gebhart/patrepeval huggingface dataset:
Bioprocess Engineering: Kinetics, Mass Transport, Reactors and Gene Expression (1994)

Classical Biotechnology. Enzyme Technology. Enzyme and Cell Based Reactors. Bioprocess Kinetics. Bioprocess Optimization and Control: Antibiotic Case Study. The New Biotechnology. Transcription and Translation of the Genetic Code. Immobilized Recombinant Microbial Cell Cultures and Bioreactors. Gene Expression with Animal Cells. Gene Expression with Plant Cells. Appendices. Postscript. Indexes.
Evaluation of Cell Proliferation in Rat Tissues with BrdU, PCNA, Ki-67(MIB-5) Immunohistochemistry and In Situ Hybridization for Histone mRNA (2003)

The standard method for assessment of cell proliferation in paraffin-embedded tissue sections is 5-bromodeoxyuridine (BrdU) immunohistochemistry (IHC). BrdU can be administered to laboratory animals via IP injections, is readily incorporated into nuclei during the DNA synthetic phase of the cell cycle, and is detected with an anti-BrdU antibody. This method has several disadvantages, and an accurate method for evaluation of proliferative activity that can substitute for BrdU IHC, when necessary, is of great interest to investigators. Alternative methods for detection of proliferating cells in tissue sections are proliferating cell nuclear antigen (PCNA) IHC, Ki-67 IHC, and in situ hybridization (ISH) for histone mRNA. To determine the optimal choice, we analyzed the correlation of anti-PCNA, anti-Ki-67(MIB-5), and histone mRNA labeling indices (LIs) with anti-BrdU LI in rat highly replicative (renewing) tissues. The correlation between anti-BrdU and histone mRNA LIs, as well as the correlation between anti-BrdU and anti-Ki-67 LIs, was statistically significant. There was no significant correlation between anti-BrdU and anti-PCNA LIs. These results suggest that both ISH for histone mRNA and IHC with MIB-5 are preferable techniques for assessment of cell proliferation in rat paraffin-embedded renewing tissues compared to PCNA IHC. They can substitute for BrdU IHC when necessary.
Decision rules and variance of response in breeding schemes (1993)

Abstract Selection decisions in breeding schemes can involve choices between candidates evaluated to different accuracies. A Bayesian framework is put forward for choosing among candidates, and it is shown that attaching loss functions for estimation errors makes this process different from selecting upon best linear unbiased predictions alone. Examples are given using both linear and quadratic loss to show that when estimation errors are penalized, the selection process tends to select more unrelated and more accurately evaluated individuals. In a dairy cattle breeding scheme response was only slightly lower than that from selection on expected breeding values but with a much reduced coefficient of variation. However, if prediction errors are preferred, with the hope of selecting individuals whose breeding value are higher than expected, extra genetic progress could be obtained by favouring the selection of individuals with low accuracy. This requires consideration of more than a single generation. With discrete generations and equal measurements on candidates the decision framework was shown to be equivalent to a single quadratic restriction on the selection scores of parents in the previous generation. A framework based on Bayes decision theory could be simply applied to produce a flexible means for producers to select according to their individual risk preferences.
EEG reveals divergent paths for speech envelopes during selective attention (2011)

This paper reports the results of an experiment that was designed to determine the effects of attention on the representation of speech signal envelopes in EEG. We recorded EEG while subjects attended to one of two concurrently presented and spatially separated speech streams. Cross- correlating the speech envelope with signals from individual EEG channels reveals clear differences between the neural representations of the envelopes of attended and unattended speech. The two concurrently presented speech signals were amplitude modulated at 40 and 41 Hz, respectively, in order to investigate the effects of attention on speech signal gain. The modulations elicited strong steady-stage responses that showed no effects of attention. We conclude that the differences between the representations in EEG of the envelopes of attended and unattended speech reflect some form of top-down attentional control.
Solution-phase immunoassay for determination of cortisol in serum by capillary electrophoresis (1995)

We describe a competitive solution-phase immunoassay for serum cortisol determination that involves capillary electrophoresis (CE) combined with laser-induced fluorescence for separation and quantification. A polyclonal antibody preparation and fluorescein-labeled cortisol are used as assay reagents. 8-Anilino-1-naphthalenesulfonic acid was added to the serum sample during the assay to promote the release of cortisol from endogenous binding proteins. Conditions for the rapid separation of free and bound labeled antigen by CE were developed. Aspects of assay performance are evaluated in this report. The resulting assay protocol allows for the analysis of serum samples without extraction or other sample preparation steps.
Pleiotropic effects of cAMP on germination, antibiotic biosynthesis and morphological development in Streptomyces coelicolor (1998)

In wild-type Streptomyces coelicolor MT1110 cultures, cyclic adenosine 3',5' monophosphate (cAMP) was synthesized throughout the developmental programme with peaks of accumulation both during germination and later when aerial mycelium and actinorhodin were being produced. Construction and characterization of an adenylate cyclase disruption mutant (BZ1) demonstrated that cAMP facilitated these developmental processes. Although pulse-labelling experiments showed that a similar germination process was initiated in BZ1 and MT1110, germ-tube emergence was severely delayed in BZ1 and never occurred in more than 85% of the spores. Studies of growth and development on solid glucose minimal medium (SMMS, buffered or unbuffered) showed that MT1110 and BZ1 produced acid during the first rapid growth phase, which generated substrate mycelium. Thereafter, on unbuffered SMMS, only MT1110 resumed growth and produced aerial mycelium by switching to an alternative metabolism that neutralized its medium, probably by reincorporating and metabolizing extracellular acids. BZ1 was not able to neutralize its medium or produce aerial mycelium on unbuffered SMMS; these defects were suppressed by high concentrations (>1 mM) of cAMP during early growth or on buffered medium. Other developmental mutants (bldA, bldB, bldC, bldD, bldG) also irreversibly acidified this medium. However, these bald mutants were not suppressed by exogenous cAMP or neutralizing buffer. BZ1 also differentiated when it was cultured in close proximity to MT1110, a property observed in cross-feeding experiments between bald mutants and commonly thought to reflect diffusion of a discrete positively acting signalling molecule. In this case, MT1110 generated a more neutral pH environment that allowed BZ1 to reinitiate growth and form aerial mycelium. The fact that actinorhodin synthesis could be induced by concentrations of cAMP (< 20 microM) found in the medium of MT1110 cultures, suggested that it may serve as a diffusible signalling molecule to co-ordinate antibiotic biosynthesis.
Computer Aided Tissue Engineering for Modeling and Design of Novel Tissue Scaffolds (2004)

Computer-Aided Design and Applications is an international journal on the applications of CAD and CAM. It publishes papers in the general domain of CAD plus in emerging fields like bio-CAD, nano-CAD, soft-CAD, garment-CAD, PLM, PDM, CAD data mining, CAD and the internet, CAD education, genetic algorithms and CAD engines. The journal is aimed at all developers and users of CAD technology to ptovide CAD solutions for various stages of design and manufacturing. The journal publishes all about Computer-Aided Design and Computer-Aided technologies.
Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors (2016)

Aberrant activation of the complement system is associated with diseases, including paroxysmal nocturnal hemoglobinuria and age-related macular degeneration. Complement factor D is the rate-limiting enzyme for activating the alternative pathway in the complement system. Recent development led to a class of potent amide containing pyrrolidine derived factor D inhibitors. Here, we used biochemical enzymatic and biolayer interferometry assays to demonstrate that the amide group improves the inhibitor potency by more than 80-fold. Our crystal structures revealed buried hydrogen bond interactions are important. Molecular orbital analysis from quantum chemistry calculations dissects the chemical groups participating in these interactions. Free energy calculation supports the differential contributions of the amide group to the binding affinities of these inhibitors. Cell-based hemolysis assay confirmed these compounds inhibit factor D mediated complement activation via the alternative pathway. Our study highlights the important interactions contributing to the high potency of factor D inhibitors reported recently.
Simple and Efficient Synthesis of Various Alkoxyamines for Stable Free Radical Polymerization (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTSimple and Efficient Synthesis of Various Alkoxyamines for Stable Free Radical PolymerizationKrzysztof Matyjaszewski, Brian E. Woodworth, Xuan Zhang, Scott G. Gaynor, and Zack MetznerView Author Information Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213 Cite this: Macromolecules 1998, 31, 17, 5955–5957Publication Date (Web):August 5, 1998Publication History Received7 May 1998Revised29 June 1998Published online5 August 1998Published inissue 1 August 1998https://pubs.acs.org/doi/10.1021/ma9807264https://doi.org/10.1021/ma9807264rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views2894Altmetric-Citations218LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Halogens,Inorganic compounds,Radical polymerization,Reaction products,Styrenes Get e-Alerts
The regulation of cytoplasmic pH in human fibroblasts. (1984)

The regulation of cytoplasmic pH (pHi) has been examined in normal human foreskin fibroblasts (HF cells) using a fluorometric technique for continuously monitoring rapid pHi transients. We previously reported that pHi in HF cells is rapidly raised by growth factors due to activation of a Na+/H+ exchange mechanism in the plasma membrane ( Moolenaar , W. H., Tsien , R. Y., van der Saag , P. T., and de Laat , S. W. (1983) Nature (Lond.) 304, 645-648). Here we characterize the ionic basis of pHi homeostasis in quiescent HF cells. When HF cells are acid-loaded by externally applied weak acids or by pretreatment with NH4+, pHi immediately recovers toward its resting value (approximately 7.05). pHi recovery follows an exponential time course and is accompanied by enhanced Na+ influx and net H+ extrusion. Recovery of pHi and concomitant Na+/H+ fluxes are reversibly inhibited by amiloride (half-maximal effect at approximately 0.1 mM). The rate of pHi recovery from an acid load depends on external Na+ (half-maximal rate at approximately 35 mM), but is independent of external anions (HCO3-, Cl-) and is not affected by membrane depolarization. Li+ can substitute for Na+ in pHi recovery. In Na+-free media, pHi spontaneously falls to a new resting value, from which it rapidly recovers after readdition of Na+. A stepwise increase in external pH (pHo) accelerates pHi recovery from an acid load and raises the resting pHi by approximately 50% of the pHo shift. The response of pHi to alkaline pHo shifts is abolished by amiloride and by Na+ removal. It is concluded that pHi in HF cells is closely regulated by an amiloride-sensitive, reversible Na+/H+ exchanger, which is driven by the transmembrane concentration gradients for Na+ and H+. Under normal conditions, the exchanger appears to be relatively inactive, while its rate is increasingly stimulated by lowering pHi or by raising pHo.
Acetylcarnitine induces heme oxygenase in rat astrocytes and protects against oxidative stress: Involvement of the transcription factor Nrf2 (2005)

Efficient functioning of maintenance and repair processes seem to be crucial for both survival and physical quality of life. This is accomplished by a complex network of the so-called longevity assurance processes, under control of several genes termed vitagenes. These include members of the heat shock protein system, and there is now evidence that the heat shock response contributes to establishing a cytoprotective state in a wide variety of human conditions, including inflammation, neurodegenerative disorders, and aging. Among the various heat shock proteins, heme oxygenase-1 has received considerable attention; it has been recently demonstrated that heme oxygenase-1 induction, by generating the vasoactive molecule carbon monoxide and the potent antioxidant bilirubin, could represent a protective system potentially active against brain oxidative injury. Acetyl-L-carnitine is proposed as a therapeutic agent for several neurodegenerative disorders. Accordingly, we report here that treatment of astrocytes with acetyl-L-carnitine induces heme oxygenase-1 in a dose- and time-dependent manner and that this effect was associated with up-regulation of heat shock protein 60 as well as high expression of the redox-sensitive transcription factor Nrf2 in the nuclear fraction of treated cells. In addition, we show that addition of acetyl-L-carnitine to astrocytes, prior to proinflammatory lipopolysaccharide- and interferon-gamma-induced nitrosative stress, prevents changes in mitochondrial respiratory chain complex activity, protein nitrosation and antioxidant status induced by inflammatory cytokine insult. Given the broad cytoprotective properties of the heat shock response, molecules inducing this defense mechanism appear to be possible candidates for novel cytoprotective strategies. Particularly, manipulation of endogenous cellular defense mechanisms via acetyl-L-carnitine may represent an innovative approach to therapeutic intervention in diseases causing tissue damage, such as neurodegeneration. We hypothesize that maintenance or recovery of the activity of vitagenes may delay the aging process and decrease the risk of age-related diseases.
Cloning and high-level expression of the glutathione-independent formaldehyde dehydrogenase gene from Pseudomonas putida (1994)

A DNA fragment of 485 bp was specifically amplified by PCR with primers based on the N-terminal sequence of the purified formaldehyde dehydrogenase (EC 1.2.1.46) from Pseudomonas putida and on that of a cyanogen bromide-derived peptide. With this product as a probe, a gene coding for formaldehyde dehydrogenase (fdhA) in P. putida chromosomal DNA was cloned in Escherichia coli DH5 alpha. Sequencing analysis revealed that the fdhA gene contained 1,197-bp open reading frame, encoding a protein composed of 399 amino acid residues whose calculated molecular weight was 42,082. The transformant of E. coli DH5 alpha harboring the hybrid plasmid, pFDHK3DN71, showed about 50-fold-higher formaldehyde dehydrogenase activity than P. putida. The predicted amino acid sequence contained several features characteristic of the zinc-containing medium-chain alcohol dehydrogenase (ADH) family. Most of the glycine residues strictly conserved within the family, including a Gly-Xaa-Gly-Xaa-Xaa-Gly pattern in the coenzyme binding domain, were well conserved in this enzyme. Regions around both the catalytic and the structural zinc atoms were also conserved. Analyses of structural and enzymatic characteristics indicated that P. putida FDH belongs to the medium-chain ADH family, with mixed properties of mammalian class I and III ADHs.
Microbial and algal oils: Do they have a future for biodiesel or as commodity oils? (2008)

Abstract We review the prospects of using yeasts and microalgae as sources of cheap oils that could be used for biodiesel. We conclude that yeast oils, the cheapest of the oils producible by heterotrophic microorganisms, are too expensive to be viable alternatives to the major commodity plant oils. Algal oils are similarly unlikely to be economic; the cheapest form of cultivation is in open ponds which then requires a robust, fast‐growing alga that can withstand adventitious predatory protozoa or contaminating bacteria and, at the same time, attain an oil content of at least 40% of the biomass. No such alga has yet been identified. However, we note that if the prices of the major plant oils and crude oil continue to rise in the future, as they have done over the past 12 months, then algal lipids might just become a realistic alternative within the next 10 to 15 years. Better prospects would, however, be to focus on algae as sources of polyunsaturated fatty acids.
Acne Fulminans and 13‐Cis‐Retinoic Acid (1992)

We report a case of acne fulminans occurring during treatment with 13-cis-retinoic acid for cystic acne. Continuing the treatment with 13-cis-retinoic acid without systemic steroid eventually cleared the systemic manifestations and skin lesions. We review the literature and discuss its pathogenesis.
Do antibodies to myelin basic protein isolated from multiple sclerosis cross-react with measles and other common virus antigens? (1983)

Immunological activity to various antigens, including brain components, measles and other viruses, has been associated with IgG in multiple sclerosis (MS). One possible explanation for the presence of anti-viral antibodies and antibody to myelin basic protein (MBP) in MS patients is that there are antigenic determinants common to certain viruses and MBP. To assess this possibility, IgG from individual brains and sera from patients with MS, subacute sclerosing panencephalitis (SSPE) and controls was isolated by protein A and MBP-Sepharose affinity chromatography. Antibody to MBP was measured with a solid phase radioimmunoassay and antibody to measles and other viruses by immunofluorescence and/or complement fixation. Anti-MBP activity was detected in brain extracts and sera of all MS patients tested. In contrast to the low levels of antibody to MBP in control brains, high levels of anti-MBP antibodies were found in most of the normal sera. There was no correlation between the presence and levels of serum anti-measles antibodies and the anti-MBP activity. None of the anti-MBP antibodies affinity purified from brain and serum of MS patients reacted with any of the viruses tested, including measles. IgG purified from SSPE patients or from a rabbit hyperimmunized with measles antigen had no reactivity to MBP, despite high levels of anti-measles antibody. It is concluded that there is not direct link between the presence of antibody to MBP and antibody to measles and other viruses in MS patients.
Comparison of the Antiviral Activities of Various Cloned Human Interferon- Subtypes in Mammalian Cell Cultures (1981)

Five human interferon-alpha (leukocyte) subtypes derived from genes cloned in Escherichia coli have been compared for their ability to induce antiviral activity against vesicular stomatitis virus infection of various mammalian cell cultures. These interferons, designated LeIF-A (IFN-alpha 2), -B, -C, -D (IFN-alpha 1) and LeIF-F, show different relative activities when assayed on human, bovine, hamster, mouse, rabbit and monkey cell lines. As with a natural human buffy-coat interferon-alpha preparation, three subtypes (LeIF-B, -C and -D) showed considerable activity on RK-13 rabbit cells, but two (LeIF-D and -F) also showed some activity on mouse L-929 cells. Of the five interferon subtypes examined, LeIF-F demonstrated the highest degree of species specificity.
Atom Transfer Radical Polymerization of Styrene Using a Novel Octafunctional Initiator: Synthesis of Well-Defined Polystyrene Stars (1998)

A novel octafunctional calixarene derivative, namely, 5,11,17,23,29,35,41,47-octa-tert-butyl-49,50,51,52,53,54,55,56-octakis(2-bromopropionyloxy)calix[8]arene (1) which was readily synthesized in one step, was used to initiate the bulk atom transfer radical polymerization (ATRP) of styrene, at 100 °C, in the presence of CuBr/2,2‘-bipyridyl. Polystyrene (PS) stars of narrow polydispersity with precisely eight arms could be synthesized by restricting the polymerization to low conversion, typically below 15−20%. At higher conversions, irreversible coupling occurred between stars as evidenced by a size exclusion chromatography line equipped with a multiangle laser light scattering detector (MALLS/SEC). Octafunctional stars of molar masses up to 340 000 g mol-1 could be prepared by using high ratios of the monomer to the initiator ([M]/[I] = 12 000). The precise octafunctional structure of the stars was confirmed, on one hand, by studying the kinetics of ATRP of styrene initiated by an equimolar mixture of 1 and its monofunctional equivalent, namely 4-tert-butylphenyl(2-bromopropionate) (2) and, on the other hand, by the characterization of the individual arms obtained upon hydrolysis of the ester link between the core and the branches of the stars.
AUF1 Binding Affinity to A+U-rich Elements Correlates with Rapid mRNA Degradation (1996)

Rapid degradation of many labile mRNAs is regulated in part by an A + U-rich element (ARE) in their 3'-untranslated regions. Extensive mutational analyses of various AREs have identified important components of the ARE, such as the nonamer motif UUAUUUAUU, two copies of which serve as a potent mRNA destabilizer. To investigate the roles of trans-acting factors in ARE-directed mRNA degradation, we previously purified and molecularly cloned the RNA-binding protein AUF1 and demonstrated that both cellular and recombinant AUF1 bind specifically to AREs as shown by UV cross-linking assays in vitro. In the present work, we have examined the in vitro RNA-binding properties of AUF1 using gel mobility shift assays with purified recombinant His6-AUF1 fusion protein. We find that ARE binding affinities of AUF1 correlate with the potency of an ARE to direct degradation of a heterologous mRNA. These results support a role for AUF1 in ARE-directed mRNA decay that is based upon its affinity for different AREs.
Supercontinuum generation in a photonic crystal fiber with two zero-dispersion wavelengths tapered to normal dispersion at all wavelengths (2005)

We numerically study supercontinuum generation in photonic crystal fibers with two zero-dispersion wavelengths, weakly tapered to have normal dispersion at all wavelengths after a certain distance. We pump with 15 fs pulses with milliwatt average power and show that two distinct smooth spectral parts are generated, with improved stability due to the normal dispersion. We characterize the two spectral parts and show how the 3 dB bandwidth, the center wavelength, and the power of the two parts depend on the taper parameters and the pump power.