gebhart/patrepeval huggingface dataset:
Correction of matrix effects for As and Se in ICP OES using a Flow Blurring® multiple nebulizer (2012)

A new and efficient multiple nebulizer based on Flow Blurring® hydrodynamics (FBMN) has been employed for elemental analysis. The aerosol generated by the FBMN has been characterized and compared with a conventional pneumatic nebulizer (MicroMist®, MM). Both nebulizers have been operated with the same cyclonic spray chamber for comparison. At a solution flow rate of 300 μL min−1 and a nebulizer gas flow rate of 0.60 L min−1 the aerosol produced by the FBMN is formed by droplets smaller than 53 μm, and the Sauter mean diameter (D3,2) and the median diameter (D50) of the primary aerosols are 16.3 and 16.8 μm, and 20.4 and 23.3 μm with the FBMN and MM, respectively. The sample introduction system based on the FBMN successfully corrects matrix effects in As and Se determination by inductively coupled plasma optical emission spectrometry. The FBMN makes feasible the implementation of an on-line internal standard (I.S.) strategy by mixing the I.S. solution with analytical reference solutions or a sample solution directly in the spray chamber. It has been demonstrated that the combination of FBMN and In as an internal standard leads to better accuracy for determining As in a lake sediment.
Effect of rare gas implantation on the magnetic properties of amorphous CoTi thin films (1987)

We report here on the effect of Xe+ ion irradiation on the magnetic properties of amorphous CoTi thin films. With increasing fluence range the in-plane K <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">u</inf> or perpendicuIar anisotropy K <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</inf> decreases continuously and disappears for 5×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">15</sup> Xe+/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , while the magnetization remains unchanged. Resonance measurements shows that even for low fluences the homogeneity along the film thickness is improved. In comparison with thermal annealing the much higher efficiency of ion irradiation in order to suppress K <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">u</inf> is displayed. Discussions on the physical origin of K <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">u</inf> are also given.
Effect of barrier width on performance of long wavelength GainAs/InP multi-quantum-well lasers (1988)

It is demonstrated that lasing thresholds in GaInAs/InP MQW lasers under electrical injection are sensitive to the InP barrier thickness and that reducing the barrier width contributes significantly to achieving low-threshold, room temperature operation. In contrast, lasing thresholdsunder optical pumping show a relative insensitivity to the barrier width. We show that this behaviour is consistent with preferential hole capture in the leading wells.
Analysis of gene amplification in human tumor cell lines. (1988)

Oncogene amplification has been observed in various primary tumors and tumor-derived cell lines. In several types of cancer, amplification of specific oncogenes is correlated with the stage of tumor progression. To estimate the frequency of gene amplification in other tumor types and to determine whether the ability to grow in vivo is associated with gene amplification in tumor cell lines, we have developed a modified version of the in-gel renaturation assay that detects human DNA sequences of unknown nature amplified as little as 7- to 8-fold. This assay was used to screen 16 cell lines derived from various solid tumors and leukemias. Amplified DNA sequences were detected in only one cell line, Calu-3 lung adenocarcinoma. This cell line was found to contain coamplified NGL (formerly termed neu) and ERBA1 oncogenes. However, when one of the amplification-negative cell lines, PC-3 prostatic carcinoma, was selected for in vivo growth in nude mice, amplified DNA sequences became detectable in these cells. The amplified sequences included the MYC oncogene, which showed no amplification in the parental cell line but was amplified 10- to 12-fold in the in vivo-selected cells. MYC amplification may, therefore, provide tumor cells with a selective advantage specific for in vivo growth.
Nanolipid Formulations of Benzoporphyrin Derivative: Exploring the Dependence of Nanoconstruct Photophysics and Photochemistry on Their Therapeutic Index in Ovarian Cancer Cells (2018)

With the rapidly emerging designs and applications of light-activated, photodynamic therapy (PDT)-based nanoconstructs, photonanomedicines (PNMs), an unmet need exists to establish whether conventional methods of photochemical and photophysical characterization of photosensitizers are relevant for evaluating new PNMs in order to intelligently guide their design. As a model system, we build on the clinical formulation of benzoporphyrin derivative (BPD), Visudyne<sup>®</sup> , by developing a panel of nanolipid formulations entrapping new lipidated chemical variants of BPD with differing chemical, photochemical and photophysical properties. These are 16:0 and 20:0 lysophosphocholine-BPD (16:0/20:0 BPD-PC), DSPE-PEG-BPD and BPD-cholesterol. We show that Visudyne<sup>®</sup> was the most phototoxic formulation to OVCAR-5 cells, and the least effective was liposomal DSPE-PEG-BPD. However, these differences did not match their optical, photophysical and photochemical properties, as the static BPD quenching was highest in Visudyne, which also exhibited the lowest generation of singlet oxygen. Furthermore, we establish that OVCAR-5 cell phototoxicity also does not correlate with rates of photosensitizer photobleaching and fluorescence quantum yields in any nanolipid formulations. These findings warrant critical future studies into subcellular targets and molecular mechanisms of phototoxicity of photodynamic nanoconstructs, as more reliable prognostic surrogates for predicting efficacy to appropriately and intelligently guide their design.
A new sensitive derivatization reagent for liquid chromatographic separation of hydroxyl compounds. (1981)

A new sensitive derivatization reagent for use in liquid chromatographic separation of hydroxyl compounds has been developed. A suitable reagent for this purpose, 4-dimethylamino-1-naphthoyl nitrile, was readily prepared from the corresponding acid chloride by the exchange reaction with trimethylsilyl cyanide. Condensation of a hydroxyl compound with the reagent was effected in the presence of triethylamine under the mild condition. The resulting ester was highly responsible for a fluorescence detector with a detection limit of 200 pg.
Compact source of coherent blue light (1994)

Generation of 22 mW of narrow-band radiation near 430 nm was achieved by frequency doubling the 100-mW output of a single-mode GaAIAs diode laser near 860 nm. A monolithic potassium niobate ring resonator serves as the nonlinear medium and at the same time as a reference cavity for the diode-laser frequency, which optically self-locks to a cavity resonance frequency. Continuous scans of the second-harmonic frequency over 330 MHz are achieved with the electro-optic effect. The results demonstrate a portable, economical, and efficient source of coherent blue light.
FLIPL induces caspase 8 activity in the absence of interdomain caspase 8 cleavage and alters substrate specificity (2011)

Caspase 8 is an initiator caspase that is activated by death receptors to initiate the extrinsic pathway of apoptosis. Caspase 8 activation involves dimerization and subsequent interdomain autoprocessing of caspase 8 zymogens, and recently published work has established that elimination of the autoprocessing site of caspase 8 abrogates its pro-apoptotic function while leaving its proliferative function intact. The observation that the developmental abnormalities of caspase 8-deficient mice are shared by mice lacking the dimerization adapter FADD (Fas-associated death domain) or the caspase paralogue FLIP(L) [FLICE (FADD-like interleukin 1β-converting enzyme)-inhibitory protein, long form] has led to the hypothesis that FADD-dependent formation of heterodimers between caspase 8 and FLIP(L) could mediate the developmental role of caspase 8. In the present study, using an inducible dimerization system we demonstrate that cleavage of the catalytic domain of caspase 8 is crucial for its activity in the context of activation by homodimerization. However, we find that use of FLIP(L) as a partner for caspase 8 in dimerization-induced activation rescues the requirement for intersubunit linker proteolysis in both protomers. Moreover, before processing, caspase 8 in complex with FLIP(L) does not generate a fully active enzyme, but an attenuated species able to process only selected natural substrates. Based on these results we propose a mechanism of caspase 8 activation by dimerization in the presence of FLIP(L), as well as a mechanism of caspase 8 functional divergence in apoptotic and non-apoptotic pathways.
A novel peptide, THALWHT, for the targeting of human airway epithelia (2001)

Targeting gene vectors to human airway epithelial cells may help to overcome the current inefficiency of gene transfer as the major problem confronting cystic fibrosis gene therapy. To elucidate novel ligands targeting abundant, apically located receptors on airway epithelial cells, a phage display library was screened for peptides binding with high affinity to such cells. This screening yielded a selectively enriched amino acid sequence, Thr-His-Ala-Leu-Trp-His-Thr (THALWHT). Subsequent binding studies confirmed that THALWHT-displaying phages bound much stronger than phages displaying control peptides to human airway epithelial cells. In contrast, no significant binding differences were observed on a variety of non-airway-derived human cell lines suggesting selective binding of the THALWHT motif to airway epithelia. Confocal microscopy of such cells after exposure to labelled synthetic THALWHT peptide indicated that its binding is followed by specific internalisation via endocytosis. A synthetic peptide comprising a cyclic CTHALWHTC domain and a DNA binding moiety enabled efficient targeted gene delivery into human airway epithelial cells. Competition assays with free THALWHT peptide confirmed the specificity of gene delivery. Thus, the THALWHT motif may prove a useful targeting moiety for both non-viral and viral gene therapy vectors.
Synthesis, Structure, Assembly, and Modulation of the CO<sub>2</sub> Adsorption Properties of a Zinc-Adeninate Macrocycle (2009)

The preparation and self-assembly of zinc adeninate macrocycles [Zn(6)(adeninate)(6)(pyridine)(6)(dimethylcarbamate)(6)] is described. The macrocycles self-assemble through adenine-adenine hydrogen bonding interactions into a 3-D porous crystalline material that maintains its structural integrity after removal of guest molecules and coordinated pyridine molecules. By adjusting the activation temperature prior to gas adsorption measurements, the size of the pore aperture can be modulated to afford unique gas sorption properties including selective gas adsorption and CO(2) sequestration.
COVID-19 and Selenium Deficiency: a Systematic Review (2021)

Several studies have indicated that selenium deficiency may be detrimental in the context of various viral disorders, and in the case of COVID-19, several studies have reported heterogeneous results concerning the association of selenium deficiency with the severity of disease. To summarize the available data surrounding the association of body selenium levels with the outcomes of COVID-19, a systematic search was performed in the Medline database (PubMed), Scopus, Cochrane Library, Embase, and Web of Science using keywords including "SARS-CoV-2," "COVID-19," and "selenium," Studies evaluating the association of COVID-19 with body selenium levels were included. Among 1,862 articles viewed in the database search, 10 articles were included after title, abstract, and full-text review. One study was further included after searching the literature again for any newly published articles. Out of 11 included studies, 10 studies measured serum selenium level, and one study investigated urinary selenium level. Three of 10 studies measured serum SELENOP level as well as selenium level. Glutathione peroxidase-3 level in serum was also assessed in one study. The reported outcomes were severity, mortality, and risk of COVID-19. Nine studies indicated that a lower serum selenium level is associated with worse outcomes. Two studies reported no significant association between serum selenium level and COVID-19. In one study, urinary selenium level was reported to be higher in severe and fatal cases compared to non-severe and recovered patients, respectively. In most cases, selenium deficiency was associated with worse outcomes, and selenium levels in COVID-19 patients were lower than in healthy individuals. Thus, it could be concluded that cautious selenium supplementation in COVID-19 patients may be helpful to prevent disease progression. However, randomized clinical trials are needed to confirm this.
High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors (2021)

A new coronavirus (SARS-CoV-2) has been identified as the etiologic agent for the COVID-19 outbreak. Currently, effective treatment options remain very limited for this disease; therefore, there is an urgent need to identify new anti-COVID-19 agents. In this study, we screened over 6,000 compounds that included approved drugs, drug candidates in clinical trials, and pharmacologically active compounds to identify leads that target the SARS-CoV-2 papain-like protease (PLpro). Together with main protease (M<sup>pro</sup>), PLpro is responsible for processing the viral replicase polyprotein into functional units. Therefore, it is an attractive target for antiviral drug development. Here we discovered four compounds, YM155, cryptotanshinone, tanshinone I and GRL0617 that inhibit SARS-CoV-2 PLpro with IC<sub>50</sub> values ranging from 1.39 to 5.63 μmol/L. These compounds also exhibit strong antiviral activities in cell-based assays. YM155, an anticancer drug candidate in clinical trials, has the most potent antiviral activity with an EC<sub>50</sub> value of 170 nmol/L. In addition, we have determined the crystal structures of this enzyme and its complex with YM155, revealing a unique binding mode. YM155 simultaneously targets three "hot" spots on PLpro, including the substrate-binding pocket, the interferon stimulating gene product 15 (ISG15) binding site and zinc finger motif. Our results demonstrate the efficacy of this screening and repurposing strategy, which has led to the discovery of new drug leads with clinical potential for COVID-19 treatments.
Oxidation of hydrogen and reduction of methanol to methane is the sole energy source for a methanogen isolated from human feces (1983)

A methanogenic coccus isolated from human feces requires H2 and CH3OH for growth and uses H2 to reduce CH3OH to CH4. Growth does not occur with CH3OH alone. The organism does not grow or produce CH4 from acetate or methylamines without or with H2 or from H2 and CO2 or formate. In a complex medium. CO2 is required for formation of approximately 50% of cell carbon, whereas the methyl carbon from methanol is not incorporated into cell carbon.
Transcription Activator-like Effectors: A Toolkit for Synthetic Biology (2014)

Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species. TALEs assist infections by binding to specific DNA sequences and activating the expression of host genes. Recent results show that TALE proteins consist of a central repeat domain, which determines the DNA targeting specificity and can be rapidly synthesized de novo. Considering the highly modular nature of TALEs, their versatility, and the ease of constructing these proteins, this technology can have important implications for synthetic biology applications. Here, we review developments in the area with a particular focus on modifications for custom and controllable gene regulation.
A simplified and robust protocol for immunoglobulin expression in <scp><i>E</i></scp><i>scherichia coli</i> cell‐free protein synthesis systems (2015)

Cell-free protein synthesis (CFPS) systems allow for robust protein expression with easy manipulation of conditions to improve protein yield and folding. Recent technological developments have significantly increased the productivity and reduced the operating costs of CFPS systems, such that they can compete with conventional in vivo protein production platforms, while also offering new routes for the discovery and production of biotherapeutics. As cell-free systems have evolved, productivity increases have commonly been obtained by addition of components to previously designed reaction mixtures without careful re-examination of the essentiality of reagents from previous generations. Here we present a systematic sensitivity analysis of the components in a conventional Escherichia coli CFPS reaction mixture to evaluate their optimal concentrations for production of the immunoglobulin G trastuzumab. We identify eight changes to the system, which result in optimal expression of trastuzumab. We find that doubling the potassium glutamate concentration, while entirely eliminating pyruvate, coenzyme A, NAD, total tRNA, folinic acid, putrescine and ammonium glutamate, results in a highly productive cell-free system with a 95% reduction in reagent costs (excluding cell-extract, plasmid, and T7 RNA polymerase made in-house). A larger panel of other proteins was also tested and all show equivalent or improved yields with our simplified system. Furthermore, we demonstrate that all of the reagents for CFPS can be combined in a single freeze-thaw stable master mix to improve reliability and ease of use. These improvements are important for the application of the CFPS system in fields such as protein engineering, high-throughput screening, and biotherapeutics.
Productive Cellulase Adsorption on Cellulose (2004)

Hydrolysis of insoluble polymeric cellulose by cellulases requires enzyme adsorption onto the substrate. Being heterogeneous on its surface, cellulose in general has different sites for different cellulases to adsorb. Only a portion of the adsorbed cellulase is productive, able to lead to subsequent glycosidic bond cleavage. We applied the dependence of initial hydrolysis rate on the concentration of enzyme and substrate to probe the "productive" adsorption of four different cellulases on two types of cellulose. We found that different celluloses could have significantly different cellulase accessibility; that different cellulases, even from the same family, could have significantly different "productive" adsorption on cellulose; and that functionally analogous cellulases could have overlapping adsorption sites, while functionally dissimilar cellulases could have separate adsorption sites. The usefulness of the method for mechanistic study and industrial application of cellulases was discussed.
Construction of Recombinant Human Collagen III Variants and Genomic Manipulations in Yeast for Collagen Yield Optimization (2015)

As the most abundant protein in the extracellular matrix, collagen is an attractive tissue engineering scaffold. IKVAV, a peptide sequence native to the protein laminin, is widely known for its roles in neuroregeneration. Using a computational algorithm, IKVAV-containing collagen variants were successfully assembled in a de novo fashion. The incorporation of IKVAV into the collagen sequence required the interruption of the characteristic Gly-X-Y repeat. These variants, however, were able to retain their triple-helical form, and the one examined yielded a melting temperature comparable to that of our baseline recombinant collagen. Accessibility of IKVAV within the collagen structure was not confirmed, and cell adhesion assays indicate a lack of cell binding to the variants tested. Further studies are necessary to draw definite conclusions. In our system, the collagen gene is expressed under the GAL1 promoter in Saccharomyces cerevisiae, necessitating cultivation of the yeast in galactose-containing medium for induction. To optimize collagen yield, the REG1 and GAL1 genes were deleted to inhibit catabolite repression and galactose consumption, allowing growth in glucose under constant inducer concentration. Unlike the ÎREG1 strain, the ÎREG1ÎGAL1 strain did not show improved growth in glucose. Upon transformation of a S. cerevisiae CEN/ARS plasmid carrying the collagen gene, the ability of both variants to produce triple-helical collagen was confirmed by circular dichroism. Initial Western blots did not show increased collagen production by the ÎREG1ÎGAL1 strain. However, the strain did allow collagen production during growth on glucose, and the concentration of the galactose inducer can likely be significantly reduced.
The role of hydrophobic interactions in positioning of peripheral proteins in membranes (2007)

Positions of diverse peripheral proteins and peptides in the lipid bilayer can be accurately predicted using their 3D structures that represent a proper membrane-bound conformation and oligomeric state, and have membrane binding elements present. The success of the implicit solvation model suggests that hydrophobic interactions are usually sufficient to determine the spatial position of a protein in the membrane, even when electrostatic interactions or specific binding of lipids are substantial. Our results demonstrate that most peripheral proteins not only interact with the membrane surface, but penetrate through the interfacial region and reach the hydrocarbon interior, which is consistent with published experimental studies.
System architecture directions for networked sensors (2000)

Technological progress in integrated, low-power, CMOS communication devices and sensors makes a rich design space of networked sensors viable. They can be deeply embedded in the physical world and spread throughout our environment like smart dust. The missing elements are an overall system architecture and a methodology for systematic advance. To this end, we identify key requirements, develop a small device that is representative of the class, design a tiny event-driven operating system, and show that it provides support for efficient modularity and concurrency-intensive operation. Our operating system fits in 178 bytes of memory, propagates events in the time it takes to copy 1.25 bytes of memory, context switches in the time it takes to copy 6 bytes of memory and supports two level scheduling. The analysis lays a groundwork for future architectural advances.
Broadband macromodelling of passive components using orthonormal vector fitting (2005)

Vector fitting is widely accepted as a robust macromodelling tool for efficient frequency domain identification of passive components. The orthonormal vector fitting technique is introduced, which improves the numerical stability of the method, by using orthonormal rational functions. This leads to better conditioned equations, reduces the numerical sensitivity to the choice of starting poles significantly, limits the number of required iterations, and reduces the overall computation time.
Phone-to-phone communication for adaptive image classification (2008)

In this paper, we present a novel technique for adapting local image classifiers that are applied for object recognition on mobile phones through ad-hoc network communication between the devices. By continuously accumulating and exchanging collected user feedback among mobile phones that are located within signal range, we show that our approach improves the overall classification rate and adapts to dynamic changes quickly. This technique is applied in the context of PhoneGuide -- an adaptive museum guidance system.