gebhart/patrepeval huggingface dataset:
Windows XP in a Nutshell, Second Edition (2005)

Windows XP in a Nutshell, Second Edition documents everything there is to know about the world's most widely used operating system. Updated to include information on the security technologies featured in Service Pack 2 (SP2), this must-have desktop reference is dedicated to making your time at the computer safer, easier, and more fun. It's the ultimate resource for IT professionals and Windows XP power users everywhere.
Recursive digital filter design via covariance sequence approximation (1981)

In this paper we propose a modified solution to the general nonlinear least-squares approximation problem for digital filter design. We choose to approximate the covariance sequence associated with an ideal filter because it arises more naturally in spectrum matching problems than does the unit pulse response sequence. The design procedure resulting from our approach requires the rooting of an nth-order polynomial, the solution of an nth-order system of linear equations, and the calculation of a (2n - 1)-point DFT for the design of an ARMA (2n, 2(n - 1)) digital filter.
Front Matter: Volume 9727 (2016)

A unique citation identifier (CID) number is assigned to each article at the time of publication. Utilization of CIDs allows articles to be
Mechanism of device degradation in n- and p-channel polysilicon TFTs by electrical stressing (1990)

The effects of electrical stress on hydrogenated n- and p-channel polysilicon thin-film transistors are discussed. The on-state caused the most significant degradation, whereas off-state and accumulation conditions resulted in negligible degradation. The on-state stress degraded the threshold voltage, trap state density, and subthreshold sharpness of both n- and p-channel devices toward perhydrogenated values, and the rates of degradation increased with stressing biases. The field-effect mobility and leakage current, however, were not degraded by stressing. The mechanism of device degradation may be attributed to the metastable creation of midgap states within the polysilicon channel, as opposed to gate dielectric charge trapping or interface state generation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Fusion Nuclear Science Facility, the Critical Step in the Pathway to Fusion Energy (2015)

The proposed Fusion Nuclear Science Facility (FNSF) represents the first facility to enter the complex fusion nuclear regime, and its technical mission and attributes are being developed. The FNSF represents one part of the fusion energy development pathway to the first commercial power plant with other major components being the pre-FNSF research and development, research in parallel with the FNSF, pre-DEMO research and development, and the demonstration power plant (DEMO). The Fusion Energy Systems Studies group is developing the technical basis for the FNSF in order to provide a better understanding of the demands on the fusion plasma and fusion nuclear science programs.
Color Errors, Metamerism and Color Ellipses (2019)

This paper is about calculation of index of metamerism for the change of observer and comparisons with various color errors and tolerances. — There are two major aspects for color measure in visual reproduction. One goal is to measure the performance of reproduction equipment. The other aspect is related to the audience visual perception. On the one hand human perception is characterized by its variability and, on the other hand, technological trends in reproduction are adding new color source characteristics. — Metamerism is ensuring the viability of trichromatic reproduction. In fact, traditionally, any reproduced color is rendered with a mix of three primaries. It is giving a perception similar to that of surfaces in front of the camera which have various complex spectra so long as those spectral surfaces lie within the trichromatic gamut of the selected reproduction primaries. — Various metamerism indexes have been defined to give a measure of the differences in color matching. The metameric index for change of observer may be used to directly evaluate human perception variability found in any audience for a given reproduction system. At least this can be computed for a set of representative colors. — But new reproduction systems are based on primaries spectra differing sensibly from the ones previously used with Xenon light source. The method for calculation of the index of metamerism for change of observer is using the Standard Deviate Observer data in addition to the Standard Observer data. — The magnitude of color errors induced by this phenomenon is compared with JND found in MacAdam study. It is also compared with existing tolerances in color accuracy. — In fact, the tolerance expressed in current standards are much larger than the variations caused by the observer variability.
On a Balanced Delta Robot for Precise Aerial Manipulation: Implementation, Testing, and Lessons for Future Designs (2022)

Using a delta-manipulator for stabilisation of an end-effector to perform precise spatial positioning is a current area of interest in aerial manipulation. High speed precision movements of a manipulator can cause disturbances to the aerial platform, which hinders trajectory tracking and in some cases could be sufficient to cause a loss of control of the vehicle. In this paper, a statically balanced delta aerial manipulator is developed and evaluated. The system is balanced using three counter-masses to reduce the force imparted onto the base and thus reduce perturbations to the movement of the drone. The system is thoroughly tested following trajectories while mounted to a force sensor and while on-board an aerial vehicle. Results show that the forces transmitted to the base in all axes are reduced considerably, however improvements in overall flight accuracy are not observed in aerial settings. Design lessons to make a balanced delta-manipulator viable for practical implementation on an aerial vehicle are discussed in depth. A video summarising the flight testing results is available at https://youtu.be/fXKnosnVKCk.
Cloning and expression of 1,4-galactosyltransferase gene from Helicobacter pylori (2000)

Helicobacter pylori, which is a human pathogen associated with gastric and duodenal ulcer, has been shown to express human oncofetal antigens Lewis X and Lewis Y. Although the mammalian glycosyltransferases that synthesize these structures are well characterized, little is known about the corresponding bacterial enzymes. We report that a novel beta1,4-galactosyltransferase gene (HpgalT) involved in the biosynthesis of lipopolysaccharides in H. pylori has been cloned and expressed in Escherichia coli. The deduced amino acid sequence of the protein (HpGal-T) encoded by HpgalT consists of 274 residues with the calculated molecular mass of 31,731 Da, which does not show significant similarity to those of beta1,4-galactosyltransferases from mammalian sources and Neisseria It was confirmed that HpGal-T catalyzed the introduction of galactose from UDP-Gal in a beta1,4 linkage to accepting N-acetylglucosamine (GlcNAc) residues by means of high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). When the E.coli cells which overexpressed HpgalT was coupled with the UDP-Gal production system, which consisted of recombinant E.coli cells overexpressing its UDP-Gal biosynthetic genes and Corynebacterium ammoniagenes, N-acetyllactosamine, a core structure of lipopolysaccharide of H.pylori, was efficiently produced from orotic acid, galactose, and GlcNAc.
Nitratireductor pacificus sp. nov., isolated from a pyrene-degrading consortium (2010)

Strain pht-3B(T) was isolated from a pyrene-degrading consortium of an enriched sediment from the Pacific Ocean, collected during the screening of polycyclic aromatic hydrocarbon-degrading bacteria. Cells were Gram-negative, short rods that were motile by means of flagella. Growth was observed at 0-7 % NaCl and 10-41 °C. The isolate was able to reduce nitrate to nitrite, but not to nitrogen. 16S rRNA gene sequence comparisons showed that strain pht-3B(T) was most closely related to Nitratireductor aquibiodomus NL21(T) (97.3 % 16S rRNA gene sequence similarity), N. indicus C115(T) (97.1 %), N. basaltis J3(T) (96.8 %) and N. kimnyeongensis KY 101(T) (96.7 %). DNA-DNA hybridization between strain pht-3B(T) and these reference strains revealed 55, 54, 28 and 42 % DNA-DNA relatedness, respectively. The dominant fatty acids were C(19 : 0)ω8c cyclo (22.6 %) and summed feature 8 (consisting of C(18 : 1)ω7c and/or C(18 : 1)ω6c; 60.4 %). The G+C content of the chromosomal DNA was 63 mol%. These characteristics were in good agreement with those of members of the genus Nitratireductor. According to cell morphology, physiology, fatty acid composition, 16S rRNA gene sequence analysis and DNA-DNA relatedness, the isolate belonged to the genus Nitratireductor but could be readily distinguished from recognized species of the genus. Therefore a novel species is proposed to accommodate strain pht-3B(T), for which the name Nitratireductor pacificus sp. nov. is proposed. The type strain is pht-3B(T) ( = CCTCC AB 209302(T) = LMG 25541(T) = MCCC 1A01024(T)).
Childhood‐onset ataxia: Testing for large CAG‐repeats in SCA2 and SCA7 (2002)

Infantile- and juvenile-onset spinal cerebellar ataxia (SCA) is associated with expansion of 130 to more than 200 CAG-repeats in the SCA2 and SCA7 genes. Routine clinical assays for SCA2 and SCA7, which use polymerase chain reaction (PCR) and denaturing PAGE (polyacrylamide gel electrophoresis), will not reliably detect such large expansions. An assay based on separation of PCR products on an agarose gel, blotting, and hybridization with a (CAG)6 oligonucleotide probe was used to test DNA from individuals more than 10 years of age who had a possible diagnosis of SCA. Among 25 cases, the PCR-blot assay confirmed the presence of SCA2 expansions between 230 and 500 repeats in four unrelated individuals, but did not detect any cases of extreme expansion in the SCA7 gene. The PCR-blot assay provides reliable detection of extreme expansion mutations. Routine incorporation of this assay in clinical laboratories may reveal that infantile-juvenile forms of SCA2 and SCA7 are more prevalent than previously recognized.
Identification of Histone Peptide Binding Specificity and Small-Molecule Ligands for the TRIM33α and TRIM33β Bromodomains (2022)

TRIM33 is a member of the tripartite motif (TRIM) family of proteins, some of which possess E3 ligase activity and are involved in the ubiquitin-dependent degradation of proteins. Four of the TRIM family proteins, TRIM24 (TIF1α), TRIM28 (TIF1β), TRIM33 (TIF1γ) and TRIM66, contain C-terminal plant homeodomain (PHD) and bromodomain (BRD) modules, which bind to methylated lysine (KMe<sub><i>n</i></sub>) and acetylated lysine (KAc), respectively. Here we investigate the differences between the two isoforms of TRIM33, TRIM33α and TRIM33β, using structural and biophysical approaches. We show that the N1039 residue, which is equivalent to N140 in BRD4(1) and which is conserved in most BRDs, has a different orientation in each isoform. In TRIM33β, this residue coordinates KAc, but this is not the case in TRIM33α. Despite these differences, both isoforms show similar affinities for H3<sub>1-27</sub>K18Ac, and bind preferentially to H3<sub>1-27</sub>K9Me<sub>3</sub>K18Ac. We used this information to develop an AlphaScreen assay, with which we have identified four new ligands for the TRIM33 PHD-BRD cassette. These findings provide fundamental new information regarding which histone marks are recognized by both isoforms of TRIM33 and suggest starting points for the development of chemical probes to investigate the cellular function of TRIM33.
Automated Generation of Hardware Accelerators with Direct Memory Access from ANSI/ISO Standard C Functions (2006)

Methodologies for synthesis of stand-alone hardware modules from C/C++ based languages have been gaining adoption for embedded system design, as an essential means to stay ahead of increasing performance, complexity, and time-to-market demands. However, using C to generate stand-alone blocks does not allow for truly seamless unification of embedded software and hardware development flows. This paper describes a methodology for generating hardware accelerator modules that are tightly coupled with a soft RISC CPU, its tool chain, and its memory system. This coupling allows for several significant advancements: (1) a unified development environment with true pushbutton switching between original software and hardware-accelerated implementations, (2) direct access to memory from the accelerator module, (3) full support for pointers and arrays, and (4) latency-aware pipelining of memory transactions. We also present results of our implementation, the C2H compiler. Eight user test cases on common embedded applications show speedup factors of 13x-73x achieved in less than a few days
Immobilization and melting point depression of imidazolium ionic liquids on the surface of nano-SiOx particles (2010)

Four kinds of imidazolium-based ionic liquids (ILs) were immobilized onto the surface of nano-SiO(x) particles (d approximately 20 nm) by grinding in an agate mortar to produce a series of weight ratios of ionic liquid to nanoparticles. The physicochemical properties of immobilized ILs were investigated by differential scanning calorimetry, powder X-ray diffraction and Raman spectroscopy. It was found that the melting points (T(m)) of the immobilized ILs depressed significantly in comparison with the bulk ionic liquids. The T(m) depressions are 10, 12, 13 and 41 degrees C for [EMIM][PF(6)], [PMIM][PF(6)], [PHMIM][BF(4)] and [EMIM][I], respectively, for a loading amount of 35 wt% ionic liquid. The T(m) depression of [EMIM][PF(6)] was independent of the weight proportion of immobilized ionic liquid up to 50 wt%, indicating that nano-SiO(x) has a large capacity for immobilized ILs. The T(m) depression of [EMIM][I] is particularly significant because the H-bonding interactions of iodine anions with surface silanol groups of nano-SiO(x) particles is much weaker than that of fluorine anions with silanol groups of other investigated ionic liquids.
Structured motifs in biological sequences: search and extraction (2006)

Searching biological sequence(s) for motifs is a fundamental task in bioinformatics. In this thesis, we develop efficient algorithms for the discovery of interesting structured motifs from biological sequences, which may play important roles in various biological functions. Such patterns include transcription factor binding sites, tandem repeats, retrotransposons, protein sites, and so on. A structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps. The motif can either be represented as a pattern or a profile (also called positional weight matrix). 
We tackle two main problems in structured motif search: (a) given a motif we search for all occurrences, (b) we discover/extract the structured motifs. We allow several variations, including approximate matching, missing components, overlap ping motifs, and length ranges of simple motifs. We propose an efficient algorithm; called SMOTIF, to solve the structured motif search problem, i.e., given one or more sequences and a structured motif, SMOTIF searches the sequences for all occurrences of the motif. Potential applications of SMOTIF include searching for long terminal repeat, (LTR) retrotransposons and composite regulatory binding sites in DNA sequences. SMOTIF can search for both pattern and profile motifs, and it is efficient in terms of both time and space; it outperforms S MARTFINDER, a, state-of-the-art algorithm for structured motif search. Experimental results show that SMOTIF is about 7 times faster and consumes 100 times less memory than S MARTFINDER. It can effectively search for LTR retrotransposons and is well suited to searching for motifs with long range gaps. 
We next look at the problem of mining structured motifs and propose an efficient algorithm, called EXMOTIF, that given some sequence(s), and a structured motif template, extracts all frequent structured motifs that have quorum q. Poten tial applications of EXMOTIF include the extraction of single/composite regulatory binding sites in DNA sequences. EXM OTIF is efficient in terms of both time and space and outperforms RISO, a state-of-the-art algorithm. Experimental results show that EXMOTIF is about 3-5 times faster than RISO.
Differential Phase Contrast Imaging in the Scanning Transmission X-ray Microscope (1991)

In the scanning transmission x-ray microscope (STXM) the specimen is scanned in a raster by an x-ray probe formed with a Fresnel zone plate. To achieve near diffraction limited resolution it is necessary to have a coherent source, even when forming an incoherent brightfield image by measuring the x-ray intensity transmitted by the object. This has so far been the only imaging mode used in the STXM and for hydrated biological specimens is well suited to soft x-ray wavelengths within the “water window” (2‧33 to 4‧36 nm) where carbon absorbs much more strongly than water. However, by the use of phase contrast rather than amplitude contrast, it is possible to form images at wavelengths where the absorption is low, resulting in lower radiation dose for the same level of contrast. Calculations made by Howells [1] and Rudolph and Schmahl [2] have demonstrated very clearly the advantages of phase contrast imaging at wavelengths outside the water window.
Tendon‐Driven Auxetic Tubular Springs for Resilient Hopping Robots (2021)

Compliance in jumping robots improves gait stability and enables energy‐efficient locomotion. Here, 3D printable auxetic tubular springs from thermoplastic polyurethane (TPU) for rapid and sustainable hopping are developed. Because the springs have negative Poisson's ratios, they become stiffer as compression proceeds and theoretically stores 35.2% more energy than a linear spring with the same stiffness. As the stress concentrates on the hinges, it is revealed through experimental, numerical, and analytical investigations that hinge geometries, for example, the lattice angle and hinge radius, governs the global stiffness and robustness of the springs. The hopping robot leg composed of three auxetic tubular springs in parallel sustains more than 1,000 cycles of repeated, one‐degree‐of‐freedom (1‐DOF) vertical hopping and two‐degree‐of‐freedom (2‐DOF) forward hopping. The 2.5 kg‐robot system requires minimum 420 mJ of elastic energy for repeated hopping. The springs are pre‐compressed by tendon‐driven actuators and stores 1.08 J during jumping and release the springs when touching the ground. The power stroke is calculated as 15–18 W. The average velocity of the hopping robot reaches 0.06 m s −1 with the increase of touchdown angle to 0.125 rad. The cost of transport is calculated as 6.7, similar to those of the living organisms.
Optimal docking area: A new method for predicting protein–protein interaction sites (2004)

Understanding energetics and mechanism of protein-protein association remains one of the biggest theoretical problems in structural biology. It is assumed that desolvation must play an essential role during the association process, and indeed protein-protein interfaces in obligate complexes have been found to be highly hydrophobic. However, the identification of protein interaction sites from surface analysis of proteins involved in non-obligate protein-protein complexes is more challenging. Here we present Optimal Docking Area (ODA), a new fast and accurate method of analyzing a protein surface in search of areas with favorable energy change when buried upon protein-protein association. The method identifies continuous surface patches with optimal docking desolvation energy based on atomic solvation parameters adjusted for protein-protein docking. The procedure has been validated on the unbound structures of a total of 66 non-homologous proteins involved in non-obligate protein-protein hetero-complexes of known structure. Optimal docking areas with significant low-docking surface energy were found in around half of the proteins. The 'ODA hot spots' detected in X-ray unbound structures were correctly located in the known protein-protein binding sites in 80% of the cases. The role of these low-surface-energy areas during complex formation is discussed. Burial of these regions during protein-protein association may favor the complexed configurations with near-native interfaces but otherwise arbitrary orientations, thus driving the formation of an encounter complex. The patch prediction procedure is freely accessible at http://www.molsoft.com/oda and can be easily scaled up for predictions in structural proteomics.
Control of partial digestion combining the enzymesdammethylase andMboI (1989)

A method is described which allows the preparation of reproducible partial digests without previous establishment of the incubation conditions. It is based on a combined application of dam methylase and the restriction endonuclease MboI, both recognizing the sequence 5'-GATC-3' but MboI unable to cut the methylated site. Due to their competition for the same substrate the DNA is partially digested, with the size of the resulting fragments strongly dependent on the ratio of enzymes. The Km of the dam methylase was determined to be 115 ng DNA/microliters indicating a variance in fragment sizes generated at low DNA-concentrations. This effect is minimized above 150 ng/microliters. Any influence of digestion time is avoided, because the reaction runs until complete modification of all sites. The dependence on enzyme concentration and presence of agarose was checked. Knowledge of these parameters allows an accurate prediction of fragment sizes generated at different conditions. The technique was successfully used to construct libraries from different sources, in particular chromosome-specific libraries from small amounts of flow-sorted material.