gebhart/patrepeval huggingface dataset:
Porcine Thyroid Peroxidase: Relationship between the Native Enzyme and an Active, Highly Purified Tryptic Fragment (1988)

We previously described the preparation of highly purified porcine thyroid peroxidase by a procedure that involved initial solubilization of the enzyme with trypsin plus detergent. Recently, the complete amino acid sequence of porcine thyroid peroxidase (TPO) was determined by cDNA cloning, and it became of interest to compare the structure of the purified trypsin-solubilized enzyme with that of the native enzyme. For this purpose we employed antibodies to the purified enzyme and to two synthetic peptides representing defined regions of the protein. We also obtained N-terminal amino acid sequence data on TPO fragments separated by gel electrophoresis. Trypsin cleavage sites in the purified enzyme were observed after arg residues 109 and 561, and also at two undetermined sites close to the putative membrane spanning region at the carboxyl end. Major fragments of approximately 60, 32, and 29 kilodaltons were observed when the purified enzyme was subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions. This observation is explained by assuming that the cleavage site after arg residue 561 occurred within a disulfide loop. The Mr of the trypsin-solubilized enzyme is approximately 88,000 compared to approximately 106,000 for the native enzyme. The difference can be accounted for by the loss of approximately 90 residues from the amino terminus and of at least 80 residues from the carboxyl end. Despite the loss of these fragments totaling approximately 18 kilodaltons and cleavage of the peptide bond after arg residue 561, the purified trypsin-solubilized TPO appears to retain full enzyme activity.
Biofunctionalized Gadolinium-Containing Prussian Blue Nanoparticles as Multimodal Molecular Imaging Agents (2013)

Molecular imaging agents enable the visualization of phenomena with cellular and subcellular level resolutions and therefore have enormous potential in improving disease diagnosis and therapy assessment. In this article, we describe the synthesis, characterization, and demonstration of core-shell, biofunctionalized, gadolinium-containing Prussian blue nanoparticles as multimodal molecular imaging agents. Our multimodal nanoparticles combine the advantages of MRI and fluorescence. The core of our nanoparticles consists of a Prussian blue lattice with gadolinium ions located within the lattice interstices that confer high relaxivity to the nanoparticles providing MRI contrast. The relaxivities of our nanoparticles are nearly nine times those observed for the clinically used Magnevist. The nanoparticle MRI core is biofunctionalized with a layer of fluorescently labeled avidin that enables fluorescence imaging. Biotinylated antibodies are attached to the surface avidin and confer molecular specificity to the nanoparticles by targeting cell-specific biomarkers. We demonstrate our nanoparticles as multimodal molecular imaging agents in an in vitro model consisting of a mixture of eosinophilic cells and squamous epithelial cells. Our nanoparticles specifically detect eosinophilic cells and not squamous epithelial cells, via both fluorescence imaging and MRI in vitro. These results suggest the potential of our biofunctionalized Prussian blue nanoparticles as multimodal molecular imaging agents in vivo.
Interior-Point Methods for Massive Support Vector Machines (2002)

We investigate the use of interior-point methods for solving quadratic programming problems with a small number of linear constraints, where the quadratic term consists of a low-rank update to a positive semidefinite matrix. Several formulations of the support vector machine fit into this category. An interesting feature of these particular problems is the volume of data, which can lead to quadratic programs with between 10 and 100 million variables and, if written explicitly, a dense Q matrix. Our code is based on OOQP, an object-oriented interior-point code, with the linear algebra specialized for the support vector machine application. For the targeted massive problems, all of the data is stored out of core and we overlap computation and input/output to reduce overhead. Results are reported for several linear support vector machine formulations demonstrating that the method is reliable and scalable.
Sexual experience alters D1 receptor–mediated cyclic AMP production in the nucleus accumbens of female Syrian hamsters (2004)

Drugs of abuse produce long-term changes in dopamine neurotransmission and receptor-effected intracellular signaling. Similar changes in neuronal activity are mediated by motivated behaviors. To explore cellular mechanisms underlying these neuroadaptations following sexual experience, cyclic AMP accumulation following stimulation of D1 dopamine receptors, G-proteins, and adenylate cyclase was compared in the nucleus accumbens and caudate nucleus of sexually naive and experienced female hamsters following sexual behavior. Direct stimulation of adenylate cyclase with forskolin or indirectly by activation of G-proteins with Gpp(NH)p produced dose-dependent increases in the formation of cyclic AMP in the nucleus accumbens and caudate nucleus, with no effects of sexual experience on these measures. Specific D1 receptor stimulation increased Gpp(NH)p-induced adenylate cyclase activity in the nucleus accumbens and caudate nucleus of all animals. Interestingly, this stimulation was further enhanced only in membranes from the nucleus accumbens, but not from the caudate nucleus, of sexually experienced hamsters compared to the response of naive females. These results demonstrate that sexual behavior experience can sensitize mesolimbic dopamine pathways and that this sensitization occurs through an increase in D1 receptor-mediated signaling.
Chiral Scars in Chaotic Dirac Fermion Systems (2013)

Do relativistic quantum scars in classically chaotic systems possess unique features that are not shared by nonrelativistic quantum scars? We report a class of relativistic quantum scars in massless Dirac fermion systems whose phases return to the original values or acquire a 2π change only after circulating twice about some classical unstable periodic orbits. We name such scars chiral scars, the successful identification of which has been facilitated tremendously by our development of an analytic, conformal-mapping-based method to calculate an unprecedentedly large number of eigenstates with high accuracy. Our semiclassical theory indicates that the physical origin of chiral scars can be attributed to a combined effect of chirality intrinsic to massless Dirac fermions and the geometry of the underlying classical orbit.
Bioinspired superhydrophobic surfaces: From molecule to materials (2015)

International audience
Synthesis and Antitumor Activity of C-7-Alkynylated and Arylated Pyrrolotriazine C-Ribonucleosides (2020)

A number of biologically active nucleoside analogues contain the adenine isostere 4-amino-pyrrolo[2,1-<i>f</i>][1,2,4]triazine connected to various sugar moieties through a C-C anomeric linkage. We employed palladium-catalyzed cross-coupling chemistry to promptly functionalize the 7-position of such a heterocyclic scaffold with various alkynyl and aryl groups starting from a common 7-iodo-pyrrolotriazine C-ribonucleoside intermediate. Analogues bearing a 7-cyclopropyl-, 7-propyl-, and 7-butylacetylene moiety displayed potent cytotoxic activity, with the latest being the most selective of this series toward cancer cells. Further insights revealed that such C-nucleosides could exert their antiproliferative action by causing dose-dependent DNA damage.
Three-Dimensional Reconstruction for Medical-CAD Modeling (2005)

Reverse engineering, the process of obtaining a geometric CAD model from measurements obtained by scanning an existing physical model, is widely used in numerous applications, such as manufacturing, industrial design and jewellery design and reproduction.For creating editable CAD models meant for manufacturing we identify that it is more appropriate to use feature-based constraint-based representations, since they capture plausible design intent.We propose this type of model representation for reverse engineering 3D point clouds of jewellery objects.In this paper we propose an approach for reverse engineering of jewellery combining skeleton construction, feature and constraint information exploitation to obtain a more robust and accurate CAD model.First we automatically construct the skeleton of the point cloud.Constraints are automatically detected based on the skeleton and then an iterative interactive process is carried out, during which features are fitted to the point cloud according to constraints.A voxel inspired technique is also employed to describe repeated patterns common to various types of traditional jewellery.
INHIBITION-BASED BIOSENSORS FOR THE DETECTION OF ENVIRONMENTAL CONTAMINANTS: DETERMINATION OF 2,4-DICHLOROPHENOXYACETIC ACID (2000)

In this work data are reported on the possibility for detection of environmental contaminants endowed with toxic effects by specifically designed electrochemical biosensors. A new bienzymatic inhibition biosensor based on the combined catalytic activity of the enzymes alkaline phosphatase and glucose oxidase is proposed and discussed for the direct determination of 2,4-dichlorophenoxyacetic acid (2,4-D), one of the most powerful and diffused defoliants, which also is endowed with estrogenic properties. A discussion on the different approaches followed to manage the experimental data obtained by enzymatic inhibition biosensors is also presented.
Human Growth Hormone: Additional Members of the Complex* (1979)

The use of urea during electrophoretic analysis of human GH (hGH) permitted detection of two previously undetected forms of the hormone. The newly recognized components were resolved at pH 10 and 7.8 but not at pH 4. Because they migrated more slowly than the major hGH component, the forms have been denoted as Slow-slow-GH and Slow-GH. They have molecular weights near 22,000 and are neither electrophoretic artifacts nor proteolytically cleaved forms. By RIA, Slowslow-GH and Slow-GH have been found to produce displacements similar to that observed with reference hGH (NIH). Both forms had growth-promoting activity (1.8 IU/mg) in the rat tibial line assay and both resembled hGH by peptide mapping and total amino acid composition. Slow-GH had definite lactogenic activity in the pigeon crop sac assay, with a suggestion that it was somewhat more active than the hGH from which it was removed. A third form of hGH was detected when the gel electrophoresis was done at pH 7.8 with or without urea. This component was denoted as Fast-GH because it migrated just slightly ahead of the major band. At pH 10, the component migrated with the major hGH band and, therefore, could not be detected. The molecular weight of Fast-GH was near 22,000 and there was no evidence of its being an enzymically cleaved form. RIA has indicated that Fast-GH is essentially as active as hGH (NIH). Tibial line assay gave a potency of 2.0 IU/mg. Peptide mapping indicated a great similarity to hGH but no free amino-terminal group could be detected. These studies bring to five the number of intact (proteolytically uncleaved) forms of hGH that can be detected in currently available preparations of hGH. The results support the view that hGH is a complex of substances and suggest that the multiple actions of GH may be in part a result of this heterogeneity. Proteolytic conversion of each of the new forms to two-chain forms is a further possibility.
Trade unions and immigrant workers (1974)

(1974). Trade unions and immigrant workers. Journal of Ethnic and Migration Studies: Vol. 4, No. 1, pp. 19-36.
A Functionally Stable RuMn Electrocatalyst for Oxygen Evolution Reaction in Acid (2022)

Abstract Proton exchange membrane water electrolysis (PEMWE) is a key technology to solve the serious energy and environmental problems. However, the poor durability of electrocatalysts in acidic oxygen evolution reaction (OER) environment hinders the large‐scale application of PEMWE. Herein, a robust RuMn electrochemical catalyst with a remarkable durability within 20 000 cyclic voltammetry cycles is reported. Furthermore, RuMn is stable for 720 h at 10 mA cm –2 current density in 0.5 M H 2 SO 4 solution with &lt;100 mV overpotential increase, outperforming the most electrocatalysts reported to date, by far. An amorphous RuO x shell is detected after the OER test, indicating a surface reconstruction process on the catalyst that inhibits steady‐state dissolution. Further study demonstrates that the excellent durability of RuMn realized by protective RuO x can be attributed to strong bond strength of Ru, which is supported by density functional theory calculations with high dissolution voltage. Thus, improving the bond strength of Ru extends the design strategy for the Ru‐based alloy catalysts with considerable stability.
Identification of novel macrolides with antibacterial, anti-inflammatory and type I and III IFN-augmenting activity in airway epithelium (2016)

The data support the idea that macrolides have antiviral properties through a mechanism that is yet to be ascertained. We also provide evidence that macrolides can be developed with anti-inflammatory, antibacterial and antiviral activity and show surprising versatility depending on the clinical need.
Power calculations for preclinical studies using a K-sample rank test and the Lehmann alternative hypothesis (2005)

Power calculations in a small sample comparative study, with a continuous outcome measure, are typically undertaken using the asymptotic distribution of the test statistic. When the sample size is small, this asymptotic result can be a poor approximation. An alternative approach, using a rank based test statistic, is an exact power calculation. When the number of groups is greater than two, the number of calculations required to perform an exact power calculation is prohibitive. To reduce the computational burden, a Monte Carlo resampling procedure is used to approximate the exact power function of a k-sample rank test statistic under the family of Lehmann alternative hypotheses. The motivating example for this approach is the design of animal studies, where the number of animals per group is typically small.
Graftings of End-alkoxysilylated Poly (styrene) s onto Inorganic Pigments and Dispersibility of the Grafted Pigments (1992)

末端にイソプロポキシシリル基やトリエトキシシリル基を有するポリスチレンの末端基を酸もしくは塩基触媒を用いて加水分解し, シリカおよびアルミナ表面へのグラフト化を試みた。酸性表面を有するシリカの場合にはn-ブチルリン酸が, 塩基性表面を有するアルミナの場合にはテトラブチルアンモニウムヒドロキシドが加水分解触媒として有効に働いた。これらのポリマーで処理されたシリカは, 主鎖中にランダムにトリエトキシシリル基を有するポリスチレンやトリメチルシリル基で処理されたシリカに比べて, トルエン溶液中やポリスチレンのトルエン溶液中において良好な分散性を示した。
Characterization of the groESL Operon in Listeria monocytogenes : Utilization of Two Reporter Systems ( gfp and hly ) for Evaluating In Vivo Expression (2001)

The ability of intracellular pathogens to sense and adapt to the hostile environment of the host is an important factor governing virulence. We have sequenced the operon encoding the major heat shock proteins GroES and GroEL in the gram-positive food-borne pathogen Listeria monocytogenes. The operon has a conserved orientation in the order groES groEL. Upstream of groES and in the opposite orientation is a gene encoding a homologue of the Bacillus subtilis protein YdiL, while downstream of groEL is a gene encoding a putative bile hydrolase. We used both reverse transcriptase-PCR (RT-PCR) and transcriptional fusions to the UV-optimized Aequorea victoria green fluorescent protein (GFP(UV)) to analyze expression of groESL under various environmental stress conditions, including heat shock, ethanol stress, and acid shock, and during infection of J774 mouse macrophage cells. Strains harboring GFP(UV) transcriptional fusions to the promoter region of groESL demonstrated a significant increase in fluorescence following heat shock that was detected by both fluorimetry and fluorescence microscopy. Using both RT-PCR and GFP technology we detected expression of groESL following internalization by J774 cells. Increased intracellular expression of dnaK was also determined using RT-PCR. We have recently described a system which utilizes L. monocytogenes hemolysin as an in vivo reporter of gene expression within the host cell phagosome (C. G. M. Gahan and C. Hill, Mol. Microbiol. 36:498-507, 2000). In this study a strain was constructed in which hemolysin expression was placed under the control of the groESL promoter. In this strain hemolysin expression during infection also confirms transcription from the groESL promoter during J774 and murine infection, albeit at lower levels than the known virulence factor plcA.
Construction of His6-Protein A/PEG Co-Immobilized Surface for High-Performance Protein Sensing (2007)

Development of the biointerface for high performance immuno-sensing methods is one of the cmrent research topics in analytical chemistty and biochemistty. We developed histidine-tagged protein A (His6-protein A)/poly(ethylene glycol) (PEG) eo-immobilized gold surface as a new class of immuno-sensor chip, where both protein A and PEG are directly immobilized on the surface by the histidine-tag and the thiol group, respectively. In this study, the resulting surface was applied to sandwich assay for specific protein detection based on surface plasmon resonance measurements. Despite the similar content of immobilized antibodies, the amount of secondmy antibody on His6-protein A/PEG surface was about eight times higher than that of physically adsorbed antibody/PEG surface. In addition, nonspecific protein absorption was extremely suppressed on His6-protein A/PEG surface, compared with Ni 2 + -nitrilotriacetic acid (NT A) surface, which was generally used for the immobilization of histidine-tagged proteins. These results clearly indicate that effective orientation of the immobilized antibody with the prevention of non-specific adsorption was achieved on the His6-protein A/PEG surface.
Self‐Adjusting Metal–Organic Framework for Efficient Capture of Trace Xenon and Krypton (2022)

Abstract The capture of the xenon and krypton from nuclear reprocessing off‐gas is essential to the treatment of radioactive waste. Although various porous materials have been employed to capture Xe and Kr, the development of high‐performance adsorbents capable of trapping Xe/Kr at very low partial pressure as in the nuclear reprocessing off‐gas conditions remains challenging. Herein, we report a self‐adjusting metal‐organic framework based on multiple weak binding interactions to capture trace Xe and Kr from the nuclear reprocessing off‐gas. The self‐adjusting behavior of ATC‐Cu and its mechanism have been visualized by the in‐situ single‐crystal X‐ray diffraction studies and theoretical calculations. The self‐adjusting behavior endows ATC‐Cu unprecedented uptake capacities of 2.65 and 0.52 mmol g −1 for Xe and Kr respectively at 0.1 bar and 298 K, as well as the record Xe capture capability from the nuclear reprocessing off‐gas. Our work not only provides a benchmark Xe adsorbent but proposes a new route to construct smart materials for efficient separations.
Fully Intermolecular Nickel-Catalyzed Three-Component Couplings via Internal Redox (2007)

Two distinct nickel-catalyzed fully intermolecular three-component couplings are described. The catalytic addition of enals, alkynes, and alcohols provides γ,δ-unsaturated esters, whereas the catalytic addition of enones, alkynes, and aldehydes provides stereodefined, unsymmetrical 2-allyl-1,3-diketones. An internal redox process allows the reactions to proceed in the absence of reducing agents. On the basis of deuterium-labeling studies, a likely mechanistic pathway is proposed.
The full-ORF clone resource of the German cDNA Consortium (2007)

The German cDNA Consortium ORFeome resource currently consists of more than 3,800 sequence-verified entry clones representing ORFs, cloned with and without stop codon, for about 1,700 different gene loci. 177 splice variants were cloned representing 121 of these genes. The entry clones have been used to generate over 5,000 different expression constructs, providing the basis for functional profiling applications. As a member of the recently formed international ORFeome collaboration we substantially contribute to generating and providing a whole genome human ORFeome collection in a unique cloning system that is made freely available in the community.
Neurosteroid Access to the GABAAReceptor (2005)

GABAA receptors are a pivotal inhibitory influence in the nervous system, and modulators of the GABAA receptor are important anesthetics, sedatives, anticonvulsants, and anxiolytics. Current views of receptor modulation suggest that many exogenous drugs access and bind to an extracellular receptor domain. Using novel synthetic steroid analogs, we examined the access route for neuroactive steroids, potent GABAA receptor modulators also produced endogenously. Tight-seal recordings, in which direct aqueous drug access to receptor was prevented, demonstrated that steroids can reach the receptor either through plasma membrane lateral diffusion or through intracellular routes. A fluorescent neuroactive steroid accumulated intracellularly, but recordings from excised patches indicated that the intracellular reservoir is not necessary for receptor modulation, although it can apparently equilibrate with the plasma membrane within seconds. A membrane impermeant neuroactive steroid modulated receptor activity only when applied to the inner membrane leaflet, demonstrating that the steroid does not access an extracellular modulatory site. Thus, neuroactive steroids do not require direct aqueous access to the receptor, and membrane accumulation is required for receptor modulation.
Comparison of sandwich and fingers-crossing type WO3/BiVO4 multilayer heterojunctions for photoelectrochemical water oxidation (2016)

Sandwich and fingers-crossing type WO<sub>3</sub>/BiVO<sub>4</sub> multilayer heterojunctions were fabricated to investigate the influence of the junction structure on their photoelectrochemical performances.
Toward solving the etiological mystery of primary biliary cholangitis (2017)

Primary biliary cholangitis (PBC) is considered a model autoimmune disease due to its signature AMA autoantibody, female predominance and relatively specific portal infiltration and cholestasis. The identification and cloning of the major mitochondrial autoantigens, recognized by AMA, have served as an immunologic platform to identify the earliest events involved in loss of tolerance. Despite the relative high concordance rate in identical twins, genome wide association studies have not proven clinically useful and have led to suggestions of epigenetic events. To understand the natural history and etiology of PBC, several murine models have been developed including spontaneous models, models induced by chemical xenobiotic immunization and by "designer" mice with altered interferon metabolism. Herein, we describe five such models including 1) NOD.c3c4 mice, 2) dominant negative form of transforming growth factor (TGF)-<i>β</i> receptor type II (dnTGF<i>β</i>RII) mice, 3) interleukin (IL)-2R<i>α</i><sup>-/-</sup> mice 4) ARE Del<sup>-/-</sup>mice and 5) 2-octynoic acid conjugated bovine serum albumin (2OA-BSA) immunized mice. Individually there is no perfect murine model but collectively the models point to loss of tolerance to PDC-D2, the major mitochondrial autoantigen, as the earliest event that occurs before clinical disease is manifest. Although there is no direct association of AMA titer and PBC disease progression it is noteworthy that the triad of PBC monocytes, biliary apotopes and AMA leads to an intense proinflammatory cytokine burst. Further the recurrence of PBC after liver transplantation indicates that, due to MHC restriction, disease activity must include not only adaptive immunity but also innate immune mechanisms. We postulate that successful treatment of PBC may require a personalized approach with therapies designed for different stages of disease.