gebhart/patrepeval huggingface dataset:
Heparan sulfate proteoglycans from mouse mammary epithelial cells. Cell surface proteoglycan as a receptor for interstitial collagens. (1985)

A heparan sulfate-rich proteoglycan is on the surface of NMuMG mouse mammary epithelial cells apparently intercalated into their plasma membranes. Mild treatment of the cells with trypsin releases the GAG-bearing region (ectodomain) of this molecule as a discrete proteoglycan which is readily purified. At physiological pH and ionic strength, the ectodomain binds collagen types I, III, and V but not types II, IV, or denatured type I. The proteoglycan binds to a single class of high affinity saturable sites on type I collagen fibrils, sites which are selective for heparin-like glycosaminoglycans. The binding of NMuMG cells to type I collagen duplicates that of their cell surface proteoglycan; cells bind to native but not denatured collagen, and binding is inhibited by heparin but not by other glycosaminoglycans. These binding properties suggest that cell surface heparan sulfate proteoglycans could act as receptors for interstitial collagens and mediate changes in cell behavior induced by collagenous matrices.
Nitric oxide synthase activity from a hematophagous insect salivary gland (1993)

The salivary glands of the hematophagous insect, Rhodnius prolixus, contain a nitrosylhemeprotein that dissociates its ligand, NO, to the host tissues while the insect is searching for a blood meal. We now report a salivary nitric oxide synthase activity in this insect. The activity is dependent on NADPH, FAD, tetrahydrobiopterin, calmodulin, Ca2+, and converts arginine to citrulline while producing vasorelaxing activity. Molecular sieving indicates a molecular weight of 185 kDa, coeluting with a diaphorase activity. Results indicate similarity of this insect activity to the vertebrate constitutive NO synthase, suggesting NO synthesis is an evolutionary old biological pathway.
Neogenin Interacts with Hemojuvelin through Its Two Membrane-Proximal Fibronectin Type III Domains (2008)

Hemojuvelin is a recently identified iron-regulatory protein that plays an important role in affecting the expression of hepcidin, a key iron regulatory hormone. Although the underlying mechanism of this process is not clear, several hemojuvelin-binding proteins, including the cell surface receptor neogenin and bone morphogenetic protein (BMP) cytokines, have been identified. The ectodomain of neogenin is composed of four immunoglobulin-like (Ig) domains followed by six fibronectin type III-like (FNIII) domains. Here we report expression of soluble versions of hemojuvelin and neogenin for biochemical characterization of their interaction and the interaction of HJV with BMP-2. Hemojuvelin normally undergoes an autocatalytic cleavage, and as in vivo, recombinant hemojuvelin exists as a mixture of cleaved and uncleaved forms. Neogenin binds to cleaved and noncleaved hemojuvelin, as verified by its binding to an uncleaved mutant hemojuvelin. We localized the hemojuvelin binding site on neogenin to the membrane-proximal fifth and sixth FNIII domains and the juxtamembrane linker and showed that a fragment containing only this region binds 2-3 orders of magnitude more tightly than the entire neogenin ectodomain. Binding to the most membrane-proximal region of neogenin may play a role in regulating the levels of soluble and membrane-bound forms of hemojuvelin, which in turn would influence the amount of free BMP-2 available for binding to its receptors and triggering transcription of the hepcidin gene. Our finding that BMP-2 and neogenin bind simultaneously to hemojuvelin raises the possibility that neogenin is part of a multiprotein complex at the hepatocyte membrane involving BMP, its receptors, and hemojuvelin.
The Bcl-Xl Inhibitor, ABT-737, Efficiently Induces Apoptosis and Suppresses Growth of Hepatoma Cells in Combination with Sorafenib (2010)

Bcl-xL inactivation by ABT-737 in combination with sorafenib was found to be safe and effective for anti-HCC therapy in preclinical models. Direct activation of the apoptosis machinery seems to unlock the antitumor potential of oncogenic kinase inhibitors and may produce durable clinical responses against HCC.
CDX2 regulation by the RNA-binding protein MEX3A: impact on intestinal differentiation and stemness (2013)

The homeobox transcription factor CDX2 plays a crucial role in intestinal cell fate specification, both during normal development and in tumorigenic processes involving intestinal reprogramming. The CDX2 regulatory network is intricate, but it has not yet been fully uncovered. Through genome-wide screening of a 3D culture system, the RNA-binding protein MEX3A was identified as putatively involved in CDX2 regulation; therefore, its biological relevance was addressed by setting up cell-based assays together with expression studies in murine intestine. We demonstrate here that MEX3A has a repressive function by controlling CDX2 levels in gastric and colorectal cellular models. This is dependent on the interaction with a specific binding determinant present in CDX2 mRNA 3'untranslated region. We have further determined that MEX3A impairs intestinal differentiation and cellular polarization, affects cell cycle progression and promotes increased expression of intestinal stem cell markers, namely LGR5, BMI1 and MSI1. Finally, we show that MEX3A is expressed in mouse intestine, supporting an in vivo context for interaction with CDX2 and modulation of stem cell properties. Therefore, we describe a novel CDX2 post-transcriptional regulatory mechanism, through the RNA-binding protein MEX3A, with a major impact in intestinal differentiation, polarity and stemness, likely contributing to intestinal homeostasis and carcinogenesis.
High resolution two-dimensional protein gel evidence of differential gene expression during Entamoeba encystation. (1992)

As an initial step of investigation into the regulatory mechanisms of encystation in Entamoeba, we compared the protein profiles of newly formed cysts and trophozoites of E. invadens using high resolution two-dimensional PAGE and digitized video image analysis of silver stained gels. A total of 155 proteins unique to trophozoites and a total of 72 proteins unique to cysts were detected. Five of the most prominent cyst specific proteins were identified as candidates for further study. These results imply that extensive changes in gene expression accompany the progression of this parasite through its life cycle.
Combination of fluorescence microscopy and nanomotion detection to characterize bacteria (2013)

Antibiotic-resistant pathogens are a major health concern in everyday clinical practice. Because their detection by conventional microbial techniques requires minimally 24 h, some of us have recently introduced a nanomechanical sensor, which can reveal motion at the nanoscale. By monitoring the fluctuations of the sensor, this technique can evidence the presence of bacteria and their susceptibility to antibiotics in less than 1 h. Their amplitude correlates to the metabolism of the bacteria and is a powerful tool to characterize these microorganisms at low densities. This technique is new and calls for an effort to optimize its protocol and determine its limits. Indeed, many questions remain unanswered, such as the detection limits or the correlation between the bacterial distribution on the sensor and the detection's output. In this work, we couple fluorescence microscopy to the nanomotion investigation to determine the optimal experimental protocols and to highlight the effect of the different bacterial distributions on the sensor.
Synthesis of trans-3,4-Dimethyl-4-(3-hydroxyphenyl)piperidine Opioid Antagonists:  Application of the Cis-Thermal Elimination of Carbonates to Alkaloid Synthesis (1996)

Improved syntheses of twotrans-3,4-dimethyl-4-(3-hydroxyphenyl)piperidine opioid antagonists from 1,3-dimethyl-4-piperidinone are described. The 1,3-dimethyl-4-arylpiperidinol 23 was selectively dehydrated in a two step process to the 1,3-dimethyl-4-aryl-1,2,3,6-tetrahydropyridine 26 by the cis-thermal elimination of the corresponding alkyl carbonate derivative at 190 degrees C. In the presence of a basic nitrogen, the success of the elimination was found to be critically dependent upon the nature of the carbonate alkyl group, with Et, i-Bu, and i-Pr being preferred (90% yield). Alkylation of the metalloenamine, formed by deprotonation of 26 with n-BuLi, proceeded regio- and stereospecifically to give the trans-3,4-dimethyl-4-aryl-1,2,3,4-tetrahydropyridine 27, which was converted in three steps to the common intermediate, (3R,4R)-3,4-dimethyl-4-(3-hydroxyphenyl)piperidine. LY255582, a centrally-active opioid antagonist, and LY246736-dihydrate, a peripherally-active opioid antagonist, were prepared from 1,3-dimethyl-4-piperidinone in 11.8% yield (8 steps) and 6.2% yield (12 steps), respectively.
Direct Patterning and Spontaneous Self-Assembly of Graphene Oxide via Electrohydrodynamic Jet Printing for Energy Storage and Sensing (2019)

The macroscopic assembly of two-dimensional materials into a laminar structure has received considerable attention because it improves both the mechanical and chemical properties of the original materials. However, conventional manufacturing methods have certain limitations in that they require a high temperature process, use toxic solvents, and are considerably time consuming. Here, we present a new system for the self-assembly of layer-by-layer (LBL) graphene oxide (GO) via an electrohydrodynamic (EHD) jet printing technique. During printing, the orientation of GO flakes can be controlled by the velocity distribution of liquid jet and electric field-induced alignment spontaneously. Closely-packed GO patterns with an ordered laminar structure can be rapidly realized using an interfacial assembly process on the substrates. The surface roughness and electrical conductivity of the LBL structure were significantly improved compared with conventional dispensing methods. We further applied this technique to fabricate a reduced graphene oxide (r-GO)-based supercapacitor and a three-dimensional (3D) metallic grid hybrid ammonia sensor. We present the EHD-assisted assembly of laminar r-GO structures as a new platform for preparing high-performance energy storage devices and sensors.
In Vitro and In Vivo Comparison of Two Suprachoroidal Shunts (2013)

In a rabbit model, suprachoroidal polypropylene and gold shunts allow access to a new drainage pathway with different IOP profiles that can be modified with antifibrotics.
631. Catalytic hydroxylation of unsaturated compounds (1949)

M. Mugdan and D. P. Young, J. Chem. Soc., 1949, 2988 DOI: 10.1039/JR9490002988
On Foundation and Construction of Physical Unclonable Functions. (2010)

Physical Unclonable Functions (PUFs) have been introduced as a new cryptographic prim-itive, and whilst a large number of PUF designs and applications have been proposed, few studies has been undertaken on the theoretical foundation of PUFs. At the same time, many PUF designs have been found to be insecure, raising questions about their design methodol-ogy. Moreover, PUFs with efficient implementation are needed to enable many applications in practice. In this paper, we present novel results on the theoretical foundation and practical construc-tion for PUFs. First, we prove that, for an ℓ-bit-input and 푚-bit-output PUF containing 푛 silicon components, if 푛 &amp;lt; 푚2 ℓ 푐 where 푐 is a constant, then 1) the PUF cannot be a random function, and 2) confusion and diffusion are necessary for the PUF to be a pseudorandom func-tion. Then, we propose a helper data algorithm (HDA) that is secure against active attacks and significantly reduces PUF implementation overhead compared to previous HDAs. Finally, we integrate PUF construction into block cipher design to implement an efficient physical un-clonable pseudorandom permutation (PUPRP); to the best of our knowledge, this is the first practical PUPRP using an integrated approach. 1
Miniproteins as Phage Display-Scaffolds for Clinical Applications (2011)

Miniproteins are currently developed as alternative, non-immunoglobin proteins for the generation of novel binding motifs. Miniproteins are rigid scaffolds that are stabilised by alpha-helices, beta-sheets and disulfide-constrained secondary structural elements. They are tolerant to multiple amino acid substitutions, which allow for the integration of a randomised affinity function into the stably folded framework. These properties classify miniprotein scaffolds as promising tools for lead structure generation using phage display technologies. Owing to their high enzymatic resistance and structural stability, miniproteins are ideal templates to display binding epitopes for medical applications in vivo. This review summarises the characteristics and the engineering of miniproteins as a novel class of scaffolds to generate of alternative binding agents using phage display screening. Moreover, recent developments for therapeutic and especially diagnostic applications of miniproteins are reviewed.
Recognition of Hyaluronan Released in Sterile Injury Involves a Unique Receptor Complex Dependent on Toll-like Receptor 4, CD44, and MD-2 (2007)

Inflammation under sterile conditions is not well understood despite its importance in trauma and autoimmune disease. To investigate this process we established mouse models of sterile injury and explored the role of hyaluronan in mediating inflammation following injury. The response of cultured monocytes to hyaluronan was different than the response to lipopolysaccharide (LPS) despite both being dependent on Toll-like receptor 4 (TLR4). Cultured cells exposed to hyaluronan showed a pattern of gene induction that mimics the response seen in mouse skin after sterile injury with an increase in molecules such as transforming growth factor-beta2 and matrix metalloproteinase-13. These factors were not induced by LPS despite the mutual dependence of both hyaluronan and LPS on TLR4. Explanation for the unique response to hyaluronan was provided by observations that a lack of TLR4 or CD44 in mice diminished the response to sterile injury, and together with MD-2, was required for responsiveness to hyaluronan in vitro. Thus, a unique complex of TLR4, MD-2, and CD44 recognizes hyaluronan. Immunoprecipitation experiments confirmed the physical association of TLR4 and CD44. Taken together, our results define a previously unknown mechanism for initiation of sterile inflammation that involves recognition of released hyaluronan fragments as an endogenous signal of tissue injury.
Broadband nonvolatile photonic switching based on optical phase change materials: beyond the classical figure-of-merit (2017)

In this Letter, we propose a broadband, nonvolatile on-chip switch design in the telecommunication C-band with record low loss and crosstalk. The unprecedented device performance builds on: 1) a new optical phase change material (O-PCM) Ge<sub>2</sub>Sb<sub>2</sub>Se<sub>4</sub>Te<sub>1</sub> (GSST), which exhibits significantly reduced optical attenuation compared to traditional O-PCMs, and 2) a nonperturbative design that enables low-loss device operation beyond the classical figure-of-merit (FOM) limit. We further demonstrate that the 1-by-2 and 2-by-2 switches can serve as basic building blocks to construct nonblocking and nonvolatile on-chip switching fabric supporting arbitrary numbers of input and output ports.
Spatial Coupling of mTOR and Autophagy Augments Secretory Phenotypes (2011)

Protein synthesis and autophagic degradation are regulated in an opposite manner by mammalian target of rapamycin (mTOR), whereas under certain conditions it would be beneficial if they occurred in unison to handle rapid protein turnover. We observed a distinct cellular compartment at the trans side of the Golgi apparatus, the TOR-autophagy spatial coupling compartment (TASCC), where (auto)lysosomes and mTOR accumulated during Ras-induced senescence. mTOR recruitment to the TASCC was amino acid- and Rag guanosine triphosphatase-dependent, and disruption of mTOR localization to the TASCC suppressed interleukin-6/8 synthesis. TASCC formation was observed during macrophage differentiation and in glomerular podocytes; both displayed increased protein secretion. The spatial coupling of cells' catabolic and anabolic machinery could augment their respective functions and facilitate the mass synthesis of secretory proteins.
Semiological Value of ABCDE Criteria in the Diagnosis of Cutaneous Pigmented Tumors (1998)

The so-called ABCD criteria have a good semiological value in the differential diagnosis of pigmented tumors. Addition of an E criterion for enlargement optimizes sensitivity and specificity of diagnosis.
Relationship of serum sex‐steroid hormones and prostate volume in African American men (2002)

Circulating serum levels of SHBG and endogenous sex-steroid hormones are correlated with prostate volume and potentially impact the natural history of BPH. However, longitudinal studies are needed to demonstrate the temporal relationships of hormones and growth factors in the pathogenesis of BPH in AA men.
Effect of ferrous and ferric chelators on transferrin‐iron‐macrophage interactions (1988)

A study was done to evaluate the effect of ferrous and ferric chelators on the interaction between transferrin-iron and cultured human blood monocytes. This interaction has been previously shown to involve a specific receptor and vesicle protonation. Transferrin-iron uptake was significantly inhibited by the hydrophobic ferrous chelator 2,2' bipyridine, and the inhibition was shown not to be a consequence of the mobilisation of intracellular iron by the chelator. Chase experiments and prolonged incubation studies suggested that the chelator prevented the iron released from transferrin from negotiating the unit membrane. The iron and transferrin then appeared to be returned independently to the incubation medium. In contrast, a hydrophilic ferrin chelator, desferrioxamine, had only a very modest effect on the interaction. These findings are compatible with the hypothesis that transferrin-iron is reduced to the ferrous state during its uptake by the culture human blood monocyte.
Isolation and characterization of a novel extracellular metalloprotease from Bacillus subtilis (1990)

We have isolated and characterized two minor extracellular proteases from culture supernatants of a strain of Bacillus subtilis containing deletion mutations of the genes for the extracellular proteases subtilisin (apr) and neutral protease (npr) and a minor extracellular protease (epr) as well as intracellular serine protease-I (isp-1). Characterization studies have revealed that one of these enzymes is the previously described protease bacillopeptidase F. The second enzyme, the subject of this report, is a novel metalloprotease, which we designate Mpr. Mpr is a unique metalloprotease that has been purified to apparent homogeneity by using both conventional and high-performance liquid chromatography procedures. Mpr has a molecular mass of approximately 28 kilodaltons on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and a basic isoelectric point of 8.7. The enzyme showed maximal activity against azocoll at pH 7.5 and 50 degrees C. Mpr was inhibited by dithiothreitol and a combination of beta-mercaptoethanol and EDTA. Activity was moderately inhibited by beta-mercaptoethanol and EDTA alone as well as by cysteine and citrate and only marginally by phosphoramidon 1,10-phenanthroline and N-[N-(L-3-trans-carboxyoxiran-2-carbonyl)-L-leucyl]-agmatine. Mpr was not inhibited by phenylmethylsulfonyl fluoride. In addition, Mpr showed esterolytic but not collagenolytic activities. Our studies suggest that Mpr is a secreted metalloprotease containing cysteine residues that are required for maximal activity.
Alveolysin, the thiol-activated toxin of Bacillus alvei, is homologous to listeriolysin O, perfringolysin O, pneumolysin, and streptolysin O and contains a single cysteine (1990)

The gene coding for alveolysin, the thiol-activated toxin produced by Bacillus alvei, has been cloned by means of an oligonucleotide based on the known N-terminal sequence of the secreted protein. The complete nucleotide sequence of the gene has been determined. The deduced amino acid sequence of alveolysin shows that alveolysin shares homologies with listeriolysin O, perfringolysin O, pneumolysin, and streptolysin O. Alveolysin, like the other members of the family, contains a single cysteine in the conserved peptide sequence ECTGLA WEWWR.
Oxidation of aniline and other primary aromatic amines by manganese dioxide (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidation of aniline and other primary aromatic amines by manganese dioxideShonali Laha and Richard G. LuthyCite this: Environ. Sci. Technol. 1990, 24, 3, 363–373Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/es00073a012https://doi.org/10.1021/es00073a012research-articleACS PublicationsRequest reuse permissionsArticle Views3335Altmetric-Citations277LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing (1976)

Valyl-tRNA synthetase from Bacillus stearothermophilus activates thereonine and forms a 1:1 complex with threonyl adenylate, but it does not catalyze the net formation of threonyl-tRNAVal at pH 7.78 and 25 degrees C in the quenched flow apparatus it decomposes at a rate constant of 36s-1. During this process there is a transient formation of Thr-tRNAVal reaching a maximum at 25 ms and rapidly falling to zero after 150 ms. At the peak, 22% of the (14C) threonine from the complex is present as (14C) Thr-tRNA. The reaction may be quenched with phenol and the partially mischarged tRNA isolated. The enzyme catalyzes its hydrolysis with a rate constant of 40s-1. The data fit a kinetic scheme in which 62% of the threonine from the threonyl adenylate is transferred to the tRNA. This may be compared with the rate constant of 12s-1 at which 84% of the valine is transferred to tRNAVal from the enzyme-bound valyl adenylate, and the rate constant of 0.015s-1 for the subsequent hydrolysis of Val-tRNAVal. Inhibition studies indicate a distinct second site for hydrolysis. The translocation of the aminoacyl moiety between the two sites could be mediated by a transfer between the 2'-and 3'-OH groups of the terminal adenosine fo the tRNA. The hyperspecificity of the enzyme is based on discriminating between the two competing substrates twice: once against the undesired substrate in the synthetic step, and once against the desired substrate in the destructive step.