gebhart/patrepeval huggingface dataset:
Surface-loop residue Lys316 in blood coagulation Factor IX is a major determinant for Factor X but not antithrombin recognition (2000)

The active site of activated Factor IX (FIXa) and related blood-coagulation enzymes is surrounded by a number of highly variable surface loops, which contribute to the characteristic substrate specificity of each individual enzyme. FIX residue Lys(316) is located in one of these loops and mutation of this residue to Glu is associated with haemophilia B. In the present study we investigated the functional role of Lys(316) in human FIXa by analysing the purified and activated FIX mutants FIXa-K316E and FIXa-K316A. FIXa-K316E was indistinguishable from normal FIXa in binding the competitive active-site inhibitor p-aminobenzamidine. In addition, substitution of Glu for Lys(316) had no significant effect on the reactivity towards various synthetic tripeptide substrates. Inhibition by the macromolecular inhibitor antithrombin was only slightly reduced for both FIXa mutants (less than 2-fold). In contrast, proteolytic activity of FIXa-K316E towards the natural substrate Factor X (FX) was virtually lacking, while the Lys(316) to Ala mutation resulted in a more than 10-fold reduction in FX activation. Thus residue Lys(316) plays a key role in FIXa activity towards FX. The requirement for Lys at position 316 for FX activation was also evident in the presence of the cofactor activated Factor VIII, although to a lesser extent than in its absence. These data demonstrate that Lys(316) specifically determines the reactivity of FIXa towards its natural substrate FX, but not to synthetic peptide substrates or antithrombin.
Complete remission of experimental arthritis by joint targeting of glucocorticoids with long‐circulating liposomes (2003)

Targeted delivery using long-circulating liposomes is a promising, novel means to successfully intervene in arthritis with glucocorticoid therapy.
Cellular Apoptosis Susceptibility Gene Expression in Endometrial Carcinoma: Correlation With Bcl-2, Bax, and Caspase-3 Expression and Outcome (2001)

Deregulation of proliferation and apoptosis is known to contribute to neoplastic transformation and growth. Using specific antibodies for the cellular apoptosis susceptibility (CAS) gene, caspase-3, Bcl-2, and Bax, we examined the protein expression in 89 endometrial carcinomas and in 56 samples of nonneoplastic adjacent endometrium for comparison. Immunostaining results were scored with regard to approximate percentage of positive tumor cells (< 10%, 10% to 50%, > 50%) and relative immunostaining intensity (1+, 2+, 3+). In nonneoplastic endometrium, CAS protein was expressed in 70.6%, Bax in 64%, caspase-3 in 52%, and Bcl-2 in 87%. In neoplastic tissue, CAS was present in 93% of the tumors, Bax in 88%, caspase-3 in 77%, and Bcl-2 in 51%. Bcl-2:Bax ratio was > 1 in 9 cases (10%). In cases of atrophy (n = 24) and simple (n = 10) and complex (n = 22) hyperplasia in the adjacent endometrium, lower levels of expression compared with carcinoma were observed for CAS (p = 0.003), caspase-3 (p = 0.034), and Bax (p = 0.04) and higher levels for Bcl-2, although for this protein the results were not statistically significant (p = 0.32). There was no association between immunoscores and FIGO stage. High caspase-3 levels were seen in endometrioid tumor type (p = 0.017). CAS expression was higher in grade 3 tumors (p = 0.002) and older patients (p = 0.013). All tumors of younger patients (< 50 years) were Bcl-2 negative (p = 0.037). Caspase-3 correlated positively with CAS (p = 0.008), Bax (p = 0.04), and low Bcl-2:Bax ratio (p = 0.043), and inversely (as a trend) with Bcl-2 (p = 0.056). Survival analysis (Kaplan-Meier and Cox regression) established a strong association between prognosis and stage, grade, and histologic type (all p < or = 0.0036). In addition, shorter survival was observed for patients whose tumors contained > 50% of positive cells for caspase-3 (p = 0.024) or for CAS (p = 0.04). Age, Bcl-2, Bax, and Bcl-2:Bax ratio did not provide prognostic information. Our results suggest a role of CAS, Bcl-2, Bax, and caspase-3, which are apparently involved in the progressive deregulation of proliferation and apoptosis leading from simple and complex hyperplasia to carcinoma. In addition, CAS and caspase-3 protein levels may be useful markers in predicting the outcome of the patients.
AC133-2, a Novel Isoform of Human AC133 Stem Cell Antigen (2002)

Human AC133 antigen, also called CD133, was recently identified as a hematopoietic stem cell marker. However, the molecular structure and function of this protein has remained unclear. Here we cloned and identified a novel isoform of AC133, which we named AC133-2. In comparison to the reported AC133 cDNA, which is referred to herein as AC133-1, a small exon of 27 nucleotides is deleted in AC133-2 by alternative mRNA splicing. Similar to the previously characterized AC133 antigen, recombinant AC133-2 expressed in 293 cells was glycosylated and transported to plasma membrane. AC133-2 mRNA was found predominant in a variety of human fetal tissue, adult tissues, and several carcinomas. In contrast, AC133-1 mRNA was more prominent in fetal brain and adult skeletal muscle but was not detected in fetal liver and kidney, adult pancreas, kidney, and placenta, suggesting different roles for the two isoforms in fetal development and mature organ homeostasis. Here, we demonstrate that AC133-2 is the isoform expressed on hematopoietic stem cells derived from fetal liver, bone marrow, and peripheral blood. The results indicate that AC133-2, not AC133-1, has been the cell surface antigen recognized by anti-AC133 monoclonal antibodies that are used for isolation of hematopoietic stem cells. To further investigate its expression in other stem cell populations, we found that AC133-2 co-expressed with beta(1) integrin in the basal layer of human neonatal epidermis. AC133-2(+)/beta(1) integrin(+) cells proliferated and differentiated in culture, which coincided with a loss of AC133-2 and gain in a terminal differentiation marker involucrin. Taken together, these results suggest that AC133-2 is expressed in multiple stem cell niches and may provide a means to isolate specific stem cell subpopulations from human tissues.
Research on the Effects of Drying Temperature on Nitrogen Detection of Different Soil Types by Near Infrared Sensors (2018)

Soil is a complicated system whose components and mechanisms are complex and difficult to be fully excavated and comprehended. Nitrogen is the key parameter supporting plant growth and development, and is the material basis of plant growth as well. An accurate grasp of soil nitrogen information is the premise of scientific fertilization in precision agriculture, where near infrared sensors are widely used for rapid detection of nutrients in soil. However, soil texture, soil moisture content and drying temperature all affect soil nitrogen detection using near infrared sensors. In order to investigate the effects of drying temperature on the nitrogen detection in black soil, loess and calcium soil, three kinds of soils were detected by near infrared sensors after 25 °C placement (ambient temperature), 50 °C drying (medium temperature), 80 °C drying (medium-high temperature) and 95 °C drying (high temperature). The successive projections algorithm based on multiple linear regression (SPA-MLR), partial least squares (PLS) and competitive adaptive reweighted squares (CARS) were used to model and analyze the spectral information of different soil types. The predictive abilities were assessed using the prediction correlation coefficients (R<sub>P</sub>), the root mean squared error of prediction (RMSEP), and the residual predictive deviation (RPD). The results showed that the loess (R<sub>P</sub> = 0.9721, RMSEP = 0.067 g/kg, RPD = 4.34) and calcium soil (R<sub>P</sub> = 0.9588, RMSEP = 0.094 g/kg, RPD = 3.89) obtained the best prediction accuracy after 95 °C drying. The detection results of black soil (R<sub>P</sub> = 0.9486, RMSEP = 0.22 g/kg, RPD = 2.82) after 80 °C drying were the optimum. In conclusion, drying temperature does have an obvious influence on the detection of soil nitrogen by near infrared sensors, and the suitable drying temperature for different soil types was of great significance in enhancing the detection accuracy.
T Cell Dysfunction in Cancer Immunity and Immunotherapy (2019)

In cancer, T cells become dysfunctional owing to persistent antigen exposure. Dysfunctional T cells are characterized by reduced proliferative capacity, decreased effector function, and overexpression of multiple inhibitory receptors. Due to the presence of various inhibitory signals in the complex tumor microenvironment, tumor-specific T cells have distinct dysfunction states. Therapeutic reactivation of tumor-specific T cells has yielded good results in cancer patients. Here, we review the hallmarks of T cell dysfunction in cancer. Also, we discuss the relationship between T cell dysfunction and cancer immunotherapy.
Schottky diode with Ag on (1120) epitaxial ZnO film (2002)

Silver Schottky contacts were fabricated on (112̄0) n-ZnO epilayers, which were grown on R-plane sapphire substrates by metalorganic chemical-vapor deposition. The flatband barrier height was determined to be 0.89 and 0.92 eV by current–voltage and capacitance–voltage measurements, respectively. The ideality factor was found to be 1.33.
Robust Image Retargeting via Axis‐Aligned Deformation (2012)

Abstract We propose the space of axis‐aligned deformations as the meaningful space for content‐aware image retargeting. Such deformations exclude local rotations, avoiding harmful visual distortions, and they are parameterized in 1D. We show that standard warping energies for image retargeting can be minimized in the space of axis‐aligned deformations while guaranteeing that bijectivity constraints are satisfied, leading to high‐quality, smooth and robust retargeting results. Thanks to the 1D parameterization, our method only requires solving a small quadratic program, which can be done within a few milliseconds on the CPU with no precomputation overhead. We demonstrate how the image size and the saliency map can be changed in real time with our approach, and present results on various input images, including the R etarget M e benchmark. We compare our results with six other algorithms in a user study to demonstrate that the space of axis‐aligned deformations is suitable for the problem at hand.
Evaluation of a nanocomposite hydrogel for water shut‐off in enhanced oil recovery applications: Design, synthesis, and characterization (2012)

Abstract This work involves the synthesis of a nanocomposite hydrogel from just polymer and clay without the use of conventional organic crosslinkers. Conventional hydrogel design usually involves a multicomponent reaction that incorporates monomer (or polymer), initiator, and an organic crosslinker. However, because of the many limitations, setbacks, and inconsistencies involved with organic crosslinkers, authors herein present a nanocomposite hydrogel that incorporates polymer and clay only. It was found that these hydrogels show surprising mechanical toughness, tensile moduli, and tensile strengths. Study of gel behavior reveal physical interaction between polymer and clay, due in part to adsorption of polymer chains onto clay surface and ionic interactions between anionic carboxylate groups of polymer chains and positive clay surface. X‐ray diffraction patterns and Scanning Electron Microscopy revealed the formation of intercalated and exfoliated clay morphology. Increase in clay concentration and gel strength had a direct proportionality. The effect of clay concentration on hydrogel decomposition temperature was also reported by thermogravimetric analysis. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
The Total Synthesis of Iboga Alkaloids1 (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Total Synthesis of Iboga Alkaloids1G. Büchi, D. L. Coffen, Karoly Kocsis, P. E. Sonnet, and Frederick E. ZieglerCite this: J. Am. Chem. Soc. 1966, 88, 13, 3099–3109Publication Date (Print):July 1, 1966Publication History Published online1 May 2002Published inissue 1 July 1966https://pubs.acs.org/doi/10.1021/ja00965a039https://doi.org/10.1021/ja00965a039research-articleACS PublicationsRequest reuse permissionsArticle Views1382Altmetric-Citations89LEARN 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
Power spectrum of current-induced magnetization dynamics in uniaxial nanomagnets (2007)

Nanomagnets with uniaxial symmetry driven by spin polarized currents are considered, in which anisotropy, applied field, and spin polarization are all aligned along the symmetry axis. Thermal fluctuations are taken into account by adding a Gaussian white noise stochastic term to the equation for the deterministic dynamics. The corresponding Fokker-Planck equation is derived and it is solved by using separation of variable and eigenfunction expansion techniques. From the solution of the Fokker-Planck equation, the autocorrelation function and the power spectral density of magnetization are computed. The position and the linewidth of the peaks in the power spectral density are discussed in detail.
Conjugation to Hyperbranched Polyglycerols Improves RGD-Mediated Inhibition of Platelet Function in Vitro (2008)

RGD (arginine-glycine-aspartic acid) is a known peptide sequence that binds platelet integrin GPIIbIIIa and disrupts platelet-fibrinogen binding and platelet cross-linking during thrombosis. RGD peptides are unsuitable for clinical applications due to their high 50% inhibitory concentration (IC50) and low in vivo residence times. We addressed these issues by conjugating RGD peptides to biocompatible macromolecular carriers: hyperbranched polyglycerols (HPG) via divinyl sulfone. The GPIIbIIIa binding activity of RGD was maintained after conjugation and the effectiveness of the HPG-RGD conjugate was dependent upon molecular weight and the number of RGD peptides attached to each HPG molecule. These polyvalent inhibitors of platelet aggregation decreased the IC50 of RGD in an inverse linear manner based on the number of RGD peptides per HPG. Since HPG-RGD conjugates do not cause platelet activation by degranulation and certain substitution ratios do not increase fibrinogen binding to resting platelets, HPG-RGD may serve as a model for a novel class of antithrombotics.
Facilitating the Culture of Mammalian Nerve Cells with Polyelectrolyte Multilayers (2006)

When neuron-like cells (NLCs) derived from pluripotent embryonal carcinoma cells (P19) are cultured on bare tissue culture substrates, they require a monolayer of fibroblast cells to exhibit normal neurite outgrowth, behavior typical of neuronal cultures. However, substrate treatment with polyelectrolyte multilayers (PEMs) composed of poly(allylamine hydrochloride) (PAH) and poly(styrenesulfonic acid) (PSS) significantly improved these cultures. Cell morphology was more spread, indicative of healthy cells, and direct attachment of neuronal cell bodies to the treated surface was observed. Neuronal outgrowth across the surface was not dependent on an underlying fibroblast monolayer with the PEMs surface treatment. Additionally, the PEMs surface treatment can be used to condition various surfaces, facilitating neuronal cultures on surfaces which are natively hydrophilic (tissue culture polystyrene) or hydrophobic (poly(dimethylsiloxane), PDMS). Microfluidic networks were used to micropattern the PEMs onto PDMS, resulting in confined regions of cellular attachment and directed neuronal outgrowth. The ability of PEMs to encourage NLC attachment without supporting cells to a variety of surfaces and surface geometries greatly simplifies neuronal culture methodology and enables neuronal investigations in new environments.
Role of Lactobacillus plantarum MTCC1325 in membrane-bound transport ATPases system in Alzheimer’s disease-induced rat brain (2016)

<i><b>Introduction:</b></i> Alzheimer's disease (AD) is a neurodegenerative disorder, clinically characterized by memory dysfunction and progressive loss of cognition. No curative therapeutic or drug is available for the complete cure of this disease. The present study was aimed to evaluate the efficacy of <i>Lactobacillus plantarum</i> MTCC1325 in ATPases activity in the selected brain regions of rats induced with Alzheimer's. <i><b>Methods:</b></i> For the study, 48 healthy Wistar rats were divided into four groups: group I as control group, group II as AD model (AD induced by intraperitoneal injection of D-Galactose, 120 mg/kg body weight for 6 weeks), group III as normal control rats which were orally administered only with <i>L. plantarum</i> MTCC1325 for 60 days, and group IV where the AD-induced rats simultaneously received oral treatment of <i>L. plantarum</i> MTCC1325 (10ml/kg body weight, 12×10<sup>8</sup> CFU/mL) for 60 days. The well known membrane bound transport enzymes including Na<sup>+</sup>, K<sup>+</sup>-ATPases, Ca<sup>2+</sup>-ATPases, and Mg<sup>2+</sup>-ATPases were assayed in the selected brain regions of hippocampus and cerebral cortex in all four groups of rats at selected time intervals. <i><b>Results:</b></i> Chronic injection of D-Galactose caused lipid peroxidation, oxidative stress, and mitochondrial dysfunction leading to the damage of neurons in the brain, finally bringing a significant decrease (-20%) in the brain total membrane bound ATPases over the controls. Contrary to this, treatment of AD-induced rats with <i>L. plantarum</i> MTCC1325 reverted all the constituents of ATPase enzymes to near normal levels within 30 days. <i><b>Conclusion:</b></i><i>Lactobacillus plantarum</i> MTCC1325 exerted a beneficial action on the entire ATPases system in AD-induced rat brain by delaying neurodegeneration.
An Antagonist of Dishevelled Protein-Protein Interaction Suppresses β-Catenin–Dependent Tumor Cell Growth (2007)

Recent progress in the development of inhibitors of protein-protein interactions has opened the door for developing drugs that act by novel and selective mechanisms. Building on that work, we designed a small-molecule inhibitor of the Wnt signaling pathway, which is aberrantly activated across a wide range of human tumors. The compound, named FJ9, disrupts the interaction between the Frizzed-7 Wnt receptor and the PDZ domain of Dishevelled, down-regulating canonical Wnt signaling and suppressing tumor cell growth. The antitumorigenic effects of FJ9 were pronounced, including induction of apoptosis in human cancer cell lines and tumor growth inhibition in a mouse xenograft model. FJ9 is thus among the first non-peptide inhibitors to show therapeutic efficacy through disruption of PDZ protein-protein interactions.
Expression of a swine class II gene in murine bone marrow hematopoietic cells by retroviral-mediated gene transfer. (1991)

As a first step in assessing the efficacy of a gene transfer approach to the induction of transplantation tolerance in our miniature swine model, double-copy retroviral vectors engineered to express a drug-resistance marker (neomycin) and a swine class II DRB cDNA were constructed. Infectious particles containing these vectors were produced at a titer of greater than 1 x 10(6) G418-resistant colony-forming units/ml using both ecotropic and amphotropic packaging cell lines. Flow cytometric analysis of DRA-transfected murine fibroblasts subsequently transduced with virus-containing supernatants demonstrated that the transferred sequences were sufficient to produce DR surface expression. Cocultivation of murine bone marrow with high-titer producer lines leads to the transduction of 40% of granulocyte/macrophage colony-forming units (CFU-GM) as determined by the frequency of colony formation under G418 selection. After nearly 5 weeks in long-term bone marrow culture, virus-exposed marrow still contained G418-resistant CFU-GM at a frequency of 25%. In addition, virtually all of the transduced and selected colonies contained DRB-specific transcripts. These results suggest that a significant proportion of very primitive myelopoietic precursor cells can be transduced with the DRB recombinant vector and that vector sequences are expressed in the differentiated progeny of these cells.
The Next Frontier (2009)

Abstract Asia is the next frontier in the campaign to end state execution because more than 95 percent of the executions in the world take place there. This book combines detailed case studies of the death penalty in major Asian nations with cross-national comparisons. It demonstrates decline in the number of Asian countries using execution as a criminal sanction and a decline in the rate of executions in most nations that retain the death penalty. Few Asian nations conduct executions with any regularity, and even major nations with death penalties in their criminal codes use the sanction rarely. What separates the low-execution nations from the very few states with high execution rates is, more than anything, politics. All of Asia's high execution states are hard-line authoritarian regimes of the left or right. When former right-wing authoritarian states experience democratic reforms, the rate of executions drops sharply and the only noncommunist government that maintains high executions is Singapore. The key question is not whether Asia will end state executions, but when it can be expected to do so. If the end of executions depends on the democratization of relatively stable hard-line communist regimes, many decades may be required, but if the stigma of state executions continues to increase, the end of capital punishment in Asia could happen before more comprehensive political change occurs.
Interactive Image Segmentation via Adaptive Weighted Distances (2007)

An interactive algorithm for soft segmentation of natural images is presented in this paper. The user first roughly scribbles different regions of interest, and from them, the whole image is automatically segmented. This soft segmentation is obtained via fast, linear complexity computation of weighted distances to the user-provided scribbles. The adaptive weights are obtained from a series of Gabor filters, and are automatically computed according to the ability of each single filter to discriminate between the selected regions of interest. We present the underlying framework and examples showing the capability of the algorithm to segment diverse images.