gebhart/patrepeval huggingface dataset:
Efficient thermoelectric performance in silicon nano-films by vacancy-engineering (2015)

The introduction of large concentrations of lattice vacancies in silicon nano-films creates more than a 20-fold reduction in thermal conductivity, while electrical conductivity and Seebeck coefficient are largely maintained. This results in thermoelectric performance comparable to silicon nanowires, but crucially leaves the silicon structure indistinguishable from bulk silicon, resulting in a robust material that is straight-forward to fabricate. This finding significantly advances the potential of silicon ultra-thin-films as a high-performance thermoelectric material.
Some electrochemical and chemical properties of methoxatin and analogous quinoquinones. (1982)

The present study establishes relationships between structure and reactivity for the pyrroloquinoline and phenanthroline quinones. The electrochemical reductions of 1,7- and 1,10-phenanthroline-5,6-quinones, like other quinones, are reversible and occur by 2e- transfer in a single step in aqueous solution and by two 1e(-)-transfer steps in aprotic media. The electron-withdrawing pyridine moieties both increase their potentials and stabilize their aprotic semiquinones. The electrochemistry of the cofactor methoxatin and its trimethylester derivative is similar to the phenanthroline quinones in aqueous solution. However, the electrochemical reductions of methoxatin and its triester in aprotic solutions are characterized by at least three potentials, each accounting for less than 1e-. This has been explained by the proposal of semiquinone complexing with itself and with quinone. Despite an electron-donating pyrrole moiety, methoxatin and its trimethylester have relatively high potentials in aprotic solution. This is presumably due to stabilization of radical anions by the aforementioned complexing or by delocalization with carboxylic acid and ester groups. The reduction potential of methoxatin, in both aqueous and aprotic solvent, suggests that oxidation of methanol should be a thermodynamically favorable process. No evidence for an electrochemically reduced state lower than the quinol was found for any of the compounds. Chemical reactivity is influenced by the orientation of the pyridine nitrogen. The two quinones with a pyridine nitrogen peri to a quinone carbonyl add and oxidize nucleophiles most readily.
G-Rich Oligonucleotides for Cancer Treatment (2009)

Oligonucleotides with guanosine-rich (G-rich) sequences often have unusual physical and biological properties, including resistance to nucleases, enhanced cellular uptake, and high affinity for particular proteins. Furthermore, we have found that certain G-rich oligonucleotides (GROs) have antiproliferative activity against a range of cancer cells, while having minimal toxic effects on normal cells. We have investigated the mechanism of this activity and studied the relationship between oligonucleotide structural features and biological activity. Our results indicate that the antiproliferative effects of GROs depend on two properties: the ability to form quadruplex structures stabilized by G-quartets and binding affinity for nucleolin protein. Thus, it appears that the antiproliferative GROs are acting as nucleolin aptamers. Because nucleolin is expressed at high levels on the surface of cancer cells, where it mediates the endocytosis of various ligands, it seems likely that nucleolin-dependent uptake of GROs plays a role in their activity. One of the GROs that we have developed, a 26-nucleotide phosphodiester oligodeoxynucleotide now named AS1411 (formerly AGRO100 or GRO26B-OH), is currently being tested as an anticancer agent in Phase II clinical trials.
Heparan Sulfate d-Glucosaminyl 3-O-Sulfotransferase-3A SulfatesN-Unsubstituted Glucosamine Residues (1999)

3-O-Sulfation of glucosamine by heparan sulfate D-glucosaminyl 3-O-sulfotransferase (3-OST-1) is the key modification in anticoagulant heparan sulfate synthesis. However, the heparan sulfates modified by 3-OST-2 and 3-OST-3A, isoforms of 3-OST-1, do not have anticoagulant activity, although these isoforms transfer sulfate to the 3-OH position of glucosamine residues. In this study, we characterize the substrate specificity of purified 3-OST-3A at the tetrasaccharide level. The 3-OST-3A enzyme was purified from Sf9 cells infected with recombinant baculovirus containing 3-OST-3A cDNA. Two 3-OST-3A-modified tetrasaccharides were purified from the 3-O-(35)S-sulfated heparan sulfate that was digested by heparin lyases. These tetrasaccharides were analyzed using nitrous acid and enzymatic degradation combined with matrix-assisted laser desorption/ionization-mass spectrometry. Two novel tetrasaccharides were discovered with proposed structures of DeltaUA2S-GlcNS-IdoUA2S-[(35)S]GlcNH(2)3S and DeltaUA2S-GlcNS-IdoUA2S-[3-(35)S]GlcNH(2)3S6S . The results demonstrate that 3-OST-3A sulfates N-unsubstituted glucosamine residues, and the 3-OST-3A modification sites are probably located in defined oligosaccharide sequences. Our study suggests that oligosaccharides with N-unsubstituted glucosamine are precursors for sulfation by 3-OST-3A. The intriguing linkage between N-unsubstituted glucosamine and the 3-O-sulfation by 3-OST-3A may provide a clue to the potential biological functions of 3-OST-3A-modified heparan sulfate.
Identification of a Novel Member (GDF-1) of the Transforming Growth Factor-β Superfamily (1990)

A cDNA clone encoding a new member (designated GDF-1) of the transforming growth factor-beta (TGF beta) superfamily was isolated from a library prepared from day 8.5 mouse embryos. The nucleotide sequence of GDF-1 predicts a protein of 357 amino acids with a mol wt of 38,600. The sequence contains a pair of arginine residues at positions 236-237, which is likely to represent a site for proteolytic processing. The C-terminus following the presumed dibasic cleavage site shows significant homology with the known members of the TGF beta superfamily, matching the other family members at all of the invariant positions, including the seven cysteine residues with their characteristic spacing. GDF-1 is most homologous to Xenopus Vg-1 (52%), but is not likely to be the murine homolog of Vg-1. In vitro translation experiments were consistent with GDF-1 being a secreted glycoprotein. Genomic Southern analysis indicated that GDF-1 may be highly conserved across species. These results suggest that GDF-1 is most likely an extracellular factor mediating cell differentiation events during embryonic development.
Genetic programming theory (2007)

Article Share on Genetic programming theory Authors: Riccardo Poli University of Essex, Colchester, United Kingdom University of Essex, Colchester, United KingdomView Profile , William B. Langdon University of Essex, Colchester, United Kingdom University of Essex, Colchester, United KingdomView Profile Authors Info & Claims GECCO '07: Proceedings of the 9th annual conference companion on Genetic and evolutionary computationJuly 2007Pages 3563–3584https://doi.org/10.1145/1274000.1274124Published:07 July 2007Publication History 44citation212DownloadsMetricsTotal Citations44Total Downloads212Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Spherical mechanism analysis of a surgical robot for minimally invasive surgery -- analytical and experimental approaches. (2005)

Recent advances in technology have led to the fusion of MIS techniques and robot devices. However, current systems are large and cumbersome. Optimizing the surgical robot mechanism will eventually lead to its integration into the operating room (OR) of the future becoming the extended presence of the surgeon and nurses in a room occupied by the patient alone. By optimizing a spherical mechanism using data collected in-vivo during MIS procedures, this study is focused on a bottom-up approach to developing a new class of surgical robotic arms while maximizing their performance and minimizing their size. The spherical mechanism is a rotational manipulator with all axes intersecting at the center of the sphere. Locating the rotation center of the mechanism at the MIS port makes this class of mechanism a suitable candidate for the first two links of a surgical robot for MIS. The required dexterous workspace (DWS) is defined as the region in which 95% of the tool motions are contained based on in-vivo measurements. The extended dexterous workspace (EDWS) is defined as the entire abdominal cavity reachable by a MIS instruments. The DWS is defined by a right circular cone with a vertex angle of 60 degrees and the EDWS is defined by a cone with an elliptical cross section created by two orthogonal vertex angles of 60 degrees and 90 degrees. A compound function based on the mechanism's isotropy and the mechanism stiffness was considered as the performance metric cost function. Optimization across both the DWS and the EDWS lead to a serial mechanism configuration with link length angles of 74 degrees and 60 degrees for a serial configuration. This mechanism configuration maximized the kinematic performance in the DWS while keeping the EDWS as its reachable workspace. Surgeons, using a mockup of two mechanisms in a MIS setup, validated these results experimentally. From these experiments the serial configuration was deemed most applicable for MIS robotic applications compared to a parallel mechanism configuration. The mechanical design of a cable actuated surgical robot was based on optimized link length angles. The system is currently being integrated into a fully operated two-arm system. Small form-factor surgical robotic arms with optimized dexterous workspaces will facilitate the integration of multiple arms while avoiding self-collision in the OR of the future.
Light-generated oligonucleotide arrays for rapid DNA sequence analysis. (1994)

In many areas of molecular biology there is a need to rapidly extract and analyze genetic information; however, current technologies for DNA sequence analysis are slow and labor intensive. We report here how modern photolithographic techniques can be used to facilitate sequence analysis by generating miniaturized arrays of densely packed oligonucleotide probes. These probe arrays, or DNA chips, can then be applied to parallel DNA hybridization analysis, directly yielding sequence information. In a preliminary experiment, a 1.28 x 1.28 cm array of 256 different octanucleotides was produced in 16 chemical reaction cycles, requiring 4 hr to complete. The hybridization pattern of fluorescently labeled oligonucleotide targets was then detected by epifluorescence microscopy. The fluorescence signals from complementary probes were 5-35 times stronger than those with single or double base-pair hybridization mismatches, demonstrating specificity in the identification of complementary sequences. This method should prove to be a powerful tool for rapid investigations in human genetics and diagnostics, pathogen detection, and DNA molecular recognition.
Cell type‐ and promoter‐dependent modulation of the Wnt signaling pathway by sodium butyrate (2001)

The Wnt signaling pathway modulates the transcription of genes linked to proliferation, differentiation and tumor progression. beta-Catenin-Tcf (BCT)-dependent Wnt signaling is influenced by the short-chain fatty acid sodium butyrate, which induces growth arrest and/or maturation of colonic carcinoma cells. We have compared the effects of sodium butyrate on BCT-dependent signaling in 2 colon carcinoma cell lines that differ in their physiologic response to butyrate, with SW620 cells responding to butyrate by undergoing terminal differentiation and apoptosis, and HCT-116 cells undergoing reversible growth arrest, but no significant apoptotic cell death. Furthermore, these colon carcinoma cell lines differ in their mechanism of Wnt pathway activation, with adenomatous polyposis coli (APC) mutant SW620 cells having high levels of BCT complexes and APC wild-type HCT-116 cells having mutant beta-catenin, low levels of BCT complexes and correspondingly higher levels of free Tcf. We have demonstrated that in SW620 cells, butyrate downregulates BCT-dependent expression of the Tcf-TK, matrilysin and cyclin D1 promoters, whereas in HCT-116 cells, butyrate upregulates expression of these promoters. Cotransfection with expression vectors that interfere with the Wnt pathway suggests that butyrate enhances BCT complex-DNA binding. Butyrate reduces the expression of Tcf4 in HCT-116 cells, consistent with the induction by butyrate of Tcf-repressible promoters in these cells. These findings indicate that sodium butyrate modulates the Wnt pathway in SW620 and HCT-116 cells in a different manner and that these differences have consequences for promoter activity that may influence the physiologic response to butyrate.
Molecular cloning and tissue distribution of PHAS-I, an intracellular target for insulin and growth factors. (1994)

Although the actions of insulin and a number of growth factors that signal via protein-tyrosine kinase receptors are believed to involve increased phosphorylation of key intracellular proteins, relatively few of the downstream phosphoproteins have been identified. In this report we describe a cDNA encoding one of the most prominent insulin-stimulated phosphoproteins in rat adipocytes. The cDNA encodes a protein, designated PHAS-I, which has 117 amino acids and a M(r) of 12,400. When translated in vitro and subjected to SDS/PAGE, PHAS-I migrates anomalously, having an apparent M(r) of 21,000. The predicted amino acid composition is interesting in that approximately 45% of the PHAS-I protein is accounted for by only four amino acids--serine, threonine, proline, and glycine. The PHAS-I gene is expressed in a variety of tissues, although the highest levels of mRNA are present in fat and skeletal muscle, two of the most insulin-responsive tissues. The nucleotide and deduced amino acid sequences of PHAS-I differ from any that have been reported, and homology screening provided no clues concerning the function of the protein. However, in view of its tissue distribution and the fact that the protein is phosphorylated in response to insulin, we speculate that PHAS-I is important in insulin action.
Immunogenicity and Safety of 13-Valent Pneumococcal Conjugate Vaccine in Infants and Toddlers (2010)

PCV13 will be as effective as PCV7 in the prevention of pneumococcal disease caused by the 7 common serotypes and could provide expanded protection against the 6 additional serotypes. The PCV13 safety profile was comparable to that of PCV7.
Basic pathogenic mechanisms operating in experimental models of acute anterior uveitis (1998)

Acute anterior uveitis is a recurrent inflammatory disease of the eye that occurs commonly, is distressing for the patient, and may have potentially blinding sequelae. The pathogenesis of the disease is poorly understood, and anti-inflammatory treatment is consequently non-specific and may be associated with significant complications. Animal models are a possible key to a better understanding of this disease. In one model, rats and mice develop a relatively short-lived anterior uveal inflammation almost immediately after systemic injection of bacterial endotoxin. Accumulating evidence suggests that cytokine production by resident uveal macrophages initiates endotoxin-induced uveitis which is characterized by an infiltration of neutrophils and mononuclear cells. A second model displays features in keeping with a delayed-type hypersensitivity immune response. Experimental melanin-induced uveitis is an acute recurrent uveitis with delayed onset but extended duration, observed when rats are immunized with bovine ocular melanin. Both animal models have clinical features in common with acute anterior uveitis, although experimental melanin-induced uveitis appears to mimic the human disease more closely. Novel treatment options to target implicated inflammatory cells and molecules are currently under consideration.
Temporal evolution of beam emittance from a field-emission electron gun (1987)

The temporal evolution of the beam emittance and beam brightness from a field-emission electron gun (1.3 MV, 0.5 kA, 30 ns) has been measured with nanosecond time resolution by using a novel Čerenkov-electro-optic diagnostic. Observations show that guns provided with velvet-backed cathodes behave differently than, and are superior to, the more conventional graphite cathodes.
Focusing of sub-micrometer particles and bacteria enabled by two-dimensional acoustophoresis (2014)

Handling of sub-micrometer bioparticles <italic>e.g.</italic> bacteria is becoming increasingly important in the biomedical field and in environmental and food analysis.
, a Winged Helix Transcriptional Repressor with Expression Restricted to Embryonic Stem Cells (1996)

A novel member of the winged helix (formerly HNF-3/Forkhead) transcriptional regulatory family, termed Genesis, was isolated and characterized. Putative translation of the complete cDNA revealed the winged helix DNA binding domain to be centrally located within the protein, with regions on either side that contain known transcriptional regulatory motifs. Extensive Northern analysis of Genesis found that the message was exclusively expressed in embryonic stem cells or their malignant equivalent, embryonal carcinoma cells. The Genesis transcript was down-regulated when these cells were stimulated to differentiate. DNA sequences that Genesis protein would interact with were characterized and were found to contain a consensus similar to that found in an embryonic stem cell enhancer sequence. Co-transfection experiments revealed that Genesis is a transcriptional repressor. Genesis mapped to mouse chromosome 4 in a region syntenic with human chromosome 1p31, a site of nonrandom abnormalities in germ cell neoplasia, neuroblastoma, and acute lymphoblastic leukemia. Genesis is a candidate for regulating the phenotype of normal or malignant embryonic stem cells.
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema (2013)

The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we performed deep RNA sequencing of the blastema over a time course in the axolotl, a species whose genome has not been sequenced. Using a novel comparative approach to analyzing RNA-seq data, we characterized the transcriptional dynamics of the regenerating axolotl limb with respect to the human gene set. This approach involved de novo assembly of axolotl transcripts, RNA-seq transcript quantification without a reference genome, and transformation of abundances from axolotl contigs to human genes. We found a prominent burst in oncogene expression during the first day and blastemal/limb bud genes peaking at 7 to 14 days. In addition, we found that limb patterning genes, SALL genes, and genes involved in angiogenesis, wound healing, defense/immunity, and bone development are enriched during blastema formation and development. Finally, we identified a category of genes with no prior literature support for limb regeneration that are candidates for further evaluation based on their expression pattern during the regenerative process.
Androgen action: molecular mechanism and medical application. (1994)

Androgen action in many organs, such as prostate and skin, is dependent on the conversion of testosterone by 5 alpha-reductase to 5 alpha-dihydrotestosterone. 5 alpha-Dihydrotestosterone then binds to the androgen receptor to regulate specific gene expression. Inhibitors of 5 alpha-reductase are useful for the selective treatment of prostatic cancer, benign prostate hyperplasia, acne, baldness and female hirsutism, without affecting spermatogenesis, sexual behavior and smooth muscle growth, that do not require the conversion of testosterone to 5 alpha-dihydrotestosterone. Certain unsaturated fatty acids, such as gamma-linolenic acid, are potent 5 alpha-reductase inhibitors, suggesting a linkage between unsaturated fatty acids and androgen action. Mutations in androgen receptor genes are responsible for many cases of androgen-insensitivity. In some prostate cancer cells, some antiandrogens may act like androgens in stimulating the proliferation of the cancer cells because these antiandrogens can bind to a mutated androgen receptor and transactivate target genes. Prostate cancers are usually androgen-dependent initially but can lose dependency and responsiveness. Tumor cells which are resistant to endocrine therapy ultimately proliferate. Androgen-independent or androgen-repressive cells can arise from androgen-sensitive prostate cancer cells by changes in specific gene expression over time in a clonal isolate. This change in androgen responsiveness was accompanied by a change in androgen receptor expression and transcriptional activity as well as expression of some oncogenes.
Interconnected Silicon Hollow Nanospheres for Lithium-Ion Battery Anodes with Long Cycle Life (2011)

Silicon is a promising candidate for the anode material in lithium-ion batteries due to its high theoretical specific capacity. However, volume changes during cycling cause pulverization and capacity fade, and improving cycle life is a major research challenge. Here, we report a novel interconnected Si hollow nanosphere electrode that is capable of accommodating large volume changes without pulverization during cycling. We achieved the high initial discharge capacity of 2725 mAh g(-1) with less than 8% capacity degradation every hundred cycles for 700 total cycles. Si hollow sphere electrodes also show a Coulombic efficiency of 99.5% in later cycles. Superior rate capability is demonstrated and attributed to fast lithium diffusion in the interconnected Si hollow structure.
KLX/KLY Reservoir Management Using Integrated Asset Modeling, Case Study (2004)

Abstract One of the most important areas in Offshore North West Java is KLX/KLY fields, considering their high contribution to the West Java total gas production. Four platforms have been developed in this field to produce gas from shallow, thick and low strength carbonate reservoir. The large gas accumulation in this field is within a thick carbonate build up formation with average gas column thickness of 350-400 ft underlain by the aquifer. The reservoir has high porosities ranging from 32 to 45% and high permeabilities up to several Darcies. As consequences of dominating gas production, reservoir pressure has dropped and gas production rate decreased in this area. To ensure production continuation, well problem anticipation and surface facility remediation, Integrated Asset Modeling (IAM) have been built. Currently, this Asset is focusing on three important sectors, which are Low Pressure Compression, Well Surveillances Planning and Subsidence Management. Low Pressure Compressor ProjectSome scenarios for Low Pressure Compressor Project had been created to optimize gas production and maximize reservoir ultimate recovery.Well Surveillance PlanningIn this section, IAM has been used to control, monitor and perform forecasting for each well. Potential well problem in the future have been predict and planned the appropriate solution through scheduled well intervention.Subsidence ManagementKLX/KLY produce from Carbonate build up reservoir with low rock compressibility. Subsidence phenomena have been observed; therefore, integrated reservoir management is very important in this area. Ultimate subsidence, facility remediation and subsidence effect have been investigated. The purpose of this paper is to present the importance of IAM for KLX/KLY asset to ensure production continuation through the integrated engineering study on reservoir modeling, core analysis, facility remediation and effect of reservoir subsidence on gas production/reservoir performance and surface facility.