gebhart/patrepeval huggingface dataset:
Visible-light-driven photocatalytic S- and C- codoped meso/nanoporous TiO2 (2010)

The first facile and efficient soft synthesis for fabricating S- and C- co-doped hierarchically meso/nanoporous TiO2 is hereby presented. The doping of sulfur is achieved through a counter strategy, in which the precursor of TiO2 is added to the sulfur hydrosol. The sulfur nanoparticles in the sulfur hydrosol serve as the seeds for the formation of bimodal meso/nanopores TiO2 upon calcination treatment. The prepared anatase TiO2 exhibited excellent thermal stability and photocatalytic activity. In comparison to commercial P25 TiO2, our S- and C- codoped meso/nanoporous anatase TiO2 exhibits remarkably enhanced visible light-driven photocatalytic activity on the decomposition of methylene blue (MB). The samples also showed excellent cyclic stability in the photocatalytic activity of degrading MB. The formation mechanism of these S-, C- codoped hierarchically meso/nanoporous TiO2 spheres is also discussed. The high photocatalytic activity in the visible light region is attributed to numerous oxygen vacancies, acidic sites on the surface of TiO2, and large specific surface area.
Induction of Apoplastic Invertase of Chenopodium rubrum by D-Glucose and a Glucose Analog and Tissue-Specific Expression Suggest a Role in Sink-Source Regulation (1995)

Photoautotrophic suspension-culture cells of Chenopodium rubrum that were shifted to mixotrophic growth by adding glucose were used as model system to investigate the influence of the source-sink transition in higher plants on the expression and enzyme activities of intracellular and extracellular invertases. The complete cDNA coding for an extracellular invertase was cloned and sequenced from C. rubrum, and its identity has been proven by heterologous expression in Saccharomyces cerevisiae. The higher activity of extracellular invertase after preincubation in the presence of glucose was paralleled by an increased expression of the corresponding gene. The induction by glucose could be mimicked by the nonmetabolizable glucose analog 6-deoxyglucose. Both enzyme activity and mRNA level of extracellular invertase showed a sink-tissue-specific distribution in plants. The activity of neutral and acidic intracellular invertases were not affected by preincubation of autotrophic tissue cultures with sugars, nor did they show a tissue-specific distribution in plants. The data suggest that apoplastic invertase not only has an important function in phloem unloading and carbohydrate partitioning between source and sink tissues but may also have a role in establishing metabolic sinks.
A lab-on-a-chip for cell detection and manipulation (2003)

This paper presents a lab-on-a-chip for electronic manipulation and detection of microorganisms based on the use of closed dielectrophoretic (DEP) cages combined with impedance sensing. A prototype has been realized using a standard printed circuit board (PCB) technology by which polystyrene microbeads have been trapped, concentrated and quantitated, in agreement with CAD simulations, without the need for external optical components. The experiment was successfully repeated with S. cerevisiae. The approach is suited to be implemented in integrated circuit technology, which would allow to manipulate and detect single cells and reduce the system dimension.
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008)

The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.
Intramolecular Resonance Dipole−Dipole Interactions in a Profluorescent Protease Substrate (1998)

In this study NorFES, an undecapeptide containing an amino acid sequence recognized by the serine protease elastase, was covalently labeled with two xanthenes, one on each side of its cleavage site, to serve as a tool for examination of intramolecular resonance dipole−dipole interactions. To this end using all possible combinations from the group of xanthenes including fluorescein, tetramethylrhodamine, and rhodamine-X, three heterobichromophoric and three homobichromophoric NorFES derivatives were synthesized; their absorption and fluorescence spectra were measured both before and after cleavage by elastase. In the heterobichromophoric substrates the fluorescence of the fluorophore that would be the nominal donor in a Förster model system was quenched. Since the fluorescence intensity of the nominal acceptor in these substrates was also decreased, these data were not consistent with the Förster model. Rather, spectra for all six doubly labeled peptides could be explained by delocalization of excitation over each substrate's two fluorophores. Thus, by taking into account dipole−dipole interactions between two dyes placed in close proximity to each other, the spectral properties observed could not be ascribed to the monomeric components but were the unique optical signature of each ground-state dimer.
Patterning of random interconnect using double exposure of strong-type PSMs (2001)

This paper discusses a new PSM algorithm to generate a pair of sub-mask patterns to achieve 2-D random patterns by double exposure. Test layout was automatically decomposed into two sub-PSMs with about 190 steps of geometrical operations including simple OPCs. Both simulation and experiments showed that 0.28-micrometer pitch random wiring is achieved with our method, suggesting local wiring at 70- (50-) nm node logic LSIs combined with ArF (F2) exposure tools.
Characterization of a novel androgen-sensitive, prostate-specific antigen-producing prostatic carcinoma xenograft: LuCaP 23. (1996)

Prostatic carcinoma has proven extremely difficult to establish as cell lines or xenografts. In this article, we describe a new series of prostate cancer xenografts propagated in athymic mice, designated LuCaP 23, developed from prostate metastases harvested at autopsy shortly after death. Tumor from three separate metastatic deposits was developed into three xenograft sublines: two from lymph node metastases (LuCaP 23.1 and 23.8) and one from a liver metastasis (LuCaP 23.12). Fluorescence in situ hybridization analysis confirms the xenografts are human. Histologically, the xenografts are comprised of columnar epithelial cells arranged in a glandular pattern. Tumor doubling times range from 11 to 21 days for the three sublines. The cells secrete large amounts of prostate-specific antigen (PSA) with PSA indices of 1.27, 1.63, and 5.21 ng/ml/mm3 for the mice bearing the LuCaP 23.1, 23.8, and 23.12 sublines, respectively. Following androgen deprivation a temporary decrease in PSA secretion and a decrease in tumor size are noted in most tumors. Eventually, the tumors become androgen independent and resume growth in castrate hosts. The degree of PSA response to castration and time to PSA nadir correlate with time to progression. Thus, unlike most existing models of prostatic carcinoma, this novel xenograft exhibits many phenotypic characteristics of clinical prostatic carcinoma, including androgen sensitivity. These properties make this xenograft an excellent model for future study.
Biosensors for Food Analysis (1992)

There has been a considerable interest in developing new assays for food analysis to meet the demands of the different regulatory health agencies. Biosensors offer a new alternative due to their inherent specificity, simplicity and quick response. Selected biosensors which have been developed recently in our laboratory featuring applications in food analysis are discussed. These include enzyme electrodes and fiber optic probes for the detection and determination of various substances (fructose, glutamate, aspartame, hydrogen peroxide, glucose and sulfite).
Fructose-Sorbitol Malabsorption and Symptom Provocation in Irritable Bowel Syndrome: Relationship to Enteric Hypersensitivity and Dysmotility (1998)

Although carbohydrate malabsorption can provoke symptoms in some IBS patients, there is no consistent association between such a phenomenon and the presence of either jejunal hypersensitivity or dysmotility.
Multimerization of a chimeric anti-CD20 single-chain Fv-Fc fusion protein is mediated through variable domain exchange (2001)

A series of single-chain anti-CD20 antibodies was produced by fusing single-chain Fv (scFv) with human IgG1 hinge and Fc regions, designated scFv-Fc. The initial scFv-Fc construct was assembled using an 18 amino acid (aa) linker between the antibody light- and heavy-chain variable regions, with the Cys residue in the upper hinge region (Kabat 233) mutagenized to Ser. Anti-CD20 scFv-Fc retained specific binding to CD20-positive cells and was active in mediating complement-dependent cytolysis. Size-exclusion HPLC analysis revealed that the purified scFv-Fc included multimeric as well as monomeric components. Variant scFv-Fcs were constructed incorporating four different hinges between the scFv and Fc regions, or three different linkers in the scFv domain. All formed multimers, with the highest level of multimerization found in the scFv-Fc with the shortest linker (8 aa). Elimination of an unusual salt bridge between residues L38 and H89 in the V(L)-V(H) domain interface failed to reduce the formation of higher order forms. Structural analysis of the scFv-Fc constructed with 18 or 8 aa linkers by pepsin or papain cleavage suggested the proteins contained a form in which scFv units had cross-paired to form a 'diabody'. Thus, domain exchange or cross-pairing appears to be the basis of the observed multimerization.
CNS immune privilege: hiding in plain sight (2006)

Central nervous system (CNS) immune privilege is an experimentally defined phenomenon. Tissues that are rapidly rejected by the immune system when grafted in sites, such as the skin, show prolonged survival when grafted into the CNS. Initially, CNS immune privilege was construed as CNS isolation from the immune system by the blood-brain barrier (BBB), the lack of draining lymphatics, and the apparent immunoincompetence of microglia, the resident CNS macrophage. CNS autoimmunity and neurodegeneration were presumed automatic consequences of immune cell encounter with CNS antigens. Recent data have dramatically altered this viewpoint by revealing that the CNS is neither isolated nor passive in its interactions with the immune system. Peripheral immune cells can cross the intact BBB, CNS neurons and glia actively regulate macrophage and lymphocyte responses, and microglia are immunocompetent but differ from other macrophage/dendritic cells in their ability to direct neuroprotective lymphocyte responses. This newer view of CNS immune privilege is opening the door for therapies designed to harness autoreactive lymphocyte responses and also implies (i) that CNS autoimmune diseases (i.e. multiple sclerosis) may result as much from neuronal and/or glial dysfunction as from immune system dysfunctions and (ii) that the severe neuronal and glial dysfunction associated with neurodegenerative disorders (i.e. Alzheimer's disease) likely alters CNS-specific regulation of lymphocyte responses affecting the utility of immune-based therapies (i.e. vaccines).
A comparative evaluation of three transfection procedures as assessed by resistance to G418 conferred to HEPG2 cells. (1994)

Three commonly used transfection techniques (electroporation, calcium phosphate precipitation and scrape loading) and a novel procedure combining the latter two methods were evaluated and conditions optimised for successful transfection of human HepG2 cells with plasmid DNA incorporating a mouse MHC Class I gene and a selectable marker (neomycin transferase gene) conferring resistance to G418. While transfection with linear DNA by scrape-loading gave satisfactory results, transfer of cloned circular DNA by electroporation, calcium phosphate precipitation or a combined use of scrape-loading and calcium phosphate gave best results for HepG2 cells.
Separation of tripalmitin from its hydrolysis products by simple isocratic reversed‐phase high‐performance liquid chromatography (1998)

Abstract An isocratic reversed‐phase high‐performance liquid‐chromatographic method was developed for monitoring the lipase‐catalyzed hydrolysis of solid triglycerides in supercritical carbon dioxide. The reaction products obtained consist of free fatty acids, monoglycerides, diglycerides, and unreacted triglycerides. For the method, developed with tripalmitin, a mobile phase of acetonitrile/chloroform/acetic acid (50:50:1, vol/vol/vol), a C 18 column, and refractive index detection were used. Analysis time is 7 min. Response factors were determined for each neutral lipid class, which permitted quantitation of the hydrolysis product mixture.
Migraine in the triptan era: progresses achieved, lessons learned and future developments (2009)

Triptans, serotonin 5-HT1B/1D receptor agonists, more than revolutionizing the treatment of migraine, stimulated also ground breaking research that provided insights into the anatomy, physiology, and molecular pharmacology of migraine. This knowledge, in turn, is stimulating research on new mechanisms of action for the treatment of migraine. Accordingly, it is opportune to critically review the main advances in migraine science that happened in the triptan era. Herein we first review and conceptualize some of the progresses achieved in migraine science during the triptan era. We then review the class of the triptans--mechanism of action and clinical evidence. We close by briefly discussing the class of CGRP receptor antagonists, which is currently being developed for the acute treatment of migraine.
Harmonic Feedback Circuit Effects on Intermodulation Products and Adjacent Channel Leakage Power in HBT Power Amplifier for 1.95 GHz Wide-Band CDMA Cellular Phones (1999)

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Proteoglycan synthesis by bovine keratocytes and corneal fibroblasts: maintenance of the keratocyte phenotype in culture. (1999)

A comparison of proteoglycan synthesis and cell morphology between keratocytes in corneas in organ culture and in cell culture indicates that keratocytes maintain a more native biosynthetic phenotype and appearance when cultured in serum-free media. These results also suggest that culturing in the presence of serum fundamentally alters the keratocyte phenotype to an activated cell, mimicking certain changes observed during wound healing.
Packaging Cell Lines for Simian Foamy Virus Type 1 Vectors (1999)

Foamy viruses are nonpathogenic retroviruses that offer several unique opportunities for gene transfer in various cell types from different species. We have previously demonstrated the utility of simian foamy virus type 1 (SFV-1) as a vector system by transient expression assay (M. Wu et al., J. Virol. 72:3451-3454, 1998). In this report, we describe the first stable packaging cell lines for foamy virus vectors based on SFV-1. We developed two packaging cell lines in which the helper DNA is placed under the control of either a constitutive cytomegalovirus (CMV) immediate-early gene or inducible tetracycline promoter for expression. Although the constitutive packaging expressing cell line had a higher copy number of packaging DNA, the inducible packaging cell line produced four times more vector particles. This result suggested that the structural gene products in the constitutively expressing packaging cell line were expressed at a level that is not toxic to the cells, and thus vector production was reduced. The SFV-1 vector in the presence of vesicular stomatitis virus envelope protein G (VSV-G) produced an insignificant level of transduction, indicating that foamy viruses could not be pseudotyped with VSV-G to generate high-titer vectors. The availability of stable packaging cell lines represents a step toward the use of an SFV-1 vector delivery system that will allow scaled-up production of vector stocks for gene therapy.
Patterns of cross-resistance to the antifolate drugs trimetrexate, metoprine, homofolate, and CB3717 in human lymphoma and osteosarcoma cells resistant to methotrexate. (1983)

Methotrexate (MTX)-resistant sublines of malignant human cells were selected in vitro by stepwise increase in drug concentration in the medium. By this procedure a subline of Burkitt's lymphoma cells (RAJI) was made 290-fold resistant (RAJI/MTX-R), T-cell leukemia cells (CCRF-CEM) were obtained 210-fold resistant (CEM/MTX-R), and 3 MTX-resistant human osteosarcoma lines were selected: TE-85/MTX-R (19-fold resistant; relative to wild-type); MG-63/MTX-R (8-fold resistant); and SAOS-2/MTX-R (200-fold resistant). We also studied a B-cell lymphoblastoid line, WI-L2/m4, that was 13,000-fold resistant. Assay of cellular dihydrofolate reductase (DHFR) showed the following pattern of activity in resistant cell lines, relative to parental cell activity: RAJI/MTX-R, 550-fold increased; CEM/MTX-R, unchanged; TE-85/MTX-R, 4-fold increased; MG-63/MTX-R, 6-fold increased; SAOS-2/MTX-R, unchanged; and WI-L2/m4, 110-fold increased. Measurement of MTX membrane transport showed decreased uptake in CEM/MTX-R and SAOS-2/MTX-R, relative to parental cell lines. The other DHFR-overproducing cells all gave normal initial MTX uptake rates but increased total uptake. The DHFR-overproducing lines all had significant cross-resistance to both metoprine and trimetrexate; the two lines with defective MTX transport were not cross-resistant, and the CEM/MTX-R cells showed collateral sensitivity to these agents. Only minor cross-resistance to homofolic acid was found in all MTX-resistant lines. The highly MTX-resistant RAJI/MTX-R and WI-L2/m4 cells showed minor cross-resistance to the dual inhibitor of thymidylate synthetase and DHFR, CB3717 (5- and 15-fold, respectively). These studies demonstrated that, depending upon the mechanism of resistance, MTX-resistant human tumor cells may be effectively killed by antifolates with different routes of uptake into cells, or with a different enzyme target. Thus, there are at least three functionally distinct classes of folate antagonist with antitumor activity.
Molecular cloning of a cDNA with a novel domain present in the tre-2 oncogene and the yeast cell cycle regulators BUB2 and cdc16. (1995)

In an effort to identify genes that are differentially regulated during mast cell development, subtracted cDNA prepared from wild-type murine P815 mastocytoma cells and a P815 subline that exhibits properties of mast cell differentiation was used to screen mast cell cDNA libraries. Several known mast cell-specific cDNAs were isolated including mast cell carboxypeptidase A (MC-CPA), murine mast cell protease-5 (MMCP-5), and gp49. A novel cDNA, designated Tbc1, was identified that showed differential expression in the two mast cell lines. The amino acid sequence predicted from the cDNA contains a 200 amino acid domain that is homologous to regions in the tre-2 oncogene and the yeast regulators of mitosis, BUB2 and cdc16. The N-terminal region contains a number of cysteine and histidine residues, potentially encoding a zinc finger domain. Tbc1 is a nuclear protein and is expressed in highest levels in hematopoietic cells, testis and kidney. Within these tissues, expression of Tbc1 is cell- and stage-specific. Based on sequence similarity, pattern of expression and subcellular localization, Tbc1 may play a role in the cell cycle and differentiation of various tissues.
Triacylglycerol synthesis by PDAT1 in the absence of DGAT1 activity is dependent on re-acylation of LPC by LPCAT2 (2012)

Collectively, the data strongly support that in AS11 it is LPCAT2 up-regulation which is primarily responsible for assisting in PDAT1-catalyzed TAG biosynthesis, maintaining a supply of PC as co-substrate to transfer sn-2 moieties to the sn-3 position of the enlarged AS11 DAG pool.
Long and Oriented Single-Walled Carbon Nanotubes Grown by Ethanol Chemical Vapor Deposition (2004)

We report the controlled chemical vapor deposition (CVD) growth of single-walled carbon nanotubes (SWNTs), using ethanol as the carbon feedstock and bimetallic CoMo-doped mesoporous silica (SBA16) as the catalyst. Ultralong (up to 4 mm) and horizontally aligned SWNTs can be grown directly on flat substrates or across slits (20−120 μm apart), and the orientation of the nanotubes is always parallel to the gas flow direction. The control of the growth direction and length also enables us to fabricate parallel nanotube arrays or two-dimensional networks on flat surfaces. The growth of the carbon nanotubes is relatively fastit is attributed to the high reactivity of ethanol and high activity of the CoMo/SBA16 catalystand no doubt contributes to increased length and orientation control. Unlike previous procedures that have been used to grow well-oriented nanotubes, neither a strong external electrical field nor a fast-heating technique is required in this ethanol CVD process. Moreover, the as-grown SWNTs have a relatively narrow size distribution of 0.8−1.8 nm, which is a result of the narrow size distribution of the CoMo nanoparticles embedded in the mesoporous SBA16 silica.
Colloquium: Looking at a soliton through the prism of optical supercontinuum (2010)

A traditional view on solitons in optical fibers as robust particlelike structures suited for information transmission has been significantly altered and broadened over the past decade when solitons have been found to play the major role in generation of octave broad supercontinuum spectra in photonic crystal and other types of optical fibers. This remarkable spectral broadening is achieved through complex processes of dispersive radiation being scattered from, emitted, and transformed by solitons. Thus solitons have emerged as the major players in nonlinear frequency conversion in optical fibers. Unexpected analogies of these processes have been found with dynamics of ultracold atoms and ocean waves. This Colloquium focuses on recent understanding and new insights into physics of soliton-radiation interaction and supercontinuum generation.
Definition and Classification of Acute Kidney Injury (2008)

Changes in urine output and glomerular filtration rate are neither necessary nor sufficient for the diagnosis of renal pathology. Yet no simple alternative for the diagnosis currently exists. Until recently, there has been no consensus as to diagnostic criteria or clinical definition of acute renal failure. Depending on the definition used, acute renal failure has been reported to affect from 1 to 25% of ICU patients and has led to mortality rates from 15 to 60%. The RIFLE criteria were developed to standardize the diagnosis of acute renal failure and in the process the term acute kidney injury (AKI) has been proposed to encompass the entire spectrum of the syndrome from minor changes in renal function to requirement for renal replacement therapy. Thus, AKI is not acute renal failure but a more general description. Small changes in kidney function in hospitalized patients are important and are associated with significant changes in short and possibly long-term outcomes. The RIFLE criteria provide a uniform definition of AKI and have now been validated in numerous studies.