gebhart/patrepeval huggingface dataset:
The murine haemopexin receptor. Evidence that the haemopexin-binding site resides on a 20 kDa subunit and that receptor recycling is regulated by protein kinase C (1991)

Haemopexin receptors from mouse hepatoma (Hepa) cells were affinity-labelled by cross-linking to haem-125I-haemopexin complexes using two homo-[disuccinimidyl suberate (DSS) and 3,3'-dithiobis(succinimidyl propionate) (DTSSP)] and one hetero-[sulphosuccinimidyl 4-(p-maleimidophenyl)butyrate (sulpho-SMPB)] bifunctional cross-linking agents. Analysis of the cross-linked products by SDS/PAGE in the absence of reducing agents revealed that 125I-haemopexin was cross-linked specifically to a protein of apparent molecular mass 85-90 kDa. Upon reduction, haemopexin remained cross-linked to a protein of 20 kDa, suggesting that the murine haemopexin receptor has a subunit structure. Two subunits were identified: alpha (p65) and beta (p20). Furthermore, because haemopexin was cross-linked by all three agents to p20, the shortest cross-linker arm being 1.1 nm (11 A), we propose that the haem-haemopexin-binding site resides on this subunit. In addition, a cysteine residue of p20 is located near the haemopexin-binding site, since haemopexin, which has no free thiol groups, is cross-linked to this subunit by the hetero-bifunctional agent sulpho-SMPB. Exposure of Hepa cells to the tumour-promoting phorbol ester 4 alpha-phorbol 12-myristate 13-acetate (PMA) causes a rapid redistribution of haemopexin receptors from the cell surface to the cell interior. Within 2-4 min of incubation with 100 nM-PMA, there was an approx. 50% decrease in cell-surface haemopexin receptors, as judged by ligand binding at 0 degrees C and affinity labelling of the receptor. This time- and dose-dependent down-regulation was fully reversible within 60-90 min after removal of PMA, and the affinity of the remaining receptors was unaltered by PMA. The specificity of PMA was demonstrated by comparison with the non-tumour-promoter 4 alpha-phorbol, which did not affect any of the parameters examined. The amine H-7, a specific inhibitor of protein kinase C, antagonised the receptor redistribution effect of PMA, suggesting that the down-regulation of haemopexin receptors on the cell surface was a consequence of protein kinase C activation. The PMA-induced decrease in surface haemopexin receptors was due to a 2-fold increase in the rate of internalization (from 0.73 min-1 to 1.32 min-1), whereas the rate of exocytosis (0.6 min-1) was unchanged. PMA treatment, like binding of the natural ligand, haem-haemopexin, results in a lower steady-state level of surface haemopexin receptors independent of receptor synthesis, and the receptors were not degraded but were recycled back to the cell surface.
The meaning of graylevels in backscattered electron images of bone (1993)

Backscattered electron (BSE) imaging is considered to be a useful technique for determining relative differences in bone tissue density. However, it is not clear how graylevel variations seen in BSE images of bone tissue, which are primarily dependent on the tissue's average atomic number, correlate to tissue density (g/cm3) and mineral content. Simulated bone tissues, ranging from 32-50% mineral by volume, were made by mixing synthetic hydroxyapatite with a simulated organic matrix. This technique allowed mineral content to be varied while mineral composition and crystallography remained constant. The densities of the simulated tissues were determined using Archimedes' principle. Average atomic numbers of the simulated tissues were interpolated from a regression of BSE graylevel against average atomic numbers of pure standard materials. A strong positive correlation was found to exist between mineral content and density (r2 = 0.978) as well as between mineral content and atomic number (r2 = 0.965). The average graylevel in the BSE image also exhibited a positive correlation to mineral content (r2 = 0.965) and density (r2 = 0.923). Graylevel variations in BSE images of simulated bone tissue were shown to be strongly correlated to density and mineral content, but only as a coincidence of their association with atomic number.
Spin Transfer Magnetization Switching Read/Write Cycle Test in MgO-Based Magnetic Tunnel Junctions (2007)

We present the results of spin transfer torque magnetization switching results for some MgO-based magnetic tunnel junctions (MTJ) with tunneling magnetoresistance (TMR) ratios of 38.6% to 200% and critical current densities of 1.032 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> down to 1.68 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . We observed 2.2 times 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> stable read/write (R/W) cycles before failure under the spin transfer torque magnetization switching. The synchronized variations in both high and low magnetoresistance (MR) over the stable R/W cycles indicate that magnetization reversal into either high or low state occurs in parallel. We made a stability analysis for high and low MR distribution matching to a normalized fraction of stable cycles.
TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal (2017)

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. <i>Cancer Res; 77(21); e111-4. ©2017 AACR</i>.
Automating Procedures for Processing, Cryopreservation, Storage, and Manipulation of Human Peripheral Blood Mononuclear Cells (2004)

Cell-mediated immune responses have been found to play a crucial role in the protection from, or amelioration of, many human diseases. There are many vaccine trials being conducted where the most important immune assessment consists of measuring T cell responses. The most readily accessible source of T cells is the peripheral blood. Thus, collection, processing, cryopreservation, storage, and manipulation of human peripheral blood mononuclear cells (PBMCs) are all key steps for assessment of vaccine and disease-induced immune responses. Automation of these procedures is not currently practiced widely. This article reviews current practices and explores the need for automation.
Kinetics and correlation analysis of reactivity in oxidation of organic sulfides by hexamethylenetetramine–bromine (2000)

The oxidation of organic sulfides by hexamethylenetetramine–bromine (HABR) to the corresponding sulfoxides is first order with respect to HABR. Michaelis–Menten-type kinetics were observed with respect to the sulfide. It is proposed that HABR itself is the oxidizing species. Correlation analyses of the rate of the oxidation of 34 sulfides were performed in terms of various single and multiparametric equations. The best correlation was obtained with Charton's LDR and LDRS equations, the polar regression coefficients being negative. The oxidation of alkyl phenyl sulfides exhibited a very good correlation in terms of the Pavelich–Taft equation. A mechanism involving the formation of a halosulfonium cation in the slow step is proposed. Copyright © 2000 John Wiley & Sons, Ltd.
GRIF-1 and OIP106, Members of a Novel Gene Family of Coiled-Coil Domain Proteins (2005)

Gamma-aminobutyric acid(A) receptor-interacting factor (GRIF-1) is a 913-amino acid protein proposed to function as a GABA(A) receptor beta(2) subunit-interacting, trafficking protein. GRIF-1 shares approximately 44% amino acid sequence identity with O-linked N-acetylglucosamine transferase interacting protein 106, OIP106. Both proteins contain predicted coiled-coil domains and probably constitute a novel gene family. The Drosophila orthologue of this family of proteins may be Milton. Milton shares approximately 44% amino acid homology with GRIF-1. Milton is proposed to function in kinesin-mediated transport of mitochondria to nerve terminals. We report here that GRIF-1 and OIP106 also associate with kinesin and mitochondria. Following expression in human embryonic kidney 293 cells, both GRIF-1 and OIP106 were shown by co-immunoprecipitation to be specifically associated with an endogenous kinesin heavy chain species of 115 kDa and exogenous KIF5C. Association of GRIF-1 with kinesin was also evident in native brain and heart tissue. In the brain, anti-GRIF-1-(8-633) antibodies specifically co-immunoprecipitated two kinesin-immunoreactive species with molecular masses of 118 and 115 kDa, and in the heart, one kinesin-immunoreactive species, 115 kDa, was immunoprecipitated. Further studies revealed that GRIF-1 was predominantly associated with KIF5A in the brain and with KIF5B in both the heart and in HEK 293 cells. Yeast two-hybrid interaction assays and immunoprecipitations showed that GRIF-1 associated directly with KIF5C with the GRIF-1/KIF5C interaction domain localized to GRIF-1-(124-283). These results further support a role for GRIF-1 and OIP106 in protein and/or organelle transport in excitable cells in a manner analogous to glutamate receptor-interacting-protein 1, in the motor-dependent transport of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate glutamate excitatory neurotransmitter receptors to dendrites.
Choline is a Selective Agonist of α7 Nicotinic Acetylcholine Receptors in the Rat Brain Neurons (1997)

In the present study, we demonstrate that choline, a precursor of acetylcholine (ACh) and a product of acetylcholine hydrolysis by acetylcholinesterase (AChE), acts as an efficient and relatively selective agonist of alpha7-containing nicotinic acetylcholine receptors (nAChR) in neurons cultured from the rat hippocampus, olfactory bulb and thalamus as well as in PC12 cells. Choline was able to activate postsynaptic and presynaptic alpha7 nAChRs, with the latter action resulting in the release of other neurotransmitters. Although choline was approximately one order of magnitude less potent than ACh (EC50 of 1.6 mM for choline and 0.13 mM for ACh), it acted as a full agonist at alpha7 nAChRs. In contrast, choline did not activate alpha4beta2 agonist-bearing nAChRs on hippocampal neurons, and acted as a partial agonist at alpha3beta4-containing nAChRs on PC12 cells. The ethyl alcohol moiety of choline is required for the selective action on alpha7 nAChR. Exposure of cultured hippocampal neurons for 10 min to choline (10-100 microM) resulted in desensitization of the native alpha7 nAChRs. Moreover, chronic exposure (10 days) of the cultured hippocampal neurons to a desensitizing concentration of choline (approximately 30 microM) decreased their responsiveness to ACh. The selective action of choline on native alpha7 nAChRs suggests that this naturally occurring compound may act in vivo as an endogenous ligand for these receptors. Putative physiological actions of choline include retrograde messenger activity during the development of the mammalian central nervous system and during periods of elevated synaptic activity that leads to long-term potentiation.
Structure–Kinetic Relationships—An Overlooked Parameter in Hit-to-Lead Optimization: A Case of Cyclopentylamines as Chemokine Receptor 2 Antagonists (2013)

Preclinical models of inflammatory diseases (e.g., neuropathic pain, rheumatoid arthritis, and multiple sclerosis) have pointed to a critical role of the chemokine receptor 2 (CCR2) and chemokine ligand 2 (CCL2). However, one of the biggest problems of high-affinity inhibitors of CCR2 is their lack of efficacy in clinical trials. We report a new approach for the design of high-affinity and long-residence-time CCR2 antagonists. We developed a new competition association assay for CCR2, which allows us to investigate the relation of the structure of the ligand and its receptor residence time [i.e., structure-kinetic relationship (SKR)] next to a traditional structure-affinity relationship (SAR). By applying combined knowledge of SAR and SKR, we were able to re-evaluate the hit-to-lead process of cyclopentylamines as CCR2 antagonists. Affinity-based optimization yielded compound 1 with good binding (Ki = 6.8 nM) but very short residence time (2.4 min). However, when the optimization was also based on residence time, the hit-to-lead process yielded compound 22a, a new high-affinity CCR2 antagonist (3.6 nM), with a residence time of 135 min.
Stromal-epithelial interactions in aging and cancer: senescent fibroblasts alter epithelial cell differentiation (2005)

Cellular senescence suppresses cancer by arresting cells at risk of malignant tumorigenesis. However, senescent cells also secrete molecules that can stimulate premalignant cells to proliferate and form tumors, suggesting the senescence response is antagonistically pleiotropic. We show that premalignant mammary epithelial cells exposed to senescent human fibroblasts in mice irreversibly lose differentiated properties, become invasive and undergo full malignant transformation. Moreover, using cultured mouse or human fibroblasts and non-malignant breast epithelial cells, we show that senescent fibroblasts disrupt epithelial alveolar morphogenesis, functional differentiation and branching morphogenesis. Furthermore, we identify MMP-3 as the major factor responsible for the effects of senescent fibroblasts on branching morphogenesis. Our findings support the idea that senescent cells contribute to age-related pathology, including cancer, and describe a new property of senescent fibroblasts - the ability to alter epithelial differentiation - that might also explain the loss of tissue function and organization that is a hallmark of aging.
Kinetic Mechanism and Enantioselectivity of Halohydrin Dehalogenase from Agrobacterium radiobacter (2003)

Halohydrin dehalogenase (HheC) from Agrobacterium radiobacter AD1 catalyzes the reversible intramolecular nucleophilic displacement of a halogen by a hydroxyl group in vicinal haloalcohols, producing the corresponding epoxides. The enzyme displays high enantioselectivity toward some aromatic halohydrins. To understand the kinetic mechanism and enantioselectivity of the enzyme, steady-state and pre-steady-state kinetic analysis was performed with p-nitro-2-bromo-1-phenylethanol (PNSHH) as a model substrate. Steady-state kinetic analyses indicated that the k(cat) of the enzyme with the (R)-enantiomer (22 s(-1)) is 3-fold higher than with the (S)-enantiomer and that the K(m) for the (R)-enantiomer (0.009 mM) is about 45-fold lower than that for the (S)-enantiomer, resulting in a high enantiopreference for the (R)-enantiomer. Product inhibition studies revealed that HheC follows an ordered Uni Bi mechanism for both enantiomers, with halide as the first product to be released. To identify the rate-limiting step in the catalytic cycle, pre-steady-state experiments were performed using stopped-flow and rapid-quench methods. The results revealed the existence of a pre-steady-state burst phase during conversion of (R)-PNSHH, whereas no such burst was observed with the (S)-enantiomer. This indicates that a product release step is rate-limiting for the (R)-enantiomer but not for the (S)-enantiomer. This was further examined by doing single-turnover experiments, which revealed that during conversion of the (R)-enantiomer the rate of bromide release is 21 s(-1). Furthermore, multiple turnover analyses showed that the binding of (R)-PNSHH is a rapid equilibrium step and that the rate of formation of product ternary complex is 380 s(-1). Taken together, these findings enabled the formulation of an ordered Uni Bi kinetic mechanism for the conversion of (R)-PNSHH by HheC in which all of the rate constants are obtained. The high enantiopreference for the (R)-enantiomer can be explained by weak substrate binding of the (S)-enantiomer and a lower rate of reaction at the active site.
Identification and Optimization of Regeneration Conditions for Affinity-Based Biosensor Assays. A Multivariate Cocktail Approach (1999)

A general regeneration, identification, and optimization (RO) protocol for Biacore systems was developed. The RO protocol uses six multi-ingredient stock solutions that represent the six most common chemical properties employed as regeneration agents. The regeneration effect of different regeneration cocktails of these six stock solutions were tested iteratively until a satisfactory result was obtained. The RO protocol was designed with an ease-of-use and multivariate approach. The RO protocol was tested on 13 different antibody-antigen systems. For 10 of these, only the first screening session was tested. For 9 of the 13 systems, the RO-protocol screening session identified cocktails that removed more than 90% of the bound analyte in a 30 s pulse. For 5 systems, the RO protocol identified cocktails that regenerated the surface completely and that were more gentle than previously used regeneration conditions. Furthermore, the regeneration optimization results can be interpreted as a characterization of the interacting molecules. The relevance of testing cocktails was justified by the fact that at least one cocktail was significantly better than all diluted stock solutions for all tested model systems. By using the multivariate approach, the risk of missing relevant combinations of stock solutions was minimized. This resulted in an unexpected discovery of excellent properties of EDTA as an additive in regeneration cocktails containing chaotropic agents and ions in high concentration.
Sugar Uptake and Transport in Rice Embryo. Expression of Companion Cell-Specific Sucrose Transporter (OsSUT1) Induced by Sugar and Light (2000)

We investigated sugar uptake and transport in rice (Oryza sativa) embryo during grain germination. Endogenous sugar levels, accumulation of starch granules, and gene expression of a rice sucrose transporter (OsSUT1) were examined using rice embryos germinated with or without exogenous sugar supply. Starch granules remarkably accumulated in the cells around vascular bundles as a consequence of the sugar taken up by the embryos, indicating that the taken-up sugars are transiently converted into starch. In situ detection for OsSUT1 mRNA indicated its localization in the phloem companion cells. Furthermore, northern-blot and in situ hybridization analyses showed that OsSUT1 expression is not detectable in embryos subjected to sugar starvation conditions, whereas its expression is enhanced by an increased endogenous sugar level. Overall results indicate that the expression of companion cell-specific sucrose transporter, OsSUT1 is regulated by the endogenous sugar status as well as light exposure.
Azathioprine and 6-Mercaptopurine in Crohn Disease (1995)

Azathioprine and 6-mercaptopurine are effective in treating active Crohn disease and in maintaining remission. Cumulative dose was an important factor in predicting response. Adverse effects were more common among patients receiving therapy.
Electronic Textiles: Wearable Computers, Reactive Fashion, and Soft Computation (2005)

Electronic textiles, also referred to as smart fabrics, are quite fashionable right now. Their close relationship with the field of computer wearables gives us many diverging research directions and possible definitions. On one end of the spectrum, there are pragmatic applications such as military research into interactive camouflage or textiles that can heal wounded soldiers. On the other end of the spectrum, work is being done by artists and designers in the area of reactive clothes: “second skins” that can adapt to the environment and to the individual. Fashion, health, and telecommunication industries are also pursuing the vision of clothing that can express aspects of people's personalities, needs, and desires or augment social dynamics through the use and display of aggregate social information.In my current production-based research, I develop enabling technology for electronic textiles based upon my theoretical evaluation of the historical and cultural modalities of textiles as they relate to future computational forms. My work involves the use of conductive yarns and fibers for power delivery, communication, and networking, as well as new materials for display that use electronic ink, nitinol, and thermochromic pigments. The textiles are created using traditional textile manufacturing techniques: spinning conductive yarns, weaving, knitting, embroidering, sewing, and printing with inks.
Expression of a calpastatin transgene slows muscle wasting and obviates changes in myosin isoform expression during murine muscle disuse (2002)

Muscle wasting is a prominent feature of several systemic diseases, neurological damage and muscle disuse. The contribution of calpain proteases to muscle wasting in any instance of muscle injury or disease has remained unknown because of the inability to specifically perturb calpain activity in vivo. We have generated a transgenic mouse with muscle-specific overexpression of calpastatin, which is the endogenous inhibitor of calpains, and induced muscle atrophy by unloading hindlimb musculature for 10 days. Expression of the transgene resulted in increases in calpastatin concentration in muscle by 30- to 50-fold, and eliminated all calpain activity that was detectable on zymograms. Muscle fibres in ambulatory, transgenic mice were smaller in diameter, but more numerous, so that muscle mass did not differ between transgenic and non-transgenic mice. This is consistent with the role of the calpain-calpastatin system in muscle cell fusion that has been observed in vitro. Overexpression of calpastatin reduced muscle atrophy by 30 % during the 10 day unloading period. In addition, calpastatin overexpression completely prevented the shift in myofibrillar myosin content from slow to fast isoforms, which normally occurs in muscle unloading. These findings indicate that therapeutics directed toward regulating the calpain-calpastatin system may be beneficial in preventing muscle mass loss in muscle injury and disease.