gebhart/patrepeval huggingface dataset:
Ras-Targeting Action of Thiopurines in the Presence of Reactive Nitrogen Species (2010)

Thiopurine drugs are commonly used in the treatment of certain cancers, autoimmune disorders, organ transplant rejection, and bowel disease. Because long-term treatment with thiopurines for certain diseases is common, the cytotoxic effects associated with chronic exposure to thiopurine drugs are inevitable. The results shown in this study indicate that the oncogenic Ras in model cancer cell lines forms a complex with thioguanine nucleotide that is derived from long-term treatment with thiopurines. This study also showed that the Ras thioguanine nucleotide binary complex is likely to be a direct target of a redox agent, resulting in downregulation of the oncogenic Ras. This study proposes a radical-based molecular mechanism for the path of Ras-targeting thiopurines used in conjunction with redox agents. Given that Ras plays a central role in cellular signaling pathways, any interference with Ras activity by thiopurines and redox agents has the potential for devastating cytotoxic effects.
Biosynthesis of Terpenes. Preparation of (E)-1-Hydroxy-2-methyl-but-2-enyl 4-Diphosphate, an Intermediate of the Deoxyxylulose Phosphate Pathway (2002)

(E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (E-6) was synthesized in six reaction steps from hydroxyacetone (9) and (ethoxycarbonylmethenyl)-triphenylphosphorane (11) with an overall yield of 38%. The compound was shown to be identical with the product of IspG protein, which serves as an intermediate in the nonmevalonate terpene biosynthetic pathway.
Manipulations of Cholinesterase Gene Expression Modulate Murine Megakaryocytopoiesis In Vitro (1990)

Megakaryocytopoiesis was selectively inhibited in cultured murine bone marrow cells by a 15-mer oligodeoxynucleotide complementary to the initiator AUG region in butyrylcholinesterase mRNA. Furthermore, conditioned medium from Xenopus oocytes producing recombinant butyrylcholinesterase stimulated megakaryocytopoiesis. These observations implicate butyrylcholinesterase in megakaryocytopoiesis and suggest application of oligodeoxynucleotides for modulating bone marrow development.
Etchant Anisotropy Controls the Step Bunching Instability in KOH Etching of Silicon (2004)

STM investigations of vicinal Si(111) surfaces etched in KOH solutions under controlled flow conditions show that step bunching instability is due to inhomogeneities that develop in the etchant as the result of highly step-site-specific etching reactions. Other previously postulated mechanisms for step bunching, including anisotropic surface diffusion, surface strain, and impurity deposition, are conclusively ruled out. The inhomogeneities locally accelerate etching near surface steps. Kinetic Monte Carlo simulations of this process qualitatively reproduce the observed morphologies.
ILR1, an Amidohydrolase That Releases Active Indole-3-Acetic Acid from Conjugates (1995)

In plants, the growth regulator indole-3-acetic acid (IAA) is found both free and conjugated to a variety of amino acids, peptides, and carbohydrates. IAA conjugated to leucine has effects in Arabidopsis thaliana similar to those of free IAA. The ilr1 mutant is insensitive to exogenous IAA-Leu and was used to positionally clone the Arabidopsis ILR1 gene. ILR1 encodes a 48-kilodalton protein that cleaves IAA-amino acid conjugates in vitro and is homologous to bacterial amidohydrolase enzymes. DNA sequences similar to that of ILR1 are found in other plant species.
Structure of anguibactin, a unique plasmid-related bacterial siderophore from the fish pathogen Vibrio anguillarum (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure of anguibactin, a unique plasmid-related bacterial siderophore from the fish pathogen Vibrio anguillarumM. A. F. Jalal, M. B. Hossain, Dick Van der Helm, J. Sanders-Loehr, L. A. Actis, and J. H. CrosaCite this: J. Am. Chem. Soc. 1989, 111, 1, 292–296Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/ja00183a044https://doi.org/10.1021/ja00183a044research-articleACS PublicationsRequest reuse permissionsArticle Views493Altmetric-Citations128LEARN 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
Cloning and Expression of a Cocaine-Sensitive Dopamine Transporter Complementary DNA (1991)

A rat dopamine (DA) transporter complementary DNA has been isolated with combined complementary DNA homology and expression approaches. The DA transporter is a 619-amino acid protein with 12 hydrophobic putative membrane-spanning domains and homology to the norepinephrine and gamma-aminobutyric acid transporters. The expressed complementary DNA confers transport of [3H]DA in Xenopus oocytes and in COS cells. Binding of the cocaine analog [3H]CFT ([3H]2 beta-carbomethoxy-3 beta-(4-fluorophenyl)tropane) to transfected COS cell membranes yields a pharmacological profile similar to that in striatal membranes.
A Part-Based Skew Estimation Method (2012)

In this paper we propose a part-based skew estimation method which is more robust to larger varieties of text images, such as camera-captured scene images. Specifically, the skew angle at each local part of the input image is estimated independently by referring the local part of upright character images stored as a database. Then the global skew angle is estimated by aggregating the estimated local skews. The proposed method does not assume that characters are laid-out in straight lines and thus have more robustness to the varieties of text images than conventional methods. The experimental results show the advantage of the proposed method over the conventional methods under several conditions.
Malignant melanoma: genetics and therapeutics in the genomic era (2006)

Cell for cell, probably no human cancer is as aggressive as melanoma. It is among a handful of cancers whose dimensions are reported in millimeters. Tumor thickness approaching 4 mm presents a high risk of metastasis, and a diagnosis of metastatic melanoma carries with it an abysmal median survival of 6-9 mo. What features of this malignancy account for such aggressive behavior? Is it the migratory history of its cell of origin or the programmed adaptation of its differentiated progeny to environmental stress, particularly ultraviolet radiation? While the answers to these questions are far from complete, major strides have been made in our understanding of the cellular, molecular, and genetic underpinnings of melanoma. More importantly, these discoveries carry profound implications for the development of therapies focused directly at the molecular engines driving melanoma, suggesting that we may have reached the brink of an unprecedented opportunity to translate basic science into clinical advances. In this review, we attempt to summarize our current understanding of the genetics and biology of this disease, drawing from expanding genomic information and lessons from development and genetically engineered mouse models. In addition, we look forward toward how these new insights will impact on therapeutic options for metastatic melanoma in the near future.
Regulation of insulin receptor signaling by protein-tyrosine dephosphorylation. (1993)

Protein-tyrosine phosphatases (PTPases) that dephosphorylate the active (autophosphorylated) form of the insulin receptor and attenuate its tyrosine kinase activity play an essential regulatory role in signaling mediated by the insulin receptor. PTPases also modulate signaling through postreceptor pathways by catalyzing the dephosphorylation of cellular substrates of the insulin receptor kinase, such as IRS-1, or other tyrosine-phosphorylated proteins along the cellular cascade of insulin action. Recent studies have provided important data regarding PTPase(s) in insulin-responsive tissues that may regulate various components of the insulin action pathway. Further studies in this area will enhance our understanding of the mechanisms involved in insulin signaling and clarify the potential involvement of PTPases in the pathophysiology of insulin-resistant disease states.
Synergistic antitumor activity of the novel SN‐38‐incorporating polymeric micelles, NK012, combined with 5‐fluorouracil in a mouse model of colorectal cancer, as compared with that of irinotecan plus 5‐fluorouracil (2008)

The authors reported in a previous study that NK012, a 7-ethyl-10-hydroxy-camptothecin (SN-38)-releasing nano-system, exhibited high antitumor activity against human colorectal cancer xenografts. This study was conducted to investigate the advantages of NK012 over irinotecan hydrochloride (CPT-11) administered in combination with 5-fluorouracil (5FU). The cytotoxic effects of NK012 or SN-38 (an active metabolite of CPT-11) administered in combination with 5FU was evaluated in vitro in the human colorectal cancer cell line HT-29 by the combination index method. The effects of the same drug combinations was also evaluated in vivo using mice bearing HT-29 and HCT-116 cells. All the drugs were administered i.v. 3 times a week; NK012 (10 mg/kg) or CPT11 (50 mg/kg) was given 24 hr before 5FU (50 mg/kg). Cell cycle analysis in the HT-29 tumors administered NK012 or CPT-11 in vivo was performed by flow cytometry. NK012 exerted more synergistic activity with 5FU compared to SN-38. The therapeutic effect of NK012/5FU was significantly superior to that of CPT-11/5FU against HT-29 tumors (p = 0.0004), whereas no significant difference in the antitumor effect against HCT-116 tumors was observed between the 2-drug combinations (p = 0.2230). Cell-cycle analysis showed that both NK012 and CPT-11 tend to cause accumulation of cells in the S phase, although this effect was more pronounced and maintained for a more prolonged period with NK012 than with CPT-11. Optimal therapeutic synergy was observed between NK012 and 5FU, therefore, this regimen is considered to hold promise of clinical benefit, especially for patients with colorectal cancer.
Cell Contact–Dependent Priming and Fc Interaction with CD32+ Immune Cells Contribute to the TGN1412-Triggered Cytokine Response (2014)

Following inconspicuous preclinical testing, the superagonistic anti-CD28 mAb TGN1412 was applied to six study participants who all developed a devastating cytokine storm. We verified that TGN1412 treatment of fresh PBMCs induced only moderate responses, whereas restoration of tissue-like conditions by high-density preculture (HDC) allowed vigorous cytokine production. TGN1412 treatment of T cells isolated from HDC-PBMCs induced moderate cytokine responses, which upon additional anti-IgG crosslinking were significantly boosted. Moreover, coincubation of TGN1412-treated T cells with B cells expressing the intermediate affinity Fcγ receptor IIB (CD32B), or coincubation with CD32B(+) transfectants, resulted in robust T cell activation. This was surprising because TGN1412 was expressed as an Ig of the subclass 4 (IgG4), which was shown before to exhibit only minor affinity to FcγRs. Transcriptome analysis of TGN1412-treated T cells revealed that similar gene signatures were induced irrespective of whether T cells derived from fresh or HDC-PBMCs were studied. Collectively, these data indicate that HDC-PBMCs and HDC-PBMC-derived T cells mount rapid TGN1412 responses, which are massively boosted by FcγR crosslinking, in particular by CD32-expressing B cells. These results qualify HDC-PBMCs as a valuable in vitro test system for the analysis of complex mAb functions.
Anti‐GPIIb/IIIa (CD41) monoclonal antibody‐induced platelet activation requires Fc receptor‐dependent cell‐cell interaction (1991)

We studied platelet activation by UR1, a murine IgG1 anti-CD41 mAb. Like thrombin and crosslinked anti-Fc gamma RII mAb IV3, UR1 initiates prompt aggregation and Ca2+ mobilization. UR1 F(ab')2 fragments failed to activate, yet inhibited UR1 IgG-mediated activation. UR1-induced activation was blocked by anti-Fc gamma RII mAb. High viscosity (15% dextran or Ficoll), which impedes cell-cell interaction, inhibited activation by UR1. Cell-cell interaction was confirmed by cell-mixing studies. UR1 binding to platelets of one pool was blocked with UR1 F(ab')2 allowing UR1 binding only to Fc gamma RII. IV3 Fab fragments blocked ligand binding to Fc gamma RII on platelets of a second pool; thus, UR1 could bind only its epitope. UR1 initiated an immediate [Ca2+]i increase in the intermixed pools at low ionic strength. These studies indicate that UR1 IgG binds CD41 on one platelet to form immune complexes which then crosslink and stimulate Fc gamma RII on nearby platelets. Two other anti-CD41 mAb, 6C9 and C17, and two anti-CD9 mAb, AG1 and mAb7, activated platelets in a UR1-like manner. We propose that platelet Fc gamma RII crosslinking that follows the interaction of IgG-opsonized platelets may be a common mechanism by which anti-platelet antibodies activate platelets.
Immunogenetic Studies of Respiratory Anaphylaxis in Selectively Bred Guinea Pigs (1985)

The genetic and immunological basis of respiratory anaphylaxis was studied in two strains of guinea pigs selectively bred for either high or low respiratory anaphylactic response to inhalation of ovalbumin. Individuals of the parental strains, F1-hybrids and backcross offspring were examined for class II MHC type and asthmatic response to ovalbumin. Analysis of the results revealed an association of asthma phenotype and MHC class II type. Apart from the gene(s) in the MHC several other genes seem to be involved in the control of guinea pig asthma.
Tissue-specific enhancer of the human glycoprotein hormone alpha-subunit gene: dependence on cyclic AMP-inducible elements. (1987)

We identified and characterized elements which confer tissue specificity and cyclic AMP (cAMP) responsiveness to the human glycoprotein alpha-subunit gene. An enhancer containing an 18-base-pair repeat conferred cAMP responsiveness in a non-tissue-specific fashion. DNase I protection assays revealed DNA-binding factors that bound to this element in both placental and nonplacental cells. It also enhanced the alpha-subunit promoter in a tissue-specific manner but had a negligible effect on a heterologous promoter. A unique element found upstream of this enhancer had no independent activity but, in combination with the cAMP-responsive enhancer, distinctly increased the tissue-specific activity of both the alpha-subunit promoter and a heterologous promoter. A factor that bound to this upstream element was found in placental but not nonplacental cells. We conclude that this novel element acts, perhaps through a specific trans-acting factor, in concert with a cAMP-responsive enhancer to confer tissue specificity to the alpha-subunit gene.
Herpes simplex virus type 1 latency-associated transcription unit promotes anatomical site-dependent establishment and reactivation from latency (1992)

Defined herpes simplex virus type 1 (HSV-1) mutants KOS/1 and KOS/62 (positive and negative, respectively, for latency-associated transcripts [LATs]) express the Escherichia coli beta-galactosidase (beta-Gal) gene during latency. These mutants were employed to assess the functions of the latency-associated transcription unit on establishment and maintenance of and reactivation from the latent state. It was found that in the trigeminal ganglia, the frequencies of hyperthermia-induced reactivation of KOS/62 and an additional LATs- mutant (KOS/29) were reduced by at least 80%. Quantification of latently infected neurons expressing the beta-Gal gene revealed that the LATs- mutant KOS/62 established approximately 80% fewer latent infections in the trigeminal ganglia than did KOS/1 (LATs+). This reduction in establishment which is evident in the trigeminal ganglia could account for the reduced frequency of reactivation from this site. In striking contrast, both LATs- mutants reactivated with wild-type frequencies from lumbosacral ganglia. Quantification of beta-Gal-positive neurons at this site revealed that KOS/62 established as many as or more latent infections than the LATs+ virus, KOS/1. Colocalization of HSV antigen and beta-Gal suggested that the decreased establishment by LATs- mutants in trigeminal ganglia was the result of inefficient viral shutoff. Thus, one function of the HSV-1 LATs transcription unit is to promote the establishment of latency in trigeminal but not lumbosacral ganglia. Such a function may be relevant to understanding the distinct clinical recurrent disease patterns of HSV-1 and HSV-2.
Au “Ink” for AFM “Dip-Pen” Nanolithography (2001)

Scanning probe lithography is a rapidly growing research field, in which atomic force microscope based “dip-pen” nanolithography (DPN) is a simple new technique for creating chemically distinct nanostructures on surfaces in a “direct-write” fashion. Previous works demonstrate the transport of alkanethiols to a gold substrate, resulting in the formation of patterned self-assembled monolayers. Here, we show that surface-induced reduction of metal ions combined with DPN can be used to create metallic nanostructures on Si surfaces. Au nanostructures with sub-100-nm resolution can be created routinely, showing that the DPN technique is a general method for nanofabrication.
Pyromellitamide Aggregates and Their Response to Anion Stimuli (2007)

The N,N',N'',N'''-1,2,4,5-tetra(ethylhexanoate) pyromellitamide is found to be capable of both intermolecular aggregation and binding to small anions. It is synthesized by aminolysis of pyromellitic anhydride with ethanolamine, followed by a reaction with hexanoyl chloride. The single-crystal X-ray structure of the pyromellitamide shows that it forms one-dimensional columnar stacks through an intermolecular hydrogen-bonding network. It also forms self-assembled gels in nonpolar solvents, presumably by a hydrogen-bonding network similar to the solid-state structure as shown by IR and XRD studies. Aggregation by intermolecular hydrogen bonding of the pyromellitamide is also observed by NMR and IR in solution. Fitting of NMR dilution data for pyromellitamide in d6-acetone to a cooperative aggregation model gave KE=232 M-1 and positive cooperativity of aggregation (rho=0.22). The pyromellitamide binds to a range of small anions with the binding strength decreasing in the order chloride>acetate>bromide>nitrate approximately iodide. The data indicate that the pyromellitamide binds two anions and that it displays negative cooperativity. The intermolecular aggregation of the pyromellitamide can also be altered using small anion stimuli; anion addition to preformed self-assembled pyromellitamide gels causes their collapse. The kinetics of anion-induced gel collapse are qualitatively correlated to the binding affinities of the same anions in solution. The cooperative anion binding properties and the sensitivity of the self-assembled gels formed by pyromellitamide toward anions could be useful in the development of sensors and switching/releasing devices.
Cell Penetrating Peptides as Molecular Carriers for Anti-Cancer Agents (2018)

Cell membranes with their selective permeability play important functions in the tight control of molecular exchanges between the cytosol and the extracellular environment as the intracellular membranes do within the internal compartments. For this reason the plasma membranes often represent a challenging obstacle to the intracellular delivery of many anti-cancer molecules. The active transport of drugs through such barrier often requires specific carriers able to cross the lipid bilayer. Cell penetrating peptides (CPPs) are generally 5-30 amino acids long which, for their ability to cross cell membranes, are widely used to deliver proteins, plasmid DNA, RNA, oligonucleotides, liposomes and anti-cancer drugs inside the cells. In this review, we describe the several types of CPPs, the chemical modifications to improve their cellular uptake, the different mechanisms to cross cell membranes and their biological properties upon conjugation with specific molecules. Special emphasis has been given to those with promising application in cancer therapy.
Recent Advances in Small-Molecule TLR7 Agonists for Drug Discovery (2018)

Medicinal Chemistry Reviews is an outstanding 680 page volume providing timely and critical reviews of important topics in medicinal chemistry. It is provided free of charge to MEDI members in electronic format. Members can also order a print copy, for the cost of printing, shipping and handling
Transcriptome Profiling of Human Ulcerative Colitis Mucosa Reveals Altered Expression of Pathways Enriched in Genetic Susceptibility Loci (2014)

Human colonic mucosa altered by inflammation due to ulcerative colitis (UC) displays a drastically altered pattern of gene expression compared with healthy tissue. We aimed to understand the underlying molecular pathways influencing these differences by analyzing three publically-available, independently-generated microarray datasets of gene expression from endoscopic biopsies of the colon. Gene set enrichment analysis (GSEA) revealed that all three datasets share 87 gene sets upregulated in UC lesions and 8 gene sets downregulated (false discovery rate <0.05). The upregulated pathways were dominated by gene sets involved in immune function and signaling, as well as the control of mitosis. We applied pathway analysis to genotype data derived from genome-wide association studies (GWAS) of UC, consisting of 5,584 cases and 11,587 controls assembled from eight European-ancestry cohorts. The upregulated pathways derived from the gene expression data showed a highly significant overlap with pathways derived from the genotype data (33 of 56 gene sets, hypergeometric P = 1.49 × 10(-19)). This study supports the hypothesis that heritable variation in gene expression as measured by GWAS signals can influence key pathways in the development of disease, and that comparison of genetic susceptibility loci with gene expression signatures can differentiate key drivers of inflammation from secondary effects on gene expression of the inflammatory process.