gebhart/patrepeval huggingface dataset:
CD164 Monoclonal Antibodies That Block Hemopoietic Progenitor Cell Adhesion and Proliferation Interact with the First Mucin Domain of the CD164 Receptor (2000)

The novel sialomucin, CD164, functions as both an adhesion receptor on human CD34+ cell subsets in bone marrow and as a potent negative regulator of CD34+ hemopoietic progenitor cell proliferation. These diverse effects are mediated by at least two functional epitopes defined by the mAbs, 103B2/9E10 and 105A5. We report here the precise epitope mapping of these mAbs together with that of two other CD164 mAbs, N6B6 and 67D2. Using newly defined CD164 splice variants and a set of soluble recombinant chimeric proteins encoded by exons 1-6 of the CD164 gene, we demonstrate that the 105A5 and 103B2/9E10 functional epitopes map to distinct glycosylated regions within the first mucin domain of CD164. The N6B6 and 67D2 mAbs, in contrast, recognize closely associated and complex epitopes that rely on the conformational integrity of the CD164 molecule and encompass the cysteine-rich regions encoded by exons 2 and 3. On the basis of their sensitivities to reducing agents and to sialidase, O-sialoglycoprotease, and N-glycanase treatments, we have characterized CD164 epitopes and grouped them into three classes by analogy with CD34 epitope classification. The class I 105A5 epitope is sialidase, O-glycosidase, and O-sialoglycoprotease sensitive; the class II 103B2/9E10 epitope is N-glycanase, O-glycosidase, and O-sialoglycoprotease sensitive; and the class III N6B6 and 67D2 epitopes are not removed by such enzyme treatments. Collectively, this study indicates that the previously observed differential expression of CD164 epitopes in adult tissues is linked with cell type specific post-translational modifications and suggests a role for epitope-associated carbohydrate structures in CD164 function.
Internalization of a Peptide into Multilamellar Vesicles Assisted by the Formation of an α‐Oxo Oxime Bond (2005)

As part of a drug-delivery project, we designed and synthesised a novel hydroxylamine cholesterol-based anchor to ensure the chemoselective ligation of recognition patterns onto multilamellar vesicles by oxime ligation. The entry of a glyoxylyl peptide into the vesicles was unexpectedly assisted by the formation of the alpha-oxo oxime bond. We studied extensively the kinetic and thermodynamic aspects of this phenomenon. Briefly, for a glyoxylyl peptide, the speed and ability to enter the vesicle were dependent upon 1) the presence of a hydroxylamine anchor of the type CholE3ONH2, 2) the amount of peptide engaged in the ligation and 3) the flip-flop motion permitted by the different formulations, in which the presence of cholesterol seems to play an important role.
Research that reinvents the corporation (1991)

It's not enough to create new products. You need to build the prototype of the continuously innovating company.
Interpretation of scattering by oceanic particles around 120 degrees and its implication in ocean color studies (2017)

Field observations and theoretical studies have found that the volume scattering functions (VSFs) of oceanic particles exhibit minimum variability at angles near 120°. However, its physical interpretation is still unknown. We find this minimum variability angle represents the intersection of two backscattering-normalized VSFs, one representing particles of sizes smaller than the wavelength of light and the other larger than the wavelength of light. This also suggests that the VSFs of oceanic particles at angles between 90° and 180°, which play a critical role in ocean color study, can be modeled by linear mixing of these two end members. We further validate this mixing model using measured VSFs in coastal and oceanic waters around the US and develop a two-component model predicting the backward shapes of the VSFs.
Pose estimation of a depth camera using plane features (2013)

We present a novel method for pose estimation of a depth camera through plane features. Since conventional features for color images, mainly points and lines, are not applicable to a depth image, we propose a new type of feature utilizing planar structures in a scene. To measure the accuracy of our method, we generated a synthetic scene and calculated a position error between an estimated location and its ground truth. We also applied our method to the real world scene captured by a depth camera verifying practical usage.
Towards Improving an Algebraic Marking Scheme for Tracing DDoS Attacks (2009)

HCV core protein enhances Wnt/β-catenin signaling activity, hence playing an important role in HCV-associated carcinogenesis.
Effects of standardized stem bark extract of Mangifera indica L. in wistar rats with 2,4-dinitrophenylhydrazine-induced haemolytic anaemia (2015)

Background: The aqueous decoction of the stem back of Mangifera indica L. has been traditionally used for the treatment of various illnesses among them includes anaemia. Aims: The aim of this study was to investigate the anti-anaemic properties of standardized stem bark extract of M. indica in animals with 2,4-dinitrophenylhydrazine-induced haemolytic anaemia. Methods and Material: An in vivo animal model was used in this experiment. 2,4-dinitrophenylhydrazine was used to induce haemolysis and treatment was done with three different concentrations (25, 50, and 100 mg/ kg b.wt) of the plant extract. Astifer® was used as a positive control. Haematological parameters such as PCV, HGb concentration, and TLC were performed and to ascertain the level of haemolysis. GC-MS was used determine the present of phytoconstituents within the crude extract. Results: PCV and HGb concentration increased significantly (p 0.05) effect was observed at a dose of 25 mg/kg b.wt. TLC was decreased significantly (p 0.05) effect was observed at a dose of 25 and 50 mg/kg b.wt respectively. GC-MS analysis revealed presence of 15 compounds viz: 2,2-Dimethoxybutane, N-Acetyl-Alpha-D-glucosamine, 1,2-Benzenediol, Phenol, 2,4-bis(1,1dimethylethyl)-, Vitamin E, Pentadecanoic acid, 13-methyl-, methyl ester, 2-Ethylacridine, Benzofuran-6-ol-3-one, 2-(4ethoxycarbonyl)benzylidene-, 9-Octadecanoic acid, (E)-, 2,4,6-Cycloheptatrien-1-one, 3,5-bis-trimethylsilyl-, and Benzo[h]quinoline,2,4-dimethyl-. Conclusion: The results of our present finding suggest the significant anti-anaemic properties of standardized stem bark extract of Mangefera indica L. This finding highlights the potentials of the extract and M. indica in the treatment of haemolytic anaemia.
Properties of RuO x Working Electrodes in Nonaqueous Solvents (1979)

Reactions intrinsic to electrodes in water are quenched in aprotic media and is a well‐behaved working electrode for electrochemistry of solutions of metal bipyridyls, methyl viologen, ferrocene, tetrathiafulvalene, and nitroaromatics. Follow‐up reactions of nitroaromatic radicals are especially sensitive to water at surfaces. Electrochemical properties are correlated to XPES‐determined surface composition.
Detection of heritable mutations as quantitative changes in protein expression. (1987)

A computerized search for the appearance of heritable mutations (as indicated by changes in protein expression) was conducted on three sets of mice, whose sires had been either untreated, exposed to 3 gray units of gamma radiation, or treated with 150 mg/kg ethylnitrosourea. Proteins from the livers of approximately 800 mice were separated by two-dimensional electrophoresis, and abundances were measured by using image analysis techniques. Heritable mutations were detected by the appearance of new proteins or by the quantitative decrease in abundance of normally occurring proteins. Measurements of the variability of the protein abundance indicate that at least 48 proteins are consistent enough to be used in searches when mutations are expected to result in a 50% reduction in the normal amount of protein. New proteins were found in four offspring from ethylnitrosourea-treated mice, and in each case a nearby spot was found to be significantly diminished. These mutations were confirmed in subsequent generations. A computer-assisted search detected three of these mutations on the basis of the abundance decrease alone. These results indicate that two-dimensional electrophoresis can be used to detect mutations reflected as quantitative changes in protein expression, provided that the proteins to be monitored are quantitatively stable when samples from different individuals are compared.
A Comparative Study of Neural and Mesenchymal Stem Cell-Based Carriers for Oncolytic Adenovirus in a Model of Malignant Glioma (2011)

Glioblastoma multiforme is a primary malignancy of the central nervous system that is universally fatal due to its disseminated nature. Recent investigations have focused on the unique tumor-tropic properties of stem cells as a novel platform for targeted delivery of anticancer agents to the brain. Neural stem cells (NSCs) and mesenchymal stem cells (MSCs) both have the potential to function as cell carriers for targeted delivery of a glioma restricted oncolytic virus to disseminated tumor due to their reported tumor tropism. In this study, we evaluated NSCs and MSCs as cellular delivery vehicles for an oncolytic adenovirus in the context of human glioma. We report the first preclinical comparison of the two cell lines and show that, while both stem cell lines are able to support therapeutic adenoviral replication intracellularly, the amount of virus released from NSCs was a log higher than the MSC (p < 0.001). Moreover, only virus loaded NSCs that were administered intracranially in an orthotopic glioma model significantly prolonged the survival of tumor bearing animals (median survival for NSCs 68.5 days vs 44 days for MSCs, p < 0.002). Loading oncolytic adenovirus into NSCs and MSCs also led to expression of both pro- and anti-inflammatory genes and decreased vector-mediated neuroinflammation. Our results indicate that, despite possessing a comparable migratory capacity, NSCs display superior therapeutic efficacy in the context of intracranial tumors. Taken together, these findings argue in favor of NSCs as an effective cell carrier for antiglioma oncolytic virotherapy.
The rate of site-site interactions in functionalized polystyrenes (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe rate of site-site interactions in functionalized polystyrenesJulius Rebek Jr. and John E. TrendCite this: J. Am. Chem. Soc. 1979, 101, 3, 737Publication Date (Print):January 1, 1979Publication History Published online1 May 2002Published inissue 1 January 1979https://pubs.acs.org/doi/10.1021/ja00497a041https://doi.org/10.1021/ja00497a041research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations22LEARN 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
Detection of estrogen receptor in breast and endometrial carcinoma by the immunoperoxidase technique (1981)

Paraffin-embedded tissues from 15 women with breast or endometrial carcinomas were analyzed in a study designed to explore the possible value and validity of an immunoperoxidase method for the detection of estrogen receptor in formalin-fixed paraffin-embedded tissue. Results were compared with biochemical assays for estrogen receptor performed on cytosols of fresh tissue from the same patients. There was complete correlation in nine of 15 (60%) of the tumors analyzed. Four cases (26.7%) were judged positive for estrogen binding sites by immunoperoxidase but were negative for estrogen receptor by biochemical assays; in two cases the converse was observed. The immunohistologic technique is relatively rapid and utilizes fixed paraffin sections of the same tissue that is used for standard histologic diagnosis. The provision of a permanent record that can be kept for future reference provides an advantage over immunofluorescence methods that have been advanced for the detection of estrogen receptors. The excellent morphology achieved permits an assessment of the staining of individual cells in relation to the usual histologic criteria employed in the diagnosis of breast and endometrial cancer. This stands in contrast to biochemical cytosol-based assays that take no account of variations in receptor expression by the tumor cells or variations in the proportion of the assayed material that is in fact neoplastic as distinct from supporting stroma and connective tissue.
Combining fine-scale social contact data with epidemic modelling reveals interactions between contact tracing, quarantine, testing and physical distancing for controlling COVID-19 (2020)

Abstract Case isolation and contact tracing can contribute to the control of COVID-19 outbreaks 1,2 . However, it remains unclear how real-world networks could influence the effectiveness and efficiency of such approaches. To address this issue, we simulated control strategies for SARS-CoV-2 in a real-world social network generated from high resolution GPS data 3,4 . We found that tracing contacts-of-contacts reduced the size of simulated outbreaks more than tracing of only contacts, but resulted in almost half of the local population being quarantined at a single point in time. Testing and releasing non-infectious individuals led to increases in outbreak size, suggesting that contact tracing and quarantine may be most effective when it acts as a ‘local lockdown’ when contact rates are high. Finally, we estimated that combining physical distancing with contact tracing could enable epidemic control while reducing the number of quarantined individuals. Our approach highlights the importance of network structure and social dynamics in evaluating the potential impact of SARS-CoV-2 control.
Overview of Biorefineries based on Co-Production of Furfural, Existing Concepts and Novel Developments (2010)

At Delft University of Technology theoretical and experimental research is carried out towards selective production of furfural from renewable biomass. Furfural is an interesting molecule that has been identified as a platform chemical for a multitude of chemical products and fuel (additives).Acidic biomass hydrolysis and subsequent dehydration of the obtained C5 sugar xylose leads to furfural. The reaction selectivity is a point of concern for reactor design, as furfural can further react to loss products. The residue of this process mainly consists of the remaining main biomass constituents, cellulose and lignin. Mineral matter is to a large extent extracted to the acid in the primary hydrolysis. This implies that the residue has the potential to be a better feedstock for thermo-chemical conversion, as e.g. alkali and chlorine speciesnow extractedpotentially cause different types of problems (slagging, fouling, agglomeration etc.).An interesting option for example might be to convert this improved feedstock into synthesis gas via a gasification process, which then needs to be conditioned and upgraded for the production of green transportation fuels. In this line, a new biorefinery generation is created, which selectively uses the hemi-cellulose part of biomass. An analysis is presented towards current (integrated) concepts for novel, improved furfural production process. This paper presents some current process concepts and a novel continuous process design.
Structure Manipulation in Triptycene-Based Polyimides through Main Chain Geometry Variation and Its Effect on Gas Transport Properties (2017)

Two new triptycene-based polyimides, 6FDA-1,4-trip_ortho and 6FDA-2,6-trip_para, were synthesized to investigate the effect of varying polymer backbone geometry on chain packing and gas transport properties. Changing the imide linkage geometry from para to ortho reduced gas permeabilities by ∼48% due to more efficient chain packing of the asymmetric ortho structure, which is demonstrated by decreased d-spacing and fractional free volume. Varying the triptycene orientation from the 1,4- to 2,6-connection also caused a decrease in permeability (e.g., 29% decrease for PCO2). This is likely the result of reduced chain mobility, as evidenced by increased Tg, and a shift in free volume distribution toward smaller cavities, as supported by smaller d-spacing. Physical aging studies show that the equilibrium specific volume of these isomeric polymers is similar, as evidenced by nearly identical gas transport properties exhibited by all aged samples.
Plasmaless etching of silicon using chlorine trifluoride (1991)

Silicon etching using ClF3 gas has been carried out at various substrate temperatures from −20 to 120 °C. The etching properties (etch rate, pressure effect, and surface morphology) depend remarkably on the temperature. Based on the mass spectroscopic measurements, SiF4 is specified as a main product. The minor product SiF2 is also found, and the ratio of the signal intensity of SiF2 to that of SiF4 decreases with temperature. From Auger electron analyses on the etched surface, the density of fluorine atoms on the surface decreases with increasing the temperature. It is concluded that the density of the fluorosilyl species greatly influences the etching reaction process.
BRCA1 mRNA is expressed highly during meiosis and spermiogenesis but not during mitosis of male germ cells. (1996)

The 17q-linked breast and ovarian cancer susceptibility gene (BRCA1) is believed to function as a tumor suppressor gene (Miki et al., 1994). In this report BRCA1 RNA expression has been analysed in adult mouse tissues with detailed attention to its expression in prepuberal and adult testis. Measurements of BRCA1 mRNA levels in highly purified somatic cells of the testis and in staged germ cells showed that high level BRCA1 mRNA expression is limited to the germ cells. Within the germ cell lineage, the high level expression was detected in meiotic cells, specifically pachytene spermatocytes and in post-meiotic round spermatids. This is in contrast to premeiotic germ cells which were found to express little or no BRCA1 mRNA. These observations, considered together with recent data on the expression of BRCA1 in breast epithelium, argues against a function for BRACA1 in early progenitor cells in both tissues and cells attention instead to roles intimately associated with terminal differentiation or with final rounds of cell division.
Substrate-Independent Growth of Atomically Precise Chiral Graphene Nanoribbons (2016)

Contributing to the need for new graphene nanoribbon (GNR) structures that can be synthesized with atomic precision, we have designed a reactant that renders chiral (3,1)-GNRs after a multistep reaction including Ullmann coupling and cyclodehydrogenation. The nanoribbon synthesis has been successfully proven on different coinage metals, and the formation process, together with the fingerprints associated with each reaction step, has been studied by combining scanning tunneling microscopy, core-level spectroscopy, and density functional calculations. In addition to the GNR's chiral edge structure, the substantial GNR lengths achieved and the low processing temperature required to complete the reaction grant this reactant extremely interesting properties for potential applications.
Specific HIV-1 TAR RNA Loop Sequence and Functional Groups Are Required for Human Cyclin T1−Tat−TAR Ternary Complex Formation (2002)

Replication of human immunodeficiency virus requires Tat protein which activates elongation of RNA polymerase II transcription at the HIV-1 promoter through interaction with the cyclin T1 (CycT1) subunit of the positive transcription elongation factor complex (P-TEFb). Tat binds directly through its transactivation domain to the CycT1 subunit of the P-TEFb and induces loop sequence specific binding of the P-TEFb onto nascent HIV-1 TAR RNA. By using a gel electrophoresis method and a comprehensive set of TAR loop mutants, we have identified the sequence and structural determinants for high-affinity CycT1-Tat-TAR ternary complex formation. Our results show that CycT1 and Tat binding to TAR RNA is highly cooperative, and a capacity of 85%, a Hill coefficient of 2.7, and a dissociation constant (K(D)) of 2.45 nM were observed. These results indicate that there are three binding sites on TAR RNA. CycT1 does not bind TAR RNA in the absence of Tat, and Tat binding to TAR, while detectable, is very inefficient in the absence of CycT1. It is conceivable that the CycT1-Tat heterodimer directly binds to TAR RNA in the U-rich RNA bulge region and this binding facilitates the interactions of the CycT1-Tat heterodimer at the other two sites in the RNA loop region. On the basis of our results, we suggest a model where CycT1 interacts with Tat protein and positions the protein complex to make contacts with the G34 region of the loop sequence; G34 is critical for CycT1-Tat binding and forms a C30.G34 base pair. Two functional groups, O6 and N7, at nucleotide positions 32 and 34 in the TAR loop are essential for CycT1-Tat interactions with TAR RNA. The identity of two nucleotides, U31 and G33, is not critical, but they contribute to the stabilization of the RNA-protein complex. The presence of a single-nucleotide bulge of A35 or C35 is essential for distortion of the backbone RNA structure as well as the accessibility of functional groups in the major groove of the double-helical region. CycT1-Tat interaction with TAR RNA represents another example of the flexibility and complexity of RNA structure involved in protein recognition.
Synthesis of α-<scp>l</scp>-Threose Nucleoside Phosphonates via Regioselective Sugar Protection (2013)

A new synthesis route to α-L-threose nucleoside phosphonates via 2-O and 3-O selectively protected L-threose is developed. The key intermediates 2-O-benzoyl-L-threonolactone and 1-O-acetyl-2-O-benzoyl-3-O-t-butyldiphenylsilyl-L-threofuranose were functionalized to synthesize 2'-deoxy-2'-fluoro- and 3'-C-ethynyl L-threose 3'-O-phosphonate nucleosides. The key intermediates developed are important intermediates for the synthesis of new L-threose-based nucleoside analogues, TNA phosphoramidites, and TNA triphosphates.
Diagnostic Techniques to Understand Hydraulic Fracturing: What? Why? and How? (2000)

Abstract In recent years there have been numerous advances in fracture mapping/diagnostic technologies. This paper details the state-of-the-art in applying both conventional and advanced technologies to better understand hydraulic fracturing and improve treatment designs. The initial portion of the paper describes the application and limitations of various diagnostic tools and methods, including well testing, net pressure analysis (fracture modeling), techniques that employ open-hole & cased-hole logs, surface & downhole tilt fracture mapping, microseismic fracture mapping, and production data analysis. The bulk of the paper is dedicated to case histories that illustrate the application of these various fracture diagnostic technologies. The case histories include examples of how several fracture diagnostics can be used in concert to provide more reliable estimates of fracture dimensions and allow better economic decisions.