gebhart/patrepeval huggingface dataset:
Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry (2009)

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three-dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of (1)H/(2)H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N- and C-terminal tails were evaluated using (1)H-(15)N HSQC and (1)H-(15)N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS-based truncated construct for a 77-residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination.
Probing the Binding of Scutellarin to Human Serum Albumin by Circular Dichroism, Fluorescence Spectroscopy, FTIR, and Molecular Modeling Method (2004)

The binding of scutellarin with human serum albumin (HSA) was investigated at four temperatures, 296, 303, 310, and 318 K, by fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR), and molecular modeling study at pH 7.40. The binding parameters were determined by Scatchard's procedure, which are approximately consistent with the results of Stern-Volmer equation. The thermodynamic parameters were calculated according to the dependence of enthalpy change on the temperature as follows: DeltaH degrees is a small negative value (-8.55 kJ/mol), whereas DeltaS degrees is a positive value (65.15 J/mol K). Quenching of the fluorescence HSA in the presence of scutellarin was observed. Data obtained by fluorescence spectroscopy and CD experiment, FT-IR experiment, and molecular modeling method suggested that scutellarin can strongly bind to the HSA and the primary binding site of scutellarin is located in site I of HSA. It is considered that scutellarin binds to site I (subdomain II) mainly by a hydrophobic interaction and there are hydrogen bond interactions between the scutellarin and the residues Arg222 and Arg257.
Maximum likelihood estimation of object location in diffraction tomography. II. Strongly scattering objects (1991)

For pt.I see ibid., vol.39, no.3, p.672-82, 1991. The problem of estimating the location of a known scattering object from noisy, limited scattering data is solved within exact, scalar wave scattering theory. The estimation procedure is shown to be a generalization of an earlier procedure developed within the Born and Rytov approximations of weak scattering theory and is compared with that earlier procedure in a computer simulation study of electromagnetic tomography.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Excess Pore Water Pressure Response in Soft Clay under Embankment (2002)

Increases in excess pore water pressure without change of surcharge load were reported in clay underneath embankment at Berthierville and Olga sites after the end of construction. These abnormal phenomena could not be explained by classical consolidation theory. This paper presents a nonlinear viscoplastic model to interpret an increase in pore water pressure on natural clay, The proposed model can consider the combined processes of pore water pressure dissipation according to Darcy's law and pore water pressure generation due to viscoplastic strain, as well as time-dependent viscoplastic behaviour and strain rate dependency of preconsolidation pressure. The calculated results using numerical analysis are compared with measured ones under embankments built on soft clay at Berthierville and Olga in Quebec, Canada. It may be possible to explain the phenomenon of excess pore water pressure increase after the end of construction using the proposed nonlinear viscoplastic model.
Efficient siRNA selection using hybridization thermodynamics (2007)

Small interfering RNA (siRNA) are widely used to infer gene function. Here, insights in the equilibrium of siRNA-target hybridization are used for selection of efficient siRNA. The accessibilities of siRNA and target mRNA for hybridization, as measured by folding free energy change, are shown to be significantly correlated with efficacy. For this study, a partition function calculation that considers all possible secondary structures is used to predict target site accessibility; a significant improvement over calculations that consider only the predicted lowest free energy structure or a set of low free energy structures. The predicted thermodynamic features, in addition to siRNA sequence features, are used as input for a support vector machine that selects functional siRNA. The method works well for predicting efficient siRNA (efficacy >70%) in a large siRNA data set from Novartis. The positive predictive value (percentage of sites predicted to be efficient for silencing that are) is as high as 87.6%. The sensitivity and specificity are 22.7 and 96.5%, respectively. When tested on data from different sources, the positive predictive value increased 8.1% by adding equilibrium terms to 25 local sequence features. Prediction of hybridization affinity using partition functions is now available in the RNAstructure software package.
Non-blocking 4&#x00D7;4 InAlGaAs/InAlAs Mach-Zehnder-type optical switch fabric (2013)

We demonstrated the full-interport connection of a non-blocking 4x4 InAlGaAs/InAlAs Mach-Zehnder-type optical switch (MZ-OS) fabric. This switch fabric is consisted of six 2x2 MZ-OS elements in a cascading configuration, and it successfully operated with high-extinction ratios of about 20dB and polarization independence.
Magnetic-Core and Air-Core Inductors on Silicon: A Performance Comparison up to 100 MHz (2011)

What is the future of integrated inductor design on silicon for power conversion applications at frequencies up to 100 MHz-is it magnetic-core or air-core inductors. This study presents measured results for two microfabricated inductors (magnetic core and air core), which have been designed to operate at 20 MHz and occupy a substrate area of less than 10 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The inductor technology and design are briefly discussed. An optimized inductor design study is, then, presented. Both magnetic-core and air-core inductor designs are compared and evaluated, in terms of inductance and efficiency per unit area for frequencies up to 100 MHz. The design of the microinductors is discussed and an analytical design optimization program is used to model the devices for the maximum efficiency and inductance. The introduction of laminations with high-frequency core inductors will also be examined within the study. A 100 MHz magnetic-core inductor design with three laminations gives a 36 nH inductance, with 96.4% efficiency and an area of 3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . A comparable air-core design also gives a 36 nH inductance, with 93.45% efficiency and an area of just 2.6 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Managing a real-time massively-parallel neural architecture (2012)

A human brain has billions of processing elements operating simultaneously; the only practical way to model this computationally is with a massively-parallel computer.A computer on such a significant scale requires hundreds of thousands of interconnected processing elements, a complex environment which requires many levels of monitoring, management and control.Management begins from the moment power is applied and continues whilst the application software loads, executes, and the results are downloaded.This is the story of the research and development of a framework of scalable management tools that support SpiNNaker, a novel computing architecture designed to model spiking neural networks of biologically-significant sizes.This management framework provides solutions from the most fundamental set of power-on self-tests, through to complex, real-time monitoring of the health of the hardware and the software during simulation.The framework devised uses standard tools where appropriate, covering hardware up / down events and capacity information, through to bespoke software developed to provide real-time insight to neural network software operation across multiple levels of abstraction.With this layered management approach, users (or automated agents) have access to results dynamically and are able to make informed decisions on required actions in real-time.Within the University, I'd like to thank all those around me, past and present, within the SpiNNaker and broader APT groups.They have provided great support, including answering my daft (and sometimes not-so-daft) questions with enthusiasm and patience.The team have been a great source of inspiration and challenges in all respects, and some have become badminton / drinking buddies.I'm particularly lucky to have chosen this group to join, it's an honour to have played a small part in the team developing the SpiNNaker architecture.More specifically I'd like to particularly thank my supervisor Prof. Steve Furber, who responded positively to my initial contact in 2008, encouraged my application, and provided support all the way through the programme.Special thanks also go to Dr. J. V. Woods and Dr. J. D. Garside for their proof-reading
End Sequencing and Chromosomal <i>in silico</i> Mapping of BAC Clones Derived from an <i>indica</i> Rice Cultivar, Kasalath (2004)

To investigate the molecular basis for the phenotypic diversity and evolutionary relationships within Oryza sativa, we performed large-scale end sequencing and chromosomal in silico mapping (mapping by sequence homology) of rice BAC (bacterial artificial chromosome) clones derived from an indica rice cultivar, ‘Kasalath’. In total, 78,427 high-quality BAC-end sequences (BESs) showing an average read-length of 482 bp with a total of 37.8 Mb of genomic sequences were obtained from 47,194 BAC clones. After removal of those BESs containing repetitive sequences and use of the high-quality genomic sequence of the japonica rice cultivar ‘Nipponbare’ as a reference standard, 12,170 clones with paired BESs were mapped in silico to the 12 chromosomes. These clones consisted of 450 contigs and showed a total physical length of 308.5 Mb, indicating a coverage of the rice genome of about 80%. Confirmation of the chromosomal positions of the Kasalath BAC clones mapped on chromosome 1 using specific DNA markers revealed that the map accuracy was extremely high: at least 94.8%. In general, the genomic composition and structure of all the chromosomes were highly conserved between the two subspecies. However, we still found evidence suggesting the existence of different components in the genome of the two subspecies within large chromosomal fragments, especially on chromosomes 11 and 12. Extensive analysis of the genomic sequences of Nipponbare and Kasalath revealed a frequency of 0.71% for single nucleotide polymorphisms (SNPs) and 1.23 sites per kilobase for indels (1–16 bp length), respectively. The BAC-based Kasalath map could become an invaluable resource, not only for the isolation of genes, but also for conducting extensive analyses of genomic sequences for comparative genomic studies within or between species.
Organisation & the Search for Community (1981)

In the opening years of the 18th century, Englishmen stood on the verge of the greatest change to society the modern world has known. Already the foundations of the Industrial Revolution had been laid, the earliest “manufacturies” had been established, the harnessing of water power to machines was much improved and the first practical steam engine had been invented by Savery & Newcomen. Science and scientific knowledge, following the great traditions of English scientific thought, was flowering; the enclosures were making available the manpower to fodder the revolution and, above all, the great markets of the Americas and the Far East were opening to English manufactured goods. The stage was set for the development of the organisations which were to change the face of Britain and eventually the world.
[V<sub>19</sub>O<sub>41</sub>(OH)<sub>9</sub>]<sup>8⊖</sup>, An Ellipsoid‐Shaped Cluster Anion Belonging to the Unusual Family of V<sup><scp>IV</scp></sup>/V<sup><scp>V</scp></sup> Oxygen Clusters (1988)

Clearly distinguishable are the VIV and VV centers of the “outer shell” of the title anion 1, whose center forms a VO4 tetrahedron and a μ3-O atom. The nine μ2-O bridges between VIV centers (black) are protonated, the six between VIV and VV centers (hatched), on the other hand, are not. The formation of 1 confirms the unusual behavior of vanadium in polycondensation. The cross-hatched atom shows the second disordered position of the central V atom.
Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU (2010)

Graphics processing units (GPUs) are gaining widespread use in high-performance computing because of their performance advantages relative to CPUs. However, the reliability of GPUs is largely unproven. In particular, current GPUs lack error checking and correcting (ECC) in their memory subsystems. The impact of this design has not been previously measured at a large enough scale to quantify soft error events. We present MemtestG80, our software for assessing memory error rates on NVIDIA graphics cards. Furthermore, we present a large-scale assessment of GPU error rate, conducted by running MemtestG80 on over 50,000 hosts on the Folding@home distributed computing network. Our control experiments on consumer-grade and dedicated-GPGPU hardware in a controlled environment found no errors. However, our survey on Folding@home finds that, in their installed environments, two-thirds of tested GPUs exhibit a detectable, pattern-sensitive rate of memory soft errors. We show that these errors persist after controlling for over clocking and environmental proxies for temperature, but depend strongly on board architecture.
<i>Trypanosoma cruzi</i> : immunity-induced in mice and rats by trypomastigote excretory-secretory antigens and identification of a peptide sequence containing a T cell epitope with protective activity. (1993)

In the present study, we investigate the immunoprotective properties of trypomastigote excretory-secretory Ag (ESA) in experimental models. In the case of BALB/c mice, the immunization with ESA resulted in the reduction of parasitemia during acute infection and a significant level of protection in terms of mortality with more than 60% survival, whereas none of the mice in the control groups survived after 39 days postinfection. The same experiments performed in Fischer rats showed a high degree of protection against acute lethal infection with 100% survival, whereas 20 to 40% of rats in the control groups survived the acute phase of T. cruzi infection. Mouse and rat immune sera presented trypanolytic activity against Trypanosoma cruzi infective forms, and recognized two major parasite components of 85 and 24 kDa. The analysis of specific isotype profiles showed a predominance of IgG1, IgG2a, and IgG2b antibody responses. Rat antisera to ESA were then used to screen a trypomastigote cDNA library. Several clones were identified, all of which encoded for the 24-kDa protein. Using a mAb (Tcr7) produced against the native protein, the 31-kDa recombinant fusion protein was purified by affinity chromatography. The antisera to the recombinant protein used in IFA and immunoelectron microscopy showed that the localization of the 24-kDa protein differs among T. cruzi developmental stages. Protection experiments were performed in BALB/c mice using two synthetic peptides (20-40 and 109-124) derived from the primary sequence of the 24-kDa polypeptide. The results obtained clearly indicated that the peptide 109 to 124 containing a putative T cell epitope represents the most protective epitope, which induced 30 to 50% of protection against mortality during acute infection, whereas the percent survival in the control groups (OVA and 20-40 OVA peptide-immunized mice) was around 16%. Moreover, analysis of T cell proliferation in response to OVA-coupled peptides clearly indicated that only the 109 to 124 peptide had the capacity to induce the proliferation of T cells from peptide-immunized mice. Interestingly, only the 109 to 124-coupled peptide induced the proliferation of T cells from T. cruzi-infected mice.
Accurate electrothermal modeling of thermoelectric generators (2015)

Thermoelectric generators (TEGs) provide a unique way for harvesting thermal energy. These devices are compact, durable, inexpensive, and scalable. Unfortunately, the conversion efficiency of TEGs is low. This requires careful design of energy harvesting systems including the interface circuitry between the TEG module and the load, with the purpose of minimizing power losses. In this paper, it is analytically shown that the traditional approach for estimating the internal resistance of TEGs may result in a significant loss of harvested power. This drawback comes from ignoring the dependence of the electrical behavior of TEGs on their thermal behavior. Accordingly, a systematic method for accurately determining the TEG input resistance is presented. Next, through a case study on automotive TEGs, it is shown that compared to prior art, more than 11% of power losses in the interface circuitry that lies between the TEG and the electrical load can be saved by the proposed modeling technique. In addition, it is demonstrated that the traditional approach would have resulted in a deviation from the target regulated voltage by as much as 59%.
A simplified simulation method for progressive collapse of reinforced concrete slabs (2016)

Floor slabs are important components of frame structures which largely affect the structural progressive collapse performance. This paper presents a simplified numerical simulation method for reinforced concrete (RC) slabs. A RC slab is discretized along two directions transferring into a beam network. The meshes at each direction are simulated by fiber beam elements to consider the composite mechanical behavior of steel reinforcement and concrete. In this method, beam-slab joints at the edge area of slabs are simulated by fiber beam elements with T/L sections, by which the effects of slabs on the bending behavior and the damage mode of the beams under small deformation in progressive collapse are considered. On the other hand, fiber beam elements with rectangle sections are used to simulate the interior area of slabs, by which the tensile membrane action of slabs under large deformation can be considered. This method can not only avoid the high stiffness problem when using shell elements, but also greatly improve the efficiency of the calculation of the whole structure. Finally, existing tests on special-shaped columns (T/L cross sections), one-way slabs and two-way slabs are simulated, respectively. The results show that the simplified method can efficiently and accurately simulate the reinforced concrete slabs under large deformation, providing a powerful tool for the simulation of progressive collapse analysis of whole structures.
Urethane–acrylate polymers in high-resolution contact printing (2016)

Polyurethane–acrylate (PUA) materials were used as printing stamps in the high-resolution contact printing of organic molecules and organic thin films to show that PUA-based printing can be used as a simple alternative to a kinetically modulated PDMS stamping.
Towards Logic-Based Question Answering under Time Constraints (2008)

Abstract—Using logic for question answering (QA) promises more accurate answers and increased flexibility of querying. However, the computational effort for a deep linguistic analysis of the involved natural language (NL) expressions and the subsequent logical inferencing makes it difficult to leverage this power for real-time QA. The paper attributes this difficulty in part to the popular answer validation paradigm, and it proposes a different solution which avoids parsing of answers at query time. The novel approach, which uses logic for assessing the relevance of extracted passages, allows better concurrency of QA subtasks since logic-based passage filtering can run in parallel with the answer extractors. Moreover the substitutions found in the proofs can guide a direct answer generation. A first implementation of logical passage filtering achieved 43 % F-measure for factual questions of CLEF07, with response times of only a few seconds. These results are especially interesting since neither aggregation (for better filtering) nor parallelization (for reducing latency) were used in the prototype yet.
Schools and Delinquency (2000)

Schools and Delinquency, first published in 2001, provides a comprehensive review and critique of the current research about the causes of delinquency, substance use, drop-out, and truancy, and the role of the school in preventing these behavior patterns. Examining school-based prevention programs and practices for grades K-12, Denise Gottfredson identifies a broad array of effective strategies improving the school environment, as well as some that specifically target youths at risk of developing problem behaviors. She also explains why several popular school-based prevention strategies are ineffective and should be abandoned. Gottfredson analyzes, within the larger context of the community, the special challenges to effective prevention programming that arise in disorganized settings, identifying ways to overcome these obstacles and to make the most troubled schools safer and more productive environments.
Scaffold-attached regions (SAR elements) mediate transcriptional effects due to butyrate (1992)

The expression of certain genes has been reported to respond positively to sodium butyrate. This study demonstrates the same feature for two marker genes under the control of five different promoters. In all examples, the stimulatory effect is largest if one or especially two scaffold/matrix-attached regions (SAR/MAR elements) are present adjacent to the gene, and in one case, the stimulation depends entirely upon this situation. These results are observed with several SAR sequences including those obtained by oligomerizing short stretches of DNA surrounding a core motif. It is suggested that butyrate exerts important actions at the level of the chromatin structure.