gebhart/patrepeval huggingface dataset:
Discovering Shared Services from Cross-Organizational Software Specifications (2010)

During a standard software development process, organizations create text-based documents that describe software requirements, design, and implementation. These text-based specifications describe the functionality of future applications as they relate to an existing IT infrastructure. We suggest that these documents also implicitly describe core underlying service-based capabilities of the organization. In this paper, we describe an approach that (when provided with software specifications from multiple organizations) can recommend services shared by the multiple organizations represented. These approaches leverage the syntactic similarity of the specification text and semantic information as inferred from WordNet. Experiments show the effectiveness of this approach when processing real software requirements specifications in operational environments.
Frequency-Dependent Locally One-Dimensional FDTD Implementation With a Combined Dispersion Model for the Analysis of Surface Plasmon Waveguides (2008)

The implicit finite-difference time-domain (FDTD) method based on the locally one-dimensional scheme is extended to the frequency-dependent version for the analysis of the Drude-Lorentz model. The piecewise linear recursive convolution method is introduced, in which a large time step can be utilized. Analyses of a metal-cladding optical waveguide supporting a surface plasmon polariton reveal that the present method provides wavelength responses comparable to those of the explicit FDTD, while reducing the computational time to less than 50%.
Synthesis and Characterization of Five‐Coordinate Gallium and Indium Complexes Stabilized by Tridentate, Substituted Pyrrole Ligands (2003)

Abstract Five‐coordinate gallium and indium complexes stabilized by tridentate, substituted pyrrole ligands have been synthesized and characterized. The reaction of MCl 3 with 1 equiv. of Li[NC 4 H 2 (CH 2 NMe 2 ) 2 ‐2,5] in diethyl ether affords [{NC 4 H 2 (CH 2 NMe 2 ) 2 ‐2,5}MCl 2 ] [M = Ga ( 1 ), In ( 2 )] in high yield. Reaction of 1 with 2 equiv. of MeLi in diethyl ether at −78 °C followed by heating to reflux for 30 min affords the alkylated product [{NC 4 H 2 (CH 2 NMe 2 ) 2 ‐2,5}GaMe 2 ] ( 3 ). Similarly, the reaction of 2 with 2 equiv. of MeLi or n BuLi affords the dialkylated complexes 4 and 5 , respectively. Complex 2 is a strong Lewis acid which readily absorbs H 2 O forming [{[C 4 H 2 N(CH 2 NMe 2 ) 2 ‐2,5]InCl 2 } 2 (μ‐OH 2 )] ( 6 ). Complexes 3 , 4 , and 6 have been characterized by X‐ray crystallography. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Growth of Pseudomonas aeruginosa on nitrous oxide (1986)

Three strains of Pseudomonas aeruginosa were grown anaerobically on exogenous N2O in a defined medium under conditions that assured the maintenance of highly anaerobic conditions for periods of 1 week or more. The bacteria were observed reproducibly to increase their cell density by factors of 3 to 9, but not more, depending on the initial amount of N2O. Growth on N2O was cleanly blocked by acetylene. Cell yields, CO2 production, and N2O uptake all increased with initial PN2O at PN2O less than or equal to 0.1 atm. Growth curves were atypical in the sense that growth rates decreased with time. This is the first observation of growth of P. aeruginosa on N2O as the sole oxidant. N2O was shown to be an obligatory, freely diffusible intermediate during growth of strains PAO1 and P1 on nitrate. All three strains used this endogenous N2O efficiently for growth. For strains PAO1 and P1, it was confirmed that exogenous N2O had little effect on the cell yields of cultures growing with nitrate; thus, for these strains exogenous N2O neither directly inhibited growth nor was used significantly for growth. On the other hand, strain P2 grew abundantly on exogenous N2O when small and growth-limiting concentrations of nitrate or nitrate (2 to 10 mM) were included in the medium. The dramatic effect of these N-anions was realized in large part even when the exogenous N2O was introduced immediately after the quantitative conversion of anion-nitrogen to N2. No evidence was found for a factor in filter-sterilized spent medium that stimulated fresh inocula to grow abundantly on N2O.(ABSTRACT TRUNCATED AT 250 WORDS)
Enantioselective Synthesis of Cyclic Enol Ethers and All‐Carbon Quaternary Stereogenic Centers Through Catalytic Asymmetric Ring‐Closing Metathesis. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
FEMORAL FRACTURE BELOW AN AUSTIN MOORE PROSTHESIS: A SIMPLE METHOD OF TREATMENT (1981)

Femur fractures below endoprostheses can be a catastrophic occurrence. Insertion of a long stem prosthesis, or bedrest with traction can both present problems in elderly patients. A simple method of treatment using Rush pins and cerclage wires is described along with a case presentation.
Standards of care for treating headache in primary care practice (1997)

The following is a summary of guidelines created under the auspices of the National Headache Foundation, in an effort to improve the care of headache patients in primary care practice. The guidelines represent the consensus of an advisory panel of practitioners chosen by the NHF for their expertise in four specialty areas. A complete set of guidelines can be obtained by calling the National Headache Foundation at 1-800-843-2256 or by writing to them at 428 W. St. James Pl., 2nd Floor, Chicago, IL 60614-2750; the cost is $10.
Design and simulation software package of switched reluctance machine systems for Windows 9x in English (2002)

A developed design and simulation software package of switched reluctance machine systems for Windows 9x in English based on the Visual Basic 6.0 tool is presented in the paper. The configuration and the smallest operational environments of the software package are introduced. The main interfaces are given. The functions of the software package are introduced, such as the 2D finite element electromagnetic field calculation for seven structures of switched reluctance motors and generators, the nonlinear simulation of ten power converter main circuits with four variable speed control strategies, the displaying and printing of some pictures.
Biochemical mechanism and molecular basis for ALS-inhibiting herbicide resistance in sugarbeet (Beta vulgaris) somatic cell selections (1998)

Three sugarbeet selections differing in cross-resistance to three classes of acetolactate synthase (ALS)-inhibiting herbicides have been developed using somatic cell selection. Sugarbeet selections resistant to imidazolinone herbicides, Sir-13 and 93R30B , do not metabolize [ 14 C]-imazethapyr any faster or differently than sensitive, wild-type sugarbeets or a sulfonylurea-resistant/imidazolinone-sensitive selection, Sur. ALS specific activity from the three herbicide-resistant selections ranged from 73 to 93% of the wild-type enzyme extracts in the absence of herbicide, indicating enzyme overexpression was not a factor in resistance. Acetolactate synthase from Sir-13 plants showed a 40-fold resistance to imazethapyr but no resistance to chlorsulfuron or flumetsulam. Polymerase chain reaction amplification and sequencing of two regions of the ALS gene spanning all known sites for ALS-based herbicide resistance in plants indicated a single nucleotide change in the Sir-13 gene (G 337 to A 337 ) resulting in a deduced substitution of threonine for alanine at position 113 in the sugarbeet amino acid sequence. Sur ALS was not significantly resistant to imazethapyr, but was 1,000- and 50-fold resistant to chlorsulfuron and flumetsulam, respectively. Sur gene sequencing indicated a single nucleotide change ( C 562 to T 562 ) resulting in a serine for proline substitution at position 188 of the ALS primary structure. The 93R30B nucleotide sequence indicated two mutations resulting in two deduced amino acid substitutions: threonine for alanine at position 113 plus serine for proline at position 188. The 93R30B double mutant incorporated the changes observed in each of the single mutants above and correlated with higher resistance levels to imazethapyr (&gt; 1,000-fold), chlorsulfuron (4,300-fold), and flumetsulam (200-fold) at the ALS level than observed in either of the single mutants. 93R30B represents the first double mutant derived by a two-step selection process that incorporates two class-specific ALS-inhibitor resistance mutations to form a single broad cross-resistance trait. The interaction of the two altered amino acids is synergistic with respect to enzyme resistance vs. the resistance afforded by each of the individual mutations.
Quantum Information Processing Based On Optically Driven Semiconductor Quantum Dots (2004)

It may one day be possible to use arrays of quantum dots driven by ultrafast laser pulses to carry out quantum information processing. The article reviews recent experimental progress in the area of coherent optical control of single dots and outlines a plan for further research.
Warp Field Mechanics 101 (2011)

This paper will begin with a short review of the Alcubierre warp drive metric and describes how the phenomenon might work based on the original paper. The canonical form of the metric was developed and published in [6] which provided key insight into the field potential and boost for the field which remedied a critical paradox in the original Alcubierre concept of operations. A modified concept of operations based on the canonical form of the metric that remedies the paradox is presented and discussed. The idea of a warp drive in higher dimensional space-time (manifold) will then be briefly considered by comparing the null-like geodesics of the Alcubierre metric to the Chung-Freese metric to illustrate the mathematical role of hyperspace coordinates. The net effect of using a warp drive technology coupled with conventional propulsion systems on an exploration mission will be discussed using the nomenclature of early mission planning. Finally, an overview of the warp field interferometer test bed being implemented in the Advanced Propulsion Physics Laboratory: Eagleworks (APPL:E) at the Johnson Space Center will be detailed. While warp field mechanics has not had a Chicago Pile moment, the tools necessary to detect a modest instance of the phenomenon are near at hand.
Electrical activity of (100) n‐type diamond with full donor site incorporation of phosphorus (2015)

In a previous work, we discovered a new set of growth parameters for fabricating (100) homoepitaxial phosphorus‐doped n‐type diamond with unique properties: full incorporation of phosphorus donors in substitutional sites together with a low surface roughness. In this work, a planar type Schottky barrier diode has been fabricated on the epilayer and C – V characteristics were measured. From the capacitance properties, the net donor density and the Schottky barrier height were experimentally determined to be ∼3.1 × 10 16 cm −3 and ∼4.65 eV, respectively. The phosphorus electrical activity in our (100) n‐type diamond epilayer is discussed in comparison with previous works on the (100) and (111) orientations.
A Matter of Compromise: The State and Territorial Authorities in French Decentralization (2007)

France has recently legislated important transfers of competences from the state to 
local authorities. These transfers have often been presented as the result of a unilateral 
strategy to lessen the administrative burden on the state by shifting it to the local 
authorities. The article questions this simplistic approach, showing that from the time it 
was put on the agenda to the time it was elaborated and the reform put in place,
Protection in operating systems (1976)

A model of protection mechanisms in computing systems is presented and its appropriateness is argued. The “safety” problem for protection systems under this model is to determine in a given situation whether a subject can acquire a particular right to an object. In restricted cases, it can be shown that this problem is decidable, i.e. there is an algorithm to determine whether a system in a particular configuration is safe. In general, and under surprisingly weak assumptions, it cannot be decided if a situation is safe. Various implications of this fact are discussed.
Therapeutic Potential of High Mobility Group Box-1 in Ischemic Injury and Tissue Regeneration (2011)

High-mobility group box-1 (HMGB1) is a nuclear protein that acts as a cytokine when released into the extracellular milieu by necrotic and inflammatory cells, and is involved in inflammatory responses and tissue repair. This protein is released passively during cellular necrosis by almost all cells that have a nucleus, but is also actively secreted by immune cells such as macrophages and monocytes. This cytokine plays a key role in mediating the local and systemic responses to several stimuli and might have therapeutic relevance. Indeed, vessel-associated stem cells, injected into the general circulation of dystrophic mice, migrate to sites of tissue damage in response to the HMGB1 signal, by a nuclear factor-κB dependent mechanism. Moreover, endogenous HMGB1 enhances angiogenesis and restores cardiac function in a murine model of myocardial infarction, and the exogenous administration of HMGB1 after myocardial infarction leads to the recovery of left ventricular function through the regeneration of cardiomyocytes. Finally, recent findings show that endogenous HMGB1 is crucial for ischemia-induced angiogenesis in diabetic mice and that HMGB1 protein administration enhances collateral blood flow in the ischemic hind limbs of diabetic mice through a VEGF-dependent manner. The mechanisms of action of this protein are complex and are not well known or defined. The objective of this review is to evaluate the data regarding the tissue regeneration effects of HMGB1, with the aim of providing practical considerations about this topic for the management of subjects affected by ischemic and degenerative diseases.
Three-Dimensional Si/Ge Quantum Dot Crystals (2007)

Modern nanotechnology offers routes to create new artificial materials, widening the functionality of devices in physics, chemistry, and biology. Templated self-organization has been recognized as a possible route to achieve exact positioning of quantum dots to create quantum dot arrays, molecules, and crystals. Here we employ extreme ultraviolet interference lithography (EUV-IL) at a wavelength of lambda = 13.5 nm for fast, large-area exposure of templates with perfect periodicity. Si(001) substrates have been patterned with two-dimensional hole arrays using EUV-IL and reactive ion etching. On these substrates, three-dimensionally ordered SiGe quantum dot crystals with the so far smallest quantum dot sizes and periods both in lateral and vertical directions have been grown by molecular beam epitaxy. X-ray diffractometry from a sample volume corresponding to about 3.6 x 10(7) dots and atomic force microscopy (AFM) reveal an up to now unmatched structural perfection of the quantum dot crystal and a narrow quantum dot size distribution. Intense interband photoluminescence has been observed up to room temperature, indicating a low defect density in the three-dimensional (3D) SiGe quantum dot crystals. Using the Ge concentration and dot shapes determined by X-ray and AFM measurements as input parameters for 3D band structure calculations, an excellent quantitative agreement between measured and calculated PL energies is obtained. The calculations show that the band structure of the 3D ordered quantum dot crystal is significantly modified by the artificial periodicity. A calculation of the variation of the eigenenergies based on the statistical variation in the dot dimensions as determined experimentally (+/-10% in linear dimensions) shows that the calculated electronic coupling between neighboring dots is not destroyed due to the quantum dot size variations. Thus, not only from a structural point of view but also with respect to the band structure, the 3D ordered quantum dots can be regarded as artificial crystal.
GRASP2: Fast and memory-efficient gene-centric assembly and homolog search (2017)

A crucial task for metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and searched against reference databases, or individually searched without assembly. The first approach may suffer due to the fragmentary and incomplete nature of nucleotide sequence assembly, while the second approach is hampered by the reduced functional signal that a short read can contain. To tackle these issues, we previously developed GRASP (Guided Reference-based Assembly of Short Peptides), which accepts a reference protein sequence as input and aims to assemble its homologs from a database containing fragmentary protein sequences. In addition to a gene-centric assembly tool, GRASP also serves as a homolog search tool when using the assembled protein sequences as templates to recruit reads. GrASP has significantly improved sensitivity (60–80% vs. 30–40%) compared to other homolog search tools such as BLAST. However, GRASP is time- and space-consuming compared to these tools, and is not scalable to large datasets. Subsequently, we developed GRASPx which is 30X faster than GRASP. Here, we present a completely redesigned algorithm, GRASP2, for this computational problem. GRASP2 utilizes Burrow-Wheeler Transformation (BWT) to assist with assembly graph generation, and reduces the search space by employing a fast ungapped alignment strategy to reduce unnecessary traversal of non-homologous paths in the assembly graph. GRASP2 is 8-fold faster than GRASPx (and 250-fold faster than GRASP) and uses 8-fold less memory while maintaining the original high sensitivity of GRASP, which makes GRASP2 a useful tool for metagenomics data analysis. GRASP2 is implemented in C++ and is freely available from http://www.sourceforge.net/projects/grasp2.
Phase‐labeled reference EPI for frequency‐segmented inhomogeneity corrections (PREFICS) (2013)

The method presented allows correcting non-Cartesian EPI from a reference scan consisting of only two phase-labeled echo planar images.
PRDM1 is a tumor suppressor gene in natural killer cell malignancies (2011)

Natural killer cell lymphoma (NKCL) constitutes a rare and aggressive form of non-Hodgkin lymphoma, and there is little insight into its pathogenesis. Here we show that PRDM1 is a tumor suppressor gene in NKCLs that is inactivated by a combination of monoallelic deletion and promoter CpG island hypermethylation. We observed monoallelic deletion of PRDM1 loci in 8 of 18 (44%) NKCL cases. The other allele showed significant promoter methylation in 12 of 17 (71%) cases. In support of its role as a tumor suppressor gene, the reconstitution of PRDM1 in PRDM1-null NK cell lines led to G2/M cell cycle arrest, increased apoptosis, and a strong negative selection pressure with progressive elimination of PRDM1-expressing cells, which was enhanced when IL-2 concentration is limiting. We observed a progressive increase in PRDM1 expression--in particular, PRDM1α--in normal NK cells in response to IL-2 and in normal NK cells activated with an engineered NK cell target, K562-Cl9-mb21, suggesting its role in NK cell homeostasis. In support of this role, knockdown of PRDM1 by shRNA in normal NK cells resulted in the positive selection of these cells. We identified MYC and 4-1BBL as targets of PRDM1 in NK cells. Disruption of homeostatic control by PRDM1 may be an important pathogenetic mechanism for NKCL.
Interferometric observations of a single stroke cloud‐to‐ground flash (1989)

VHF radiation source location measurements using an interferometric technique are presented for a single stroke cloud‐to‐ground lightning discharge. The discharge began with 100 ms of preliminary activity during which several horizontal streamers developed inside the cloud, one of which culminated in the development of a negative leader to ground and a return stroke. The return stroke was followed by a 10 ms quiet period in the radiation and by a single, fast ‘k‐type‧ event which appeared to transport negative charge horizontally into the region of initial breakdown, completing the flash.
Mechanisms of involvement in calmodulin in regulation of affinity for Ca/sup 2 +/ and maximum activity of Ca pump of erythrocyte membranes (1986)

The activity of the Ca pump of inside-out vesicles of human erythrocyte membranes was studied using /sup 45/Ca and membrane filters. It was found that trifluoperazine completely inhibits the increase in the maximum activity of the Ca pump caused by the addition of calmodulin and has no effect on the calmodulin-stimulated increase in the affinity of the Ca pump for Ca/sup 2 +/. A comparison of characteristic curves of the calmodulin-stimulated components of the activity of the Ca pump, inhibited and not inhibited by trifluoperazine, and the fluorescence intensity of N-phenyl-1-naphthylamine in the presence of calmodulin showed that the mechanisms of action of calmodulin on the maximum activity of the Ca pump and its affinity for Ca/sup 2 +/ differ significantly. In the first case the activation was due to the Ca-calmodulin complex and in the second to the calcium-free form of calmodulin. This conclusion is supported by data on the dependence of the activity of the Ca pump on the calmodulin concentration at low and saturating Ca/sup 2 +/ concentrations as well as by the results obtained in the case of moderate treatment of the membranes with trypsin.
Dynamic reconfigurable bit-parallel architecture for large-scale regular expression matching (2010)

In this paper, we propose a novel FPGA-based architecture for large-scale regular expression matching, called dynamic reconfigurable bit-parallel NFA architecture (Dynamic BP-NFA) that allows dynamic reconfiguration of the patterns using bit-parallel NFA-simulation. This is the first dynamic reconfigurable FPGA-based hardware with guaranteed performance for the class of extended patterns, where an extended pattern is a restricted regular expression in linear form consisting of letters, classes of letters, don't cares, optional letters, bounded and unbounded length gaps and repeatable letters. The key to our architecture is the use of bit-parallel pattern matching approach that has been developed in string matching communities for the decades. In this approach, the information of an input NFA is compactly encoded in bit-masks stored in a collection of registers and block RAMs. Then, the NFA is efficiently simulated by a fixed circuitry using a combination of bit- and arithmetic-operations on these bit-masks consuming one input letter per clock. As compared with the previous approaches of DFA-based dynamic reconfigurable architectures, experimental results show that the proposed architecture achieves higher throughput for the class of exact string patterns and comparable for the class of extended patterns.
Fabrication of midgap metal gates compatible with ultrathin dielectrics (1998)

A process has been described which can produce a midgap tungsten gate compatible with the current and future complementary metal–oxide–semiconductor technology. The tungsten was deposited directly onto a 3.0 nm SiO2 gate dielectric without measurable degradation of any of its electrical properties. The tungsten deposition process yields no reactive or corrosive by-products that affect the gate dielectric integrity. The tungsten film is found to be pure within the limits of several analytical techniques and the resistivity of the tungsten films was found to be within a factor of 2 of the bulk value.
Prediction of subtle thermal histopathological change using a novel analysis of Gd‐DTPA kinetics (2003)

Our results suggest Gd-DTPA kinetics can predict different histopathological changes following FUS ablation and may be valuable for early prediction.