gebhart/patrepeval huggingface dataset:
Formation and stability kinetics of calcium phosphate–fetuin-A colloidal particles probed by time-resolved dynamic light scattering (2011)

Fetuin-A/α2-HS glycoprotein is a major systemic inhibitor of unwanted calcium phosphate deposition in the soft tissue. Fetuin-A mediates the formation of initially ∼100 nanometre sized colloidal protein–mineral particles, denoted as calciprotein particles. After a lag period, these particles rapidly grow to elongated particles of about twice the initial size. Similar particles can be generated with other acidic macromolecules as well. However, fetuin-A is more potent regarding activity and specificity of inhibition. Given the widely recognized physiological relevance of fetuin-A as an inhibitor of pathological mineralization both in vitro, in cells, in animals and in humans, and its ready availability in large quantities, fetuin-A is a prototypic model protein to investigate protein–calcium phosphate interactions and mineral colloid stabilization, respectively. Several studies have concentrated on the pathophysiological relevance and the structural details of particle formation and mineral ripening. The principles governing calciprotein particle formation and ripening are nevertheless poorly understood. Here we present a systematic and quantitative investigation by time-resolved dynamic light scattering of the three major parameters: fetuin-A concentration, mineral ion concentration and temperature. Changes in temperature had only a weak effect on calciprotein particle size. Increased mineral ion concentrations and especially increased fetuin-A concentration led to smaller particles. An increased temperature, mineral ion concentration and a reduced fetuin-A concentration, respectively, all accelerated the particle ripening process. Our investigation demonstrates that calciprotein particle formation and ripening are two separate and successive processes and that particle ripening follows Arrhenius law. Furthermore it provides concepts to control the particle size and stability.
Identification and characterization of two enhancers of the human albumin gene. (1992)

A 12.5-kilobase pair (kb) segment upstream of the human albumin gene was analyzed for transcription enhancing activity using transient transfection analysis, gel mobility shift assays, DNase I footprinting, and site-specific mutagenesis. Two enhancer regions were identified, one 1.7 kb upstream of the transcription initiation site (E1.7) and the other 6 kb upstream (E6). In E1.7, a nuclear protein from HuH-7 hepatoma cells binds to an AT-rich sequence, GTTACTAATTGAC. Competition gel mobility shift assays suggested that this protein is HNF-1, which regulates the promoter of the albumin gene and several other liver-specific genes. A 60-base pair E1.7 fragment carrying the AT-rich sequence stimulates a heterologous (alpha-fetoprotein) promoter in a dose-dependent manner. In E6, a HuH-7 nuclear protein binds to a GT-rich sequence, TGTTTGGC.A 27-base pair E6 fragment carrying this sequence is able to stimulate the SV40 promoter in an orientation-independent manner. An alteration of this sequence by site-specific mutagenesis resulted in the loss of transcriptional activity as well as binding to the HuH-7 nuclear protein. Competition gel mobility shift assays showed that homologous elements exist in the albumin promoter. These results show that the promoter and enhancer of the human albumin gene are regulated by two common transcription factors through two shared cis-acting elements, one AT-rich and the other GT-rich.
Another stemmer (1990)

In natural language processing, conflation is the process of merging or lumping together nonidentical words which refer to the same principal concept. This can relate both to words which are entirely different in form (e.g., "group" and "collection"), and to words which share some common root (e.g., "group", "grouping", "subgroups"). In the former case the words can only be mapped by referring to a dictionary or thesaurus, but in the latter case use can be made of the orthographic similarities between the forms. One popular approach is to remove affixes from the input words, thus reducing them to a stem ; if this could be done correctly, all the variant forms of a word would be converted to the same standard form. Since the process is aimed at mapping for retrieval purposes, the stem need not be a linguistically correct lemma or root (see also Frakes 1982).
Analysis of phonons in graphene sheets by means of HREELS measurement and ab initio calculation (2005)

Abstract We have grown epitaxial thin sheets of graphene on BC 3 /NbB 2 (0001) and measured phonon dispersion curves of the graphene sheets by means of high‐resolution electron energy‐loss spectroscopy (HREELS). The phonon dispersion curves have been calculated on the basis of ab initio calculations. The observed curves were in good agreement with theoretical curves. The quality of crystallinity of the graphene layers was high compared with the bulk graphite crystals. In this paper, we demonstrate that the combination of HREELS measurement and ab initio calculations is extremely effective for investigation of honeycomb‐structured materials. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Capnography screening for sleep apnea in patients with acute stroke (2005)

Sleep apnea syndrome (SAS) is a prominent clinical feature in acute stroke patients. Diagnosis is usually established by polysomnography or cardio-respiratory polygraphy (CRP). Both diagnostic procedures produce high costs, are dependent on the access to a specialized sleep laboratory, and are poorly tolerated by patients with acute stroke. In this study we therefore investigated whether capnography may work as a simple screening tool in this context. In addition to conventional CRP, 27 patients with acute stroke were studied with capnography provided by our standard monitoring system. The trend graphs of the end-tidal CO(2) values (EtCO(2)) were used to determine the capnography-based estimate of the apnea-hypopnea index (AHI(CO2)). Index events were scored when the EtCO(2) value dropped for > 50% of the previous baseline value. We found that the AHI(CO2) correlated significantly with the apnea-hypopnea index measured with conventional CRP (AHI(CRP)) (r = 0.94; p < 0.001). An AHI(CO2) > 5 turned out to be highly predictive of an AHI(CRP) > 10. According to our findings, routinely acquired capnography may provide a reliable estimate of the AHI(CRP). The equipment needed for this screening procedure is provided by the monitoring systems of most intensive care units and stroke units where stroke patients are regularly treated during the first days of their illness. Therefore, early diagnosis of SAS in these patients is made substantially easier.
ChemInform Abstract: Cationic Liposomes for Gene Therapy (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Purification, partial characterization of rat kidney hyaluronic acid binding protein and its localization on the cell surface. (1991)

Hyaluronic acid binding protein (HABP) has been purified to homogeneity from normal adult rat kidney by hyaluronate Sepharose affinity chromatography, and its apparent molecular mass was found to be 68 kDa. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis of HABP under reducing as well as nonreducing conditions revealed a single protein band of 34 kDa, thus indicating that kidney HABP is a homodimer and lacks interchain disulfide bond. Its glycoprotein nature was demonstrated by Con-A binding analysis. The pI value of kidney HABP was 6, indicating its acidic nature. Polyclonal antibodies were raised against it, and the monospecificity of the antibodies towards HABP was confirmed by Western blot analysis of tissue extracts. Immunoblot analysis has elucidated the occurrence of this glycoprotein in various tissues. Moreover, HABP present in these tissues are shown to be structurally and immunologically identical. However, this glycoprotein is antigenically distinct from other well characterized extracellular proteins, e.g., fibronectin, laminin and collagen type IV. With the help of enzyme-linked immunosorbent assay (ELISA) and iodinated [125I]HABP, it has been shown that kidney HABP binds specifically to hyaluronic acid (HA) amongst all the glycosaminoglycans (GAGs), however, HABP can interact with other matrix proteins, e.g., laminin, fibronectin, and collagen type IV. The apparent dissociation constants of HABP for HA, laminin, fibronectin, and collagen type IV were approximately in the range of 10(-9) M, and kinetic analysis showed that these binding interactions were complex and of positive cooperative nature. Indirect immunofluorescence staining demonstrated its localization on human fetus lung fibroblast cell surface. Detection of 34 kDa HABP in the serum-free supernatant culture medium of fibroblasts was further evident by immunoblot analysis, thus confirming the secretory nature of HABP and its occurrence in the extracellular matrix.
The future of cytotoxic therapy: selective cytotoxicity based on biology is the key (2003)

Although mortality from breast cancer is decreasing, 15% or more of all patients ultimately develop incurable metastatic disease. It is hoped that new classes of target-based cytotoxic therapeutics will significantly improve the outcome for these patients. Many of these novel agents have displayed cytotoxic activity in preclinical and clinical evaluations, with little toxicity. Such preferential cytotoxicity against malignant tissues will remain tantamount to the Holy Grail in oncologic therapeutics because this portends improved patient tolerance and overall quality of life, and the capacity to deliver combination therapy. Combinations of such rationally designed target-based therapies are likely to be increasingly important in treating patients with breast carcinoma. The anticancer efficacy of these agents will, however, remain dependent on the involvement of the targets of these agents in the biology of the individual patient's disease. Results of DNA microarray analyses have raised high hopes that the analyses of RNA expression levels can successfully predict patient prognosis, and indicate that the ability to rapidly 'fingerprint' the oncogenic profile of a patient's tumor is now possible. It is hoped that these studies will support the identification of the molecules driving a tumor's growth, and the selection of the appropriate combination of targeted agents in the near future.
Functional domains in Fok I restriction endonuclease. (1992)

The PCR was used to alter transcriptional and translational signals surrounding the Flavobacterium okeanokoites restriction endonuclease (fokIR) gene, so as to achieve high expression in Escherichia coli. By changing the ribosome-binding site sequence preceding the fokIR gene to match the consensus E. coli signal and by placing a positive retroregulator stem-loop sequence downstream of the gene, Fok I yield was increased to 5-8% of total cellular protein. Fok I was purified to homogeneity with phosphocellulose, DEAE-Sephadex, and gel chromatography, yielding 50 mg of pure Fok I endonuclease per liter of culture medium. The recognition and cleavage domains of Fok I were analyzed by trypsin digestion. Fok I in the absence of a DNA substrate cleaves into a 58-kDa carboxyl-terminal and 8-kDa amino-terminal fragment. The 58-kDa fragment does not bind the DNA substrate. Fok I in the presence of a DNA substrate cleaves into a 41-kDa amino-terminal fragment and a 25-kDa carboxyl-terminal fragment. On further digestion, the 41-kDa fragment degrades into 30-kDa amino-terminal and 11-kDa carboxyl-terminal fragments. The cleaved fragments both bind DNA substrates, as does the 41-kDa fragment. Gel-mobility-shift assays indicate that all the protein contacts necessary for the sequence-specific recognition of DNA substrates are encoded within the 41-kDa fragment. Thus, the 41-kDa amino-terminal fragment constitutes the Fok I recognition domain. The 25-kDa fragment, purified by using a DEAE-Sephadex column, cleaves nonspecifically both methylated (pACYCfokIM) and nonmethylated (pTZ19R) DNA substrates in the presence of MgCl2. Thus, the 25-kDa carboxyl-terminal fragment constitutes the Fok I cleavage domain.
The file system of an integrated local network (1985)

The distributed file system component of the DOMAIN system is described. The DOMAIN system is an architecture for networks of personal workstations and servers which creates an integrated distributed computing environment. The distinctive features of the file system include: objects addressed by unique identifiers (UIDs); transparent access to objects, regardless of their location in the network; the abstraction of a single level store for accessing all objects; and the layering of a network wide hierarchical name space on top of the UID based flat name space. The design of the facilities is described, with emphasis on techniques used to achieve performance for access to objects over the network.
Molecular and Cellular Mechanisms of Receptor-Mediated Endocytosis (1991)

In general, receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clathrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors and ligands are sorted, and then either recycle to the cell surface, become stored intracellularly, or are degraded in lysosomes. The internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of certain viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Although endocytosis is common to all nucleated eukaryotic cells, the factors that regulate these receptor-mediated endocytic pathways are not fully understood. Defective receptors that are not capable of undergoing normal endocytosis can lead to certain disease states, as in the case of familial hypercholesteremia (FH). This review has three objectives: (i) to describe the different routes that receptors and ligands follow after internaliation; (ii) to describe the potential mechanisms which regulate the initiation and subsequent sorting of receptors and ligands so they reach their final destination; and (iii) to describe the potential functions of receptor-mediated endocytosis.
Edge Transfer Lithography of Molecular and Nanoparticle Materials (2002)

A simple and general method which we call edge transfer lithography has been developed for large-area patterning of molecular and nanoparticle materials with line widths as small as 60 nm. The procedure employs standard “ink” and “stamp” microcontact printing techniques and takes advantage of the intrinsic topographic character of micropatterned elastomeric stamps and discontinuous dewetting behavior of ink solutions to selectively apply ink within the recesses of the stamp. In this way, molecules or particles are delivered from the stamp to a solid substrate of interest selectively along the edges of the stamp features. Siloxane self-assembled monolayers (SAMs) and titanium dioxide (TiO2) nanoparticle materials are directly patterned on glass substrates at nanometer resolution. Alkyl siloxane patterned SAM surfaces are used as a template structure for the guided self-assembly of molecular and nanoparticle materials. The surfaces are characterized by lateral force microscopy and noncontact atomic force microscopy.
Automatic synthesis of data storage and control structures for FPGA-based computing engines (2002)

Mapping computations written in high-level programming languages to FPGA-based computing engines requires programmers to create the datapath responsible for the core of the computation as well as the control structures to generate the appropriate signals to orchestrate its execution. This paper addresses the issue of automatic generation of data storage and control structures for FPGA-based reconfigurable computing engines using existing compiler data dependence analysis techniques. We describe a set of parameterizable data storage and control structures used as the target of our prototype compiler. We present a compiler analysis algorithm to derive the parameters of the data storage structures to minimize the required memory bandwidth of the implementation. We also describe a complete compilation scheme for mapping loops that manipulate multi-dimensional array variables to hardware. We present preliminary simulation results for complete designs generated manually using the results of the compiler analysis. These preliminary results show that it is possible to successfully integrate compiler data dependence analysis with existing commercial synthesis tools.
The Heidelberg classification of renal cell tumours (1997)

This paper presents the conclusions of a workshop entitled 'Impact of Molecular Genetics on the Classification of Renal Cell Tumours', which was held in Heidelberg in October 1996. The focus on 'renal cell tumours' excludes any discussion of Wilms' tumour and its variants, or of tumours metastatic to the kidneys. The proposed classification subdivides renal cell tumours into benign and malignant parenchymal neoplasms and, where possible, limits each subcategory to the most commonly documented genetic abnormalities. Benign tumours are subclassified into metanephric adenoma and adenofibroma, papillary renal cell adenoma, and renal oncocytoma. Malignant tumours are subclassified into common or conventional renal cell carcinoma; papillary renal cell carcinoma; chromophobe renal cell carcinoma; collecting duct carcinoma, with medullary carcinoma of the kidney; and renal cell carcinoma, unclassified. This classification is based on current genetic knowledge, correlates with recognizable histological findings, and is applicable to routine diagnostic practice.
pH-민감 고분자 미셀을 이용한 효율적인 항암제 전달 (2007)

Polymeric micelles from pH-sensitive block copolymers have been designed for targeting tumor acidity or endosomal pH in tumor cells. The micelles are core-shell types formed by self-organization of the blocks in an aqueous medium or under specific experimental conditions. They possess a segment that has physical or chemical properties responding to small changes in environmental pH. The segment induces to the fast release kinetics from the micelles at tumor sites by particle shrunk/disruption. Furthermore, it can alter the biodistribution of the micelles and the interactions with tissues and cells by utilizing small pH changes. Such properties lead to overcome the problems associated with free chemo-agents, such as nonspecific toxicity, lack of tumor selectivity, and the development of multidrug resistance in various tumor cells. Therefore, the micelles have been considered as promising anti-cancer drug carriers. This review summarizes the recent progress in pH-sensitive micelles for tumor chemotherapy, particularly for those responding to tumor pH and endosomal/lysosomal pH for the treatment of multidrug resistance (MDR). (Korean J Gastroenterol 2007;49:314-319)
Decomposition of Noise Sources in Recording Applications Using Symbol-Rate Readback Samples (2004)

Noise in recording applications is often modeled as a combination of additive noise and medium noise. In addition to the total noise power, the nature of the different noise processes and their relative contributions to the total noise affect detection performance. Two methods for noise decomposition that are based on symbol-rate readback samples of arbitrary channel input sequences are presented. They rely on the estimation of the variance of an ensemble of noise samples as a function of sample index, and its cross correlation with the input data sequence. Performance is assessed by using well-established models of the magnetic recording channel.
Isocitrate Dehydrogenase of Bradyrhizobium japonicum Is Not Required for Symbiotic Nitrogen Fixation with Soybean (2006)

A mutant strain of Bradyrhizobium japonicum USDA110 lacking isocitrate dehydrogenase activity was created to determine whether this enzyme was required for symbiotic nitrogen fixation with soybean (Glycine max cv. Williams 82). The isocitrate dehydrogenase mutant, strain 5051, was constructed by insertion of a streptomycin resistance gene cassette. The mutant was devoid of isocitrate dehydrogenase activity and of immunologically detectable protein, indicating there is only one copy in the genome. Strain 5051 grew well on a variety of carbon sources, including arabinose, pyruvate, succinate, and malate, but, unlike many microorganisms, was a glutamate auxotroph. Although the formation of nodules was slightly delayed, the mutant was able to form nodules on soybean and reduce atmospheric dinitrogen as well as the wild type, indicating that the plant was able to supply sufficient glutamate to permit infection. Combined with the results of other citric acid cycle mutants, these results suggest a role for the citric acid cycle in the infection and colonization stage of nodule development but not in the actual fixation of atmospheric dinitrogen.
The Human Glucocorticoid Receptor β Isoform (1996)

Alternative splicing of the human glucocorticoid receptor (hGR) primary transcript produces two receptor isoforms, hGRalpha and hGRbeta, which differ at their carboxyl termini. The hGRalpha isoform conveys endocrine information to target tissues by altering patterns of gene expression in a hormone-dependent fashion. In contrast to hGRalpha, very little is known about the hGRbeta splice variant. Using hGRalpha- and hGRbeta-specific riboprobes on human multiple tissue Northern blots, we show that the hGRbeta message has a widespread tissue distribution. We also prove by reverse transcriptase-polymerase chain reaction that the alternative splicing event underlying the formation of the hGRbeta message occurs in these tissues. Because the hGRbeta protein differs from hGRalpha at the extreme COOH terminus, we investigated several of the biochemical properties of hGRbeta expressed in transfected cells. hGRbeta does not bind the glucocorticoid agonist dexamethasone nor the glucocorticoid antagonist RU38486 in vivo. Moreover, in contrast to hGRalpha, hGRbeta is located primarily in the nucleus of transfected cells independent of hormone administration. Finally, in the absence of hGRalpha, hGRbeta is transcriptionally inactive on a glucocorticoid-responsive enhancer. However, when both isoforms are expressed in the same cell, hGRbeta inhibits the hormone-induced, hGRalpha-mediated stimulation of gene expression. Thus, hGRbeta potentially functions as a dominant negative inhibitor of hGRalpha activity.
Autoantibodies to fibrillin 1 in systemic sclerosis: Ethnic differences in antigen recognition and lack of correlation with specific clinical features or HLA alleles (2000)

There are striking ethnic differences in antigenic epitope specificity of anti-fibrillin 1 antibodies in patients with SSc, and the majority of SSc patients, except for Caucasians, produce antibodies to fibrillin 1. The antifibrillin response thus far remains specific for scleroderma syndromes, but it does not correlate with any major clinical features, other autoantibodies, or HLA class II alleles.
Pfinder: real-time tracking of the human body (2002)

Pfinder is a real-time system for tracking and interpretation of people. It runs on a standard SGI Indy computer, and has performed reliably on thousands of people in many different physical locations. The system uses a multi-class statistical model of color and shape to obtain a 2-D representation of head and hands in a wide range of viewing conditions. These representations are useful for applications such as wireless interfaces, video databases, and low-bandwidth coding, without cumbersome wires or attached sensors.