gebhart/patrepeval huggingface dataset:
Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions (2016)

From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary target to be neutralized by vaccine. Vaccine is the most effective immunologic intervention. In this study, we use the epitope-based vaccine design from hemagglutinin and neuraminidase of H5N1 Indonesian strain virus by using immunoinformatics approach in order to predict the binding of B-cell and T-cell epitopes (class I and class II human leukocyte antigen [HLA]). BCPREDS was used to predict the B-cell epitope. Propred, Propred I, netMHCpan, and netMHCIIpan were used to predict the T-cell epitope. Two B-cell epitopes of hemagglutinin candidates and one B-cell epitope of neuraminidase candidates were obtained to bind T-cell CD4(+) (class II HLA), and also five T-cell epitope hemagglutinin and four T-cell epitope neuraminidase were obtained to bind T-cell CD8(+) (class I HLA). The visualization of epitopes was done using MOE 2008.10. It shows that the binding affinity of epitope-HLA was based on minimum binding free energy (ΔG binding). Based on this result, visualization, and dynamic simulation, four hemagglutinin epitopes (MEKIVLLLA, CPYLGSPSF, KCQTPMGAI, and IGTSTLNQR) and two neuraminidase epitopes (NPNQKIITI and CYPDAGEIT) were computed as having the best binding affinity from HLA ligand. The results mentioned above are from in silico experiments and need to be validated using wet experiment.
Solid-State Sensor and Actuator Workshop Held at Hilton Head Island, South Carolina on June 6-9, 1988 (1988)

Abstract : Partial contents: Quartz microbalance studies of solvent and ion transport in thin polymer films in sensor applications of the QCM; Multiple- Frequency Surface Acoustic Wave Devices as Sensors; Performance Characteristics of Second Generation Polysilicon Resonating Beam Force Transducers; Friction and Wear in Microfabricated Harmonic Side-Drive Motors; Electrostatically Balanced Comb Drive for Controlled Levitation; A Micromachined Silicon Scan Tip for an Atomic Force Microscope; Pressure Sensor Design and Simulation using the CAEMEMS-D Module; Automatic Generation of a 3-D Solid Model of a Microfabricated Structure; The Mechanism of Anisotropic Electrochemical Silicon Etching in Alkaline Solutions; An Implantable CMOS Analog Signal Processor for Multiplexed Microelectrode Recording Arrays; 2-D Magnetic Field Sensor Based on Vertical Hall Device; Deep X-Ray Lithography for Micromechanics; RF Telemetry Powering and Control of Hermetically-Sealed Integrated Sensors and Actuators; Wide Dynamic Range Direct Digital Output Accelerometer; A Multi-Element Monolithic Mass Flowmeter with On-Chip CMOS Readout Electronics; Silicon Micromachining in the Fabrication of Biosensors Using Living Cells; and Secondary Sensitivities and Stability of Ultrasensitive Silicon Pressure Sensors. Symposia.
Dengue in Greece in 1927 and 1928 and the Pathogenesis of Dengue Hemorrhagic Fever: New Data and a Different Conclusion (1986)

A massive outbreak of dengue, with a high incidence of hemorrhagic manifestations and a high death rate, occurred in Athens and neighboring areas of Greece in 1927 and 1928. For many years it was believed that the episode had been caused by dengue type 1 virus. Recently, it was claimed that dengue type 2 virus also was present in Athens in 1928, and this report is cited in support of the hypotheses that dengue hemorrhagic fever is almost always the result of sequential infection with different dengue serotypes and that infection with dengue type 2 following dengue type 1 is particularly pathogenic. In the present study of 258 Greek residents born from 1914 to 1938, it was also found that dengue type 2 had occurred in Greece--but after 1928. No evidence was found that that virus had occurred in the country during, or within 13 years before, the 1927-1928 epidemic.
Lipid and Biomass Distribution and Recovery from Two Microalgae by Aqueous and Alcohol Processing (2011)

Abstract The objective of this study was to determine lipid and biomass distribution during aqueous and alcohol processing of oleaginous microalgae, with the intention of fully extracting lipid from the dewatered cell paste. Two species, Nannochloropsis and Schizochytrium , were used. It is shown that most of the total lipid, 73% for Nannochloropsis and 87% for Schizochytrium , was held by the cell solids obtained by centrifugation during the aqueous process, justifying the need to develop a more effective lipid‐extraction method. Use of ethanol at elevated temperature enabled efficient extraction of lipid from the cell mass and at the same time improved biomass precipitation and recovery in the solid or cake fraction. More than 68 and 95% of total lipid was recovered on a 50‐g scale (as‐is paste basis) from Nannochloropsis and Schizochytrium , respectively. Approximately 65% of the biomass was recovered in the solid fraction for both algae from the alcohol process, compared with the much lower biomass recovery, 38 and 16% for Nannochloropsis and Schizochytrium by the aqueous process. Therefore, oil and biomass fractionation by use of pure water is far less effective than fractionation by use of alcohol, and the alcohol process has great promise in algal oil recovery.
Structural Basis of Wnt Recognition by Frizzled (2012)

Wnts are lipid-modified morphogens that play critical roles in development principally through engagement of Frizzled receptors. The 3.25 angstrom structure of Xenopus Wnt8 (XWnt8) in complex with mouse Frizzled-8 (Fz8) cysteine-rich domain (CRD) reveals an unusual two-domain Wnt structure, not obviously related to known protein folds, resembling a "hand" with "thumb" and "index" fingers extended to grasp the Fz8-CRD at two distinct binding sites. One site is dominated by a palmitoleic acid lipid group projecting from serine 187 at the tip of Wnt's thumb into a deep groove in the Fz8-CRD. In the second binding site, the conserved tip of Wnt's "index finger" forms hydrophobic amino acid contacts with a depression on the opposite side of the Fz8-CRD. The conservation of amino acids in both interfaces appears to facilitate ligand-receptor cross-reactivity, which has important implications for understanding Wnt's functional pleiotropy and for developing Wnt-based drugs for cancer and regenerative medicine.
A Potent and Highly Selective Inhibitor of Human α-1,3-Fucosyltransferase via Click Chemistry (2003)

Potent inhibitors of fucosyltransferases, and glycosyltransferases in general, have been elusive due to the inherent barriers surrounding the family of glycosyltransfer reactions. The problems of weak substrate affinity and low catalytic proficiency of fucosyltransferase was offset by recruiting additional binding features, in this case hydrophobic interactions, to produce a high affinity inhibitor, 24, with Ki = 62 nM. The molecule was identified from a GDP-triazole library of 85 compounds, which was produced by the Cu(I)-catalyzed [2 + 3] cycloaddition reaction between azide and acetylene reactants, followed by in situ screening without product isolation.
Stimulatory effect of insulin-like growth factor-I on [3H]thymidine incorporation, DNA content and insulin biosynthesis and secretion of isolated pancreatic rat islets (1988)

The influence of insulin-like growth factor-I (IGF-I) on both the growth and function of isolated pancreatic rat islets was studied. As a measure of islet cell replication, [3H]thymidine incorporation and DNA content was estimated at the same time as parameters for (pro)insulin biosynthesis and secretion as a measure of the functional capacity of B cells. Incorporation of [3H]thymidine was measured after tissue solubilization; DNA was determined fluorometrically. (Pro-)insulin biosynthesis was determined by incorporation of [3H]leucine after immunoprecipitation and binding to protein A-Sepharose. There was a significant increase in both [3H]thymidine incorporation and DNA content after the culture of islets with IGF-I. IGF-I resulted also in an increase in insulin biosynthesis and secretion from isolated pancreatic islets. These results demonstrate a role of IGF-I in regulating the growth and function of pancreatic islets.
Humanization of an anti-p185HER2 antibody for human cancer therapy. (1992)

The murine monoclonal antibody mumAb4D5, directed against human epidermal growth factor receptor 2 (p185HER2), specifically inhibits proliferation of human tumor cells overexpressing p185HER2. However, the efficacy of mumAb4D5 in human cancer therapy is likely to be limited by a human anti-mouse antibody response and lack of effector functions. A "humanized" antibody, humAb4D5-1, containing only the antigen binding loops from mumAb4D5 and human variable region framework residues plus IgG1 constant domains was constructed. Light- and heavy-chain variable regions were simultaneously humanized in one step by "gene conversion mutagenesis" using 311-mer and 361-mer preassembled oligonucleotides, respectively. The humAb4D5-1 variant does not block the proliferation of human breast carcinoma SK-BR-3 cells, which overexpress p185HER2, despite tight antigen binding (Kd = 25 nM). One of seven additional humanized variants designed by molecular modeling (humAb4D5-8) binds the p185HER2 antigen 250-fold and 3-fold more tightly than humAb4D5-1 and mumAb4D5, respectively. In addition, humAb4D5-8 has potency comparable to the murine antibody in blocking SK-BR-3 cell proliferation. Furthermore, humAb4D5-8 is much more efficient in supporting antibody-dependent cellular cytotoxicity against SK-BR-3 cells than mumAb4D5, but it does not efficiently kill WI-38 cells, which express p185HER2 at lower levels.
Mutation and Cancer: A Model for Wilms' Tumor of the Kidney<xref ref-type="fn" rid="FN2">2</xref> (1972)

Statistical analysis of cases of Wilms' tumor supports a 2-mutation model previously reported for retinoblastoma. Comparison of data for familial, bilateral, unilateral, and unselected cases reveals that familial and bilateral cases have an early average age of diagnosis, with a distribution suggestive of a single-event process, while unilateral and unselected cases do not. Familial cases have an incidence of bilaterality higher than that of unselected cases and a pattern consistent with autosomal dominant inheritance. These findings suggest that Wilms' tumor may be attributed to a 2-mutational model; i.e., 2 mutations are required in all cases, but, in approximately 38%, one mutation has occurred in the germinal line of a parent and is inherited. Persons acquiring this germinal mutant develop an average of one second mutation each, which gives rise to tumor. Approximately 37% of gene carriers do not develop tumor, and 15% develop bilateral tumors. About 62% of cases of Wilms' tumor are non-hereditary, both of the mutations occurring in somatic cells. The association of Wilms' tumor with aniridia, hemihypertrophy, and genitourinary anomalies is fitted to the model. The familial pattern is noted to be similar to that of a delayed mutation; new germinal mutations may be attributable to a vertically transmitted tumor virus resembling the virus causing embryonal renal sarcoma in chickens.
Mixed chimerism through donor bone marrow transplantation (2011)

This review will address the recent advances in murine models as well as findings from the first clinical trials for the induction of tolerance through mixed chimerism. Both the potential for more widespread clinical application and the remaining hurdles and challenges of this tolerance approach will be discussed.
Candidate Gene Associated with a Mutation Causing Recessive Polycystic Kidney Disease in Mice (1994)

A line of transgenic mice was generated that contains an insertional mutation causing a phenotype similar to human autosomal recessive polycystic kidney disease. Homozygotes displayed a complex phenotype that included bilateral polycystic kidneys and an unusual liver lesion. The mutant locus was cloned and characterized through use of the transgene as a molecular marker. Additionally, a candidate polycystic kidney disease (PKD) gene was identified whose structure and expression are directly associated with the mutant locus. A complementary DNA derived from this gene predicted a peptide containing a motif that was originally identified in several genes involved in cell cycle control.
Fluorescence studies of the stationary-phase chemical environment in reversed-phase liquid chromatography (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorescence studies of the stationary-phase chemical environment in reversed-phase liquid chromatographyJ. W. Carr and J. M. HarrisCite this: Anal. Chem. 1986, 58, 3, 626–631Publication Date (Print):March 1, 1986Publication History Published online1 May 2002Published inissue 1 March 1986https://pubs.acs.org/doi/10.1021/ac00294a031https://doi.org/10.1021/ac00294a031research-articleACS PublicationsRequest reuse permissionsArticle Views90Altmetric-Citations70LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Regio- and Chemoselective Covalent Immobilization of Proteins through Unnatural Amino Acids (2006)

A general approach was developed for the regio- and chemoselective covalent immobilization of soluble proteins on glass surfaces through an unnatural amino acid created by post-translationally modifying the cysteine residue in a CaaX recognition motif with functional groups suitable for "click" chemistry or a Staudinger ligation. Farnesyl diphosphate analogues bearing omega-azide or omega-alkyne moieties were attached to the cysteine residue in Cys-Val-Ile-Ala motifs at the C-termini of engineered versions of green fluorescent protein (GFP) and glutathione S-transferase (GST) by protein farnesyltransferase. The derivatized proteins were attached to glass slides bearing linkers containing azide ("click" chemistry) or phosphine (Staudinger ligation) groups. "Click"-immobilized proteins were detected by fluorescently labeled antibodies and remained attached to the slide through two cycles of stripping under stringent conditions at 80 degrees C. GFP immobilized by a Staudinger ligation was detected by directly imagining the GFP fluorophore over a period of 6 days. These methods for covalent immobilization of proteins should be generally applicable. CaaX recognition motifs can easily be appended to the C-terminus of a cloned protein by a simple modification of the corresponding gene, and virtually any soluble protein or peptide bearing a CaaX motif is a substrate for protein farnesyltransferase.
Nonsteroidal antiinflammatory drugs cause apoptosis and induce cyclooxygenases in chicken embryo fibroblasts. (1995)

Programmed cell death (apoptosis) is an intrinsic part of organismal development and aging. Here we report that many nonsteroidal antiinflammatory drugs (NSAIDs) cause apoptosis when applied to v-src-transformed chicken embryo fibroblasts (CEFs). Cell death was characterized by morphological changes, the induction of tissue transglutaminase, and autodigestion of DNA. Dexamethasone, a repressor of cyclooxygenase (COX) 2, neither induced apoptosis nor altered the NSAID effect. Prostaglandin E2, the primary eicosanoid made by CEFs, also failed to inhibit apoptosis. Expression of the protooncogene bcl-2 is very low in CEFs and is not altered by NSAID treatment. In contrast, p20, a protein that may protect against apoptosis when fibroblasts enter G0 phase, was strongly repressed. The NSAID concentrations used here transiently inhibit COXs. Nevertheless, COX-1 and COX-2 mRNAs and COX-2 protein were induced. In some cell types, then, chronic NSAID treatment may lead to increased, rather than decreased, COX activity and, thus, exacerbate prostaglandin-mediated inflammatory effects. The COX-2 transcript is a partially spliced and nonfunctional form previously described. Thus, these findings suggest that COXs and their products play key roles in preventing apoptosis in CEFs and perhaps other cell types.
[The treatment of Parkinson's disease--adenosine A2A receptor antagonists]. (2002)

The primary pathology of Parkinson's disease is the degeneration of dopaminergic neurons in the nigrostriatal pathway, resulting in a significant reduction in striatum dopamine concentration which is responsible for the altered motor functions. With time and disease progression, efficacy of dopaminergic therapy becomes unpromising. Since adenosine A2A receptor is selectively localized in striatum for controlling motor activity, it appeared to be an attractive target for a novel treatment in Parkinson's disease. Several lines of evidence indicated that KW-6002, highly selective antagonist of adenosine A2A receptor, showed anti-parkinsonian effect in vivo and in vitro without any problematic side effect which is observed in dopaminergic therapy. Further investigation will be necessary to make sure the effect in ongoing progressive nature of Parkinson's disease or the long treatment periods in Parkinson's disease.
Polynuclear zinc(II) complexes of phenol–imine and –amine macrocycles (1995)

The template condensation of 2,6-diformyl-4-methylphenol with 1,11-diamino-3,6,9-trioxaundecane using zinc(II) acetate as the metal source, followed by addition of an excess of NaClO4, gave a tetranuclear zinc(II) complex [Zn4L1(µ-O2CMe)4][ClO4]21, where H2L1 is a [2 + 2] tetra-Schiff-base macrocycle. A single-crystal X-ray analysis of the dichloromethane adduct, 1·2CH2Cl2, revealed that this complex cation is centrosymmetric and contains two pairs of zinc ions bridged by a phenolic oxygen and two acetate ligands. Recrystallisation of this complex from a hydrous methanolic solution gave another tetranuclear complex, [Zn4L1(µ-OH)2(µ-O2CMe)2][ClO4]2·2H2O 2, which was also structurally characterised. While the four zinc ions are encapsulated in the macrocycle as observed for 1, in complex 2 the two dimeric units formed by phenoxo- and acetato-bridges are further connected by two hydroxyo bridges. Proton NMR spectroscopy has shown that this structural conversion is reversible and depends on the presence of water or acetic acid in solution. Treatment of complex 1(or 2) with NaBH4 in methanol gave a dinuclear zinc complex, [Zn2L2][ClO4]2·H2O3, together with a metal-free phenol–amine macrocycle, H2L2, which is a reduced form of H2L1. Both complex 3 and H2L2, have been characterised on the basis of spectroscopic data.
Short-term forecasting of life-threatening arrhythmias with finite time Lyapunov exponents (2002)

Ventricular tachycardia or fibrillation (VT/VF) are fatal cardiac arrhythmias which are the main triggering factors for a sudden cardiac death. The objective of this study was to find early signs of VT/VF in patients with an implantable cardioverter-defibrillator (ICD) to enable a prediction for an improved antiarrhythmic therapy. Therefore, we studied the interbeat intervals of 17 chronic heart failure ICD patients with and without (control) VT/VF event. To detect typical signs of an immediately following malignant arrhythmia we calculated HRV parameters from time and frequency domain as well as the averaged finite time Lyapunov exponent and the Shannon entropy of the finite time Lyapunov exponents distribution. The results of this study show that neither the time nor the frequency domain parameters show significant differences between the VT/VF and the control time series. However, the averaged finite time Lyapunov exponents and the Shannon entropy discriminate significantly both groups (p<0.01 resp. p<0.04). These findings could be of importance in algorithms for next generation ICDs to improve the diagnostics and therapy of VT/VF.
Tailored Near-Infrared Contrast Agents for Image Guided Surgery (2015)

The success of near-infrared (NIR) fluorescence to be employed for intraoperative imaging relies on the ability to develop a highly stable, NIR fluorescent, nontoxic, biocompatible, and highly excreted compound that retains a reactive functionality for conjugation to a cancer-recognizing peptide. Herein, systematic modifications to previously detailed fluorophore ZW800-1 are explored. Specific modifications, including the isosteric replacement of the O atom of ZW800-1, include nucleophilic amine and sulfur species attached to the heptamethine core. These novel compounds have shown similar satisfactory results in biodistribution and clearance while also expressing increased stability in serum. Most importantly, all of the synthesized and evaluated compounds display a reactive functionality (either a free amino group or carboxylic acid moiety) for further bioconjugation. The results obtained from the newly prepared derivatives demonstrate that the central substitution with the studied linking agents retains the ultralow background in vivo performance of the fluorophores regardless of the total net charge.
Nitric Oxide (NO)- and Nitroxyl (HNO)-Generating Diazeniumdiolates (NONOates): Emerging Commercial Opportunities (2005)

Diazeniumdiolate ions are convenient and, for a variety of applications, uniquely advantageous nitric oxide (NO) dosage forms. Ionic diazeniumdiolates generate bioactive NO in physiological fluids truly spontaneously (i. e., without metabolism or redox activation), with reliable half-lives ranging from 2 seconds to 20 hours depending on the ion's structure. They are generally simple-to-prepare solids with excellent shelf life and high NO content - up to 40% by weight. Very importantly from the pharmaceutical point of view, the ionic diazeniumdiolates can be easily derivatized to prodrug forms that can be activated for NO release enzymatically, photolytically, or by slowed hydrolysis, allowing for rational design of strategies for targeting pharmacological delivery of NO to sites of need without unwanted collateral exposure of other NO-sensitive compartments. In addition to their world-wide sale for use in probing the chemical biology of NO, published proof-of-concept studies with diazeniumdiolates suggest several more lucrative applications. These include: converting existing drugs and biologicals to NO-releasing form to improve performance and/or extend patent life; diazeniumdiolating medical devices for improved biocompatibility; anticancer drug discovery; use as surgical aids and for wound repair; field generation of NO gas; and non-medical uses such as extending the post-harvest life of cut flowers. Future work aimed at exploiting the full clinical potential of diazeniumdiolate technology will be pursued in this laboratory and strongly encouraged in others, with a concurrent fundamental research effort to broaden the knowledge base from which further opportunities can be inferred [e. g., exploiting the very recent finding that some diazeniumdiolates appear to offer a versatile platform from which nitroxyl (HNO)-generating prodrugs can be developed].