gebhart/patrepeval huggingface dataset:
T7 phage protein Gp2 inhibits the <i>Escherichia coli</i> RNA polymerase by antagonizing stable DNA strand separation near the transcription start site (2010)

Infection of Escherichia coli by the T7 phage leads to rapid and selective inhibition of the host RNA polymerase (RNAP)--a multi-subunit enzyme responsible for gene transcription--by a small ( approximately 7 kDa) phage-encoded protein called Gp2. Gp2 is also a potent inhibitor of E. coli RNAP in vitro. Here we describe the first atomic resolution structure of Gp2, which reveals a distinct run of surface-exposed negatively charged amino acid residues on one side of the molecule. Our comprehensive mutagenesis data reveal that two conserved arginine residues located on the opposite side of Gp2 are important for binding to and inhibition of RNAP. Based on a structural model of the Gp2-RNAP complex, we propose that inhibition of transcription by Gp2 involves prevention of RNAP-promoter DNA interactions required for stable DNA strand separation and maintenance of the "transcription bubble" near the transcription start site, an obligatory step in the formation of a transcriptionally competent promoter complex.
Conductivité électrique des gels argileux et anisométrie de leurs éléments (1965)

La conductivité électrique de gels monocationiques formés de solution d’un chlorure et d’une argile choisie parmi deux montinorillonites et deux kaolinites a été étudiée en faisant varier les teneurs en argile et en électrolytes. Au-dessous d’une concentration saline critique, la conductivité électrique croît avec la teneur en argile, le contraire étant vrai au-dessus de cette concentration ; la conductivité des gels est la somme d’une conductivité due au mouvement des ions dans la solution imbibant les pores du gel et d’une conductance de surface due à leur mouvement le long de la surface des pores. On a calculé le rapport du premier terme de cette somme à la conductivité de la solution d’électrolyte, ce qui a permis d’évaluer les rapports de longueurs d’axes des particules argileuses assimilées à des ellipsoïdes de révolution aplatis. Les valeurs ainsi calculées sont en accord avec les résultats tirés de méthodes indépendantes (mesures de viscosité de suspensions ou de surfaces spécifiques par isothermes d’adsorption d’azote, observations au microscope électronique). Cet accord justifie les hypothèses faites.
Biological Parameters for the Choice of Antiangiogenic Therapy and Efficacy Monitoring (1999)

Angiogenesis is a tightly controlled process which depends on the balance between stimulating and inhibiting factors. When this balance is disrupted, angiogenesis acquires a pathological meaning. The list of molecules able to induce angiogenesis is heterogeneous with respect to their chemical characteristics and biological properties. Quantitative measurement of tumor angiogenesis is necessary for the choice of therapeutic strategies and as an endpoint for antiangiogenic therapy. We are developing a quantitative RT-PCR with measures the expression of specific factors in real time. With the use of this rapid technique, measurement of the expression of the angiogenic factors and inhibitors is also possible in specimens as small as biopsies.
CFTR Inhibitors (2013)

The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a cAMP-regulated Cl- channel whose major function is to facilitate epithelial fluid secretion. Loss-of-function mutations in CFTR cause the genetic disease cystic fibrosis. CFTR is required for transepithelial fluid transport in certain secretory diarrheas, such as cholera, and for cyst expansion in autosomal dominant polycystic kidney disease. High-throughput screening has yielded CFTR inhibitors of the thiazolidinone, glycine hydrazide and quinoxalinedione chemical classes. The glycine hydrazides target the extracellular CFTR pore, whereas the thiazolidinones and quinoxalinediones act at the cytoplasmic surface. These inhibitors have been widely used in cystic fibrosis research to study CFTR function at the cell and organ levels. The most potent CFTR inhibitor has IC50 of approximately 4 nM. Studies in animal models support the development of CFTR inhibitors for antisecretory therapy of enterotoxin-mediated diarrheas and polycystic kidney disease.
Virtual reality visualization of patient specific heart model (2016)

Background The diagnostic dilemma that arises with congenital cardiac anomalies is visualizing the 3-D complexity of a child’s heart with 2-D tools. The complicated intracardiac relationships and extracardiac connections make it challenging to diagnose the defect and plan treatment for the child. It has been demonstrated that it is difficult to reconstruct an accurate mental 3D model from 2D images [Guillot 2007], yet we rely on this imperfect modality to make critical surgical decisions. 3D printed models are proving to be highly valuable in improving the understanding of these complex defects, but require many resources. In this project we have explored 3D immersive virtual reality technology to provide deeper understanding and visualization of cardiac models and supplant the need for a physical printed model. Using stereoscopic 3D in the form of 3D displays on head mounted displays (HMDs) excellent intuitive model was created. Models were generated from patient specific MRI which was converted to format that was compatible with virtual reality rendering.
A laser-based investigation of higher-order modes in transient Lamb waves (1993)

This Letter describes the integration of laser and fiber optic methods for generating and detecting broadband, transient Lamb waves in a steel plate. The generated Lamb waves are shown to be a superposition of different Lamb modes including the zeroth-order symmetric together with the zeroth- and first-order antisymmetric modes. Signal processing techniques are used to extract the phase velocities for each of these modes over a continuous, broadband frequency spectrum from the transient time histories of the waves recorded at two locations on a steel plate. The results are found to be in excellent agreement with theoretical phase velocities for each of the three modes evaluated.
A Comparison of Cell Populations at Various Depth Levels in Cerebral Cortex of Young Adult and Aged Long-Evans Rats (1968)

Journal Article A Comparison of Cell Populations at Various Depth Levels in Cerebral Cortex of Young Adult and Aged Long-Evans Rats Get access Kenneth R. Brizzee, Ph.D., M.D., Kenneth R. Brizzee, Ph.D., M.D. 2Department of Neurology And Anatomy, University Of Utah College Of MedicineSalt Lake City, Utah Search for other works by this author on: Oxford Academic PubMed Google Scholar Nancy Sherwood, Ph.D., Nancy Sherwood, Ph.D. Search for other works by this author on: Oxford Academic PubMed Google Scholar Paola S. Timiras, M.D., Ph.D. Paola S. Timiras, M.D., Ph.D. 3Department of Physiology, University Of CaliforniaBerkeley, California Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Gerontology, Volume 23, Issue 3, July 1968, Pages 289–297, https://doi.org/10.1093/geronj/23.3.289 Published: 01 July 1968
Preventive effect of isocitrate on glucocorticoid-induced cataract formation of developing chick embryo (1991)

Glucocorticoid-induced cataract formation appears to proceed via oxidation or peroxidation steps possibly caused by multiple activities of glucocorticoid in the living system. Attempts were made to modify GC-induced metabolic changes and prevent cataract formation using intermediates of the citric acid cycle. The compounds were applied to the embryos at 3, 10 and 20 hr after the administration of hydrocortisone succinate sodium (HC:0.25 mumol/egg) to 15-day-old eggs. At 48 hr after HC treatment the lenses were classified and analyzed. Almost all lenses were classified as stage IV-V (greater than 94%). However, the application of sodium isocitrate (IC:15 mumol/egg) which was the most potent among several intermediates tested showed a significant preventive effect against cataract formation. The administration of IC prevented the decline of GSH, the elevations of LPO and reduced the marked elevation of glucose in the lens caused by HC. The IC treatment also diminished the elevation of LPO in blood and liver. The above effects by IC on HC-induced events may be due to the action of IC in preventing the early decline of hepatic GSH caused by HC. Possibly IC was utilized as an intermediate of the citric acid cycle and a substrate for isocitrate dehydrogenase in cytosol to modify GC-induced metabolic changes.
Energy Scalability of On-Chip Interconnection Networks in Multicore Architectures (2008)

On-chip interconnection networks (OCNs) such as point-to-point networks and buses form the communication backbone in systems-on-a-chip, multicore processors, and tiled processors. OCNs can consume significant portions of a chip's energy budget, so analyzing their energy consumption early in the design cycle becomes important for architectural design decisions. Although numerous studies have examined OCN implementation and performance, few have examined energy. This paper develops an analytical framework for energy estimation in OCNs and presents results based on both analytical models of communication patterns and real network traces from applications running on a tiled multicore processor. Our analytical framework supports arbitrary OCN topologies under arbitrary communication patterns while accounting for wire length, switch energy, and network contention. It is the first to incorporate the effects of communication locality and network contention, and use real traces extensively. This paper compares the energy of point-to-point networks against buses under varying degrees of communication locality. The results indicate that, for 16 or more processors, a one-dimensional and a two-dimensional point-to-point network provide 66% and 82% energy savings, respectively, over a bus assuming that processors communicate with equal likelihood. The energy savings increase for patterns which exhibit locality. For the two-dimensional point-to-point OCN of the Raw tiled microprocessor, contention contributes a maximum of just 23% of the OCN energy, using estimated values for channel, switch control logic, and switch queue buffer energy of 34.5pJ, 17pJ, and 12pJ, respectively. Our results show that the energy-delay product per message decreases with increasing processor message injection rate.
Nanoceria – Energetics of Surfaces, Interfaces and Water Adsorption (2011)

The surface and interface enthalpies of CeO 2 were studied by high temperature oxide melt solution calorimetry combined with water adsorption calorimetry. The surface enthalpies of the hydrated and anhydrous surfaces are 0.86 ± 0.02 and 1.16 ± 0.02 J/m 2 , respectively. The water adsorption enthalpies are similar for nano and bulk ceria; for the nano ceria the integral adsorption enthalpy for chemisorbed water relative to water vapor is −59.82 ± 0.74 kJ/mol with coverage of 8.79 ± 0.39 H 2 O /nm 2 and for the bulk it is −61.69 ± 1.26 kJ/mol with coverage of 8.15 ± 0.66 H 2 O /nm 2 . The interfacial enthalpy is 0.81 ± 0.14 J/m 2 . The obtained energies are in good agreement with reported data from atomistic simulations and less direct experimental determinations.
Should blood transport kinetics be modeled in metabolic processes? (1984)

We analyze the interaction between blood transport phenomena and uptake processes when drug kinetics are studied with compartmental models. Relevant advantages in the physiological interpretation of the model parameters are obtained when blood transport is explicitly included in the model. This is done by aggregating into a single compartment all the blood spaces where no exchange with extravascular spaces takes place and separating into different blood compartments those spaces where some uptake and/or return occurs. The proposed strategy extensively uses all available a priori information about the physiological system, instead of considering only the information available in the measurements. This modeling approach has three main advantages: it provides greater insight into the identified quantities; it allows the introduction of quantitative a priori information; and it facilitates the experiment design task.
Prior Medications and the Cardiovascular Benefits From Combination Angiotensin‐Converting Enzyme Inhibition Plus Calcium Channel Blockade Among High‐Risk Hypertensive Patients (2018)

Peer Reviewed
Generalized Bregman divergence and gradient of mutual information for vector Poisson channels (2013)

We investigate connections between information-theoretic and estimation-theoretic quantities in vector Poisson channel models. In particular, we generalize the gradient of mutual information with respect to key system parameters from the scalar to the vector Poisson channel model. We also propose, as another contribution, a generalization of the classical Bregman divergence that offers a means to encapsulate under a unifying framework the gradient of mutual information results for scalar and vector Poisson and Gaussian channel models. The so-called generalized Bregman divergence is also shown to exhibit various properties akin to the properties of the classical version. The vector Poisson channel model is drawing considerable attention in view of its application in various domains: as an example, the availability of the gradient of mutual information can be used in conjunction with gradient descent methods to effect compressive-sensing projection designs in emerging X-ray and document classification applications.
Advanced treatment of the reverse osmosis concentrate by the Fenton and O3/UV oxidation processes (2010)

Due to their process stability and the excellent effluent quality, the use of membrane processes for wastewater treatment and reuse is rapidly expanding. However, a drawback of the membrane processes is the production of concentrates and their proper disposal. In this study, an industrial wastewater is treated by an activated sludge process combined with reverse osmosis (RO). The RO concentrate is characterised by recalcitrant COD and a low biodegradability. The effect of partial Fenton and ozone/UV oxidation of RO concentrate to increase the concentrate biodegradability is examined. Comparing all the investigated dosages of Fenton reagent, the hydrogen peroxide dosage of 2.4 mM has the most positive impact on both the BOD/COD ratio and the biodegradation rate. However the partial Fenton oxidation results in a better mineralisation of the organic matter in the concentrate, the oxidation by ozone and UV achieves a more positive effect on the enhancement of the biodegradability. Finally, a similar degradation of AOX compounds in the concentrate by both oxidation processes can be observed. Hence, it can be concluded that the partial oxidation is more selective in the degradation of complex, non-biodegradable compounds compared to the mineralisation of organic matter.
Imaging techniques in metabolic bone disease (1992)

Log in or Register Get new issue alertsGet alerts Enter your Email address: Wolters Kluwer Health may email you for journal alerts and information, but is committed to maintaining your privacy and will not share your personal information without your express consent. For more information, please refer to our Privacy Policy. Subscribe to eTOC Secondary Logo Journal Logo All Articles Images Videos Podcasts Blogs Advanced Search Toggle navigation Register Login HomeCurrent IssuePrevious Issues Current Orthopaedic PracticeCurrent Opinion in Orthopaedics (1999-2007)Clinical Orthopaedics and Related Research (1976-2007) Published Ahead-of-PrintCOP eNewsMy CollectionsJournal Info About the JournalEditorial BoardInformation for AuthorsAdvertisingOpen AccessSubscription ServicesReprintsRights and Permissions All Articles Images Videos Podcasts Blogs Advanced Search
Tyrosine Phosphorylation Is an Early and Specific Event Involved in Primary Keratinocyte Differentiation (1990)

Very little is known about early molecular events triggering epithelial cell differentiation. We have examined the possible role of tyrosine phosphorylation in this process, as observed in cultures of primary mouse keratinocytes after exposure to calcium or 12-O-tetradecanoylphorbol-13-acetate (TPA). Immunoblotting with phosphotyrosine-specific antibodies as well as direct phosphoamino acid analysis revealed that induction of tyrosine phosphorylation occurs as a very early and specific event in keratinocyte differentiation. Very little or no induction of tyrosine phosphorylation was observed in a keratinocyte cell line resistant to the differentiating effects of calcium. Treatment of cells with tyrosine kinase inhibitors prevented induction of tyrosine phosphorylation by calcium and TPA and interfered with the differentiative effects of these agents. These results suggest that specific activation of tyrosine kinase(s) may play an important regulatory role in keratinocyte differentiation.
Author response: Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA (2013)

Hundreds of cell growth and stress response genes are controlled by a rare small RNA component of an ancient splicing machinery, providing a raison d'être for its previously unexplained evolutionary conservation.
Marsh: min-area retiming with setup and hold constraints (1999)

This paper describes a polynomial time algorithm for min-area retiming for edge-triggered circuits to handle both setup and hold constraints. Given a circuit G and a target clock period c, our algorithm either outputs a retimed version of G satisfying setup and hold constraints or reports that such a solution is not possible, in O(|V/sup 3/|log|V|log(|V|C)) steps, where |V| corresponds to number of gates in the circuit and C is equal to the number of registers in the circuit. This is the first polynomial time algorithm ever reported for min-area retiming with constraints on both long and short-paths. An alternative problem formulation that takes practical issues in to consideration and lowers the problem complexity is also developed. Both the problem formulations have many parallels with the original formulation of long-path only retiming by Leiserson and Saxe and all the speed improvements that have been obtained on that technique are likely to be valid for improving the performance of the technique described in this paper.
Effects of self-radiation damage on electronic properties of {sup 244}Cm{sup 3+} in an orthophosphate crystal of YPO{sub 4} (1997)

Electronic energy level of alpha-emitting isotope {sup 244}Cm{sup 3+} (t{sub {1/2}}=18.1 y) doped into single crystals of YPO{sub 4} has been studied using site-selected laser spectroscopic methods. Electronic transitions between the nominal {sup 8}S{sub 7/2} state of Cm{sup 3+} were utilized to characterize the effects of alpha-decay induced structural damage. The total splitting of the four crystal field doublets in the ground multiplet is 12.5 cm{sup -1} and that of the excited multiplet is 611 cm{sup -1}. Due to radiation damage accumulated in 17 years since the crystals were grown, the inhomogeneous line width of the {sup 8}S{sub 7/2} {leftrightarrow} {sup 6}D{sub 7/2} transitions in broader than 50 cm{sup -1} as measured without site selection. The line width of resonant fluorescence line narrowing (RFLN) is less than 1 cm{sup -1} at 4 K. A total of 12 satellite lines were observed symmetrically spacing about the RFLN line. The position, width, and intensity of these satellite lines have been analyzed to gain information on the electronic and structural properties of the actinide ions in the metamict phases of Cm{sup 3+}:YPO{sub 4}.
A Rational Method of Project Selection by Post-Graduate Students* (2003)

A critical part, and sometimes the whole, of any postgraduate programme is the undertaking by the students of a project. One of the most crucial phases in this undertaking is the project selection. It is also this phase where students, invariably, receive no formal training and this could delay the whole undertaking substantially; in some cases leading to premature abandonment of the project or the degree programme altogether. This paper attempts to fill this gap by providing a framework and a methodology that would enable the student to develop a greater comprehension of the problem and to make a rational choice. The framework is based on decision analysis and comprises a two-stage procedure: (a) technical uncertainty and dominance screening and (b) the application of SMART (Simple Multi-Attribute Rating Technique). A hypothetical case is considered to illustrate the methodology and the results are discussed.
RFID threshold accelerometer (2008)

This paper presents the design, manufacture, and testing of a battery-free, wireless threshold accelerometer based on a fully compliant bistable mechanism (FCBM). The FCBM stores threshold acceleration measurements mechanically, eliminating the need for electrical power. The sensorpsilas state can be read wirelessly via a passive RFID tag. Because information can be stored in these tags for over 25 years, the sensor can be left unattended for long periods of time. The FCBM portion of the sensor is laser cut from a single sheet of plastic (Delrin) and integrated with an Atmel ATA5570 RFID chip. Both elements can be manufactured at low cost. The G-force needed to exceed the shock threshold can be varied by changing the mass of the FCBM. Multiple sensors were tested using three different methods. The first method was a centrifuge, providing a constant force input. The second method was a drop test that gave an impulse input to the sensor. The final method used a shaker table to provide a sinusoidal input. In each of these tests, it was found that the FCBM sensed the correct acceleration and retained its mechanical state. A number of prototype sensors were constructed with different masses resulting in threshold accelerations between 15 and 180 Gpsilas. The overall size of these sensors was approximately 28 mm x 26 mm. The RFID tags operate at 150 kHz and were read using a commercial off-the-shelf reader with a range of approximately 3 cm. Longer range readers are readily available at higher operating frequencies.
ChemInform Abstract: Pyrazolotrithiadiazepines and Their Unexpected Rearrangement to 1,2,3‐ Dithiazoles. (1991)

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.