gebhart/patrepeval huggingface dataset:
Multicenter approach to the exchange-correlation interactions inab initiotight-binding methods (2005)

An approximate method to calculate exchange-correlation contributions in the framework of first-principles tight-binding molecular dynamics methods has been developed. In the proposed scheme on-site (off-site) exchange-correlation matrix elements are expressed as a one-center (two-center) term plus a correction due to other neighboring atoms. The one-center (two-center) term is evaluated directly, while the correction is calculated using a generalization of the [Sankey-Niklewski Phys. Rev. B 40, 3979 (1989)] approach valid for arbitrary atomiclike basis sets. The proposed scheme for exchange-correlation terms, called the multi-center weighted exchange-correlation density approximation (McWEDA), permits the accurate and computationally efficient calculation of corresponding tight-binding matrices and atomic forces for complex systems. We calculate bulk properties of selected transition (W,Pd), noble (Au), and simple (Al) metals, a semiconductor (Si), and the transition metal oxide $\mathrm{Ti}{\mathrm{O}}_{2}$ with the method to demonstrate its flexibility and accuracy.
Leaf‐Like V2O5 Nanosheets Fabricated by a Facile Green Approach as High Energy Cathode Material for Lithium‐Ion Batteries (2013)

Leaf-like V2O5 nanosheets are fabricated by a facile green approach. Used as cathode material for lithium-ion batteries, this nano-structured material exhibits superior performance, i.e., high rate capability and good capacity retention upon cycling. Thus, the leaf-like V2O5 Nanosheets are promising as a cathode material for high power lithium batteries.
EGF-R antisense RNA blocks expression of the epidermal growth factor receptor and suppresses the transforming phenotype of a human carcinoma cell line. (1992)

We have used an antisense approach to investigate the role of overexpression of the normal human epidermal growth factor (EGF) receptor in the transformed phenotype of KB cells, which are a tumor derived human cell line. Initial experiments performed in vitro, showed that antisense RNA complementary to the entire coding region (AS-FL) or to parts of the EGF-R mRNA (AS-3', AS-5', and AS-K) effectively blocked translation of EGF-R mRNA. In addition, upon microinjection into KB cells, the in vitro synthesized antisense RNAs were able to inhibit transiently the synthesis of EGF-R. Inhibition was concentration-dependent, both in vitro and in cells, and the most effective constructs were those complementary to the entire coding region (AS-FL) or to the 3'-coding end of the mRNA (AS-3'). Transfection of the same EGF-R antisense RNA constructs into the human epidermoid carcinoma KB cell line gave rise to several clones stably expressing elevated levels of antisense RNA and resulting in low residual levels of EGF receptor. The most reduced clones exhibited a totally restored serum-dependent growth and were severely impaired in colony formation and growth in agar. In addition the severity of the phenotype was directly proportional to the residual amount of EGF-R expressed. We conclude that over-expression of normal EGF-R plays a direct primary role in the development of the transformed phenotype of this human cancer cell line.
A histidin alanine rich recombinant antigen protects Aotus monkeys from P. falciparum infection. (1988)

We have isolated a cDNA clone coding for 165 amino acids of a histidine alanine rich protein. An extended repeat region of this clone codes for the tripeptide Ala-His-His, which is extremely conserved, and for the tripeptide Ala-Ala-Asp, which shows only slight variability among the repeat units. This antigen exhibits high homology to the HRPII antigen described by Wellems and Howard (1986). The coding region was expressed in E. coli as a MS2-polymerase fusion protein, which was purified and used for immunization of Aotus monkeys. The animals immunized with this fusion protein showed only low parasitemias (less than 2%) after infection with P. falciparum, while animals from the control group or animals immunized with a MS2-fusion protein carrying other malaria specific sequences were not protected. The result suggests that this antigen is a good candidate for a malaria vaccine.
Potato spindle tuber viroid as Inducer of RNA Silencing in Infected Tomato (2001)

Potato spindle tuber viroid (PSTVd), an RNA plant pathogen encoding no known proteins, induces systemic symptoms on tomato plants. We report detection of small RNAs of approximately 25 nucleotides with sequence specificity to PSTVd in infected plants: an indication of the presence of RNA silencing. RNA silencing, however, did not appear to be responsible for the differing symptoms induced by a mild and a severe strain of PSTVd. The unique structural and biological features of viroids make them attractive experimental tools to investigate mechanisms of RNA silencing and pathogen counterdefense.
Anti-tumor agents. 136. Cumingianosides A-F, potent antileukemic new triterpene glucosides, and cumindysosides A and B, trisnor- and tetranortriterpene glucosides with a 14,18-cycloapoeuphane-type skeleton from Dysoxylum cumingianum (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnti-tumor agents. 136. Cumingianosides A-F, potent antileukemic new triterpene glucosides, and cumindysosides A and B, trisnor- and tetranortriterpene glucosides with a 14,18-cycloapoeuphane-type skeleton from Dysoxylum cumingianumYoshiki Kashiwada, Toshihiro Fujioka, Jer Jang Chang, Ih Sheng Chen, Kunihide Mihashi, and Kuo Hsiung LeeCite this: J. Org. Chem. 1992, 57, 25, 6946–6953Publication Date (Print):December 1, 1992Publication History Published online1 May 2002Published inissue 1 December 1992https://pubs.acs.org/doi/10.1021/jo00051a050https://doi.org/10.1021/jo00051a050research-articleACS PublicationsRequest reuse permissionsArticle Views182Altmetric-Citations41LEARN 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
Importance of the loop connecting A and B helices of human interferon-gamma in recognition by interferon-gamma receptor. (1994)

Characterization of murine-human hybrid interferon-gamma (IFN-gamma) molecules suggests that substitution of the peptide connecting the A and B helices in human IFN-gamma with the murine sequence significantly blocks the protein's binding to the human interferon-gamma receptor. Mutagenesis showed that this effect is localized to the central part of this A-B loop peptide, particularly Ser20, Asp21, Val22, and Ala23. One mutant, IFN-gamma/A23E,D24E,N25K, was examined by NMR. This "EEK" mutation does not significantly alter the conformation of interferon-gamma, suggesting that the effects of these mutations are not the result of global conformational changes. The A-B loop is near histidine 111, a residue previously shown to be important in receptor-ligand interaction (Lunn, C. A., Fossetta, J., Dalgarno, D., Murgolo, N., Windsor, W., Zavodny, P. J., Narula, S. K., and Lundell, D. (1992) Protein Eng. 5, 253-257). We show that copper forms a complex between histidine 19 in the A-B loop and histidine 111. This metal complex lacks the ability to interact with the interferon-gamma receptor. These results suggest that the A-B loop contains important structural information needed for receptor-ligand binding and hence biological activity of human interferon-gamma.
Nucleotide sequence and predicted amino acid sequence of a protein encoded in a small herpes simplex virus DNA fragment capable of trans-inducing alpha genes. (1985)

The five alpha genes of herpes simplex virus 1 are the first set of genes to be expressed after infection. Previous studies have shown that alpha genes resident in eukaryotic cells are induced by infection with herpes simplex virus 1 or 2 but not by other herpesviruses and indicate that the alpha trans-inducing factor was a structural component of the virion. This factor induces genes linked to a bona fide promoter and containing at the 5' end a small sequence derived from the promoter-regulatory domains of alpha genes. We report the sequence of a small DNA fragment shown previously to be capable of expressing the alpha trans-inducing factor in transient expression systems. The only gene encoded in its entirety in this fragment is predicted to specify a 479 amino acid protein with a Mr of 53,053. The precise termini of the 1.74-kilobase mRNA specifying this protein were determined in our 5' and 3' S1 nuclease protection studies.
Charge Storage Mechanism of MnO2 Electrode Used in Aqueous Electrochemical Capacitor (2004)

The charge storage mechanism in MnO2 electrode, used in aqueous electrolyte, was investigated by cyclic voltammetry and X-ray photoelectron spectroscopy. Thin MnO2 films deposited on a platinum substrate and thick MnO2 composite electrodes were used. First, the cyclic voltammetry data established that only a thin layer of MnO2 is involved in the redox process and electrochemically active. Second, the X-ray photoelectron spectroscopy data revealed that the manganese oxidation state was varying from III to IV for the reduced and oxidized forms of thin film electrodes, respectively, during the charge/discharge process. The X-ray photoelectron spectroscopy data also show that Na+ cations from the electrolyte were involved in the charge storage process of MnO2 thin film electrodes. However, the Na/Mn ratio for the reduced electrode was much lower than what was anticipated for charge compensation dominated by Na+, thus suggesting the involvement of protons in the pseudofaradaic mechanism. An important finding of this work is that, unlike thin film electrodes, no change of the manganese oxidation state was detected for a thicker composite electrode because only a very thin layer is involved in the charge storage process.
“De Novo” Engineering of Peptide Immunogenic and Antigenic Determinants as Potential Vaccines (1994)

In this chapter, we summarize some current approaches to the de novo design of structurally defined polypeptides with emphasis on their application to synthetic peptide vaccine development and review our attempts at engineering conformational peptides for vaccines. The purpose of this review is twofold: 1. to briefly enumerate strategies of synthetic peptide design as it pertains to elucidating and mapping B-cell antigenic determinants, and 2. to view this field, and specifically synthetic vaccines from design principles and perspectives, as it relates to the topographic nature of antigenic sites recognized by B cells. KeywordsMajor Histocompatibility ComplexMeasle VirusAntigenic SitePeptide VaccineCompetitive ELISAThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Analysis of CD36 Binding Domains: Ligand Specificity Controlled by Dephosphorylation of an Ectodomain (1993)

The protein CD36 is a membrane receptor for thrombospondin (TSP), malaria-infected erythrocytes, and collagen. Three functional sequences were identified within a single disulfide loop of CD36: one that mediates TSP binding (amino acids 87 to 99) and two that support malarial cytoadhesion (amino acids 8 to 21 and 97 to 110). One of these peptides (p87-99) is a consensus protein kinase C (PKC) phosphorylation site. Dephosphorylation of constitutively phosphorylated CD36 in resting platelets and a megakaryocytic cell line led to the loss of collagen adhesion and platelet reactivity to collagen, with a reciprocal increase in TSP binding. PKC-mediated phosphorylation of this ectodomain resulted in a loss of TSP binding and the reciprocal acquisition of collagen binding. In site-directed mutagenesis studies, when the threonine phosphorylation site was changed to alanine, CD36 was expressed in a dephosphorylated state and bound to TSP constitutively.
Neuropeptide Y and Sympathetic Neurotransmissiona (1990)

The coexistence of neuropeptide Y (NPY) with noradrenaline (NA) in perivascular nerves as well as in sympathetic nerves to muscle in the heart, spleen and vas deferens suggests a role for NPY in autonomic transmission. Sympathetic nerve stimulation or reflexogenic activation in experimental animals or man are associated with NPY release as revealed by overflow mainly upon strong activation. This difference between NPY and NA secretion may be related to the partly separate subcellular storage whereby NPY seems to be exclusively present in the large dense-cored vesicles. The NPY secretion is likely to be regulated by the local biophase concentrations of NA acting on prejunctional alpha-2-adrenoceptors since alpha-2 agonists inhibit and antagonists enhance NPY overflow, respectively. Furthermore, after NA has been depleted by reserpine, the nerve stimulation-evoked release of NPY is enhanced leading to a progressive depletion of tissue content of NPY. Exogenous NPY binds to both pre- and postjunctional receptors, inhibits NA and NPY release, enhances NA-evoked vasoconstriction and induces vasoconstriction per se. The prejunctional action of NPY which is especially noticeable in the vas deferens may serve to reduce transmitter secretion upon excessive stimulation. The long-lasting vasoconstriction evoked by sympathetic stimulation in several tissues including skeletal muscle, nasal mucosa and spleen, which remains in animals pretreated with reserpine (to deplete NA) combined with preganglionic denervation (to prevent the concomitant excessive NPY release and depletion), is mimicked by NPY and highly correlated to NPY release. Under these circumstances the NPY content in the local venous effluent reaches levels at which exogenous NPY evokes vasoconstriction.
Engineered red blood cells as carriers for systemic delivery of a wide array of functional probes (2014)

We developed modified RBCs to serve as carriers for systemic delivery of a wide array of payloads. These RBCs contain modified proteins on their plasma membrane, which can be labeled in a sortase-catalyzed reaction under native conditions without inflicting damage to the target membrane or cell. Sortase accommodates a wide range of natural and synthetic payloads that allow modification of RBCs with substituents that cannot be encoded genetically. As proof of principle, we demonstrate site-specific conjugation of biotin to in vitro-differentiated mouse erythroblasts as well as to mature mouse RBCs. Thus modified, RBCs remain in the bloodstream for up to 28 d. A single domain antibody attached enzymatically to RBCs enables them to bind specifically to target cells that express the antibody target. We extend these experiments to human RBCs and demonstrate efficient sortase-mediated labeling of in vitro-differentiated human reticulocytes.
Bacterial Heat-Stable Enterotoxins: Translation of Pathogenic Peptides into Novel Targeted Diagnostics and Therapeutics (2010)

Heat-stable toxins (STs) produced by enterotoxigenic bacteria cause endemic and traveler's diarrhea by binding to and activating the intestinal receptor guanylyl cyclase C (GC-C). Advances in understanding the biology of GC-C have extended ST from a diarrheagenic peptide to a novel therapeutic agent. Here, we summarize the physiological and pathophysiological role of GC-C in fluid-electrolyte regulation and intestinal crypt-villus homeostasis, as well as describe translational opportunities offered by STs, reflecting the unique characteristics of GC-C, in treating irritable bowel syndrome and chronic constipation, and in preventing and treating colorectal cancer.
Safety of Fecal Microbiota Transplantation (FMT) in Immunocompromised (Ic) Patients with Inflammatory Bowel Disease (IBD): Presidential Poster (2013)

Purpose: To date, more than 500 cases of FMT have been reported worldwide. Adverse events (AEs) of FMT have been minimal, and predominantly consist of transient abdominal cramping and bloating, increased flatus, and altered bowel habits. Transient fever and chills are rarely encountered, and norovirus infection, aspiration pneumonia, weight gain, and IBD flare have been reported in isolated cases. The safety of FMT in Ic patients, particularly those with IBD treated with immunosuppressive agents, has not been previously addressed. The purpose of this study was to determine the safety of FMT in IBD patients on immunosuppressive medications (IBD-Ic). Methods: This study included all patients undergoing FMT for the treatment of IBD who were on immunosuppressive agents. Data were collected from Montefiore Medical Center in New York and the Centre for Digestive Diseases in Australia. Twelve of 12 eligible patients were identified and included in the study. Pre-FMT data included demographics, type of immunosuppressive agents used, and duration of therapy. Measured outcomes post-FMT included hospitalization within 12 weeks, death, and all reported AEs related or unrelated to FMT. Specifically, data were obtained on AEs of the procedure to administer FMT (e.g., sedation-related, perforation) and AEs of FMT (e.g., new infections, diseases, or symptoms), important medical events, and life-threatening experiences. Results: Fifty-eight percent of patients were men, with an average age of 41 years (range: 26-75 years). 92% (n=11) of patients had UC, and 8% (n=1) had Crohn's disease. On average, patients had IBD for 9 years (range: 3-33 years) before FMT. FMT was pursued in all patients because of refractory disease. Sixty-seven percent were outpatients, and 33% were inpatients at the time of FMT. The average follow-up period between FMT and data collection was 14.7 months (range: 7-31 months). Immunosuppressive medications used were oral steroids (n=9, 75%), azathioprine or 6-mercaptopurine (6-MP) (n=6, 50%), infliximab (n=2, 17%), and methotrexate (n=1, 8%). All IBD-Ic pts were on these medications at the time of FMT, and the average duration of their use prior to FMT was 28.5 months (range: 0.5-108 months). No patients were hospitalized within 12 weeks of FMT, and no patients died within the follow-up period. There were no procedural or FMT-related complications. The only AE was transient abdominal distension with bloating in two patients (17%), one of whom was on oral steroids for 1 month; the other was on 6-MP for 48 months before FMT. Conclusion: FMT was safe in this IBD-Ic cohort; the only reported AE being transient abdominal distension with bloating (17%). Future studies are needed to determine if longer-term AEs will emerge.
Tricyclic Heteroaromatic Systems. Pyrazolo[3,4‐c]quinolin‐4‐ones and Pyrazolo[3,4‐c]quinoline‐1,4‐diones: Synthesis and Benzodiazepine Receptor Activity (1997)

Some pyrazolo[3,4-c]quinoline-4-ones 1-14 and pyrazolo[3,4-c]-quinoline-1,4-diones 15-17 were prepared and biologically evaluated for their binding at the benzodiazepine receptor (BZR) in rat cortical membranes. The moderate binding activity of 1-5, 7, 9-10, 13 is attributable to the lack of the optional proton acceptor at position-1, while the inactivity of the 1,4-dione derivatives 15-17 is due to the lack of the essential proton acceptor at position-3. These conclusions confirm the validity of our proposed pharmacophoric model.
Pseudomonas aeruginosa pili bind to asialoGM1 which is increased on the surface of cystic fibrosis epithelial cells. (1993)

The basis for the unique association of Pseudomonas aeruginosa and the cystic fibrosis (CF) lung has remained obscure despite major advances in the understanding of the molecular genetic cause of this disease. There is evidence to suggest that abnormalities in CF transmembrane conductance regulator function result in alterations in the glycosylation of epithelial components. The number of asialoGM1 residues, as representative of a class of glycolipids which contain a GalNAc beta 1-4Gal sequence for P. aeruginosa attachment, was quantified by flow cytometric studies of respiratory epithelial cells in primary culture from both CF patients and normal subjects. Superficial asialoGM1 was detected on 12% of the CF cells as compared with 2.9% of the cells from normal control subjects (P = 0.03, chi 2 = 4.73), and more asialoGM1 residues were exposed on CF cells after modification by P. aeruginosa exoproducts. AsialoGM1, but not the sialylated glycolipid GM1, was demonstrated to be a receptor for 125I-labeled P. aeruginosa pilin, a major adhesin for this organism, and exogenous asialoGM1 was found to competitively inhibit P. aeruginosa adherence to epithelial cells, thus, confirming the biological role of the asialoGM1 receptor. Quantitative and qualitative differences in the sialylation of superficial glycolipids in CF epithelial cells may directly contribute to the colonization of the CF lung by P. aeruginosa.
Paracrine glucocorticoid activity produced by mouse thymic epithelial cells (1999)

Previous data have suggested that glucocorticoids (GCs) are involved in the differentiation of thymocytes into mature T cells. In this report we demonstrate that the mouse thymic epithelial cells (TEC) express the cytochrome P450 hydroxylases Cyp11A1, Cyp21, and Cyp11B1. These enzymes, in combination with 3beta-hydroxysteroid dehydrogenase (3betaHSD), convert cholesterol into corticosterone, the major GC in rodents. In addition, when TEC were cocultured with 'reporter cells' containing the glucocorticoid receptor (GR) and a GR-dependent reporter gene, a specific induction of reporter gene activity was observed. Induction of reporter gene activity was blocked when the TEC and reporter cells were incubated in the presence of the Cyp11B1 inhibitor metyrapone or the 3betaHSD inhibitor trilostane, as well as by the GR antagonist RU486. Coculturing of TEC with thymocytes induced apoptosis in the latter, which was partially blocked by the enzyme inhibitors and RU486. We conclude that TEC secrete a GC hormone activity and suggest a paracrine role for this in thymocyte development.