gebhart/patrepeval huggingface dataset:
Dietary constituents altering the responses to chemical carcinogens. (1976)

This paper deals with two categories of compounds having the capacity to inhibit the neoplastic effects of chemical carcinogens on the host. The first are inducers of increased microsomal mixed function oxidase activity. An increasing number of these inducers are being found in natural products. Cruciferous vegetables including brussels sprouts, cabbage, and cauliflower contain such compounds. Recently indole-3-acetonitrile, indole-3-carbinol and 3,3'-diindolylmethane have been identified as inducers in these three plants. Other naturally occurring inducers include flavones, safrole, isosafrole, beta-ionone, and oxidized sterols. Since previous work has shown that synthetic inducers may protect against chemical carcinogens, the composition of the diet could play a role in inhibiting the neoplastic response to these carcinogenic agents. The second category of inhibitors comprises the antioxidants. Several of these compounds have been found to inhibit the carcinogenic effects of a variety of chemical carcinogens. Considerable work of this nature has been done with butylated hydroxyanisole and butylated hydroxytoluene two antioxidants extensively used as food additives. Other antioxidants having carcinogen inhibiting capacities include ethoxyquin, disulfiram, and dimethyldithiocarbamate.
The Medicinal Chemistry of Therapeutic Oligonucleotides (2016)

Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
CikA, a Bacteriophytochrome That Resets the Cyanobacterial Circadian Clock (2000)

The circadian oscillator of the cyanobacterium Synechococcus elongatus, like those in eukaryotes, is entrained by environmental cues. Inactivation of the gene cikA (circadian input kinase) shortens the circadian period of gene expression rhythms in S. elongatus by approximately 2 hours, changes the phasing of a subset of rhythms, and nearly abolishes resetting of phase by a pulse of darkness. The CikA protein sequence reveals that it is a divergent bacteriophytochrome with characteristic histidine protein kinase motifs and a cryptic response regulator motif. CikA is likely a key component of a pathway that provides environmental input to the circadian oscillator in S. elongatus.
Circadian Rhythms Confer a Higher Level of Fitness to Arabidopsis Plants (2002)

Circadian rhythms have been demonstrated in organisms across the taxonomic spectrum. In view of their widespread occurrence, the adaptive significance of these rhythms is of interest. We have previously shown that constitutive expression of the CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) gene in Arabidopsis plants (CCA1-ox) results in loss of circadian rhythmicity. Here, we demonstrate that these CCA1-ox plants retain the ability to respond to diurnal changes in light. Thus, transcript levels of several circadian-regulated genes, as well as CCA1 itself and the closely related LHY, oscillate robustly if CCA1-ox plants are grown under diurnal conditions. However, in contrast with wild-type plants in which transcript levels change in anticipation of the dark/light transitions, the CCA1-ox plants have lost the ability to anticipate this daily change in their environment. We have used CCA1-ox lines to examine the effects of loss of circadian regulation on the fitness of an organism. CCA1-ox plants flowered later, especially under long-day conditions, and were less viable under very short-day conditions than their wild-type counterparts. In addition, we demonstrate that two other circadian rhythm mutants, LHY-ox and elf3, have low-viability phenotypes. Our findings demonstrate the adaptive advantage of circadian rhythms in Arabidopsis.
DNA Vaccine Against Tumor Endothelial Marker 8 Inhibits Tumor Angiogenesis and Growth (2009)

Numerous evidences indicated that angiogenesis was a crucial step in the development of tumor, thus the immunotherapy of antiangiogenesis has been involved as potentially relevant candidate targets of cancer immunotherapy. Recently, tumor endothelial marker 8 (TEM8) was discovered to be dominantly expressed in tumor endothelium, which presented a new strategy to antiangiogenesis therapy. However, up to date, the related study of TEM8 on antiangiogenesis is very few. In this study, we constructed a xenogenic DNA vaccine encoding human TEM8 carried by attenuated Salmonella typhimurium. The results demonstrated that oral administration of this xenogenic vaccine overcame peripheral immune tolerance and generated TEM8-specific CD8 cytotoxic T-cell response. Moreover, this vaccine effectively protected mice from lethal challenges against tumor cells, reducing tumor growth, and increasing the mice life span. In addition, angiogenesis in the tumors was suppressed without obvious side effect. These results indicated that DNA vaccine encoding xenogenic TEM8 might act as a potential strategy for antiangiogenesis immunotherapy of tumors.
Dkk-1-derived Synthetic Peptides and Lithium Chloride for the Control and Recovery of Adult Stem Cells from Bone Marrow (2004)

It is established that human mesenchymal stem cells (hMSCs) from bone marrow are a source of osteoblast progenitors in vivo and under appropriate conditions, differentiate into osteoblasts ex vivo. Because hMSCs are recovered by iliac crest aspirate and enriched by virtue of their adherence to tissue culture plastic, the cells provide a convenient ex vivo model for the study of osteogenic tissue repair in an experimentally accessible system. Recent advances in the field of skeletal development and osteogenesis have demonstrated that signaling through the canonical wingless (Wnt) pathway is critical for the differentiation of progenitor cell lines into osteoblasts. Inhibition of such signals can predispose MSCs to cell cycle entry and inhibit osteogenesis. Here, we report that synthetic peptides derived from the second cysteine-rich domain of the canonical Wnt inhibitor Dickkopf-1 (Dkk-1) have utility in controlling the growth and recovery of hMSCs from bone marrow stroma. Three peptides corresponding to residues 217-269 in Dkk-1 were each found to enhance the proliferation of hMSCs in culture over 2 days. The most active peptide exhibited agonistic characteristics in that it ablated the proliferation lag observed when cultures of hMSCs receive fresh medium. It also reduced the expression of endogenous Dkk-1 (Gregory, C. A., Singh, H., and Prockop, D. J. (2003) J. Biol. Chem. 278, 28067-28078). When the cytosolic level of beta-catenin was elevated by addition of LiCl to cultures of hMSCs, the peptide also accelerated degradation of beta-catenin on withdrawal of lithium. A second peptide, corresponding to residues 184-204 had preferential and high affinity for hMSCs in the log phase of proliferation. Peptide overlay assays on hMSC lysates confirmed that the peptide bound to a 184-kDa protein corresponding to the molecular mass of LRP6. Cells recovered by this peptide had enhanced osteogenic potential but less chondrogenic potential compared with controls. Because Wnt antagonists increase the number of non-committed hMSCs in culture, they may be of use in increasing the rate of osseous wound healing in vivo by increasing the level of systemically migrating hMSCs. Therefore, such molecules could contribute to the development of a novel family of pharmaceutical agents for the improvement of the healing process in humans.
Jet Impingement Systems for Electroplating Applications: Mass Transfer Correlations (1983)

A study is presented of mass transfer rates in some jet impingement systems which are suitable for electrochemical processes where high transfer rates are required. Experimental data are presented and an empirical correlating equation is proposed. An application to high speed electroplating of printed circuit boards is described.
A decentralized solution to the Security Constrained DC-OPF problem of multi-area power systems (2005)

This paper presents a new method for the decentralized solution of the Security Constrained Optimal Power Flow (SCOPF) problem in large interconnected power systems. The method decomposes the overall SCOPF problem of a multi- area system into independent SCOPF sub-problems, one for each area. The solutions of the SCOPF sub-problems of the different areas are coordinated through a pricing mechanism until they converge to a reduced scope central SCOPF solution. The prices used for the coordination of the sub-problem solutions are the prices of electricity exchanges between adjacent areas. The reduced scope SCOPF of a multi-area power system is a SCOPF with a reduced set of security constraints, in which the effects of contingencies outside an area on monitored elements within the area are ignored. Test results from the application of the method to the IEEE 3-area RTS-96 and to the Balkan power system are presented.
Late versus early repair of Achilles tendon rupture. Clinical and biomechanical evaluation. (1995)

Eleven patients who had late reconstruction for Achilles tendon rupture were compared with 10 patients who had immediate repair. The followup period averaged 8 years for both groups. Results, based on a clinical score, were successful (excellent or good) for all but 1 patient. Although manual testing demonstrated normal plantar flexion strength in all but 1 patient, significant differences were seen in isometric and isokinetic plantar flexion strength of the involved sides as compared with the uninvolved sides of these patients. The patient with the unsuccessful result had abnormalities in vertical, foreaft, and medial-lateral force components of the ground reaction force. Three-dimensional motion analysis showed decreased total motion in the sagittal plane on the operated side as compared with the unoperated side in this patient. The data indicated that patients with late reconstruction of Achilles tendon rupture have successful clinical results comparable with those of early repair.
Brain deposition of beta-amyloid is a common pathologic feature in HIV positive patients (2005)

We propose that prolonged HAART and aging may contribute to an overall increase in amyloid deposition, potentially mediated by inhibition of insulin degradation enzyme (IDE) or disruption of the axonal transport of the amyloid precursor protein.
A multi-gene approach to differentiate papillary thyroid carcinoma from benign lesions: gene selection using support vector machines with bootstrapping (2007)

Selection of novel molecular markers is an important goal of cancer genomics studies. The aim of our analysis was to apply the multivariate bioinformatical tools to rank the genes - potential markers of papillary thyroid cancer (PTC) according to their diagnostic usefulness. We also assessed the accuracy of benign/malignant classification, based on gene expression profiling, for PTC. We analyzed a 180-array dataset (90 HG-U95A and 90 HG-U133A oligonucleotide arrays), which included a collection of 57 PTCs, 61 benign thyroid tumors, and 62 apparently normal tissues. Gene selection was carried out by the support vector machines method with bootstrapping, which allowed us 1) ranking the genes that were most important for classification quality and appeared most frequently in the classifiers (bootstrap-based feature ranking, BBFR); 2) ranking the samples, and thus detecting cases that were most difficult to classify (bootstrap-based outlier detection). The accuracy of PTC diagnosis was 98.5% for a 20-gene classifier, its 95% confidence interval (CI) was 95.9-100%, with the lower limit of CI exceeding 95% already for five genes. Only 5 of 180 samples (2.8%) were misclassified in more than 10% of bootstrap iterations. We specified 43 genes which are most suitable as molecular markers of PTC, among them some well-known PTC markers (MET, fibronectin 1, dipeptidylpeptidase 4, or adenosine A1 receptor) and potential new ones (UDP-galactose-4-epimerase, cadherin 16, gap junction protein 3, sushi, nidogen, and EGF-like domains 1, inhibitor of DNA binding 3, RUNX1, leiomodin 1, F-box protein 9, and tripartite motif-containing 58). The highest ranking gene, metallophosphoesterase domain-containing protein 2, achieved 96.7% of the maximum BBFR score.
Differences in the Protease Activities of Tetanus and Botulinum B Toxins Revealed by the Cleavage of Vesicle-Associated Membrane Protein and Various Sized Fragments (1994)

Botulinum neurotoxin serotype B (BoNT/B) and tetanus toxin (TeTx) block neuroexocytosis through selective endoproteolysis of vesicle-associated membrane protein (VAMP). The enzymological properties of both toxins were compared for the first time in their cleavage of VAMP and various sized fragments using a sensitive chromatographic assay. The optimal substrate sizes for the zinc-dependent protease activities of the light chains of TeTx and BoNT/B were established using synthetic peptides corresponding to the hydrophilic core of VAMP (30-62 amino acids in length). TeTx was found to selectively cleave the largest peptide at a single site, Gln76-Phe77. It exhibited the most demanding specificity, requiring the entire hydrophilic domain (a 62-mer) for notable hydrolysis, whereas BoNT/B efficiently cleaved the much smaller 40-mer. Thus, an unusually long N-terminal sequence of 44 amino acids upstream of the scissile bond is required for the selective hydrolysis of VAMP by TeTx. Using the largest peptide, BoNT/B and TeTx exhibited approximately 50% and 35%, respectively, of the activities shown toward intact VAMP, detergent solubilized from synaptic vesicles. Given the large size of the smallest substrates, it is possible that these neurotoxins recognize and require a three-dimensional structure. Although both toxins were inactivated by divalent metal chelators, neither was antagonized by phosphoramidon or ASQFETS (a substrate-related peptide that spans the cleavage site), and TeTx was only feebly inhibited by captopril; also, they were distinguishable in their relative activities at different pHs, temperatures, and ionic strengths. These collective findings are important in the design of effective inhibitors for both toxins, as well as in raising the possibility that TeTx and BoNT/B interact somewhat differently with VAMP.
The RNA Molecule CsrB Binds to the Global Regulatory Protein CsrA and Antagonizes Its Activity in Escherichia coli (1997)

The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay. A recombinant CsrA protein containing a metal-binding affinity tag (CsrA-H6) was purified to homogeneity and authenticated by N-terminal sequencing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and other studies. This protein was entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single approximately 350-nucleotide RNA, CsrB. cDNA cloning and nucleotide sequencing revealed that the csrB gene is located downstream from syd in the 64-min region of the Escherichia coli K-12 genome and contains no open reading frames. The purified CsrA-CsrB ribonucleoprotein complex was active in regulating glg (glycogen biosynthesis) gene expression in vitro, as was the RNA-free form of the CsrA protein. Overexpression of csrB enhanced glycogen accumulation in E. coli, a stationary phase process that is repressed by CsrA. Thus, CsrB RNA is a second component of the Csr system, which binds to CsrA and antagonizes its effects on gene expression. A model for regulatory interactions in Csr is presented, which also explains previous observations on the homologous system in Erwinia carotovora. A highly repeated nucleotide sequence located within predicted stem-loops and other single-stranded regions of CsrB, CAGGA(U/A/C)G, is a plausible CsrA-binding element.
Increasing the Number of Thyroid Lesions Classes in Microarray Analysis Improves the Relevance of Diagnostic Markers (2009)

We show that diagnostic tools defined on the basis of microarray data are more relevant when a large number of samples and tissue classes are used. Taking into account the relationships between the thyroid tumor pathologies, together with the main biological functions and pathways involved, improved the diagnostic accuracy of the samples. Our approach was particularly relevant for the classification of microfollicular adenomas.
Recent Advances in Photo-Crosslinkable Hydrogels for Biomedical Applications (2019)

Photo-crosslinkable hydrogels have recently attracted significant scientific interest. Their properties can be manipulated in a spatiotemporal manner through exposure to light to achieve the desirable functionality for various biomedical applications. This review article discusses the recent advances of the most common photo-crosslinkable hydrogels, including poly(ethylene glycol) diacrylate, gelatin methacryloyl and methacrylated hyaluronic acid, for various biomedical applications. We first highlight the advantages of photopolymerization and discuss diverse photosensitive systems used for the synthesis of photo-crosslinkable hydrogels. We then introduce their synthesis methods and review their latest state of development in biomedical applications, including tissue engineering and regenerative medicine, drug delivery, cancer therapies and biosensing. Lastly, the existing challenges and future perspectives of engineering photo-crosslinkable hydrogels for biomedical applications are briefly discussed.
Activity‐Fed Translation (AFT) Assay: A New High‐Throughput Screening Strategy for Enzymes in Droplets (2015)

There is an increasing demand for the development of sensitive enzymatic assays compatible with droplet-based microfluidics. Here we describe an original strategy, activity-fed translation (AFT), based on the coupling of enzymatic activity to in vitro translation of a fluorescent protein. We show that methionine release upon the hydrolysis of phenylacetylmethionine by penicillin acylase enabled in vitro expression of green fluorescent protein. An autocatalytic setup where both proteins are expressed makes the assay highly sensitive, as fluorescence was detected in droplets containing single PAC genes. Adding a PCR step in the droplets prior to the assay increased the sensitivity further. The strategy is potentially applicable for any activity that can be coupled to the production of an amino acid, and as the microdroplet volume is small the use of costly reagents such as in vitro expression mixtures is not limiting for high-throughput screening projects.
Whole Genome Amplification with Phi29 DNA Polymerase to Enable Genetic or Genomic Analysis of Samples of Low DNA Yield (2008)

In many large genetic studies, the amount of available DNA can be one of the criteria for selecting samples for study. In the case of large population cohorts, selecting samples based on their DNA yield can lead to biased sample selection. In addition, many valuable clinical and research sample collections exist in which the amount of DNA is very small. Unbiased whole genome amplification (WGA) of such unique samples enables genomewide scale genetic studies that would have been impossible otherwise. Multiply primed rolling circle amplification (MPRCA) and multiple displacement amplification (MDA) methods are based on the same principle. The DNA amplification is non-PCR based and uses Phi29 DNA polymerase and random hexamer primers for unbiased whole genome amplification. MDA is used for linear DNA molecules, such as genomic DNA. This chapter reviews the various applications in which whole genome amplified DNA can be used, the types of commercial kits available, and the quality control steps necessary before using the DNA in the genetic studies.
Diazoethenes: their attempted synthesis from aldehydes and aromatic ketones by way of the Horner-Emmons modification of the Wittig reaction. A facile synthesis of alkynes (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiazoethenes: their attempted synthesis from aldehydes and aromatic ketones by way of the Horner-Emmons modification of the Wittig reaction. A facile synthesis of alkynesJ. C. Gilbert and U. WeerasooriyaCite this: J. Org. Chem. 1982, 47, 10, 1837–1845Publication Date (Print):May 1, 1982Publication History Published online1 May 2002Published inissue 1 May 1982https://pubs.acs.org/doi/10.1021/jo00349a007https://doi.org/10.1021/jo00349a007research-articleACS PublicationsRequest reuse permissionsArticle Views7142Altmetric-Citations228LEARN 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
Elevated Conformational Rigidity in Dipeptides Incorporating Piperazic Acid Derivatives (1998)

N-Acyl derivatives of piperazic acids display an unusual degree of conformational rigidity. As a consequence, α-N-coupling of a piperazic acid of given configuration (d or l) with an α-aminoacyl unit of opposite configuration (l or d) produces a “heterochiral” dipeptide that exists in a conformation conducive to the formation of a peptide turn. Piperazic acids and related compounds may thus be regarded as conformationally rigid analogues of proline, and because they are readily available in either antipodal form by synthesis, they should become of great interest in the study of peptide turns.