gebhart/patrepeval huggingface dataset:
A model for the reaction mechanism of the transglutaminase 3 enzyme (2003)

Transglutaminase enzymes (TGases) catalyze the calcium dependent formation of an isopeptide bond between protein-bound glutamine and lysine substrates. Previously we have shown that activated TGase 3 acquires two additional calcium ions at site two and three. The calcium ion at site three results in the opening of a channel. At this site, the channel opening and closing could modulate, depending on which metal is bound. Here we propose that the front of the channel could be used by the two substrates for enzyme reaction. We propose that the glutamine substrate is directed from Trp236 into the enzyme, shown by molecular docking. Then a lysine substrate approaches the opened active site to engage Trp327, leading to formation of the isopeptide bond. Further, direct comparisons of the structures of TGase 3 with other TGases have allowed us to identify several residues that might potentially be involved in generic and specific recognition of the glutamine and lysine substrates.
Early Detection of Pancreatic Cancer (2012)

Despite treatment advances pancreatic cancer remains one of the most lethal malignancies. It is expected that early detection and screening of high risk patient population may have the most significant impact on altering overall survival in this disease. Serologic biomarkers may be the most useful in early detection and histology-based markers may have the most significant role in differentiating benign, pre-malignant and malignant lesions. Here we review several serum and tissue-based biomarkers and summarize new data presented at the 2012 ASCO Gastrointestinal Cancers Symposium (Abstracts #151, #164, #188) on the potential role of PAM4 in pancreatic cancer screening and diagnosis.
Expression of FGF receptor gene in rat development (1991)

We examined the expression of FGF-receptor (FGF-R) mRNA during rat development with in situ hybridization histochemistry. Embryonic tissues (E9, E12, E14, E17) and postnatal neural tissues (P1, P7, P14, adult) were examined. We detected significant levels of FGF-R mRNA in various tissues at different developmental stages. As postulated by previous studies using other methods, FGF-R gene expression was observed primarily in mesoderm- and neuroectoderm-derived tissues. In the nervous system, the pattern of gene expression was developmentally regulated; in embryos, FGF-R mRNA was mainly detected in the ependymal layer of the central nervous system (CNS). Postnatally, FGF-R transcripts were observed in specific neuronal populations, such as hippocampal neurons. FGF-R mRNA was also found in sensory systems such as trigeminal and dorsal root ganglia in late stage embryos; however, FGF-R mRNA decreased in the postnatal period. FGF-R mRNA expression was modulated in the developing retina: FGF-R messages were observed in the pigment epithelium and neuroblast layer at embryonic stages; in the postnatal period, they were found in the ganglion cell and inner granular layer. In non-neuronal embryonic tissues, a wide variety of organs expressed FGF-R message. Particularly, the prevertebral column, bone, kidney and skin showed high levels of expression. These observations reinforce the idea that FGF exerts effects on the development of various tissues.
Design and evaluation of a wireless electronic health records system for field care in mass casualty settings (2011)

Overall, the results of WIISARD show that wireless EMR systems for care of the victims of disasters would be complex to develop but potentially feasible to build and deploy, and likely to improve the quality of information available for the delivery of care during disasters.
Footprints for mobile communications (1991)

One of the many requirements of the asynchronous transfer mode (ATM) standard being defined for a broadband integrated services digital network (B-ISDN) is that it be able to support all the services currently provided by existing separate networks. One service of particular interest is mobile communications. In order to support this projected expansion it will be necessary to progressively reduce the size of the radio cells in areas of high traffic density. The burden placed on the existing hand-over protocols will become insurmountable and new techniques will be required. One such technique is to disseminate the call information to the adjacent base-stations, called the footprint, by use of a selective broadcast facility in the ATM network so that when an hand-over is required all the details about the connexion already exist at the new base-station. The protocol described has been implemented on the ATM network simulator developed in Durham, and some of the findings are reported.<
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Evaluation of Overexpressed Cannabinoid 1 Receptor in Liver Fibrosis Tissues via Detecting CB1R Antagonist, AM251, by MALDI-TOF MS in Vitro (2013)

Background: Liver fibrosis leads to liver cirrhosis and even cancer progressively, but can be prevented through early detection. A reliable tissue biomarker is desirable in order to design a non-invasive diagnosing tool to complement invasive liver biopsy. Presently many studies have reported that the cannabinoid 1 receptor (CB1R) is associated with liver fibrosis, and therefore it is possible to measure the expression of CB1R for detecting the stages of liver fibrosis. The aim of this study was to measure the protein expression of CB1R via detecting its antagonist, AM251, utilizing biomedical techniques and matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometer in vitro. Methods: The rats were treated with/without 0.04% thioacetamide to induce each stage of liver fibrosis (F0-F4) which was determined by hematoxylin and eosin (H&E) staining according to METAVIR Classification. Immunohistochemistry was used to detect the expression and position of CB1R. Fluorescent microscopy was used to observe the binding capacity of tocriflour 1117 (T1117), a fluorescent analogue of AM251, to CB1R. MALDI-TOF MS was used to measure the amount of AM251 after incubating with liver fibrosis tissue sections. Results: CB1R overexpressed in the liver fibrosis tissues and increased from F0 to F4 stage. T1117 binding assay showed that AM251 could interact with CB1R specifically. Moreover, the quantification analysis of MALDITOF MS indicated that AM251 could present the amount of CB1R in each stage of liver fibrosis with increase from F0 to F4 (p＜0.05). Conclusion: We showed that CB1R overexpressed in liver fibrosis tissues as a reliable biomarker. The data imply that in vitro measurement of CB1R antagonist, AM251, may help distinguish the stages of liver fibrosis. Furthermore, we suggest that AM251 may be used as a detecting ligand and applied in nuclear imaging technique for diagnosing liver fibrosis.
Broadly neutralizing anti-HIV-1 antibodies disrupt a hinge-related function of gp41 at the membrane interface (2009)

A vaccine capable of stimulating protective antiviral antibody responses is needed to curtail the global AIDS epidemic caused by HIV-1. Although rarely elicited during the course of natural infection or upon conventional vaccination, the membrane-proximal ectodomain region (MPER) of the HIV-1 glycoprotein of M(r) 41,000 (gp41) envelope protein subunit is the target of 3 such human broadly neutralizing antibodies (BNAbs): 4E10, 2F5, and Z13e1. How these BNAbs bind to their lipid-embedded epitopes and mediate antiviral activity is unclear, but such information might offer important insight into a worldwide health imperative. Here, EPR and NMR techniques were used to define the manner in which these BNAbs differentially recognize viral membrane-encrypted residues configured within the L-shaped helix-hinge-helix MPER segment. Two distinct modes of antibody-mediated interference of viral infection were identified. 2F5, like 4E10, induces large conformational changes in the MPER relative to the membrane. However, although 4E10 straddles the hinge and extracts residues W672 and F673, 2F5 lifts up residues N-terminal to the hinge region, exposing L669 and W670. In contrast, Z13e1 effects little change in membrane orientation or conformation, but rather immobilizes the MPER hinge through extensive rigidifying surface contacts. Thus, BNAbs disrupt HIV-1 MPER fusogenic functions critical for virus entry into human CD4 T cells and macrophages either by preventing hinge motion or by perturbing MPER orientation. HIV-1 MPER features important for targeted vaccine design have been revealed, the implications of which extend to BNAb targets on other viral fusion proteins.
Enhancement of hydrothermal stability of Cu-ZSM5 catalyst for NO decomposition (2006)

RECu-ZSM5 samples (RE = La, Sm or Ce) have been prepared by ion-exchange of H-ZSM5 with rare earth and copper ions in an aqueous solution both simultaneously and consecutively (RE before copper), and their physico-chemical and catalytic properties in NO decomposition have been compared with those of a Cu-ZSM5 with a similar copper content. The catalysts have been characterized by N2 adsorption at 77 K (BET) and XRD before and after aging cycles under wet (2–2.5 vol % H2O) conditions at 450–500°C. NO decomposition tests have been carried out in a fixed bed reactor at 450°C under dry or wet conditions on both fresh and aged catalysts. NO adsorption tests have been performed at 120°C on the same samples. The addition of RE does not affect the crystalline structure, surface area, and porosity but strongly enhances the catalytic activity and the hydrothermal stability of Cu-ZSM5, which, on the contrary, is completely deactivated under wet conditions. The two-step exchanged catalysts provide better performances likely due to the larger RE exchange level obtained with this method. A unique linear correlation between the amount of N2O produced in the NO adsorption tests, related to the reoxidation of prereduced Cu+ sites, and the TOF, estimated from the catalytic activity tests, has been found for both fresh and aged catalysts.
Enzyme‐catalyzed synthesis of structured phospholipids with conjugated linoleic acid (2005)

Structured phospholipids were synthesized with the functional lipid conjugated linoleic acid (CLA). The lipase- and phospholipase A2-catalyzed enzymatic acidolysis reaction between phospholipids (PL) and CLA was used for fatty acid modification. Enzymatic processes were an effective way to produce structured PL. Screening of four lipases and immobilized phospholipase A2 and a combination of lipase and phospholipase showed that only Lipozyme RM IM and Lipozyme TL IM were effective in incorporation of CLA into PL. The maximum incorporation achieved by the latter enzyme was 16% with soy PL in 72 h.
Expression of the Listeria monocytogenes EGD inlA and inlB genes, whose products mediate bacterial entry into tissue culture cell lines, by PrfA-dependent and -independent mechanisms (1995)

Internalization of Listeria monocytogenes into nonphagocytic cell lines in vitro requires the products of the inlAB locus (J.-L. Gaillard, P. Berche, C. Frehel, E. Gouin, and P. Cossart, Cell 65:1127-1141, 1991). By generating isogenic mutants with a chromosomal in-frame deletion in either inlA or inlB, we have identified InlA and InlB as surface-bound proteins of L. monocytogenes with molecular weights of 88,000 and 65,000, respectively. These results were obtained with monoclonal antibodies raised against either protein and corroborated by N-terminal end sequencing of InlA and InlB. By immunoblot analysis, the production of both polypeptides was found to be strongly dependent on growth temperature and, particularly for InlB, on the presence of the PrfA regulator protein. Expression of InlA was not strictly dependent on the presence of the PrfA regulator protein. Transcription analysis of the inlAB locus revealed that the inlA gene was transcribed by several promoters, of which only one is PrfA dependent. This PrfA-dependent inlA promoter, which contains two base substitutions within its putative PrfA DNA-binding palindrome, is responsible for transcription of both inlA and inlB genes. A hitherto unrecognized promoter located 51 bp upstream of the GTG start codon of the inlB gene was also detected. Hence, inlA and inlB are transcribed both individually and in an operon by PrfA-dependent and -independent mechanisms. Tissue culture invasion assays employing various epithelial cell lines demonstrated that both InlA and InlB are required for invasion. In vivo studies using the mouse infection model revealed that both internalin mutants were attenuated for virulence.
Iron Overload and Iron Chelation Therapy in Thalassaemia and Sickle Cell Haemoglobinopathies (1987)

This paper reviews the factors governing the rate of iron loading and iron toxicity in the thalassaemia syndromes and sickle cell disease. It outlines the main determinants of iron mobilization by the iron-chelating drug, desferrioxamine, together with the effects of this drug in clinical practice.
Resolution of macular oedema in occult choroidal neovascularization under oral Sorafenib®treatment (2007)

Resolution of macular oedema and stabilization of VA under oral treatment with the multikinase inhibitor Sorafenib was observed. This observation warrants further investigation.
Neurogenesis in the Neocortex of Adult Primates (1999)

In primates, prefrontal, inferior temporal, and posterior parietal cortex are important for cognitive function. It is shown that in adult macaques, new neurons are added to these three neocortical association areas, but not to a primary sensory area (striate cortex). The new neurons appeared to originate in the subventricular zone and to migrate through the white matter to the neocortex, where they extended axons. These new neurons, which are continually added in adulthood, may play a role in the functions of association neocortex.
URIEL and lang2vec: Representing languages as typological, geographical, and phylogenetic vectors (2017)

Patrick Littell, David R. Mortensen, Ke Lin, Katherine Kairis, Carlisle Turner, Lori Levin. Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 2, Short Papers. 2017.
Catalytic Asymmetric Cyclopropanation of Heteroaryldiazoacetates (2001)

Rh(2)(S-DOSP)(4)-catalyzed decomposition of heteroaryldiazoacetates in the presence of styrene results in highly diastereoselective and enantioselective cyclopropanations. Heteroaryldiazoacetates containing both electron-rich and electron-deficient heterocycles, such as thiophene, furan, pyridine, indole, oxazole, isoxazole, and benzoxazole, are effective in this chemistry. These studies broaden the range of diazo compounds containing both electron-withdrawing and electron-donating groups, which undergo highly diastereoselective cyclopropanations.
Image based obstacle detection for automatic train supervision (2012)

This paper focuses on the track obstacle detection based on image processing, analyzes and improves the Image gray-scale algorithm, Image binarization algorithm, Canny edge detection algorithm, and designs the detection window to rule out the useless information. As a result, we come up with three obstacle detection algorithms based on image feature extraction and feature analysis: Method based on Gray Level Histogram, Method based on the Proportion of Black and White Pixels, Method based on the integrity of the Rails and Sleepers. Finally, we take use of the server/client distributed model to design an automatically track detection system, which uses wireless communications. Through the experiment, the desired results have been obtained.
Field-Effect Transistors Based on a Benzothiadiazole−Cyclopentadithiophene Copolymer (2007)

We present a solution processed organic field-effect transistor based on a benzothiadiazole (BTZ)−cyclopentadithiophene (CDT) copolymer with mobilities as high as 0.17 cm2/Vs and an on/off ratio of 105. This pronounced performance together with the lack of macroscopic order in the thin film makes this conjugated copolymer an attractive candidate for low-cost organic electronics due to its facile processing.
Recurrence of left atrium-pulmonary vein conduction following successful disconnection in asymptomatic patients (2004)

Successful pulmonary vein isolation with abolition of paroxysmal atrial fibrillation does not confer permanent disconnection of the pulmonary vein musculature from the left atrium.
Fibronectin's III-1 module contains a conformation-dependent binding site for the amino-terminal region of fibronectin. (1994)

Cultured fibroblasts express binding sites for the amino-terminal region of fibronectin on their cell surface that mediate the assembly of soluble fibronectin into disulfide-stabilized fibrils. These binding sites have been termed matrix assembly sites and have been studied in binding assays using a 125I-labeled 70-kDa fragment derived from the amino terminus of fibronectin. In an attempt to isolate the protein(s) responsible for binding the 70-kDa fragment, cell surface proteins were cleaved from fibroblast monolayers by mild trypsinization. Trypsinization of monolayers generated a series of fibronectin fragments that bound the 125I-labeled 70-kDa fragment by ligand blot assay and affinity chromatography. All of the fibronectin fragments that bound the 70-kDa fragment contained the III-1 module. In solid phase binding assays, the 125I-labeled 70-kDa fragment bound preferentially to reduced fibronectin as compared with unreduced fibronectin fragments. Binding of the 125I-labeled 70-kDa fragment to reduced fibronectin was inhibited by a monoclonal antibody directed against the III-1 domain. Isolated III-1, however, did not bind the 125I-labeled 70-kDa fragment when adsorbed to plastic tissue culture wells. Heat denaturation of III-1 prior to adsorption conferred 70-kDa fragment binding properties on the isolated module. The 125I-labeled 70-kDa fragment did not bind to heat-denatured III-2, suggesting that 70-kDa fragment binding was a property of the III-1 module and not a general characteristic of all type III modules. The binding of 125I-labeled 70-kDa fragment to III-1 was of high affinity (KD = 1.8 x 10(-8) M). These results indicate that a binding site for the 70-kDa amino terminus of fibronectin is contained within a cryptic site found in the first type III module of fibronectin. Unfolding of the III-1 module on the cell surface may control matrix assembly site expression and represent an important step in the initiation of cell-dependent fibronectin polymerization.
Flat-plate solar array project. Volume 3: Silicon sheet: Wafers and ribbons (1986)

The primary objective of the Silicon Sheet Task of the Flat-Plate Solar Array (FSA) Project was the development of one or more low cost technologies for producing silicon sheet suitable for processing into cost-competitive solar cells. Silicon sheet refers to high purity crystalline silicon of size and thickness for fabrication into solar cells. Areas covered in the project were ingot growth and casting, wafering, ribbon growth, and other sheet technologies. The task made and fostered significant improvements in silicon sheet including processing of both ingot and ribbon technologies. An additional important outcome was the vastly improved understanding of the characteristics associated with high quality sheet, and the control of the parameters required for higher efficiency solar cells. Although significant sheet cost reductions were made, the technology advancements required to meet the task cost goals were not achieved.
Rendering barium titanate semiconductive by doping with rareearth elements (1988)

Abstract Distribution of doping cations between A and B sites of perovskite ABO3 structure obeys certain conditions derived in terms of energy. These can be applied to predict semiconducting BaTiO3-based compositions, to account for yet unexplained anomalies in concentrational dependencies of electrical resistivity and Curie temperature, and to understand the relatively unimportant effect of doping in the case of solid solutions such as Ba1−x Sr x TiO3 and Ba1−x Ca x TiO3.
Nitric oxide synthase activity in hyperthyroid and hypothyroid rats (2002)

These data indicated that NOS activity was upregulated in tissues primarily related to blood pressure control in hyperthyroid rats, suggesting that an increased NO production may contribute to the hyperdynamic circulation in hyperthyroidism and may have a protective homeostatic effect in the target organs of the hypertension that accompanies this endocrine disease. The aortic and renal findings in hypothyroid rats suggested a possible role for NOS in the increased peripheral resistance and the normal pressure-diuresis-natriuresis response of these hypotensive animals, although hypothyroidism produced a heterogeneous tissue response in NOS activity.
Obesity and endothelial function (2004)

Purpose of review The growing prevalence of diabetes and coronary artery disease (CAD) parallels the increased prevalence of obesity. This review explains the pathogenic role of excessive fat accumulation, especially the visceral fat in altering endothelial function. It clarifies the link between adipose tissue function, insulin resistance, and vascular reactivity. In addition, it demonstrates the role of lifestyle modification in improving endothelial function in obese individuals. Recent findings We demonstrated our most recent understanding of the pathogenesis of endothelial dysfunction as an initial step in the atherosclerotic process, and how inflammation plays a major important role in its development. The emerging hypothesis that increased secretion of adipokines by adipose tissue, particularly visceral adipocytes, are responsible for initiating subclinical inflammatory status that contribute to the development of both insulin resistance and endothelial dysfunction are covered. We also reviewed several recent studies that showed the effect of weight reduction by diet restriction, increased physical activity, medications, or surgical intervention in changing insulin sensitivity and endothelial function. Summary Better understanding of the link between obesity and endothelial function may help clinicians to build a comprehensive strategy aiming at reducing the cardiovascular mortality among type 2 diabetic patients through lifestyle modification with or without medications. It will also serve as background to further research projects aiming at selective reduction of adipose tissues burden by identifying the modifiable and the nonmodifiable targets.
Differentiation among spotted fever group rickettsiae species by analysis of restriction fragment length polymorphism of PCR-amplified DNA (1994)

Restriction fragment length polymorphism (RFLP) analysis of PCR-amplified genes was used to study spotted fever group (SFG) rickettsiae, extending the previous work of Regnery et al. (R.L. Regnery, C.L. Spruill, and B.D. Plikaytis, J. Bacteriol. 173:1576-1589, 1991). Twenty-six strains of SFG rickettsia were studied, including several recognized species which have never been studied (R. parkeri, R. helvetica, and R. japonica) as well as strains which are not currently classified. Two previously used primer pairs derived from the R. prowazekii citrate syntase gene and the R. rickettsii 190-kDa protein antigen gene were studied, as were primer pairs obtained from the R. rickettsii 120-kDa protein antigen gene. By using three amplifications and three enzyme digestions, it was possible to differentiate between almost all of the known SFG rickettsia species and to differentiate between several strains of the R. conorii complex. Two human pathogens, "R. africae" and the Israeli tick typhus rickettsia, were first separated by using BG-12 pair primer amplification and then RsaI restriction endonuclease digestion. The proposed simplified model of identification may be useful in studying the geographical distributions of SFG rickettsiae.