gebhart/patrepeval huggingface dataset:
Construction of SARS-CoV-2 Virus-Like Particles by Mammalian Expression System (2020)

Virus-like particle (VLP) is a self-assembled nanostructure incorporating key viral structural proteins. VLP resembles molecular and morphological features of authentic viruses but is non-infectious and non-replicating due to lack of genetic materials. Successful applications of VLP has been shown in vaccinological and virological research. As an accessibly safe and relevant substitute of naturally pathogenic viruses, the construction of SARS-CoV-2 VLPs is much in demand in the ongoing fight against 2019 Coronavirus disease (COVID-19) pandemics. In the current study, using mammalian expression system, which is advantageous in maintaining correct protein glycosylation patterns, we efficiently constructed SARS-CoV-2 VLPs. We showed that among four SARS-CoV-2 structural proteins, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs. Moreover, the corona-like structure presented in SARS-CoV-2 VLPs from Vero E6 cells is more stable and unified, as compared to those from HEK-293T cells. Our data demonstrate that SARS-CoV-2 VLPs possess molecular and morphological properties of native virion particles, which endow such VLPs with a promising vaccine candidate and a powerful tool for the research of SARS-CoV-2.
Analitički i numerički proračun dodatne mase kod analize vibracije broda (2013)

Comparison between analytical and numerical determination of the added hydrodynamic mass in ship vibration analysis is performed. Analytical analysis was done on a semi- submerged cylinder of a circular cross section. Numerical calculations were carried out by the boundary element method (BEM) implemented in NX Nastran finite element (FE) software. Fairly good agreement was found between the two methods for added mass calculation. Also, analysis of the real ship vibrations is performed. Free vertical vibrations of a 9200TEU containership are analyzed where the hull was modelled by the beam finite elements (FE), while the shell plating was modelled by the plate FE without stiffness to define boundary elements of the wetted surface. Such calculated results are compared with the ones obtained by software DYANA which uses Timoshenko's beam FE and in which the added mass is determined by traditional analytically- based method. Comparative analysis shows some moderate differences in the calculation of added mass between the two approaches, indicating the need for further research on this topic.
Resistance to Oxidation of White Wines Assessed by Voltammetric Means (2007)

This work concerns the development of a methodology suited to measure the resistance to oxidation of white wines by cyclic voltammetry. The voltammetric responses of several white wines of different origin and age were analyzed in the oxidation potential range (0.2-1.2 V vs SCE). Currents measured at fixed potentials were correlated to the concentration of ascorbic acid, SO2, and total phenolics. A forced degradation study was monitored by cyclic voltammetry; from plots of current versus time, the consumption rates of oxidizable species in wine were estimated.
Purification and Properties of Rabbit Skeletal Muscle Phosphorylase b Kinase* (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurification and Properties of Rabbit Skeletal Muscle Phosphorylase b Kinase*Edwin G. Krebs, David S. Love, Gloria E. Bratvold, Kenneth A. Trayser, William L. Meyer, and Edmond H. FischerCite this: Biochemistry 1964, 3, 8, 1022–1033Publication Date (Print):August 1, 1964Publication History Published online1 May 2002Published inissue 1 August 1964https://pubs.acs.org/doi/10.1021/bi00896a003https://doi.org/10.1021/bi00896a003research-articleACS PublicationsRequest reuse permissionsArticle Views486Altmetric-Citations475LEARN 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
P58 molecules as putative receptors for major histocompatibility complex (MHC) class I molecules in human natural killer (NK) cells. Anti-p58 antibodies reconstitute lysis of MHC class I-protected cells in NK clones displaying different specificities. (1993)

Human CD3-16+56+ natural killer (NK) cells have been shown to display a clonally distributed ability to recognize major histocompatibility complex (MHC) class I alleles. Opposite to T lymphocytes, in NK cells, specific recognition of MHC class I molecules appears to induce inhibition of cytolytic activity and, thus, to protect target cells. Since a precise correlation has been established between the expression of the NK-specific GL183 and EB6 surface molecules (belonging to the novel p58 molecular family) and the specificity of NK clones, we analyzed whether p58 molecules could function as receptors for MHC in human NK cells. NK clones displaying the previously defined "specificity 2" and characterized by the GL183+EB6+ phenotype, specifically recognize the Cw3 allele and thus fail to lyse the Fc gamma R+ P815 target cells transfected with Cw3. On the other hand, NK clones displaying "specificity 1" and expressing the GL183-EB6+ phenotype failed to lyse Cw4+ target cells. Addition of the F(ab')2 fragments of either GL183 or EB6 mAb as well as the XA141 mAb of IgM isotype (specific for the EB6 molecules) completely restored the lysis of Cw3-transfected P815 cells by the Cw3-specific NK clones EX2 and EX4. Similarly, both the entire EB6 mAb, its F(ab')2 fragment and the XA141 mAb reconstituted the lysis of C1R, a Fc gamma R- target cell expressing Cw4 as the only serologically detected class I antigen. Thus, it appears that masking of different members of p58 molecules prevents recognition of "protective" MHC class I alleles and thus the delivering of inhibitory signals. Further support to the concept that p58 molecules represent a NK receptor delivering a negative signal was provided by experiments in which the entire anti-p58 mAbs (of IgG isotype) could inhibit the lysis of unprotected Fc gamma R+ P815 target cells, thus mimicking the inhibitory effect of MHC class I molecules.
In Vitro Differentiated Adult Human Liver Progenitor Cells Display Mature Hepatic Metabolic Functions: A Potential Tool for in Vitro Pharmacotoxicological Testing (2010)

The potential use of stem/progenitor cells as alternative cell sources to mature hepatocytes remains basically dependent on their ability to exhibit some, if not all, the metabolic liver functions. In the current study, four major liver functions were investigated in adult derived human liver stem/progenitor cell (ADHLSCs) populations submitted to in vitro hepatogenic differentiation: gluconeogenesis, ammonia detoxification, and activity of phase I and phase II drug-metabolizing enzymes. These acquired hepatic activities were compared to those of primary adult human hepatocytes, the standard reference. Amino acid content was also investigated after hepatogenic differentiation. Differentiated ADHLSCs display higher de novo synthesis of glucose correlated to an increased activity of glucose-6 phosphatase and mRNA expression of key related enzymes. Differentiated ADHLSCs are also able to metabolize ammonium chloride and to produce urea. This was correlated to an increase in the mRNA expression of relevant key enzymes such arginase. With respect to drug metabolism, differentiated ADHLSCs express mRNAs of all the major cytochromes investigated, among which the CYP3A4 isoform (the most important drug-metabolizing enzyme). Such increased expression is correlated to an enhanced phase I activity as independently demonstrated using fluorescence-based assays. Phase II enzyme activity and amino acid levels also show a significant enhancement in differentiated ADHLSCs. The current study, according to data independently obtained in different labs, demonstrates that in vitro differentiated ADHLSCs are able to display advanced liver metabolic functions supporting the possibility to develop them as potential alternatives to primary hepatocytes for in vitro settings.
A directed evolution approach to engineering recombinant protein production in S. cerevisiae (2006)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006.
Mechanisms of quorum sensing and strategies for quorum sensing disruption in aquaculture pathogens (2014)

In many countries, infectious diseases are a considerable threat to aquaculture. The pathogenicity of micro-organisms that infect aquaculture systems is closely related to the release of virulence factors and the formation of biofilms, both of which are regulated by quorum sensing (QS). Thus, QS disruption is a potential strategy for preventing disease in aquaculture systems. QS inhibitors (QSIs) not only inhibit the expression of virulence-associated genes but also attenuate the virulence of aquaculture pathogens. In this review, we discuss QS systems in important aquaculture pathogens and focus on the relationship between QS mechanisms and bacterial virulence in aquaculture. We further elucidate QS disruption strategies for targeting aquaculture pathogens. Four main types of QSIs that target aquaculture pathogens are discussed based on their mechanisms of action.
Structure and Function of the Fo Complex of the ATP Synthase from Escherichia Coli (2000)

The membrane-bound ATP synthase (F(1)F(o)) from mitochondria, chloroplasts and bacteria plays a crucial role in energy-transducing reactions. In the case of Escherichia coli, the reversible, proton-translocating ATPase complex consists of two different entities, F(1) and F(o). The water-soluble F(1) part carries the catalytic sites for ATP synthesis and hydrolysis. It is associated with the membrane-embedded F(o) complex, which functions as a proton channel and consists of subunits a, b and c present in a stoichiometry of 1:2:12. Subunit b was isolated by preparative gel electrophoresis, acetone-precipitated and renatured in a cholate-containing buffer. Reconstituted subunit b together with purified ac subcomplex is active in proton translocation and F(1) binding, thereby demonstrating that subunit b had recovered its native conformation. Circular dichroism spectroscopy of subunit b reconstituted into liposomes revealed a rather high degree of alpha -helical conformation of 80%. After addition of a His(6)-tag to the N terminus of subunit a, a stable ab(2) subcomplex was purified instead of a single subunit a, arguing in favour of a direct interaction between these subunits. After addition of subunit c and reconstitution into phospholipid vesicles, an F(o) complex was obtained exhibiting rates of proton translocation and F(1) binding comparable with those of wild-type F(o). The epitopes of monoclonal antibodies against subunit c are located in the hydrophilic loop region (cL31-Q42) as mapped by enzyme-linked immunosorbent assay using overlapping synthetic heptapeptides. Binding studies revealed that all monoclonal antibodies (mAbs) bind to everted membrane vesicles irrespective of the presence or absence of F(1). Although the hydrophilic region of subunit c, and especially the highly conserved residues cA40, cR41, cQ42 and cP43, are known to interact with subunits gamma and epsilon of the F(1) part, the mAb molecules have no effect on the function of F(o), either in proton translocation or in F(1) binding. However, the F(1) part and the mAb molecule(s) are bound simultaneously to the F(o) complex, suggesting that not all c subunits are involved in the interaction with F(1).
Allele-specific in situ hybridization (ASISH) analysis: a novel technique which resolves differential allelic usage of H19 within the same cell lineage during human placental development (1996)

Precursory studies of H19 transcription during human foetal development have demonstrated maternally derived monoallelic expression. Analyses in extra-embryonic tissues, however, have been more equivocal, with discernible levels of expression of the paternal allele of H19 documented in the first trimester placenta. By refining the in situ hybridization technique we have developed an assay to enable the functional imprinting status of H19 to be determined at the cellular level. This assay involves the use of oligonucleotide DNA probes that are able to discriminate between allelic RNA transcripts containing sequence polymorphisms. Biallelic expression of H19 is confined to a subpopulation of cells of the trophoblast lineage, the extravillous cytotrophoblast, while the mesenchymal stroma cells maintain the imprinted pattern of monoallelic expression of H19 throughout placental development. This data demonstrates that the low level of paternal H19 expression previously detected in normal human placenta is not due to a random loss of functional imprinting, but appears to result from a developmentally regulated cell type-specific activation of the paternal allele. In addition, biallelic expression of H19 does not seem to affect the functional imprinting of the insulin-like growth factor II gene, which is monoallelically expressed at relatively high levels in the extra-villous cytotrophoblasts. These results imply that the allelic usage of these two genes in normal human placental development may not be directly analogous to the situation previously documented in the mouse embryo.
The EGF-CFC family: novel epidermal growth factor-related proteins in development and cancer. (2000)

The EGF-CFC gene family encodes a group of structurally related proteins that serve as important competence factors during early embryogenesis in Xenopus, zebrafish, mice and humans. This multigene family consists of Xenopus FRL-1, zebrafish one-eyed-pinhead (oep), mouse cripto (Cr-1) and cryptic, and human cripto (CR-1) and criptin. FRL-1, oep and mouse cripto are essential for the formation of mesoderm and endoderm and for correct establishment of the anterior/posterior axis. In addition, oep and cryptic are important for the establishment of left-right (L/R) asymmetry. In zebrafish, there is strong genetic evidence that oep functions as an obligatory co-factor for the correct signaling of a transforming growth factor-beta (TGFbeta)-related gene, nodal, during gastrulation and during L/R asymmetry development. Expression of Cr-1 and cryptic is extinguished in the embryo after day 8 of gestation except for the developing heart where Cr-1 expression is necessary for myocardial development. In the mouse, cryptic is not expressed in adult tissues whereas Cr-1 is expressed at a low level in several different tissues including the mammary gland. In the mammary gland, expression of Cr-1 in the ductal epithelial cells increases during pregnancy and lactation and immunoreactive and biologically active Cr-1 protein can be detected in human milk. Overexpression of Cr-1 in mouse mammary epithelial cells can facilitate their in vitro transformation and in vivo these Cr-1-transduced cells produce ductal hyperplasias in the mammary gland. Recombinant mouse or human cripto can enhance cell motility and branching morphogenesis in mammary epithelial cells and in some human tumor cells. These effects are accompanied by an epithelial-mesenchymal transition which is associated with a decrease in beta-catenin function and an increase in vimentin expression. Expression of cripto is increased several-fold in human colon, gastric, pancreatic and lung carcinomas and in a variety of different types of mouse and human breast carcinomas. More importantly, this increase can first be detected in premalignant lesions in some of these tissues. Although a specific receptor for the EGF-CFC proteins has not yet been identified, oep depends upon an activin-type RIIB and RIB receptor system that functions through Smad-2. Mouse and human cripto have been shown to activate a ras/raf/MAP kinase signaling pathway in mammary epithelial cells. Activation of phosphatidylinositol 3-kinase and Akt are also important for the ability of CR-1 to stimulate cell migration and to block lactogenic hormone-induced expression of beta-casein and whey acidic protein. In mammary epithelial cells, part of these responses may depend on the ability of CR-1 to transactivate erb B-4 and/or fibroblast growth factor receptor 1 through an src-like tyrosine kinase.
Apo AI/ABCA1‐Dependent and HDL3‐Mediated Lipid Efflux from Compositionally Distinct Cholesterol‐Based Microdomains (2002)

We have investigated whether a raft heterogeneity exists in human monocyte-derived macrophages and fibroblasts and whether these microdomains are modulated by lipid efflux. Triton X-100 (Triton) or Lubrol WX (Lubrol) detergent-resistant membranes from cholesterol-loaded monocytes were associated with the following findings: (i) Lubrol-DRM contained most of the cellular cholesterol and at least 75% of Triton-detergent-resistant membranes. (ii) 'Lubrol rafts', defined by their solubility in Triton but insolubility in Lubrol, were enriched in unsaturated phosphatidylcholine and showed a lower cholesterol to choline-phospholipid ratio compared to Triton rafts. (iii) CD14 and CD55 were recovered in Triton- and Lubrol-detergent-resistant membranes, whereas CD11b was found exclusively in Triton DRM. ABCA1 implicated in apo AI-mediated lipid efflux and CDC42 were partially localized in Lubrol- but not in Triton-detergent-resistant membranes. (iv) Apo AI preferentially depleted cholesterol and choline-phospholipids from Lubrol rafts, whereas HDL3 additionally decreased the cholesterol content of Triton rafts. In fibroblasts, neither ABCA1 nor CDC42 was found in Lubrol rafts, and both apo AI and HDL3 reduced the lipid content in Lubrol- as well as in Triton-detergent-resistant membranes. In summary, we provide evidence for the existence of compositionally distinct membrane microdomains in human cells and their modulation by apo AI/ABCA1-dependent and HDL3-mediated lipid efflux.
Evidence-Based And Value-Based Formulary Guidelines (2004)

Health plans and hospitals have long used drug formularies, but the processes by which formulary committees made decisions have typically lacked transparency and scientific rigor. A growing number of organizations have begun implementing formulary guidelines issued by the Academy of Managed Care Pharmacy (AMCP). These guidelines call for health plans to request formally that drug companies present a standardized "dossier" that contains detailed information not only on the drug's effectiveness and safety but also on its economic value relative to alternative therapies. This paper describes the guidelines, reviews progress to date, and analyzes several critical issues for the future.
Terminal Complement Inhibitor Eculizumab in Atypical Hemolytic–Uremic Syndrome (2013)

Eculizumab inhibited complement-mediated thrombotic microangiopathy and was associated with significant time-dependent improvement in renal function in patients with atypical hemolytic-uremic syndrome. (Funded by Alexion Pharmaceuticals; C08-002 ClinicalTrials.gov numbers, NCT00844545 [adults] and NCT00844844 [adolescents]; C08-003 ClinicalTrials.gov numbers, NCT00838513 [adults] and NCT00844428 [adolescents]).
A new class of lower bounds to information rates of stationary sources via conditional rate-distortion functions (1973)

A new class of lower bounds to rate-distortion functions of stationary processes with memory and single-letter vector-valued distortion measures is derived. This class is shown to include or imply all other well-known lower bounds to rates of such sources and distortion measures. The derivation is based on the definition and properties of the conditional rate-distortion function. In addition to providing a unified and intuitive approach to lower bounds, this approach yields several interesting relations among conditional, joint, and marginal rates that are similar to and sometimes identical with the analogous relations among the corresponding entropies.
Fine-needle aspiration biopsy-RT-PCR expression analysis of prothymosin alpha and parathymosin in thyroid: novel proliferation markers? (2007)

Fine-needle aspiration biopsy-based cytology has become an established and reliable diagnostic preoperative test in the evaluation of thyroid nodules. Despite the high specificity and sensitivity of the method, results might be doubtful in a significant number of cases. Genetic analysis of the aspirates by RT-PCR may contribute, in parallel to the cytology report, to a more precise diagnosis. Prothymosin alpha and parathymosin are two homologous chromatin remodeling proteins essential for cell cycle progression and proliferation of either normal or malignant cells. A semi-quantitative RT-PCR assay was developed to determine prothymosin alpha and parathymosin mRNA expression patterns in thyroid follicular cells obtained from the fine-needle aspiration biopsy specimens of patients diagnosed with simple nodular goitre, follicular adenoma, papillary and follicular well-differentiated carcinomas. Prothymosin alpha and parathymosin mRNA levels were found significantly elevated in well-differentiated carcinomas in relation to adenomas (p<0.05) and goitres (p<0.05), an event possibly linked to the proliferation activity of thyroid follicular cells. Further studies are required to establish prothymosin alpha and parathymosin as diagnostic proliferation markers in thyroid cancer, especially in cases of undetermined cellular morphology of follicular origin which reflect the most common cytohistopathological discrepancies.
Immune cells in term and preterm labor (2014)

Labor resembles an inflammatory response that includes secretion of cytokines/chemokines by resident and infiltrating immune cells into reproductive tissues and the maternal/fetal interface. Untimely activation of these inflammatory pathways leads to preterm labor, which can result in preterm birth. Preterm birth is a major determinant of neonatal mortality and morbidity; therefore, the elucidation of the process of labor at a cellular and molecular level is essential for understanding the pathophysiology of preterm labor. Here, we summarize the role of innate and adaptive immune cells in the physiological or pathological activation of labor. We review published literature regarding the role of innate and adaptive immune cells in the cervix, myometrium, fetal membranes, decidua and the fetus in late pregnancy and labor at term and preterm. Accumulating evidence suggests that innate immune cells (neutrophils, macrophages and mast cells) mediate the process of labor by releasing pro-inflammatory factors such as cytokines, chemokines and matrix metalloproteinases. Adaptive immune cells (T-cell subsets and B cells) participate in the maintenance of fetomaternal tolerance during pregnancy, and an alteration in their function or abundance may lead to labor at term or preterm. Also, immune cells that bridge the innate and adaptive immune systems (natural killer T (NKT) cells and dendritic cells (DCs)) seem to participate in the pathophysiology of preterm labor. In conclusion, a balance between innate and adaptive immune cells is required in order to sustain pregnancy; an alteration of this balance will lead to labor at term or preterm.