gebhart/patrepeval huggingface dataset:
Minimal genome: Worthwhile or worthless efforts toward being smaller? (2015)

Microbial cells are versatile hosts for the production of value-added products due to the well-established background knowledge, various genetic tools, and ease of manipulation. Despite those advantages, efficiency of newly incorporated synthetic pathways in microbial cells is frequently limited by innate metabolism, product toxicity, and growth-mediated genetic instability. To overcome those obstacles, a minimal genome harboring only the essential set of genes was proposed, which is a fascinating concept with potential for use as a platform strain. Here, we review the currently available artificial reduced genomes and discuss the prospects for extending use of the genome-reduced strains as programmable chasses. The genome-reduced strains generally showed comparable growth to and higher productivity than their ancestral strains. In Escherichia coli, about 300 genes are estimated as the minimal number of genes under laboratory conditions. However, recent advances revealed that there are non-essential components in essential genes, suggesting that the design principle of minimal genomes should be reconstructed. Current technology is not efficient enough to reduce large amount of interspaced genomic regions or to synthesize the genome. Furthermore, construction of minimal genome frequently has failed due to lack of genomic information. Technological breakthroughs and intense systematic studies on genomes remain tasks.
Jafnea pallida (Pezizales), a new name for a cup fungus rediscovered in Tasmania (2016)

A modern description is provided for Geopyxis pallidus, a species described by L. Rodway in 1920, from the here selected lectotype and additional recent collections from Tasmania. Based on its morphology, we recombine G. pallidus into the genus Jafnea. Recent records of Jafnea pallida comb. nov. from Tasmania have been misnamed as the morphologically similar Tarzetta jafneospora. The two species can be distinguished by their different spore ornamentation
VI-Based Appliance Classification Using Aggregated Power Consumption Data (2018)

Non-intrusive load monitoring detects active appliances in a household (and their power consumption) from measuring the aggregated power at just one point in that household. Our previous works focused on classifying a single appliance, assuming that the voltage and current trace could be isolated from an aggregated signal by considering the difference in current before and after the event. In this paper, we show that this assumption holds and that it is a viable approach in practice. We experimentally validate this for two classification methods we proposed earlier: (1) random forests using elliptical Fourier descriptors of the appliances' VI trajectories and (2) convolutional neural networks using the appliances' VI images. We benchmark these approaches on the aggregated data from the 2018 version of PLAID. We obtain, respectively for each of these classifiers, a maximal Fmacro-measure of 85.31% and 87.95%. We also show that using submetered data for training does not improve the performance.
Coupled Split-Ring Resonator Circular Polarization Selective Surface (2017)

A novel class of circular polarization selective surfaces (CPSSs) consisting of a pair of planar split-ring resonator arrays is proposed. A significant advantage of the proposed structure over existing designs is its manufacturing simplicity compatible with standard printed technology processes. Its operating principle is reviewed alongside that of the Pierrot cell and in light of the linear polarization reflection and transmission characteristics of CPSSs. Guidelines for the initial design of the proposed CPSS concept are thus derived. Further design considerations and tradeoffs are also discussed. The validity of the concept is confirmed by means of a design example entailing a right-hand CPSS at 20 GHz. Full-wave simulation results and experimental testing on a fabricated prototype are presented and agree well with the theoretical predictions.
Laboratory-size three-dimensional water-window x-ray microscope with Wolter type I mirror optics (2016)

We constructed a laboratory-size three-dimensional water-window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques. It consists of an electron-impact x-ray source emitting oxygen Kα x-rays, Wolter type I grazing incidence mirror optics, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit better than 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm-scale three-dimensional fine structures were resolved.
Fabrication of photonic crystal structures by tertiary-butyl arsine-based metal–organic vapor-phase epitaxy for photonic crystal lasers (2016)

Abstract The fabrication of air/semiconductor two-dimensional photonic crystal structures by air-hole-retained crystal regrowth using tertiary-butyl arsine-based metal–organic vapor-phase epitaxy for GaAs-based photonic crystal lasers is investigated. Photonic crystal air holes with filling factors of 10–13%, depths of ∼280 nm, and widths of 120–150 nm are successfully embedded. The embedded air holes exhibit characteristic shapes due to the anisotropy of crystal growth. Furthermore, a low lasing threshold of ∼0.5 kA/cm 2 is achieved with the fabricated structures.
Encapsulation, delegation and inheritance in object-oriented languages (1992)

For the reuse of software to become routine, it is essential that all modules have well defined interfaces and that all users of these modules respect these interfaces. This paper examines the interfaces in object-oriented programs. It uses the notion of delegation, which can be thought of as underlying all inheritance mechanisms, to provide a framework for the examination of encapsulation mechanisms in object-oriented languages. Using delegation, the encapsulation mechanisms in class-based languages are reviewed, and suggestions are made as to how they might be improved.
Plasma Treatment of Silver Impregnated Mesoporous Aluminosilicate Nanoparticles for Adsorptive Desulfurization (2015)

We report a regenerable adsorbent for the removal of refractory organosulfur compounds from fossil fuels. The material is composed of well-dispersed silver nanoparticles confined within the mesochannels of aluminum-doped MCM-41 nanoparticles. With an average initial desulfurization capacity of 15 mg S·g–1, 79% desulfurization capacity is retained after six cycles for the removal of dibenzothiophene from n-decane. The addition of intraframework aluminum to form a mesoporous aluminosilicate nanoparticle (MASN) aids in the retention and dispersion of silver ions within the mesochannels (Ag-MASN). The nanoparticles are subsequently reduced by glow discharge plasma treatment in argon (PT-Ag-MASN). The size dispersion, surface area, and structural integrity were characterized by scanning electron microscopy, annular dark-field scanning transmission electron microscopy (ADF-STEM), nitrogen adsorption analysis (BET), and powder X-ray diffraction. Silver nanoparticle formation within the mesochannels of MASN was confirmed by ADF-STEM and diffuse reflectance UV–vis spectroscopy. Model fuel testing revealed that PT-Ag-MASN had the highest regeneration capacity after six cycles compared to non-plasma-treated (Ag-MASN) and aluminum-free materials (Ag-MSN and PT-Ag-MSN). Initial testing of the military jet fuel JP-8 also shows a high desulfurization capacity of 41 mg S·g–1.
Bayesian Network Inference Modeling Identifies TRIB1 as a Novel Regulator of Cell-Cycle Progression and Survival in Cancer Cells (2017)

Molecular networks governing responses to targeted therapies in cancer cells are complex dynamic systems that demonstrate nonintuitive behaviors. We applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell-cycle arrest caused by inhibition of MEK1/2. Through simulation of a reverse-engineered Bayesian network model, we generated predictions of G<sub>1</sub>-S transition. The model identified known components of the cell-cycle machinery, such as CCND1, CCNE2, and CDC25A, as well as revealed novel regulators of G<sub>1</sub>-S transition, IER2, TRIB1, TRIM27. Experimental validation of model predictions confirmed 10 of 12 predicted genes to have a role in G<sub>1</sub>-S progression. Further analysis showed that TRIB1 regulated the cyclin D1 promoter via NFκB and AP-1 sites and sensitized cells to TRAIL-induced apoptosis. In clinical specimens of breast cancer, TRIB1 levels correlated with expression of NFκB and its target genes (<i>IL8, CSF2</i>), and TRIB1 copy number and expression were predictive of clinical outcome. Together, our results establish a critical role of TRIB1 in cell cycle and survival that is mediated via the modulation of NFκB signaling. <i>Cancer Res; 77(7); 1575-85. ©2017 AACR</i>.
Design and measurement of 2.5 gsps digital receiver (2004)

1ABsfrarf - A design of 2.5 GSPS digifal receiver using fhe superresolufion fechnique to improve fhe insfanfaneous dynamic range is presenfed The digifal design can cover 1 GHz bandwidfh (125 MHz - 1125 MHZ) and can correcffy process fwo simultaneous signals. This design uses a fast Fourier fransform (FFV fo obfain frequencies on two simultaneous signals. If has a beffer sensiriviry than IFM receivers because fhe FFT channelizes the input info narrower bandwidth It has fine frequency resolufion (able fo separaie two closefrequencies) and goodfrequency accuracy. The single signal, fwo signal spur free dynamic ranges, 'and two signal insfanfaneous dynamic ranges are high.
Episodes from the Continuous Search for Solutions against Downy Mildew Diseases (2019)

Discovery background, lead optimization pathways, synthesis and structure-activity relationships of three different research projects searching for new active ingredients against downy mildew diseases are reported. These case studies, on which the author worked in three different decades in the research departments of Syngenta Crop Protection AG and its legacy company Novartis Crop Protection AG deal with inhibitors of cellulose synthase, tubulin polymerization and oxysterol-binding protein. Rarely used reactions, which have been applied within these projects, such as Seebach's variation of the Passerini reaction, the Bogert quinazoline synthesis and the carbonyldiimidazole-mediated Lossen rearrangement give proof of the significance of synthetic organic chemistry for modern crop protection.
ChemInform Abstract: Na+‐Glucose Cotransporter (SGLT) Inhibitors as Antidiabetic Agents. Part 4. Synthesis and Pharmacological Properties of 4′‐Dehydroxyphlorizin Derivatives Substituted on the B Ring. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Recruitment of the Putative Transcription-Repair Coupling Factor CSB/ERCC6 to RNA Polymerase II Elongation Complexes (1997)

Cockayne's syndrome (CS) is a disease characterized by developmental and growth defects, sunlight sensitivity, and a defect in transcription-coupled nucleotide excision repair. The two principle proteins involved in CS, CSA and CSB/ERCC6, have been hypothesized to bind RNA polymerase II (Pol II) and link transcription to DNA repair. We have tested CSA and CSB in assays designed to determine their role in transcription-coupled repair. Using a unique oligo(dC)-tailed DNA template, we provide biochemical evidence that CSB/ERCC6 interacts with Pol II molecules engaged in ternary complexes containing DNA and nascent RNA. CSB is a DNA-activated ATPase, and hydrolysis of the ATP beta-gamma phosphoanhydride bond is required for the formation of a stable Pol II-CSB-DNA-RNA complex. Unlike CSB, CSA does not directly bind Pol II.
Synthesis and characterization of 3,3′‐disulfonated‐4,4′‐dichlorodiphenyl sulfone (SDCDPS) monomer for proton exchange membranes (PEM) in fuel cell applications (2006)

Abstract A systematic study of the synthesis and characterization of 3,3′‐disulfonated‐4,4′‐dichlorodiphenyl sulfone (SDCDPS) monomer was conducted by varying reactant stoichiometries (molar ratios of 4,4′‐dichlorodiphenyl sulfone (DCDPS) to SO 3 1 : 2.2, 1 : 2.9, and 1 : 3.3), reaction temperature (90–120°C), and reaction time (4–6 h). The optimum synthesis batch process variables were 1 : 3.3 reactant molar ratio (DCDPS : SO 3 ) at 110°C for 6 h. In earlier studies, recrystallization of the “crude” disulfonated monomer from alcohol–water mixture was necessary to remove the monosulfonated and DCDPS impurities that lowered yield. However, in the current research, SDCDPS was successfully synthesized at nearly 100% conversion, which effectively eliminated the need for recrystallization. Recrystallization of SDCDPS from several alcohol–water mixtures (methanol–, ethanol–, and isoproponal–water mixtures) was investigated to compare product purities. Several characterization methods including proton NMR, HPLC, UV–visible, and fast atom bombardment mass spectroscopy confirmed that the crude SDCDPS was completely disulfonated and identical to recrystallized SDCDPS, without having any monosulfonated or starting material DCDPS impurities. Hence, it was demonstrated that the crude SDCDPS monomer by the current one‐step process and the recrystallized SDCDPS monomer were identical. This optimized monomer synthesis has been used to scale up the SDCDPS and poly(arylene ether sulfone) random and statistical copolymers at controlled disulfonation (35 and 45 mol %) levels, which were then used to fabricate proton exchange membranes for fuel cell applications. The intrinsic viscosity data confirmed that high molecular weight film forming copolymers were synthesized. The calculated degree of disulfonations by proton NMR was in close agreement with target disulfonations. It may be concluded that this optimized SDCDPS synthesis eliminates the need for recrystallization, which would be expected to improve process economics. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 4595–4602, 2006
Growth and survival signaling by lipid kinases (2008)

The phosphoinositide 3‐kinase (PI3K) pathway plays a critical role in cell growth regulation. PI3K generates the lipid, phosphatidylinositol‐3,4,5‐trisphosphate (PIP3), that acts as a membrane bound second messenger to activate AKT/PKB family protein Ser/Thr kinases as well Tec family protein‐Tyr kinases. PIP3 also regulates proteins that control Arf, Rac and Ras family GTP‐binding proteins. This lipid is elevated in cancers, either due to loss of PTEN, the phosphatases that degrades it, or due to constitutive PI3K activity because of activating mutations in PIK3CA or an upstream activator of PI3K. The ultimate consequence of activating PI3K is to generate changes in signaling networks and gene expression patterns that promote cell growth, cell survival and cell movement. In order to elucidate the role of the PI3K pathway in normal cell growth and in cancer, we have generated mice in which genes for PI3K are deleted or activated in specific tissues. In addition, we have investigated the biochemical mechanisms by which PI3K becomes activated in human cancers. Our progress in these areas will be summarized.
Changes in Laboratory Variables in Rheumatoid Arthritis Patients During a Trial of Fasting and One-year Vegetarian Diet (1995)

We have previously reported that significant improvement may be obtained in rheumatoid arthritis patients by fasting followed by a vegetarian diet for one year. The present study was carried out to examine to what extent biochemical and immunological variables changed during the clinical trial of fasting and vegetarian diet. For the patients who were randomised to the vegetarian diet there was a significant decrease in platelet count, leukocyte count, calprotectin, total IgG, IgM rheumatoid factor (RF), C3-activation products, and the complement components C3 and C4 after one month of treatment. None of the measured parameters changed significantly during this period in the group of omnivores. The course of 14 of 15 measured variables favored the vegetarians compared with the omnivores, but the difference was only significant for leukocyte count, IgM RF, and the complement components C3 and C4. Most of the laboratory variables declined considerably in the vegetarians who improved according to clinical variables, indicating a substantial reduction in inflammatory activity. The leukocyte count, however, decreased in the vegetarians irrespective of the clinical results. Thus, the decline in leukocyte count may be attributed to vegetarian diet per se and not to the reduction in disease activity. The results of the present study are in accordance with the findings from the clinical trial, namely that dietary treatment can reduce the disease activity in some patients with rheumatoid arthritis.
Optimized high-power diode laser, laser arrays, and bars for pump applications (2009)

Broad area diode laser and diode laser bars are the most efficient light sources. In comparison to solid state laser or gas laser systems the over all beam quality of the diode laser is poor. Thus most application of diode laser bars is high efficient pumping of solid state lasers converting the beam quality and scaling the power of laser systems within the kW range. The pump efficiency and the beam coupling efficiency of the diode laser pumped systems has to be increased to meet the increasing laser market demands for reduced costs. JENOPTIK Diode Lab GmbH (JDL) has optimized their high power brilliance bars to enable reliable high power operation especially, for the 9xx nm wavelength range and low far field divergences. Superior reliability with long operation time of 13,000 hours and high power operation of 200 W are demonstrated for high power bars high filling factor mounted on passively cooled heat sinks. Smaller far field divergence at high power levels requires longer cavity length and higher efficiencies in the beam coupling needs requires lower filling factors. The new high brilliance bars and arrays with 20% filling factor are showing high power operation up to 95 W and a slow axis beam divergence of less than 8&deg; (95% power content).
Seismic Response of Multistory Buildings with Self-Centering Energy Dissipative Steel Braces (2007)

This paper examines the seismic response of 2-, 4-, 8-, 12-, and 16-story steel framed buildings with self-centering energy dissipative (SCED) bracing members. The structures are assumed to be located in Los Angeles, California. Identical buildings equipped with buckling restrained braces (BRB) are also studied for comparison purposes. Incremental static analysis and nonlinear dynamic analysis under ground motion ensembles corresponding to three hazard levels were performed. The SCED frames generally experienced smaller peak story drifts, less damage concentration over the building height, and smaller residual lateral deformations compared to the BRB system. Higher floor acceleration peaks were observed in the SCED frames due to the sharper transitions between elastic and inelastic response assumed in the analysis. The study also indicated that higher design seismic loads may be needed for low-rise SCED and BRB frames in order to improve their collapse prevention performance.
An all-silicon transmitter with co-designed modulator and DC-coupled driver (2019)

We present a co-designed silicon traveling wave modulator with a SiGe driver with 6Vpp effective swing. 34GBaud DP-16QAM is demonstrated with comparable ROSNR performance to a commercial CFP2-ACO.
Preparation and comparison of bulk and membrane hydrogels based on Kraft- and ionic-liquid-isolated lignins (2016)

Lignin-based hydrogels in both bulk and membrane forms for potential drug delivery, food packaging, and wound dressing applications have been designed by crosslinking ionic-liquid-isolated lignin with epoxide-terminated polyethylene glycol (ETPEG) in alkaline solution.
Predicting the Suitability of Service Animals Using Instrumented Dog Toys (2018)

Working dogs1 are significantly beneficial to society; however, a substantial number of dogs are released from time consuming and expensive training programs because of unsuitability in behavior. Early prediction of successful service dog placement could save time, resources, and funding. Our research focus is to explore whether aspects of canine temperament can be detected from interactions with sensors, and to develop classifiers that correlate sensor data to predict the success (or failure) of assistance dogs in advanced training. In a 2-year longitudinal study, our team tested a cohort of dogs entering advanced training in the Canine Companions for Independence (CCI) Program with 2 instrumented dog toys: a silicone ball and a silicone tug sensor. We then create a logistic model tree classifier to predict service dog success using only 5 features derived from dog-toy interactions. During randomized 10-fold cross validation where 4 of the 40 dogs were kept in an independent test set for each fold, our classifier predicts the dogs' outcomes with 87.5% average accuracy. We assess the reliability of our model by performing the testing routine 10 times over 1.5 years for a single suitable working dog, which predicts that the dog would pass each time. We calculate the resource benefit of identifying dogs who will fail early in their training, and the value for a cohort of 40 dogs using our toys and our methods for prediction is over $70,000. With CCI's 6 training centers, annual savings could be upwards of $5 million per year.