gebhart/patrepeval huggingface dataset:
Role of D-ribose as a cometabolite in D-xylose metabolism by Saccharomyces cerevisiae (1993)

The influence of D-ribose as a cosubstrate on the uptake and metabolism of the non-growth substrate D-xylose by Saccharomyces cerevisiae ATCC 26602 was investigated. Xylose was taken up by means of low- and high-affinity glucose transport systems. In cells exposed for 2 days to a mixture of xylose and ribose, only the high-affinity system could be detected. Glucose strongly inhibited the transport of xylose by both systems. Starvation or exposure to either xylose or ribose resulted in inactivation of xylose transport, which did not occur in the presence of a mixture of ribose and xylose. A constitutive non-glucose-repressible NADPH2-dependent xylose reductase with a specific activity of ca. 5 mU/mg of protein that converted xylose to xylitol was present in a glucose-grown culture. No activity converting xylitol to xylulose or vice versa was found in crude extracts. Both xylose and ribose were converted to their corresponding polyols, xylitol and ribitol, as indicated by 13C nuclear magnetic resonance spectroscopy. Furthermore, ethanol was detected, and this implied that pathways for the complete catabolism of xylose and ribose exist. However, the NADPH2 required for the conversion of xylose to xylitol is apparently not supplied by the pentose phosphate pathway since the ethanol produced from D-[1-13C]xylose was labelled only in the C-2 position. Acetic acid was produced from ribose and may assist in the conversion of xylose to xylitol by cycling NADPH2.
A Convenient Synthesis of Amino Acid Methyl Esters (2008)

A series of amino acid methyl ester hydrochlorides were prepared in good to excellent yields by the room temperature reaction of amino acids with methanol in the presence of trimethylchlorosilane. This method is not only compatible with natural amino acids, but also with other aromatic and aliphatic amino acids.
ZnO Doped With Transition Metal Ions (2007)

Spin-dependent phenomena in ZnO may lead to devices with new or enhanced functionality, such as polarized solid-state light sources and sensitive biological and chemical sensors. In this paper, we review the experimental results on transition metal doping of ZnO and show that the material can be made with a single phase at high levels of Co incorporation (~15 at.%) and exhibits the anomalous Hall effect. ZnO is expected to be one of the most promising materials for room-temperature polarized light emission; but to date, we have been unable to detect the optical spin polarization in ZnO. The short spin relaxation time observed likely results from the Rashba effect. Possible solutions involve either cubic phase ZnO or the use of additional stressor layers to create a larger spin splitting in order to get a polarized light emission from these structures or to look at alternative semiconductors and fresh device approaches
Applications of random PCR. (1995)

Since the technique of PCR was developed in 1985 (Saiki et al). many new forms of applications have been described in the literature. Of particular interest are PCR approaches, allowing amplification of unknown sequences. In this review these approaches are generally termed "Random PCR"s. While "conventional PCR" in the form that was first described by Saiki et al. is utilized for the amplification and subsequent detection of specific DNA sequences, which are precisely characterized in length and sequence, Random PCR is either used for universal amplification of prevailing DNA or for amplification of unknown intervening sequences which are not generally defined in length or sequence. We depict criteria for discrimination between conventional PCR and Random PCR. Furthermore, we have compiled a classification system for Random PCR approaches based on differentiation by primer structure (degenerate--non-degenerate). According to this classification system a general overview of published Random PCR approaches is given. Future aspects of application of Random PCR are mentioned and commented. Own investigations, combining Random PCR with the technique of chromosome microdissection and thus allowing characterization of unknown chromosomes or chromosome fragments via FISH, are presented. Results are briefly summarized.
Modeling the Cycles of Growth and Detachment of Bubbles in Carbonated Beverages (2006)

In this paper, a model for the formation of bubbles in carbonated beverages is presented. It has previously been shown that bubbles form from cellulose fibers within such beverages and the passage of such bubbles from the fibers to the liquid surface has been modeled. A model is thus presented here that considers the process of formation, which is governed by diffusion through the fiber and bubble surfaces. The model comprises two stages, growth and detachment, and it is shown here that both play an important role. The latter process is found to occur over a much shorter time scale than the former, enabling the models to be partially decoupled. The total number of bubbles released from individual fibers over time is found to be approximated well by an exponential relationship, and the parameters in this relationship are presented for a range of different detachment angles and fiber sizes. It is found that bubble formation is promoted in narrow, long tubes, but that the time constant is solely determined by the rate of diffusion across the liquid surface. The surface tension is found to have minimal influence on the number of bubbles produced.
Role of Circulating Fibroblast Growth Factor 23 in the Development of Secondary Hyperparathyroidism (2005)

It would be useful to predict the future development of hyperparathyroidism before treatment with active vitamin D agents. Fibroblast growth factor 23 (FGF23) is a newly identified humoral phosphaturic factor. Positive correlation was found between parathyroid function and serum FGF23 levels in dialysis patients. Interestingly, FGF23 levels showed even better correlation with intact parathyroid hormone (iPTH) levels 2 years after the sample collection for the FGF23 measurement. In long-term dialysis patients with mild secondary hyperparathyroidism, serum FGF23 level was the best screening test to discriminate patients with future advanced secondary hyperparathyroidism within 2 years. In dialysis patients with advanced secondary hyperparathyroidism, the pretreatment FGF23 levels, as well as iPTH levels, significantly affected the outcome of calcitriol therapy. Thus, the measurement of serum FGF23 level is a promising laboratory examination to predict the future development of secondary hyperparathyroidism. The mechanism of this phenomenon, however, remains to be revealed.
Fluorinated retinoic acids and their analogs. 3. Synthesis and biological activity of aromatic 6-fluoro analogs (1982)

Ethyl (E,Z,E,E)-3,7-dimethyl-4-fluoro-9-(4-methoxy-2,3,6-trimethylphenyl)nonatetraenoate (10a) has been found to cause a marked regression of chemically induced skin papillomas in mice. A new synthesis of this compound was achieved by condensation of 4-fluoro aldehyde 7 or 8 with the aromatic phosphonium salt 9a. Several analogues (101-e) having different substituted aromatic moieties were also prepared and tested for their antipapilloma effect. The monochloro analogue 10b was shown to have comparable activity to the parent compound 10a.
Hybrid microfluidics combined with active and passive approaches for continuous cell separation (2016)

Microfluidics, which is classified as either active or passive, is capable of separating cells of interest from a complex and heterogeneous sample. Active methods utilise external fields such as electric, magnetic, acoustic, and optical to drive cells for separation, while passive methods utilise channel structures, intrinsic hydrodynamic forces, and steric hindrances to manipulate cells. However, when processing complex biological samples such as whole blood with rare cells, separation with a single module microfluidic device is difficult. Hybrid microfluidics is an emerging technique, which utilises active and passive methods whilst fulfilling higher requirements for stable performance, versatility, and convenience, including (i) the ability to process multi-target cells, (ii) enhanced ability for multiplexed separation, (iii) higher sensitivity, and (iv) tunability for a wider operational range. This review introduces the fundamental physics and typical formats for subclasses of hybrid microfluidic devices based on their different physical fields; presents current examples of cell sorting to highlight the advantage and usefulness of hybrid microfluidics on biomedicine, and then discusses the challenges and perspective of future development and the promising direction of research in this field.
Flow-dependent effect of formoterol dry-powder inhaled from the Aerolizer (1997)

The output and size distribution of aerosols from dry powder inhalers are dependent on the flow rate through the device. Therefore, in an in vivo study, we examined the flow-dependency of the effect of formoterol when delivered from a dry powder inhaler, the Aerolizer, in a flow range relevant to schoolchildren. In a preliminary study comprising 126 asthmatic children aged 3-10 yrs, the relationship between age and peak inspiratory flow (PIF) rate through the Aerolizer was determined. Mean PIF was 104 L.min-1 and all children aged > 5 yrs performed a PIF > 60 L.min-1. Sixteen children aged 8-15 yrs with exercise-induced asthma (EIA) took part in the main trial comparing the protective effect of 12 micrograms formoterol inhaled at 60 and 120 L.min-1. The effect from high and low inspiratory flow was judged from the protective effect against EIA 12 h after drug administration. The decrease in forced expiratory volume in one second (FEV1) after exercise was 34% on the placebo day, but only 15% when formoterol was inhaled at the high flow rate. This difference was statistically significant. The decrease in FEV1 was 23% after treatment with formoterol inhaled at the low flow rate, that was not significantly different from placebo or from high-flow formoterol treatment. These clinical findings correspond with the in vitro findings of flow-dependent fine particle mass from the Aerolizer, and corroborate the relationship between fine particle mass of aerosol and clinical effect. The results indicate a flow-dependent effect of formoterol dry powder inhaled from the Aerolizer, within the range of inspiratory flow rate obtainable by school-children. This questions its applicability in children with asthma.
Potential of ceramic materials as permanently implantable skeletal prostheses (1970)

Abstract The feasibility of the use of porous ceramic materials in the permanent repair of skeletal defects was studied from the standpoint of physiological compatibility and in growth of natural bone. High‐fired calcium aluminate samples in the form of quarter‐inch diameter cylindrical pellets containing interconnecting porous networks were implanted in vivo into canine femurs for 4‐, 11‐, and 22‐week periods. The implants had 65% porosity with pore size falling within one of five distinct ranges from less than 45 μ to about 200 μ in diameter. Thin sections were prepared by grinding (poly) methyl methacrylate‐mounted cross sections of the femurs containing the implanted ceramic samples and adjacent soft tissues. Tissue‐prosthetic compatibility was determined using standard histological thin section procedures, electron microbeam probe examinations, autoradiographic techniques, microfadiographic techniques, microchemistry techniques, and ultra‐violet fluorescent techniques. Optical microscopic evaluations of each section showed the ceramic samples to be bound lightly by natural bone and gave no detectable signs of tissue incompatibility. Minimum pore size for significant ingrowth of natural bone was indicated to be between 75 and 100 μ.
Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics (2007)

Most studies involving prebiotic oligosaccharides have been carried out using inulin and its fructo-oligosaccharide (FOS) derivatives, together with various forms of galacto-oligosaccharides (GOS). Although many intestinal bacteria are able to grow on these carbohydrates, most investigations have demonstrated that the growth of bifidobacteria, and to a lesser degree lactobacilli, is particularly favoured. Because of their safety, stability, organoleptic properties, resistance to digestion in the upper bowel and fermentability in the colon, as well as their abilities to promote the growth of beneficial bacteria in the gut, these prebiotics are being increasingly incorporated into the Western diet. Inulin-derived oligosaccharides and GOS are mildly laxative, but can result in flatulence and osmotic diarrhoea if taken in large amounts. However, their effects on large bowel habit are relatively minor. Although the literature dealing with the health significance of prebiotics is not as extensive as that concerning probiotics, considerable evidence has accrued showing that consumption of GOS and FOS can have significant health benefits, particularly in relation to their putative anti-cancer properties, influence on mineral absorption, lipid metabolism, and anti-inflammatory and other immune effects such as atopic disease. In many instances, prebiotics seem to be more effective when used as part of a synbiotic combination.
InP/InGaAs uni-travelling-carrier photodiode with310 GHz bandwidth (2000)

The authors have fabricated an InP/InGaAs uni-travelling-carrier photodiode that exhibits a 3 dB bandwidth of 310 GHz and a pulse width (FWHM) of 0.97 ps, both of which are record values for photodetectors operating at a wavelength of 1.55 µm. The average electron velocity in the depletion region is estimated to be 3.0 × 107 cm/s.
Natural human interferon-α2 is O-glycosylated (1991)

Natural human interferon alpha 2 (IFN-alpha 2) was isolated from a preparation of partially purified human leucocyte IFN by monoclonal-antibody immunoaffinity chromatography. The purified protein had a specific activity of 1.5 x 10(8) i.u./mg; it was estimated to constitute 10-20% of the total antiviral activity of leucocyte IFN. N-Terminal amino-acid-sequence analysis identified the subspecies IFN-alpha 2b and/or IFN-alpha 2c, whereas IFN-alpha 2a was not detectable. The structure of natural IFN-alpha 2 was found to differ from that of its recombinant (Escherichia coli-derived) equivalent. First, reverse-phase h.p.l.c. showed that natural IFN-alpha 2 was significantly more hydrophilic then expected. Secondly, the apparent molecular mass of the natural protein determined by SDS/PAGE was higher than that of recombinant IFN-alpha 2; incubation under mild alkaline conditions known to eliminate O-linked carbohydrates resulted in a reduction of the apparent molecular mass to that of the recombinant protein. On sequence analysis of proteolytic peptides, Thr-106 was found to be modified. These results suggested that Thr-106 of natural IFN-alpha 2 carries O-linked carbohydrates. Reverse-phase h.p.l.c. as well as SDS/PAGE of natural IFN-alpha 2 showed that glycosylation is heterogeneous. For characterization of the carbohydrate moieties, the protein was treated with neuraminidase and/or O-glycanase and analysed by gel electrophoresis; in addition, glycopeptides obtained by proteinase digestion and separated by h.p.l.c. were characterized by sequence analysis and m.s. Further information on the composition of the glycans was obtained by monosaccharide analysis. The results indicate that natural IFN-alpha 2 contains the disaccharide galactosyl-N-acetylgalactosamine (Gal-GalNAc) linked to Thr-106. In part of the molecules, this core carbohydrate carries (alpha-)N-acetylneuraminic acid, whereas a disaccharide, probably N-acetyl-lactosamine, is bound to Gal-GalNAc in another proportion of the protein. Further glycosylation isomers are present in small amounts. As IFN-alpha 2 is the only IFN-alpha species with a threonine residue at position 106, it may represent the only O-glycosylated human IFN-alpha protein.
Correlations between the Sonic Hedgehog Pathway and basal cell carcinoma (2007)

The Hedgehog (HH) family of intercellular signaling proteins has some essential functions in patterning both invertebrate and vertebrate embryos. Identified as an important regulator of segment polarity and tissue organization in flies, the HH pathway can also play a significant role in human development and in cutaneous carcinogenesis. The family received their name because when the D. melanogaster HH protein malfunctions the mutant fly ends up looking like a small prickly ball, similar to a curled up hedgehog. The Sonic hedgehog (SHH) pathway is implicated in the etiology of the most common human cancer, the basal cell carcinoma (BCC). Mutations in the receptor of SHH, the patched gene (PTCH), have been characterized in sporadic BCCs as well as those from patients with the rare genetic syndrome nevoid BCC. Human PTCH is mutated in sporadic as well as hereditary BCCs, and inactivation of this gene is probably a necessary if not sufficient step for tumorigenesis. Delineation of the biochemical pathway in which PTCH functions may lead to rational medical therapy for skin cancer and possibly other tumors.
Identification and quantitative analyses of microRNAs located in the distal axons of sympathetic neurons (2010)

microRNAs (miRNAs) constitute a novel class of small, noncoding RNAs that act as negative post-transcriptional regulators of gene expression. Although the nervous system is a prominent site of miRNA expression, little is known about the spatial expression profiles of miRNAs in neurons. Here, we employed compartmentalized Campenot cell culture chambers to obtain a pure axonal RNA fraction of superior cervical ganglia (SCG) neurons, and determined the miRNA expression levels in these subcellular structural domains by microarray analysis and by real-time reverse-transcription polymerase chain reaction. The data revealed stable expression of a number of mature miRNAs that were enriched in the axons and presynaptic nerve terminals. Among the 130 miRNAs identified in the axon, miR-15b, miR-16, miR-204, and miR-221 were found to be highly abundant in distal axons as compared with the cell bodies of primary sympathetic neurons. Moreover, a number of miRNAs encoded by a common primary transcript (pri-miRNA) were differentially expressed in the distal axons, suggesting that there is a differential subcellular transport of miRNAs derived from the same coding region of the genome. Taken together, the data provide an important resource for future studies on the regulation of axonal protein synthesis and the role played by miRNAs in the maintenance of axonal structure and function as well as neuronal growth and development.
A wide host‐range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase (2005)

Using DNA obtained from the metagenome of an anaerobic digestor in a waste water treatment plant, we constructed a gene library cloned in the wide host-range cosmid pLAFR3. One cosmid enabled Rhizobium leguminosarum to grow on ethanol as sole carbon and energy source, this being due to the presence of a gene, termed adhEMeta. The AdhEMeta protein most closely resembles the AdhE alcohol dehydrogenase of Clostridium acetobutylicum, where it catalyses the formation of ethanol and butanol in a two-step reductive process. However, cloned adhEMeta did not confer ethanol utilization ability to Escherichia coli or to Pseudomonas aeruginosa, even though it was transcribed in both these hosts. Further, cell-free extracts of E. coli and R. leguminosarum containing cloned adhEMeta had butanol and ethanol dehydrogenase activities when assayed in vitro. In contrast to the well-studied AdhE proteins of C. acetobutylicum and E. coli, the enzyme specified by adhEMeta is not inactivated by oxygen and it enables alcohol to be catabolized. Cloned adhEMeta did, however, confer one phenotype to E. coli. AdhE- mutants of E. coli fail to ferment glucose and introduction of adhEMeta restored the growth of such mutants when grown under fermentative conditions. These observations show that the use of wide host-range vectors enhances the efficacy with which metagenomic libraries can be screened for genes that confer novel functions.
Important role of the proline residue in the signal sequence that directs the secretion of human lysozyme in Saccharomyces cerevisiae (1989)

To elucidate the role of the proline residue in the engineered signal sequence that directs the secretion of human lysozyme in Saccharomyces cerevisiae, we have remodeled an idealized signal sequence L8 = Met-Arg-(Leu)8-Pro-Leu-Ala-Ala-Leu-Gly [Yamamoto, Y., Taniyama, Y., Kikuchi, M., & Ikehara, M. (1987) Biochem. Biophys. Res. Commun. 149, 431-436] in the vicinity of the proline residue. By analyzing the secretory capability of 10 engineered signal sequences, we have shown the following. (1) The proline residue is important for the secretion of human lysozyme and is allowed at position -4, -5, or -6. (2) The secretory capability of the engineered signal sequences is correlated with their predicted conformations. (3) The functional signal sequences that we have investigated can be generalized as follows: Met-Arg-(Leu)n-Pro-(Xaa)-Ala-Leu-Gly where n equals 6-12 and Xaa is Leu, Ala, or Leu-Ala or can be omitted.
Engineering Biomaterials for Synthetic Neural Stem Cell Microenvironments (2008)

ADVERTISEMENT RETURN TO ISSUEPREVReviewEngineering Biomaterials for Synthetic Neural Stem Cell MicroenvironmentsLauren Little, †, Kevin E. Healy, *‡§, and David Schaffer, *†‡∥View Author Information Departments of Chemical Engineering, Bioengineering, and Material Science and Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720-1760* To whom correspondence should be addressed. (D.S.) Tel: 510-643-5963 . Fax: 510-642-4778. E-mail: [email protected]. (K.E.H.) Tel: 510-643-3559 . Fax: 510-643-5792. E-mail: [email protected]†Department of Chemical Engineering.‡Department of Bioengineering.§Department of Material Science and Engineering.∥Helen Wills Neuroscience Institute.Cite this: Chem. Rev. 2008, 108, 5, 1787–1796Publication Date (Web):May 14, 2008Publication History Received13 February 2008Published online14 May 2008Published inissue 1 May 2008https://pubs.acs.org/doi/10.1021/cr078228thttps://doi.org/10.1021/cr078228treview-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views3239Altmetric-Citations84LEARN 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 SUBJECTS:Biopolymers,Cells,Differentiation,Extracellular matrix,Rodent models Get e-Alerts