gebhart/patrepeval huggingface dataset:
Baculovirus gp64 gene expression: analysis of sequences modulating early transcription and transactivation by IE1 (1991)

Expression of the baculovirus major envelope glycoprotein gene (gp64) is regulated by transcription from both early and late promoters. To characterize the early promoter and identify sequences involved in the regulation of gp64 early transcription, promoter-reporter gene fusions were generated from the Orygia pseudotsugata nuclear polyhedrosis virus gp64 promoter and were analyzed by transient expression in uninfected insect cells. For these analyses, 5' deletion mutations were constructed in the gp64 upstream regulatory region. Larger promoter constructs were functional in uninfected Lymantria dispar cells, indicating that transcription from the gp64 early promoter required no additional viral gene products. Deletion analysis of the gp64 upstream region revealed several regulatory regions. These included a putative negative regulatory element between -319 and -166 nucleotides (nt) and multiple positive regulatory elements between -166 and -77 nt. Deletion of the TATA box located between -77 and -62 nt resulted in the loss of transcriptional activity. Cotransfections of reporter constructs and a plasmid containing a baculovirus transcriptional transactivator gene (Autographa californica nuclear polyhedrosis virus IE1) resulted in transcriptional transactivation of all constructs containing an intact TATA box. These data demonstrate that sequences upstream of the gp64 TATA box are not essential for IE1 transactivation and that only 34 nt upstream of the early transcription start site were necessary for basal levels of transcription and for transactivation by IE1. Function of the gp64 early promoter was also examined in cell lines from Spodoptera frugiperda and Drosophila melanogaster.
Ultrastrong Capacitive Coupling of Flux Qubits (2022)

A flux qubit can interact strongly when it is capacitively coupled to other circuit elements. This interaction can be separated into two parts, one acting on the qubit subspaces and one in which excited states mediate the interaction. The first term dominates the interaction between the flux qubit and an $LC$ resonator, leading to ultrastrong couplings of the form ${\ensuremath{\sigma}}^{y}(a+{a}^{\ifmmode\dagger\else\textdagger\fi{}})$, which complement the inductive ${\ensuremath{\sigma}}^{x}i({a}^{\ifmmode\dagger\else\textdagger\fi{}}\ensuremath{-}a)$ coupling. However, when coupling two flux qubits capacitively, all terms need to be taken into account, leading to complex nonstoquastic ultrastrong interaction of types ${\ensuremath{\sigma}}_{1}^{y}{\ensuremath{\sigma}}_{2}^{y}$, ${\ensuremath{\sigma}}_{1}^{z}{\ensuremath{\sigma}}_{2}^{z}$, and ${\ensuremath{\sigma}}_{1}^{x}{\ensuremath{\sigma}}_{2}^{x}$. Our theory explains all these interactions, describing them in terms of general circuit properties---coupling capacitances, qubit gaps, inductive, Josephson and capacitive energies---that apply to a wide variety of circuits and flux qubit designs.
Inhibition of glycosidases by aldonolactones of corresponding configuration. 2. Inhibitors of β-N-acetylglucosaminidase (1958)

Conchie & Levvy (1957) found that, in general, the enzymic hydrolysis of a simple glycoside was in- hibited by the aldonolactone corresponding in configuration to the sugar residue of the substrate. This suggested that the structural requirements necessary for a specific inhibitor of fl-N-acetyl-
Purification of the photosynthetic pigment C‐phycocyanin from heterotrophic Galdieria sulphuraria (2013)

C-PC from heterotrophic G. sulphuraria shows similar properties to cyanobacterial C-PC and can be purified to the same standards, despite initial C-PC concentrations being low and impurity concentrations high in G. sulphuraria extracts.
Isolation of Hofbauer Cells from Human Term Placentas with High Yield and Purity (2011)

PROBLEM Placental villus macrophages (i.e., Hofbauer cells, HBCs) were identified more than 100 years ago. Alterations in their numbers and characteristics are associated with several complications of pregnancy. Although HBCs have previously been isolated and cultured, there is no consensus methodology to obtain these cells with high yield and purity for in vitro studies. METHOD OF STUDY Hofbauer cells were isolated from human term placentas using protocols in which cytotrophoblasts (CTs) and fibroblasts (FIBs), other major villous cell types, were isolated in parallel. Enzymatic digestion, Percoll gradients, and immunoselection were used to isolate the three cell types. Purity was assessed by morphology, flow cytometry, and phagocytosis assays. RESULTS Hofbauer cells were isolated with 98-99% purity and a yield of 130-200 × 10(6) cells/80-100 g of tissue. HBCs exhibited a pleiomorphic and vacuolated appearance for at least 5 days in culture medium with and without serum. High levels of phagocytosis in HBCs, but not in CTs or FIBs, confirmed macrophage function in HBCs. Phagocytotic activity was maintained across several days in culture. CONCLUSION Hofbauer cells were isolated from term placenta with high yield and purity using protocols in which CTs and FIBs were also obtained. This methodology will foster future studies that examine the role of HBCs in regulating villus function.
A 35 amino acid fragment of leptin inhibits feeding in the rat (1996)

Peptide fragments of the larger 167 amino acid obesity gene related peptide (OBGRP), leptin, were tested for their ability to inhibit feeding in the rat.The C-terminal fragment, OBGRP 116-167 exerted only minimal inhibition of feeding when administered into the lateral cerbroventricle.No alteration in feeding was observed following admir&ration of OBGRP 57-92.We hypothesized that the satiety etTect.s of leptin reside in the N-ten&al region of the peptide sequence.Significant, dose-related, and reversible inhibition of food intake was observed following central administration of the 35 amino acid fragment OBGRP 22-56.These results suggest that a small, readily synthesized fragment of the 167 amino acid peptide leptin may exert physiologically relevant satiety effects in brain revealing an endocrine feedback mechanism by which the adipocyte may modulate hypothalamic function.
1-Deoxy-5-hydroxysphingolipids as New Anticancer Principles:  An Efficient Procedure for Stereoselective Syntheses of 2-Amino-3,5-diols (2005)

[reaction: see text]. Enantioselective preparation of the linear homoallylic alcohol I allows efficient formation of the 2-amino-3,5-diol moiety present in several biologically active compounds, including 1-deoxy-5-hydroxysphingosine analogue IV, which has exhibited excellent biological activity against colon cancer. The conversion of I into IV involves a sequence of enantioselective epoxidation of the O-tert-butoxycarbonyl derivative of I, followed by regioselective and stereospecific oxacyclization of II to introduce differentiated oxygens in III.
Induction of Cytoprotective Genes Through Nrf2 / Antioxidant Response Element Pathway: A New Therapeutic Approach for the Treatment of Inflammatory Diseases (2004)

In the last decade, it has become recognized that reactive oxygen species (ROS) play important roles in the multiple biological processes involved in the pathophysiology of chronic inflammation such as cell proliferation, adhesion molecule expression, cytokine and chemoattractant production and matrix metalloproteinase generation. Intracellular redox homeostasis is maintained by balancing the production of ROS with their removal through cellular antioxidant defense systems. The antioxidant response element (ARE) is a cis-acting DNA regulatory element located in the regulatory regions of multiple genes including phase II detoxification enzymes as well as antioxidant proteins including glutathione-S-transferases, NAD(P)H:quinone oxidoreductase-1, gamma-glutamylcysteine synthase, ferritin, and heme oxygenase-1. Nrf2 is the primary transcription factor that binds to the ARE, and through heterodimerization with other leucine-zipper containing transcription factors, activates the expression of these genes. It is evident that activation of ARE-regulated genes contributes to the regulation of cellular antioxidant defense systems. More importantly, there is a growing body of evidence suggesting that modulation of these cytoprotective genes has profound effects on immune and inflammatory responses. Activation of cytoprotective Nrf2/ARE-regulated genes can suppress inflammatory responses, whereas decreased expression of these genes results in autoimmune disease and enhanced inflammatory responses to oxidant insults. Thus, coordinate induction of cytoprotective genes through Nrf2/ARE pathway may represent a novel therapeutic approach for the treatment of immune and inflammatory diseases.
The Mitochondrial Benzodiazepine Receptor as a Potential Target Protein for Drug Development: Demonstration of Functional Significance with Cell Lines Exhibiting Differential Expression of Bcl-2 (2003)

The article highlighted in this issue is "Reversal of Bcl-2 Mediated Resistance of the EW36 Human B-Cell Lymphoma Cell Line to Arsenite and Pesticide-Induced Apoptosis by PK11195, a Ligand of the Mitochondrial Benzodiazepine Receptor" by Donna E. Muscarella, Kerry A. O'Brien, Ann T. Lemley, and Stephen E Bloom from Cornell University in Ithaca, NY (pp. 66-73). The following brief review summarizes their findings, highlights the novel biological model and experimental approach used, and explores potential mechanistic and therapeutic implications of these findings.
CdSe–CdS Nanoheteroplatelets with Efficient Photoexcitation of Central CdSe Region through Epitaxially Grown CdS Wings (2013)

We synthesized a new type of optically active semiconductor nanoheterostructure based on CdSe nanoplatelets with epitaxially grown CdS flat branches or wings. CdS branches work as efficient photonic antenna in the blue spectral region, enhancing the excitation of CdSe band edge emission. The formation of CdSe-CdS nanoheteroplatelets instead of CdSe/CdS core-shell nanoplatelets was achieved using short-chain Cd ethylhexanoate and sulfur in octadecene as precursors for CdS overgrowth in the presence of acetate salt.
Prognostic Significance of Autoimmunity during Treatment of Melanoma with Interferon (2006)

The appearance of autoantibodies or clinical manifestations of autoimmunity during treatment with interferon alfa-2b is associated with statistically significant improvements in relapse-free survival and overall survival in patients with melanoma.
Repurposing Diflunisal for Familial Amyloid Polyneuropathy (2013)

clinicaltrials.gov Identifier: NCT00294671.
Nanowire electrodes for high-density stimulation and measurement of neural circuits (2013)

Brain-machine interfaces (BMIs) that can precisely monitor and control neural activity will likely require new hardware with improved resolution and specificity. New nanofabricated electrodes with feature sizes and densities comparable to neural circuits may lead to such improvements. In this perspective, we review the recent development of vertical nanowire (NW) electrodes that could provide highly parallel single-cell recording and stimulation for future BMIs. We compare the advantages of these devices and discuss some of the technical challenges that must be overcome for this technology to become a platform for next-generation closed-loop BMIs.
Kinetics of Formation for n-Alkanethiolate Self-Assembled Monolayers onto Gold in Aqueous Micellar Solutions of C12E6 and C12E7 (2002)

We have investigated the kinetics of formation for n-alkanethiolate self-assembled monolayers (SAMs) onto gold from aqueous micellar solutions of hexaethylene glycol monododecyl ether (C12E6) and heptaethylene glycol monododecyl ether (C12E7). Micelles provide hydrophobic domains to solubilize the alkanethiols in aqueous solution and facilitate their delivery to the gold surface. The kinetics of SAM formation depends on the micellar size, the concentration of solubilized thiol, and the alkanethiol chain length. The kinetics data for SAM formation in aqueous micellar solutions of C12E6 and C12E7 are best fit by a diffusion-limited, second-order Langmuir adsorption model that accounts for diffusion of the thiol-laden micelles and release of the alkanethiols from the micelles. The observed rate constant for SAM formation decreases exponentially with alkanethiol chain length, consistent with an activated diffusion process for the release of the alkanethiol from the micelle. The activation energy for release of the thiols from the C12E6 and C12E7 micelles to the metal surface is ∼0.22 kcal/mol per CH2 group in the alkanethiol. This relatively small barrier is consistent with a mechanism in which alkanethiols release from micelles to admicelles that are present on the gold surface through a collision-induced process.
Construction of a Shuttle Vector for, and Spheroplast Transformation of, the Hyperthermophilic Archaeon Pyrococcus abyssi (2002)

ABSTRACT Our understanding of the genetics of species of the best-studied hyperthermophilic archaea, Pyrococcus spp . , is presently limited by the lack of suitable genetic tools, such as a stable cloning vector and the ability to select individual transformants on plates. Here we describe the development of a reliable host-vector system for the hyperthermophilic archaeon Pyrococcus abyssi . Shuttle vectors were constructed based on the endogenous plasmid pGT5 from P. abyssi strain GE5 and the bacterial vector pLitmus38. As no antibiotic resistance marker is currently available for Pyrococcus spp., we generated a selectable auxotrophic marker. Uracil auxotrophs resistant to 5-fluoorotic acid were isolated from P. abyssi strain GE9 (devoid of pGT5). Genetic analysis of these mutants revealed mutations in the pyrE and/or pyrF genes, encoding key enzymes of the pyrimidine biosynthetic pathway. Two pyrE mutants exhibiting low reversion rates were retained for complementation experiments. For that purpose, the pyrE gene, encoding orotate phosphoribosyltransferase (OPRTase) of the thermoacidophilic crenarchaeote Sulfolobus acidocaldarius , was introduced into the pGT5-based vector, giving rise to pYS2. With a polyethylene glycol-spheroplast method, we could reproducibly transform P. abyssi GE9 pyrE mutants to prototrophy, though with low frequency (10 2 to 10 3 transformants per μg of pYS2 plasmid DNA). Transformants did grow as well as the wild type on minimal medium without uracil and showed comparable OPRTase activity. Vector pYS2 proved to be very stable and was maintained at high copy number under selective conditions in both Escherichia coli and P. abyssi .
Rapid antidepressant effects of the psychedelic ayahuasca in treatment-resistant depression: a randomized placebo-controlled trial (2018)

To our knowledge, this is the first controlled trial to test a psychedelic substance in treatment-resistant depression. Overall, this study brings new evidence supporting the safety and therapeutic value of ayahuasca, dosed within an appropriate setting, to help treat depression. This study is registered at http://clinicaltrials.gov (NCT02914769).
Aneurysm of the rabbit common carotid artery induced by periarterial application of calcium chloride in vivo. (1988)

Experimental aneurysmatic dilatation of the rabbit common carotid artery was induced by a single, periarterial application of calcium chloride in vivo. Vessels were fixed in situ after 3 d, 1 wk, 3 wk, 6 wk, and 12 wk by intracardiac perfusion of glutaraldehyde and tissues prepared for light, scanning, and transmission electron microscopy. Progressive focal aneurysmal dilatation was seen limited to the site of calcium application with endothelial damage and thrombus formation in areas of irregular luminal contour. Disruption of the elastic network of the intima and media was seen with varying degrees of intimal fibromuscular hyperplasia and medial disorganization. The calcium-elastic tissue complex was the focus of the inflammatory, arteriosclerotic reaction and subsequent aneurysm formation. The inflammatory cell infiltration initially included primarily neutrophils followed by lymphocytes, plasma cells, monocytes, and multinucleated giant cells. These studies support the hypothesis that disruption of the elastic tissue network of the vascular wall represents an important pathogenetic factor in the initiation of aneurysmal dilatation. In addition, the results of these studies suggest that interaction of calcium with the elastica of the arterial wall may represent an important pathogenetic factor in the initiation of giant cell arteritis.
Distribution and Particle Size of Type A Botulinum Toxin in Body Fluids of Intravenously Injected Rabbits. (1961)

SummaryIn rabbits which were given type A botulinum toxin intravenously, and which died rapidly of acute poisoning the toxin was found in lymph and plasma with no tendency to diffuse into erythrocytes. Ratio of toxin in lymph to plasma ranged between 1:6 to 1:12. Sedimentation coefficients of the toxin in these body fluids were similar and had the dimensions of a protein. The particle size was decreased in relation to crystalline toxin, was similar to toxin in lymph from rats given toxin intraduodenally, but was not sufficiently smaller to warrant the assumption of complete dissociation of toxin from the hemagglutinin present in crystalline toxin.Toxin was absent from fetal blood, but appeared in small quantities in urine and bile. Cerebrospinal fluid was free of toxin except for a small amount at death. In the normal eye none or only a small quantity of toxin appears in the intraocular fluid. By experimental reduction of intraocular pressure toxin in intraocular fluid tends to approach concentrations pre...
Cloning and Comparison of fliC Genes and Identification of Glycosylation in the Flagellin of Pseudomonas aeruginosa a-Type Strains (1998)

Pseudomonas aeruginosa a-type strains produce flagellin proteins which vary in molecular weight between strains. To compare the properties of a-type flagellins, the flagellin genes of several Pseudomonas aeruginosa a-type strains, as determined by interaction with specific anti-a monoclonal antibody, were cloned and sequenced. PCR amplification of the a-type flagellin gene fragments from five strains each yielded a 1.02-kb product, indicating that the gene size is not likely to be responsible for the observed molecular weight differences among the a-type strains. The flagellin amino acid sequences of several a-type strains (170,018, 5933, 5939, and PAK) were compared, and that of 170,018 was compared with that of PAO1, a b-type strain. The former comparisons revealed that a-type strains are similar in amino acid sequence, while the latter comparison revealed differences between 170,018 and PAO1. Posttranslational modification was explored for its contribution to the observed differences in molecular weight among the a-type strains. A biotin-hydrazide glycosylation assay was performed on the flagellins of three a-type strains (170,018, 5933, and 5939) and one b-type strain (M2), revealing a positive glycosylation reaction for strains 5933 and 5939 and a negative reaction for 170,018 and M2. Deglycosylation of the flagellin proteins with trifluoromethanesulfonic acid (TFMS) confirmed the glycosylation results. A molecular weight shift was observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis for the TFMS-treated flagellins of 5933 and 5939. These results indicate that the molecular weight discrepancies observed for the a-type flagellins can be attributed, at least in part, to glycosylation of the protein. Anti-a flagellin monoclonal antibody reacted with the TFMS-treated flagellins, suggesting that the glycosyl groups are not a necessary component of the epitope for the human anti-a monoclonal antibody. Comparisons between a-type sequences and a b-type sequence (PAO1) will aid in delineation of the epitope for this monoclonal antibody.
2,4,6-Triphenylpyrylium Tetrafluoroborate as an Electron-Transfer Photosensitizer (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2,4,6-Triphenylpyrylium Tetrafluoroborate as an Electron-Transfer PhotosensitizerMiguel A. Miranda and Hermenegildo GarciaCite this: Chem. Rev. 1994, 94, 4, 1063–1089Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/cr00028a009https://doi.org/10.1021/cr00028a009research-articleACS PublicationsRequest reuse permissionsArticle Views4766Altmetric-Citations303LEARN 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
Programmable Single and Multiplex Base-Editing in Bombyx mori Using RNA-Guided Cytidine Deaminases (2018)

Genome editing using standard tools (ZFN, TALEN, and CRISPR/Cas9) rely on double strand breaks to edit the genome. A series of new CRISPR tools that convert cytidine to thymine (C to T) without the requirement for DNA double-strand breaks was developed recently and quickly applied in a variety of organisms. Here, we demonstrate that CRISPR/Cas9-dependent base editor (BE3) converts C to T with a high frequency in the invertebrate <i>Bombyx mori</i> silkworm. Using BE3 as a knock-out tool, we inactivated exogenous and endogenous genes through base-editing-induced nonsense mutations with an efficiency of up to 66.2%. Furthermore, genome-scale analysis showed that 96.5% of <i>B. mori</i> genes have one or more targetable sites that can be edited by BE3 for inactivation, with a median of 11 sites per gene. The editing window of BE3 reached up to 13 bases (from C1 to C13 in the range of gRNA) in <i>B. mori</i> Notably, up to 14 bases were substituted simultaneously in a single DNA molecule, with a low indel frequency of 0.6%, when 32 gRNAs were co-transfected. Collectively, our data show for the first time that RNA-guided cytidine deaminases are capable of programmable single and multiplex base editing in an invertebrate model.
Wireless Networking for Control and Automation of Off-road Equipment (1999)

This paper describes new wireless networking technology and its applications to off-road equipment. We present an overview of current wireless networking equipment as well as a description of a commercially available voice recognition package. We then demonstrate several examples of the use of wireless networking for control and automation on an agricultural platform. These examples include telecasting of vehicle information, control in a virtual environment, web-based steering control, and remote voice-based steering control. We conclude by listing several possibilities and extensions for this work.
Therapy for severe interstitial lung disease in systemic sclerosis. a retrospective study (1994)

This retrospective study shows that patients treated with CYC had a significant improvement in FVC over time. Prospective controlled studies of CYC treatment in early disease are necessary to determine if it can significantly alter the natural history of interstitial lung disease.