gebhart/patrepeval huggingface dataset:
A hypermutator phenotype attenuates the virulence of <i>Listeria monocytogenes</i> in a mouse model (2002)

The integrity of the genetic material of bacteria is guaranteed by a set of distinct repair mechanisms. The participation of these repair systems in bacterial pathogenicity has been addressed only recently. Here, we study for the first time the participation in virulence of the MutSL mismatch repair system of Listeria monocytogenes. The mutS and mutL genes, which are contiguous in the L. monocytogenes chromosome, were identified after in silico analysis. The deduced MutS shares 62% identity with MutS of Bacillus subtilis and 50% identity with HexA, its homologue in Streptococcus pneumoniae; MutL shares 59% identity with MutL of B. subtilis and 47% identity with HexB of S. pneumoniae. Functional analysis of the mutSL locus was studied by constructing a double knock-out mutant. We showed that the deletion DeltamutSL induces: (i) a 100- to 1000-fold increase in the spontaneous mutation rate; and (ii) a 10- to 15-fold increase in the frequency of transduction, thus demonstrating the role of mutSL of L. monocytogenes in both mismatch repair and homologous recombination. We found that the deletion DeltamutSL moderately affected bacterial virulence, with a 1-log increase in the lethal dose 50% (LD50) in the mouse. Strikingly, repeated passages of the mutant strain in mice reduced virulence further. Competition assays between wild-type and mutant strains showed that the deletion DeltamutSL reduced the capacity of L. monocytogenes to survive and multiply in mice. These results thus demonstrate that, for the intracellular pathogen L. monocytogenes, a hypermutator phenotype is more deleterious than profitable to its virulence.
Transfer of Monovalent and Divalent Cations in Salt Solutions by Electrodialysis (2007)

Abstract The selectivity mechanism of transport of Na+, Ca2+ and Mg2+ through commercial monovalent‐cation permselective membranes is investigated in batch electrodialysis experiments with synthetic salt solutions containing monovalent and divalent cations. The role of hydration energy, steric effect, kinetic effect as well as effects of permselectivity of cation exchange membrane has been elucidated with electrodialysis of single solutions (NaCl, CaCl2, MgCl2). The mechanism of interferences is investigated in (Na+/Ca2+, Na+/Mg2+, Ca2+/Mg2+ and Na+/Ca2+/Mg2+) mixtures.
Production of Solvents by <i>Clostridium acetobutylicum</i> Cultures Maintained at Neutral pH (1984)

The formation of acetone and n-butanol by Clostridium acetobutylicum NCIB 8052 (ATCC 824) was monitored in batch culture at 35 degrees C in a glucose (2% [wt/vol]) minimal medium maintained throughout at either pH 5.0 or 7.0. At pH 5, good solvent production was obtained in the unsupplemented medium, although addition of acetate plus butyrate (10 mM each) caused solvent production to be initiated at a lower biomass concentration. At pH 7, although a purely acidogenic fermentation was maintained in the unsupplemented medium, low concentrations of acetone and n-butanol were produced when the glucose content of the medium was increased (to 4% [wt/vol]). Substantial solvent concentrations were, however, obtained at pH 7 in the 2% glucose medium supplemented with high concentrations of acetate plus butyrate (100 mM each, supplied as their potassium salts). Thus, C. acetobutylicum NCIB 8052, like C. beijerinckii VPI 13436, is able to produce solvents at neutral pH, although good yields are obtained only when adequately high concentrations of acetate and butyrate are supplied. Supplementation of the glucose minimal medium with propionate (20 mM) at pH 5 led to the production of some n-propanol as well as acetone and n-butanol; the final culture medium was virtually acid free. At pH 7, supplementation with propionate (150 mM) again led to the formation of n-propanol but also provoked production of some acetone and n-butanol, although in considerably smaller amounts than were obtained when the same basal medium had been fortified with acetate and butyrate at pH 7.
Planning in the large: efficient generation of IT change plans on large infrastructures (2012)

Change Management, a core process of the Information Technology Infrastructure Library (ITIL), is concerned with the management of changes to networks and services to minimize costly disruptions on the business. As part of Change Management, IT changes need to be planned. Previous approaches to automatically generate IT change plans struggle, in terms of scalability, to properly deal with large Configuration Management Databases (CMDBs). To enable IT change planning in the large, in this paper we discuss and analyze optimizations for refinement-based IT change planning over object-oriented CMDBs. Our optimizations reduce the runtime complexity of several key operations part of refinement-based IT change planning algorithms. A sensitivity analysis shows that our optimizations outperform SHOP2 - the winner of a previous comparison among IT change planners - in terms of runtime complexity for several important characteristics of IT changes and CMDBs. A cloud deployment case study of a Three-tier application and a virtual network configuration case study demonstrate the feasibility of our approach and confirm the results from the sensitivity analysis: IT change planning has evolved from planning in the small to planning in the large.
Using image references in radiology reports to support enhanced report-to-image navigation. (2013)

Radiology reports frequently contain references to image slices that are illustrative of described findings, for instance, "Neurofibroma in superior right extraconal space (series 5, image 104)". In the current workflow, if a report consumer wants to view a referenced image, he or she needs to (1) open prior study, (2) open the series of interest (series 5 in this example), and (3) navigate to the corresponding image slice (image 104). This research aims to improve this report-to-image navigation process by providing hyperlinks to images. We develop and evaluate a regular expressions-based algorithm that recognizes image references at a sentence level. Validation on 314 image references from general radiology reports shows precision of 99.35%, recall of 98.08% and F-measure of 98.71%, suggesting this is a viable approach for image reference extraction. We demonstrate how recognized image references can be hyperlinked in a PACS report viewer allowing one-click access to the images.
P22 Arc Repressor: Transition State Properties Inferred from Mutational Effects on the Rates of Protein Unfolding and Refolding (1995)

The kinetics of unfolding and refolding have been measured for a set of Arc repressor mutants bearing single amino acid substitutions at 44 of the 53 residue positions. Roughly half of the mutations cause significant changes in the unfolding and/or refolding rate constants. These substitutions alter the hydrophobic core, tertiary hydrogen bonds and salt bridges, and glycines with restricted backbone conformations. Overall, the mutations cause larger changes in the unfolding rates than the refolding rates, indicating that significantly less side-chain information is used between the denatured state and transition state than between the transition state and native state. The set of mutants displays reasonable Brønsted behavior, suggesting that many native interactions are partially formed in the transition state. Taken together, these observations suggest that the overall structure of most of the protein must be somewhat native-like in the transition state but without close, complementary packing of the hydrophobic core or good hydrogen bond geometry. Such a transition state is inconsistent with a model in which monomers fold to their correct conformations and then dock to form the dimer but supports a model in which folding and dimerization are concurrent processes.
FPGA Prototyping by VHDL Examples (2007)

A hands-on introduction to VHDL synthesis and FPGA prototyping

Hardware Descriptive Language (HDL) and Field Programmable Gate Array (FPGA) devices

allow designers to quickly develop and simulate a sophisticated digital circuit, realize it on a prototyping device, and verify the operation of its physical implementation. As these technologies have matured, they have become accepted mainstream practice so that it is possible to use a PC and an inexpensive FPGA prototyping board to construct a complex digital system.

This book uses a by doing approach to introduce the concepts and techniques of VHDL and FPGA to designers through a series of hands-on experiments. FPGA Prototyping by VHDL Examples provides: 


A collection of clear, easy-to-follow templates for quick code development 
A large number of practical examples to illustrate and reinforce the concepts and design techniques 
Realistic projects that can be implemented and tested on a Xilinx prototyping board 
A thorough exploration of the Xilinx PicoBlaze soft-core microcontroller 



Although the book is an introductory text, the examples are developed in a rigorous manner and the derivations follow strict design guidelines and coding practices used for large, complex systems. It lays a solid foundation for students and new engineers and prepares them for future development tasks. FPGA Prototyping by VHDL Examples is an indispensable companion text for introductory digital design courses and also serves as a valuable self-teaching guide for practicing engineers who wish to learn more about this emerging area of interest.
Heart rate variability is a trait marker of major depressive disorder: evidence from the sertraline vs. electric current therapy to treat depression clinical study (2013)

Decreased heart rate variability (HRV) is a cardiovascular predictor of mortality. Recent debate has focused on whether reductions in HRV in major depressive disorder (MDD) are a consequence of the disorder or a consequence of pharmacotherapy. Here we report on the impact of transcranial direct current stimulation (tDCS), a non-pharmacological intervention, vs. sertraline to further investigate this issue. The employed design was a double-blind, randomized, factorial, placebo-controlled trial. One hundred and eighteen moderate-to-severe, medication-free, low-cardiovascular risk depressed patients were recruited for this study and allocated to either active/sham tDCS (10 consecutive sessions plus two extra sessions every other week) or placebo/sertraline (50 mg/d) for 6 wk. Patients were age and gender-matched to healthy controls from a concurrent cohort study [the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil)]. The impact of disorder, treatment and clinical response on HRV (root mean square of successive differences and high frequency) was examined. Our findings confirmed that patients displayed decreased HRV relative to controls. Furthermore, HRV scores did not change following treatment with either a non-pharmacological (tDCS) or pharmacological (sertraline) intervention, nor did HRV increase with clinical response to treatment. Based on these findings, we discuss whether reduced HRV is a trait-marker for MDD, which may predispose patients to a host of conditions and disease even after response to treatment. Our findings have important implications for our understanding of depression pathophysiology and the relationship between MDD, cardiovascular disorders and mortality.
An iterative procedure based on the donnan equilibrium for calculating the polymer‐subphase volume of alginic acid (1989)

Abstract A numerical iterative procedure is presented to predict the polymer‐subphase volume that is formed when anionic polysaccharides such as alginic acid (polyuronic acid from kelp) are suspended in an aqueous solution. (The aqueous region surrounding the polymer chain where a strong electrostatic attractive force for counterions exists is defined as the separate polymer subphase within the colloidal phase enclosed by the polymer coil.) Based on the phase‐partition model of Marinsky et al. 5 and Donnan equilibrium theory, this iterative procedure utilizes the base titration data of the acidic polysaccharide at different ionic strengths as well as the osmotic properties of the sodium form of the polysaccharide. No detailed structural information of alginic acid is required. The resulting calculations show that the polymer subphase, which accounts for a small fraction of the total solution volume, should be regarded as the reaction zone for acid dissociation and metal binding reactions. The volume of polymer subphase thus calculated may also serve as an excellent index for the morphology of the polymer molecule at different ionic strengths, degrees of ionization, polymer concentrations, and extent of polymer‐metal binding.
Maximizing a Transport Platform Through Computer Technology (2003)

One of the most recent innovations coalescing computer technology and medical care is the further development of integrated medical component technology coupled with a computer subsystem. One such example is the self-contained patient transport system known as the Life Support for Trauma and Transport (LSTAT(tm)). The LSTAT creates a new transport platform that integrates the most current medical monitoring and therapeutic capabilities with computer processing capacity, creating the first "smart litter". The LSTAT is built around a computer system that is network capable and acts as the data hub for multiple medical devices and utilities, including data, power, and oxygen systems. The system logs patient and device data in a simultaneous, time-synchronized, continuous format, allowing electronic transmission, storage, and electronic documentation. The third-generation LSTAT includes an oxygen system, ventilator, clinical point-of-care blood analyzer, suction, defibrillator, infusion pump, and physiologic monitor, as well as on-board power and oxygen systems. The developers of LSTAT and other developers have the ability to further expand integrative component technology by developing and integrating clinical decision support systems.
Imaging and focusing of atoms by a fresnel zone plate (1991)

Focusing of and imaging with atoms by means of a spherical Fresnel zone plate has been observed for the first time. An intense beam of metastable helium atoms with atomic de Broglie wavelength ${\ensuremath{\lambda}}_{\mathrm{dB}}$=0.5--2.5 \AA{} is passed through either a single or a double slip with dimensions in the 10-\ensuremath{\mu}m range. This transverse intensity distribution is imaged by a Fresnel zone plate, 210 \ensuremath{\mu}m in diameter and with an innermost zone diameter of 18.76 \ensuremath{\mu}m. For ${\ensuremath{\lambda}}_{\mathrm{dB}}$=1.96 \AA{} the focal length is 0.45 m. The imaging properties of the zone plate are presented and compared with numerical calculations.
Solution‐Processed Organic n‐Type Thin‐Film Transistors (2003)

An organic n‐type transistor , where both insulating and active layer were processed from solution, has been produced. As the active layer the C 60 ‐derivative, [6,6]‐phenyl C 61 ‐butyric acid methyl ester (PCBM), was used. Its electron mobility was determined to be as high as μ e = 4.5 × 10 –3 cm 2 V –1 s –1 when calcium drain/source contacts were used. If these contacts are formed from more air‐stable metals, the device performance decreases.
An All-Solid-State Flow Cytometer for Counting Fluorescent Microspheres (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn All-Solid-State Flow Cytometer for Counting Fluorescent MicrospheresStefan. Niehren, Wolfgang. Kinzelbach, Stefan. Seeger, and Juergen. WolfrumCite this: Anal. Chem. 1995, 67, 15, 2666–2671Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/ac00111a027https://doi.org/10.1021/ac00111a027research-articleACS PublicationsRequest reuse permissionsArticle Views193Altmetric-Citations28LEARN 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
Formation of CO2 Hydrate in Pure and Sea Waters. (1993)

The formation of CO2 hydrates in both pure and sea waters along the three-phase coexistence of CO2, H2O, and hydrate is measured by use of a convenient temperature-cycle method proposed in the present study. Four kinds of three-phase coexisting curves are investigated in the temperature range from 270 to 283 K and pressures up to 9 MPa. By applying the Langmuir adsorption model based on statistical thermodynamics, the three-phase coexisting pressures obtained are correlated satisfactorily. The enthalpy changes of hydration in both systems are calculated from the Clapeyron equation of the three-phase coexisting curve. The apparent rate constant of hydration is estimated under the assumption of pseudo-first order reaction with respect to CO2 concentration.
The ezrin-like family of tyrosine kinase substrates: receptor-specific pattern of tyrosine phosphorylation and relationship to malignant transformation. (1993)

A method for the isolation of tyrosine kinases substrates was developed. The method takes advantage of immuno-affinity purification of an entire set of proteins phosphorylated by tyrosine kinases, followed by generation of antisera against the purified protein pool and immunological screening of bacterial expression libraries with these antisera. By applying this methodology to the study of the phosphorylation events triggered by activation of the epidermal growth factor receptors, we have isolated several cDNAs encoding novel putative tyrosine kinase substrates. One of these cDNAs encodes radixin, a protein belonging to the band 4.1 family of proteins and highly related to ezrin and moesin. We demonstrated that, despite a high degree of relatedness, these three proteins exhibit a distinct receptor-specific pattern of phosphorylation, raising the possibility that they might mediate receptor-specific cellular changes. In addition the generation of antibodies specific for either radixin, ezrin or moesin allowed us to show that a previously described tumor transplantation antigen is indeed ezrin, thus implicating this protein in the determination of the biological phenotype of certain tumors.
A micro power management system and maximum output power control for solar energy harvesting applications (2007)

A micro power management system is presented for solar energy harvesting applications. An inductor-less solution is proposed which facilitates on-chip integration of the system. We target at applications working in different lighting environments ranging from strong sunlight to dim indoor lighting where the output voltage from the photovoltaic (PV) cells is low. A charge pump is used to step the PV voltage up to charge a battery or directly operate the circuit. The power management system behavior is theoretically analyzed and the control strategy is derived to transfer maximum power from the PV cells to the battery or the circuit. Circuit design and low power techniques for the maximum output power control are proposed for the system. The system was implemented using 0.35μm CMOS process. With the measured PV cells output characteristics, HSPICE simulations for the power management system were carried out to verify the control strategy and to demonstrate the system operation.
Extended Brownian dynamics of diffusion controlled reactions (1985)

The Brownian dynamics simulation method of Northrup et al. is extended so that dynamical trajectories can be initiated with the reactants in close proximity to one another. A more general analysis is presented which shows that this procedure is exact in cases where the first-time encounter flux to the more proximal starting surface is isotropic, such as cases where interparticle forces are centrosymmetric, but is approximate otherwise. Diffusion controlled rate constants for three model systems obtained by this procedure are compared with analytic results or with exact rate constants derived from simulations following the original Northrup procedure. Agreement is good to excellent in all cases considered. The extended method is expected to be of considerable practical importance in systems with highly anisotropic reactivity where it is computationally inefficient to obtain rate constants by the original method.
Atomic Layer Deposition of Vanadium Oxide on Carbon Nanotubes for High-Power Supercapacitor Electrodes (2012)

Abstract not Available.
Subcutaneous Rodding for Progressive Spinal Curvatures: Early Results (2002)

This study retrospectively reviewed the clinical records and radiographs of 11 patients with progressive early-onset scoliosis who failed to respond to nonoperative management and who underwent consecutive distraction of subcutaneous rods. Eleven children were treated by consecutive distraction of subcutaneous rods, and in two patients with rodding and anterior apical fusion. At surgery, the average patient age was 5.66 years, with a mean Cobb angle of 74 degrees and an average Pedriole angle of 39 degrees. The etiology of the scoliosis included four syndromic and one each congenital, post-rib resection, post-spinal tumor resection, neurofibromatosis, myelomeningocele, infantile idiopathic, and juvenile idiopathic. Subcutaneous rodding halted curve progression in all patients. At an average of 5.1 years after surgery, one patient showed no deterioration of the curve and nine patients showed an improvement of > or =40% in the magnitude of the original curvature. Eight of these patients had already had definitive surgery performed with segmental spinal instrumentation and fusion. Spinal growth occurred in all 11 patients and ranged from 0.5 to 4.5 cm (mean 2.0). Early results from these patients show that subcutaneous rodding with consecutive distraction allows correction of progressive early-onset scoliosis that failed to respond to nonsurgical management, preserving the individual growth potential of the spinal column and delaying definitive surgical treatment. Rotational deformity did not deteriorate radiographically, but clinical deformity increased subjectively. The amount of growth achieved and the number of procedures required to obtain these results raises the question of whether patients would be better served by a single anterior, posterior fusion and instrumentation at a young age.
Managing Dynamic Service Dependencies (2001)

We anticipate that software development will be service-centric in the near future. Applications will be created from existing services that are distributed throughout a network. Sure enough, management of those components will be mandatory. While service management is usually service-specific, a few areas can be identified that can be addressed in a generic way. One of these areas is the management of dependencies between services. Despite its genericity, this problem is currently mostly addressed in a service-specific way. This paper details the need for a generic dependency management approach, identifies the key properties of dependencies as well as the requirements for dependency management schemes, describes the model derived from the requirements, and presents an implementation using the Jini connection technology.