gebhart/patrepeval huggingface dataset:
Oxidative degradation of collagen and its model peptide by ultraviolet irradiation (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidative degradation of collagen and its model peptide by ultraviolet irradiationYoji. Kato, Koji. Uchida, and Shunro. KawakishiCite this: J. Agric. Food Chem. 1992, 40, 3, 373–379Publication Date (Print):March 1, 1992Publication History Published online1 May 2002Published inissue 1 March 1992https://pubs.acs.org/doi/10.1021/jf00015a003https://doi.org/10.1021/jf00015a003research-articleACS PublicationsRequest reuse permissionsArticle Views482Altmetric-Citations42LEARN 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
Human cytogenetic biomonitoring using flow-cytometric analysis of micronuclei in transferrin-positive immature peripheral blood reticulocytes (2000)

We have developed a method to isolate and analyze nascent human reticulocytes in peripheral blood for the presence of micronuclei (MN). For a very short time peripheral reticulocytes show residual expression of the transferrin receptor. Using immunomagnetic separation of cells expressing the transferrin receptor, a population of immature reticulocytes (Trf-Ret) was isolated from peripheral blood. In humans, the spleen actively removes micronucleated erythrocytes but during the short lifetime of the isolated Trf-Ret only a fraction (less than about 20%) of the MN-containing reticulocytes will have been eliminated. Cells were stained with the fluorescent dyes Thiazole Orange for RNA and Hoechst 33342 for DNA and analyzed by flow cytometry and fluorescence microscopy. Baseline frequencies of MN-Trf-Ret on a group of healthy donors were found to be 1.1% for males and 1.4% for females; however, the gender difference was not significant. The frequency of MN-Trf-Ret in the studied group increased with age, and was dependent on blood group. In three donors studied over 4 months, the baseline level remained stable. In cancer patients treated with radiation or chemotherapy, the frequency of MN-Trf-Ret increased 10- to 20-fold after 1-4 days, depending on the treatment. A high correlation between flow and manual analysis of MN-Trf-Ret was seen. We believe the method has a high potential as a sensitive and rapid method for biological monitoring in presumed exposed groups and individuals.
Structure-Based Optimization of Naphthyridones into Potent ATAD2 Bromodomain Inhibitors (2015)

ATAD2 is a bromodomain-containing protein whose overexpression is linked to poor outcomes in a number of different cancer types. To date, no potent and selective inhibitors of the bromodomain have been reported. This article describes the structure-based optimization of a series of naphthyridones from micromolar leads with no selectivity over the BET bromodomains to inhibitors with sub-100 nM ATAD2 potency and 100-fold BET selectivity.
Retinoic acid induces sodium/iodide symporter gene expression and radioiodide uptake in the MCF-7 breast cancer cell line (2000)

The sodium/iodide symporter (NIS) stimulates iodide uptake in normal lactating breast, but is not known to be active in nonlactating breast or breast cancer. We studied NIS gene regulation and iodide uptake in MCF-7 cells, an estrogen receptor (ER)-positive human breast cancer cell line. All-trans retinoic acid (tRA) treatment stimulated iodide uptake in a time- and dose-dependent fashion up to approximately 9.4-fold above baseline. Stimulation with selective retinoid compounds indicated that the induction of iodide uptake was mediated by retinoic acid receptor. Treatment with tRA markedly stimulated NIS mRNA and immunoreactive protein ( approximately 68 kDa). tRA stimulated NIS gene transcription approximately 4-fold, as shown by nuclear run-on assay. No induction of iodide uptake was observed with RA treatment of an ER-negative human breast cancer cell line, MDA-MB 231, or a normal human breast cell line, MCF-12A. The iodide efflux rate of tRA-treated MCF-7 cells was slow (t(1/2) = 24 min), compared with that in FRTL-5 thyroid cells (t(1/2) = 3.9 min), favoring iodide retention in MCF-7 cells. An in vitro clonogenic assay demonstrated selective cytotoxicity with (131)I after tRA stimulation of MCF-7 cells. tRA up-regulates NIS gene expression and iodide uptake in an ER-positive breast cancer cell line. Stimulation of radioiodide uptake after systemic retinoid treatment may be useful for diagnosis and treatment of some differentiated breast cancers.
Control of growth orientation for carbon nanotubes (2003)

Laterally aligned carbon nanotubes were synthesized on substrates over iron nanoparticles using chemical vapor deposition. In addition, aligned carbon nanotubes grown vertically and with tilt angle to the substrates were produced, which means that it is possible to grow aligned carbon nanotubes at any angle relative to the substrate. The growth direction of the carbon nanotubes was controlled by a magnetic field that is applied in the process of adhering catalyst particles on silicon oxide substrates from dispersion. The ferromagnetic property of the iron nanoparticles fixes them in a defined orientation under magnetic field, which results in aligned growth of the carbon nanotubes. These results indicate that carbon nanotubes preferentially grow from certain facets of the catalyst particles, suggesting a crucial clue in investigating the growth mechanism of carbon nanotubes. The laterally aligned carbon nanotubes could make it possible to integrate them in nanoelectronic devices, such as a channel for field-effect transistors.
Regulation of WNT signaling molecules by retinoic acid during neuronal differentiation in NT2 cells: Threshold model of WNT action (Review) (2002)

NT2/NTera2 cells, derived from human embryonal tumor, differentiate into neuronal cells after treatment with all-trans-retinoic acid (ATRA). We have cloned and characterized 13 out of 19 human WNT genes, and also 9 out of 10 human Frizzled (FZD) genes encoding seven-transmembrane-type WNT receptors, which are potent targets for pharmacogenomics in the post-genomic era, especially in the field of regenerative medicine and clinical oncology. Because WNT signals are implicated in morphogenesis of neural tissues, regulation of 19 WNT genes and 10 FZD genes during the early phase of neuronal differentiation in NT2 cells is reviewed. Multiple WNTs and FZDs are expressed in NT2 cells. WNT2B/WNT13 gene encode 2 isoforms due to alternative splicing of alternative promoter type, and WNT2B isoform 2 (WNT2B2) rather than WNT2B isoform 1 (WNT2B1) is expressed in NT2 cells. WNT3A, WNT8A, WNT8B, WNT10B and WNT11 are down-regulated in NT2 cells after ATRA treatment, while WNT2, WNT7B and WNT14B are up-regulated. FZD4 and FZD10 are up-regulated in NT2 cells after ATRA treatment. Expression of multiple WNT signaling molecules are dramatically changed during the early phase of neuronal differentiation in NT2 cells. Each WNT activates the beta-catenin - TCF pathway, the JNK pathway or the Ca2+-releasing pathway in NT2 cells, and summed effects of multiple WNTs might determine the fate of NT2 cells (self-renewal or differentiation) through switching intracellular WNT signaling pathways. The author proposes the threshold model of WNT action.
Water-Soluble Phosphinothiols for Traceless Staudinger Ligation and Integration with Expressed Protein Ligation (2007)

The traceless Staudinger ligation is an effective means to synthesize an amide bond between two groups of otherwise orthogonal reactivity: a phosphinothioester and an azide. An important application of the Staudinger ligation is in the ligation of peptides at a variety of residues. Here, we demonstrate that the traceless Staudinger ligation can be achieved in water with a water-soluble reagent. Those reagents that provide a high yield of amide product discourage protonation of the nitrogen in the key iminophosphorane intermediate. The most efficacious reagent, bis(p-dimethylaminoethyl)phosphinomethanethiol, mediates the rapid ligation of equimolar substrates in water. This reagent is also able to perform a transthioesterification reaction with the thioester intermediate formed during intein-mediated protein splicing. Hence, the traceless Staudinger ligation can be integrated with expressed protein ligation, extending the reach of modern protein chemistry.
β‐Carbolin‐Alkaloide, I. Synthese von 1‐Aryl‐ und 1‐Alkenyl‐β‐carbolinen durch Palladium‐katalysierte Kupplungsreaktionen (1992)

β‐Carboline Alkaloids, I. — Syntheses of 1‐Aryl‐ and 1‐Alkenyl‐β‐carbolines by Palladium‐Catalyzed Coupling Reactions 1‐Chloro‐β‐carboline ( 6 ) is prepared in three steps starting from tryptamine ( 3 ). Palladium‐catalyzed coupling reactions of 6 with aryl boronic acids offer an easy access to the alkaloids komaroine ( 11 ) and perlolyrine ( 15 ). Pavettine ( 16 ) is prepared by coupling of 6 with tributylvinylstannane.
Scheduling transient periods of dual-armed cluster tools (2012)

Modern semiconductor manufacturing industry tends to reduce the lot size; that is, a lot has a small number of identical wafers, because of demands for small lots and an increased die yield per wafer due to the larger wafer size. Therefore, cluster tools for wafer processing, mostly repeating identical work cycles, are subject to frequent lot changes. We thus examine dual-armed cluster tool scheduling problems for transient periods. We first develop a Petri net model for the tool's operational behavior in a transient period. We then develop a mixed integer programming model for finding an optimal schedule in terms of makespan of a transient period. We also examine how to adapt the conventional swap sequence, which is mostly used for scheduling steady work cycles, for a transient period. This is important to guarantee the compatibility between schedules of steady-state and transient periods because most tools are scheduled by the swap sequence in steady-state periods. To do this, we identify a deadlock-free condition and also propose two efficient scheduling algorithms by modifying the swap sequence. Finally, we experimentally analyze the efficiency of the proposed algorithms.
Photoelectrochemical Behavior of n-Type Porous-Si Electrodes (1986)

A prolonged photoanodic operation of n-type Si in aqueous electrolytes was observed with porous-structure Si electrodes. The n-type porous-Si layers (n-PSL) were formed on n-Si substrates (1-2 Ωcm in resistivity) by anodic treatments in an HF solution. The total output charge Q obtainable from a n-PSL photoelectrochemical cell increased in proportion to the n-PSL thickness d . At d = 50 µm, Q reached 12.5 C/cm 2 ; this was four orders of magnitude greater than was obtained from naked n-Si photoanodes. The H 2 evolution rate from the Pt counterelectrode was about 60 µmol/2 h at d = 30 µm. The experimental results of the spectral response suggest an increase in the surface state density of the n-PSL surface with increasing d .
Synthesis, Proton-Affinity and Anti-Cancer Properties of the Prodigiosin-Group Natural Products (2001)

The prodigiosin-group natural products are a family of tripyrrole red-pigments that are produced by microorganisms such as Streptomyces and Serratia and contain a common 4-methoxy-2,2'-bipyrrole ring system. They were first isolated in 1929 and studied as antibiotic and cytotoxic agents in the 1960s, but were not developed clinically due to their high systemic toxicity. However, during the past decade some prodigiosins have shown potentially useful immunosuppressive activity when administered at doses that are not toxic. They have also been found to exhibit selective cytotoxicity against melanoma and liver cancer cells. These results have fueled various studies on the biological mechanisms of the prodigiosins and it has now been established that they inhibit phosphorylation and activation of JAK-3, a cytoplasmic tyrosine kinase associated with the cell surface receptor component called common gamma-chain. They also uncouple lysosomal vacuolar-type ATPases through promotion of H(+)/Cl(-) symport and facilitate oxidative double-strand DNA cleavage in the presence of copper. A simple and elegant synthesis of the prodigiosins has also been developed, which has allowed a number of the natural prodigiosins and synthetic analogues to be prepared. These studies have served to renew interest in the prodigiosin-group natural products. In this review the recent advances on the synthesis, proton-affinity and biological activities of the prodigiosins are discussed. With regard to their anti-cancer properties, particular attention is given to their ability to facilitate oxidative DNA damage, which provides a rationale for the cytotoxic properties of the prodigiosin-group natural products.
<title>New chemistry of BODIPY dyes and BODIPY dye cassettes featuring through-bond energy transfer</title> (2000)

We are attempting to design and prepare a new class of dyes for biomedical/biotechnological applications, including detection of oligonucleotides in DNA sequencing and diagnostics. The dyes use through-bond energy transfer to harvest short wavelength irradiation, and fluoresce at much longer wavelengths. Excellent resolution of fluorescent emissions from a 266 nm laser source is observed, with apparent Stokes' shifts of up to 408 nm.
Reduced collagen VI causes Bethlem myopathy: a heterozygous COL6A1 nonsense mutation results in mRNA decay and functional haploinsufficiency (1998)

We have identified a new pathogenic mechanism for an inherited muscular dystrophy in which functional haploinsufficiency of the extracellular matrix protein collagen VI causes Bethlem myopathy. The heterozygous COL6A1 mutation results in a single base deletion from the mRNA and a premature stop codon. The mutant mRNA is unstable, subject to nonsense-mediated mRNA decay, and is almost completely absent both from patient fibroblasts and skeletal muscle, resulting in haploinsufficiency of the alpha1(VI) subunit and reduced production of structurally normal collagen VI. This is the first example of a muscular dystrophy caused by haploinsufficiency of a structural protein or member of the dystrophin-glycoprotein complex, and identifies collagen VI as a critical contributor to cell-matrix adhesion in skeletal muscle.
Ultra-Rapid Absorption of Recombinant Human Insulin Induced by Zinc Chelation and Surface Charge Masking (2012)

The combination of rapid dissociation of insulin hexamers upon dilution due to the zinc chelating effects of disodium EDTA followed by the inhibition of insulin monomer/dimer reassociation due to the charge-masking effects of citrate provides the basis for the ultra-rapid absorption of this novel insulin formulation.
Signalling through Class I PI3Ks in mammalian cells (2006)

It is now accepted that activation of Class I PI3Ks (phosphoinositide 3-kinases) is one of the most important signal transduction pathways used by cell-surface receptors to control intracellular events. The receptors which access this pathway include those that recognize growth factors, hormones, antigens and inflammatory stimuli, and the cellular events known to be regulated include cell growth, survival, proliferation and movement. We have learnt a great deal about the family of Class I PI3K enzymes themselves and the structural adaptations which allow a variety of cell-surface receptors to regulate their activity. Class I PI3Ks synthesize the phospholipid PtdIns(3,4,5)P3 in the membranes in which they are activated, and it is now accepted that PtdIns(3,4,5)P3 and its dephosphorylation product PtdIns(3,4)P2 are messenger molecules which regulate the localization and function of multiple effectors by binding to their specific PH (pleckstrin homology) domains. The number of direct PtdIns(3,4,5)P3/PtdIns(3,4)P2 effectors which exist, even within a single cell, creates an extremely complex signalling web downstream of PI3K activation. Some key players are beginning to emerge, however, linking PI3K activity to specific cellular responses. These include small GTPases for the Rho and Arf families which regulate the cytoskeletal and membrane rearrangements required for cell movement, and PKB (protein kinase B), which has important regulatory inputs into the regulation of cell-cycle progression and survival. The importance of the PI3K signalling pathway in regulating the balance of decisions in cell growth, proliferation and survival is clear from the prevalence of oncogenes (e.g. PI3Kalpha) and tumour suppressors [e.g. the PtdIns(3,4,5)P3 3-phosphatase, PTEN (phosphatase and tensin homologue deleted on chromosome 10)] found in this pathway. The recent availability of transgenic mouse models with engineered defects in Class I PI3K signalling pathways, and the development of PI3K isoform-selective inhibitors by both academic and pharmaceutical research has highlighted the importance of specific isoforms of PI3K in whole-animal physiology and pathology, e.g. PI3Kalpha in growth and metabolic regulation, PI3Kbeta in thrombosis, and PI3Kdelta and PI3Kgamma in inflammation and asthma. Thus the Class I PI3K signalling pathway is emerging as an exciting new area for the development of novel therapeutics.
Selective androgen receptor modulators: in pursuit of tissue-selective androgens. (2006)

The androgen receptor mediates the androgenic and anabolic activity of the endogenous steroids testosterone and 5alpha-dihydrotestosterone. Current knowledge of the androgen receptor protein structure, and the molecular mechanisms surrounding the binding properties and activities of agonists and antagonists has led to the design and development of novel nonsteroidal ligands with selected tissue-specific androgen receptor agonist and antagonist activities. The activity of these compounds, termed selective androgen receptor modulators (SARMs), is directed toward the maintenance or enhancement of anabolic effects on bone and muscle with minimal androgenic effects on prostate growth. SARMs are of potential therapeutic value in the treatment of male hypogonadism, osteoporosis, frailty and muscle wasting, burn injury and would healing, anemia, mood and depression, benign prostatic hyperplasia and prostate cancer.
Fermentation of Glycerol to Succinate by Metabolically Engineered Strains of Escherichia coli (2010)

The fermentative metabolism of Escherichia coli was reengineered to efficiently convert glycerol to succinate under anaerobic conditions without the use of foreign genes. Formate and ethanol were the dominant fermentation products from glycerol in wild-type Escherichia coli ATCC 8739, followed by succinate and acetate. Inactivation of pyruvate formate-lyase (pflB) in the wild-type strain eliminated the production of formate and ethanol and reduced the production of acetate. However, this deletion slowed growth and decreased cell yields due to either insufficient energy production or insufficient levels of electron acceptors. Reversing the direction of the gluconeogenic phosphoenolpyruvate carboxykinase reaction offered an approach to solve both problems, conserving energy as an additional ATP and increasing the pool of electron acceptors (fumarate and malate). Recruiting this enzyme through a promoter mutation (pck*) to increase expression also increased the rate of growth, cell yield, and succinate production. Presumably, the high NADH/NAD(+) ratio served to establish the direction of carbon flow. Additional mutations were also beneficial. Glycerol dehydrogenase and the phosphotransferase-dependent dihydroxyacetone kinase are regarded as the primary route for glycerol metabolism under anaerobic conditions. However, this is not true for succinate production by engineered strains. Deletion of the ptsI gene or any other gene essential for the phosphotranferase system was found to increase succinate yield. Deletion of pflB in this background provided a further increase in the succinate yield. Together, these three core mutations (pck*, ptsI, and pflB) effectively redirected carbon flow from glycerol to succinate at 80% of the maximum theoretical yield during anaerobic fermentation in mineral salts medium.
Alternatively Folded Choriogonadotropin Analogs (2001)

Most heterodimeric proteins are stabilized by intersubunit contacts or disulfide bonds. In contrast, human chorionic gonadotropin (hCG) and other glycoprotein hormones are secured by a strand of their beta-subunits that is wrapped around alpha-subunit loop 2 "like a seatbelt." During studies of hCG synthesis in COS-7 cells, we found that, when the seatbelt was prevented from forming the disulfide that normally "latches" it to the beta-subunit, its carboxyl-terminal end can "scan" the surface of the heterodimer and become latched by a disulfide to cysteines substituted for residues in the alpha-subunit. Analogs in which the seatbelt was latched to residues 35, 37, 41-43, and 56 of alpha-subunit loop 2 had similar lutropin activities to those of hCG; that in which it was latched to residue 92 at the carboxyl terminus had 10-20% the activity of hCG. Attachment of the seatbelt to alpha-subunit residues 45-51, 86, 88, 90, and 91 reduced lutropin activity substantially. These findings show that the heterodimer can form before the beta-subunit has folded completely and support the notions that the carboxyl-terminal end of the seatbelt, portions of alpha-subunit loop 2, and the end of the alpha-subunit carboxyl terminus do not participate in lutropin receptor interactions. They suggest also that several different architectures could have been sampled without disrupting hormone activity as the glycoprotein hormones diverged from other cysteine knot proteins.
Plant and soil nematodes: societal impact and focus for the future. (1994)

Plant and soil nematodes significandy impact our lives. Therefore, we must understand and manage these complex organisms so that we may continue to develop and sustain our food production systems, our natural resources, our environment, and our quality of life. This publication looks specifically at soil and plant nematology. First, the societal impact of nematodes and benefits of nematology research are briefly presented. Next, the opportunities facing nematology in the next decade are outlined, as well as the resources needed to address these priorities. The safety and sustainability of U.S. food and fiber production depends on public and administrative understanding of the importance of nematodes, the drastic effects of nematodes on many agricultural and horticultural crops, and the current research priorities of nematology.
Fabrication of nanoscale zero-mode waveguides using microlithography for single molecule sensing (2012)

We present a novel approach to the fabrication of zero-mode waveguides (ZMWs) using inexpensive processing techniques. Our method is capable of rapid fabrication of circular nanoapertures with diameters ranging from 70 nm to 2 μm, allowing us to perform a detailed characterization of the dependence of the fluorescence emission on the waveguide diameter. We also validated the use of the fabricated ZMWs by detecting single molecule binding events with a signal-to-noise ratio of ten.
T/TCP -- TCP Extensions for Transactions Functional Specification (1994)

based UDP.