gebhart/patrepeval huggingface dataset:
Solution Structures and Integrin Binding Activities of an RGD Peptide with Two Isomers (2001)

The Arg-Gly-Asp (RGD) sequence serves as the primary integrin recognition site in extracellular matrix proteins, and peptides containing this sequence can mimic the activities of the matrix proteins. Depending on the context of the RGD sequence, an RGD-containing peptide may bind to all of the RGD-directed integrins, to a few, or to only a single one. We have previously isolated from a phage-displayed peptide library a cyclic peptide that binds avidly to the alpha(v)beta3 and alpha(v)beta5 integrins but does not bind to other closely related integrins. This peptide, ACDCRGDCFCG, exists in two natural configurations depending on internal disulfide bonding. The peptide with the 1-4; 2-3 disulfide bond arrangement accounts for most of the alpha(v) integrin binding activity, whereas the 1-3; 2-4 peptide is about 10-fold less potent. Solution structure analysis by nuclear magnetic resonance reveals an entirely different presentation of the RGD motif in the two isomers of RGD-4C. These results provide new insight into the ligand recognition specificity of integrins.
Hematopoietic stem cell differentiation affects expression and function of MRP4 (ABCC4), a transport protein for signaling molecules and drugs (2008)

Several types of peripheral blood cells express ABC transporters. ABCC4 (MRP4) and ABCC5 (MRP5) localize to different cellular sites and fulfill lineage-specific functions such as mediator storage in platelets' dense granules. All mature blood cells originate from the same precursor and specific functionalities arise during differentiation. To characterize this process, expression, localization and function of MRP4 and MRP5 were assessed in differentiating human CD34+ progenitors and leukemia cell lines using real time polymerase chain reaction (PCR), immunofluorescence microscopy and cell viability assays. Median MRP4 mRNA copy numbers were significantly enhanced by megakaryocytic differentiation from 7.9 x 10(3) to 5.8 x 10(4) copies per nanograms of total RNA (p < 0.05) in CD34+ progenitors and in M-07e cells (MRP4 mRNA/18S rRNA ratios: 5.4 +/- 3.8 x 10(-4) vs. 2.7 +/- 0.9 x 10(-3) for native and differentiated cells, respectively, p < 0.05), and MRP4 protein was localized to granular structures and to the plasma membrane both in differentiated progenitors and bone marrow megakaryocytes. In contrast, expression of MRP4 decreased during maturation to leukocytes (MRP4 mRNA/18S rRNA ratios: 5.2 x 10(-3) for native vs. 3.5 x 10(-3) for CD34+ cells in the presence of G-CSF, p < 0.05) and was significantly reduced in mature monocytes and granulocytes compared with progenitors (MRP4 mRNA/18S rRNA ratios: 8.1 +/- 5.4 x 10(-5) and 2.8 +/- 1.6 x 10(-4) vs. 1.2 +/- 0.7 x 10(-3), respectively, p < 0.05). Expression of MRP5 was not significantly altered under all differentiation conditions. These results indicate that MRP4 expression is differentially regulated during hematopoiesis. The increase of MRP4 together with its specific localization during differentiation toward megakaryocytes supports the concept of platelet specific functions whereas decreased transporter expression in leukocyte differentiation may have implications for chemotherapy.
Induction of Apoptosis by Alkaloids, Non-Protein Amino Acids, and Cardiac Glycosides in Human Promyelotic HL-60 Cells (2007)

The induction of apoptosis by 66 alkaloids of the quinoline, quinolizidine, pyrrolizidine, isoquinoline, indole, terpene, tropane, steroid, purine, and piperidine type, of 9 cardiac glycosides, 11 non-protein amino acids and 10 further secondary metabolites was assayed in HL-60 cell cultures and measured by quantification of the subdiploid DNA content by flow cytometry, detection of DNA fragmentation by gel electrophoresis, and cell morphology. Several alkaloids of the isoquinoline, quinoline, and indole type were active, whereas quinol-izidine, tropane, pyrrolizidine, terpene and piperdine alkaloids were mostly inactive. The proapoptotic alkaloids can be characterized by their property to inhibit protein biosynthesis and their intercalation into DNA at the same time, or by their inhibition of microtubule formation. All cardiac glycosides, which are both membrane detergents and Na+,K+-ATPase inhibitors, are potent apoptosis inducers. Also proapoptotic were a few non-protein amino acids, podophyllotoxin and the flavonoid quercetin.
Diels-Alder Additions with Dialkyl Azodicarboxylates and Azo-Bis-Formamidine (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiels-Alder Additions with Dialkyl Azodicarboxylates and Azo-Bis-FormamidineJ. C. J. MacKenzie, Alan Rodgman, and George F. WrightCite this: J. Org. Chem. 1952, 17, 12, 1666–1674Publication Date (Print):December 1, 1952Publication History Published online1 May 2002Published inissue 1 December 1952https://doi.org/10.1021/jo50012a015RIGHTS & PERMISSIONSArticle Views272Altmetric-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 InReddit PDF (617 KB) Get e-Alertsclose Get e-Alerts
Molar Extinction Coefficient of Single-Wall Carbon Nanotubes (2011)

The molar extinction coefficient of single-wall carbon nanotubes (SWNTs) is determined using fluorescence tagging, as well as atomic force microscopy (AFM) imaging, which facilitate the correlation of nanotube concentrations with absorption spectra. Tagging of SWNTs is achieved using fluorescence-labeled single-strand DNA oligomers as the dispersion additive, while AFM imaging is used to determine the mass of SWNTs in the retentate of vacuum-filtered colloidal SWNT suspensions. The resulting absorption cross section for the first exciton transition of (6,5) nanotubes of 1.7 × 10–17 cm2 per C-atom corresponds to an extinction coefficient of (4400 ± 1000) M–1·cm–1, which is equivalent to an oscillator strength of 0.010 per carbon atom.
Adoptive immunotherapy with genetically modified lymphocytes in allogeneic stem cell transplantation (2013)

Hematopoietic stem cell transplantation from a healthy donor (allo-HSCT) represents the most potent form of cellular adoptive immunotherapy to treat malignancies. In allo-HSCT, donor T cells are double edge-swords: highly potent against residual tumor cells, but potentially highly toxic, and responsible for graft versus host disease (GVHD), a major clinical complication of transplantation. Gene transfer technologies coupled with current knowledge on cancer immunology have generated a wide range of approaches aimed at fostering the immunological response to cancer cells, while avoiding or controlling GVHD. In this review, we discuss cell and gene therapy approaches currently tested in preclinical models and in clinical trials.
Hyperglycemia: An Independent Marker of In-Hospital Mortality in Patients with Undiagnosed Diabetes (2002)

Admission hyperglycemia has been associated with increased hospital mortality in critically ill patients; however, it is not known whether hyperglycemia in patients admitted to general hospital wards is associated with poor outcome. The aim of this study was to determine the prevalence of in-hospital hyperglycemia and determine the survival and functional outcome of patients with hyperglycemia with and without a history of diabetes. We reviewed the medical records of 2030 consecutive adult patients admitted to Georgia Baptist Medical Center, a community teaching hospital in downtown Atlanta, GA, from July 1, 1998, to October 20, 1998. New hyperglycemia was defined as an admission or in-hospital fasting glucose level of 126 mg/dl (7 mmol/liter) or more or a random blood glucose level of 200 mg/dl (11.1 mmol/liter) or more on 2 or more determinations. Hyperglycemia was present in 38% of patients admitted to the hospital, of whom 26% had a known history of diabetes, and 12% had no history of diabetes before the admission. Newly discovered hyperglycemia was associated with higher in-hospital mortality rate (16%) compared with those patients with a prior history of diabetes (3%) and subjects with normoglycemia (1.7%; both P < 0.01). In addition, new hyperglycemic patients had a longer length of hospital stay, a higher admission rate to an intensive care unit, and were less likely to be discharged to home, frequently requiring transfer to a transitional care unit or nursing home facility. Our results indicate that in-hospital hyperglycemia is a common finding and represents an important marker of poor clinical outcome and mortality in patients with and without a history of diabetes. Patients with newly diagnosed hyperglycemia had a significantly higher mortality rate and a lower functional outcome than patients with a known history of diabetes or normoglycemia.
Structural Basis for the Substrate Specificity of Endo-β-N-acetylglucosaminidase F3, (2000)

Endo-beta-N-acetylglucosaminidase F(3) cleaves the beta(1-4) link between the core GlcNAc's of asparagine-linked oligosaccharides, with specificity for biantennary and triantennary complex glycans. The crystal structures of Endo F(3) and the complex with its reaction product, the biantennary octasaccharide, Gal-beta(1-4)-GlcNAc-beta(1-2)-Man-alpha(1-3)[Gal-beta(1-4)-GlcNAc-be ta(1-2)-Man-alpha(1-6)]-Man-beta(1-4)-GlcNAc, have been determined to 1.8 and 2.1 A resolution, respectively. Comparison of the structure of Endo F(3) with that of Endo F(1), which is specific for high-mannose oligosaccharides, reveals highly distinct folds and amino acid compositions at the oligosaccharide recognition sites. Binding of the oligosaccharide to the protein does not affect the protein conformation. The conformation of the oligosaccharide is similar to that seen for other biantennary oligosaccharides, with the exception of two links: the Gal-beta(1-4)-GlcNAc link of the alpha(1-3) branch and the GlcNAc-beta(1-2)-Man link of the alpha(1-6) branch. Especially the latter link is highly distorted and energetically unfavorable. Only the reducing-end GlcNAc and two Man's of the trimannose core are in direct contact with the protein. This is in contrast with biochemical data for Endo F(1) that shows that activity depends on the presence and identity of sugar residues beyond the trimannose core. The substrate specificity of Endo F(3) is based on steric exclusion of incompatible oligosaccharides rather than on protein-carbohydrate interactions that are unique to complexes with biantennary or triantennary complex glycans.
T cell epitope specificity in human allergic and nonallergic subjects to bee venom phospholipase A2 (1993)

Phospholipase A2 (PLA) is a biochemically fully defined glycoprotein, representing the main allergen of bee venom. We have established CD4+ T cell clones specific to PLA from subjects allergic and nonallergic to bee sting. By screening the epitope specificity of these clones with 62 synthetic overlapping dodecapeptides representing the PLA molecule, two immunogenic epitopes, PLA81-92 and PLA113-124, were identified. Additional screening, using longer peptides of up to 18 residues, revealed a third epitope at position PLA 45-62. These epitopes are recognized by specific T cell clones in association with HLA-DP and -DQ molecules, although HLA-DR-associated responses to PLA exist. Primary in vitro proliferation of unfractionated PBMC from bee sting allergic, hyposensitized, or hyperimmune subjects to PLA-derived peptides revealed the same immunogenic sites as found in the T cell clones. Among the different groups of individuals, proliferative responses to the PLA molecule and fragments thereof were generally higher in allergic patients than in nonallergic subjects. Thus, at least three linear epitopes are involved in T cell recognition of PLA, independently whether or not subjects are allergic.
Differential expression of a novel protein kinase in human B lymphocytes. Preferential localization in the germinal center (1994)

B lymphocytes which reside in the germinal center region of lymphoid follicles are functionally and phenotypically distinct from the surrounding mantle zone B cells. We have isolated cDNA clones for several genes that are differentially expressed between these two populations of B lymphocytes. One such gene, BL44, is preferentially expressed in germinal center B cells. The nucleotide sequence of a 2,874-base pair BL44 cDNA was determined and a 2,451-bp open reading frame found that encodes for a 97-kDa serine/threonine protein kinase referred to as GC kinase. It has an NH2-terminal catalytic domain most similar to that of the Drosophila NinaC protein and the yeast STE20 protein. GC kinase mRNA transcripts are not unique to germinal center B cells and are found in several other tissues, including brain, lung, and placenta. The GC kinase protein was immunoprecipitated from transfected COS cells and from the Burkitt cell line RAMOS. GC kinase immunoprecipitated from transfected COS cells phosphorylated the substrates casein and myelin basic protein. In addition, a 97-kDa phosphoprotein likely to be GC kinase itself was detected. GC kinase may participate in an important signal transduction pathway in germinal center B cells.
Detailed analysis of p53 pathway defects in fludarabine-refractory chronic lymphocytic leukemia (CLL): dissecting the contribution of 17p deletion, TP53 mutation, p53-p21 dysfunction, and miR34a in a prospective clinical trial (2009)

The prognosis of fludarabine (F)-refractory chronic lymphocytic leukemia (CLL) is very poor, and underlying mechanisms are only partly understood. To assess the contribution of p53 abnormalities to F-refractory CLL, we studied TP53 mutations in the CLL2H trial (subcutaneous alemtuzumab; n = 99). We found TP53 mutations in 37% of patients. Twelve of 67 (18%) patients without the 17p deletion showed a TP53 mutation and 50% showed evidence of uniparental disomy. A total of 75% of cases with TP53 mutation (without 17p-) showed clonal evolution/expansion. TP53 mutations had no impact on overall survival (P = .48). CLL with the 17p deletion or TP53 mutation showed very low miR-34a expression. To investigate the mechanisms underlying refractory CLL beyond p53, we studied cases without 17p-/TP53 mutation in detail. In several paired samples before and after F-refractory disease, no change in p21/p53 induction was observed after DNA damage. Although TP53 mutations and 17p deletions are found in a high proportion of F-refractory CLL, more than half of the cases cannot be explained by p53 defects (deletion or mutation), and alternative mechanisms need to be investigated. Alemtuzumab is effective irrespective of genetic high-risk subgroups with TP53 mutations. These clinical trials are registered at www.clinicaltrials.gov as #NCT00274976.
Intermolecular Cross‐Linking in Fibrotic Collagen (1985)

The extent, nature and location of the cross-links involved in the stabilization of collagen in fibrotic lesions are crucial to its subsequent removal, naturally or induced by treatment. Stabilization is achieved initially by divalent aldimine and keto-imine intermolecular cross-links located at the end-overlap region in the quarter-stagger alignment of the molecules in the fibre. Elucidation of the location of the cross-links also provides chemical evidence for the organization of the collagen molecule in the fibre. All the fibrous collagens are stabilized by these cross-links, the more stable keto-imine cross-link predominating in the types I and II collagens present in the initial stages of fibrosis. Further stabilization of the lesion usually follows, increasing the resistance to degradative enzymes, thus rendering the fibrosis irreversible. This maturation process, which also occurs in normal ageing, involves the formation of multivalent cross-links derived from the initial aldimine and keto-imine cross-links to form a three-dimensional network through a polymeric peptide (poly-alpha 1CB6 in type I collagen). The nature of these cross-links has not yet been elucidated. The so-called mature cross-link, 3-hydroxypyridinoline, could not be identified in this polymeric network. A secondary process involving non-enzymic glycosylation of lysine residues and subsequent intermolecular cross-linking has also been demonstrated, although the nature and extent of this type of cross-link remain to be determined.
Adversarial Examples Are a Natural Consequence of Test Error in Noise (2019)

Over the last few years, the phenomenon of adversarial examples --- maliciously constructed inputs that fool trained machine learning models --- has captured the attention of the research community, especially when the adversary is restricted to small modifications of a correctly handled input. Less surprisingly, image classifiers also lack human-level performance on randomly corrupted images, such as images with additive Gaussian noise. In this paper we provide both empirical and theoretical evidence that these are two manifestations of the same underlying phenomenon, establishing close connections between the adversarial robustness and corruption robustness research programs. This suggests that improving adversarial robustness should go hand in hand with improving performance in the presence of more general and realistic image corruptions. Based on our results we recommend that future adversarial defenses consider evaluating the robustness of their methods to distributional shift with benchmarks such as Imagenet-C.
Total Synthesis of Epothilone B (2001)

[structure-see text] A convergent and stereoselective total synthesis of epothilone B (2) is described. The key steps are Normant reaction, Wadsworth-Emmons reaction of a methyl ketone 14 with the phosphonate reagent 7, diastereoselective aldol condensation of aldehyde 3 with enolate 4 to form the C6-C7 bond, and macrolactonization.
True-motion estimation with 3-D recursive search block matching (1993)

A new recursive block-matching motion estimation algorithm with only eight candidate vectors per block is presented. A fast convergence and a high accuracy, also in the vicinity of discontinuities in the velocity plane, was realized with such new techniques as bidirectional convergence and convergence accelerators. A new search strategy, asynchronous cyclic search, which allows a highly efficient implementation, is presented. A new block erosion postprocessing proposal further effectively eliminates block structures from the generated vector field. Measured with criteria relevant for the field rate conversion application, the new motion estimator is shown to have a superior performance over alternative algorithms, while its complexity is significantly less.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clinical worsening in multiple sclerosis is associated with increased frequency and area of gadopentetate dimeglumine–enhancing magnetic resonance imaging lesions (1993)

Abstract It is now well established that clinically stable patients with relapsing–remitting multiple sclerosis have ongoing disease activity when evaluated by serial gadolinium–enhanced (Gd‐DTPA) magnetic resonance imaging (MRI) scans. Despite this, the relationship between clinical disease and MRI lesions, though suspected, has not been extensively documented. The relationship between Gd‐DTPA MRI lesions, and clinical disease was examined in this study of 9 patients with mild relapsing–remitting multiple sclerosis (Expanded Disability Status Scale [EDSS] &lt;3.5) who had 24 to 37 monthly Gd‐DTPA MRI scans, neurological examinations, and EDSS score assignments. The area and frequency of Gd‐DTPA lesions were examined during months with and without clinical worsening as measured by EDSS. Forty‐one episodes of clinical worsening were noted during the study. A significant association was observed between these periods of clinical worsening and MRI parameters, including increases in total number, number of new lesions, and the total area of enhancement. Logistic regression analysis showed a signficant effect of the number and area of Gd‐DTPA MRI lesions on both the onset and continuation of clinical worsening, confirming an imporant relationship between clinical disease and an increase in cerebral Gd‐DTPA MRI activity. A relationship with long‐term disability was suggested, but cannot be confirmed without longer follow‐up of these patients.
Phosphorylation of the protein kinase C-theta activation loop and hydrophobic motif regulates its kinase activity, but only activation loop phosphorylation is critical to in vivo nuclear-factor-κB induction (2002)

Protein kinase C (PKC)-theta, a member of the 'novel' subfamily of PKC isoforms, is of singular importance in transducing signals in T-lymphocytes. Since understanding of regulatory phosphorylation of novel PKCs is fragmentary and inconsistent with findings for 'classical' PKC isoforms, we investigated three potential phosphorylation sites on PKC-theta; in the activation loop (Thr(538)), turn motif (Ser(676)) and hydrophobic motif (Ser(695)). Combined evidence from phospho-specific antisera and MS demonstrates phosphorylation at all three sites. Unlike its closest paralogue, PKC-delta, lack of negative charge in the activation loop of PKC-theta results in a profound catalytic defect (>100-fold reduction in the T538A mutant); the high sequence similarity between PKC-theta and -delta assists in the formulation of structural hypotheses to account for this major difference. In contrast with mechanisms proposed for other PKC isoforms, phosphorylation at the other two sites does not reconstitute catalytic activity. Activation loop phosphorylation is critical in vivo, since the T538A mutant completely lost its capacity to mediate T-cell receptor-stimulation of nuclear factor kappaB (NF-kappaB) activation in Jurkat T-cells. Hydrophobic motif phosphorylation also substantially influences PKC-theta catalytic activity (5-fold reduction in the S695A mutant), but does not impair NF-kappaB activation in Jurkat T-cells. Its mechanism is independent of secondary effects on activation loop phosphorylation and cannot be explained by thermal instability. Turn motif phosphorylation has a limited effect on kinase activity, but negatively regulates other aspects of PKC-theta function, since the S676A mutant is more efficient than wild-type in inducing NF-kappaB activation in Jurkat T-cells. These findings expand our understanding of the roles of phosphorylation in novel PKCs, and indicate that PKC-theta is a constitutively competent kinase as a consequence of constitutive phosphorylation of its activation loop.