gebhart/patrepeval huggingface dataset:
Electrochemical biofilm control: a review (2015)

One of the methods of controlling biofilms that has widely been discussed in the literature is to apply a potential or electrical current to a metal surface on which the biofilm is growing. Although electrochemical biofilm control has been studied for decades, the literature is often conflicting, as is detailed in this review. The goals of this review are: (1) to present the current status of knowledge regarding electrochemical biofilm control; (2) to establish a basis for a fundamental definition of electrochemical biofilm control and requirements for studying it; (3) to discuss current proposed mechanisms; and (4) to introduce future directions in the field. It is expected that the review will provide researchers with guidelines on comparing datasets across the literature and generating comparable datasets. The authors believe that, with the correct design, electrochemical biofilm control has great potential for industrial use.
Stability of Copigmented Anthocyanins and Ascorbic Acid in a Grape Juice Model System (2004)

The stability of red grape anthocyanins (Vitis vinifera) was evaluated in a model juice system during normal (25 degrees C) and accelerated storage (35 degrees C) in the presence of ascorbic acid. Rosemary polyphenolic cofactors (0, 0.2, and 0.4% v/v) were evaluated as anthocyanin stabilizing agents. Cofactor addition resulted in concentration-dependent hyperchromic (up to 178%) and bathochromic (up to 23 nm) shifts, indicating a more intense red coloration of the models. Anthocyanin and ascorbic acid degradation followed first-order kinetics during storage. Results showed that copigmented treatments underwent a lower conversion of L-ascorbic acid into dehydroascorbic acid during storage when compared to the control, favorably impacting the vitamin retention of these models. Copigmentation did not affect anthocyanin degradation in the absence of ascorbic acid but in its presence aided to retain a higher anthocyanin content than the control. This study indicated that the addition of anthocyanin cofactors could be used to reduce the pigment and vitamin degradation while masking detrimental color changes in anthocyanin containing products.
Preparation of Red Dyes Derived from Quinacridone Pigment by Introducing N-substituent and Their Characteristics as a Colorant for LCD Color Filter (2012)

Six red dyes derived from quinacridone pigment (C. I. Pigment Red 122) were prepared by introducing an N-alkyl group or N-acyl group in the quinacridone ring. The characteristics of the synthesized dyes were examined by absorption maxima, solubility and thermogravimetric analysis (TGA). The introduction of N-alkyl group gave very little bathochromic shift of 2∼3 nm, whereas the presence of a withdrawing group at the nitrogen exhibited a large hypsochromic shift of 60∼45nm comparing to that of C. I. Pigment Red 122 which is unsubstitued at the nitrogen atom. In terms of weight reduction at 250°C, N-alkyl groups withstood to the thermal decomposition in comparison with the behavior of withdrawing groups at the position of nitrogen atom. The solubility of six dyes was dramatically increased by the introduction of N-substituent which clearly indicates their character as a dye rather than a pigment.
High Plasma Fibrinogen is Correlated With Poor Response to Trastuzumab Treatment in HER2 Positive Breast Cancer (2015)

Some of HER-2 positive breast cancer patients failed to trastuzumab treatment. Recent reports have indicated the correlation between plasma coagulation parameters and clinical characteristics in breast cancer. The aim of this study was to analyze the role of coagulation parameters in trastuzumab treated patients. Coagulation parameters from trastuzumab treated breast cancer patients were retrospectively studied from 2006 to 2010. The correlation between routine coagulation levels and clinical characteristics were analyzed, including prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT), fibrinogen (Fib) and D-dimer (DD). The Kaplan-Meier analysis and Cox regression hazard model were applied to assess their effect on prognosis. Totally 102 hospitalized breast cancer patients who received trastuzumab were collected and followed-up. All patients were HER-2 positive advanced breast cancer, with a median age of 45 years old. Extended PT, APTT, and TT were found in trastuzumab treatment non-effective group, as well as increased Fib and DD. But significant increase was only found in Fib. High Fib status (Fib > 2.88 g/L) was correlated with clinical characteristics, such as pathological grade, and reversely correlated with PTEN expression. More importantly, poor disease-free survival (DFS) and overall survival (OS) to trastuzumab treatment were found in high Fib breast cancer patients. This retrospective study suggests high Fib status was correlated with poor treatment response to trastuzumab. Our findings indicated that Fib > 2.88 should alert physicians to consider a pretreatment for reducing Fib levels before trastuzumab treatment in HER-2 positive breast cancer patients.
Bifunctional Carbon Nanotubes by Sidewall Protection (2005)

Abstract A vertically aligned array of multiwalled carbon nanotubes (MWCNTs) impregnated with polystyrene is utilized to independently functionalize each end of the MWCNTs. The presence of the polystyrene matrix prevents sidewall oxidation of the CNTs, resulting in carboxylate derivatization at the CNT tips during processing via plasma oxidation. The membrane is subsequently dissolved in toluene, resulting in a suspension of CNTs with carboxylate‐derivatized tips. The CNT tips are further functionalized using carbodiimide‐mediated linking of carboxylate at the CNT tips with an amine of 2‐aminoethanethiol. This treatment results in thiol functionality and Fourier‐transform infrared (FT‐IR) studies confirm amide‐bond formation. Gold nanoparticles that are readily observed using transmisison electron microscopy (TEM) are then covalently linked to the thiol functional groups. Estimates of the average nanoparticle density are observed to decrease from ∼ 526 particles μm –1 near the CNT tips to negligible values (&lt; 7 particles μm –1 ) at locations beyond 700 nm from the CNT tips. This is consistent with a membrane geometry where CNTs tips are above the polystyrene surface owing to differing oxidation rates. Bifunctional CNTs (with different chemical functionality at either end of each CNT) is achieved by thiol functionalization on only one side of the oxidized CNT membrane floating on top of a 2‐aminoethanethiol functionalization reaction solution. After dissolution of the polystyrene matrix, TEM analysis shows gold‐nanoparticle decoration at the thiol‐functionalized end of the CNT.
Corrosion inhibition approach of oil production systems in offshore oilfields (2004)

Abstract Synthesis and modification of imidazoline were carried out based on review of the corrosion inhibitor development and application for oilfields. A series of imidazoline compounds were synthesised through the solvent dewatering and vacuum dewatering methods. After reaction of imidazoline with ethane oxide, the produced compound was used to react with halogen hydrocarbon and polyphosphoric acid respectively. Finally an agent with performance of corrosion‐inhibition, sterilisation and anti‐scaling was obtained. The structures of the compounds were characterised by the Fourier transformation infrared spectrum. The relationships between corrosion inhibition effectiveness of the compounds and their structures were investigated so as to determine the structure of a novel corrosion inhibitor. The selected corrosion inhibitor was evaluated by a series of experiments to understand the characteristics of imidazoline derivative and some major factors associated with oil production in the oilfields of China. The experimental results showed that this corrosion inhibitor has outstanding performance of corrosion inhibition and sterilization, and is suitable for corrosion inhibition of the oil abstraction systems with high water‐content in the offshore oilfields.
Ultrasound-Mediated Transfection of Mammalian Cells (1996)

Mammalian cells were successfully transfected with plasmid DNA in vitro using ultrasound transmitted through the walls of cell culture flasks or plates. Primary rat fibroblasts or chondrocytes were exposed to ultrasound in the presence of plasmids containing lacZ or neo genes. The transfection efficiency was evaluated by counting the number of beta-galactosidase (beta-Gal) positive cells or neomycin-resistant colonies. Transfection efficiency was optimized by varying ultrasound conditions, ambient temperatures (room temperature or 37 degrees C), plasmid concentrations, and initial cell populations. Additional experiments were performed performed to elucidate the mechanism of the ultrasound-mediated transfection. Maximal gene transfection was seen with two ultrasound conditions: 1-MHz carrier frequency 411 +/- 189 kPascal continuous wave with 20 or 30 sec of exposure time, and 1 MHz carrier frequency 319 +/- 157 kPascal continuous wave with 40 or 60 sec of exposure time. Gene expression was negligible when transfection procedures were performed at room temperature. The average stable transfection rate was 0.34% of surviving cells with a plasmid concentration of 40 micrograms/ml in primary fibroblasts. The transient transfection rate was 2.4% of surviving cells for primary chondrocytes. Data suggest that increasing plasmid concentration will increase efficiency. Identical treatment with 3.5 MHz produced no transfection, implying that cavitation produced by the ultrasound pressure wave appeared to play a critical role in mediating transfection. Ultrasound-mediated transfection was effective for suspended cells as well as for plated cells. This transfection method is simple, easy to keep sterile, and convenient. Ultrasound-mediated transfection appears to be a promising method for gene transfer into mammalian cells.
Growth Rate Patterns of Solid Tumors and Their Relation to Responsiveness to Therapy (1978)

The clinical doubling times of human solid tumors are reviewed. Methods are also described for estimating subclinical tumor doubling times, and these methods are applied to Wilms' tumor, choriocarcinoma, Burkitt's tumor, and breast cancer. Rapidly growing tumors are often responsive to therapy, and such complete responses are often quite durable. Slowly growing tumors respond less favorably to therapy, and responses are generally not durable. Rapidly growing tumors in advanced stages are similar in their response behavior to the slowly growing tumors. A strategy based on cell kinetics principles and tumor doubling time data is proposed for improving therapeutic results in responsive tumors. Data on clinical and subclinical tumor doubling times are used to distinguish early recurrences from late recurrences in a given tumor type. Early recurrences call for intensification of induction therapy, whereas late recurrences call for prolongation of consolidative therapy. This strategy may also apply in adjuvant therapy of slowly growing tumors.
Myxobacterial Epothilones and Tubulysins as Promising Anticancer Agents (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
The α/β hydrolase fold (1992)

We have identified a new protein fold--the alpha/beta hydrolase fold--that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta sheet, not barrel, of eight beta-sheets connected by alpha-helices. These enzymes have diverged from a common ancestor so as to preserve the arrangement of the catalytic residues, not the binding site. They all have a catalytic triad, the elements of which are borne on loops which are the best-conserved structural features in the fold. Only the histidine in the nucleophile-histidine-acid catalytic triad is completely conserved, with the nucleophile and acid loops accommodating more than one type of amino acid. The unique topological and sequence arrangement of the triad residues produces a catalytic triad which is, in a sense, a mirror-image of the serine protease catalytic triad. There are now four groups of enzymes which contain catalytic triads and which are related by convergent evolution towards a stable, useful active site: the eukaryotic serine proteases, the cysteine proteases, subtilisins and the alpha/beta hydrolase fold enzymes.
Mastro studio (2013)

Ontology-based data access (OBDA) is a novel paradigm for accessing large data repositories through an ontology, that is a formal description of a domain of interest. Supporting the management of OBDA applications poses new challenges, as it requires to provide effective tools for (i) allowing both expert and non-expert users to analyze the OBDA specification, (ii) collaboratively documenting the ontology, (iii) exploiting OBDA services, such as query answering and automated reasoning over ontologies, e.g., to support data quality check, and (iv) tuning the OBDA application towards optimized performances. To fulfill these challenges, we have built a novel system, called MASTRO STUDIO, based on a tool for automated reasoning over ontologies, enhanced with a suite of tools and optimization facilities for managing OBDA applications. To show the effectiveness of MASTRO STUDIO, we demonstrate its usage in one OBDA application developed in collaboration with the Italian Ministry of Economy and Finance.
Adenovirus-Mediated Transfer of the CFTR Gene to Lung of Nonhuman Primates: Toxicity Study (1993)

In preparation for human trials of gene therapy for cystic fibrosis (CF), we performed a preclinical study of gene transfer into the lungs of baboons. Recombinant adenovirus vectors containing expression cassettes for human cystic fibrosis transmembrane conductance regulator (CFTR) and Escherichia coli beta-galactosidase (lacZ) were instilled through a bronchoscope into limited regions of lung in 14 baboons. A detailed accounting of the extent, distribution, and duration of gene expression is contained in a companion article (Engelhardt et al., 1993b). In this article, we report the results of toxicity studies in which clinical laboratory tests, chest radiographs, and necropsy studies were used to detect adverse effects. The only adverse effect noted was a mononuclear cell inflammatory response within the alveolar compartment of animals receiving doses of virus that were required to induce detectable gene expression. Minimal inflammation was seen at 10(7) and 10(8) pfu/ml, but at 10(9) and more prominently at 10(10) pfu/ml, a perivascular lymphocytic and histiocytic infiltrate was seen. The intensity of inflammation increased between 4 and 21 days. At its greatest intensity, there was diffuse alveolar wall damage with intra-alveolar edema. Airways were relatively spared, despite the intensity of alveolar inflammation. Clinical tests did not accurately reflect the presence of lung inflammation, with the exception of chest radiographs which revealed alveolar infiltrates, but only in regions of lung having the greatest intensity inflammation. We conclude that adenovirus-mediated gene transfer into the lungs of baboons is associated with development of alveolar inflammation at high doses of virus.
Thermodynamic and kinetic examination of protein stabilization by glycerol (1981)

The effect of concentrated glycerol on the thermal transitions of chymotrypsinogen and ribonuclease has been examined by differential spectrophotometry at 293 and 287 mm, respectively. It was found that for both proteins addition of glycerol raises the transition temperature, the increase in Tm being greater for ribonuclease than for chymotrypsinogen. This increase in the free energy of denaturation appears to reflect primarily a decrease in the entropy change. Analysis in terms of the Wyman linkage equation shows that, for both proteins, the exclusion of glycerol from the protein domain increases on denaturation i.e., the chemical potential of glycerol becomes even more positive when the protein unfolds relative to the native structure. This provides the thermodynamic stabilization free energy. Results of the kinetic examination of the slow unfolding reaction are consistent with the concept that the preferential exclusion of glycerol is related, at least in part, to enhanced solvent ordering.
Comprehensive Expression Profiling of Rice Grain Filling-Related Genes under High Temperature Using DNA Microarray (2007)

To elucidate the effect of high temperature on grain-filling metabolism, developing rice (Oryza sativa) "Nipponbare" caryopses were exposed to high temperature (33 degrees C/28 degrees C) or control temperature (25 degrees C/20 degrees C) during the milky stage. Comprehensive gene screening by a 22-K DNA microarray and differential hybridization, followed by expression analysis by semiquantitative reverse transcription-PCR, revealed that several starch synthesis-related genes, such as granule-bound starch synthase I (GBSSI) and branching enzymes, especially BEIIb, and a cytosolic pyruvate orthophosphate dikinase gene were down-regulated by high temperature, whereas those for starch-consuming alpha-amylases and heat shock proteins were up-regulated. Biochemical analyses of starch showed that the high temperature-ripened grains contained decreased levels of amylose and long chain-enriched amylopectin, which might be attributed to the repressed expression of GBSSI and BEIIb, respectively. SDS-PAGE and immunoblot analysis of storage proteins revealed decreased accumulation of 13-kD prolamin, which is consistent with the diminished expression of prolamin genes under elevated temperature. Ripening under high temperature resulted in the occurrence of grains with various degrees of chalky appearance and decreased weight. Among them, severely chalky grains contained amylopectin enriched particularly with long chains compared to slightly chalky grains, suggesting that such alterations of amylopectin structure might be involved in grain chalkiness. However, among high temperature-tolerant and sensitive cultivars, alterations of neither amylopectin chain-length distribution nor amylose content were correlated to the degree of grain chalkiness, but rather seemed to be correlated to grain weight decrease, implying different underlying mechanisms for the varietal difference in grain chalkiness. The possible metabolic pathways affected by high temperature and their relevance to grain chalkiness are discussed.
p130Cas interacts with estrogen receptor α and modulates non-genomic estrogen signaling in breast cancer cells (2004)

Steroid hormones bind to their receptors and trans-activate target genes. Rapid non-genomic action of steroid hormones has been proposed in addition to the one at the genomic level. Estrogen has been described to activate c-Src kinase and this activation has been shown to be responsible for estrogen-dependent mitogenicity. A major substrate of c-Src kinase activity is the cytoskeletal protein p130Cas, originally identified in v-Src-transformed cells. We show that in the human breast carcinoma T47D cells, upon estrogen treatment, p130Cas rapidly and transiently associates with the estrogen receptor alpha in a multi-molecular complex containing the c-Src kinase and the p85 subunit of PI 3-kinase. Association of p130Cas with the estrogen receptor alpha occurs within 3 minutes of estrogen treatment and is dependent on c-Src kinase activation. Transient overexpression of p130Cas in T47D cells increases estrogen-dependent Src kinase and Erk1/2 MAPKs activities and accelerates their kinetics of stimulation. A similar effect was detected on estrogen-dependent cyclin D1 expression, suggesting a role for p130Cas in regulating estrogen-dependent cell cycle progression. Double-stranded small RNA interference (siRNA) by silencing endogenous p130Cas protein, was sufficient to inhibit estrogen-dependent Erk1/2 MAPKs activity and cyclin D1 induction, demonstrating the requirement of p130Cas in such events. Therefore, our data show that the adaptor protein p130Cas associates with the estrogen receptor transducing complex, regulating estrogen-dependent activation of c-Src kinase and downstream signaling pathways.
Influence of nucleotide sequence adjacent to duplex DNA termini on 3′ terminal labeling by terminal transferase (1979)

We have analyzed the effect of base-pairing at the exposed ends of Hinc II fragments of SV40 DNA on the efficiency of ribonucleotide incorporation catalyzed by terminal transferase. Wide variations in the labeling efficiency of individual DNA fragments have been observed. To elucidate the nature of this variation at the molecular level, we have correlated this effect with nucleotide sequence adjacent to the cleavage site. We found that a G:C base pair right at the exposed end drastically reduces the incorporation of ribonucleotides. Furthermore, the higher the number of G:C base pairs adjacent to the exposed end, the greater the reduction in labeling efficiency. From these results, we conclude that the labeling efficiency is determined by the degree of 'terminal breathing' of the DNA molecule at the exposed end of the duplex.
A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers (2006)

The secreted protein sonic hedgehog (Shh) plays an integral role in forming the ventral midline of the vertebrate central nervous system (CNS). In the absence of Shh function, ventral midline development is perturbed resulting in holoprosencephaly (HPE), a structural malformation of the brain, as well as in neuronal patterning and path finding defects along the length of the anteroposterior neuraxis. Central to the understanding of ventral neural tube development is how Shh transcription is regulated in the CNS. To address this issue, we devised an enhancer trap assay to systematically screen 1 Mb of DNA surrounding the Shh locus for the ability to target reporter gene expression to sites of Shh transcription in transgenic mouse embryos. This analysis uncovered six enhancers distributed over 400 kb, the combined activity of which covered all sites of Shh expression in the mouse embryonic CNS from the ventral forebrain to the posterior extent of the spinal cord. To evaluate the relative contribution of these enhancers to the overall pattern of Shh expression, individual elements were deleted in the context of a transgenic Bac reporter assay. Redundant mechanisms were found to control Shh-like reporter activity in the ventral spinal cord, hindbrain and regions of the telencephalon, whereas unique elements regulated Shh-like expression in the ventral midbrain, the majority of the ventral diencephalon and parts of the telencephalon. Three ventral forebrain enhancers locate on the distal side of translocation breakpoints that occurred upstream of Shh in human cases of HPE, suggesting that displacement of these regulatory elements from the Shh promoter is a likely cause of HPE in these individuals.