gebhart/patrepeval huggingface dataset:
The Bone Extracellular Matrix in Bone Formation and Regeneration (2020)

Bone regeneration repairs bone tissue lost due to trauma, fractures, and tumors, or absent due to congenital disorders. The extracellular matrix (ECM) is an intricate dynamic bio-environment with precisely regulated mechanical and biochemical properties. In bone, ECMs are involved in regulating cell adhesion, proliferation, and responses to growth factors, differentiation, and ultimately, the functional characteristics of the mature bone. Bone ECM can induce the production of new bone by osteoblast-lineage cells, such as MSCs, osteoblasts, and osteocytes and the absorption of bone by osteoclasts. With the rapid development of bone regenerative medicine, the osteoinductive, osteoconductive, and osteogenic potential of ECM-based scaffolds has attracted increasing attention. ECM-based scaffolds for bone tissue engineering can be divided into two types, that is, ECM-modified biomaterial scaffold and decellularized ECM scaffold. Tissue engineering strategies that utilize the functional ECM are superior at guiding the formation of specific tissues at the implantation site. In this review, we provide an overview of the function of various types of bone ECMs in bone tissue and their regulation roles in the behaviors of osteoblast-lineage cells and osteoclasts. We also summarize the application of bone ECM in bone repair and regeneration. A better understanding of the role of bone ECM in guiding cellular behavior and tissue function is essential for its future applications in bone repair and regenerative medicine.
The genomic binding sites of a noncoding RNA (2011)

Long noncoding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed capture hybridization analysis of RNA targets (CHART), a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly cross-linked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from flies and humans. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the male-specific lethal complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to chromatin immunoprecipitation for proteins.
Pt−Ag Catalysts as Cathode Material for Oxygen-Depolarized Electrodes in Hydrochloric Acid Electrolysis (2010)

Pt-Ag nanoparticles were prepared on a glassy carbon (GC) surface by pulsed electrodeposition and tested using cyclic voltammetry and scanning electrochemical microscopy (SECM) with respect to their possible use as catalyst material for oxygen reduction in 400 mM HCl solution. For comparison, a Pt catalyst was investigated under similar conditions. The redox competition mode of scanning electrochemical microscopy (RC-SECM) was adapted to the specific conditions caused by the presence of Cl(-) ions and used to visualize the local catalytic activity of the Pt-Ag deposits. Similarly prepared Pt deposits were shown to dissolve underneath the SECM tip. Pt-Ag composites showed improved long-term stability toward oxygen reduction as compared with Pt even under multiple switching off to open-circuit potential in 400 mM HCl.
No association between Glu/Asp polymorphism of <i>NOS3</i> gene and ischemic stroke (1999)

Endothelial nitric oxide synthase (NOS3) gene has been shown to modulate the degree of cerebral ischemia following stroke in animal models and is thus a candidate genetic risk factor for stroke. We compared 265 ischemic stroke cases with 293 controls and found no difference in distribution of the common structural variant Glu/Asp in codon 298 of exon 7 in the NOS3 gene. Our data do not support the hypothesis that NOS3 is a genetic risk factor for stroke.
Micromachining of {111} plates in [001] oriented silicon (1998)

There are basically two ways to etch silicon: dry and wet chemical etching. In micromachining, the control of the shape of the structure is accomplished by anisotropic etching through mask openings. The anisotropy of wet chemical etching is related to the crystal structure of silicon, while that of dry etching stems from the momentum of ions impinging the substrate. The latter gives us much more freedom of design, however, the control of dry etching is much more cumbersome and the equipment much more expensive. Therefore, any new process trick to increase the number of geometries that can be obtained by wet chemical anisotropic etching is of interest. In this paper, techniques are demonstrated to etch thin {111} plates in 〈100〉 silicon. These plates can be used as building blocks in, for example, microfluidic systems for valves and pumps. All micromaching processes described in this paper are accomplished in 25 wt% KOH at 78 ◦C.
Global roaming and personal mobility with COPS architecture in SuperDHLR (2002)

Personal mobility removes the fixed association between a terminal and a user (a characteristic of traditional fixed and mobile networks), thereby adding one more degree of mobility on top of terminal mobility. Global roaming allows a user to roam in communication networks of different technologies. These two mobility options provide users with ubiquitous services across networks of different types. This paper identifies the technical challenges to achieving global roaming and personal mobility. We propose common operations (COPS) architecture to allow effective multiprotocol support and efficient protocol interworking among disparate networks and compare it with other approaches. SuperDHLR embodies the COPS architecture. It keeps track of user location, manages user profiles for multiple networks, and incorporates service logic for global roaming. It serves as a home location register (HLR) for wireless networks and a mobility management server for Internet protocol (IP) networks. SuperDHLR enables terminal and user mobility and facilitates seamless roaming across circuit and packet switched wireless networks, the Internet and wireline networks.
The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models (2015)

The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation.
Accelerated learning in layered neural networks (1988)

Abst ract . Learning in layered neu ral networks is posed as the mini­ miz at ion of an error function defined over t he training set. A proba­ bilistic interpretation of the target act ivities sugges ts th e use of rela­ t ive entro py as an error measure. We investigate t he merits of using this error function over t he traditional quad ratic function for gradient descent learni ng. Com parative numerical sim ulations for the conrf­ guity problem show marked redu ct ion s in learn ing t imes. This im ­ provement is explained in terms of the characteristic steepness of the landscape defined by the error function in configuration space.
2D‐DIGE proteomic characterization of head and neck squamous cell carcinoma (2009)

Downregulation of cornulin is a prominent feature of the molecular signature of HNSCC identified by comparative proteomics. Cornulin may represent a link between HNSCC and other pathologies arising in stratified squamous epithelium.
Effect of pravastatin on body composition and markers of cardiovascular disease in HIV-infected men—a randomized, placebo-controlled study (2006)

Despite limited effects on cholesterol, 12 weeks use of pravastatin 40 mg each night in HIV-infected men with hypercholesterolaemia resulted in significant increases in subcutaneous fat.
Characterization of an antiserum to guinea pig antithrombin III (AT III). I. Reactivity with guinea pig T lymphocytes. (1981)

In the course of studies investigating the effects of antisera prepared against a variety of guinea pig proteins on lymphocyte function, a goat antiserum prepared against a guinea pig gamma-globulin preparation was found to react with guinea pig T lymphocytes. This antiserum, serum 592, contained a significant titer of antibodies that were cytotoxic for a subpopulation of lymph node cells and thymocytes, and mitogenic for lymph node T cells. Immunoelectrophoretic analysis and selective absorptions of the antiserum demonstrated that the antigen recognized on thymocytes was also present on an alpha 2 globulin in guinea pig plasma, which, on the basis of physiochemical characteristics and heparin-binding affinity, appeared to be guinea pig antithrombin III (AT III). Although the antiserum was shown to contain antibodies to both protein and carbohydrate determinants on the AT III molecule, studies comparing the effects of 7 M guanidine and periodate oxidation on the antigenicity of the AT III determinant also recognized on the thymocytes indicated that this shared antigenic determinant was carbohydrate in nature. The thymocyte membrane molecule bearing this determinant was also isolated and was found to be a 210,000-dalton macromolecule that was very sensitive to proteolytic and/or autolytic degradation. These data raise the interesting possibility that guinea pig lymphoid cells may have a membrane-associated protease inhibitor related to plasma AT III.
Roughness improvement and hardness enhancement in nanoscale Al/AlN multilayered thin films (1997)

Al/AlN multilayered thin films with periodic thickness λ less than 24 nm were developed by ion beam assisted deposition. A considerably small surface roughness comparable to that of the silicon substrate and much smaller than those of both monolithic Al and AlN films was obtained. Over the investigated range of λ, all the multilayers are harder than the homogeneous AlN film, and a significant hardness enhancement by a factor of ∼2 over that of the AlN film was observed in the multilayer with λ of 6 nm. Moreover, the hardness enhancement is not at the expense of the multilayer toughness, with the multilayer Al/AlN films showing improved plasticity as compared with the AlN film.
2,3-Diphosphoglycerate Phosphatase from Human Erythrocytes (1970)

Abstract 2,3-Diphosphoglycerate phosphatase has been purified from human red blood cells. It has been separated from phosphoglycerate mutase and acid phosphatase. The reaction catalyzed is 2,3-PGA + H2O → 3-PGA + Pi. In the absence of activators, 1 mµmole of substrate can be converted to products per min at 37° by enzyme from 1 ml of packed cells. The activity is increased by certain anions. There is activation by chloride or phosphate individually, which is enhanced by the simultaneous presence of both anions. In the presence of 0.1 m chloride, phosphate activates with a Ka of 0.7 mm. Fluoride or bromide, but not iodide, and bicarbonate can substitute for chloride. Anions that can substitute for phosphate and activate in the presence of chloride include arsenate, fluorophosphate, and sulfite. The most potent activator found is glycolate-2-P which can give a 1600-fold stimulation. In the presence of this activator, chloride is an inhibitor with respect to glycolate-2-P. Phosphate is a competitive inhibitor with respect to glycolate-2-P and the inhibition is related to the square of the phosphate concentration. The monophosphoglycerates are competitive inhibitors with respect to phosphate with enzyme activated by phosphate and chloride with a Ki of 3 µm. Monophosphoglycerates are competitive with respect to glycolate-2-P with enzyme activated by glycolate-2-P and chloride with a Ki of 2 µm. Glycine or taurine (at high pH) or pyrophosphate are activators in the presence of which there is inhibition by chloride. The Km of 2,3-diphosphoglycerate depends on the conditions of activation, varying from 0.08 µm with phosphate and 0.1 m chloride activation to 25 µm with glycolate-2-P and 0.1 m chloride. The apparent Vmax varies over a 500-fold range. Phosphoglycerate increases the Km of 2,3-PGA and inhibits with a Ki of 6 µm. The maximal velocity of the enzyme is obtained at pH 6.4 with either phosphate and chloride or glycolate-2-P as activators. With fluorophosphate and chloride, the optimum rate is at pH 6. It is suggested that the phosphate and phosphoglycerate levels are important for determining the rate of hydrolysis of 2,3-diphosphoglycerate in the human red blood cell.
A New Read Channel Model for Patterned Media Storage (2007)

It is conceivable that early generations of patterned media will utilize read heads whose dimensions are several times larger than an "island" of magnetization. For such a scenario, we propose a "multiple islands per read head" model where the output from the read head is a function of the magnetization from several independently written tracks of islands. In particular, we focus on a "3 islands per read head" model where the output from the read head is a function of the magnetization from three independently written tracks of islands. The readback signal is determined from a finite track-width magnetoresistive (MR) head model using reciprocity calculations, and two noise sources - island position jitter and AWGN electronics noise - are considered. By sampling the noisy signal at intervals corresponding to the down-track island separation, we obtain a discrete-time readback channel model whose performance is obtained under maximum-likelihood sequence detection.
A Metadata Management Method Base on Directory Path Code (2014)

Metadata distribution is important in mass storage system. Sub-tree partition and hash are two traditional metadata distribution algorithms used in file system. But they both have a defect in system scalability. This paper presents a new metadata management method, Directory Path Code Hash (DPCH). This method is to store directory and file metadata separately, and effectively solving the unbalanced metadata distribution and access hot point problems in Sub-tree partition and the excessive reading times and large metadata migration amount after directory property modification in hash algorithm. The experiment indicates that this method proposed significantly outweighs other algorithms in terms of throughput rate, metadata distribution, reading times, etc.
Chemistry of epoxy compounds. XXI. Reaction of potassium cyanate with epoxides (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of epoxy compounds. XXI. Reaction of potassium cyanate with epoxidesMartin E. Dyen and Daniel SwernCite this: J. Org. Chem. 1968, 33, 1, 379–384Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://pubs.acs.org/doi/10.1021/jo01265a076https://doi.org/10.1021/jo01265a076research-articleACS PublicationsRequest reuse permissionsArticle Views347Altmetric-Citations11LEARN 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
A Materials Engineering Technology Approach to Alloy Design (2007)

Materials engineers use published properties of commercial alloys, laboratory data, and computational models to develop metal alloys. In recent decades, computer modeling has focused on predicting the compositions of solid phases in alloy systems from thermodynamic data (CALPHAD). Houerer, a broader range of materials properties can be predicted using a "materials engineering technology" approach instead of a "materials science" approach. These materials properties include liquidus and solidus temperatures, thermal and electrical conductivity, and color The materials technology approach is based on prior work by Zotos, which used mnltirariable linear regression. 'The proposed method uses a spreadsheet to calculate the coefficients of a mullirariable polynomial regression equation. Next, an alloy design program uses the regression equation recursively to predict the properties of all possible alloys within a search field. Results are sorted according to the target properly range. One benefit of using a spreadsheet is that a small company or educational institution with limited resources can develop and run its own alloy property prediction program at relatively low cost. Unlike commercially-available phase diagram prediction software, this method can be applied to any composition-dependent property of an alloy system.
Separations of Metallic and Semiconducting Carbon Nanotubes by Using Sucrose as a Gradient Medium (2008)

The separation of metallic and semiconducting single-wall carbon nanotubes (SWCNTs) was achieved using sucrose as a gradient medium in density-gradient ultracentrifugations (sucrose-DGU). By lowering the temperature during sucrose-DGU and tuning the concentrations of the surfactants, metallic and semiconducting SWCNT samples were obtained in high purity. The purity of the metallic and the semiconducting SWCNTs obtained by the sucrose-DGU was estimated to be 69% and 95%, respectively, from their optical absorption spectra. It is well-known that the amounts and types of surfactants significantly influence the separations. However, the authors found that the temperature during centrifugation was also an important parameter that improved the metal−semiconductor separation capability.
Potential impact of dengue vaccination: Insights from two large-scale phase III trials with a tetravalent dengue vaccine (2016)

Our analysis suggests that dengue vaccination can significantly reduce the public health impact of dengue in countries where the disease is endemic.
Studies on the mechanism of uncoupling by amine local anesthetics. Evidence for mitochondrial proton transport mediated by lipophilic ion pairs. (1983)

The hydrophobic weak acid, carbonyl cyanide m-chlorophenylhydrazone (CCCP), induced rapid swelling of mitochondria suspended in NH4SCN, as predicted from the protonophoretic property of CCCP. Butacaine and other hydrophobic amines produced the same response as CCCP. As expected of a protonophore, CCCP (a) induced swelling in mitochondria suspended in potassium acetate and valinomycin, (b) induced rapid K+ efflux from mitochondria treated with valinomycin, and (c) caused an 8-fold stimulation of respiration. Butacaine alone was unable to mimic these effects of CCCP; however, all of these effects were observed with butacaine when SCN- or tetraphenylboron were added to the assay medium. We conclude that amine local anesthetics are not protonophores; rather, their uncoupler-like activity derives from their ability to form lipophilic ion pairs with certain anions. Depending on conditions, ion pair transport may result in electroneutral anion uptake or in electrophoretic proton transport. Uncoupling results from transmembrane cycling of neutral amine, charged anion, and neutral ion pair. Dose response studies were carried out for several pharmacologically important amines with local anesthetic properties. Their relative potencies in the NH4SCN swelling assay followed the order: chlorpromazine much greater than quinine greater than dibucaine greater than quinidine greater than butacaine greater than propranolol greater than tetracaine much greater than lidocaine, procaine, procainamide. Neutral anesthetics (progesterone and benzocaine) and an amine with low anesthetic potency (timolol) were found ineffective. Among hydrophobic drugs, swelling rates in NH4SCN correlate poorly with octanol:water partition coefficients, suggesting that the rate of ion pair transport is determined by the formation constant for lipophilic ion pairs.
NB4S, a Member of the TBC1 Domain Family of Genes, is Truncated as a Result of a Constitutional t(1;10)(p22;q21) Chromosome Translocation in a Patient with Stage 4S Neuroblastoma (1998)

Molecular cloning of the breakpoints of a t(1;10)(p22q21) constitutional translocation breakpoint in a patient with stage 4S neuroblastoma has identified two genes which are fused in-frame to generate a novel gene. The 1p22 gene, which we have called NB4S , encodes a 7.5 kb transcript with an 810 amino acid open reading frame and is expressed in a wide variety of tissues. NB4S has >88% homology with the mouse EVI -5 gene within the coding region and shows strong homology over a 200 amino acid region with TBC1 box motif genes involved in cell growth and differentiation. The C-teminal end of the protein contains a number of coiled coil domains, indicating a possible protein-protein binding function. The chromosome 10 breakpoint interrupts a novel transcript (TRNG10) which could only be detected in tumor cells. This transcript has no exon/intron structure or significant open reading frame, suggesting that it is a structural RNA which is transcribed but not translated. The chromosome rearrangement creates a fusion gene product which combines the TBC1 motif of NB4S with a polyadenylation signal from TRNG10 , potentially generating a truncated protein with oncogenic properties.