gebhart/patrepeval huggingface dataset:
Unusual Helix-Containing Greek Keys in Development-Specific Ca2+-Binding Protein S. 1H, 15N, and 13C Assignments and Secondary Structure Determined with the Use of Multidimensional Double and Triple Resonance Heteronuclear NMR Spectroscopy (1994)

Multidimensional heteronuclear NMR spectroscopy has been used to determine almost complete backbone and side-chain 1H, 15N, and 13C resonance assignments of calcium loaded Myxococcus xanthus protein S (173 residues). Of the range of constant-time triple resonance experiments recorded, HNCACB and CBCA(CO)NH, which correlate C alpha and C beta with backbone amide resonances of the same and the succeeding residue respectively, proved particularly useful in resolving assignment ambiguities created by the 4-fold internal homology of the protein S amino acid sequence. Extensive side-chain 1H and 13C assignments have been obtained by analysis of HCCH-TOCSY and 15N-edited TOCSY-HMQC spectra. A combination of NOE, backbone amide proton exchange, 3JNH alpha coupling constant, and chemical shift data has been used to show that each of the protein S repeat units consists of four beta-strands in a Greek key arrangement. Two of the Greek keys contain a regular alpha-helix between the third and fourth strands, resulting in an unusual and possibly unique variation on this common folding motif. Despite similarity between two nine-residue stretches in the first and third domains of protein S and one of the Ca(2+)-binding sequences in bovine brain calmodulin [Inouye, S., Franceschini, T., & Inouye, M. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 6829-6833], the protein S topology in these regions is incompatible with an EF-hand calmodulin-type Ca(2+)-binding site.
Spreadsheet functional programming (2007)

Abstract The functional programming community has shown some interest in spreadsheets, but surprisingly no one seems to have considered making a standard spreadsheet, such as Excel, work with a standard functional programming language, such as Haskell. In this paper, we show one way that this can be done. Our hope is that by doing so, we might get spreadsheet programmers to give functional programming a try.
MOCVD growth of BaTiO/sub 3/ in an 8" single-wafer CVD reactor (2003)

A reduced-pressure MOCVD (metal-organic chemical vapor deposition) process for the growth of BaSrTiO/sub 3/ thin films was developed in a 2-in inverted-vertical reactor was developed, and preliminary studies were carried out to scale this process to a commercially available single-wafer tool. Novel process technology was used as the CVD sources were dissolved in a liquid which was measured into a vaporizer with a high-precision pump. Implementation of this process gave uniform deposition of perovskite-phase BaTiO/sub 3/ over the entire surface of a 150-mm Pt-metallized Si wafer. These films exhibited crystallographic texture in the
Complete FcRn dependence for intravenous Ig therapy in autoimmune skin blistering diseases (2005)

Numerous mechanisms of action have been proposed for intravenous Ig (IVIG). In this study, we used IgG passive transfer murine models of bullous pemphigoid (BP), pemphigus foliaceus (PF), and pemphigus vulgaris (PV) to test the hypothesis that the effect of IVIG in autoantibody-mediated cutaneous bullous diseases is to accelerate the degradation of pathogenic IgG by saturation of the MHC-like Fc receptor neonatal Fc receptor (FcRn). BP, PF, and PV are organ-specific antibody-mediated diseases in which autoantibodies target the hemidesmosomal antigen BP180 and desmosomal antigens Dsg1 and Dsg3, respectively. Antibodies against BP180, Dsg1, and Dsg3, when injected into neonatal mice, induce the BP, PF, and PV disease phenotypes, respectively. We found that FcRn-deficient mice were resistant to experimental BP, PF, and PV. Circulating levels of pathogenic IgG in FcRn-deficient mice were significantly reduced compared with those in WT mice. Administration of high-dose human IgG (HDIG) to WT mice also drastically reduced circulating pathogenic IgG levels and prevented blistering. In FcRn-deficient mice, no additional protective effect with HDIG was realized. These data demonstrate that the therapeutic efficacy of HDIG treatment in the pemphigus and pemphigoid models is dependent on FcRn. Thus, FcRn is a promising therapeutic target for treating such IgG-mediated autoimmune diseases.
Minimizing information overload: the ranking of electronic messages (1989)

The decision to examine a message at a particular point in time should be made rationally and economically if the mes sage recipient is to operate efficiently. Electronic message distribution systems, electronic bulletin board systems, and telephone systems capable of leaving digitized voice messages can contribute to "information overload", defined as the eco nomic loss associated with the examination of a number of non- or less-relevant messages. Our model provides a formal method for minimizing expected information overload. The proposed adaptive model predicts the usefulness of a message based on the available message features and may be useful to rank messages by expected importance or economic worth. The assumptions of binary and two Poisson indepen dent probabilistic distributions of message feature frequencies are examined, and methods of incorporating these distributions into the ranking model are examined. Ways to incorporate user supplied relevance feedback are suggested. Analytic perfor mance measures are proposed to predict system quality. Other message handling models, including rule based expert systems, are seen as special cases of the model. The performance is given for a set of UNIX shell programs which rank USENET messages. Problems with the use of this formal model are examined, and areas for future research are suggested.
STUDY OF HEAT TRANSFER THROUGH MULTILAYER CLOTHING ASSEMBLIES: A THEORETICAL PREDICTION (2011)

Abstract It has long been recognised that heat transfer through clothing is a main constraint to the comfort properties of clothing. The present work relates to the development of a mathematical model for the prediction of heat transmission through multilayer clothing with air in between two successive layers of fabric in a multilayered clothing assembly. A mathematical model was developed using general equations of heat transfer through porous media and was validated using experimental results. A series of multilayered fabric assemblies were created with different combinations of fabric layers and air gaps of different thicknesses. The predicted total thermal resistance of these fabric assemblies was obtained from the model and the values were compared with experimental results. The total thermal resistance of these fabric assemblies were measured using a guarded hot plate for validating the model. Fairly good correlations between the predicted and experimental values of thermal resistance were observed.
Control of polyhydroxyalkanoate synthesis in Azotobacter vinelandii strain UWD (1994)

To better understand the reasons for the hyper-accumulation of polyhydroxyalkanoate (PHA) in mutant Azotobacter vinelandii UWD, the kinetic properties of 3-ketothiolase, acetoacetyl-CoA reductase, and β-hydroxybutyrate dehydrogenase were examined. The regulation of the condensation of acetyl-CoA mediated by 3-ketothiolase was normal, in that it was negatively regulated by free CoA, but inhibition was overcome by higher concentrations of acetyl-CoA. Acetoacetyl-CoA from this reaction was reduced to 3-hydroxybutyryl-CoA by an NADPH-specific acetoacetyl-CoA reductase. This enzyme also reduced 3-ketovaleryl-CoA derived from the β-oxidation of C5, C7 or C9 n-alkanoates, but at only 16% of the rate found with the C4-substrate. The acetoacetyl-CoA reductase was determined to be an allosteric enzyme that bound NADPH and acetoacetyl-CoA at multiple binding sites in a general hybrid Ping-Pong random mechanism. The enzyme was negatively regulated by acetoacetyl-CoA, but this was overcome at high concentrations of NADPH. The activity of pyridine nucleotide transhydrogenase was determined to be important for the conversion of NADH in these mutant cells to NADPH and for decreasing the availability of NADP+, which was a negative regulator of the acetoacetyl-CoA reductase. The combination of high acetoacetyl-CoA, the UWD mutation, transhydrogenase activity, and high NADPH appeared to be the conditions promoting PHA formation by strain UWD during active growth on glucose. Degradation of PHA in strain UWD did not appear to be regulated at the level of β-hydroxybutyrate dehydrogenase. This enzyme was unaffected by NADH, was inhibited only 13% by pyruvate and its activity was enhanced by NADPH. The thiolysis of acetoacetyl-CoA also was unusual, in that 3-ketothiolase was not inhibited by acetoacetyl-CoA, but free CoA was a competitive inhibitor in a bireactant Ping-Pong mechanism. This inhibition was overcome by higher concentrations of the normal first substrate, acetoacetyl-CoA. Thus a single thiolase was used for the condensation of acetyl-CoA and the thiolysis of acetoacetyl-CoA, derived from PHA depolymerization or from the β-oxidation of n-alkanoates.
Direct Preparation of 3-Thienyl Organometallic Reagents:  3-Thienylzinc and 3-Thienylmagnesium Iodides and 3-Thienylmanganese Bromides and Their Coupling Reactions (1997)

3-Thienylzinc and 3-thienylmagnesium iodides can be generated from the direct oxidative addition of Rieke zinc and magnesium to 3-iodothiophene, respectively. The direct preparation of 3-thienylmanganese bromides from the reaction of Rieke manganese with 3-bromothiophene and 3,4-dibromothiophene is also performed. These 3-thienyl organometallic reagents have been found to be regiostable intermediates and undergo coupling reactions with a variety of versatile electrophiles such as acid chlorides, aryl iodides, aldehydes, and disulfide.
Supplementation of N -Acetylcysteine Fails to Increase Glutathione in Lymphocytes and Plasma of Patients with AIDS (1995)

Because glutathione (GSH) in plasma and lymphocytes of HIV-infected patients is low, adjunct therapy with N-acetylcysteine (NAC) to restore GSH homeostasis has been proposed. To investigate the effect of NAC on the GSH status we treated six patients with AIDS with 1.8 g/day of NAC for 2 weeks. During treatment the plasma concentration of cysteine, a precursor for GSH synthesis, increased significantly. Nevertheless, there was no significant increase in GSH in plasma and peripheral blood mononuclear cells. The failure of sulfhydryl supplementation to increase GSH suggests that the low concentrations of the tripeptide are not the result of an increased consumption secondary to an oxidant stress, but rather the consequence of a decreased rate of synthesis of GSH in HIV infection.
Polymer substrates for controlled biological interactions (1994)

The identification of a myriad of small peptide and carbohydrate ligands recognized by cell surface receptors has generated enthusiasm for the use of these ligands of components of biomaterials for controlling cellular interactions. Achieving control of cell interactions via ligand modification of materials also requires that nonspecific interactions of cells with these materials due to surface adsorption of biological macromolecules is minimized. Polyethylene oxide (PEO) exhibits extraordinary inertness toward most biological macromolecules and is thus receiving increasing attention as a component of new materials for controlling cell behavior. Both surface and bulk modifications with PEO are being applied to develop a range of bland substrate materials as vehicles for ligand immobilization.
Myogenic satellite cells: physiology to molecular biology (2001)

Adult skeletal muscle has a remarkable ability to regenerate following myotrauma. Because adult myofibers are terminally differentiated, the regeneration of skeletal muscle is largely dependent on a small population of resident cells termed satellite cells. Although this population of cells was identified 40 years ago, little is known regarding the molecular phenotype or regulation of the satellite cell. The use of cell culture techniques and transgenic animal models has improved our understanding of this unique cell population; however, the capacity and potential of these cells remain ill-defined. This review will highlight the origin and unique markers of the satellite cell population, the regulation by growth factors, and the response to physiological and pathological stimuli. We conclude by highlighting the potential therapeutic uses of satellite cells and identifying future research goals for the study of satellite cell biology.
Genetic factors predicting response to interferon treatment for viral hepatitis C (2008)

Since completion of the human genome and HapMap projects it is likely that an increasing number of studies dealing with genetic associations in specific diseases will be published in medical journals. Hepatitis C and especially its response to antiviral treatment does not constitute an exception to this rule. It has been known for quite a long time that viral factors such as genotype and viral load have a major influence on the outcome of antiviral treatment.1 Nevertheless, researchers have become increasingly aware that host genetic factors including ethnicity, human leucocyte antigens, cytokine production and differences in T cell immune responses can modulate the response to antiviral treatment and viral clearance.2 3 In this issue of Gut ( see page 10.1136/gut.2007.129478 ), Persico et al report on single nucleotide polymorphisms (SNPs) of suppressor of cytokine signalling 3 (SOCS3) being positively and negatively associated with response to antiviral therapy in hepatitis C virus (HCV) genotype-1-infected patients.4 Interestingly, these data were generated from peripheral mononuclear blood cells (PMBCs), a material that would be easily available for large-scale studies in the future. The concept of SOCS3 being involved in modulating antiviral response mechanisms is appealing to the scientific community. SOCS3 acts as a negative regulator of the cytokine-induced JAK–STAT (Janus kinase–signal transducer and activator of transcription) pathway. As a consequence of a classical negative feedback circuit, SOCS3 inhibits the cytokine receptor-associated JAK tyrosine kinase through either direct interaction with JAKs or indirect inhibition by binding to specific sites on the receptor.5 6 Inhibition of JAKs leads in turn to deficient STAT phosphorylation and dimerisation required for nuclear translocation of STATs and ultimately to blockage of transcriptional activity of STAT-responsive genes involved in regulation of immune responses and maintaining immunological homeostasis.6 Interferons (IFNs) are naturally occurring proteins that induce an antiviral state …
Antibody response to the pneumococcal proteins pneumococcal surface adhesin A and pneumolysin in children with acute otitis media (2001)

We showed that infants are capable of developing a specific antibody response to the pneumococcal proteins PsaA and Ply during AOM.
Clogging-free microfluidics for continuous size-based separation of microparticles (2016)

In microfluidic filtration systems, one of the leading obstacles to efficient, continuous operation is clogging of the filters. Here, we introduce a lateral flow microfluidic sieving (μ-sieving) technique to overcome clogging and to allow continuous operation of filter based microfluidic separation. A low frequency mechanical oscillation was added to the fluid flow, which made possible the release of aggregated unwanted polystyrene (PS) particles trapped between the larger target PS particles in the filter demonstrating continuous μ-sieving operation. We achieved collection of the target PS particles with 100% separation efficiency. Also, on average, more than 98% of the filtered target particles were retrieved after the filtration showing high retrieval rates. Since the oscillation was applied to the fluid but not to the microfluidic filter system, mechanical stresses to the system was minimized and no additional fabrication procedures were necessary. We also applied the μ-sieving technique to the separation of cancer cells (MDA-MB-231) from whole blood and showed that the fluidic oscillations prevented the filters from being blocked by the filtered cancer cells allowing continuous microfluidic separation with high efficiency.
Chemicopharmacological Studies on Antispasmodic Action. XII. Structure-Activity Relationship of Aralkylamines. (1958)

1. Fifty-eight aralkylamines were tested for atropine-like activity against acetylcholine-stimulated ileal strips of mice. 2. Papaverine-like activity of the aralkylamines was tested against excess acetylcholine-stimulated ileal strips of mice. 3. The relationship between chemical structure and pharmacological activity has been discussed. In almost all the compounds tested here, atropine-like activities change somewhat parallel with the papaverine-like activities of the compounds. The effect of quaternization of tertiary amines is the only exception, where the quaternary ammonium compounds have stronger atropine-like and weaker papaverine-like action than the corresponding tertiary amines. It is suggested that some physicochemical properties such as lipoid solubility would influence the papaverine-like activity and also participate even in intensifying the atropine-like antiacetylcholine activity.
Treat LPGs with Amines (1997)

In recent years, there has been increasing interest in sweetening liquefied petroleum gases (LPGs) with amines. However, limited data and design information are available in the literature. This article reviews the fundamental aspects of LPG amine treaters and includes guidelines, design considerations and alternatives for static mixers, jet eductor mixers and columns with structured packing, random packing and sieve trays. All of these current design methods are compared based on plant operating data. Guidelines are given for sweetening LPGs with amines including amine type, concentration, filtration, temperature, loading, circulation rate and water-wash systems. Also covered is the contacting method used in the absorber. Any of the commonly available amines such as monoethanolamine (MEA), diethanolamine (DEA), diglycolamine (DGA), methyl diethanolamine (MDEA) and MDEA-based solvents usually perform satisfactorily. Design criteria for distributors and LPG disperser plates, amine filtration and LPG settlers and coalescers are important. The contacting method is also important and includes jet eductor mixers, static mixers, and columns with sieve trays, random packing and structured packing.
Expression of Recombinant Antibodies (2013)

Recombinant antibodies are highly specific detection probes in research, diagnostics, and have emerged over the last two decades as the fastest growing class of therapeutic proteins. Antibody generation has been dramatically accelerated by in vitro selection systems, particularly phage display. An increasing variety of recombinant production systems have been developed, ranging from Gram-negative and positive bacteria, yeasts and filamentous fungi, insect cell lines, mammalian cells to transgenic plants and animals. Currently, almost all therapeutic antibodies are still produced in mammalian cell lines in order to reduce the risk of immunogenicity due to altered, non-human glycosylation patterns. However, recent developments of glycosylation-engineered yeast, insect cell lines, and transgenic plants are promising to obtain antibodies with "human-like" post-translational modifications. Furthermore, smaller antibody fragments including bispecific antibodies without any glycosylation are successfully produced in bacteria and have advanced to clinical testing. The first therapeutic antibody products from a non-mammalian source can be expected in coming next years. In this review, we focus on current antibody production systems including their usability for different applications.
High Glycolytic Flux Improves Pyruvate Production by a Metabolically Engineered Escherichia coli Strain (2008)

We report pyruvate formation in Escherichia coli strain ALS929 containing mutations in the aceEF, pfl, poxB, pps, and ldhA genes which encode, respectively, the pyruvate dehydrogenase complex, pyruvate formate lyase, pyruvate oxidase, phosphoenolpyruvate synthase, and lactate dehydrogenase. The glycolytic rate and pyruvate productivity were compared using glucose-, acetate-, nitrogen-, or phosphorus-limited chemostats at a growth rate of 0.15 h(-1). Of these four nutrient limitation conditions, growth under acetate limitation resulted in the highest glycolytic flux (1.60 g/g . h), pyruvate formation rate (1.11 g/g h), and pyruvate yield (0.70 g/g). Additional mutations in atpFH and arcA (strain ALS1059) further elevated the steady-state glycolytic flux to 2.38 g/g h in an acetate-limited chemostat, with heterologous NADH oxidase expression causing only modest additional improvement. A fed-batch process with strain ALS1059 using defined medium with 5 mM betaine as osmoprotectant and an exponential feeding rate of 0.15 h(-1) achieved 90 g/liter pyruvate, with an overall productivity of 2.1 g/liter h and yield of 0.68 g/g.
Mo-O bond doping and related-defect assisted enhancement of photoluminescence in monolayer MoS2 (2014)

In this work, we report a strong photoluminescence (PL) enhancement of monolayer MoS2 under different treatments. We find that by simple ambient annealing treatment in the range of 200 °C to 400 °C, the PL emission can be greatly enhanced by a factor up to two orders of magnitude. This enhancement can be attributed to two factors: first, the formation of Mo-O bonds during ambient exposure introduces an effective p-doping in the MoS2 layer; second, localized electrons formed around Mo-O bonds related defective sites where the electrons can be effectively localized with higher binding energy resulting in efficient radiative excitons recombination. Time resolved PL decay measurement showed that longer lifetime of the treated sample consistent with the higher quantum efficiency in PL. These results give more insights to understand the luminescence properties of the MoS2.
Microfluidic Systems for Biosensing (2010)

In the past two decades, Micro Fluidic Systems (MFS) have emerged as a powerful tool for biosensing, particularly in enriching and purifying molecules and cells in biological samples. Compared with conventional sensing techniques, distinctive advantages of using MFS for biomedicine include ultra-high sensitivity, higher throughput, in-situ monitoring and lower cost. This review aims to summarize the recent advancements in two major types of micro fluidic systems, continuous and discrete MFS, as well as their biomedical applications. The state-of-the-art of active and passive mechanisms of fluid manipulation for mixing, separation, purification and concentration will also be elaborated. Future trends of using MFS in detection at molecular or cellular level, especially in stem cell therapy, tissue engineering and regenerative medicine, are also prospected.
Frequent 7q gains in flow cytometric multiploid/hypertetraploid breast carcinomas: a study of chromosome imbalances by comparative genomic hybridisation (2006)

There is a very high incidence of genetic aberrations, mainly related to chromosomal gains, in this subgroup of aneuploid breast cancer patients, associated with a poor clinical outcome. The 7q locus, not previously reported as showing frequent changes in breast cancer, was found to be a potential site for some candidate oncogenes.