gebhart/patrepeval huggingface dataset:
Characterization of Retroviral and Lentiviral Vectors Pseudotyped with Xenotropic Murine Leukemia Virus-Related Virus Envelope Glycoprotein (2010)

Retroviral and lentiviral vectors are effective gene delivery vehicles that are being evaluated in clinical trials. Variations in the viral envelope (Env) glycoproteins, which are used to pseudotype retroviral or lentiviral vectors, can alter vector performance, including stability, titers, host range, and tissue tropism. Xenotropic murine leukemia virus (MLV)-related virus (XMRV) is a novel human retrovirus identified in patients with prostate cancer. XMRV targets XPR1 cell surface receptor, which is expressed in a broad range of human tissues including hematopoietic stem cells. Pseudotyping with XMRV Env would allow targeting of XPR1-expressing tissues. Here, we characterized XMRV Env-pseudotyped retroviral and lentiviral vectors. Although HIV and MLV vectors were poorly pseudotyped with wild-type XMRV Env, replacement of the C-terminal 11 amino acid residues in the transmembrane domain of XMRV Env with the corresponding 6 amino acid residues of amphotropic MLV Env (XMRV/R(ampho)) significantly increased XMRV Env-pseudotyped HIV and MLV vector titers. The transduction efficiency in human CD34(+) cells when using the XMRV/R(ampho)-pseudotyped HIV vector (10-20%) was comparable to that achieved when using the same infectious units of vesicular stomatitis virus G glycoprotein-pseudotyped vector (25%); thus the modified XMRV Env offers an alternative pseudotyping strategy for XPR1-mediated gene delivery.
miR-200a Regulates Nrf2 Activation by Targeting Keap1 mRNA in Breast Cancer Cells (2011)

NF-E2-related factor 2 (Nrf2) is an important transcription factor that activates the expression of cellular detoxifying enzymes. Nrf2 expression is largely regulated through the association of Nrf2 with Kelch-like ECH-associated protein 1 (Keap1), which results in cytoplasmic Nrf2 degradation. Conversely, little is known concerning the regulation of Keap1 expression. Until now, a regulatory role for microRNAs (miRs) in controlling Keap1 gene expression had not been characterized. By using miR array-based screening, we observed miR-200a silencing in breast cancer cells and demonstrated that upon re-expression, miR-200a targets the Keap1 3'-untranslated region (3'-UTR), leading to Keap1 mRNA degradation. Loss of this regulatory mechanism may contribute to the dysregulation of Nrf2 activity in breast cancer. Previously, we have identified epigenetic repression of miR-200a in breast cancer cells. Here, we find that treatment with epigenetic therapy, the histone deacetylase inhibitor suberoylanilide hydroxamic acid, restored miR-200a expression and reduced Keap1 levels. This reduction in Keap1 levels corresponded with Nrf2 nuclear translocation and activation of Nrf2-dependent NAD(P)H-quinone oxidoreductase 1 (NQO1) gene transcription. Moreover, we found that Nrf2 activation inhibited the anchorage-independent growth of breast cancer cells. Finally, our in vitro observations were confirmed in a model of carcinogen-induced mammary hyperplasia in vivo. In conclusion, our study demonstrates that miR-200a regulates the Keap1/Nrf2 pathway in mammary epithelium, and we find that epigenetic therapy can restore miR-200a regulation of Keap1 expression, therefore reactivating the Nrf2-dependent antioxidant pathway in breast cancer.
Overlaps and parallels in the regulation of intrinsic multiple‐antibiotic resistance in Escherichia coli (1996)

Chromosomally encoded systems present in a variety of bacteria appear to play a central role in determining the Intrinsic level of resistance to many commonly used antibiotics. Work with the Gram-negative bacterium Escherichia coli has shown that there is significant similarity at the amino acid sequence level among the structural components of these resistance systems as well as among their genetic regulators. This review describes two of the better-studied regulatory systems, marRAB and soxRS, as well as two regulated multidrug-efflux systems, encoded by emrAB and acrAB, and focuses on conserved themes in their primary structures and environmental stimuli. The observed resistance to clinically important antibiotics appears to reflect an overlap with broad-ranged adaptive responses by free-living bacteria to noxious plant materials in their natural environment.
Phase I and Pharmacokinetic Study of a New Taxoid, RPR 109881A, Given as a 1-Hour Intravenous Infusion in Patients With Advanced Solid Tumors (2000)

RPR 109881A was found to be a well-tolerated and promising taxoid agent. The MTD was 75 mg/m(2), and the recommended dose for phase II study was 60 mg/m(2) as a 1-hour infusion every 3 weeks.
Development of the Intranet-based SCADA (supervisory control and data acquisition system) for power system (2002)

This paper proposes to apply the Intranet technology to SCADA (supervisory control and data acquisition system) for power system and presents the result of development of the Intranet-based SCADA trial system. The Intranet-based SCADA is concerned with real-time performance and reliability of supervisory control. How the trial system resolved these issues is discussed and various measurements at the trial system including picture display time, supervisory control response time and failover time are presented. Real time performance, system cost and maintainability of the Intranet-based SCADA are evaluated based upon the trial system. The feature of the Intranet-based SCADA such as failover between geographically separated servers and capability of supervisory control at night from another control center are discussed. Information security of the Intranet-based SCADA that should be paid particular attention to is also discussed.
Confession session: Learning from others mistakes (2011)

People rarely put in their papers the things that didn't work, the mistakes they made, and how they found out what went wrong. Such confessions can help others learn how to avoid similar mistakes. Twenty-six confessions were collected to form the bulk of this paper. Themes that arise are errors that result from not understanding the limitations of simulation tools in modeling physical reality, chip verification errors that result from lack of clear communication between designers, and projects that are considered in their own isolated environment of technical challenges rather than the broader context of their environment or application.
Acne is Not Associated with Yet-Uncultured Bacteria (2008)

Current clinical and microbiological information on acne fails to demonstrate a clear association between particular species, including Propionibacterium acnes, and disease, and the disease continues to be a considerable problem. To test if acne is associated with hitherto uncultured bacteria residing in diseased skin follicles, sequencing and phylogenetic analysis of approximately 5,700 amplified and cloned 16S rRNA genes were used to determine the microbial diversity in follicles from acne patients and healthy individuals and from the superficial skin of acne patients. Follicles from healthy skin were exclusively colonized by P. acnes, whereas the follicular microbiota of acne patients included, in addition, Staphylococcus epidermidis and minor proportions of other species. In comparison, samples from superficial skin showed a complex microbiota represented by 12 to 16 bacterial species. The findings of the study exclude the possibility that acne is associated with yet-uncultured bacteria and shows that healthy skin follicles constitute a remarkably exclusive habitat allowing colonization only by P. acnes.
Crown ethers in inorganic chemistry. Preparation and characterization of the Group 6 pentacarbonyl hydroxides and fluorides (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrown ethers in inorganic chemistry. Preparation and characterization of the Group 6 pentacarbonyl hydroxides and fluoridesJohn L. Cihonski and Robert A. LevensonCite this: Inorg. Chem. 1975, 14, 7, 1717–1720Publication Date (Print):July 1, 1975Publication History Published online1 May 2002Published inissue 1 July 1975https://pubs.acs.org/doi/10.1021/ic50149a059https://doi.org/10.1021/ic50149a059research-articleACS PublicationsRequest reuse permissionsArticle Views83Altmetric-Citations17LEARN 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
Safety and efficacy of a novel high‐intensity focused electromagnetic technology device for noninvasive abdominal body shaping (2018)

Observed waist size reduction and aesthetic improvement appear to be a combination of fat reduction and increased muscle definition of abdominal wall. In lower BMI patients, the increased abdominal muscle definition was largely responsible for the improvement. This novel energy device provides an additional tool for body contouring with primary application for lower and medium BMI patients.
Experiments on Gram-Schmidt Orthogonalization (1966)

The present paper contains in Table 1 a somewhat shortened version of that summary, and lists all values of | k \ for which six or more solutions were found.We summarize some of our results as follows:(1) For positive k g 100, no solution could be appended to the Table in [3].(2) For negative k 2ï -9999, the last solution found was(1,775,104)3 -(2,365,024,826)2 = -5412;whilst, for positive fc ^ 9999, the last solution was(939,787)3 -(911,054,064)2 = 307.(3) In addition to solutions for | k | ^ 9999, we have solutions, for y ^ 104and | k | g 99999; there are 1221 for positive k and 799 for negative k.The vast majority of solutions are with y < 100 and Table 2 gives the number of solutions for various ranges of y.The fact that the number of solutions is a rapidly decreasing function of y suggests that for at least some k the solution set may be complete.
Translational repression of aC. elegansNotch mRNA by the STAR/KH domain protein GLD-1 (2003)

In C. elegans, the Notch receptor GLP-1 is localized within the germline and early embryo by translational control of glp-1 mRNA. RNA elements in the glp-1 3'untranslated region (3' UTR) are necessary for repression of glp-1 translation in germ cells, and for localization of translation to anterior cells of the early embryo. The direct regulators of glp-1 mRNA are not known. Here, we show that a 34 nucleotide region of the glp-1 3' UTR contains two regulatory elements, an element that represses translation in germ cells and posterior cells of the early embryo, and an element that inhibits repressor activity to promote translation in the embryo. Furthermore, we show that the STAR/KH domain protein GLD-1 binds directly and specifically to the repressor element. Depletion of GLD-1 activity by RNA interference causes loss of endogenous glp-1 mRNA repression in early meiotic germ cells, and in posterior cells of the early embryo. Therefore, GLD-1 is a direct repressor of glp-1 translation at two developmental stages. These results suggest a new function for GLD-1 in regulating early embryonic asymmetry. Furthermore, these observations indicate that precise control of GLD-1 activity by other regulatory factors is important to localize this Notch receptor, and contributes to the spatial organization of Notch signaling.
Design of microstrip antennas covered with a dielectric layer (1982)

The design of a microstrip antenna covered with a dielectric layer is presented. Due to loading, the resonant frequency of the antenna changes. The absolute value of the change increases with the operating frequency, the relative permittivity (except plasma), and the thickness of the dielectric layer. This change may cause degradation in performance due to the inherent narrow bandwidth of microstrip antennas if the effect of loading is not considered in the design. The curves presented here may be used to design microstrip antennas that may be subjected to icing or a plasma environment or coated with protective layers. Numerical and experimental results for the fractional change in the resonant frequency are round to be in good agreement.
Hyperthermia in tissue-cultured cells of malignant origin. (1957)

Summary Three permanent human neoplastic cell strains were cultured in a fluid medium. Their reactions to elevated temperatures were studied. HeLa and J96 showed the same tolerance to heat, while H.Ep. #2 was more resistant. The three strains reacted to elevated temperatures at first with increased rate of growth (maximum at 38° C.), then with temporary interruption of the mitotic cycle in metaphase (39°–40° C.), finally with irreversible heat injury. The lethal exposure times were determined between 42° and 46° C. for single and divided heat application. The thermotolerance increased by culturing the cells at 39° C. previous to the experiment and was decreased by culturing them at 31° C. Cells surviving heat application became considerably more thermoresistant for at least 3 months. Sublines with higher thermotolerance were developed from all three strains. The morphologic changes during and after heat treatment were described.
A Novel Sialic Acid Binding Site on Factor H Mediates Serum Resistance of Sialylated Neisseria gonorrhoeae (1998)

Factor H (fH), a key alternative complement pathway regulator, is a cofactor for factor I-mediated cleavage of C3b. fH consists of 20 short consensus repeat (SCR) domains. Sialic acid binding domains have previously been localized to fH SCRs 6-10 and 13. To examine fH binding on a sialylated microbial surface, we grew Neisseria gonorrhoeae in the presence of 5'-cytidinemonophospho-N-acetylneuraminic acid, which sialylates lipooligosaccharide and converts to serum resistance gonococci previously sensitive to nonimmune serum killing. fH domains necessary for binding sialylated gonococci were determined by incubating organisms with recombinant human fH (rH) and nine mutant rH molecules (deletions spanning the entire fH molecule). rH and all mutant rH molecules that contained SCRs 16-20 bound to the sialylated strain; no mutant molecule bound to serum-sensitive nonsialylated organisms. Sialic acid was demonstrated to be the fH target by flow cytometry that showed a fourfold increase in fH binding that was reversed by neuraminidase-mediated cleavage of sialic acid off gonococci. Functional specificity of fH was confirmed by decreased total C3 binding and almost complete conversion to iC3b on sialylated gonococci. Sialic acid can therefore bind fH uniquely through SCRs 16-20. This blocks complement pathway activation for N. gonorrhoeae at the level of C3.
Gene Expression in the Normal Adult Human Kidney Assessed by Complementary DNA Microarray (2003)

The kidney is a highly specialized organ with a complex, stereotyped architecture and a great diversity of functions and cell types. Because the microscopic organization of the nephron, the functional unit of the kidney, has a consistent relationship to the macroscopic anatomy of the kidney, knowledge of the characteristic patterns of gene expression in different compartments of the kidney could provide insight into the functions and functional organization of the normal nephron. We studied gene expression in dissected renal lobes of five adult human kidneys using cDNA microarrays representing approximately 30,000 different human genes. Total RNA was isolated from sections of the inner and outer cortex, inner and outer medulla, papillary tips, and renal pelvis and from glomeruli isolated by sieving. The results revealed unique and highly distinctive patterns of gene expression for glomeruli, cortex, medulla, papillary tips, and pelvic samples. Immunohistochemical staining using selected antisera confirmed differential expression of several cognate proteins and provided histological localization of expression within the nephron. The distinctive patterns of gene expression in discrete portions of the kidney may serve as a resource for further understanding of renal physiology and the molecular and cellular organization of the nephron.
Specific Interaction between Bovine Cyclophilin A and Synthetic Analogues of Cyclolinopeptide A (1998)

Like cyclosporin A, cyclolinopeptide A binds specifically bovine cyclophilin A, inhibiting its peptidyl-prolyl cis-trans isomerase activity. We describe here the protein interaction with several synthetic analogues of cyclolinopeptide A, which are either homodetic or disulphide bridged heterodetic cyclopeptides characterized by different ring dimensions, in terms of dissociation and inhibition constants evaluated by fluorescence and inhibition of the enzyme activity, respectively. Dissociation constants from fluorescence experiments are practically identical and about 20-fold lower than for cyclosporin A. On the other hand, inhibition constants differ from compound to compound and are higher than for cyclosporin A. This result is therefore difficult to rationalize, but we would suggest decoupling between binding and inhibitory ability of cyclopeptides. The Pro1 residue of cyclolinopeptide A seems to play a fundamental role in determining the inhibition of the rotamase activity of cyclophilin A, as the homodetic analogue lacking this residue does not show any inhibitory ability. Similarly, heterodetic analogues with a ring size smaller than 7 residues do not display inhibition. We presume that the sequence -Pro-Pro-Phe-Phe- and a ring size of 8 residues for homodetic cyclic peptides could be used as starting points in the targeted synthesis of cyclopeptides able to bind both cyclosporin A and calcineurin. The only peptide showing similar values of the dissociation and inhibition constant is cyclolinopeptide A. This compound can be considered a novel model for the molecular design of immunosuppressant drugs.
Brain somatic representation of phantom and intact limb: a fMRI study case report (2000)

Reports on phantom limb patients concerning neuronal reorganization using non-invasive methods have focused mainly on the cortical regions and suggest the presence of pain as the cause of this reorganization. The phantom limb, however, includes other somatic and motor sensations other than pain. Here we describe the results of non-painful stimulation in cortical and subcortical lateralization and reorganization and also examine the involvement of subcortical structures in phantom limb telescoping perception. We describe an enlarged contralateral cortical representation of the stump, a cortical and thalamic bilateral representation of the remaining leg, and a neuronal correlate of a telescoping perception of the phantom limb. The missing leg produces an enlarged cortical representation due to abnormal information and the remaining leg has a bilateral SII representation, which could be related to new, compensatory functions. The telescoping perception of a phantom limb by the stimulation of misallocation points was correlated with lenticular nuclei, thalamic and cingulate gyrus activation. We therefore propose that the reorganization concept of a phantom limb, applied mainly to the cortex, must extend to the thalamic and the somatosensory and motor systems (pathways and relay nuclei).
Prediction of immunogenicity for therapeutic proteins: state of the art. (2007)

Immunogenicity is a significant problem associated with protein therapeutics, but can be predicted in advance by in silico, in vitro, and in vivo tools, which can identifiy sequences within the therapeutic protein that, when processed by T-cells, elicit an immune response. Recent developments in T-cell-dependent immunology relating to the immunogenicity of therapeutic products include the description of toll-like receptor ligands and the identification and classification of regulatory T-cells. A limitation in determining the relative immunogenicity of potential therapeutic proteins is the variance in the immunogenicity determined by in vitro or in vivo techniques in animal and human models. However, given the sophistication and high-throughput capacity of existing in silico tools and the availability of precise in vitro validation assays, accurate prediction of immunogenicity for therapeutic protein products, and more rapid translation of research discoveries into clinical success, may be within reach.
Cyclodextrin as Carrier of Peptide Hormones. Conformational and Biological Properties of β-Cyclodextrin/Gastrin Constructs (1998)

The C-terminal tetrapeptide amide of gastrin, the shortest sequence of this gastrointestinal hormone capable of exhibiting all the biological properties even though at reduced potency, and the related heptapeptide amide were covalently linked to mono-(6-succinylamino-6-deoxy)-β-cyclodextrin to analyze the effect of the bulky cyclic carbohydrate moiety on recognition of the peptides by the G-protein-coupled CCK−B/gastrin receptor and on their signal transduction potencies. With the four-carbon succinyl spacer and particularly with the additional tripeptide spacer in the heptapeptide/β-cyclodextrin conjugate, full recognition by the receptor was obtained with binding affinities identical to those of the unconjugated tetrapeptide and with a potency comparable to that of full agonists. Docking of this conjugate onto a structure of the human CCK−B receptor derived by homology modeling indicates sufficient free space of the peptide moiety for intermolecular interaction at the putative gastrin binding site, whereby additional interactions of the cyclodextrin with the receptor surface apparently suffice for stabilizing the complex and thus for triggering the full hormonal message. The host/guest complexation of the peptide moiety by the β-cyclodextrin which seems to occur at least in the case of the tetrapeptide conjugate does not suffice in its strength for competing with the receptor recognition. However, multiple presentation of the tetragastrin by its covalent linkage to the heptakis-(6-succinylamino-6-deoxy)-β-cyclodextrin leads to peptide/peptide and/or peptide/cyclodextrin collapses with strong interferences in the receptor recognition process. Retention of full agonism by suitably designed monoconjugates of bioactive peptides with cyclodextrins suggests a highly promising approach for targeting host/guest complexed or covalently bound cytotoxic drugs to specific tumor cells for receptor-mediated internalization.