gebhart/patrepeval huggingface dataset:
Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention (2017)

Abstract Specificity of CRISPR/Cas9 tools has been a major concern along with the reports of their successful applications. We report unexpected observations of high frequency off-target mutagenesis induced by CRISPR/Cas9 in T1 Arabidopsis mutants although the sgRNA was predicted to have a high specificity score. We also present evidence that the off-target effects were further exacerbated in the T2 progeny. To prevent the off-target effects, we tested and optimized two strategies in Arabidopsis , including introduction of a mCherry cassette for a simple and reliable isolation of Cas9-free mutants and the use of highly specific mutant SpCas9 variants. Optimization of the mCherry vectors and subsequent validation found that fusion of tRNA with the mutant rather than the original sgRNA scaffold significantly improves editing efficiency. We then examined the editing efficiency of eight high-specificity SpCas9 variants in combination with the improved tRNA-sgRNA fusion strategy. Our results suggest that highly specific SpCas9 variants require a higher level of expression than their wild-type counterpart to maintain high editing efficiency. Additionally, we demonstrate that T-DNA can be inserted into the cleavage sites of CRISPR/Cas9 targets with high frequency. Altogether, our results suggest that in plants, continuous attention should be paid to off-target effects induced by CRISPR/Cas9 in current and subsequent generations, and that the tools optimized in this report will be useful in improving genome editing efficiency and specificity in plants and other organisms.
Additive spanners and (α, β)-spanners (2010)

An (α, β)-spanner of an unweighted graph G is a subgraph H that distorts distances in G up to a multiplicative factor of α and an additive term β. It is well known that any graph contains a (multiplicative) (2 k −1, 0)-spanner of size O ( n 1+1/ k ) and an (additive) (1,2)-spanner of size O ( n 3/2 ). However no other additive spanners are known to exist. In this article we develop a couple of new techniques for constructing (α, β)-spanners. Our first result is an additive (1,6)-spanner of size O ( n 4/3 ). The construction algorithm can be understood as an economical agent that assigns costs and values to paths in the graph, purchasing affordable paths and ignoring expensive ones, which are intuitively well approximated by paths already purchased. We show that this path buying algorithm can be parameterized in different ways to yield other sparseness-distortion tradeoffs. Our second result addresses the problem of which (α, β)-spanners can be computed efficiently, ideally in linear time. We show that, for any k , a ( k , k −1)-spanner with size O ( kn 1+1/ k ) can be found in linear time, and, further, that in a distributed network the algorithm terminates in a constant number of rounds. Previous spanner constructions with similar performance had roughly twice the multiplicative distortion.
Expression profiling and comparative sequence derived insights into lipid metabolism (2001)

Expression profiling and genomic DNA sequence comparisons are increasingly being applied to the identification and analysis of the genes involved in lipid metabolism. Not only has genome-wide expression profiling aided in the identification of novel genes involved in important processes in lipid metabolism such as sterol efflux, but the utilization of information from these studies has added to our understanding of the regulation of pathways participating in the process. Coupled with these gene expression studies, cross species comparison, searching for sequences conserved through evolution, has proven to be a powerful tool to identify important non-coding regulatory sequences as well as the discovery of novel genes relevant to lipid biology. An example of the value of this approach was the recent chance discovery of a new apolipoprotein gene (apo AV) that has dramatic effects upon triglyceride metabolism in mice and humans.
Oficinas de Programação para Meninas: Despertando o Interesse Pela Computação (2018)

O presente relato descreve as atividades realizadas em um projeto de extensão que vem atuando na educação de alunas do primeiro ano do ensino médio, promovendo, através de oficinas de programação, o contato real com a área de computação. Dados coletados durante os três anos do projeto mostram que a maioria das alunas não tem conhecimento prévio sobre programação e consideram a atividade difícil; observou-se ainda que elas se mostram motivadas, interessadas e desafiadas em aprender a programar e percebem que a área de computação também é para elas. A partir da avaliação ao final da ação, pôde-se constatar que as oficinas vem cumprindo seu papel na promoção do empoderamento feminino bem como contribuindo com a formação cidadã das meninas.
On the Characterization of Urban Freight Transport (2011)

The current life in urban centers has led to increasing and demanding freight requirements, and manufactures, retailers and other urban agents have thus tended towards more frequent and smaller deliveries, which result in a growing use of light freight vehicles (<3.5 ton). In this paper the authors characterize and analyse urban freight mobility. Based on a 2-city case, which gathers data from global positioning systems (GPS) and complementary interviews, the authors first propose a categorization of urban freight movement, after which the authors carry out a speed analysis. Finally, this multi-factor study allows us to link dangerous behavior (out-of-limit-speed) with movement characteristics. The authors confirm that routine movements lead to safer driving behavior, while the lack of patterns and of previous route planning promote higher and, even worse, out-of-limit speeds. The results of this research could make an important contribution for setting appropriate and more specific safety policies.
Privacy Assessment in Android Apps: A Systematic Mapping Study (2021)

Android apps are daily installed by billions of users worldwide, who grant access to an extensive set of sensitive personal data. Different techniques have been developed over the years to understand how apps protect or harm their users’ privacy. However, these results have been produced in different research domains and addressing privacy from different perspectives, resulting in a growing but scattered body of knowledge. To bridge this gap, we have carried out a systematic mapping study to provide practitioners and researchers with an overview of the state-of-the-art technique, published between 2016 and 2020, to assess privacy in Android apps. In this paper, we highlight the most relevant findings, identify and analyse the most pressing gaps, and discuss the promising research directions.
Ion-microfield-induced effects on the satellite line spectra from laser-produced plasmas (1989)

The authors investigate the combined effect of the static perturbation due to a plasma ion microfield and the level population processes in determining the intensity of the dielectronic satellite lines (2p2) 1D to (1s2p) 1P and (2s2p) 1P to (1s2s) 1S in hot and dense plasmas. The results confirm that besides the different mechanisms of level population, the quasistatic ions of the plasma must be taken into account in the calculation of the intensities of these satellites.
Monitoring Damage Accumulation in Filament-Wound Graphite/Epoxy Laminate Coupons During Fatigue Loading Through Acoustic Emission (1984)

Damage accumulation during low cycle tension-tension fatigue loading has been monitored through acoustic emission for filament-wound graphite/epoxy [±24/90/0/ ±45/0/90/±24] T laminate coupons. Test frequency was 0.1 and 1.0 Hz at different dynamic load levels and specimens were cycled up to 5,000 and 15,000 cycles at a fatigue load ratio of 0.1. Unnotched and double edge notched specimens (300 × 25 mm in dimensions) were tested, with notch length-to-width ratios of 0.15 and 0.25.
A new species of Dendroblatta Rehn, 1916 from northern Brazil (Blattaria: Ectobiidae) collected in wasp nests (2013)

Currently sixteen species of Dendroblatta Rehn, 1916 are known, twelve of them occurring in Brazil. In this paper, one new species, D. spiculata sp. nov., is described from material collected from the Acre and Amazonas states in northern Brazil, in wasp nests. The new species differs from all other members of the genus by the male genitalia pieces. Illustrations of the genital pieces are presented. In Brazil, the genus is now known from the states of Acre, Amazonas, Bahia, Mato Grosso, Minas Gerais, Pará, Rio de Janeiro, and Rondônia.
tRNA over-expression in breast cancer and functional consequences (2009)

Increased proliferation and elevated levels of protein synthesis are characteristics of transformed and tumor cells. Though components of the translation machinery are often misregulated in cancers, what role tRNA plays in cancer cells has not been explored. We compare genome-wide tRNA expression in cancer-derived versus non-cancer-derived breast cell lines, as well as tRNA expression in breast tumors versus normal breast tissues. In cancer-derived versus non-cancer-derived cell lines, nuclear-encoded tRNAs increase by up to 3-fold and mitochondrial-encoded tRNAs increase by up to 5-fold. In tumors versus normal breast tissues, both nuclear- and mitochondrial-encoded tRNAs increase up to 10-fold. This tRNA over-expression is selective and coordinates with the properties of cognate amino acids. Nuclear- and mitochondrial-encoded tRNAs exhibit distinct expression patterns, indicating that tRNAs can be used as biomarkers for breast cancer. We also performed association analysis for codon usage-tRNA expression for the cell lines. tRNA isoacceptor expression levels are not geared towards optimal translation of house-keeping or cell line specific genes. Instead, tRNA isoacceptor expression levels may favor the translation of cancer-related genes having regulatory roles. Our results suggest a functional consequence of tRNA over-expression in tumor cells. tRNA isoacceptor over-expression may increase the translational efficiency of genes relevant to cancer development and progression.
Negative Poisson's Ratios for Extreme States of Matter (2000)

Negative Poisson's ratios are predicted for body-centered-cubic phases that likely exist in white dwarf cores and neutron star outer crusts, as well as those found for vacuumlike ion crystals, plasma dust crystals, and colloidal crystals (including certain virus crystals). The existence of this counterintuitive property, which means that a material laterally expands when stretched, is experimentally demonstrated for very low density crystals of trapped ions. At very high densities, the large predicted negative and positive Poisson's ratios might be important for understanding the asteroseismology of neutron stars and white dwarfs and the effect of stellar stresses on nuclear reaction rates. Giant Poisson's ratios are both predicted and observed for highly strained coulombic photonic crystals, suggesting possible applications of large, tunable Poisson's ratios for photonic crystal devices.
An improved Q-PLL to overcome the speed reversal problems in sensorless PMSM drive (2016)

Many existing sensorless control methods are based on flux observers, where phase-locked loops (PLLs) were used to extract the position information from the estimated rotor flux. This paper proposes an improved quadrature-component-based phase locked loop (Q-PLL) scheme for sensorless control of permanent magnet synchronous motor (PMSM) drives. To show the superiority of the proposed method in solving the problem of speed reversal, other three kinds of PLLs are also presented for the aim of comparison. This improved PLL is integrated with SMO-based sensorless control of PMSM drives. Compared to conventional Q-PLL, the main advantage of the proposed PLL is that it can work well without a gain scheduling remedial strategy or a judgment of the sign of speed in terms of speed reversal. Furthermore, it has a better performance in the transient and steady state response. Both Simulation and experimental results are presented to demonstrate the good performances of the proposed Q-PLL.
Efficient Synthesis of the Very‐Long‐Chain n‐3 Fatty Acids, Tetracosahexaenoic Acid (C24:6n‐3) and Tricosahexaenoic Acid (C23:6n‐3) (2011)

Tetracosahexaenoic acid (C(24):6n-3, THA, 3) is an essential biosynthetic precursor in mammals of docosahexaenoic acid (C(22):6n-3, DHA, 1), the end-product of the metabolism of n-3 fatty acids. THA 3 is present in commercially valuable fishes, such as flathead flounder. Tricosahexaenoic acid (C(23):6n-3, TrHA, 2), an odd-numbered-chain fatty acid, has been identified from marine organisms such as the dinoflagellate, Amphidinium carterae. To date, few studies have examined THA 3 and TrHA 2 due to difficulties in detecting and identifying these compounds, so their chemical and biological properties remain poorly characterized. Only one methodology for the chemical synthesis of THA 3 has been presented, and no method for the synthesis of TrHA 2 has been reported. We report here the efficient synthesis of THA 3 in four steps in 56% overall yield, and the synthesis of TrHA 2 in six steps in 48% overall yield. We also present the synthesis of Δ(2)-THA 4, an intermediate of β-oxidation of THA 3 to DHA 1, in three steps in 73% overall yield.
Electrochemical degradation modes in bifacial silicon photovoltaic modules (2021)

Abstract Motivated by the rapidly rising deployment of bifacial monocrystalline‐silicon photovoltaics (PV), we investigate the durability of various PV module packaging configurations with transparent coverings on both the front and rear sides of the module. We use a series of bifacial passivated emitter and rear cell (p‐PERC) mini‐modules with systematically varying outer cover materials (glass/glass, G/G, or glass/transparent backsheet, G/TB) and encapsulant chemistries (poly [ethylene‐co‐vinyl acetate], EVA; or polyolefin, POE). We study degradation modes over 1,000 hours of combined damp heat (DH) exposure and high system voltages that can cause potential‐induced degradation (PID) under positive, zero, or negative 1,000 V cell‐to‐frame bias. We analyze the degradation modes using a combination of current–voltage measurements, impedance spectroscopy, external quantum efficiency, and spatially resolved luminescence and thermal imaging. Our results highlight various types of degradation including shunting, enhanced recombination, and series resistance increases, and we use spatially resolved characterization to separately identify the localized effects. We show that multiple PID and moisture‐ingress degradation modes severely affect EVA‐containing modules, with previously reported PID processes under negative‐bias DH and a unique observation of rear‐side surface recombination in G/EVA/G modules under positive‐bias DH. We observe significantly less degradation in POE‐containing modules, where the G/POE/G configuration exhibits minimal degradation under all stress conditions that we employ.
Laser calibration and kinematical analysis and synthesis of robots. Selected problems (2002)

The paper presents kinematic analysis and synthesis of a multilink robot using a general multibody approach. The multibody analysis is based on the absolute coordinate formulation. For the numerical calculation the general purpose ADAMS/sup TM/ computer package was used. Separately the problem of calibration of a serial-parallel robot is discussed. For the calibration the ROBOTEST laser system was adapted which is primarily intended for measurements of other robot accuracy characteristics. The original calibration algorithm enables calibration using this system.
Data pruning for template-based automatic speech recognition (2010)

In this paper we describe and analyze a data pruning method in combination with template-based automatic speech recognition. We demonstrate the positive effects of polishing the template database by minimizing the word error rate scores. Data pruning allowed to effectively reduce the database size, and therefore the model size, by an impressive 30%, with consequent benefits on the computation time and memory usage. Index Terms: pruning, template, automatic speech recognition
Microgravity Effects on Plant Boundary Layers (2005)

The goal of these series of experiment was to determine the effects of microgravity conditions on the developmental boundary layers in roots and leaves and to determine the effects of air flow on boundary layer development. It is hypothesized that microgravity induces larger boundary layers around plant organs because of the absence of buoyancy-driven convection. These larger boundary layers may affect normal metabolic function because they may reduce the fluxes of heat and metabolically active gases (e.g., oxygen, water vapor, and carbon dioxide. These experiments are to test whether there is a change in boundary layer associated with microgravity, quantify the change if it exists, and determine influence of air velocity on boundary layer thickness under different gravity conditions.
Reflection-type Q factor measurement of transmission-type cavities (2002)

The traditional method of measuring the unloaded Q factor of a transmission cavity is the so-called insertion-loss method. The accuracy of that method deteriorates when the coupling becomes strong and when the input and output coupling coefficients differ from each other. To circumvent these difficulties, it is proposed to terminate one of the cavity ports with a matched load and measure the Q factor of the other port by the reflection-type method. The ports are then exchanged, and the measurement repeated from the other side. Such measurement provides an estimate of the uncertainty of the unloaded Q factor, and also works well when the input and output coupling coefficients differ from each other.
Morphology of PDMS−PMAA IPN Membranes (2003)

Direct visualization of IPN morphology formed during polymerization-induced phase separation (PIPS) of PDMS−PMAA IPNs is reported. Laser scanning confocal microscopy (LSCM) and hydrophilic fluorescent probes of varying molecular weights were used to image hydrophilic domains in PDMS−PMAA IPNs. The images reveal complex, superimposed structures of hydrophilic domains of varying sizes and spatial distributions. This morphology is attributed to the phase-separated structures formed and partially arrested at continuously varying quench depths during the PIPS process. These observations contribute to the understanding of morphology development in IPNs.
Effects of Nitrogen Availability on the Antioxidant Activity and Carotenoid Content of the Microalgae Nephroselmis sp (2020)

<i>Nephroselmis</i> sp. was previously identified as a species of interest for its antioxidant properties owing to its high carotenoid content. In addition, nitrogen availability can impact biomass and specific metabolites' production of microalgae. To optimize parameters of antioxidant production, <i>Nephroselmis</i> sp. was cultivated in batch and continuous culture conditions in stirred closed photobioreactors under different nitrogen conditions (N-repletion, N-limitation, and N-starvation). The aim was to determine the influence of nitrogen availability on the peroxyl radical scavenging activity (oxygen radical absorbance capacity (ORAC) assay) and carotenoid content of <i>Nephroselmis</i> sp. Pigment analysis revealed a specific and unusual photosynthetic system with siphonaxanthin-type light harvesting complexes found in primitive green algae, but also high lutein content and xanthophyll cycle pigments (i.e., violaxanthin, antheraxanthin, and zeaxanthin), as observed in most advanced chlorophytes. The results indicated that N-replete conditions enhance carotenoid biosynthesis, which would correspond to a higher antioxidant capacity measured in <i>Nephroselmis</i> sp. Indeed, peroxyl radical scavenging activity and total carotenoids were higher under N-replete conditions and decreased sharply under N-limitation or starvation conditions. Considering individual carotenoids, siphonaxanthin, neoxanthin, xanthophyll cycle pigments, and lycopene followed the same trend as total carotenoids, while β-carotene and lutein stayed stable regardless of the nitrogen availability. Carotenoid productivities were also higher under N-replete treatment. The peroxyl radical scavenging activity measured with ORAC assay (63.6 to 154.9 µmol TE g<sup>-1</sup> DW) and the lutein content (5.22 to 7.97 mg g<sup>-1</sup> DW) were within the upper ranges of values reported previously for other microalgae. Furthermore, contents of siphonaxanthin ere 6 to 20% higher than in previous identified sources (siphonous green algae). These results highlight the potential of <i>Nephroselmis</i> sp. as a source of natural antioxidant and as a pigment of interest.
Preparation and characterization of photoactivable heterobifunctional fluorescent reagents. (1984)

Two new photoactivable heterobifunctional reagents, 1-azido-5-naphthalene sulfonyl chloride (ANS-C1) and the N-hydroxysuccinimide ester of 1 -azido-5-naphthalene sulfonyl aminopropionate (NHS-ANS-AP), were synthesized and characterized. The reagents were applicable to the groupdirected modification of ligands. Upon exposure to ultraviolet light, the non-fluorescent modified ligands generated reactive nitrene intermediates which could react with neighboring molecules to form fluorescent products. This was demonstrated by the covalent modification of bovine serum albumin with ANS-AP by photolysis. NHS-ANS-AP was used for the preparation of a photoreactive invertebrate lectin.
Human imaging of phosphorus in cortical and trabecular bone in vivo (2004)

Phosphorus was imaged in vivo in human cortical and trabecular bone and the T(1) and T(2) (*) were measured. An ultrashort TE (UTE) pulse sequence (TE = 70 microm) was used with half pulse excitation and radial mapping of k-space from the center out. T(2) (*) was measured using multiple echo times and T(1) was measured both by saturation recovery and by a method using different RF pulse amplitudes. Seven normal subjects (32-85 years) were examined. Phosphorus was imaged, with a true in-plane resolution of 2.9 x 2.9 mm and a signal-to-noise ratio (SNR) of 19:1, in both cortical and trabecular bone. The mean T(2) (*) value was 207 +/- 12 micros, and the mean T(1) value was 8.6 +/- 3.0 sec. Images and measurements were obtained in realistic times on a clinical MR system. This may provide a new approach to characterizing disease of bone.
Charge Buildup In Lossy Dielectrics With Induced Inhomogeneities (1997)

In addition to their normal inhomogeneities, insulation may also become inhomogeneous under stress, for instance if their temperature is not uniform. Then, a charge density builds up wherever material properties such as conductivity and permittivity are not uniform. This is the case of HVDC cables, in which the core is heated by the Joule effect, while the sheath remains at near ambient temperature, so that an average temperature gradient of /spl les/50 K/cm may occur in the insulation, under a field which can reach 100 kV/cm. If the conductivity of the insulation is assumed to depend only on temperature, with an activation energy of 1 eV, the steady charge density predicted by electrostatics may reach levels easily measurable by the techniques now available. This charge density is somehow lowered in non-ohmic insulation. An early analysis of the transient charge build-up is discussed here, and extended to the case of a non-ohmic insulation. This allows calculation of the transient current generated in the external circuit by the accumulating charge, in the cases of ohmic and non-ohmic insulation. Finally, other manifestations of the space charges in question are mentioned. Among these, unexpected results on electroconvection in slightly ionic liquids in the presence of a temperature gradient are analyzed in terms of these charges, and suggest practical applications.