gebhart/patrepeval huggingface dataset:
Aranea (2006)

Currently there exist dozens of web controller frameworks that are incompatible, but at the same time have large portions of overlapping functionality that is implemented over and over again. Web programmers are facing limitations on code reuse, application and framework integration, extensibility, expressiveness of programming model and productivity.In this paper we propose a minimalistic component model Aranea that is aimed at constructing and integrating server-side web controller frameworks in Java. It allows assembling most of available web programming models out of reusable components and patterns. We also show how to integrate different existing frameworks using Aranea as a common protocol. In its default configuration Aranea supports both developing sophisticated user interfaces using stateful components and nested processes as well as high-performance stateless components.We propose to use this model as a platform for framework development, integration and research. This would allow combining different ideas and avoid reimplementing the same features repeatedly. An open source implementation of Aranea framework together with reusable controls, such as input forms and data lists, and a rendering engine are ready for real-life applications.
Wildlife Strikes to Civil Aircraft in the United States 1990-2005 (2006)

Table of Contents List of Tables List of Figures List of Appendices Acknowledgments Preface Wildlife Strikes to Civil Aircraft in the United States, 1990–2005 Literature Cited Tables Figure 1 Appendix A. Bird Strikes to Civil Helicopters in the United States, 1990–2005
An experimental study on the performance of visual information retrieval similarity models (2004)

This paper is an experimental study on the performance of the two major methods for macro-level similarity measurement: linear weighted merging and logical retrieval. Performance is measured as the average query execution time for a significant number of tests. The two models were implemented in the standard version (as they are applied in a number of prototypes) and in an optimized version. The results show that optimized logical retrieval clearly outperforms optimized linear weighted merging.
Evidence that defective gamma interferon production in patients with primary immunodeficiencies is due to intrinsic incompetence of lymphocytes. (1988)

We have selected 11 patients with primary immunodeficiency disorders predominantly affecting T lymphocyte function (four with ataxia-telangiectasia (AT), four with common variable immunodeficiency (CVI) and one each with Wiskott-Aldrich syndrome, hyper-IgE syndrome and combined immunodeficiency) with defective gamma interferon (IFN-gamma) production in vitro. Induction with phytohaemagglutinin showed low interleukin 2 (IL-2) production concomitant with reduced IFN-gamma titres. However the addition of 10 U/ml of rIL-2 to cultures stimulated with staphylococcal enterotoxin B or galactose oxidase failed to restore IFN-gamma production in defective cases. IFN-gamma was titrated by both bioassay and immunoradiometric assay, ruling out the possible release of inactive or altered IFN-gamma molecules. Normal levels of IFN-gamma were found in patients of patients with AT, as well as in two AT and two CVI cases, demonstrating heterogeneity of defects within these syndromes. Soluble inhibitors or cellular suppression of IFN-gamma were not observed in mixing experiments. The possibility that defective interaction between accessory cells and T lymphocytes might account for the poor response to the inducing agents was ruled out as no IFN-gamma was produced using a calcium ionophore--which bypasses this step--in seven patients with absolute IFN-gamma deficiency.
Effects of temporal association on recognition memory (2001)

The influence of temporal association on the representation and recognition of objects was investigated. Observers were shown sequences of novel faces in which the identity of the face changed as the head rotated. As a result, observers showed a tendency to treat the views as if they were of the same person. Additional experiments revealed that this was only true if the training sequences depicted head rotations rather than jumbled views; in other words, the sequence had to be spatially as well as temporally smooth. Results suggest that we are continuously associating views of objects to support later recognition, and that we do so not only on the basis of the physical similarity, but also the correlated appearance in time of the objects.
Organising meetings (2010)

Schedule regular meetings. Ideally, try and find a regular time to meet at the start of the project so people can build it in to their schedule (and remember it!)
Efficient Cache Performance Modeling in GPUs Using Reuse Distance Analysis (2018)

Reuse distance analysis (RDA) is a popular method for calculating locality profiles and modeling cache performance. The present article proposes a framework to apply the RDA algorithm to obtain reuse distance profiles in graphics processing unit (GPU) kernels. To study the implications of hardware-related parameters in RDA, two RDA algorithms were employed, including a high-level cache-independent RDA algorithm, called HLRDA, and a detailed RDA algorithm, called DRDA. DRDA models the effects of reservation fails in cache blocks and miss status holding registers to provide accurate cache-related performance metrics. In this case, the reuse profiles are cache-specific. In a selection of GPU kernels, DRDA obtained the L1 miss-rate breakdowns with an average error of 3.86% and outperformed the state-of-the-art RDA in terms of accuracy. In terms of performance, DRDA is 246,000× slower than the real GPU executions and 11× faster than GPGPU-Sim. HLRDA ignores the cache-related parameters and its obtained reuse profiles are general, which can be used to calculate miss rates in all cache sizes. Moreover, the average error incurred by HLRDA was 16.9%.
Intradiscal temperature monitoring using double gradient‐echo pulse sequences at 1.0T (2010)

Intradiscal temperature monitoring with an unspoiled dual-echo sequence is most accurate with PRF-thermometry in combination with the long echo time. Magnitude images with an initial short echo time permit high image detail of the heat-induced lesion.
A Novel Role for Stat1 in Phagosome Acidification and Natural Host Resistance to Intracellular Infection by Leishmania major (2009)

Intracellular parasites of the genus Leishmania generate severe diseases in humans, which are associated with a failure of the infected host to induce a protective interferon gamma (IFNgamma)-mediated immune response. We tested the role of the JAK/STAT1 signaling pathway in Leishmania pathogenesis by utilizing knockout mice lacking the signal transducer and activator of transcription 1 (Stat1) and derived macrophages. Unexpectedly, infection of Stat1-deficient macrophages in vitro with promastigotes from Leishmania major and attenuated LPG1 knockout mutants (lpg(-)) specifically lacking lipophosphoglycan (LPG) resulted in a twofold increased intracellular growth, which was independent of IFNgamma and associated with a substantial increase in phagosomal pH. Phagosomes in Stat1-/- macrophages showed normal maturation as judged by the accumulation of the lysosomal marker protein rab7, and provided normal vATPase activity, but were defective in the anion conductive pathway required for full vesicular acidification. Our results suggest a role of acidic pH in the control of intracellular Leishmania growth early during infection and identify for the first time an unexpected role of Stat1 in natural anti-microbial resistance independent from its function as IFNgamma-induced signal transducer. This novel Stat1 function may have important implications to studies of other pathogens, as the acidic phagolysosomal pH plays an important role in antigen processing and the uncoating process of many viruses.
Myocardial Sympathetic Innervation in Patients with Symptomatic Coronary Artery Disease: Follow-up After 1 Year with Neurostimulation (2008)

In patients with stable chronic coronary artery disease, sympathetic innervation of the myocardium is almost unchanged in both diabetic and nondiabetic patients in a 1-y follow-up. In myocardial segments with severely altered blood supply, a small but significant decrease in (11)C-HED retention most probably reflects ischemic neuronal damage. The prognostic relevance of sympathetic denervation in viable myocardium still has to be determined.
Quantitative characterization of intermolecular dipolar interactions of two-component systems in solution nuclear magnetic resonance (2001)

Liquid nuclear magnetic resonance behaviors related to intermolecular dipolar interactions were investigated theoretically and experimentally in highly polarized two-component spin systems. A modified CRAZED pulse sequence was designed to investigate relative signal intensities with considerations of spin transverse relaxation, longitudinal relaxation, molecular diffusion, and optimal radio-frequency flip angles. The dissipation of the demagnetizing field due to relaxation and diffusion processes during the detection period was taken into account as well. For the first time, vigorous analytical expressions of the spin dynamics, including all the effects mentioned above, were derived from the combination of the demagnetizing field model and product operator formalism. In the regime where the linear approximation (γμ0M0t≪1) is valid, these explicit analytical expressions can quantitatively describe the signal behaviors related to intermolecular dipolar interactions. All the theoretical predictions based on the analytical expressions for the directly excited component are in excellent agreement with experimental observations reported previously. Several valuable insights for the indirectly excited component were gained from the analytical expressions and verified by experimental measurements, including optimal radio-frequency flip angles, unusual relative signal intensities for n=−2 and n=2, and unconventional diffusion and multi-exponential longitudinal relaxation processes, where n is the ratio of the coherence-selection gradient areas in the CRAZED pulse sequence. In addition, n-order diffusion coefficients of the directly and indirectly excited spins during the evolution period predicted by the demagnetizing field picture are found to be the same as those obtained with the combination of the intermolecular multiple-quantum picture and Gaussian phase distribution approximation which is valid in the case of unrestricted isotropic diffusion. These results suggest that a combination of the demagnetizing field model and product operator formalism provides excellent predictive power and computational convenience for diffusion and relaxation behaviors in two-component systems. These quantitative studies may also provide an opportunity to probe specific sources of new contrast for medical MR imaging.
Implementation and implications of a stealth hard-drive backdoor (2013)

Modern workstations and servers implicitly trust hard disks to act as well-behaved block devices. This paper analyzes the catastrophic loss of security that occurs when hard disks are not trustworthy. First, we show that it is possible to compromise the firmware of a commercial off-the-shelf hard drive, by resorting only to public information and reverse engineering. Using such a compromised firmware, we present a stealth rootkit that replaces arbitrary blocks from the disk while they are written, providing a data replacement back-door. The measured performance overhead of the compromised disk drive is less than 1% compared with a normal, non-malicious disk drive. We then demonstrate that a remote attacker can even establish a communication channel with a compromised disk to infiltrate commands and to ex-filtrate data. In our example, this channel is established over the Internet to an unmodified web server that relies on the compromised drive for its storage, passing through the original webserver, database server, database storage engine, filesystem driver, and block device driver. Additional experiments, performed in an emulated disk-drive environment, could automatically extract sensitive data such as /etc/shadow (or a secret key file) in less than a minute. This paper claims that the difficulty of implementing such an attack is not limited to the area of government cyber-warfare; rather, it is well within the reach of moderately funded criminals, botnet herders and academic researchers.
Second-harmonic generation for dispersive elastic waves in a discrete granular chain (2013)

The propagation of nonlinear compressional waves in a one-dimensional granular chain driven at one end by a harmonic excitation is studied. The chain is described by a Fermi-Pasta-Ulam (FPU) lattice model with quadratic nonlinearity (α-FPU model), valid for strong initial compression of the chain by an external static force. A successive approximations method is used to obtain the analytical expressions for the amplitudes of the static displacement field and of the fundamental and second harmonics propagating through the lattice. Both propagating and evanescent second harmonics are shown to influence the nonlinear propagation characteristics of the fundamental frequency. The propagating regime is characterized by a periodic energy transfer between first and second harmonics, resulting from dispersion, which disappears when the second harmonic becomes evanescent.
The Protein Mutant Database (1999)

Currently the protein mutant database (PMD) contains over 81 000 mutants, including artificial as well as natural mutants of various proteins extracted from about 10 000 articles. We recently developed a powerful viewing and retrieving system (http://pmd.ddbj.nig.ac.jp), which is integrated with the sequence and tertiary structure databases. The system has the following features: (i) mutated sequences are displayed after being automatically generated from the information described in the entry together with the sequence data of wild-type proteins integrated. This is a convenient feature because it allows one to see the position of altered amino acids (shown in a different color) in the entire sequence of a wild-type protein; (ii) for those proteins whose 3D structures have been experimentally determined, a 3D structure is displayed to show mutation sites in a different color; (iii) a sequence homology search against PMD can be carried out with any query sequence; (iv) a summary of mutations of homologous sequences can be displayed, which shows all the mutations at a certain site of a protein, recorded throughout the PMD.
A Multi-View Stereo Measurement System Based on a Laser Scanner for Fine Workpieces (2019)

A new solution to the high-quality 3D reverse modeling problem of complex surfaces for fine workpieces is presented using a laser line-scanning sensor. Due to registration errors, measurement errors, deformations, etc., a fast and accurate method is important in machine vision measurement. This paper builds a convenient and economic multi-view stereo (MVS) measurement system based on a linear stage and a rotary stage to reconstruct the measured object surface completely and accurately. In the proposed technique, the linear stage is used to generate the trigger signal and synchronize the laser sensor scanning; the rotary stage is used to rotate the object and obtain multi-view point cloud data, and then the multi-view point cloud data are registered and integrated into a 3D model. The measurement results show a measurement accuracy of 0.075 mm for a 360° reconstruction in 34 s, and some evaluation experiments were carried out to demonstrate the validity and practicability of the proposed technique.
A four-blade light-driven plastic mill based on hydrazone liquid-crystal networks (2017)

The first light-driven plastic mill is developed, which converts the incoming light directly into a continuous rotation. This device is composed of four blades made of hydrazone-based liquid crystal polymer films able to bend under focused light irradiation and to create a force causing the rotation of the mill. The mechanism of motion originates from the fast photo-thermal isomerization around the C[dbnd]N bond of hydrazones. We show that by accelerating the rate of the thermal Z to E back-isomerization of hydrazones, macroscopic deformation with fast strain rate can be obtained. The rapid motion of the film is the key factor in obtaining the continuous rotatory motion of the mill. These results broaden the range of molecular switches available for macroscopic motion of light-driven organic devices and offer new insights for single-step energy conversion in soft robotics and automated systems.
The Rho Guanine Nucleotide Exchange Factor Lsc Homo-oligomerizes and Is Negatively Regulated through Domains in Its Carboxyl Terminus That Are Absent in Novel Splenic Isoforms (2003)

Rho GTPases control fundamental cellular processes, including cytoskeletal reorganization and transcription. Rho guanine nucleotide exchange factors (GEFs) compose a large (>65) and diverse family of related proteins that activate Rho GTPases. Lsc/p115-RhoGEF is a Rho-specific GEF required for normal B and T lymphocyte function. Despite its essential role in lymphocytes, Lsc/p115-RhoGEF signaling in vivo is not well understood. To define Lsc/p115-RhoGEF signaling pathways in vivo, we set out to identify proteins that interact with regulatory regions of Lsc. The 146-amino acid C terminus of Lsc contains a predicted coiled-coil domain, and we demonstrated that deletion of this C terminus confers a gain of function in vivo. Surprisingly, a yeast two-hybrid screen for proteins that interact with this regulatory C terminus isolated a larger C-terminal fragment of Lsc itself. Co-immunoprecipitation experiments in mammalian cells demonstrated that Lsc specifically homo-oligomerizes and that the coiled-coil domain in the C terminus is required for homo-oligomerization. Mutagenesis experiments revealed that homo-oligomerization and negative regulation are distinct functions of the C terminus. Two novel isoforms of Lsc found in the spleen lack portions of this C terminus, including the coiled-coil domain. Importantly, the C termini of both isoforms confer a gain of function and eliminate homo-oligomerization. These results define two important features of Lsc signaling. First, Lsc homo-oligomerizes and is negatively regulated through domains in its C terminus; and second, functionally distinct isoforms of Lsc lacking these domains are present in the spleen.
Daily supplementation of tocotrienol-rich fraction or α-tocopherol did not induce immunomodulatory changes in healthy human volunteers (2008)

Vitamin E is divided into two subgroups; tocopherols and tocotrienols. Both have protective roles in biological systems. The present study was conducted to compare the effect of short-term supplementation at 200 mg/d of either alpha-tocopherol or a tocotrienol-rich fraction (TRF) from palm oil on immune modulation and plasma vitamin E levels in normal healthy Asian volunteers. In a randomised, double-blind placebo-controlled trial conducted, fifty-three healthy volunteers aged 20-50 years were recruited based on the study's inclusion and exclusion criteria. They were randomly assigned into three groups, i.e. two experimental groups that received daily supplementation at 200 mg of either alpha-tocopherol or the TRF, and the control group that received a placebo. Blood was drawn on days 0, 28 and 56 for several laboratory analyses. Differences in the production of IL-4 or interferon-gamma by concanavalin A-stimulated lymphocytes isolated from these volunteers were not significant (P>0.05). There were no significant differences observed in immune parameters between the healthy volunteers who received daily supplementation with either alpha-tocopherol or the TRF. As these observations were made in the absence of any immunogenic challenge, we feel it would be of benefit to study if there would be any differences observed when an immunogenic challenge such as vaccination were introduced.
Synthesis and Solution Studies of Silver(I)‐Assembled Porphyrin Coordination Cages (2014)

The synthesis and the characterization of two porphyrin coordination cages are reported. The design of the cage formation is based on the coordination of silver(I) ions to the pyridyl units of 3-pyridyl appended porphyrins. (1)H/(109)Ag NMR spectroscopy, and diffusion-ordered spectroscopy (DOSY) experiments demonstrate that both the free base porphyrin 2H-TPyP and the Zn-porphyrin Zn-TPyP form the closed cages, [Ag4(2H-TPyP)2](4+) and [Ag4(Zn-TPyP)2](4+), respectively, upon addition of two equivalents of Ag(+). The complexation processes are characterized in details by means of absorption and emission spectroscopy in diluted CH2Cl2 solutions. The data are discussed in the frame of the point-dipole exciton coupling theory; the two porphyrin monomers, in fact, experience a rigid face-to-face geometry in the cages and a weak inter-porphyrin exciton coupling. An intermediate species is observed, for Zn-TPyP, in a porphyrin/Ag(+) stoichiometric ratio of about 1:0.5 and is tentatively ascribed to an oblique open form. The occurrence of a photoinduced electron-transfer reaction within the cages is excluded on the basis of the experimental outcomes and thermodynamic evaluations. Photophysical experiments evidence different reactivities of singlet and triplet excited states in the assemblies. A lower fluorescence quantum yield and triplet formation is discussed in relation to the constrained geometry of the complexes. Unusually long triplet excited state lifetimes are measured for the assemblies.
SAT05-6: NAMEPS: N -Tier Satellite Multicast Security Protocol Based on Signcryption Schemes (2006)

In this paper, we propose a new N-tier sAtellite Multicast sEcurity Protocol based on multi-recipient Signcryption schemes (NAMEPS). Our protocol is especially designed for very large and highly dynamic satellite multicast systems which require high security and reliability. Our N-tier architecture significantly reduces workload of the satellite layers especially for bandwidth consumption, computation resources and storage requirements. N-tier approach localizes effects of the rekeying operation (forward-backward security) and provides significant performance gain. Moreover, batch keying and ticketing mechanisms are used which additionally reduce workload of the satellite and terrestrial layers. Also, as a novel approach for cryptographic method, our protocol uses multi-recipient signcryption scheme, which provides confidentiality, authentication, unforgeability and non-repudiation together, more efficiently than classical sign-then-encrypt approaches. As a result, NAMEPS has many advantages for very large, dynamic and security critic satellite multicast systems.
Endoplasmic Reticulum Stress Triggers Gametocytogenesis in the Malaria Parasite (2014)

The malaria parasite experiences a significant amount of redox stress during its growth in human erythrocytes and heavily relies on secretory functions for pathogenesis. Most certainly, the parasite is equipped with machinery to tackle perturbations in the secretory pathway, like the unfolded protein response pathway in higher eukaryotes. Our bioinformatics analysis revealed the complete absence of genes involved in the canonical unfolded protein response pathway in Plasmodium falciparum. Accordingly, the parasite was unable to up-regulate endoplasmic reticulum (ER) chaperones or ER-associated degradation in response to DTT-mediated ER stress. Global profiling of gene expression upon DTT treatment revealed a network of AP2 transcription factors and their targets being activated. The overall outcome was up-regulation of genes involved in protein export and the sexual stage of the parasite life cycle culminating in gametocytogenesis. Our results suggest that the malaria parasite uses ER stress as a cue to switch to the transmissible sexual stages.