gebhart/patrepeval huggingface dataset:
Analysis of enzyme specificity by multiple substrate kinetics (1993)

Multiple approaches for screening large sets of compounds for a specific function are of growing interest. The use of substrate mixtures to characterize the specificity of enzymes has been limited so far to compounds with similar kinetic parameters, because the data were analyzed by applying the kinetics of two competing substrates. In this study we introduce a statistical method for the analysis of reactions with many competing substrates which makes use of the specific features of multiple substrate kinetics. It is assumed that the relative concentrations of all substrates in a mixture can be monitored by high-performance liquid chromatography or a similar technique. Relative second-order rate constants, i.e., kcat/KM values, can be calculated for all substrates in the mixture from the resulting data set. The calculation uses the fact that there is a relationship between the concentrations of all pairs of substrates in the mixture. As a result, the precision of the calculated parameters is increased and the range of kinetic constants that can be obtained from one experiment is considerably expanded. Simulations demonstrate that the precision in the kinetic parameters increases with the number of substrates in the mixture. In fact, estimation of ratios of rate constants can be improved (or made possible) for substrates with order of magnitude differences in reactivity by adding "dummy" substrates with intermediate reactivities, even though the rate constants for dummy substrates are themselves of no intrinsic interest.
Prediction of Psilocybin Response in Healthy Volunteers (2012)

Responses to hallucinogenic drugs, such as psilocybin, are believed to be critically dependent on the user's personality, current mood state, drug pre-experiences, expectancies, and social and environmental variables. However, little is known about the order of importance of these variables and their effect sizes in comparison to drug dose. Hence, this study investigated the effects of 24 predictor variables, including age, sex, education, personality traits, drug pre-experience, mental state before drug intake, experimental setting, and drug dose on the acute response to psilocybin. The analysis was based on the pooled data of 23 controlled experimental studies involving 409 psilocybin administrations to 261 healthy volunteers. Multiple linear mixed effects models were fitted for each of 15 response variables. Although drug dose was clearly the most important predictor for all measured response variables, several non-pharmacological variables significantly contributed to the effects of psilocybin. Specifically, having a high score in the personality trait of Absorption, being in an emotionally excitable and active state immediately before drug intake, and having experienced few psychological problems in past weeks were most strongly associated with pleasant and mystical-type experiences, whereas high Emotional Excitability, low age, and an experimental setting involving positron emission tomography most strongly predicted unpleasant and/or anxious reactions to psilocybin. The results confirm that non-pharmacological variables play an important role in the effects of psilocybin.
ANTHOCYANINS OF MANGOSTEEN, Garcinia mangostana (1977)

ABSTRACT Mangosteen rinds contain a substantial amount of red pigment. The major pigment is cyanidin‐3‐sophoroside, and a minor pigment is cyanidin‐3‐glucoside.
Internal initiation of translation in retroviral vectors carrying picornavirus 5' nontranslated regions (1991)

Previous work has shown that picornavirus 5' nontranslated regions (NTRs) can initiate internal translation of downstream coding regions both in vitro and in transient in vivo assays. We have used 5' NTR sequences from encephalomyocarditis virus and poliovirus to construct retroviral vectors that are designed to express two proteins from a single mRNA. Inclusion of 5' NTR sequences did not adversely affect vector titer. Protein expression was studied with stable cell lines generated by vector infection of mouse NIH 3T3 cells and human and canine skin fibroblasts. Expression of a coding region in the downstream position was at levels from 25 to 100% of the same coding region in the upstream position. Expression of downstream coding regions in control vectors that did not contain the 5' NTR sequences was very low, in agreement with the predictions of the scanning model for eukaryotic translation. These experiments demonstrate coordinate expression of two coding regions from a single mRNA in stable cell lines and provide further support for the model of internal translation initiation by sequences in the 5' NTRs of picornaviruses.
[3H]Dihydrotetrabenazine, a New In Vitro Monoaminergic Probe for Human Brain (1988)

The monoamine transporter of dopamine (DA), noradrenaline, and 5-hydroxytryptamine synaptic vesicles was assayed in rat and human brain homogenates by in vitro binding of [3H]dihydrotetrabenazine. [3H]Reserpine, a second ligand of the vesicular monoamine transporter, could not be used. [3H]Dihydrotetrabenazine binding in rat brain was stable after 72 h at 22 degrees C postmortem. In major human brain regions, [3H]dihydrotetrabenazine binding was specific and saturable (KD, 2.7 nM). Displacement constants by substrates or inhibitors of vesicular monoamine uptake, and regional distribution in human brain were similar to those found in rodents. The highest densities of binding sites were observed in caudate nucleus, putamen, and accumbens nucleus. In caudate nucleus and in putamen from normal human subjects, [3H]dihydrotetrabenazine binding and homovanillic acid concentration were significantly or nearly significantly correlated. A weaker correlation was found between [3H]dihydrotetrabenazine binding and DA, in association with a higher variability of DA. [3H]Dihydrotetrabenazine binding in caudate nucleus and in putamen decreased significantly with age, unlike DA and homovanillic acid concentrations. The results establish [3H]dihydrotetrabenazine as a presynaptic monoaminergic ligand of interest for studies on postmortem human brain.
Chromosomal Variations Within Aneuploid Cancer Lines (2003)

Aneuploid cancers exhibit a wide spectrum of clinical aggressiveness, possibly because of varying chromosome compositions. To test this, karyotypes from the diploid CCD-34Lu fibroblast and the aneuploid A549 and SUIT-2 cancer lines underwent fluorescence in situ hybridization (FISH) and DAPI counterstaining. The number of DAPI-stained and FISH-identified chromosomes, 1-22, X,Y, as well as structural abnormalities, were counted and compared using the chi(2), Mann-Whitney rank sum test and the Levene's equality of variance. Virtually all of the evaluable diploid CCD-34Lu karyotypes had 46 chromosomes with two normal-appearing homologues. The aneuploid chromosome numbers per karyotype were highly variable, averaging 62 and 72 for the A549 and SUIT-2 lines, respectively. However, the A549 chromosome numbers were more narrowly distributed than the SUIT-2 karyotype chromosome numbers. Furthermore, 25% of the A549 chromosomes had structural abnormalities compared to only 7% of the SUIT-2 chromosomes. The chromosomal compositions of the aneuploid A549 and SUIT-2 cancer lines are widely divergent, suggesting that diverse genetic alterations, rather than chance, may govern the chromosome makeups of aneuploid cancers.
A heterodimer-selective agonist shows in vivo relevance of G protein-coupled receptor dimers (2005)

There has been much speculation regarding the functional relevance of G protein-coupled receptor heterodimers, primarily because demonstrating their existence in vivo has proven to be a considerable challenge. Here we show that the opioid agonist ligand 6'-guanidinonaltrindole (6'-GNTI) has the unique property of selectively activating only opioid receptor heterodimers but not homomers. Importantly, 6'-GNTI is an analgesic, thereby demonstrating that opioid receptor heterodimers are indeed functionally relevant in vivo. However, 6'-GNTI induces analgesia only when it is administered in the spinal cord but not in the brain, suggesting that the organization of heterodimers is tissue-specific. This study demonstrates a proof of concept for tissue-selective drug targeting based on G protein-coupled receptor heterodimerization. Importantly, targeting opioid heterodimers could provide an approach toward the design of analgesic drugs with reduced side effects.
Evolving video skims into useful multimedia abstractions (1998)

This paper reports two studies that measured the effects of ,different "video skim" techniques on comprehension, navigation, and user satisfaction. Video skims are compact, ,content-rich abstractions of longer videos, condensations that preserve frame rate while greatly reducing viewing time. Their characteristics depend on the image-and audioprocessing techniques used to create them. Results from the initial study helped refine video skims, which were then reassessed in the second experiment. Significant benefits were found for skims built from audio sequences meeting certain criteria. Keyworck
Identification of a temperature-sensitive asparaginyl-transfer ribonucleic acid synthetase mutant of Escherichia coli (1977)

A temperature-sensitive mutant of Escherichia coli K-12 isolated previously (H. Ohsawa and B. Maruo, J. Bacteriol. 127:1157-1166, 1976) was found to have an alteration in asparaginyl-transfer ribonucleic acid synthetase. This alteration can account for the temperature-sensitive phenotype of the mutant. No evidence was obtained to support the previous suggestion that ribosomal protein S1 is altered in this mutant. Combined with the previous genetic studies, we conclude that the newly defined genetic locus, asnS, for the asparaginyl-transfer ribonucleic acid synthetase maps near pyrD at 21 min on the E. coli chromosome.
Vertical profiles and CD loss control in deep RIE technology (2005)

Deep reactive ion etching (DRIE) technology is widely used to fabricate high aspect ratio structures in MEMS devices. The vertical profiles of the trenches etched by normal advanced silicon etching are not always satisfactory enough for some applications such as a vibratory lateral gyroscope. Bad vertical profiles will decrease the capacitance signal of a lateral comb, change the designed stress of a cantilever beam, reduce the weight of the mass and finally affect the sensitivity and stability of MEMS devices, especially small dimension MEMS structures. We introduce a new technology to improve the vertical profiles, which is realized by decreasing the etching time each cycle. This anisotropy parameter improves from 25 to 175. Moreover, we introduce a method to reduce CD loss. It is realized by adding descending passivation gasses C/sub 4/F/sub 8/ in the first several minutes and decreasing the etching time in the switch periods. The CD loss is decreased from 145 nm to 55 nm.
Microtubule Binding and Trapping at the Tip of Neurites Regulate Tau Motion in Living Neurons (2009)

During the development of neurons, the microtubule-associated tau proteins show a graded proximo-distal distribution in axons. In tauopathies such as Alzheimer's disease, tau accumulates in the somatodendritic compartment. To scrutinize the determinants of tau's distribution and motion, we constructed photoactivatable green fluorescent protein (GFP)-tagged tau fusion proteins and recorded their distribution after focal activation in living cells. Simulation showed that the motion of tau was compatible with diffusion/reaction as opposed to active transport/reaction. Effective diffusion constants of 0.7-0.8 microm(2)/second were calculated in neurites of PC12 cells and primary cortical neurons. Furthermore, tau's amino terminal projection domain mediated binding and enrichment of tau at distal neurites indicating that the tip of a neurite acts as an adsorber trapping tau protein. Treatment with taxol, incorporation of disease-related tau modifications, experimentally induced hyperphosphorylation and addition of preaggregated amyloid beta peptides (Abeta) increased the effective diffusion constant compatible with a decreased binding to microtubules. Distal enrichment was present after taxol treatment but was suppressed at disease-relevant conditions. The data suggest that (i) dynamic binding of tau to microtubules and diffusion along microtubules and (ii) trapping at the tip of a neurite both contribute to its distribution during development and disease.
An improved flow cytometry-based natural killer cytotoxicity assay involving calcein AM staining of effector cells. (2012)

Several flow cytometric methods for measuring natural killer cell activity have been developed. Commonly used protocols involve the staining of target cells with various fluorescent dyes. However, these protocols are not applicable to certain experimental settings. Therefore, we used Calcein AM (CAM), which has been reported to be the most suitable dye for use in target cell staining protocols, as a means of developing an improved flow cytometry-based NK cytotoxicity assay involving effector cell staining. Peripheral blood mononuclear cells (PBMCs) isolated by gradient density centrifugation and expanded NK cells were used as effector cells. Cytotoxicity against K562 cells and several hematologic cancer cell lines was measured by a flow cytometry-based method using CAM and propidium iodide. The new assay was compared with a standard (51)Cr release assay (CRA) in terms of its ability to measure the cytotoxicity of NK cells in PBMCs and expanded NK cells against K562 cells. The optimal concentration of CAM for staining effector cells was 0.05 μM, and CAM fluorescence intensity in effector cells was maintained for 4 hours. CAM staining had no significant effect on NK cell activity in human PBMCs or expanded NK cells. Comparison of the CRA and this new assay using K562 cells revealed a good correlation (PBMCs, r = 0.894; expanded NK cells, r = 0.887). Distinct separation between target tumor cells (Daudi, Raji, RPMI8226, U266, U937, and K562 cells) and CAM-stained PBMCs (E:T ratio, 12.5:1 to 50:1) or expanded NK cells (E:T ratio, 0.5 to 4:1) was observed after incubation for 1 or 4 hours. In summary, we successfully developed an effective flow cytometry-based assay for assessing the activity of NK cells in PBMCs and expanded NK cells against K562 cells and various types of hematologic cancer cells.
Endothelial cell regulation of matrix metalloproteinases (2005)

The process of sprouting angiogenesis requires that the endothelial cells degrade the basement membrane matrix and migrate into the interstitial matrix. Matrix metalloproteinases are enzymes capable of cleaving numerous extracellular matrix proteins. Increased production and activity of matrix metalloproteinases in any cell type is associated with a more migratory and invasive phenotype. This paper describes results of recent in-vitro studies of the regulation of transcription and activation of MMP-2 and MT1-MMP in endothelial cells, as well as studies that examined roles of matrix metalloproteinases in activity-induced angiogenesis.
Influence of sex and disease severity on gene expression profiles in individuals with idiopathic pulmonary fibrosis. (2014)

Epidemiological studies suggest sex-specific trends in the prevalence and mortality of idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) that are distinct for each disease. While the expression of numerous immune and extracellular matrix (ECM) genes in the lung have been well characterized in these diseases, associations elucidating their sex-specific expression patterns by disease type and severity, and the evaluation of hormone-related genes, have not been well studied. Here we performed targeted transcriptional profiling of 48 genes was performed on lung tissue samples from males and females with mild or medium severity IPF or COPD. The genes assessed included those involved in inflammation, ECM remodeling and hormonal processes. Data for 36 lung tissue samples were obtained that were stratified by disease and sex. Expression levels revealed a subset of genes which show differential expression among sexes, disease type, and disease severity. The most significant observations were the increased expression primarily of ECM genes in medium severity IPF (CATHK, COL1A1, COL3, MMP1, MMP7, IL-1RN) compared to mild IPF and COPD. Two genes, CH3L1 and MMP7 showed a tendency of interaction between sex and disease in IPF severity. Surprisingly, there were no significant differences in any of the sex genes measured between the IPF groups; however, ESR1 and AR expression levels were higher and lower, respectively, compared to COPD samples. Overall, this work highlights two genes, CH3L1 and MMP7, that may contribute to gender trends observed for IPF and COPD and are potential targets for future research.
Alignment layers with variable anchoring strengths from Polyvinyl Alcohol (2012)

In the study of polyvinyl alcohol (PVA) alignment layers for liquid crystal devices, we found that the anchoring strength can be greatly varied by changing the alignment film thickness. Both the polar and azimuthal anchoring strengths increased with increasing film thickness; however, they had different film thickness dependences. It was also noticed that the quartic term in the expansion of the Rapini-Papoular anchoring energy was important for describing the polar anchoring. In the experiment, solid PVA was dissolved in a thinner and spin-coated on glass substrates to create alignment layers. The substrates were assembled to make electrically-controlled birefringence liquid crystal cells. The polar anchoring strength of the alignment layer was measured using the high field method and the azimuthal anchoring strength using the twist angle method.
Strong and Selective Glomerular Localization of CD134 Ligand and TNF Receptor-1 in Proliferative Lupus Nephritis (2000)

CD134 (OX40) is a member of the tumor necrosis factor (TNF) receptor (TNFR) family that can be expressed on activated T lymphocytes. Interaction between CD134 and its ligand (CD134L) is involved in costimulation of T and B lymphocyte activation, and in T cell adhesion to endothelium. To examine the possible role of this interaction in the pathogenesis of systemic lupus erythematosus (SLE), expression of CD134 and CD134L on peripheral blood leukocytes was studied, and no significant differences between SLE patients and control individuals were found. Immunohistology on renal biopsies from patients with lupus nephritis or other renal disorders, using a recombinant human CD134-containing chimeric molecule to detect CD134L, demonstrated the abundant presence of CD134L in all cases of proliferative lupus nephritis in a granular distribution predominantly along the epithelial side of the glomerular capillary wall. Confocal laser scanning microscopy indicated colocalization with subepithelial immune deposits. In none of the other renal disorders examined, including nonproliferative forms of lupus nephritis, was glomerular staining for CD134L detected in a similar pattern. Endothelial CD134L expression was frequently observed in different types of vasculitis. CD134 was detected on perivascular infiltrating leukocytes and on part of the tubular epithelium, but not on glomerular resident cells. Immunohistology for several other TNF(R) family members revealed in proliferative lupus nephritis a similar distribution for TNFR1 as was observed for CD134L. In contrast, glomerular expression of TNFR2 was similar in all cases examined. The glomerular presence of CD134L and TNFR1 in proliferative lupus nephritis in association with subepithelial immune deposits may be of pathogenetic significance and have diagnostic value.
Iron Oxide Nanoparticles Grafted with Sulfonated Copolymers are Stable in Concentrated Brine at Elevated Temperatures and Weakly Adsorb on Silica (2013)

Magnetic nanoparticles that can be transported in subsurface reservoirs at high salinities and temperatures are expected to have a major impact on enhanced oil recovery, carbon dioxide sequestration, and electromagnetic imaging. Herein we report a rare example of steric stabilization of iron oxide (IO) nanoparticles (NPs) grafted with poly(2-acrylamido-2-methylpropanesulfonate-co-acrylic acid) (poly(AMPS-co-AA)) that not only display colloidal stability in standard American Petroleum Institute (API) brine (8% NaCl + 2% CaCl2 by weight) at 90 °C for 1 month but also resist undesirable adsorption on silica surfaces (0.4% monolayer NPs). Because the AMPS groups interacted weakly with Ca(2+), they were sufficiently well solvated to provide steric stabilization. The PAA groups, in contrast, enabled covalent grafting of the poly(AMPS-co-AA) chains to amine-functionalized IO NPs via formation of amide bonds and prevented polymer desorption even after a 40,000-fold dilution. The aforementioned methodology may be readily adapted to stabilize a variety of other functional inorganic and organic NPs at high salinities and temperatures.
Receptor-transporting Protein 1 Short (RTP1S) Mediates Translocation and Activation of Odorant Receptors by Acting through Multiple Steps (2012)

Odorant receptor (OR) proteins are retained in the endoplasmic reticulum when heterologously expressed in cultured cells of non-olfactory origins. RTP1S is an accessory protein to mammalian ORs and facilitates their trafficking to the cell-surface membrane and ligand-induced responses in heterologous cells. The mechanism by which RTP1S promotes the functional expression of ORs remains poorly understood. To obtain a better understanding of the role(s) of RTP1S, we performed a series of structure-function analyses of RTP1S in HEK293T cells. By constructing RTP1S deletion and chimera series and subsequently introducing single-site mutations into the protein, we found the N terminus of RTP1S is important for the endoplasmic reticulum exit of ORs and that a middle region of RTP1S is important for OR trafficking from the Golgi to the membrane. Using sucrose gradient centrifugation, we found that the localization of RTP1S to the lipid raft microdomain is critical to the activation of ORs. Finally, in a protein-protein interaction analysis, we determined that the C terminus of RTP1S may be interacting with ORs. These findings provide new insights into the distinct roles of RTP1S in OR translocation and activation.
Community acquired bacterial meningitis in Cuba: a follow up of a decade (2010)

The results of the National Program for Control and Prevention of the Neurological Infectious Syndrome evidenced a reduction of the BM incidence, but not the CFR. Multivariate analysis identified an association of mortality with some societal groups as well as with S. pneumoniae.
Cost-effective depolarized diode pump unit designed for C-band flat-gain Raman amplifiers to control EDFA gain profile (2002)

A cost-effective pumping unit with only two depolarized pump LDs for C-band flat-gain Raman amplifiers is proposed. The Raman gain in DCF is applied to simultaneously control the overall gain and gain flatness of an in-line EDFA.