gebhart/patrepeval huggingface dataset:
[Novel biomarker for pathological immature cells--soluble form of LR11]. (2012)

LR11 (also called SorLA or SORL1), a member of the LDL receptor family, was originally discovered in 1996 from genes specifically expressed in the intimal smooth muscle cells of atherosclerotic plaques. The soluble form of LR11 (sLR11) as well as the membrane-bound form plays a key role in the phenotype conversion of medial smooth muscle cells into intimal smooth muscle cells through the activation of urokinase receptor/integrin-mediated intracellular pathways. The levels of sLR11 in serum or CSF are increased in patients with atherosclerotic diseases, Alzheimer's disease or malignant diseases including acute leukemias. The recently developed ELISA system using two specific antibodies against LR11 made it possible to measure sLR11 quantitatively and stably for many samples. Thus, a novel clinical examination is expected to detect the pathological immature cells important for the pathophysiology of the above diseases. The soluble receptor-based clinical approach, together with basic studies about the structure-function relationship, may shed light on the development of novel target therapy against pathological immature cells in the science fields of so far independently categorized diseases.
Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases (1988)

DNA polymerases catalyze the addition of deoxyribonucleotides onto DNA primers in a template-directed manner. The requirement for template instruction distinguishes these enzymes from other nucleotidyl transferases, such as terminal deoxynucleotidyl transferase, that do not utilize a template. An oligonucleotide substrate was used to characterize a novel, non-templated nucleotide addition reaction carried out by DNA polymerases from a variety of procaryotic and eucaryotic sources. The products of the reaction, in which a deoxyribonucleotide was added to the 3' hydroxyl terminus of a blunt-ended DNA substrate, were analyzed by electrophoresis on high resolution, denaturing polyacrylamide gels. DNA polymerase from Thermus aquaticus, polymerase alpha from chick embryo, rat polymerase beta, reverse transcriptase from avian myeloblastosis virus, and DNA polymerase I from Saccharomyces cerevisiae all carried out the blunt-end addition reaction. The reaction required a duplex DNA substrate but did not require coding information from the template strand. These results demonstrate that template instruction is not an absolute requirement for the catalysis of nucleotidyl transfer reactions by DNA polymerases.
A two-channel molecular dosimeter for the optical detection of copper(ii) (2003)

A cyclam-like macrocycle with an integrated push-pull chromophore selectively detects Cu2+ inclusion through both orange-to-yellow colour change and quenching of the green fluorescence.
Clonality Assay (X-CIP) and JAK 2 V617P Mutation: Clustering Patients with Essential Thrombocythemia at High Risk for Thrombosis. (2005)

Abstract We have previously demonstrated that clonal hemopoiesis in female ET patients was significantly associated to the risk of thrombosis. When data on JAK2 V617P mutation became available we aimed to evaluate the incidence of this mutation according to clonality status. Ninety-two female patients, median age 32 (19–65) with a diagnosis of ET according to PVSG criteria were studied for clonality with X-CIP, 83 patients were evaluable for endogenous erythroid colonies (EECs) growth and 44 patients were evaluable for JAK2 V617P mutation. Twenty episodes of thromboses (21.7%) were detected and they include splanchnic (11), CNS (5), limb (3) thromboses and pulmonary embolism (1). Thromboses were mainly detected at diagnosis. Thirthy-seven patients showed clonal hemopoiesis (40%), 27 had polyclonal hemopoiesis (29.5%) and 28 were considered uninterpretable due to constitutional skewing (30.5%). Thromboses were overrepresented in the monoclonal group in respect to the polyclonal one (15/37 vs 2/27, p=0.003). DNA for analysis of JAK2 V617P by allele-specific PCR was available for 44 of these patients. Thirty-two patients of 44 (73%) showed JAK2 V617P mutation; JAK2 V617P was found in 16/21 patients with monoclonal hemopoiesis (76%), in 9/13 in the polyclonal group (69%) and in 7/10 (70%) in patients with constitutional skewing. Thirteen of the 32 patients with JAK2 V617P mutation (41%) had thromboses while no thrombotic event was recorded in wild type patients (p=0.008); among the 13 patients with thrombosis and JAK2 V617P mutation, 9 (69%) had monoclonal hemopoiesis, 2 (15%) had polyclonal hemopoiesis, and 2 had constitutive skewing. Thus there was a significant increase in thrombotic events in patients with JAK2 V617P mutation and monoclonal hemopoiesis (p=0.04). JAK2 V617P mutation was also significantly associated to the presence of EECs (p=0.02); in fact 22/26 patients with EECs growth showed JAK2 mutation (85%). Finally when patients with splanchnic thromboses were analyzed 9/11 had a monoclonal X-CIP (81.8%) and 7 of them who were evaluable for JAK2 V617P mutation were invariably carriers of the mutation. Thus we confirm that X-CIP in young female ET is correlated to the risk of thrombosis. JAK2 V617P mutation is significantly associated to the development of thrombosis and is present in the vast majority of patients with monoclonal hemopoiesis. The mechanisms underlying monoclonal hemopoiesis in the absence of JAK2 V617P mutation are unclear, notwithstanding these patients are clinically characterized by both absence of EECs and thrombosis.
Synchronization: A Universal Concept in Nonlinear Science (2002)

First Page
CMOS-compatible RF-MEMS tunable capacitors (2003)

New CMOS-MEMS tunable capacitors have been designed, fabricated and tested. Large-tuning range and high quality factor, Q, are achieved. The structures were made from the CMOS interconnect stack using a maskless CMOS micromachining process. Our tunable capacitor designs can be classified into two categories based on their tuning schemes as gap&area tuning and gap-only tuning. The capacitors with gap&area tuning were fabricated using Austria Microsystems (AMS) 0.6 /spl mu/m and Agilent 0.5 /spl mu/m CMOS processes. These devices have a measured nominal capacitance of 209 fF and a measured Q of 28 at 1.5 GHz. The capacitance change is measured from 209 fF to 294 fF within a 24 V control voltage, and 72.4 mW power at 1.5 GHz. The capacitors with gap-only tuning were fabricated in the TSMC 0.35 /spl mu/m CMOS process and have larger tuning range and more power efficiency than the 1st generation designs. For these new designs, 3.52 to 1 tuning range has been measured with tuning from 42 fF to 148 fF within a 12 V control voltage and 34 mW power and Q of 52 at 1.5 GHz. The tuning mechanism uses electro-thermal actuation. The essential differences between this work and prior work are the CMOS compatibility and more area efficiency at several gigahertz.
Solvent-Free Mechanochemical Reaction of [60]Fullerene with Phenylhydrazine Hydrochlorides (2008)

The solvent-free reaction of [60]fullerene with phenylhydrazine hydrochlorides 1a-e in the presence of sodium carbonate under high-speed vibration milling conditions afforded 1-aryl-1,2-dihydro[60]fullerenes 2a-e, amongst them 1- (4-nitrophenyl)-1,2-dihydro[60]fullerene 2e could not be obtained in the liquid-phase reaction. When excess sodium nitrite was employed to replace sodium carbonate, fullerotriazoline 3 was formed. Product 3 tended to decompose via the loss of molecular nitrogen to give azafulleriod 4. Keywords: [60]Fullerene, mechanochemistry, phenylhydrazine hydrochlorides, solvent-free
Triple quadrupole mass spectrometry for direct mixture analysis and structure elucidation (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTriple quadrupole mass spectrometry for direct mixture analysis and structure elucidationR. A. Yost and C. G. EnkeCite this: Anal. Chem. 1979, 51, 12, 1251–1264Publication Date (Print):October 1, 1979Publication History Published online21 September 2008Published inissue 1 October 1979https://pubs.acs.org/doi/10.1021/ac50048a002https://doi.org/10.1021/ac50048a002research-articleACS PublicationsRequest reuse permissionsArticle Views2708Altmetric-Citations248LEARN 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
The Mode of Action of Bacillus Thuringiensis Endotoxins (1992)

The use of synthetic organic insecticides developed during the last half of this century may pose risks to human health and can cause environmental prob­ lems. Consequently, interest has developed in using alternative strategies for insect pest management. One contemporary approach that has received atten­ tion is the development of Bacillus thuringiensis (Bt) toxins as insecticides. B. thuringiensis, a gram-positive bacteria, produces a proteinaceous paraspor­ al crystalline inclusion during sporulation. Upon ingestion by insects, this crystalline inclusion is solubilized in the midgut, releasing proteins called S-endotoxins. These proteins (protoxins) are activated by midgut proteases, and the activated toxins interact with the larval midgut epithelium causing a disruption in membrane integrity and ultimately leading to insect death. In spite of significant efforts directed towards the study of Bt, its use in pest control is restricted, in part because of the selectivity of Bt and in part because of its moderate efficacy. Attempts to improve these two qualities have met with only moderate success because inadequate effort has been devoted to understanding the molecular basis of selectivity and insecticidal properties of these toxins.
A bit-rate/bandwidth scalable speech coder based on ITU-T G.723.1 standard (2004)

The paper presents a new scalable coder based on the ITU-T G.723.1 standard which is one of the most famous speech coders for VoIP applications. In order to support both bit-rate scalability and bandwidth scalability, the proposed coder adopts a split-band approach, where the input signal, sampled at 16 kHz, is decomposed into two equal frequency bands. The lower-band speech is coded with a standard coder, such as the G.723.1 standard. In addition, the low-band enhancement layer for lower-band speech improves the perceptual quality of decoded speech by employing additional coding units based on a cascaded codebook approach. The higher-band signal is encoded using an MDCT-based transform coding scheme. The proposed coder, at a bit-rate of 19.4 kbit/s, provides speech quality comparable to the ITU-T 24 kbit/s G.722.1 coder, while it also has interoperability with G.723.1.
The collagen receptor alpha 2 beta 1, from MG-63 and HT1080 cells, interacts with a cyclic RGD peptide (1992)

Several receptors for the extracellular matrix protein collagen have been described which belong to the superfamily of receptors collectively known as integrins. Although several integrins have been shown to interact with extracellular matrix molecules via a common recognition site, arginine-glycine-aspartic Acid (RGD), within the beta 1 integrin subfamily, only the fibronectin receptor (alpha 5 beta 1) has been convincingly shown to interact with RGD. In the present study, we tested whether a collagen receptor could interact with RGD. Adhesion of an osteosarcoma cell line, MG-63, to immobilized collagen I was inhibited by the cyclic RGD-containing peptide, C*GRGDSPC* (where C* indicates that Cys participates in disulfide), and not by the linear GRGDSP or the non-RGD-containing cyclic peptide, C*GKGESPC*. Similarly, using collagen-Sepharose affinity chromatography, a heterodimeric protein could be specifically eluted from the column by the cyclic RGD peptide. Immunoprecipitations of the eluted material with monoclonal antibodies showed reactivity with the collagen receptor alpha 2 beta 1 and not alpha 3 beta 1. Our data demonstrate that RGD peptides can interact with the collagen receptor, and the differences seen with the linear and cyclic peptide suggest that the cyclic C*GRGDSPC* has a higher avidity for the receptor than the more flexible linear GRGDSP. In this paper, we provide supportive evidence that one possible mode of collagen interaction with alpha 2 beta 1 is via the RGD recognition sequence.
Deciphering the structural code for proteins: Helical propensities in domain classes and statistical multiresidue information in α‐helices (1998)

We made several statistical analyses in a large sample of nearly 4,000 helices (from 546 redundancy-controlled PDB protein subunits), which give new insights into the helical properties of globular proteins. In a first experiment, the amino acid composition of the whole sample was compared with the composition of two helical sample subgroups (the "mainly-alpha" and the "(alpha/beta)8 barrel" domain classes); we reached the conclusion that composition-based helical propensities for secondary structure prediction do not depend on the structural class. Running a five-residue window through the whole sample, the positional composition revealed that positive and negative residues are located throughout the helices and tend to neutralize the macrodipole effect. On this basis, we analyzed charged triplets using a running five-residue window. The conclusion was that only mixed charged residues [positive (+) and negative (-)] located at positions 1-2-5 and 1-4-5 are clearly favored. In these locations the most abundant are (- -..+) and (-..+ +), and this shows the existence of side chain microdipoles, which neutralize the large macrodipole of the helix. We made a systematic statistical analysis of charged, dipolar, and hydrophobic + aromatic residues, which enabled us to work out rules that should be useful for modeling and design purposes. Finally, we analyzed the relative abundance of all the different amphipathic double-arcs that are present in helices formed by octapeptides (8) and nonapeptides (18). All of the double-arcs that make up Schiffer and Edmundson's classical helical wheel are found in abundance in the sample.
AMD3100 mobilizes hematopoietic stem cells with long-term repopulating capacity in nonhuman primates (2006)

AMD3100, a bicyclam antagonist of the chemokine receptor CXCR4, has been shown to induce rapid mobilization of CD34(+) hematopoietic cells in mice, dogs, and humans, offering an alternative to G-CSF mobilization of peripheral-blood hematopoietic stem cells. In this study, AMD3100-mobilized CD34(+) cells were phenotypically analyzed, marked with Neo(R)-containing retroviral vectors, and subsequently transplanted into myeloablated rhesus macaques. We show engraftment of transduced AMD3100-mobilized CD34(+) cells with Neo(R) gene marked myeloid and lymphoid cells up to 32 months after transplantation, demonstrating the ability of AMD3100 to mobilize true long-term repopulating hematopoietic stem cells. More AMD3100-mobilized CD34(+) cells are in the G(1) phase of the cell cycle and more cells express CXCR4 and VLA-4 compared with G-CSF-mobilized CD34(+) cells. In vivo gene marking levels obtained with AMD3100-mobilized CD34(+) cells were better than those obtained using CD34(+) cells mobilized with G-CSF alone. Overall, these results indicate that AMD3100 mobilizes a population of hematopoietic stem cells with intrinsic characteristics different from those of hematopoietic stem cells mobilized with G-CSF, suggesting fundamental differences in the mechanism of AMD3100-mediated and G-CSF-mediated hematopoietic stem cell mobilization. Thus, AMD3100-mobilized CD34(+) cells represent an alternative source of hematopoietic stem cells for clinical stem cell transplantation and genetic manipulation with integrating retroviral vectors.
Drug Metabolism Handbook: Concepts and Applications (2009)

Drug metabolism handbook , Drug metabolism handbook , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Experimental Rhinovirus 16 Infection (1997)

Asthma exacerbations are often associated with respiratory virus infections, particularly with rhinovirus. In the present study we investigated the effect of experimental rhinovirus 16 (RV16) infection on airway inflammation as assessed by analysis of hypertonic saline-induced sputum. Twenty-seven nonsmoking atopic, mildly asthmatic subjects participated in a placebo-controlled parallel study. RV16 (n = 19) or its diluent (n = 8) was nasally administered. Sputum inductions were performed at entry and on Days 2 and 9 after inoculation, and airway responsiveness to histamine (PC20) was measured on Days 4 and 11. Cell differentials and levels of albumin, eosinophil cationic protein (ECP), IL-8, and IL-6 were determined. The cellular origin of IL-8 was investigated by intracellular staining. RV infection was confirmed by culture and/or by antibody titer rise in each of the RV16-treated subjects. There were no significant changes in the sputum differentials of nonsquamous cells (MANOVA, p > or = 0.40). In the RV16 group, there was a significant increase in the levels of ECP, IL-8, and IL-6 at Day 2 after infection (p < 0.05), whereas the albumin levels did not change (p = 0.82). The levels of IL-8 and IL-6 remained elevated for as long as 9 d after infection (p < 0.05). The increase in the percentage of IL-8 positive cells at Day 2 after infection could be attributed to the increase in IL-8 positive neutrophils (p < 0.02). There was a significant decrease in PC20 at Day 4 (p = 0.02), which was no longer significant at Day 11 (p = 0.19). The decrease in PC20 correlated significantly with the increase in ECP in the first week (r = -0.60) and with the change in the percentage eosinophils in the second week after inoculation (r = -0.58). We conclude that experimental RV16 infection in atopic asthmatic subjects increases airway hyperresponsiveness in conjunction with augmented airway inflammation, as reflected by an increase in ECP, IL-8, and IL-6 in sputum. Our results suggest that the RV16-enhanced airway hyperresponsiveness is associated with eosinophilic inflammation.
Increased expression of TGF-beta 2 in osteoblasts results in an osteoporosis-like phenotype. (1996)

The development of the skeleton requires the coordinated activities of bone-forming osteoblasts and bone-resorbing osteoclasts. The activities of these two cell types are likely to be regulated by TGF-beta, which is abundant in bone matrix. We have used transgenic mice to evaluate the role of TGF-beta 2 in bone development and turnover. Osteoblast-specific overexpression of TGF-beta 2 from the osteocalcin promoter resulted in progressive bone loss associated with increases in osteoblastic matrix deposition and osteoclastic bone resorption. This phenotype closely resembles the bone abnormalities seen in human hyperparathyroidism and osteoporosis. Furthermore, a high level of TGF-beta 2 overexpression resulted in defective bone mineralization and severe hypoplasia of the clavicles, a hallmark of the developmental disease cleidocranial dysplasia. Our results suggest that TGF-beta 2 functions as a local positive regulator of bone remodeling and that alterations in TGF-beta 2 synthesis by bone cells, or in their responsiveness to TGF-beta 2, may contribute to the pathogenesis of metabolic bone disease.
A Latent Dirichlet Model for Unsupervised Entity Resolution (2006)

Entity resolution has received considerable attention in recent years. Given many references to underlying entities, the goal is to predict which references correspond to the same entity. We show how to extend the Latent Dirichlet Allocation model for this task and propose a probabilistic model for collective entity resolution for relational domains where references are connected to each other. Our approach differs from other recently proposed entity resolution approaches in that it is a) generative, b) does not make pair-wise decisions and c) captures relations between entities through a hidden group variable. We propose a novel sampling algorithm for collective entity resolution which is unsupervised and also takes entity relations into account. Additionally, we do not assume the domain of entities to be known and show how to infer the number of entities from the data. We demonstrate the utility and practicality of our relational entity resolution approach for author resolution in two real-world bibliographic datasets. In addition, we present preliminary results on characterizing conditions under which relational information is useful.
The Epidemiology of Antiretroviral Drug Resistance among Drug‐Naive HIV‐1–Infected Persons in 10 US Cities (2004)

Depending on the characteristics of the patients tested, HIV-genotype testing prior to the initiation of therapy would identify a substantial number of infected persons with mutations associated with reduced antiretroviral-drug susceptibility.
Condensation and Wetting Transitions on Microstructured Ultrahydrophobic Surfaces (2007)

On rough surfaces, two distinct wetting modes can appear. These two states are usually described by the theories of Cassie (drops suspended on top of roughness features) and Wenzel (drops impaled on roughness features). Whereas the wetting transition from the Cassie to the Wenzel state has been relatively well studied both experimentally and theoretically, the question of whether metastable Wenzel drops exist and how they transition to the Cassie state has remained open. In this work, we study the wetting behavior of microstructured post surfaces coated with a hydrophobic fluoropolymer. Through condensation, the formation of metastable Wenzel droplets is induced. We show that under certain conditions drops can transition from the Wenzel to the Cassie state.
Low-power operation using self-timed circuits and adaptive scaling of the supply voltage (1994)

Recent research has demonstrated that for certain types of applications like sampled audio systems, self-timed circuits can achieve very low power consumption, because unused circuit parts automatically turn into a stand-by mode. Additional savings may be obtained by combining the self-timed circuits with a mechanism that adaptively adjusts the supply voltage to the smallest possible, while maintaining the performance requirements. This paper describes such a mechanism, analyzes the possible power savings, and presents a demonstrator chip that has been fabricated and tested. The idea of voltage scaling has been used previously in synchronous circuits, and the contributions of the present paper are: 1) the combination of supply scaling and self-timed circuitry which has some unique advantages, and 2) the thorough analysis of the power savings that are possible using this technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>