gebhart/patrepeval huggingface dataset:
Review on microfluidic studies for EOR application (2019)

All the time the flow of fluids happens below the surface of the earth. These flow processes can only be imagined, but not be fully visualised on how fluid flow behaviour occurs though the porous medium of the rocks. Hence comes the play of microfluidic micromodels. These are a transparent version of slices (2 dimensional) porous structure of rocks such as sandstone duplicated onto materials such as glass, polymers and silicon wafers. Fluids such as crude oil, surfactant and polymer solutions and gases such as carbon dioxide (CO2) are injected through special pumps into these transparent micromodels. The flow patterns and behaviours hence developed inside the micromodels are studied and analysed. Micromodels have helped in different branches of science such as medicine, genetics, liquid channelling and enhanced oil recovery (EOR). The concern of this paper is to study the flow behaviour and EOR in micromodels. Micromodels can be made to represent a micro version of a partially saturated rock with crude oil. The various chemical EOR processes such as surfactant flooding, polymer flooding, gas flooding injected into crude oil filled micromodels with water saturation is studied. The advancement of front developed between displacing and displaced fluids, the fingering effect, the presence of high permeability streaks is observed. Also the breakthrough of the flood front is analysed from the various experiments reviewed. This review paper is undertaken so as to help researchers find a consolidated and concise literature of the trends and developments in microfluidics especially in EOR.
The pyruvate formate lyase family: sequences, structures and activation (2004)

We cloned and expressed in Escherichia coli the Archaeglobus fulgidus gene that encodes pyruvate formate lyase 2 (PFL2). PFL2, despite its homology to the other glycyl radical enzymes, differs from them by exhibiting a completely different oligomerization. The most abundant form of PFL2 when expressed in E.coli is a trimer. The closest homologue of PFL2 with a known structure is E. coli PFL, which is a dimer. Sequence comparisons allowed us to reclassify PFL-like enzymes and the consensus sequences allowed us to propose an activation route for PFL-like glycyl radical enzymes. Surprisingly, most of the conserved residues in PFL-like enzymes appear to be involved in preserving the structure, rather than forming the active site.
Origin of nitrite and nitrate in nasal and exhaled breath condensate and relation to nitric oxide formation (2005)

Besides the salivary glands, plasma nitrate is taken up by the lower airways but not the nasal airways. Nitrate levels in EBC are thus influenced by dietary intake. Nitrate is reduced to nitrite by bacterial activity which takes place primarily in the oropharyngeal tract of healthy subjects. Only oropharyngeal nitrite seems to contribute to exhaled NO in non-inflamed airways, and there is also a substantial contribution of nitrite from the oropharyngeal tract during standard collection of EBC.
Interleukin 2 gene transfer into tumor cells abrogates tumorigenicity and induces protective immunity. (1990)

To study the effects of localized secretion of cytokines on tumor progression, the gene for human interleukin 2 (IL-2) was introduced via retroviral vectors into CMS-5 cells, a weakly immunogenic mouse fibrosarcoma cell line of BALB/c origin. Secretion of low levels of IL-2 from the tumor cells abrogated their tumorigenicity and induced a long-lasting protective immune response against a challenge with a tumorigenic dose of parental CMS-5 cells. Co-injection of IL-2-producing CMS-5 cells with unmodified tumor cells inhibited tumor formation even when highly tumorigenic doses of CMS-5 cells were used. Cytolytic activity in mice injected with parental CMS-5 cells was transient and was greatly diminished 3 wk after injection, as commonly observed in tumor-bearing animals. However, in mice injected with IL-2-producing cells, tumor-specific cytolytic activity persisted at high levels for the duration of the observation period (at least 75 d). High levels of tumor-specific cytolytic activity could also be detected in parental CMS-5 tumor-bearing animals 18 d after inoculation with tumor cells, if IL-2-producing CMS-5 cells but not unmodified parental tumor cells were used as targets. These studies highlight the potential advantages of localized secretion of cytokines mediated via gene transfer to induce potent anti-tumor immune responses.
Role of a Class Dhc1b Dynein in Retrograde Transport of Ift Motors and Ift Raft Particles along Cilia, but Not Dendrites, in Chemosensory Neurons of Living Caenorhabditis elegans (1999)

The heterotrimeric motor protein, kinesin-II, and its presumptive cargo, can be observed moving anterogradely at 0.7 microm/s by intraflagellar transport (IFT) within sensory cilia of chemosensory neurons of living Caenorhabditis elegans, using a fluorescence microscope-based transport assay (Orozco, J.T., K.P. Wedaman, D. Signor, H. Brown, L. Rose, and J.M. Scholey. 1999. Nature. 398:674). Here, we report that kinesin-II, and two of its presumptive cargo molecules, OSM-1 and OSM-6, all move at approximately 1.1 microm/s in the retrograde direction along cilia and dendrites, which is consistent with the hypothesis that these proteins are retrieved from the distal endings of the cilia by a retrograde transport pathway that moves them along cilia and then dendrites, back to the neuronal cell body. To test the hypothesis that the minus end-directed microtubule motor protein, cytoplasmic dynein, drives this retrograde transport pathway, we visualized movement of kinesin-II and its cargo along dendrites and cilia in a che-3 cytoplasmic dynein mutant background, and observed an inhibition of retrograde transport in cilia but not in dendrites. In contrast, anterograde IFT proceeds normally in che-3 mutants. Thus, we propose that the class DHC1b cytoplasmic dynein, CHE-3, is specifically responsible for the retrograde transport of the anterograde motor, kinesin-II, and its cargo within sensory cilia, but not within dendrites.
Prevention and treatment of non-steroidal anti-inflammatory drug-induced gastro-duodenal damage: rationale for the use of antisecretory compounds. (1999)

Gastro-duodenal mucosa possesses an array of defensive mechanisms and non-steroidal anti-inflammatory drugs have a deleterious effect on most of them. This results in a mucosa less able to cope with even a reduced acid load. The presence of acid appears to be a conditio sine qua non for non-steroidal anti-inflammatory drug-injury, which is in fact pH-dependent. The acute damage induced by acid non-steroidal anti-inflammatory drugs, like aspirin, can be markedly reduced or even prevented by raising intragastric pH with antacids or antisecretory compounds. Animal studies have clearly shown that not only the degree, but also the duration, of acid inhibition is an important factor for prevention of non-steroidal anti-inflammatory drug-induced mucosal damage. As a consequence, proton pump inhibitors (PPIs) appear to be more effective that H2-receptor antagonists both in preventing and treating gastro-duodenal lesions. While acid suppression seems to be the only effective mechanism for ulcer healing, prevention of non-steroidal anti-inflammatory drug-injury might also rely on the mucosal protective activity of these compounds. Clinical pharmacological studies, performed in healthy volunteers, have shown that--as in laboratory animals--elevation of intragastric pH by means of antacids or antisecretory compounds protects against acute NSAID-induced damage. Unlike H2-blockers, PPIs protect from non-steroidal anti-inflammatory drug-injury not only the duodenum, but also the stomach, where the majority of mucosal lesions are usually located. Although elevation of intragastric pH affects non-steroidal anti-inflammatory drug pharmacokinetics and pharmacodynamics in laboratory animals, a lack of drug-to-drug interaction between PPIs and some of these compounds has been reported in humans. To summarize, clinical and experimental pharmacology support the use of PPIs for the prevention and treatment of non-steroidal anti-inflammatory drug-induced gastro-duodenal damage. Acid suppression could, however, represent only one of the many mechanisms by which these compounds protect gastro-duodenal mucosa. Further studies are, therefore, needed to better elucidate the respective role of the various pharmacological actions in their mucosal protective activity as well as to assess the clinical relevance of each of them.
Nanotubule-Based Molecular-Filtration Membranes (1997)

Polymeric membranes that contain a collection of monodisperse gold nanotubules, with inside diameters of molecular dimensions (less than 1 nanometer), were used in a simple membrane-permeation experiment to cleanly separate small molecules on the basis of molecular size. For example, when such a membrane was presented with an aqueous feed solution containing pyridine (molecular weight 79) and quinine (molecular weight 324), only the smaller pyridine molecule was transported through the nanotubules and into a receiver solution on the other side of the membrane.
Bioreactor Production of Human α 1 ‐Antitrypsin Using Metabolically Regulated Plant Cell Cultures (2002)

Transgenic rice cell cultures, capable of producing recombinant human alpha(1)-antitrypsin (rAAT), were scaled up from shake flasks to a 5-L bioreactor. The maximum specific growth rates (mu(max)) observed from two bioreactor runs were 0.40 day(-1) (doubling time of 1.7 days) and 0.47 day(-1) (doubling time of 1.5 days), and the maximum specific oxygen uptake rates were 0.78 and 0.84 mmol O(2)/(g dw h). Using a metabolically regulated rice alpha-amylase (RAmy3D) promoter, signal peptide, and terminator, sugar deprivation turned on rAAT expression, and rAAT was secreted into the culture medium. After 1 day of culture in sugar-free medium, there was still continued biomass growth, oxygen consumption, and viability. Extracellular concentrations of 51 and 40 mg active rAAT/L were reached 1.7 and 2.5 days, respectively, after induction in a sugar-free medium. Volumetric productivities for two batch cultures were 7.3 and 4.6 mg rAAT/(L day), and specific productivities were 3.2 and 1.6 mg rAAT/(g dw day). Several different molecular weight bands of immunoreactive rAAT were observed on immunoblots.
Killing Bacterial Spores with Blue Light: When Innate Resistance Meets the Power of Light (2012)

This article is a highlight of the study by Maclean et al. in this issue of Photochemistry and Photobiology describing the sporicidal effects 405 nm visible light alone on endospores of the Clostridium and Bacillus genera. 1.73 kJ cm(-2) was capable of reducing endospore colony-forming units by up to 4-log(10). These findings have never been previously demonstrated and may be incorporated into decontamination methods that span medical, military and food preparatory applications.
Demonstration of inter- and intraspecies differences in serotonin binding sites by antibodies from an autistic child. (1985)

Serotonin (5-HT) binding sites from bovine and rat cerebral cortex membranes share pharmacological properties that allow both to be subclassified by the same criteria. We show here that [3H]5-HT binding sites from human cortex also possess pharmacological properties that follow the same subclassification scheme as for bovine and rat cortex. In addition, we show that solubilized 5-HT1 and 5-HT3 sites from all three species have an s20,w value of 3.4. Despite these similar pharmacological and physical characteristics, we can demonstrate antigenic differences between receptor types and species. Human 5-HT1A sites can be distinguished from human 5-HT1B, 5-HT2, and 5-HT3 sites and from equivalent sites in rat and bovine cortex. The anti-human 5-HT1A antibodies were discovered in the blood of an autistic child and may have clinical or etiologic significance for this disorder.
Small-Angle X-Ray Scattering from RNA, Proteins, and Protein Complexes (2007)

Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D scattering profiles have made possible the generation of useful low-resolution molecular models from SAXS data. Furthermore, SAXS is well suited for the study of unfolded or partially folded conformational ensembles as a function of time or solution conditions. Here, we review recently developed algorithms for 3-D structure modeling and applications to protein complexes. Furthermore, we discuss the emerging use of SAXS as a tool to study membrane protein-detergent complexes. SAXS is proving useful to study the folding of functional RNA molecules, and finally we discuss uses of SAXS to study ensembles of denatured proteins.
Detection of integrated papillomavirus sequences by ligation‐mediated PCR (DIPS‐PCR) and molecular characterization in cervical cancer cells (2001)

Human papillomavirus (HPV) genomes usually persist as episomal molecules in HPV associated preneoplastic lesions whereas they are frequently integrated into the host cell genome in HPV-related cancers cells. This suggests that malignant conversion of HPV-infected epithelia is linked to recombination of cellular and viral sequences. Due to technical limitations, precise sequence information on viral–cellular junctions were obtained only for few cell lines and primary lesions. In order to facilitate the molecular analysis of genomic HPV integration, we established a ligation-mediated PCR assay for the detection of integrated papillomavirus sequences (DIPS-PCR). DIPS-PCR was initially used to amplify genomic viral–cellular junctions from HPV-associated cervical cancer cell lines (C4-I, C4-II, SW756, and HeLa) and HPV-immortalized keratinocyte lines (HPKIA, HPKII). In addition to junctions already reported in public data bases, various new fusion fragments were identified. Subsequently, 22 different viral–cellular junctions were amplified from 17 cervical carcinomas and 1 vulval intraepithelial neoplasia (VIN III). Sequence analysis of each junction revealed that the viral E1 open reading frame (ORF) was fused to cellular sequences in 20 of 22 (91%) cases. Chromosomal integration loci mapped to chromosomes 1 (2n), 2 (3n), 7 (2n), 8 (3n), 10 (1n), 14 (5n), 16 (1n), 17 (2n), and mitochondrial DNA (1n), suggesting random distribution of chromosomal integration sites. Precise sequence information obtained by DIPS-PCR was further used to monitor the monoclonal origin of 4 cervical cancers, 1 case of recurrent premalignant lesions and 1 lymph node metastasis. Therefore, DIPS-PCR might allow efficient therapy control and prediction of relapse in patients with HPV-associated anogenital cancers. © 2001 Wiley-Liss, Inc.
Chimeras of the Homing Endonuclease PI‐SceI and the Homologous Candida tropicalis Intein: A Study to Explore the Possibility of Exchanging DNA‐Binding Modules to Obtain Highly Specific Endonucleases with Altered Specificity (2004)

Homing endonucleases are extremely specific endodeoxyribonucleases. In vivo, these enzymes confer mobility on their genes by inducing a very specific double-strand cut in cognate alleles that lack the cooling sequence for the homing endonuclease; the cellular repair of the double-strand break with the endonuclease-containing allele as a template leads to integration of the endonuclease gene, completing the homing process. As a result of their extreme sequence specificity, homing endonucleases are promising tools for genome engineering. For this purpose, it is desirable to design enzymes with defined new specificities. To analyse which DNA-binding elements are potential candidates for use in the design of enzymes with modified or even new specificity, we produced several chimeric proteins derived from the Saccharomyces cerevisiae VMA1 intein (PI-SceI) and the related Candida tropicalis VMA1 intein. Although the mature Candida intein is devoid of endonucleolytic activity, the exchange of two DNA-binding modules of PI-SceI with the homologous elements from the Candida intein results in an active endonuclease. The low sequence homology in these modules indicates that different protein-DNA contacts are responsible for the recognition of related DNA sequences. This flexibility in DNA recognition should, in principle, allow endonucleases to be produced with new specificities useful for genome engineering.
Direct pattern fabrication on silicone resin by vapor phase electron beam polymerization (1983)

A new technique for high resolution lithography with a dry-developed multilayer resist system is demonstrated. The technique involves a direct pattern fabrication by electron beam-induced vapor phase graft polymerization. The selective pattern formation in irradiated areas was performed using PMMA or silicone resin as a base film and styrene as a grafting monomer. The base film patterns can be fabricated by dry etching with the mask of grafted patterns. However, because of isotropic behavior in the growth of grafted polymer, the base film thickness to be directly etched with the mask of graft-polymerized film is severely limited by the resolution to be achieved. The combination of thin silicone resin as a directly etched layer using graft-polymerized film and thick organic polymer as the bottom layer can solve the conflict between resolution and overall resist thickness, because the silicone resin has an excellent durability against oxygen RIE of organic polymers. Submicron pattern formation with a high aspect ratio was demonstrated with this dry-developed multilayer resist system.
Solid‐Phase Syntheses of Unnatural Biopolymers Containing Repeating Urea Units (1995)

New “oligourea”-based peptidomimetics are the subject of this communication. Two new derivatives of this type, including the Leu-enkephalin analog 1, have been prepared by addition of suitably protected isocyanates to amino acids supported on Rink's amide resin. The chemistry described is designed for solid-phase approaches to combinatorial libraries by split syntheses.
Developing directly photodefinable substrate guiding layers for block copolymer directed self-assembly (DSA) patterning (2011)

Directed self-assembly (DSA) of block copolymers has gained significant attention in recent years as a possible alternative for large area fabrication of future sub-30 nm lithographic patterns. To achieve this patterning, at least three critical pieces are needed: (1) a block copolymer with sufficient immiscibility of the two blocks to drive phase separation at the low molecular weights required to achieve such small phase domains, (2) a method for selectively removing one of the blocks after phase separation to achieve formation of a relief pattern, and (3) a method for producing the templated surfaces used to guide and register the phase separated patterns on the substrate of interest. Current methods for achieving the patterned substrate template, whether they are of chemoepitaxial or graphoepitaxial nature, are generally complex involving a large number of steps that are not easily applied to a variety of different substrate surfaces. For example, numerous substrates have been studied to provide neutral wettability to the styrene-methacrylate (PS-b- PMMA) block copolymers, such as random styrene-methacrylate copolymer films (PS-r-PMMA) or self-assembled monolayer (SAM) modified surfaces, which induce perpendicularly oriented morphologies for PS-b-PMMA self-assembly. In the case of chemical epitaxy processes, a layer of photoresist is generally then coated on such neutral substrate films and patterned to render commensurability to the periodicity of the PS-b-PMMA being used. The open (i.e. space) regions in the resist are then exposed to alter their chemistry, e.g. soft X-ray or oxygen plasma exposures have been used, to achieve hydrophilicity which should preferentially wet PMMA. Finally, the resist is stripped and the block copolymer is coated and assembled on the template surface. Obviously such multi-step processes would not be preferred if alternatives existed. As a step toward that goal of making DSA processes simpler, a photodefinable substrate film that can be used for PS-b-PMMA self-assembly has been developed in this work that is coated, exposed, and baked in a manner analogous to current optical photoresists. The polymer resin for this material is a form of protected poly(hydroxystyrene) that is cross-linkable. The new material is suitable for DSA processes using both solvent and thermal annealing methods. Results of PS-b-PMMA DSA on this new material will be discussed.
Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE): Determining Therapeutic Goals for Treat-to-Target (2015)

Evidence- and consensus-based recommendations for selecting the goals for treat-to-target strategies in patients with IBD are made available. Prospective studies are needed to determine how these targets will change disease course and patients' quality of life.
About modus ponens and aggregation of rules (2002)

There exists some paradoxal situation about aggregation of rules, when solving this problem either by use of some conjunction operator or by use of some disjunction one, depending on the choice of the ply operator. A unified framework is proposed for aggregating rules by the introduction of a new modus ponens based on conditional formulae.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
All-trans retinoic acid in acute promyelocytic leukemias. II. In vitro studies: structure-function relationship (1990)

All-trans retinoic acid induces leukemic cells from patients with acute promyelocytic leukemia (M3) to differentiate in vitro to mature granulocytes which express the CD15 antigen and are capable of respiratory burst function. Of 35 M3 samples, only one failed to respond. In eight cases, we compared the efficacy of two naturally occurring isomers of retinoic acid, all-trans RA and 13-cis RA. Both isomers induce maximal differentiation at 10(-6) mol/L. The maximal response was maintained at 10(-7) mol/L for the all-trans but not for the 13-cis RA. We also observed that the metabolites 4-oxo-all-trans and 4-oxo-13-cis were effective at 10(-6) mol/L. This 1 order of magnitude difference in the in vitro differentiating potencies of all-trans RA and 13-cis RA in the blasts of promyelocytic leukemias predicts a difference in the clinical efficacy of the two drugs.