gebhart/patrepeval huggingface dataset:
Batch production of a silk-elastin-like protein in E. coli BL21(DE3): key parameters for optimisation (2013)

We have identified the optimal conditions for the shake flask production of a novel SELP with the final production levels obtained being the highest reported to date. While this study is focused on SELPs, we believe that it could also be of general interest to any study where the pET (ampicillin selective marker)-E. coli BL21(DE3) expression system is used. In particular, we show that induction time is critical in this system with, in contrast to that which is generally believed, optimal production being obtained by induction at the beginning of the stationary phase. Furthermore, we believe that we are at or near the maximum productivity for the system used, with rapid degradation of the selective agent by plasmid encoded β-lactamase, plasmid instability on induction and high acetate production levels being the principal limiting factors for further improved production.
Use of vasopressin in refractory hypotension in children with vasodilatory shock: Five cases and a review of the literature (2002)

This article describes case studies of five children treated with vasopressin for refractory hypotension. In addition, physiology and pharmacology of vasopressin are reviewed in a comprehensive survey of the literature from 1966 until the present. In all five children, blood pressure increased immediately after vasopressin administration. The preliminary success of vasopressin for hypotension the setting of vasodilatory shock is promising. This limited use of vasopressin in the setting of refractory hypotension in these patients appears to be safe; the appropriate patient population and dose regimen are not yet determined.
A Device for Dried Blood Microsampling in Quantitative Bioanalysis: Overcoming The Issues Associated Blood Hematocrit (2014)

The novel volumetric absorptive microsampling device has the potential to deliver the advantages of dried blood spot sampling while overcoming some of the issues associated with the technology.
Multiple dipole modeling and localization from spatio-temporal MEG data (1992)

An array of biomagnetometers may be used to measure the spatio-temporal neuromagnetic field or magnetoencephalogram (MEG) produced by neural activity in the brain. A popular model for the neural activity produced in response to a given sensory stimulus is a set of current dipoles, where each dipole represents the primary current associated with the combined activation of a large number of neurons located in a small volume of the brain. An important problem in the interpretation of MEG data from evoked response experiments is the localization of these neural current dipoles. We present here a linear algebraic framework for three common spatio-temporal dipole models: i) unconstrained dipoles, ii) dipoles with a fixed location, and iii) dipoles with a fixed orientation and location. In all cases, we assume that the location, orientation, and magnitude of the dipoles are unknown. With a common model, we show how the parameter estimation problem may be decomposed into the estimation of the time invariant parameters using nonlinear least-squares minimization, followed by linear estimation of the associated time varying parameters. A subspace formulation is presented and used to derive a suboptimal least-squares subspace scanning method. The resulting algorithm is a special case of the well-known MUltiple SIgnal Classification (MUSIC) method, in which the solution (multiple dipole locations) is found by scanning potential locations using a simple one dipole model. Principal components analysis (PCA) dipole fitting has also been used to individually fit single dipoles in a multiple dipole problem. Analysis is presented here to show why PCA dipole fitting will fail in general, whereas the subspace method presented here will generally succeed. Numerically efficient means of calculating the cost functions are presented, and problems of model order selection and missing moments are discussed. Results from a simulation and a somatosensory experiment are presented.
Purification of Recombinant Adeno-Associated Virus by Iodixanol Gradient Ultracentrifugation Allows Rapid and Reproducible Preparation of Vector Stocks for Gene Transfer in the Nervous System (1999)

Recombinant adeno-associated virus (rAAV) vectors have become attractive tools for in vivo gene transfer. The production and purification of high-titer rAAV vector stocks for experimental and therapeutic gene transfer continue to undergo improvement. Standard rAAV vector purification protocols include the purification of the vector by cesium chloride (CsCl)-density gradient centrifugation followed by extensive desalination via dialysis against a physiological buffer for in vivo use. These procedures are extremely time consuming and frequently result in a substantial loss of the infectious vector titer. As an alternative to CsCl we have investigated the use of Iodixanol, an X-ray contrast solution, as the density-gradient medium. Purification of rAAV vectors by Iodixanol shortened the centrifugation period to 3 hr and resulted in reproducible concentration and purification of rAAV-vector stocks. We show that injection of rAAV derived from an Iodixanol gradient can be used for in vivo gene transfer applications in the brain and spinal cord without detectable cytopathic effects and directing stable transgene expression for at least 2 months.
Gene transfer in astrocytes: Comparison between different delivering methods and expression of the HIV‐1 protein Nef (1999)

To identify a good system to introduce foreign genes into normal and tumoral astrocytes, we studied the efficiency of two chemical methods, calcium phosphate precipitation and lipofection, and of a viral-mediated transfer by a vector derived from the highly attenuated modified vaccinia virus Ankara (MVA). Using the β-galactosidase (β-gal) gene (lacZ) as reporter, we searched for optimal experimental conditions to obtain an efficient gene transfer into human embryonic and neonatal rat astrocytes and into a human astrocytoma cell line (U373 MG). The β-gal protein production was evaluated by cytochemical staining and enzymatic activity assay. Among chemical methods, lipofection was the most efficient system to transfect astrocytes in providing up to 60% of β-gal-positive cells in all the cell types analyzed. MVA infection also proved to be an efficient system to introduce heterologous genes into human embryonic astrocytes that appeared 80–100% positive 48–96 hr after an infection at a multiplicity of 1–10. In contrast, only a limited infection was observed with rat astrocytes, human astrocytoma cells, and human leptomeningeal cells. A recombinant MVA vector expressing the human immunodeficiency virus-1 (HIV-1) regulatory protein Nef was used to transfect human embryonic astrocytes, and the resulting Nef expression was compared with that detected after lipofection in the same cells. By Western blot analysis, Nef expression was observed in human astrocytes 24–96 hr after infection and was similar to that present in stably HIV-1–infected astrocytoma cells. Lipofection resulted in lower Nef expression. In spite of these promising results, the negative effects of MVA infection on cell viability and the possibility that a productive infection occurs in human embryonic astrocytes limit the use of this vector for gene delivery in developmentally immature human glial cells. J. Neurosci. Res. 55:569–577, 1999. © 1999 Wiley-Liss, Inc.
Amino Acid Active Esters. III. Base-Catalyzed Racemization of Peptide Active Esters1,2 (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAmino Acid Active Esters. III. Base-Catalyzed Racemization of Peptide Active Esters1,2Murray Goodman and Kenneth C. StuebenCite this: J. Org. Chem. 1962, 27, 10, 3409–3416Publication Date (Print):October 1, 1962Publication History Published online1 May 2002Published inissue 1 October 1962https://pubs.acs.org/doi/10.1021/jo01057a006https://doi.org/10.1021/jo01057a006research-articleACS PublicationsRequest reuse permissionsArticle Views992Altmetric-Citations39LEARN 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
PROANTHOCYANIDIN-FREE BARLEY-MALTING AND BREWING (1986)

Colloidal haze in beer is due to the precipitation of proteins by proanthocyanidins. Carlsberg Research Center reported in 1977 that the use of barley mutants which block the biosynthesis of catechins and proanthocyanidins in the grain prevents the formation of haze in beer. The results from ten years of malting and brewing research with proanthocyanidin-free barley and malt are reviewed.
The Primary Structure of Porcine Cu-Zn Superoxide Dismutase. Evidence for Allotypes of Superoxide Dismutase in Pigs (1985)

Cu-Zn superoxide dismutase was purified to homogeneity from mixed pig blood and from a single pig. The isolated product had an absorption ratio 280/260 nm of 0.91, a specific activity of 3 000 +/- 200 units (cytochrome c reduction test), and an isoelectric point of 7.5 (chromatofocusing) or 7.25 (isoelectric focusing), respectively. Sequence determination was performed by automated solid-phase Edman degradation of fragments of the reduced S-carboxymethylated proteins obtained by digestion with trypsin or Staphylococcus aureus proteinase V8 or treatment with cyanogen bromide. Acetylation of the N-terminus was confirmed by comparing high performance liquid chromatography retention times of N-terminal peptides with those of authentic samples. Sequencing of the superoxide dismutase of mixed porcine blood revealed heterogeneity (70% Leu; 30% Val at position 29), whereas the sample derived from a single French pig proved to be homogeneous (100% Leu at position 29). The complete sequence of pig superoxide dismutase comprised 152 amino-acid residues, which corresponds to a theoretical molecular mass of 15 800 Da per subunit, and exhibited the expected high homology with those of other mammals. The aspartate and all 7 histidine residues known to complex the metal ions in bovine superoxide dismutase are conserved in the porcine sequence at the homologous positions Asp82 and His45, His47, His62, His70, His79, His119, respectively.
Poly I:CLC Induction of the Interferon System in Mice: An Initial Study of Four Detection Methods (2002)

Induction of a large number of the components of the interferon (IFN) system (IFN genes, their mRNAs, IFN proteins, IFN receptors, IFN signaling molecules, the IFN response genes, and their effector proteins) has been studied. Less well studied is the comparative induction of these components in vivo. Induction of IFN by double-stranded RNA (dsRNA) treatment mimics certain aspects of viral infection and induces the components of the IFN system. To determine the comparative sensitivity of detection of induction in mice, we initially studied the limiting concentrations of polyribinosinic-polyribocytidylic acid, polylysine complex (poly I:CLC, a synthetic dsRNA preparation), for induction of four representative components of the IFN system: (1) IFN in serum, (2) the IFN response gene mRNA ISG54 in spleen and liver, (3) the IFN-beta mRNA in spleen, and (4) resistance of mice to Banzi viral infection. The results of this initial study showed that resistance to infection was 7-fold more sensitive for detection of the IFN response than was ISG54 mRNA and 70-fold more sensitive than either IFN-beta mRNA or IFN production in serum. In comparison, mouse cells in vitro treated with poly I:CLC were 3-10-fold less sensitive to its antiviral action than is the mouse. The results demonstrate that in the four tests in mice, the most sensitive indicator of poly I:CLC induction of the IFN system was protection against Banzi viral infection, followed by ISG54 mRNA levels, IFN-beta mRNA, and IFN protein levels. It is hypothesized that the highest sensitivity of mouse protection may be due to priming by the initial poly I:CLC-induced IFN of the subsequent Banzi virus-induced IFN, resulting in rapid and high concentrations of IFN at the local site of viral replication. Future studies are needed to study other molecular components of the IFN system to identify those that cause the unanticipated high sensitivity of mice to protection against Banzi virus.
Stress diagnostics and crack detection in full-size silicon wafers using resonance ultrasonic vibrations (2005)

Non-destructive monitoring of residual elastic stress in silicon wafers is a matter of strong concern for modern photovoltaic industry. The excess stress can generate cracks within the crystalline structure, which further may lead to wafer breakage. Cracks diagnostics and reduction in multicrystalline silicon, for example, are ones of the most important issues in photovoltaics now. The industry is intent to improve the yield of solar cells fabrication. There is a number of techniques to measure residual stress in semiconductor materials today. They include Raman spectroscopy, X-ray diffraction and infrared polariscopy. None of these methods are applicable for in-line diagnostics of residual elastic stress in silicon wafers for solar cells. Moreover, the method has to be fast enough to fit in solar cell sequential production line. In photovoltaics, fast in-line quality control has to be performed within two seconds per wafer to match the throughput of the production lines.\nDuring this Ph.D. research we developed the resonance ultrasonic vibration (RUV) approach to diagnose residual stress non-destructively in full-size multicrystalline silicon wafers used in solar cell manufacturing. This method is based on excitation of longitudinal resonance ultrasonic vibrations in the material using an external piezoelectric transducer combined with high sensitive ultrasonic probe and data acquisition of the frequency response to make the method suitable for in-line diagnostics during wafer and cell manufacturing. Theoretical and experimental analyses of the vibration mode in single crystal and multicrystalline silicon wafers were used to provide a benchmark reference analysis and validation of the approach. Importantly, we observed a clear trend of increasing resonance frequency of the longitudinal vibration mode with higher average in-plane stress obtained with scanning infrared polariscopy.\nUsing the same experimental approach we assessed a fast crack detection and length determination in full-size solar-grade crystalline silicon wafers. We demonstrated on a set of identical non-processed crystalline Si wafers with introduced periphery cracks that the crack shifts a selected RUV peak to a lower frequency and increases the resonance peak’s half-width. Both characteristics are gradually increased with the length of the crack. This was confirmed also theoretically by performing finite element analysis of longitudinal vibrations of wafers with cracks. The frequency shift and peak half-width were found to be reliable indicators of the crack appearance in silicon wafers suitable for mechanical quality control and fast wafer’s inspection.\nResonance ultrasonic vibrations metrology is a promising technique to provide quality control in full-size silicon wafers. This approach has the potential to be further developed into a diagnostic tool to address the needs of silicon wafer manufacturers, both in the microelectronic and the solar cell industries
Characterization of sheep afferent lymph dendritic cells and their role in antigen carriage. (1989)

We have ablated peripheral lymph nodes in sheep and subsequently cannulated the pseudo-afferent lymphatic vessel that arises as a consequence of afferent lymphatic vessels reanastomosing with the former efferent duct. This technique allows the collection of lymph with a cellular composition that resembles true afferent fluid, and in particular, containing 1-10% dendritic cells. A 16-h collection of this lymph may contain between 10(6) and 10(7) dendritic cells. This dendritic cell population may be enriched to greater than 75% by a single-density gradient centrifugation step. We have generated a mAb that recognizes sheep CD1. This monoclonal not only reacts with afferent dendritic cells, but with dendritic cells in the skin and paracortical T cell areas of lymph nodes. The expression of CD1 suggests afferent dendritic cells are related to skin Langerhans' cells and other dendritic cells that act as accessory cells for T cell responses. Consistent with this is the high level of expression by dendritic cells of molecules involved in antigen recognition by T cells, including MHC class I and class II. Afferent dendritic cells express high levels of the cellular adhesion molecule LFA-3, and at the same time express a ligand for this molecule, namely CD2. The accessory functions of afferent dendritic cells resemble those displayed by mature Langerhans' cells and by lymph node interdigitating cells. These include clustering with resting T cells and stimulating their proliferation in a primary response to antigen. Afferent dendritic cells are capable of acquiring soluble protein antigen in vivo or in vitro and presenting the material directly to autologous T cells in an antigen-specific manner. We conclude that afferent dendritic cells represent a lymph-borne Langerhans' cell involved in antigen carriage to the lymph node.
Mild iron deficiency does not ameliorate the phenotype of a murine erythropoietic protoporphyria model (2020)

Reduced ferrochelatase activity in erythropoietic protoporphyria (EPP) causes the accumulation of protoporphyrin IX (PPIX) leading to acute cutaneous photosensitivity and liver injury. Many EPP patients also have a mild hypochromic, microcytic anemia and iron deficiency. Iron deficiency can lead to decreased PPIX accumulation in another erythropoietic porphyria, congenital erythropoietic porphyria (CEP). Expression of the iron regulatory peptide hepcidin is negatively regulated by the serine protease TMPRSS6. Hepcidin induction by siRNA-mediated inhibition of TMPRSS6 expression reduces iron availability and induces iron deficiency. To interrogate the therapeutic potential of iron deficiency to modify EPP, we treated an ethylnitrosourea-induced mouse model of EPP, Fech <sup>m1Pas</sup> , with a GalNAc-conjugated Tmprss6 siRNA and PPIX levels, anemia and iron parameters were monitored. The GalNAc-RNAi therapeutic reduces Tmprss6 expression and induces mild iron deficiency in Fech <sup>m1Pas</sup> animals. However, decreases in erythrocyte PPIX levels and liver PPIX accumulation were not seen. These results indicate short-term induction of iron deficiency, at least in a murine model of EPP, does not lead to decreased PPIX production.
Mechanical properties of shale-gas reservoir rocks — Part 2: Ductile creep, brittle strength, and their relation to the elastic modulus (2013)

ABSTRACT We studied the elastic moduli, ductile creep behavior, and brittle strength of shale-gas reservoir rocks from Barnett, Haynesville, Eagle Ford, and Fort St. John shale in a series of triaxial laboratory experiments. We found a strong correlation between the shale compositions, in particular, the volume of clay plus kerogen and intact rock strength, frictional strength, and viscoplastic creep. Viscoplastic creep strain was approximately linear with the applied differential stress. The reduction in sample volume during creep suggested that the creep was accommodated by slight pore compaction. In a manner similar to instantaneous strain, there was more viscoplastic creep in samples deformed perpendicular to the bedding than parallel to the bedding. The tendency to creep also correlated well with the static Young’s modulus. We explained this apparent correlation between creep behavior and elastic modulus by appealing to the stress partitioning that occurs between the soft components of the shales (clay and kerogen) and the stiff components (quartz, feldspar, pyrite, and carbonates). Through a simple 1D analysis, we found that a unique relation between the creep compliance and elastic modulus, independent of composition and orientation, can be established by considering the individual creep behavior of the soft and stiff components that arises from the stress partitioning within the rock. This appears to provide a mechanical explanation for why long-term ductile deformational properties can appear to correlate with short-term elastic properties in shale-gas reservoir rocks.
Comparison of dry etch techniques for GaN (1996)

Dry etching of GaN in Cl2/H2/CH4/Ar has been compared using electron cyclotron resonance (ECR), inductively coupled plasma (ICP), and reactive ion etch (RIE) systems. GaN etch rates and surface morphology were obtained as a function of RF power, and showed significant improvements under high density plasma conditions.
Active stage of autoimmune diabetes is associated with the expression of a novel cytokine, IGIF, which is located near Idd2. (1997)

Recently, interferon-gamma-inducing-factor (IGIF) has been described as a novel monokine that is a more potent interferon-gamma (IFN-gamma) inducer than IL-12. By cloning IGIF from affected tissue and studying IGIF gene expression, we describe for the first time a close association of this cytokine with an autoimmune disease. The non-obese diabetic (NOD) mouse spontaneously develops autoimmune insulitis and diabetes which can be accelerated and synchronized by a single injection of cyclophosphamide. IGIF mRNA was demonstrated by reverse transcriptase PCR in NOD mouse pancreas during early stages of insulitis. Levels of IGIF mRNA increased rapidly after cyclophosphamide treatment and preceded a rise in IFN-gamma mRNA, and subsequently diabetes. Interestingly, these kinetics mimick that of IL-12p40 mRNA, resulting in a close correlation of individual mRNA levels. Cloning of the IGIF cDNA from pancreas RNA followed by sequencing revealed identity with the IGIF sequence cloned from Kupffer cells and in vivo preactivated macrophages. When extending our study to macrophages of the spleen we observed that NOD mouse macrophages responded to cyclophosphamide with IGIF gene expression while macrophages from Balb/c mice treated in parallel did not. The IGIF gene position is located within the Idd2 interval on mouse chromosome 9 and therefore it is a candidate for the Idd2 susceptible gene. We conclude that IGIF expression is abnormally regulated in autoimmune NOD mice and closely associated with diabetes development.