gebhart/patrepeval huggingface dataset:
Correlation between Molecular Weight Distribution of Oligo-L-methionine Prepared by, Papain-catalyzed Polymerization and Its Supplementary Effect in a Low Protein Diet (1992)

"Correlation between Molecular Weight Distribution of Oligo-L-methionine Prepared by, Papain-catalyzed Polymerization and Its Supplementary Effect in a Low Protein Diet." Bioscience, Biotechnology, and Biochemistry, 56(11), pp. 1884–1885
A novel capacitance control design of tunable capacitor using multiple electrostatic driving electrodes (2002)

A novel method that is capable of linearly electrostatic driving a tunable capacitor is proposed in this paper. By extending the derivation of electrostatic theory and elastic theory in constructing the tunable capacitor, the nonlinear relationship between applied voltages and displacement (air gap) between two parallel plates of the capacitor is obtained. To suppress the nonlinearity so that the gap between the capacitor can vary linearly with the applied voltage, a control design method based on the variation of the multi-rectangular electrodes and applied voltages is proposed. By varying the number of rectangular electrodes that are evenly divided according to the size of the upper plate of the capacitor, the working space of the tunable capacitor with nonlinear characteristics is obtained. With this working space, linear control design method based on fixed or linearly varied applied voltages can be used to determine the number of the multi-rectangular electrodes such that stepping effect of the tunable capacitor can be achieved. Examples are used to demonstrate the feasibility of the present control design.
Click Conjugation of Cloaked Peptide Ligands to Microbubbles (2018)

Interest in the use of targeted microbubbles for ultrasound molecular imaging (USMI) has been growing in recent years as a safe and efficacious means of diagnosing tumor angiogenesis and assessing response to therapy. Of particular interest are cloaked microbubbles, which improve specificity by concealing the ligand from blood components until they reach the target vasculature, where the ligand can be transiently revealed for firm receptor-binding by ultrasound acoustic radiation force pulses. Herein, a bio-orthogonal "click" conjugation chemistry is introduced to decorate the surface of cloaked 4-5-μm-diameter microbubbles as part of a sterile and reproducible production process. Azido-functionalized antagonists for the angiogenic biomarkers α<sub>V</sub>β<sub>3</sub> integrin (cRGD) and VEGFR2 (A7R) proteins were conjugated to bimodal-brush microbubbles via strain-promoted [3 + 2] azide-alkyne cycloaddition (SPAAC) click chemistry. Ligand conjugation was validated by epifluorescent microscopy, flow cytometry, and Fourier-transform infrared spectroscopy. Sterility was validated by bacterial culture and endotoxin analysis. Additionally, clinically normal dogs receiving escalating microbubble doses were shown to experience no pathologic changes in physical examination, complete blood count, serum biochemistry profile, or coagulation panel. This bio-orthogonal microbubble conjugation process for cloaked peptide ligands may be leveraged for future USMI studies of tumor angiogenesis for translation to preclinical and clinical applications.
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks (2014)

One ultimate goal of metabolic network modeling is the rational redesign of biochemical networks to optimize the production of certain compounds by cellular systems. Although several constraint-based optimization techniques have been developed for this purpose, methods for systematic enumeration of intervention strategies in genome-scale metabolic networks are still lacking. In principle, Minimal Cut Sets (MCSs; inclusion-minimal combinations of reaction or gene deletions that lead to the fulfilment of a given intervention goal) provide an exhaustive enumeration approach. However, their disadvantage is the combinatorial explosion in larger networks and the requirement to compute first the elementary modes (EMs) which itself is impractical in genome-scale networks. We present MCSEnumerator, a new method for effective enumeration of the smallest MCSs (with fewest interventions) in genome-scale metabolic network models. For this we combine two approaches, namely (i) the mapping of MCSs to EMs in a dual network, and (ii) a modified algorithm by which shortest EMs can be effectively determined in large networks. In this way, we can identify the smallest MCSs by calculating the shortest EMs in the dual network. Realistic application examples demonstrate that our algorithm is able to list thousands of the most efficient intervention strategies in genome-scale networks for various intervention problems. For instance, for the first time we could enumerate all synthetic lethals in E.coli with combinations of up to 5 reactions. We also applied the new algorithm exemplarily to compute strain designs for growth-coupled synthesis of different products (ethanol, fumarate, serine) by E.coli. We found numerous new engineering strategies partially requiring less knockouts and guaranteeing higher product yields (even without the assumption of optimal growth) than reported previously. The strength of the presented approach is that smallest intervention strategies can be quickly calculated and screened with neither network size nor the number of required interventions posing major challenges.
In vitro characterization of the reaction of four psoralen derivatives with DNA. (1984)

Four psoralen derivatives were radiolabeled and used for in vitro DNA binding studies. The derivatives were compared for their dark-binding ability to DNA, photoreactivity, and for unwinding angles. The dark-binding dissociation constants we determined were 1.4 X 10(-3) M for 8-methoxypsoralen (8-MOP), 3.5 X 10(-4) M for 5-methoxypsoralen (5-MOP), and 5.5 X 10(-4) M for 5-methylisopsoralen (5-MIP). We did not detect any dark binding to DNA for 3-carbethoxypsoralen (3-CP). Photoaddition experiments indicated that the relative rates of photoaddition by psoralen to DNA (measured as psoralens bound per base pair per second) are 4.4 X 10(-5) for 5-MIP, 9.2 X 10(-6) for 5-MOP, 7.8 X 10(-6) for 8-MOP, and 4.6 X 10(-6) for 3-CP. We found the peak level of binding (for an initial base pair-to-psoralen ratio of 22) to be 27, 32.2, 31.2, and 1,538 base pairs per psoralen bound for 5-MOP, 8-MOP, 5-MIP, and 3-CP, respectively. In addition, 3-CP adducts could be photoreversed by prolonged irradiation at 360 nm. After 10 hours of irradiation, the amounts of 3-CP bound to DNA had fallen to less than 50% of the peak amount bound. In the same time, the amount of 8-MOP and 5-MOP bound had fallen to 95% of their peak values, and 5-MIP had fallen to 85% of its peak value. We also performed unwinding angle experiments to determine the amount of unwinding of the DNA helix induced per photobound derivative molecule; the unwinding angles +/- 3 degrees were 25 for 5-MOP, 28 for 8-MOP, 26 for 3-CP, and 18 for 5-MIP.
Efficiently Inducing Features of Conditional Random Fields (2012)

Conditional Random Fields (CRFs) are undirected graphical models, a special case of which correspond to conditionally-trained finite state machines. A key advantage of these models is their great flexibility to include a wide array of overlapping, multi-granularity, non-independent features of the input. In face of this freedom, an important question that remains is, what features should be used? This paper presents a feature induction method for CRFs. Founded on the principle of constructing only those feature conjunctions that significantly increase log-likelihood, the approach is based on that of Della Pietra et al [1997], but altered to work with conditional rather than joint probabilities, and with additional modifications for providing tractability specifically for a sequence model. In comparison with traditional approaches, automated feature induction offers both improved accuracy and more than an order of magnitude reduction in feature count; it enables the use of richer, higher-order Markov models, and offers more freedom to liberally guess about which atomic features may be relevant to a task. The induction method applies to linear-chain CRFs, as well as to more arbitrary CRF structures, also known as Relational Markov Networks [Taskar &amp; Koller, 2002]. We present experimental results on a named entity extraction task.
Targeting novel antigens for prostate cancer treatment: focus on prostate-specific membrane antigen (2005)

Prostate-specific membrane antigen (PSMA) is a relatively omnipresent, but unique Type II dimeric transmembrane protein with a multiplicity of functions and has been shown to be a reasonable target for immunological approaches such as vaccines or more directed therapy with radioactively labelled monoclonal antibodies against PSMA. Given the abundance of various glycoprotein and carbohydrate antigens expressed on the surface of prostate cancer cells and cell lines, PSMA stands out as another 'self' antigen which is not only expressed on cancer cells, but on neovasculature. Although vaccines are varied in their design and target goal, recent technology has afforded researchers the opportunity to induce recruitment of multiple effector cell populations, cytokines and factors which can elicit both cellular and humoral responses. This review serves to present unique approaches in vaccine development which can induce immunological responsiveness with potential impact on disease progression and to introduce PSMA as a potential target for multimodality therapies.
FURTHER INSIGHT INTO PRODUCTION AND DIARRHEAGENICITY OF ZONULA OCCLUDENS TOXIN (ZOT) BY VIBRIO CHOLERAE (1991)

Fasano, A.; Baudry, B.; Kaper, J. B.; Ciarla, C.; Ferraro, L.; Guandalini, S. Author Information
THE DEVELOPMENT OF THE MOUSE OVARY FROM BIRTH TO MATURITY (1969)

ABSTRACT Changes occur in the infant ovary which develop the structurally simple organ at birth to a highly complex one in the maturing animal. The ovary in the immature mouse is not a dormant organ but one that is characterized by a continuous growth and development and a concurrent continuous degeneration of oocytes and follicles. The stroma cells which are present in the ovary at birth are apparently a pool of cells with multiple potentialities, which contribute to the development of the earliest granulosa and theca cells. The interfollicular stroma of the juvenile ovary, however, originates from collapsing and contracting follicles. The quantitative changes in the oocyte and follicle population during the immature period lead to a marked reduction in the total number of oocytes and a simultaneous numerical increase in follicles at different stages of development. Factors influencing oocyte atresia and follicle development in the immature mouse are discussed.
Contemporary definitions of tumor specific antigens, immunogens and markers as related to the adaptive responses of the cancer-bearing host. (2005)

This review describes clear parameters for designating the correct use of the term Tumor Rejection Antigen [TRA] to define the role of tumor cell constituents which activate adaptive anti-tumor immune reactions in the cancer-bearing host. This is important, especially in defining immunogens which activate the patient's cytotoxic T-cells that are important to immunotherapeutic applications in human cancer treatment. The focus of the review is to correctly delineate the immunogenic properties of 37 kDa oncofetal antigen [OFA], one of only a few true TRAs expressed on human and experimental rodent cancers. The purpose of this review is to provide a background for publication reviewers, journal and text editors, and scientists reporting on TRAs to avoid creating further confusion that has proliferated in the cancer literature to imply traits of so-called tumor-associated antigens that do not qualify as TRAs.
Biomolecule and Nanoparticle Transfer on Patterned and Heterogeneously Wetted Superhydrophobic Silicon Nanowire Surfaces (2008)

We report on the use of patterned superhydrophobic silicon nanowire surfaces for the efficient, selective transfer of biological molecules and nanoparticles. Superhydrophilic patterns are prepared on superhydrophobic silicon nanowire surfaces using standard optical lithography. The resulting water-repellent surface allows material transfer and physisorption to the superhydrophilic islands upon exposure to an aqueous solution containing peptides, proteins, or nanoparticles.
Neuronal mRNAs travel singly into dendrites (2012)

RNA transport granules deliver translationally repressed mRNAs to synaptic sites in dendrites, where synaptic activity promotes their localized translation. Although the identity of many proteins that make up the neuronal granules is known, the stoichiometry of their core component, the mRNA, is poorly understood. By imaging nine different dendritically localized mRNA species with single-molecule sensitivity and subdiffraction-limit resolution in cultured hippocampal neurons, we show that two molecules of the same or different mRNA species do not assemble in common structures. Even mRNA species with a common dendritic localization element, the sequence that is believed to mediate the incorporation of these mRNAs into common complexes, do not colocalize. These results suggest that mRNA molecules traffic to the distal reaches of dendrites singly and independently of others, a model that permits a finer control of mRNA content within a synapse for synaptic plasticity.
Phosphorylation results in activation of a cAMP phosphodiesterase in human platelets. (1988)

Agents such as prostaglandins E1 and I2 which elevate cAMP levels in platelets also increase cAMP phosphodiesterase activity. Since much of the cAMP phosphodiesterase activity in human platelets is due to the cGMP-inhibited isozyme (Macphee, C. H., Harrison, S. A., and Beavo, J. A. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 6600-6663), we examined the regulation of this isozyme by prostaglandins E1 and I2 in intact platelets. Because this isozyme is a minor component of platelet protein, normally requiring several thousand-fold purification to achieve homogeneity, a specific monoclonal antibody (CGI-5) was utilized to identify and isolate the cGMP-inhibited phosphodiesterase activity. Treatment of intact platelets with the prostaglandins promoted an increase in the phosphorylation state of the cGMP-inhibited phosphodiesterase and a corresponding increase in phosphodiesterase activity. The effect on activity and phosphorylation of the cGMP-inhibited phosphodiesterase was observed within 2 min after intact platelets were exposed to the prostaglandins. The half-maximal effective dose for prostaglandin I2 (10 nM) was approximately 10-fold lower than that for prostaglandin E1. The phosphorylated, cGMP-inhibited isozyme migrated as a 110-kDa peptide following sodium dodecyl sulfate gel electrophoresis. Direct in vitro phosphorylation of the platelet cGMP-inhibited phosphodiesterase by the catalytic subunit of cAMP-dependent protein kinase caused a similar increase in phosphodiesterase activity. Treatment with PKI peptide, a specific inhibitor of cAMP-dependent protein kinase, blocked the phosphorylation and the effect on activity. Taken together, the data strongly suggest that the effects of prostaglandins E1 and I2 on platelet phosphodiesterase activity are mediated by a direct cAMP-dependent protein kinase-catalyzed phosphorylation of the cGMP-inhibited phosphodiesterase isozyme.
Implications of Antigen Selection on T Cell-Based Immunotherapy (2021)

Many immunotherapies rely on CD8+ effector T cells to recognize and kill cognate tumor cells. These T cell-based immunotherapies include adoptive cell therapy, such as CAR T cells or transgenic TCR T cells, and anti-cancer vaccines which expand endogenous T cell populations. Tumor mutation burden and the choice of antigen are among the most important aspects of T cell-based immunotherapies. Here, we highlight various classes of cancer antigens, including self, neojunction-derived, human endogenous retrovirus (HERV)-derived, and somatic nucleotide variant (SNV)-derived antigens, and consider their utility in T cell-based immunotherapies. We further discuss the respective anti-tumor/anti-self-properties that influence both the degree of immunotolerance and potential off-target effects associated with each antigen class.
Synthesis of P-thioadenylyl-(2'-5')-adenosine and P-thioadenylyl-(2'-5')-P-thioadenylyl-(2'-5')-adenosine (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of P-thioadenylyl-(2'-5')-adenosine and P-thioadenylyl-(2'-5')-P-thioadenylyl-(2'-5')-adenosinePaul S. Nelson, Chinh T. Bach, and Julien P. H. VerheydenCite this: J. Org. Chem. 1984, 49, 13, 2314–2317Publication Date (Print):June 1, 1984Publication History Published online1 May 2002Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/jo00187a003https://doi.org/10.1021/jo00187a003research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations28LEARN 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
Sunitinib Suppress Neuroblastoma Growth through Degradation of MYCN and Inhibition of Angiogenesis (2014)

Neuroblastoma, a tumor of the peripheral sympathetic nervous system, is the most common and deadly extracranial tumor of childhood. The majority of high-risk neuroblastoma exhibit amplification of the MYCN proto-oncogene and increased neoangiogenesis. Both MYCN protein stabilization and angiogenesis are regulated by signaling through receptor tyrosine kinases (RTKs). Therefore, inhibitors of RTKs have a potential as a treatment option for high-risk neuroblastoma. We used receptor tyrosine kinase antibody arrays to profile the activity of membrane-bound RTKs in neuroblastoma and found the multi-RTK inhibitor sunitinib to tailor the activation of RTKs in neuroblastoma cells. Sunitinib inhibited several RTKs and demonstrated potent antitumor activity on neuroblastoma cells, through induction of apoptosis and cell cycle arrest. Treatment with sunitinib decreased MYCN protein levels by inhibition of PI3K/AKT signaling and GSK3β. This effect correlates with a decrease in VEGF secretion in neuroblastoma cells with MYCN amplification. Sunitinib significantly inhibited the growth of established, subcutaneous MYCN-amplified neuroblastoma xenografts in nude mice and demonstrated an anti-angiogenic effect in vivo with a reduction of tumor vasculature and a decrease of MYCN expression. These results suggest that sunitinib should be tested as a treatment option for high risk neuroblastoma patients.
Performance limits of nonlinear RZ and NRZ coded transmission at 1O and 40 Gb/s on different fibers (2002)

We compare single-channel systems on standard and non-zero dispersion-shifted fiber (NZDSF). Upgrading from NRZ to RZ, the transmission range is increased by 2 to 6 dB. RZ coding balances the benefits of NZDSF over standard fiber at high data rates.
Point Mutations in theablSH2 Domain Coordinately Impair Phosphotyrosine Binding In Vitro and Transforming Activity In Vivo (1992)

We have constructed a series of point mutations in the highly conserved FLVRES motif of the src homology 2 (SH2) domain of the abl tyrosine kinase. Mutant SH2 domains were expressed in bacteria, and their ability to bind to tyrosine-phosphorylated proteins was examined in vitro. Three mutants were greatly reduced in their ability to bind both phosphotyrosine itself and tyrosine-phosphorylated cellular proteins. All of the mutants that retained activity bound to the same set of tyrosine-phosphorylated proteins as did the wild type, suggesting that binding specificity was unaffected. These results implicate the FLVRES motif in direct binding to phosphotyrosine. When the mutant SH2 domains were inserted into an activated abl kinase and expressed in murine fibroblasts, decreased in vitro phosphotyrosine binding correlated with decreased transforming ability. This finding implies that SH2-phosphotyrosine interactions are involved in transmission of positive growth signals by the nonreceptor tyrosine kinases, most likely via the assembly of multiprotein complexes with other tyrosine-phosphorylated proteins.
Targeted Exon Sequencing by In‐Solution Hybrid Selection (2010)

Abstract This unit describes a protocol for the targeted enrichment of exons from randomly sheared genomic DNA libraries using an in‐solution hybrid selection approach for sequencing on an Illumina Genome Analyzer II. The steps for designing and ordering a hybrid selection oligo pool are reviewed, as are critical steps for performing the preparation and hybrid selection of an Illumina paired‐end library. Critical parameters, performance metrics, and analysis workflow are discussed. Curr. Protoc. Hum. Genet . 66:18.4.1‐18.4.24 © 2010 by John Wiley &amp; Sons, Inc.
Characteristics of the Human Lymphocyte Insulin Receptor (1973)

Abstract Insulin interactions with human lymphocytes in established cultures and with isolated peripheral lymphocytes have been studied using 125I-insulin. Receptors in circulating lymphocytes are indistinguishable from those found in cultured cells, and the lymphocyte receptors show striking similarities to those structures described in fat cell and liver preparations. In lymphocytes, the ability of insulin or insulin analogues to inhibit binding of 125I-insulin is directly proportional to the ability of that preparation to inhibit binding of labeled hormone to purified liver membranes or to stimulate glucose oxidation in the fat cell. Binding of 125I-insulin to lymphocytes is a rapid and reversible process. Binding is maximal at 15°. Dissociation rate studies revealed a biphasic curve and the constants obtained were 8.3 x 10-5 s-1 and 8.3 x 10-4 s-1. The apparent affinity constants of the two orders of binding sites in the cultured lymphocytes were 1.2 x 1010 m-1 and 1.1 x 109 m-1, whereas in the normal circulating lymphocytes the values were 2.0 x 109 m-1 and 1.4 x 108 m-1. At 30° there is very little degradation of labeled insulin by lymphocytes, and at 15° there is no detectable degradation with cultured or circulating cells. Binding of 125I-insulin to cultured lymphocytes is unaffected by Ca++, Mg++, or EDTA. The optimum pH for binding occurs at about 7.8. Insulin binding to cells is unaffected by digestion with DNase, RNase, or neuraminidase. However, tryptic digestion destroys the capacity of the cells to bind insulin.
Novel topical drug delivery systems and their potential use in acne vulgaris. (2008)

A vast spectrum of topical anti-acne agents has emerged in response to new insights that have been gained through the understanding of disease pathophysiology and the need for clinicians to adopt an individualized therapeutic approach. Because topical agents are most commonly used for acne management, this article reviews some novel vehicle delivery advances that are poised to further enhance the efficacy of topical acne formulations, and/or offer the possibility of simplified dosing regimens that may improve treatment outcomes.