free studies of isolated membrane proteins in a native like environment using neutron reflectometry (NR). This method exceeds studies of membrane proteins in vesicle or supported lipid bilayer because membrane proteins can be selectively adsorbed with controlled orientation. As a proof of concept, the mechanism of action of the membrane-anchored cytochrome P450 reductase (POR) is studied here. This enzyme is responsible for catalyzing the transfer of electrons from NADPH to cytochrome P450s and thus is a key enzyme in the biosynthesis of numerous primary and secondary metabolites in plants. Neutron reflectometry shows a coexistence of two different POR conformations, a compact and an extended form with a thickness of 44 and 79 Å, respectively. Upon complete reduction by NADPH, the conformational equilibrium shifts toward the compact form protecting the reduced FMN cofactor from engaging in unspecific electron transfer reaction.
Compiler and runtime support for efficient software transactional memory (2006)

Programmers have traditionally used locks to synchronize concurrent access to shared data. Lock-based synchronization, however, has well-known pitfalls: using locks for fine-grain synchronization and composing code that already uses locks are both difficult and prone to deadlock. Transactional memory provides an alternate concurrency control mechanism that avoids these pitfalls and significantly eases concurrent programming. Transactional memory language constructs have recently been proposed as extensions to existing languages or included in new concurrent language specifications, opening the door for new compiler optimizations that target the overheads of transactional memory.This paper presents compiler and runtime optimizations for transactional memory language constructs. We present a high-performance software transactional memory system (STM) integrated into a managed runtime environment. Our system efficiently implements nested transactions that support both composition of transactions and partial roll back. Our JIT compiler is the first to optimize the overheads of STM, and we show novel techniques for enabling JIT optimizations on STM operations. We measure the performance of our optimizations on a 16-way SMP running multi-threaded transactional workloads. Our results show that these techniques enable transactional memory's performance to compete with that of well-tuned synchronization.
Pharmacokinetics of Cannabinoids (2005)

Delta-9-tetrahydrocannabinol (Delta-9-THC) is the main psychoactive ingredient of cannabis (marijuana). The present review focuses on the pharmacokinetics of THC, but also includes known information for cannabinol and cannabidiol, as well as the synthetic marketed cannabinoids, dronabinol (synthetic THC) and nabilone. The variability of THC in plant material (0.3% to 30%) leads to variability in tissue THC levels from smoking, which is, in itself, a highly individual process. THC bioavailability averages 30%. With a 3.55% THC cigarette, a peak plasma level of 152±86.3 ng/mL occured approximately 10 min after inhalation. Oral THC, on the other hand, is only 4% to 12% bioavailable and absorption is highly variable. THC is eliminated from plasma in a multiphasic manner, with low amounts detectable for over one week after dosing. A major active 11-hydroxy metabolite is formed after both inhalation and oral dosing (20% and 100% of parent, respectively). THC is widely distributed, particularly to fatty tissues, but less than 1% of an administered dose reaches the brain, while the spleen and body fat are long-term storage sites. The elimination of THC and its many metabolites (from all routes) occurs via the feces and urine. Metabolites persist in the urine and feces for several weeks. Nabilone is well absorbed and the pharmacokinetics, although variable, appear to be linear from oral doses of 1 mg to 4 mg (these doses show a plasma elimination half-life of approximately 2 h). As with THC, there is a high first-pass effect, and the feces to urine ratio of excretion is similar to other cannabinoids. Pharmacokinetic-pharmacodynamic modelling with plasma THC versus cardiac and psychotropic effects show that after equilibrium is reached, the intensity of effect is proportional to the plasma THC profile. Clinical trials have found that nabilone produces less tachycardia and less euphoria than THC for a similar antiemetic response.
Primary and .beta.-secondary deuterium isotope effects in N-deethylation reactions (1975)

Lidocaine (1), labeled specifically with deuterium in the alpha-methylene (lidocaine-d4,2) and beta-methyl (lidocaine-d6,3) carbon atoms of the terminal amino group, was used to probe the mechanism of oxidative N-deethylation by rat liver microsomes. The reaction rates were determined by measuring the formation of acetaldehyde colorimetrically. This general assay for oxidative N-deethylation reactions has the advantages of being rapid, producing a relatively stable colored derivative and being linear over the range of 0.25-4 mug of acetaldehyde formed per milliliter of incubate. Deuterium substitution at the methylene carbon atoms, the presumed site of initial oxygen insertion, revealed a kH/kD = 1.49 +/- 0.11 and a KmD/KmH = 1.23. Deuterium substitution on the terminal methyl groups showed a kH/kD = 1.52 +/- 0.10 and a KmD/KmH = 0.92. The results are explained in terms of both primary and secondary isotope effects on a possible rate-determining step in the N-deethylation sequence.
Structural and kinetic alterations in adenosine deaminase associated with the differentiation of rat intestinal cells. (1977)

Summary Forms of the enzyme adenosine deaminase (ADase) in rapidly dividing versus differentiated epithelial cells of rat intestinal mucosa were compared. Two variants with isolectric points at pH ca. 4.85 (ADase I) and 4.80 (ADase II) were resolved by preparative and analytical isoelectric focusing. These forms, which could also be partially resolved by molecular exclusion chromatography, displayed apparent molecular weight values of 37,000 and 33,500, respectively. K m values for adenosine for the two forms were significantly different (0.07 mm for ADase I and 0.38 mm for ADase II). Small differences were also observed in relative substrate specificity, while the pH-activity profiles for the two forms were essentially identical, with broad maxima between pH values of 6.5 and 9.0. The intensity of ADase I observed in analytical isoelectric focusing increased dramatically with respect to ADase II as the epithelial cells differentiated. The specific adenosine deaminase activity also increased with cellular differentiation by over 30-fold, expressed per mg DNA, or over 6-fold, expressed per mg protein. Cycloheximide, sharply reduced this increase in specific activity. Cycloheximide was also shown to prevent the increase in the activity of ADase I that is normally associated with differentiation in rat intestines. The data imply the formation of a particular enzyme variant characteristic of the differentiated cell by a mechanism related to active protein synthesis.
Iron-Deficiency Anemia (2015)

Iron-deficiency anemia is the most common form of anemia in the world. This article reviews the global nature of the disease, iron homeostasis in normal and iron-deficient states, clinical findings, treatment, and causes of iron-resistant iron deficiency.
Immunodepression following neurosurgical procedures (1995)

A decrease of monocytic human leukocyte antigen-DR expression occurs after neurosurgery and is associated with a preceding, strong, intracranial (but not systemic) inflammatory response. A very low monocytic human leukocyte antigen-DR expression (< 30% positive monocytes) suggests the possibility of infection. Measurement of monocytic human leukocyte antigen-DR expression could help to detect patients with a high risk of infection after neurosurgery. Our results suggest that even sterile central nervous system surgery may contribute to general immunodepression. The local intracranial inflammatory response may be involved in this process.
My grandmother on the other side of the lake notions of absence and presence at the cultural interface a work in progress (2000)

My grandmother on the Other Side of the Lake is a cross-cultural oral history project that investigates the recent social history of My Grandmother on the Other Side of the Lake Alexandrina region of South Australia from a cross-cultural and post-colonial perspective. The project is being undertaken with broad community consultation and involvement as part of an interdisciplinary Masters of Arts in Australian Studies and Screen Studies at Flinders University. It explores the ability of oral narratives to form dialogues of resistance to the dominant historical records which have sought to represent, erase, exclude and marginalize Indigenous voices, women's voices and, more pointedly, Indigenous women's voices.
The interferon signature in autoimmune diseases (2012)

The observed IFN signature in several autoimmune diseases is a biomarker of active disease and is investigated as a tool when selecting treatment for individual patients.
Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes for the propanediol dehydratase (1997)

The propanediol utilization (pdu) operon of Salmonella typhimurium encodes proteins required for the catabolism of propanediol, including a coenzyme B12-dependent propanediol dehydratase. A clone that expresses propanediol dehydratase activity was isolated from a Salmonella genomic library. DNA sequence analysis showed that the clone included part of the pduF gene, the pduABCDE genes, and a long partial open reading frame (ORF1). The clone included 3.9 kbp of pdu DNA which had not been previously sequenced. Complementation and expression studies with subclones constructed via PCR showed that three genes (pduCDE) are necessary and sufficient for propanediol dehydratase activity. The function of ORF1 was not determined. Analyses showed that the S. typhimurium propanediol dehydratase was related to coenzyme B12-dependent glycerol dehydratases from Citrobacter freundii and Klebsiella pneumoniae. Unexpectedly, the S. typhimurium propanediol dehydratase was found to be 98% identical in amino acid sequence to the Klebsiella oxytoca propanediol dehydratase; this is a much higher identity than expected, given the relationship between these organisms. DNA sequence analyses also supported previous studies indicating that the pdu operon was inherited along with the adjacent cobalamin biosynthesis operon by a single horizontal gene transfer.
Heat-mediated immune complex dissociation and enzyme-linked immunosorbent assay signal amplification render p24 antigen detection in plasma as sensitive as HIV-1 RNA detection by polymerase chain reaction. (1996)

Heat-mediated ICD combined with a signal-amplification-boosted ELISA detects HIV-1 expression as sensitively as a polymerase chain reaction kit for viral RNA, but at only a fraction of the cost. The procedure uses a 50 microliters plasma sample and should be fully automatable.
Nuclear Factor E2-Related Factor 2-Dependent Antioxidant Response Element Activation bytert-Butylhydroquinone and Sulforaphane Occurring Preferentially in Astrocytes Conditions Neurons against Oxidative Insult (2004)

Binding of the transcription factor nuclear factor E2-related factor 2 (Nrf2) to the antioxidant response element (ARE) in neural cells results in the induction of a battery of genes that can coordinate a protective response against a variety of oxidative stressors. In this study, tert-butylhydroquinone (tBHQ) and sulforaphane were used as activators of this pathway. Consistent with previous studies, treatment of primary cortical cultures from ARE reporter mice revealed selective promoter activity in astrocytes. This activation protected neurons from hydrogen peroxide and nonexcitotoxic glutamate toxicity. tBHQ treatment of cultures from Nrf2 knock-out animals resulted in neither ARE activation nor neuroprotection. By reintroducing Nrf2 via infection with a replication-deficient adenovirus (ad), both the genetic response and neuroprotection were rescued. Conversely, infection with adenovirus encoding dominant-negative (DN) Nrf2 (ad-DN-Nrf2) or pretreatment with the selective phosphatidylinositol-3 kinase inhibitor LY294002 inhibited the tBHQ-mediated promoter response and corresponding neuroprotection. Interestingly, the adenoviral infection showed a high selectivity for astrocytes over neurons. In an attempt to reveal some of the cell type-specific changes resulting from ARE activation, cultures were infected with adenovirus encoding green fluorescent protein (GFP) (ad-GFP) or ad-DN-Nrf2 (containing GFP) before tBHQ treatment. A glia-enriched population of GFP-infected cells was then isolated from a population of uninfected neurons using cell-sorting technology. Microarray analysis was used to evaluate potential glial versus neuron-specific contributions to the neuroprotective effects of ARE activation and Nrf2 dependence. Strikingly, the change in neuronal gene expression after tBHQ treatment was dependent on Nrf2 activity in the astrocytes. This suggests that Nrf2-dependent genetic changes alter neuron-glia interactions resulting in neuroprotection.
Severe cachexia in mice inoculated with interferon‐γ‐producing tumor cells (1991)

Nude mice were inoculated with CHO/IFN-gamma cells, a line of Chinese hamster ovary tumor cells, that had been genetically engineered to produce murine IFN-gamma. Severe cachexia, as evident from body weight loss and reduced food intake, occurred in these mice, but not in those injected with CHO/control cells, i.e. the original, non-IFN-gamma-producing line. The essential role of IFN-gamma in the pathogenesis of cachexia was confirmed by the demonstration that monoclonal antibodies (MAbs) against IFN-gamma, given prior to injection of the tumor cells, prevented cachexia. In addition to IFN-gamma, the presence of the tumor cells was also required for cachexia to develop. As evident from pair-feeding experiments, reduced food intake could only partially account for the rapid and extensive body-weight loss. Cachexia was characterized by a marked reduction in the amount of interscapular fat tissue. Injected tumor cells exclusively invaded intraperitoneal adipose tissue and elicited an inflammatory cell infiltrate, indicating that interscapular fat loss was due to humoral factors. Our data suggest that, among the humoral factors responsible for cancer-associated cachexia, IFN-gamma plays a prominent role.
Major histocompatibility complex – dependent T cell epitopes of lymphocytic choriomeningitis virus nucleoprotein and their protective capacity against viral disease (1989)

In mice the immune response to infection with lymphocytic choriomeningitis virus (LCMV), a member of the arenavirus family, is mainly based on the activity of cytotoxic T cells. The immunogenic epitopes of the viral nucleoprotein recognized by cytotoxic T cells in various inbred strains of mice were defined. These epitopes were located in H-2d and H-2q mice in the amino-terminal region and in H-2b mice in the carboxy-terminal region of the nucleoprotein. A detailed analysis with synthetic peptides allowed the definition of a common epitope of 9 amino acids in H-2d and H-2q mice and of about 15 amino acids in H-2b mice. These T cell epitopes were all recognized in association with H-2 D or L transplantation antigen. The protective capacity of recombinant vaccinia viruses expressing these epitopes was documented by assaying prevention of virus replication, protection against LCM and prevention of the local footpad swelling reaction. Thus, distinct T cell epitopes on the same internal viral protein mediate protection in a major histocompatibility complex-restricted manner.