gebhart/patrepeval huggingface dataset:
Helicase dissociation and annealing of RNA-DNA hybrids by <i>Escherichia coli</i> Cas3 protein (2011)

CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) is a nucleic acid processing system in bacteria and archaea that interacts with mobile genetic elements. CRISPR DNA and RNA sequences are processed by Cas proteins: in Escherichia coli K-12, one CRISPR locus links to eight cas genes (cas1, 2, 3 and casABCDE), whose protein products promote protection against phage. In the present paper, we report that purified E. coli Cas3 catalyses ATP-independent annealing of RNA with DNA forming R-loops, hybrids of RNA base-paired into duplex DNA. ATP abolishes Cas3 R-loop formation and instead powers Cas3 helicase unwinding of the invading RNA strand of a model R-loop substrate. R-loop formation by Cas3 requires magnesium as a co-factor and is inactivated by mutagenesis of a conserved amino acid motif. Cells expressing the mutant Cas3 protein are more sensitive to plaque formation by the phage λvir. A complex of CasABCDE ('Cascade') also promotes R-loop formation and we discuss possible overlapping roles of Cas3 and Cascade in E. coli, and the apparently antagonistic roles of Cas3 catalysing RNA-DNA annealing and ATP-dependent helicase unwinding.
Shear Modulus and Yield Stress Measurements of Attractive Alumina Particle Networks in Aqueous Slurries (1996)

The shear modulus and yield stress of attractive alumina particle networks in aqueous slurries was determined as a function of volume fraction (0.1 to 0.5), pH (2, 4, 5, 6, and 9), and salt (NH 4 l) concentration (0.25M to 2.34) using both vane and couette rheological tools. Consistent with previous observations concerning the relative strength of attractive particle networks, the shear modulus increased to a plateau value with salt concentration. In this work we have shown that the salt concentration at which this plateau value is achieved is a function of the pH, and thus, the surface charge density. The values of the shear modulus [G′], yield stress [τ y ], and yield strain [γ y ] of the attractive networks can be described with power law functions for particle volume fraction [φ] (G′∝φ 4.75 , τ y ∝φ 3.6 , and γ y ∝φ −1.1 ) and salt concentration [c] (G′∝ [c] 2.0 , τ, ∝ [c] 1.15 , and γ y ∝ [c] −0.85 ).
Efficient Synthesis of S‐Linked Glycopeptides in Aqueous Solution by a Convergent Strategy. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Phase Angle Effects on Fracture Toughness of Polymer Interfaces Reinforced with Block Copolymers (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhase Angle Effects on Fracture Toughness of Polymer Interfaces Reinforced with Block CopolymersFei Xiao, Chung-Yuen Hui, Junichiro Washiyama, and Edward J. KramerCite this: Macromolecules 1994, 27, 15, 4382–4390Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/ma00093a045https://doi.org/10.1021/ma00093a045research-articleACS PublicationsRequest reuse permissionsArticle Views329Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Human climbing with efficiently scaled gecko-inspired dry adhesives (2014)

Since the discovery of the mechanism of adhesion in geckos, many synthetic dry adhesives have been developed with desirable gecko-like properties such as reusability, directionality, self-cleaning ability, rough surface adhesion and high adhesive stress. However, fully exploiting these adhesives in practical applications at different length scales requires efficient scaling (i.e. with little loss in adhesion as area grows). Just as natural gecko adhesives have been used as a benchmark for synthetic materials, so can gecko adhesion systems provide a baseline for scaling efficiency. In the tokay gecko (Gekko gecko), a scaling power law has been reported relating the maximum shear stress σmax to the area A: σmax ∝ A(-1/4). We present a mechanical concept which improves upon the gecko's non-uniform load-sharing and results in a nearly even load distribution over multiple patches of gecko-inspired adhesive. We created a synthetic adhesion system incorporating this concept which shows efficient scaling across four orders of magnitude of area, yielding an improved scaling power law: σmax ∝ A(-1/50). Furthermore, we found that the synthetic adhesion system does not fail catastrophically when a simulated failure is induced on a portion of the adhesive. In a practical demonstration, the synthetic adhesion system enabled a 70 kg human to climb vertical glass with 140 cm(2) of adhesive per hand.
Hydrophobic supplements in cell‐free systems: Designing artificial environments for membrane proteins (2014)

Membrane proteins (MPs) are of central interest for the pharmaceutical industry but their production is usually a challenging task. The complex folding mechanisms of newly synthesized MPs often require interactions with specific compounds for improved stability. Conditions for the production of high‐quality samples are therefore difficult to predict and frequently cannot be provided in conventional protein expression platforms. Cell‐free (CF) biosynthetic systems allow, in contrast to living cells, nonrestricted access to the protein production machinery. Reaction conditions can be adjusted according to particular requirements and modified by supplementing single additives or even cocktails of compounds. These options have initiated completely new research fields for the cotranslational stabilization and folding of MPs in artificial environments. Based on established and efficient CF production protocols, a recent focus was to explore and define suitable supplements for CF expression reactions that are useful for the generation of high‐quality MP samples. Besides classical detergents and lipids, a variety of new compounds with interesting properties have been discovered and synthesized. We compile the currently available toolbox for MP solubilization in CF systems and summarize new developments and perspectives for the directed modulation of CF biosynthetic environments.
INVESTIGATION OF ARRAY AND LENS-TYPE SCANNING ANTENNAS (1961)

An investigation was made of arr y and lens-type scanning an e na High-resolution antenna arrays were developed with relatively few antenna elements by using interferometer techniques combi with uitable signalprocessing circuitry. Further, theoretical and experimental design information was derived for a novel beam-scanning lens antenna that is useful at frequencies as low as he HF ban . The lens consist of a pair of wire grids with square, hexagonal, or triangular mesh. Some work was done on nonuniformly spaced arrays. The results of this stu y, however, were not very promising. (Author)
EL SURGIMIENTO DE LA MODERNIDAD (2012)

En este articulo el autor hace una sinopsis del surgimiento de la sociedad moderna a partir de una serie de siete cambios que se producen en Europa y luego se extienden por el resto del mundo en un periodo de 400 anos que van aproximadamente desde 1430 a 1830. Esos siete procesos fueron: la exploracion y expansion geografica, el Renacimiento, la reforma protestante, la revolucion cientifica, las revoluciones politicas de Inglaterra y Francia, la Ilustracion y la Revolucion Industrial. Finalmente se sintetizan las tres oleadas de cambios paralelos, sociojuridicos y tecnologicos, acontecidos en los ultimos 200 anos que dan lugar a la denominada sociedad post-industrial o sociedad de la informacion y el conocimiento en la cual nos encontramos. Normal 0 21 false false false ES X-NONE X-NONE /* Style Definitions */
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<b>The leader peptide is essential for the post‐translational modification of the DNA‐gyrase inhibitor microcin B17</b> (1997)

Microcin B17 (MccB17) is a ribosomally encoded DNA-gyrase inhibitor. Ribosomally encoded antibiotics are derived from precursors containing an N-terminal leader, which is removed during maturation, and a C-terminal structural peptide. PreMccB17, the translational product of mcbA, is modified into proMccB17 by the action of three enzymes, McbB, McbC, and McbD. A chromosomally encoded peptidase then converts proMccB17 into MccB17. The role of McbB, McbC, and McbD is to convert glycine, cysteine, and serine residues present in preMccB17 into four thiazole and four oxazole rings. Using a modification-specific antibody rather than antimicrobial activity, we show that the 26-amino-acid N-terminal leader of preMccB17 is essential for the conversion of preMccB17 into proMccB17. Neither a preMccB17 peptide lacking the leader nor a preMccB17-beta-galactosidase fusion lacking the leader are post-translationally modified.
Etiolation aids rooting of <i>Protea cynaroides</i> cuttings (2006)

The role that starch content and blanching play in the rooting of Protea cynaroides cuttings was studied.P. cynaroides stems were blanched on the motherplant in the field, which resulted in a higher starch concentration in the cuttings.The relationship between starch content and rooting was also established, whereby the ability of the blanched cuttings to maintain a consistent starch level throughout the rooting period, resulted in the acceleration of the rooting process.The blanched cuttings had a higher dry root mass than the control at day 90 when the cuttings were ready to be transplanted.The untreated cuttings were only suitable for transplanting after 120 days.Blanching the cuttings also resulted in a higher rooting percentage (100%) than the control (60%).
Design Of A Robust Controller For Agc With Combined Intelligence Techniques (2008)

In this work Artificial Intelligence (AI) techniques like Fuzzy logic, Genetic Algorithms and Particle Swarm Optimization have been used to improve the performance of the Automatic Generation Control (AGC) system. Instead of applying Genetic Algorithms and Particle swarm optimization independently for optimizing the parameters of the conventional AGC with PI controller, an intelligent tuned Fuzzy logic controller (acting as the secondary controller in the AGC system) has been designed. The controller gives an improved dynamic performance for both hydrothermal and thermal-thermal power systems under a variety of operating conditions.
Diagnostic Value of Electromyography in Children and Adolescents (2005)

The diagnostic accuracy in pediatric neurology has been considerably improved by new methods such as magnetic resonance imaging and molecular genetic analysis. However, standard diagnostic techniques continue to play an important role. The authors analyzed the diagnostic value of electromyography (EMG) and nerve conduction studies (NCS) in a retrospective study of 498 pediatric patients. The overall consistency between EMG results and the final clinical diagnosis in all children examined was 98%. In myogenic diseases, the concordance between EMG and clinical findings was lower (80%), because some patients with congenital myopathies showed normal EMG findings in this group. Peripheral neurogenic diseases were in all but one of the cases diagnosed correctly (99.5%). No decrease in diagnostic reliability was found in the younger age group. EMG and NCS examinations have to be adapted to the needs of children by an experienced examiner, but continue to be valuable diagnostic methods in pediatric neurology.
Image-guided periacetabular osteotomy: computer-assisted navigation compared with the conventional technique: A randomized study of 36 patients followed for 2 years (2006)

A computer-assisted navigation system is a feasible tool to provide real-time image guidance and facilitate PAO. However, it offers little additional benefit when the surgery is done by an experienced surgeon.
Direct observation of the critical state field profile in a YBa2Cu3O7-y single crystal (1992)

We report direct imaging of the critical state in a ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathit{y}}$ single crystal. The self-field profiles are obtained by mechanically scanning a high-spatial-resolution Hall-probe array above the crystal surface. The measured field distributions confirm Bean's assumption of homogeneity, setting the relevant length scale for the evaluation of the critical currents as the sample size, and are a proof against the weak-link behavior in such crystals.
International migration: a new challenge. (1992)

This is a general review of global trends in international migration, including its current volume and its implications.
Empowering Visual Categorization With the GPU (2010)

Visual categorization is important to manage large collections of digital images and video, where textual metadata is often incomplete or simply unavailable. The bag-of-words model has become the most powerful method for visual categorization of images and video. Despite its high accuracy, a severe drawback of this model is its high computational cost. As the trend to increase computational power in newer CPU and GPU architectures is to increase their level of parallelism, exploiting this parallelism becomes an important direction to handle the computational cost of the bag-of-words approach. When optimizing a system based on the bag-of-words approach, the goal is to minimize the time it takes to process batches of images. this paper, we analyze the bag-of-words model for visual categorization in terms of computational cost and identify two major bottlenecks: the quantization step and the classification step. We address these two bottlenecks by proposing two efficient algorithms for quantization and classification by exploiting the GPU hardware and the CUDA parallel programming model. The algorithms are designed to (1) keep categorization accuracy intact, (2) decompose the problem, and (3) give the same numerical results. In the experiments on large scale datasets, it is shown that, by using a parallel implementation on the Geforce GTX260 GPU, classifying unseen images is 4.8 times faster than a quad-core CPU version on the Core i7 920, while giving the exact same numerical results. In addition, we show how the algorithms can be generalized to other applications, such as text retrieval and video retrieval. Moreover, when the obtained speedup is used to process extra video frames in a video retrieval benchmark, the accuracy of visual categorization is improved by 29%.
XXV.—Synthesis of indene, hydrindene, and some of their derivatives (1894)

W. H. Perkin and G. Révay, J. Chem. Soc., Trans., 1894, 65, 228 DOI: 10.1039/CT8946500228
Site-Directed Disulfide Cross-Linking Shows that Cleft Flexibility in the Periplasmic Domain Is Needed for the Multidrug Efflux Pump AcrB of <i>Escherichia coli</i> (2007)

Escherichia coli AcrB is a multidrug efflux transporter that recognizes multiple toxic chemicals having diverse structures. Recent crystallographic studies of the asymmetric trimer of AcrB suggest that each protomer in the trimeric assembly goes through a cycle of conformational changes during drug export. However, biochemical evidence for these conformational changes has not been provided previously. In this study, we took advantage of the observation that the external large cleft in the periplasmic domain of AcrB appears to become closed in the crystal structure of one of the three protomers, and we carried out in vivo cross-linking between cysteine residues introduced by site-directed mutagenesis on both sides of the cleft, as well as at the interface between the periplasmic domains of the AcrB trimer. Double-cysteine mutants with mutations in the cleft or the interface were inactive. The possibility that this was due to the formation of disulfide bonds was suggested by the restoration of transport activity of the cleft mutants in a dsbA strain, which had diminished activity to form disulfide bonds in the periplasm. Furthermore, rapidly reacting, sulfhydryl-specific chemical cross-linkers, methanethiosulfonates, inactivated the AcrB transporter with double-cysteine residues in the cleft expressed in dsbA cells, and this inactivation could be observed within a few seconds after the addition of a cross-linker in real time by increased ethidium influx into the cells. These observations indicate that conformational changes, including the closure of the external cleft in the periplasmic domain, are required for drug transport by AcrB.
Past exposure to vaccines and subsequent risk of Alzheimer's disease. (2001)

Past exposure to vaccines against diphtheria or tetanus, poliomyelitis and influenza may protect against subsequent development of Alzheimer's disease.
Towards Markerless Augmented Medical Visualization (2004)

This work describes a technique to merge 3D virtual models onto real scenes without tracking markers. Real scene is acquired using stereovision technique and the region of interest in the real scene is selected by means of applying color and spatial filters. The registration algorithm operates by minimizing the mean square distance between the points from stereovision and the surface from the virtual model. It is an approach suitable for applications requiring focused user%92s attention and high accuracy in the registration process. This approach has been integrated into a multi-platform framework for visualization and processing of medical image. The achieved spatial accuracy (e.g. rotation and translation) and time performance are encouraging for real time applications.
The renal elimination of rifampicin as a function of the oral dose. A convenient way to assess relative bioavailability. (1978)

A spectrophotometric method for the quantitative determination of rifampicin in urine is described and its specificity and precision are discussed. It is shown that the mean cumulative urinary elimination of rifampicin is reproducible when the same dose is administered twice in two different experiments to the same group of volunteers. The percentage of the amount eliminated increases with increasing dose. The renal elimination of apparent rifampicin can be used as a parameter for assessment of relative bioavailability of rifampicin from oral dosage forms of the same nominal strength if an appropriate number of volunteers is involved in the test.
HIV-1 regulation of latency in the monocyte-macrophage lineage and in CD4+ T lymphocytes (2009)

The introduction in 1996 of the HAART raised hopes for the eradication of HIV-1. Unfortunately, the discovery of latent HIV-1 reservoirs in CD4+ T cells and in the monocyte-macrophage lineage proved the optimism to be premature. The long-lived HIV-1 reservoirs constitute a major obstacle to the eradication of HIV-1. In this review, we focus on the establishment and maintenance of HIV-1 latency in the two major targets for HIV-1: the CD4+ T cells and the monocyte-macrophage lineage. Understanding the cell-type molecular mechanisms of establishment, maintenance, and reactivation of HIV-1 latency in these reservoirs is crucial for efficient therapeutic intervention. A complete viral eradication, the holy graal for clinicians, might be achieved by strategic interventions targeting latently and productively infected cells. We suggest that new approaches, such as the combination of different kinds of proviral activators, may help to reduce dramatically the size of latent HIV-1 reservoirs in patients on HAART.
A Multi-stream Bi-directional Recurrent Neural Network for Fine-Grained Action Detection (2016)

We present a multi-stream bi-directional recurrent neural network for fine-grained action detection. Recently, twostream convolutional neural networks (CNNs) trained on stacked optical flow and image frames have been successful for action recognition in videos. Our system uses a tracking algorithm to locate a bounding box around the person, which provides a frame of reference for appearance and motion and also suppresses background noise that is not within the bounding box. We train two additional streams on motion and appearance cropped to the tracked bounding box, along with full-frame streams. Our motion streams use pixel trajectories of a frame as raw features, in which the displacement values corresponding to a moving scene point are at the same spatial position across several frames. To model long-term temporal dynamics within and between actions, the multi-stream CNN is followed by a bi-directional Long Short-Term Memory (LSTM) layer. We show that our bi-directional LSTM network utilizes about 8 seconds of the video sequence to predict an action label. We test on two action detection datasets: the MPII Cooking 2 Dataset, and a new MERL Shopping Dataset that we introduce and make available to the community with this paper. The results demonstrate that our method significantly outperforms state-of-the-art action detection methods on both datasets.
Inactivation of the 2-ketoglutarate and pyruvate dehydrogenase complexes of beef heart by branched chain keto acids. (1983)

Incubation of 2-ketoglutarate dehydrogenase complex with 2-ketoisovalerate, 2-keto-4-methylvalerate, or 2-keto-3-methylvalerate leads to the appearance of a lag phase and of a progressive loss of activity in subsequent measurements of the initial rate of oxidation of 2-ketoglutarate. In the case of 2-ketoisovalerate these effects are shown to be due to the formation of an isobutyryllipoate derivative of the enzyme, as a result of the very slow oxidation of 2-ketoisovalerate by the enzyme complex (Vmax congruent to 0.15% of that for 2-ketoglutarate). Incubation of the enzyme complex with 2-keto[14C]isovalerate or 2-keto[14C]glutarate results in comparable incorporation of radioactivity, amounting to 3.5 to 5.3 nmol of isobutyryl or succinyl residues per mg of protein in the complex. Isobutyryl residues are also incorporated in the enzyme during the simultaneous oxidation of both of these substrates. During the early phase of incubation of the complex with 2-ketoisovalerate the incorporation of isobutyryl residues is much faster than the loss of enzyme activity. This observation seems to support the suggestion that each 2-ketoglutarate decarboxylase subunit of the complex may catalyze the succinylation of more than one lipoate succinyltransferase subunit. Results are also presented showing the inactivation of pyruvate dehydrogenase complex on preincubation with 2-ketoisovalerate and of 2-ketoglutarate dehydrogenase complex with methylenecyclopropylpyruvate, the keto acid corresponding to the toxic amino acid hypoglycin. The relevance of covalent modifications of the two keto acid dehydrogenase complexes to the pathological manifestations of maple syrup urine disease are discussed.