gebhart/patrepeval huggingface dataset:
De-immunization of therapeutic proteins by T-cell epitope modification. (2005)

Many therapeutic proteins in clinical use have been shown to elicit antibody responses which in some cases have been linked to adverse events. Conventional animal models, although convenient, have rarely been predictive of immunogenicity in humans. New methods for predicting the potential immunogenicity of therapeutic proteins are needed. This treatise proposes a new approach which pairs in silico T-cell epitope analysis with in vitro studies. T-cell epitope mapping algorithms such as EpiMatrix can be used to evaluate a candidate therapeutic protein for T-helper epitopes, followed by confirmation of the T-helper epitopes using in vitro methods such as MHC binding assays and T-cell assays. Once these are identified, substitution of key amino acids in the T-cell epitopes may attenuate the immunogenicity of the protein, since modification of the amino acids in anchor position(s) can abrogate binding to human class II MHC molecules and presentation of the peptides, in the context of MHC, to T-helper cells. Following substitution of the key amino acids, immunogenicity of the modified protein can be evaluated in vitro. In parallel, the potential effect of the modifications on the structure of the protein can be evaluated using in silico modeling methods. This multi-step process has been termed DeFT for de-immunization of functional therapeutics. In this article we review the rationale for the approach, provide several retrospective examples that prove the approach in principle, and describe potential applications to therapeutic protein design. The demand for pre-clinical means of evaluating therapeutic proteins is expected to increase with the number of therapeutic proteins and monoclonal antibodies entering the pre-clinical pipeline. Examples provided offer some preliminary proof that the de-immunization approach may improve clinical outcomes.
Long-term transgene expression in the RPE after gene transfer with a high-capacity adenoviral vector. (2002)

In contrast to previous results with earlier generation adenoviral vectors, subretinal injection of an HC-Ad vector in immunocompetent rats resulted in long-term transgene expression without evidence of adverse immune reactions or significant toxicity, probably because of the absence of expression of the viral gene from this vector. Thus, HC-Ad vectors are suitable for the treatment of eye disorders that require durable gene expression in the RPE.
T cell receptor engagement induces tyrosine phosphorylation of FAK and Pyk2 and their association with Lck (1997)

Stimulation through the TCR is known to induce tyrosine phosphorylation of a number of proteins, which leads to functional activation of T cells. Identification of the substrates that become phosphorylated and defining their interactions with other signaling molecules will provide insight into the mechanisms controlling T cell activation. Focal adhesion kinase (FAK) and the recently described Pyk2 kinase are homologous members of a non-receptor protein tyrosine kinase family. FAK has been shown to become phosphorylated upon TCR stimulation, but its role, if any, in T cell activation remains to be defined. Although Pyk2 has been shown to play a role in neuronal cell activation stimulated through G-protein-coupled receptors, a role in T cell activation has not been described. In this study we show that FAK and Pyk2 are two of the major 115-to-120-kDa proteins that become tyrosine phosphorylated in T cells following TCR complex stimulation. Furthermore, coincident with the increase in tyrosine phosphorylation, we show an association of these kinases with the SH2 domain of the tyrosine kinase Lck in vivo. The increase in tyrosine phosphorylation of both FAK and Pyk2, however, occurs in Lck-deficient cells suggesting that phosphorylation of both of these kinases does not require Lck. Taken together, these results suggest that FAK and Pyk2, perhaps in coordination with Lck, play a role in T cell activation.
Beta Cell Culture on Synthetic Capillaries: an Artificial Endocrine Pancreas (1975)

Beta cells from neonatal rats were cultured on bundles of artificial capillaries perfused with tissue culture medium. Cells continued to release insulin and remained responsive to changes in glucose concentration. The quantity of insulin released was similar to that of conventional flask cultures.
Purification and characterization of a pp60c-src-related tyrosine kinase that effectively phosphorylates a synthetic peptide derived from p34cdc2 (1991)

A protein tyrosine kinase has been purified from the particulate fraction of bovine spleen to a specific activity of 0.217 mumol/min/mg at 100 microM ATP and 3 mM [Val5] angiotensin II. Both the angiotensin phosphorylation activity and immunoreactivity towards an antibody preparation raised against a synthetic peptide containing the autophosphorylation site of pp60c-src, Cys-src(403-421), were monitored during the purification. The purified sample displayed three closely spaced protein bands with molecular weights of 50-55 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. All bands could be phosphorylated exclusively on tyrosine residues under autophosphorylation conditions. All reacted on immunoblots with an antibody raised against a synthetic peptide corresponding to the consensus autophosphorylation site of members of the pp60c-src family of tyrosine kinases. Tryptic phosphopeptide maps of the three proteins were essentially indistinguishable. The results suggest that the purified enzyme preparation contained mainly three closely related pp60c-src-family protein tyrosine kinases or a pp60src-family protein tyrosine kinase modified posttranslationally to give three closely spaced protein bands on sodium dodecyl sulfate gel. Neither of these proteins appears to be pp60c-src or p56lck. The spleen protein tyrosine kinase was found to phosphorylate a p34cdc2 kinase peptide, Cys-cdc2(8-20), which contained the regulatory tyrosine residue Tyr-15 about 20 times better than [Val5]angiotensin II or Cys-src(403-421) peptide at a peptide substrate concentration of 1 mM. In contrast, epidermal growth factor receptor kinase partially purified from A431 cells did not show preference for Cys-cdc2(8-20) as its substrate. Although Cys-cdc2(8-20) contained two tyrosine residues, only the tyrosine corresponding to Tyr-15 in p34cdc2 was phosphorylated by the spleen tyrosine kinase. The observation suggests that the primary structure surrounding Tyr-15 of p34cdc2 contains substrate structural determinants specific for the spleen tyrosine kinase.
Transfection of constitutively active mitogen-activated protein/extracellular signal-regulated kinase kinase confers tumorigenic and metastatic potentials to NIH3T3 cells. (2000)

Cellular growth and differentiation are controlled by multiple extracellular signals, many of which activate extracellular signal-regulated kinase (ERK)/mitogen-activated protein (MAP) kinases. Components of the MAP kinase pathways also cause oncogenic transformation in their constitutively active forms. Moreover, expression of activated ras can confer metastatic potential upon some cells. Activation of MAP kinases requires phosphorylation of both Thr and Tyr in the catalytic domain by a family of dual-specificity kinases, called MEKs (MAP kinase/ERK kinase). MEK1 is activated by phosphorylation at Ser218 and Ser222 by Raf. Mutation of these two sites to acidic residues, specifically [Asp218], [Asp218, Asp222], and [Glu218, Glu222], results in constitutively active MEK1. Using these mutant variants of MEK1, we showed previously that transfection of NIH/3T3 or Swiss 3T3 cells causes morphological transformation and increases growth on soft agar, independent of ERK activity. The transformed cell lines show increased expression of matrix metalloproteinases 2 and 9 and cathepsin L, proteinases that have been implicated in the metastatic process. We tested NIH3T3 cells transfected with the [Asp218] or [Asp218, Asp222] for metastatic potential after i.v. injection into athymic mice. Parental 3T3 cells formed no tumors grossly or histologically. However, all MEK1 mutant transformants formed macroscopic metastases. Thus, like activated Ras, MEK1 can confer both tumorigenic and metastatic potential upon NIH3T3 cells. These results refine the mechanism through which ras could confer tumorigenic and metastatic potential (ie., the critical determinants of tumorigenic and metastatic potential are downstream of MEK1).
Amino Acid Sequence of a Lectin from Japanese Frog (Rana japonica) Eggs1 (1990)

The complete amino acid sequence and the location of disulfide bonds of a lectin from Japanese frog (Rana japonica) eggs, which specifically agglutinates transformed cells, are presented. The sequence was determined by analysis of peptides generated by digestion of the S-carboxyamidomethylated protein with Achromobacter protease I, or chymotrypsin, and by chemical cleavage with BNPS-skatole or cyanogen bromide. The lectin is a single-chain protein consisting of 111 residues, with a pyroglutamyl residue at the amino terminus. Four disulfide bonds link half-cystinyl residue 19 to 72, 34 to 82, 52 to 97, and 94 to 111. The sequence and the location of the disulfide bonds are highly homologous to those of bull frog (Rana catesbeiana) egg S-lectin. They are also homologous to human angiogenin, a tumor angiogenesis factor, and a family of pancreatic ribonucleases.
THE ACTION POTENTIAL OF SPINAL AXONS IN VITRO (1954)

Despite the trauma of dissection and special metabolic requirements, the physiological properties of funiculi of the mammalian spinal cord can be studied in vitro. They are adequately oxygenated by diffusion at 0.88 atm. pO(2) and remain in a functionally normal state for over 12 hours. The internal consistency of several kinds of data presented in this and the foregoing papers (5, 38) serves to characterize certain properties of central myelinated axons whether excised or in situ. (1) Spinal tracts support a large spike potential in vitro whose form, duration, and velocity are comparable to those of alpha fibers in vitro and spinal tracts in vivo. (2) Properties consistent with a large L fraction are found in central axons whether excised or in situ. (3) Following conduction there has been identified post-spike supernormality with exponential time course (7.5 msecs. half-time) which is the result of activity intrinsic to parent fibers of dorsal columns. The supernormality is similar in form and magnitude both in excised and intact funiculi. (4) In excised funiculi the action potential of parent axons includes a large negative after-potential whose form and duration correspond satisfactorily with this supernormality. This potential appears not to result from activity arising in broken collaterals. (5) Central axons, excised or intact, fire spontaneously in the presence of citrate ion, and when synchronized by stimulation develop periodic oscillations at about 400 C.P.S. but show no such behavior in the presence of excess potassium ion. Certain characteristics peculiar to central axons indicate that they occupy an extreme position in the spectrum of properties encountered in conducting tissues. Dorsal column myelinated axons differ from their peripheral counterparts, even though they are parts of the same cell, in the following ways. The maintenance of the column spike potential is more critically dependent on CO(2) and the entire tissue mass has a higher oxygen consumption. The negative after-potential is much larger and the positive after-potential, non-existent following a single volley, is more difficult to develop by repetitive stimulation. Unlike peripheral nerve, central axons are not incited to spontaneous activity by manipulation of certain constituents normally present in their environment. However, when induced by the application of citrate the resulting rhythmic behavior has twice the frequency of that in peripheral nerve. In general, the recovery process in central axons is more invariant than that in peripheral axons when they are subjected to similar changes in their artificial environments.
Search for mutations in the β1 GABAA receptor subunit gene in patients with schizophrenia (1994)

As alterations in GABAergic neurotransmission have been indirectly implicated in the pathogenetics of schizophrenia, GABAA receptor subunit genes are plausible candidate genes for the illness. We undertook a search for sequence variations in the coding region of beta 1 subunit gene by designing intron-based primers to amplify its 9 exons. Using single strand conformation polymorphism (SSCP) analysis, we found an exon 9 variant present in 3 of 86 unrelated schizophrenic cases derived from families having at least 2 first-degree relatives with schizophrenia. Direct sequencing of the SSCP variant revealed a C-->G nucleotide transversion at codon 396 predicting a histidine to glutamine substitution in the beta 1 peptide. The predicted amino acid substitution occurs at a highly conserved site, 9 residues from a cAMP-dependent serine phosphorylation consensus sequence. All known GABAA beta 1 subunit genes including human, bovine, and rat, code for histidine at position 396. Although the variant cosegregated with disease in a family with 2 affected sibs, it was only transmitted to 2 of 3 affected sibs in a multiplex family. The variant was not found in an additional sample comprising 155 unrelated schizophrenics and the sequence variant was present at a low frequency (approximately 1.1%) in control groups. Although these results indicate that the sequence variant is likely to be a natural polymorphism, it is possible that the variant may be a predisposing allele in rare instances. It is also possible that the variant may change the function or regulation of the GABAA receptor complex and it may be of pharmacogenetic relevance.
A SYNTHETIC APPROACH TO (+)-THIENAMYCIN FROM METHYL (R)-3-HYDROXYBUTANOATE. A NEW ENTRY TO (3R, 4R)-3-[(R)-1-HYDROXYETHYL]-4-ACETOXY-2-AZETIDINONE (1985)

Abstract A new entry to the O-silylated form of the title azetidinone, a well-established key intermediate for thienamycin synthesis, is described which relies on the stereocontrolled transformation of the 2-azetidinone obtained via the condensation of methyl (R)-3-hydroxybutanoate with the N-silylimine of trimethylsilylpropynal.
Cycloadditions of cyanoketenes to cinnamylidenamines and benzylidenamines. Synthetic scope, stereochemistry, and mechanism (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCycloadditions of cyanoketenes to cinnamylidenamines and benzylidenamines. Synthetic scope, stereochemistry, and mechanismHarold W. Moore, Gregory Hughes, Kasturi Srinivasachar, Mario Fernandez, Nghi V. Nguyen, Doug Schoon, and Anne TranneCite this: J. Org. Chem. 1985, 50, 22, 4231–4238Publication Date (Print):November 1, 1985Publication History Published online1 May 2002Published inissue 1 November 1985https://pubs.acs.org/doi/10.1021/jo00222a010https://doi.org/10.1021/jo00222a010research-articleACS PublicationsRequest reuse permissionsArticle Views460Altmetric-Citations79LEARN 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 Get e-Alerts
Improving the tumor retention of radioiodinated antibody: aryl carbohydrate adducts. (1990)

Improved methods for attaching radioiodine to monoclonal antibodies have been developed. Ten aryl carbohydrate adducts were synthesized by the reductive amination of a carbohydrate with an aryl amine, using sodium cyanoborohydride as a reducing agent. After purification by chromatography and characterization by nuclear magnetic resonance they were iodinated using the chloramine-T method. Iodinated adducts were activated with cyanuric chloride and incubated with protein at room temperature. The immunoreactivity and avidity of radioiodinated tyramine cellobiose (TCB) labeled antibody were fully preserved when compared to electrophilically radioiodinated antibody. Radioiodinated TCB-and tyramine glucose-labeled monoclonal antibodies showed much greater intracellular retention of radioiodine when compared to electrophilically radioiodinated monoclonal antibodies. Neither radioiodinated tyramine nor radioiodinated TCB had any specific tissue uptake or retention. In mice the retention of radioiodinated TCB labeled anti-Thy-1.1 antibody (1A14) by Thy-1.1-bearing lymphoma cells was 2 times greater than that of chloramine-T labeled 1A14 antibody, whereas the plasma clearance curve and uptake in normal tissues was not changed. This method of radioiodinating monoclonal antibodies increases the retention time of radioiodine in tumor and thus may obviate the problem of intracellular deiodination, a perceived disadvantage of electrophilically iodinated antibodies, with respect to tumor retention of radioactivity.
Chemistry and Physics in One Dimension:  Synthesis and Properties of Nanowires and Nanotubes (1999)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry and Physics in One Dimension: Synthesis and Properties of Nanowires and NanotubesJiangtao Hu, Teri Wang Odom, and Charles M. LieberView Author Information Department of Chemistry and Chemical Biology and Division of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138 Cite this: Acc. Chem. Res. 1999, 32, 5, 435–445Publication Date (Web):February 20, 1999Publication History Received24 September 1998Published online20 February 1999Published inissue 1 May 1999https://pubs.acs.org/doi/10.1021/ar9700365https://doi.org/10.1021/ar9700365research-articleACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views20976Altmetric-Citations3091LEARN 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 SUBJECTS:Carbon nanotubes,Catalysts,Crystallization,Nanostructures,Nanowires Get e-Alerts
The Role of NSAIDs in the Prevention of Colon Cancer (2002)

The treatment of colorectal cancer continues to improve, but it still remains the second leading cause of cancer-related death in the United States. In 2001, there will be over 135,000 new cases of colorectal cancer in the United States alone. Prevention is not only a realistic option for colon cancer, but also one that offers significant hope for this dreadful disease.Cancer prevention is concerned with the identification of preventable causes of cancer in a target population and with the effective application of strategies to reduce its incidence. Prevention may be categorized as primary, secondary, or tertiary. Primary prevention modifies genetic, environmental, and biological factors etiological in a given tumor to alter their effects on tumorigenesis. For example, elimination of chemicals, radiation, and viruses constitutes primary prevention. Unfortunately, culprit agents, e.g., smoking, are rarely identified. Secondary prevention deals with screening for premalignant and early neoplastic lesions, symptomatic or asymptomatic, and their expeditious treatment. Screening a large population becomes worthwhile if the disease represents a significant health problem, and a cost-effective treatment is available and acceptable to patients and doctors. For example, screening for colorectal cancer reduces mortality by 15–33%. Tertiary prevention utilizes specific pharmacological agents or nutrients to prevent, delay, or retard the development of cancer. This is also called chemoprevention. Nonsteroidal antiinflammatory drugs (NSAIDs) are emerging as the prototypical chemopreventive agents against colorectal cancer, a notion now supported by a considerable body of epidemiological, animal, and basic science data.In this review, we summarize our current understanding of the role of NSAIDs in the prevention of colorectal cancer and present efforts to develop safer alternatives to traditional NSAIDs.
Pegylated peptides I: Solid-phase synthesis of N alpha-pegylated peptides using Fmoc strategy. (1993)

The feasibility of pegylating peptides by the solid-phase procedure was examined. Although polyethyleneglycol (PEG) was shown to be partially degraded by HF, the use of TFA was fully compatible with the PEG system. Therefore, the Fmoc/tBu solid-phase strategy was utilized for the synthesis of a series of model tetra-, octa- and dodecapeptides, and the corresponding N alpha-pegylated peptides, which were prepared from common peptide-resin intermediates. PEG-OCH2-CO-Nle-OH, 3, proved to be an ideal reagent for N-terminal pegylation. This intermediate served as a diagnostic for the determination of the number of PEG units/mole of peptide. Solid-phase coupling reactions proceeded by standard procedures using BOP-activation. The authentic pegylated peptides (readily purified by conventional methods of preparative HPLC) were fully characterized by amino acid analysis, 1H-NMR spectroscopy, analytical HPLC and laser desorption ionization mass spectrometry, leading to the values that are identical with the expected structures.
A 1-V 46-ns 16-Mb SOI-DRAM with body control technique (1997)

A low-voltage high-speed 16-Mb SOI-DRAM has been developed using a 0.5-/spl mu/m CMOS/SIMOX technology. A newly introduced "FD-PD mode switching" transistor dynamically switches its operation mode between fully depleted (FD) and partially depleted (PD) according to the body bias voltage, thus it has both PD-mode large current drivability and FD-mode small leakage current. By the body bias control, the transistor operates as if it has an S-factor of 30 mV/decade. Enabling both high speed and low power at a low voltage, 30 mV is only one-half the theoretical value. By utilizing the transistor, we have developed body pulsed sense amplifier (BPS), body driven equalizer (BDEQ), body current clamper (BCC), and body pulsed transistor logic (BPTL) to achieve 46 ns access time at 1 V power supply with suppressed standby current.