gebhart/patrepeval huggingface dataset:
Assessment of methods for covalent binding of nucleic acids to magnetic beads, DynabeadsTM, and the characteristics of the bound nucleic acids in hybridization reactions (1988)

Dynabeads are magnetic monosized beads with high stability, high uniformity, unique paramagnetic properties, low particle-particle interaction, and high dispersibility. Different reactive groups; hydroxyl, carboxyl and amino groups can be attached to the surface. Several methods for covalent attachment of DNA or oligonucleotides to the beads were investigated. Best coupling yields were obtained by carbodiimide-mediated end-attachment of 5'-phosphate and 5'-NH2 modified nucleic acids to respectively amino and carboxyl beads. The carboxyl beads showed a low degree of non-specific binding, while a better yield of end-attached nucleic acids was obtained using the amino beads. The DNA-beads worked efficiently in hybridization experiments, and the kinetics of hybridization approach those of solution hybridization.
Anti-Kaposi’s Sarcoma and Antiangiogenic Activities of Sulfated Dextrins (1999)

Delivery of the sulfated polysaccharide dextrin 2-sulfate by the intraperitoneal route to the lymphatic circulation resulted in a clinically significant improvement in Kaposi's sarcoma in three patients. Our in vitro studies show that although sulfated dextrins do not interfere with the growth of isolated human umbilical vein endothelial cells, they do inhibit the morphological differentiation of endothelial cells into tubes as well as reduce new vessel formation in a placental angiogenesis assay. The antiangiogenic effect of dextrin 6-sulfate is greater than that of dextrin 2-sulfate and is independent of their anti-human immunodeficiency virus type 1 activities.
Apoptosis in resolution of inflammation (1997)

The last few years have seen the accumulation of compelling evidence that apoptosis (programmed cell death) plays a major role in promoting resolution of the acute inflammatory response. Neutrophils are constitutively programmed to undergo apoptosis, which limits their pro-inflammatory potential and leads to rapid, specific, and non-phlogistic recognition by macrophages and semi-professional phagocytes. Similar mechanisms have been implicated in clearance of eosinophils, lymphocytes, and monocytes and apoptosis also plays a role in remodeling the inflamed site by deletion of myofibroblasts. A growing understanding of the mechanisms regulating leukocyte apoptosis and of the molecules mediating safe phagocytic clearance of dying cells may yield new insights into the pathogenesis and therapy of inflammatory diseases.
Significance of cyclin D1 overexpression for the diagnosis of mantle cell lymphoma: a clinicopathologic comparison of cyclin D1-positive MCL and cyclin D1-negative MCL-like B-cell lymphoma. (2000)

Mantle cell lymphoma (MCL) is a distinct clinicopathologic entity of non-Hodgkin's lymphoma, characterized by a monotonous proliferation of small to medium-sized lymphocytes with co-expression of CD5 and CD20, an aggressive and incurable clinical course, and frequent t(11;14)(q13;q32) translocation. We examined 151 cases of lymphoma with MCL morphology from a viewpoint of cyclin D1 overexpression, which is now easily detectable by immunohistochemistry. 128 cases (85%) showed positive nuclear staining for cyclin D1, while the remaining 23 (15%) were negative. Except for cyclin D1 immunohistochemistry, current diagnostic methods, including morphological and phenotypical examinations, could not make this distinction. Although both the cyclin D1-positive and -negative groups were characterized by male predominance, advanced stages of the disease, frequent extranodal involvement, and low CD23 reactivity, the cyclin D1-positive group showed a higher age distribution (P =.04), larger cell size (P =.02), higher mitotic index (P =.01), more frequent gastrointestinal involvement (P =.05), higher international prognostic index score (P =.05), and lower p27(KIP1) expression (P <.0001). Of particular interest is that cyclin D1-positive MCL showed significantly worse survival than cyclin D1-negative lymphoma (5-year survival: 30% versus 86%, P =.0002), which was confirmed by multivariate analysis to be independent of other risk factors. These data suggest that cyclin D1-positive and -negative groups may represent different entities and that the former closely fits the characteristics of classical, typical MCL. We therefore propose that cyclin D1-positivity should be included as one of the standard criteria for MCL, and that innovative therapies for this incurable disease should be explored on the basis of the new criteria.
Histone deacetylase inhibitors reduce polyglutamine toxicity (2001)

Polyglutamine diseases include at least nine neurodegenerative disorders, each caused by a CAG repeat expansion in a different gene. Accumulation of mutant polyglutamine-containing proteins occurs in patients, and evidence from cell culture and animal experiments suggests the nucleus as a site of pathogenesis. To understand the consequences of nuclear accumulation, we created a cell culture system with nuclear-targeted polyglutamine. In our system, cell death can be mitigated by overexpression of full-length cAMP response element binding protein (CREB)-binding protein (CBP) or its amino-terminal portion alone. CBP is one of several histone acetyltransferases sequestered by polyglutamine inclusions. We found histone acetylation to be reduced in cells expressing mutant polyglutamine. Reversal of this hypoacetylation, which can be achieved either by overexpression of CBP or its amino terminus or by treatment with deacetylase inhibitors, reduced cell loss. These findings suggest that nuclear accumulation of polyglutamine can lead to altered protein acetylation in neurons and indicate a novel therapeutic strategy for polyglutamine disease.
Tissue-dependent regulation of protein tyrosine kinase activity during embryonic development. (1991)

Protein tyrosine kinase activity was assayed in a variety of chicken tissues during embryonic development and in the adult. In some tissues protein tyrosine kinase activity decreased during embryonic development; however, in other tissues it remained high throughout development, it contrast to the level of protein tyrosine phosphorylation, which decreased during development. The highest levels of tyrosine kinase activity were detected in 17-d embryonic brain although only low levels of protein tyrosine phosphorylation were observed in this tissue. Several alternatives were examined in an effort to determine the mechanism responsible for the low levels of tyrosine phosphorylated proteins in most older embryonic and adult chicken tissues despite the presence of highly active tyrosine kinases. The results show that the regulation of protein tyrosine phosphorylation during embryonic development is complex and varies from tissue to tissue. Furthermore, the results suggest that protein tyrosine phosphatases play an important role in regulating the level of phosphotyrosine in proteins of many older embryonic and adult tissues.
In Situ Vaccination With a TLR9 Agonist Induces Systemic Lymphoma Regression: A Phase I/II Study (2010)

In situ tumor vaccination with a TLR9 agonist induces systemic antilymphoma clinical responses. This maneuver is clinically feasible and does not require the production of a customized vaccine product.
Graphene Analogues of BN: Novel Synthesis and Properties (2010)

Enthused by the fascinating properties of graphene, we have prepared graphene analogues of BN by a chemical method with a control on the number of layers. The method involves the reaction of boric acid with urea, wherein the relative proportions of the two have been varied over a wide range. Synthesis with a high proportion of urea yields a product with a majority of 1-4 layers. The surface area of BN increases progressively with the decreasing number of layers, and the high surface area BN exhibits high CO(2) adsorption, but negligible H(2) adsorption. Few-layer BN has been solubilized by interaction with Lewis bases. We have used first-principles simulations to determine structure, phonon dispersion, and elastic properties of BN with planar honeycomb lattice-based n-layer forms. We find that the mechanical stability of BN with respect to out-of-plane deformation is quite different from that of graphene, as evident in the dispersion of their flexural modes. BN is softer than graphene and exhibits signatures of long-range ionic interactions in its optical phonons. Finally, structures with different stacking sequences of BN have comparable energies, suggesting relative abundance of slip faults, stacking faults, and structural inhomogeneities in multilayer BN.
Human Vascular Adhesion Protein-1 (VAP-1) Plays a Critical Role in Lymphocyte–Endothelial Cell Adhesion Cascade Under Shear (2000)

Lymphocyte binding to vascular endothelium is a prerequisite for the movement of immune cells from the blood into lymphoid tissues and into sites of inflammation. Human vascular adhesion protein-1 (VAP-1) is an endothelial glycoprotein involved in this interaction. It also displays an enzymatic (monoamine oxidase) activity. Here we examined how recombinant human VAP-1 mediates lymphocyte binding using rotatory and flow chamber binding assays. VAP-1 cDNA transfected into an endothelial cell line, which does not bind lymphocytes, renders the cell line capable of binding lymphocytes in a shear-dependent manner. VAP-1 transfectants bound lymphocytes 5 times better than monocytes with a preference for T killer cells, and no specific granulocyte adherence was detectable. The binding is partially inhibited by anti-VAP-1 monoclonal antibodies or by blocking lymphocyte L-selectin and CD18 integrins, but not by inhibition of several other homing-associated molecules. In contrast, CD44 ligation on lymphocytes markedly upregulates their VAP-1-dependent adhesion, suggesting that the VAP-1 counterreceptor can be activated via CD44. The transfectant model also allowed us to perform detailed structure-function analyses of VAP-1. We show that the exposed integrin-binding motif RGD or the enzymatic activity is not indispensable for VAP-1-dependent adhesion. Together, these data show that VAP-1 can reconstitute the lymphocyte-endothelial adhesion cascade under shear and propose a critical role for VAP-1 in lymphocyte emigration from the blood.
The type‐III Fe receptor from Streptococcus dysgalactiae is also an α2‐macroglobulin receptor (1994)

We have cloned and sequenced the gene for a type‐III Fe receptor from a Streptococcus dysgalactiae strain isolated from bovine mastitis and report here the complete sequence of the gene. The 1992‐nucleotides‐long open reading frame codes for a protein of 664 amino acids with a predicted molecular mass of 72 kDa (including the signal peptide). The C‐terminal part of the protein is very similar to other streptococcal type‐III receptors but contains five homologous IgG‐binding domains compared to two or three in earlier reported Fe receptors of this type. Upstream of the IgG‐binding domains, there is a unique sequence containing short repeated motifs. Subeloning different parts of the gene and expressing them as maltose‐binding fusion proteins revealed that the upstream part is mediating binding to the plasma proteinase inhibitor α 2 ‐macroglobulin after its complex formation with proteases. In contrast to earlier described type‐III Fe receptors, this molecule does not bind human serum albumin.
Wnt-signaling and skeletogenesis. (2002)

Members of the Wnt gene family, encoding secreted cystein-rich glycoproteins, have been isolated from a variety of organisms. They serve as important developmental signaling molecules and have been implicated to play crucial roles in such diverse processes as cancer, organogenesis and pattern formation. Experiments by Zakany and Duboule, and Rudnicki and Brown have suggested a role for Wnt molecules in negatively regulating chondrogenesis. However, neither of the two Wnt genes used in these studies is endogenously expressed in chondrogenic regions. We and others have found that in the chick limb at least four members of the Wnt gene family, Wnt-4, Wnt-5a, Wnt-5b, and Wnt-14, are expressed in defined regions of the developing chondrogenic elements. With the exception of Wnt-5b, which is expressed in perichondrial cells and prehypertrophic chondrocytes, the expression of the three other Wnt genes is restricted to the perichondrium surrounding the cartilage element. Viral misexpression studies in the chick suggested that Wnt-4 acts as a positive signal originating from the joint region and when misexpressed accelerates chondrocyte maturation, while Wnt-5a and Wnt-5b both negatively regulate chondrocyte maturation. We have further shown that they utilize different signaling pathways; while Wnt-4 signals through the canonical Wnt-pathway, Wnt-5a and Wnt-5b do not. Interestingly, the delay in chondrocyte maturation due to Wnt-5a misexpression is associated with an up regulation of Wnt-5b expression in the prehypertropic chondrocytes. Concomitantly, Wnt-5b misexpression also delays chondrocyte maturation. However, preliminary studies suggest that the two Wnt genes affect different steps in the maturation process. Wnt signaling, however, is not only regulating chondrogenesis but is also involved in the segmentation process of the appendicular skeleton. Localized misexpression of the fourth Wnt gene, Wnt-14, which is expressed early in the presumptive joint region, induces morphological and molecular changes indicative of an early joint interzone, suggesting that Wnt-14 plays a pivotal role in the induction of the joint interzone.
Development of HIV-1 Drug Resistance Through 144 Weeks in Antiretroviral-Naïve Subjects on Emtricitabine, Tenofovir Disoproxil Fumarate, and Efavirenz Compared With Lamivudine/Zidovudine and Efavirenz in Study GS-01-934 (2009)

Study 934 was an open-label, randomized Phase III study of emtricitabine + tenofovir DF + efavirenz (FTC + TDF + EFV) compared with lamivudine + zidovudine + efavirenz (3TC + ZDV + EFV) in antiretroviral therapy-naïve HIV-1 infected subjects. Baseline genotyping revealed the presence of primary nonnucleoside reverse transcriptase inhibitor resistance (NNRTI-R) in 22 of 509 enrolled patients (4.3%, 11 subjects in each group). The 487 subjects without baseline NNRTI-R formed the primary efficacy population (modified intent-to-treat population). Through 144 weeks, 50 of 487 modified intent-to-treat subjects (FTC + TDF + EFV, n = 19; 3TC + ZDV + EFV, n = 31) were analyzed for resistance development after virologic failure. NNRTI-R, primarily the K103N mutation, was the most common form of resistance that developed in both groups. No subject on FTC + TDF + EFV developed the K65R mutation. Significantly fewer subjects on FTC + TDF + EFV compared with 3TC + ZDV + EFV developed the M184V/I mutation (two versus 10, respectively, P = 0.021). Thymidine analog mutations developed in two subjects on 3TC + ZDV + EFV. Subjects with baseline NRTI genotypic resistance (TAMs, n = 13) or non-B HIV-1 subtypes (n = 28) showed no evidence of reduced treatment responses in either group. Nine of 22 patients with baseline NNRTI-R experienced virologic failure (FTC + TDF + EFV, n = 4; 3TC + ZDV + EFV, n = 5); seven of nine developed M184V/I and/or additional NNRTI-R, but none developed K65R. Baseline NNRTI-R was significantly associated with virologic failure in both groups (P < 0.001).
BPSK to ASK Signal Conversion Using Injection-Locked Oscillators—Part I: Theory (2005)

This paper presents a new method and circuit for the conversion of binary phase-shift keying (BPSK) signals into amplitude shift keying signals. The basic principles of the conversion method are the superharmonic injection and locking of oscillator circuits, and interference phenomena. The first one is used to synchronize the oscillators, while the second is used to generate an amplitude interference pattern that reproduces the original phase modulation. When combined with an envelope detector, the proposed converter circuit allows the coherent demodulation of BPSK signals without need of any explicit carrier recovery system. The time response of the converter circuit to phase changes of the input signal, as well as the conversion limits, are discussed in detail.
An Acellular, Allograft‐Derived Meniscus Scaffold in an Ovine Model (2010)

This meniscus scaffold has potential for future clinical application as a meniscus transplant construct.
Increased Tissue Factor Expression is an Independent Predictor of Mortality in Clear Cell Carcinoma of the Kidney (2014)

Increased immunohistochemical expression of TF was an important independent predictor of mortality in a contemporary cohort of patients with clear cell carcinoma of the kidney. Further studies are necessary to define the role of TF in clinical practice.
Very Large G Protein-coupled Receptor-1, the Largest Known Cell Surface Protein, Is Highly Expressed in the Developing Central Nervous System (2002)

We previously identified a member of the G protein-coupled receptor family, very large G protein-coupled receptor-1 (VLGR1). VLGR1 has a large ectodomain containing multiple calcium exchanger beta repeats that resemble regulatory domains of sodium-calcium exchanger proteins. Similar repeats are found in the extracellular aggregation factor of marine sponges, which mediates species-specific cell aggregation. We now report that the protein encoded by the originally described human cDNA (now termed VLGR1a) is, in fact, at 1967 amino acids, the smallest of three expressed human isoforms. It is encoded by an alternative transcript that begins within intron 64 of the VLGR1 gene. The longest gene product, VLGR1b, is 6307 amino acids (6298 amino acids in mice) due to a much larger ectodomain containing 35 calcium exchanger beta repeats and a pentraxin homology domain. VLGR1b is apparently the largest known cell surface protein. The VLGR1 gene comprises 90 exons and is >600 kb long. In situ hybridization studies with mouse embryo sections show that high level expression of VLGR1 is restricted to the developing central nervous system and eye. Strong expression in the ventricular zone, home of neural progenitor cells during embryonal neurogenesis, suggests a fundamental role for VLGR1 in the development of the central nervous system.
Synthesis, Characterization, and Electron-Transport Property of Perfluorinated Phenylene Dendrimers (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis, Characterization, and Electron-Transport Property of Perfluorinated Phenylene DendrimersYouichi Sakamoto, Toshiyasu Suzuki, Atsushi Miura, Hisayoshi Fujikawa, Shizuo Tokito, and Yasunori TagaView Author Information Institute for Molecular Science, Myodaiji Okazaki 444-8585, Japan Toyota Central Research and Development Laboratories Inc. Nagakute, Aichi 480-1192, Japan Cite this: J. Am. Chem. Soc. 2000, 122, 8, 1832–1833Publication Date (Web):February 15, 2000Publication History Received22 November 1999Published online15 February 2000Published inissue 1 March 2000https://pubs.acs.org/doi/10.1021/ja994083zhttps://doi.org/10.1021/ja994083zrapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views2849Altmetric-Citations153LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Dendrons,Diodes,Layers,Materials Get e-Alerts
Six-Step Synthesis of (S)-Brevicolline from (S)-Nicotine (2006)

[reaction: see text] A six-step synthesis of (S)-brevicolline from (S)-nicotine is reported. Regioselective trisubstitution of the pyridine ring of nicotine, followed by successive Suzuki cross-coupling and Buchwald amination reactions, afforded the enantiopure beta-carboline alkaloid, brevicolline.
Hierarchical asynchronous genetic algorithms for parallel/distributed simulation-based optimization (1995)

The objective of this dissertation is to develop a multi-resolution optimization strategy based on the evolution algorithms in the parallel/distributed simulation environment. The system architecture is constructed hierarchically with multiple clusters which consist of an expert system (controller) and set of genetic algorithm optimizers (agents). We propose an asynchronous genetic algorithm (AGA) which continuously updates the population in parallel genetic algorithms. Asynchronous evaluation of population in a parallel computer improves the utilization of the processors and reduces search time when the evaluation time of individuals is highly variable. Further, we have devised a noise assignment scheme which resolves the pre-convergence drawback of the genetic algorithms. In this scheme, binary representation (discrete sampling) of an individual is combined with a random number (analog sampling), so that the genetic algorithm can investigate the entire search space regardless of the bit-size of an individual. Real application problems require the evaluation of a large number of parameters and their search complexity grows beyond the capability of a single level GA-optimizer. In response, we have developed a novel scheme called Hierarchical Genetic Algorithms. This multilevel GA optimization strategy is based on an Intelligent Machine Architecture which supporting non-deterministic computation, intensive and irregular memory access patterns, and large potential for parallel computing. The clusters in the Hierarchical GAs are coordinated hierarchically and creation and deletion of nodes are performed dynamically based upon performance. During the optimization process, the clusters cooperate together to solve different levels of the abstracted problem. A candidate solution at a higher level creates a lower level cluster which utilizes previously optimized parameter information. It can also contribute to the search process of a higher level by sending the feedback information. Hierarchical GAs demonstrate performance with various experiments. We have compared the performance of the Hierarchical GAs and simple GA (single-level). The Hierarchical GAs adaptively changes its structure to allocate more computing resources to the promising nodes. With the same amount of memory size for population, the simulation results shows that the Hierarchical GAs find a solution faster than the simple GA.
Antigenic Variation Of A Relapsing Fever Borrelia Species (1990)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More