gebhart/patrepeval huggingface dataset:
Antibodies against the CD44 p80, lymphocyte homing receptor molecule augment human peripheral blood T cell activation. (1990)

The CD44 inhibitor Lutheran [In(Lu)]-related p80 molecule has recently been shown to be identical to the Hermes-1 lymphocyte homing receptor and to the human Pgp-1 molecule. We have determined the effect of addition of CD44 antibodies to in vitro activation assays of PBMC. CD44 antibodies did not induce PBMC proliferation alone, but markedly enhanced PBMC proliferation induced by a mitogenic CD2 antibody pair or by CD3 antibody. CD44 antibody addition had no effect upon PBMC activation induced by PHA or tetanus toxoid. CD44 antibody enhancement of CD2 antibody-induced T cell activation was specific for mature T cells as thymocytes could not be activated in the presence of combinations of CD2 and CD44 antibodies. CD44 antibody enhancement of CD2-mediated T cell triggering occurred if CD44 antibody was placed either on monocytes or on T cells. In experiments with purified monocyte and T cell suspensions, CD44 antibodies A3D8 and A1G3 augmented CD2-mediated T cell activation by three mechanisms. First, CD44 antibody binding to monocytes induced monocyte IL-1 release, second, CD44 antibodies enhanced the adhesion of T cells and monocytes in CD2 antibody-stimulated cultures, and third, CD44 antibodies augmented T cell IL-2 production in response to CD2 antibodies. Thus, ligand binding to CD44 molecules on T cells and monocytes may regulate numerous events on both cell types that are important for T cell activation. Given that recent data suggest that the CD44 molecule may bind to specific ligands on endothelial cells (vascular addressin) and within the extracellular matrix (collagen, fibronectin), these data raise the possibility that binding of T cells to endothelial cells or extracellular matrix proteins may induce or up-regulate T cell activation in inflammatory sites.
Protein Complex Identification by Integrating Protein-Protein Interaction Evidence from Multiple Sources (2013)

We conclude that incorporating PPI information from other sources can improve the effectiveness of protein complex identification.
1,2-Dithiolan-3-one 1-Oxides:  A Class of Thiol-Activated DNA-Cleaving Agents That Are Structurally Related to the Natural Product Leinamycin (1996)

Leinamycin is a recently discovered, thiol-dependent DNA-cleaving natural product. The mechanism of DNA cleavage by leinamycin is unknown. Inspired by this intriguing natural product, we have investigated the DNA-cleaving properties of three 1,2-dithiolan-3-one 1-oxides (1-3) that are structurally related to the suspected DNA-cleaving "core" of leinamycin. It was found that, similar to leinamycin, these three 1,2-dithiolan-3-one 1-oxides are thiol-dependent DNA-cleaving agents. At the concentrations of 1-3 used in these experiments (approximately 100 microM), efficient DNA cleavage is absolutely dependent on added thiol, with optimum cleavage occurring at 5-10 equiv (500 microM-1 mM) of added thiol. 2-Mercaptoethanol, glutathione, dithiothreitol, and thiophenol function with approximately equal efficiency as triggering agents for the cleavage reaction. DNA cleavage by 1-3 is not highly pH-dependent. Cleavage of DNA by these sulfur heterocycles is diminished by the removal of molecular oxygen from the reaction medium, by the radical scavengers methanol, ethanol, and mannitol, and by the enzyme catalase. Superoxide dismutase does not suppress DNA cleavage by these compounds. When diethylenetriaminepentaacetic acid is employed in these reactions as a chelator of adventitious trace metal ions, DNA cleavage is efficiently inhibited. The S-deoxy analog of 1 does not cleave DNA under conditions where 1 effects efficient thiol-mediated cleavage of DNA. These experiments indicate that, in concert with thiols, 1,2-dithiolan-3-one 1-oxides convert molecular oxygen to DNA-cleaving oxygen radicals. The marked effect of catalase further suggests that molecular oxygen is converted to hydrogen peroxide which ultimately cleaves DNA via a trace metal-dependent Fenton reaction. This work demonstrates that 1,2-dithiolan-3-one 1-oxides represent a general class of thiol-potentiated DNA-cleaving molecules.
Discovery and functional characterization of two diterpene synthases for sclareol biosynthesis in Salvia sclarea(L.) and their relevance for perfume manufacture (2012)

SsLPPS and SsSS are two monofunctional diTPSs which, together, produce the diterpenoid specialized metabolite sclareol in a two-step process. They represent two of the first characterized hydroxylating diTPSs in angiosperms and generate the dihydroxylated labdane sclareol without requirement for additional enzymatic oxidation by activities such as cytochrome P450 monoxygenases. Yeast-based production of sclareol by co-expresssion of SsLPPS and SsSS was efficient enough to warrant the development and use of such technology for the biotechnological production of scareol and other oxygenated diterpenes.
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution (1999)

This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly different from random sequences with the same dinucleotide distribution. For random sequences with the same mononucleotide distribution it has previously been shown that the native mRNA sequences have a lower predicted free energy, which indicates a more stable structure than random sequences. However, dinucleotide content is important when assessing the significance of predicted free energy as the physical stability of RNA secondary structure is known to depend on dinucleotide base stacking energies. Even known RNA secondary structures, like tRNAs, can be shown to have predicted free energies indistinguishable from randomized sequences. This suggests that the predicted free energy is not always a good determinant for RNA folding.
Microarchitecture-level power management (2002)

In this paper, we present a strategy for run-time profiling to optimize the configuration of a superscalar microprocessor dynamically so as to save power with minimum-performance penalty. The configuration of the processor is changed according to the parallelism and power profile of the running application. To identify the optimal configuration, additional hardware with minimal overhead is used to detect the parts of the running application which have good potential for energy savings. Experiments on some benchmark programs show good savings in total energy consumption; we have observed a mean decrease of 18% in average power, and 9% in total energy. Our proposed approach can be used for energy-aware computing in either portable applications or in desktop environments where power density is becoming a concern. This approach can also be incorporated in power-management strategies like advanced configuration and power interface (ACPI) as a replacement for classic thermal management schemes such as static-clock throttling. Our approach is shown to be better than static-throttling methods presently used in power management.
GUN4, a Regulator of Chlorophyll Synthesis and Intracellular Signaling (2003)

Nuclear genes control plastid differentiation in response to developmental signals, environmental signals, and retrograde signals from plastids themselves. In return, plastids emit signals that are essential for proper expression of many nuclear photosynthetic genes. Accumulation of magnesium-protoporphyrin IX (Mg-Proto), an intermediate in chlorophyll biosynthesis, is a plastid signal that represses nuclear transcription through a signaling pathway that, in Arabidopsis, requires the GUN4 gene. GUN4 binds the product and substrate of Mg- chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. Thus, GUN4 participates in plastid-to-nucleus signaling by regulating Mg-Proto synthesis or trafficking.
Single Turn Peptide Alpha Helices with Exceptional Stability in Water (2005)

Cyclic pentapeptides are not known to exist in alpha-helical conformations. CD and NMR spectra show that specific 20-membered cyclic pentapeptides, Ac-(cyclo-1,5) [KxxxD]-NH(2) and Ac-(cyclo-2,6)-R[KxxxD]-NH(2), are highly alpha-helical structures in water and independent of concentration, TFE, denaturants, and proteases. These are the smallest alpha-helical peptides in water.
Optimal ion channel clustering for intracellular calcium signaling (2003)

Ion channels and receptors in the cell membranes and internal membranes are often distributed in discrete clusters. One particularly well-studied example is the distribution of inositol 1,4,5-triphosphate receptors in the plasma membrane that controls the flux of Ca2+ from the endoplasmic reticulum into the cytosol. By using mathematical modeling, we show that channel clustering can enhance the cell's Ca2+ signaling capability. Furthermore, we predict optimal signaling cellular capability at cluster sizes and distances that agree with experimentally found values in Xenopus oocyte.
Review article Multisensor image fusion in remote sensing: Concepts, methods and applications (1998)

With the availability of multisensor, multitemporal, multiresolution and multifrequency image data from operational Earth observation satellites the fusion of digital image data has become a valuable tool in remote sensing image evaluation. Digital image fusion is a relatively new research field at the leading edge of available technology. It forms a rapidly developing area of research in remote sensing. This review paper describes and explains mainly pixel based image fusion of Earth observation satellite data as a contribution to multisensor integration oriented data processing.
Dihydro(alkylthio)(naphthylmethyl)oxopyrimidines:  Novel Non-Nucleoside Reverse Transcriptase Inhibitors of the S-DABO Series (1997)

Novel compounds related to 2-(cyclohexylthio)-3,4-dihydro-5-methyl-6-(3-methylbenzyl)-4-ox opyrimidine (3c, MC 639) have been synthesized and tested as inhibitors of human immunodeficiency virus type-1 (HIV-1). Reaction of thiourea with ethyl arylmethylacetoacetates furnished 5-alkyl-6-(arylmethyl)-3,4-dihydro-2-mercapto-4-oxopyrimidines which were then alkylated at the sulfur atom to afford the required 2-alkylthio or 2-cycloalkylthio derivatives (S-DABOs). Chemical modifications at N-3, C-4, and C-6 of the pyrimidine ring were attempted with the aim of improving antiretroviral activity. In particular, replacement of the benzyl group with the 1-naphthylmethyl moiety enhanced the activity of S-DABOs, whereas N-3 alkylation and C=O transformation into C=S at position 4 of the pyrimidine ring led to compounds devoid of anti-HIV-1 activity. Lower activity was generally observed when 1-naphthylmethyl was replaced by the isomeric 2-naphthylmethyl moiety. The most active compounds showed activity in the low micromolar range with EC50 values comparable to that of nevirapine.
Unusual Sp1-GC box interaction in a parvovirus promoter (1991)

The P4 promoter of the parvovirus minute virus of mice contains a single degenerate GC box sequence which binds the transcription factor Sp1 with high affinity. The two promoters of murine Sp1 were affinity purified, and their interactions with the P4 promoter were examined. Several unusual features were observed. Methylation interference experiments demonstrated that Sp1 makes contacts with both DNA strands, including the central guanine as well as an adenine residue on the cytidine-rich strand of the GC box. UV photocross-linking revealed that the 95- and the 105-kDa promoters cross-link exclusively to opposite strands of the GC box. These results suggest that the phosphorylation of the 95-kDa Sp1 promoter results in a change in the way Sp1 is positioned on the P4 GC box and identifies a high-affinity GC box motif.
Immunoglobulin Replacement Therapy in Primary Antibody Deficiency Diseases – Maximizing Success (2005)

Antibody or humoral immunodeficiencies comprise the largest group of primary immunodeficiency diseases. Since the first description of patients with low gammaglobulin levels more than four decades ago, a great wealth of information has been accumulated. Especially in the last several years, the application of molecular and genetic techniques has unraveled many of these disorders, identifying disorders of B cell development, failure of class switch recombination and abnormalities of specific antibody production. Regardless of the underlying defect, the mainstay of therapy has been and remains immunoglobulin (Ig) replacement therapy, currently by intravenous infusion or subcutaneous injection. With advances in manufacturing, a number of products are not only safe for intravenous administration but doses can be increased to provide even more effective infection prophylaxis. However, manufacturing processes, methods of viral inactivation and removal and final composition differ widely among the available preparations. How these variables impact clinical outcome is not clear, but they have the potential to do so. As a result, careful selection of an intravenous immunoglobulin (IVIG), matching patient needs and risks to those risks associated with a specific IVIG, is necessary to optimize outcomes and maximize the success of Ig replacement therapy.
Circulating tumor and cancer stem cells in hepatitis C virus-associated liver disease (2014)

CTC counts and AFP, CK19, telomerase, and MAGE1/MAGE3 expression predict disease progression in patients with HCV, whereas telomerase, MAGE3, CD90, CD133 and CK19 are prognostic markers in HCC.
Designing highly active siRNAs for therapeutic applications (2010)

The discovery of RNA interference (RNAi) generated considerable interest in developing short interfering RNAs (siRNAs) for understanding basic biology and as the active agents in a new variety of therapeutics. Early studies showed that selecting an active siRNA was not as straightforward as simply picking a sequence on the target mRNA and synthesizing the siRNA complementary to that sequence. As interest in applying RNAi has increased, the methods for identifying active siRNA sequences have evolved from focusing on the simplicity of synthesis and purification, to identifying preferred target sequences and secondary structures, to predicting the thermodynamic stability of the siRNA. As more specific details of the RNAi mechanism have been defined, these have been incorporated into more complex siRNA selection algorithms, increasing the reliability of selecting active siRNAs against a single target. Ultimately, design of the best siRNA therapeutics will require design of the siRNA itself, in addition to design of the vehicle and other components necessary for it to function in vivo. In this minireview, we summarize the evolution of siRNA selection techniques with a particular focus on one issue of current importance to the field, how best to identify those siRNA sequences likely to have high activity. Approaches to designing active siRNAs through chemical and structural modifications will also be highlighted. As the understanding of how to control the activity and specificity of siRNAs improves, the potential utility of siRNAs as human therapeutics will concomitantly grow.
Stem cells in pathobiology and regenerative medicine (2008)

This issue of the Journal of Pathology contains 16 articles largely dealing with the role of tissue-specific adult stem cells in the pathogenesis of disease, notably cancer. These authoritative reviews begin by describing the current knowledge regarding the identity and molecular regulation of normal tissue-specific stem cells, before itemizing their role in the aetiology and progression of disease. Fundamental concepts regarding the stem cell niche have been gleaned from studies of germ line stem cells in Drosophila and Caenorhabditis elegans, and these are described in detail in this issue. Somatic cell reprogramming, a process underlying not only therapeutic cloning but also the production of induced pluripotent stem (iPS) cells, is further discussed. Much attention is given to embryonic stem (ES) and iPS cells within the scientific community; this issue of the Journal of Pathology redresses this imbalance by illustrating the pivotal role of adult stem cells in much of human disease.
Growth of aligned carbon nanotubes with controlled site density (2002)

Pulse-current electrochemical deposition has been used to prepare Ni nanoparticles that are used as the catalysts for the growth of aligned carbon nanotubes. The nucleation site density of the Ni nanoparticles was controlled by changing the magnitude and duration of the pulse current. The aligned carbon nanotubes from the nickel nanoparticles were grown by plasma enhanced hot filament chemical vapor deposition. The site density of the aligned carbon nanotubes varied from 105 to 108 cm−2. The achievement of controlling the site density is significant for applications of carbon nanotubes as field emitters, nanoelectrodes array, etc.
Marked dependence of enzyme prochiral selectivity on the solvent (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMarked dependence of enzyme prochiral selectivity on the solventFernand Terradas, Michelle Teston-Henry, Paul A. Fitzpatrick, and Alexander M. KlibanovCite this: J. Am. Chem. Soc. 1993, 115, 2, 390–396Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/ja00055a004https://doi.org/10.1021/ja00055a004research-articleACS PublicationsRequest reuse permissionsArticle Views293Altmetric-Citations81LEARN 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
Modern superabsorbent polymer technology (1998)

Absorbency and Superabsorbency (F. Buchholz). Chemistry of Superabsorbent Polyacrylates (T. Staples, et al.). Commercial Processes for the Manufacture of Superabsorbent Polymers (A. Graham & L. Wilson). Analysis and Characterization of Superabsorbent Polymers (S. Cutie, et al.). The Structure and Properties of Superabsorbent Polyacrylates (F. Buchholz). Other Superabsorbent Polymer Forms and Types (D. Allan). Applications of Superabsorbent Polymers (F. Buchholz).
Differential expression of insulin-like growth factor II mRNA in human primary liver cancers, benign liver tumors, and liver cirrhosis. (1988)

We investigated insulin-like growth factor II (IGF-II) mRNA in three groups of human liver samples including primary liver cancers, benign liver tumors and cirrhosis; indeed these pathological conditions would allow us to distinguish between different steps in liver carcinogenesis. A 40- to 100-fold increase in IGF-II mRNA was shown in 9/40 of the liver cancer samples as compared to normal adult liver. RNA blot analysis using both IGF-II cDNA and oligonucleotide probes showed the reexpression of two fetal (6 and 5 kilobases) IGF-II transcripts in primary liver cancers and in some cirrhotic adjacent tissues; these included all the samples with enhanced IGF-II expression. By contrast the adult (5.3 kilobases) IGF-II transcript was identified in most of the benign liver tumors and liver cirrhosis; in addition, in some of these samples, the 5-kilobase fetal transcript was also detected. The increase of IGF-II mRNA in some liver cancers is consistent with an autocrine mechanism conferring a selective growth advantage to tumorous liver cells. Furthermore, these results indicate a differential expression of IGF-II transcripts in nonmalignant hepatocyte proliferation (benign liver tumors and cirrhosis) as compared to liver cancer. Finally this study suggests that, in liver cirrhosis and in some benign liver tumors, premalignant proliferative states might be identified by the presence of IGF-II fetal transcripts.
Analgesic activity of high-dose intravenous calcitonin in cancer patients with bone metastases (2006)

We undertook a prospective, nonrandomized study with the objective to evaluate the efficacy of salmon calcitonin (sCT) in controlling pain secondary to bone metastases. Our study population consisted of 45 cancer patients with bone metastases (26 men) with a mean age of 64 years (range, 48-70) who had completed chemotherapy, hormonal therapy and radiation therapy at least 30 days prior to enrollment in the study, and had intractable pain despite the use of common analgesics (acetaminophen, nonsteroidal anti-inflammatory agents, opioids) and bisphosphonates. The study medication was a 300-IU dose of sCT administered intravenously daily for 5 consecutive days and repeated every two weeks until no response was noticeable. The analgesic efficacy of sCT was evaluated by means of Huskisson's visual analogue scale and Keele's pain scale; the daily consumption of analgesic drugs and performance status were also monitored. None of the patients managed to completely discontinue the use of other analgesics, but 5 patients (11% of the total number) had an analgesic response that lasted 4 weeks and less than 5% of the patients continued to respond for 6 weeks. No significant side effects were observed. Our data show that intravenous calcitonin administered in a relatively high dose has a very limited therapeutic potential as an adjuvant analgesic for a short period of time in selected cancer patients with bone metastases.