gebhart/patrepeval huggingface dataset:
Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports (2014)

Poor partitioning of macromolecules into the holes of holey carbon support grids frequently limits structural determination by single particle cryo-electron microscopy (cryo-EM). Here, we present a method to deposit, on gold-coated carbon grids, a self-assembled monolayer whose surface properties can be controlled by chemical modification. We demonstrate the utility of this approach to drive partitioning of ionotropic glutamate receptors into the holes, thereby enabling 3D structural analysis using cryo-EM methods.
The theory of ground vehicles - 3rd edition (2001)

This book focuses on applying engineering principles to the analysis of vehicle behavior. A large number of practical examples and problems are included throughout to help readers bridge the gap between theory and practice. The chapters include information on the mechanics of pneumatic tyres, vehicle-terrain interaction, vehicle performance on roads, performance of off-road vehicles, handling characteristics, steering of tracked vehicles, vehicle ride characteristics, and an introduction to air cushion vehicles.Revised information in the third edition includes: the 'magic formula' for characterizing pneumatic tire behavior from test data for vehicle handling simulations; computer-aided methods for performance and design evaluation of off-road vehicles; updated data on road vehicle transmissions and operating fuel economy; fundamentals of road vehicle stability control; optimization of the performance of four-wheel-drive off-road vehicles and experimental substantiation; and a new theory on skid-steering of tracked vehicles.
Cyberspaces and Global Affairs (2013)

info:eu-repo/semantics/published
An Error-Localization, Validation and Optimization Tool for Embedded Code Augmentation: an Architecture Oriented Approach (2011)

interpretation is a theory of effective abstraction and/or approximation of discrete mathematical structures as found in the semantics of programming languages, modelling program executions, hence program properties, at various levels of abstraction [102]. Abstract interpretation has been applied to static program analysis of embedded control software by P. Cusot, that is the automatic (without any human intervention), static (at compile time) determination of dynamic program properties (that always hold at runtime) involving complex Review of Debugging and Optimization Technologies Cochin University of Science and Technology 41 abstractions of the infinite state operational semantics [102]. This approach was successfully illustrated by the ASTR EE static analyzer which is specialized for proving the absence of run-time errors in synchronous, time triggered, real-time, safety critical, embedded software written or automatically generated in the C programming language [103]. It was able to prove the absence of run-time errors in large industrial avionic control-command programs [102] without any hypotheses on the controlled systems (but, maybe, for ranges of variation of very few volatile input variables). This means that the software will go on functioning without any runtime error whatever the behavior of the controlled system can be, as long as the processor on which the program is running does not fail (a situation which can be handled by fault-tolerance techniques). Several general static analysis techniques allow specification of code patterns which may be used to find bugs in programs. Bug patterns are code idioms that are often errors. Hovemeyer and Pugh [43] have implemented automatic detectors for a variety of bug patterns found in Java programs. They have found that the effort required to implement a bug pattern detector tends to be low, and that even extremely simple detectors find bugs in real applications. They have found that even well tested code written by experts contains a surprising number of obvious bugs and that simple automatic techniques can be effective at countering the impact of both ordinary mistakes and misunderstood language features. Automatic detectors for many bug patterns can be implemented using relatively simple static analysis techniques. In many ways, using static analysis to find occurrences of bug patterns is like an automated code inspection. They have implemented a number of automatic bug pattern detectors in a tool called FindBugs [43]. Automatic techniques to find bugs in software have been extensively studied in previous research [9, 43, 98, 100, 104]. Often, these techniques rely on formal
Robust video scene detection using multimodal fusion of optimally grouped features (2017)

Video scene detection, the task of temporally dividing a video into its semantic sections, is an important process for effective analysis of heterogeneous video content. With the increased amount of video available for consumption, video scene detection becomes more and more important by providing means for effective video summarization, search and retrieval, browsing, and video understanding. We formulate the problem of video scene detection as a generic optimization problem aimed at partitioning a video given a set of features derived from multiple modalities. By optimally grouping consecutive shots into scenes, our method presents an effective and efficient solution for dividing a video into sections using a unique dynamic programming scheme. Unlike existing methods, it allows us to directly obtain temporally consistent video scene detection and has the advantage of being parameter-free, making it robust and applicable to various types of video content. Our experimental results show that our proposed multimodal approach can provide a significant gain compared to using only a single modality (e.g., either video or audio alone). Additionally, our method outperforms the state of the art in video scene detection, clearly demonstrating the effectiveness of the proposed method. As part of this work, we also provide a significant extension to our Open Video Scene Detection dataset (OVSD), which comprises open licensed videos freely available for academic and industrial use. This extension, which increases the OVSD's cumulative duration from the original 2.5 hours to over 17 hours, makes this dataset the most extensive evaluation tool for the problem of video scene detection.
ZNN -- A Fast and Scalable Algorithm for Training 3D Convolutional Networks on Multi-core and Many-Core Shared Memory Machines (2016)

Convolutional networks (ConvNets) have become a popular approach to computer vision. It is important to accelerate ConvNet training, which is computationally costly. We propose a novel parallel algorithm based on decomposition into a set of tasks, most of which are convolutions or FFTs. Applying Brent's theorem to the task dependency graph implies that linear speedup with the number of processors is attainable within the PRAM model of parallel computation, for wide network architectures. To attain such performance on real shared-memory machines, our algorithm computes convolutions converging on the same node of the network with temporal locality to reduce cache misses, and sums the convergent convolution outputs via an almost wait-free concurrent method to reduce time spent in critical sections. We implement the algorithm with a publicly available software package called ZNN. Benchmarking with multi-core CPUs shows that ZNN can attain speedup roughly equal to the number of physical cores. We also show that ZNN can attain over 90× speedup on a many-core CPU (Xeon Phi™ Knights Corner). These speedups are achieved for network architectures with widths that are in common use. The task parallelism of the ZNN algorithm is suited to CPUs, while the SIMD parallelism of previous algorithms is compatible with GPUs. Through examples, we show that ZNN can be either faster or slower than certain GPU implementations depending on specifics of the network architecture, kernel sizes, and density and size of the output patch. ZNN may be less costly to develop and maintain, due to the relative ease of general-purpose CPU programming.
Realistic simulations of CDMA mobile radio systems using joint detection and coherent receiver antenna diversity (2002)

Due to time variant multipath propagation, both intersymbol interference and multiple access interference occur at CDMA receivers. These degrading effects can be combatted by joint detection (JD) techniques. In order to reduce the performance impairments resulting from time variance, coherent receiver antenna diversity (CRAD) can be used. A system model of CDMA mobile radio systems using various JD techniques in combination with CRAD is introduced. This system model is an evolution of the pan-European GSM and takes important real world aspects such as imperfect channel estimation, nonlinear amplification and D/A and A/D conversion into account. The viability of JD with CRAD is demonstrated by bit error rate simulations of this system model. It is shown that by using JD with two receiver antennas in bad urban areas, E/sub bN/sub 0/<8 dB per antenna is sufficient for a bit error rate of 10/sup -2/, and E/sub bN/sub 0/<11 dB per antenna is required for a bit error rate of 10/sup -3/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Wavefront reconstruction by adding modulation capabilities of two liquid crystal devices (2004)

We analyze the behavior of complex information in the Fresnel domain, taking into account the limited capability to display complex values of liquid crystal devices when they are used as holographic displays. To do this analysis we study the reconstruction of Fresnel holograms at several distances using the different parts of the complex distribution. We also use the information adjusted with a method that combines two configurations of the devices in an adding architecture. The results of the error analysis show different behavior for the reconstructions when using the different methods. Simulated and experimental results are presented.
Human H1 histones: conserved and varied sequence elements in two H1 subtype genes. (1989)

The genes coding for two different human H1 histones were isolated, and the primary structures were deduced from the nucleotide sequences. The genes differ from each other and from any other vertebrate H1 structure described until now. The differences occur mainly within the N- and C-terminal H1 domains, whereas the central part of the protein is highly conserved. Within the flanking domains, however, some sequence elements are shared by different H1 subtype genes. An octapeptide, which has been described in C-terminal domains of most H1 histones, is found in both H1 subtypes. The nucleotide sequences of the flanking portions of both H1 genes show conserved motifs at established regulatory sites, but otherwise these 3' and 5' noncoding sequences of both genes differ substantially.
Program synthesis using natural language (2016)

Interacting with computers is a ubiquitous activity for millions of people. Repetitive or specialized tasks often require creation of small, often one-off, programs. End-users struggle with learning and using the myriad of domain-specific languages (DSLs) to effectively accomplish these tasks.
LSTM-based GNSS Spoofing Detection Using Low-cost Spectrum Sensors (2021)

GNSS/GPS is a positioning system widely used nowadays in our lives for real-time localization in Earth. This technology is highly vulnerable to spoofing/jamming attacks caused by malicious intruders. In the recent years, commodity and low-cost radio-frequency hardware have been used to interfere with the legitimate GPS signal. Existing spoofing detection solutions use costly receivers and computationally expensive algorithms which limit the large-scale deployment. In this work we propose a GNSS spoofing detection system that can run on spectrum sensors with Software-Defined Radio (SDR) capabilities and cost in the order of 20 euros. Our approach exploits the predictability of the Doppler characteristics of the received GPS signals to determine the presence of anomalies or malicious attackers. We propose an artificial recurrent neural network (RNN) based on Long short-term memory (LSTM) for anomaly detection. We use data received by low-cost SDR receivers that are processed locally by low-cost embedded machines such as Nvidia Jetson Nano to provide inference capabilities. We show that our solution predicts very accurately the Doppler shift of GNSS signals and can determine the presence of a spoofing transmitter.
The antidepressant-like effect induced by sigma(1)-receptor agonists and neuroactive steroids in mice submitted to the forced swimming test. (2001)

The interaction of neuroactive steroids with the sigma(1)-receptor was investigated in Swiss mice submitted to the forced swimming test. The sigma(1)-agonists igmesine and (+)-SKF-10,047 and the steroid dehydroepiandrosterone sulfate (DHEAS) showed some antidepressant-like activity by shortening the immobility time, these effects being blocked by the sigma(1)-antagonist BD1047 or progesterone. The sigma(1)-agonist PRE-084 or pregnenolone sulfate failed to affect the immobility time. In adrenalectomized/castrated (AdX/CX) mice, the effects of igmesine and DHEAS were significantly potentiated, and PRE-084 or pregnenolone sulfate induced significant decreases of immobility time. The augmented effects in AdX/CX were fully blocked by BD1047. The effects of the classical antidepressants, desipramine or fluoxetine, were unchanged in AdX/CX mice. The effect of stress on the sigma(1)-receptor binding and neurosteroid levels was then examined in different brain structures, in terms of in vivo (+)-[(3)H]SKF-10,047 binding to sigma(1)-sites and neurosteroids levels. In the hippocampus, but not in the cortex or cerebellum, inhibition of in vivo (+)-[(3)H]SKF-10,047 binding was measured in parallel to the extent of progesterone levels according to the endocrine conditions. These data confirmed the antidepressant ability of sigma(1)-receptor agonists and revealed that the endogenous steroidal levels tonically interfere with the efficacy of the sigma(1)-system. It was observed that local modifications in progesterone levels are directly related to the changes of in vivo sigma(1)-binding. Such observations may be of major importance in view of the therapeutic use of selective sigma(1)-agonists in depression.
Preparation of Discrete Oligoethers:  Synthesis of Pentabutylene Glycol and Hexapropylene Glycol by Two Complementary Methods (2003)

Two experimentally facile methods for the preparation of discrete oligoethers are reported. The first involves an iterative sequence of oxidation, acetal formation, and reductive ring opening for the synthesis of penta-1,4-butylene glycol. The second method is also iterative, comprising phase-transfer etherification and end-group deprotection to form hexa-1,3-propylene glycol. These methods offer significantly improved yields and purification protocols over previously reported syntheses.
[Zd 1839 "Iressa"]. (2000)

ZD 1839 is a highly specific EGF receptor tyrosine kinase inhibitor. Inhibition of EGF receptor transphosphorylation by ZD 1839 blocks the signal transduction at the first step, thus providing antiproliferative effects. Preclinical studies demonstrated efficacy and good bioavailability. The terminal half-life of the compound in patients is ranging from 27 to 41 hours, allowing single oral dosing. Tolerance in healthy volunteers was excellent. In phase I studies, toxicity was manageable. Most common side effects were skin rash, nausea, vomiting, and diarrhea. During those studies, clinical responses were observed in patients with various malignant tumors, in particular non small cell lung cancer. Phase II and III studies are ongoing.
Evaluation of the incident angle of the beam into 30° electrostatic energy analyzer directly during HIBP operation in plasma experiments (2003)

The resolution of the plasma potential measurements by a 30° electrostatic energy analyzer of a heavy-ion beam probe (HIBP) is strongly related to the accuracy of knowledge of the incident angle of the beam (θ). Initially it is determined by the calculations of the beam trajectories in the confining magnetic field of the plasma device. However, because the magnetic-field simulation codes are not exact, an uncertainty in θ always exists. A common practice to reduce the influence of this uncertainty consists in tuning the analyzer geometry parameters in such a way as to minimize the dependence on the variation of θ that results from a scan of the beam across the plasma. Still, the attachment of the energy analyzer to the diagnostic port cannot be controlled with enough precision and, therefore, an unknown shift out from the chosen optimal range of θ is predictable. This article proposes a method for the direct evaluation of the incident angles during operation of HIBP in plasma experiments. It is based on the addition of a second split-plate detector along a 30° exit axis of the analyzer, and on the comparison of the respective normalized beam currents. The experimental verification of the method on a test facility has shown that an accuracy better than Δθ=0.1° can be attained.
Absorption of Calcium Fumarate Salts Is Equivalent to Other Calcium Salts When Measured in the Rat Model (2002)

Calcium absorption from fumarate salts (calcium fumarate and calcium malate fumarate), which have recently been considered for use as sources for food and beverage enrichment, was compared to that from calcium citrate malate, calcium citrate, and calcium carbonate. Salts were instrinsically labeled with 45Ca and orally administered to Sprague-Dawley rats. Fractional absorption of calcium from each salt was determined using the femur uptake model. Fractional absorption from the five salts (0.30-0.27) was not significantly different (p > 0.05). Thus, when measured in the rat model, calcium from calcium fumarate and calcium malate fumarate is absorbed equally well as compared to other salts, which are common calcium sources in many foods, beverages, and supplements.
Localization Studies of Bioactive Cyclic Peptides in the Ascidian <i>Lissoclinum </i><i>p</i><i>atella</i> (2002)

A Palauan specimen of the ascidian Lissoclinum patella contained the cyclic peptides patellamides A-C. In contrast to previous reports concerning the location of cyclic peptides in L. patella and L. bistratum, it has been demonstrated that these cyclic peptides were not located in the symbiotic cyanobacterium Prochloron sp. but were instead distributed throughout the ascidian tunic. The relevance of these results with respect to the biosynthetic origins of the patellamides is discussed.
A tau-like protein interacts with stress fibers and microtubules in human and rodent cultured cell lines (1993)

The cytoskeletal integrity of human and rodent cell lines was analyzed using site-directed monoclonal antibodies prepared from hybridomas. Secreting hybridomas were produced by immunizing mice with synthetic peptides from the C-terminal domain of the beta II-tubulin isotype, beta II(422-434), YQQYQDATADEQG, and the first imperfect repeat from brain tau, Tau-I(187-204), VRSKIGSTENLKHQPGGG. Two hybridomas were selected for this work: MTB6.22, an anti-idiotypic monoclonal antibody, which was obtained from a mouse immunized with the beta II-peptide and recognizes specific tubulin-binding domains on MAP-2 and tau; and Tau-I/1, which recognizes the repetitive binding sequences on tau and MAP-2. Immunoblots of cytoskeletal protein preparations from the five different tumor cell lines studied, showed the interaction of the site-directed antibodies MTB6.22 and Tau-I/1 with a group of proteins that co-migrate with brain tau. Immunoreactive tau components were also identified using an anti-tau monoclonal antibody (clone Tau-2), and several polyclonal anti-tau antibodies that interact with tau epitopes, other than those of the tubulin-binding domains. These tau-like proteins bound to a calmodulin-Sepharose affinity column and were eluted using 2 mM EGTA. Interestingly, washing the extracted cytoskeleton pellet with 5 x 10(-3) M Ca2+ for short periods of time selectively released the tau-like protein components, whilst most of the other cytoskeletal proteins remained in the pellet. On the other hand, immunofluorescence microscopy of detergent-extracted cells showed immunostaining of MAP components that appear to be co-localized in a discrete dot-like distribution along the stress fibers, which were revealed using rhodamine-phallacidin. Further support for the specificity of tau interaction with sites on tubulin and actin polymers was obtained with double-immunofluorescence, using the MAP-reactive monoclonal antibody MTB6.22 and a polyclonal antibody to a tubulin peptide containing part of the tau-binding domain on tubulin. Considering the anti-idiotypic nature of the MTB6.22 monoclonal antibody, our studies indicate that, in all the cell lines analyzed, a tau-like protein component is involved in mediating the interaction of both actin and tubulin polymers.
Solvent induced shape recovery of shape memory polymer based on chemically cross-linked poly(vinyl alcohol) (2010)

A shape memory polymer based on poly(vinyl alcohol) (SM-PVA) chemically cross-linked with glutaraldehyde exhibits good temperature responsive shape memory behavior. In the present investigation, solvent-induced shape memory behavior is observed by immersing this kind of SM-PVA in good or poor solvents (including water, DMF, and EG etc.) for PVA. A significant indication of shape memory is the decrease of the glass transition temperature (Tg), which is caused by PVA swelling in certain solvents. Differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), swelling equilibrium and bending tests are carried out to find the mechanism behind this interesting phenomenon. Factors that influence the permeation of solvents in the polymer depend on the rate and degree of swelling and whether swelling will occur, which determines the shape recovery ratio in different solvents. Water can induce shape recovery in a shorter time than organic solvents. The structure of water and PVA, and the interaction between them, contribute to the shorter recovery time. SM-PVA has an excellent shape recovery ratio even after several test cycles. Using solvents as a stimulus for shape memory behavior will extend applications of SMPs, especially in the field of medical devices, where stimulus instead of heat is highly desired.
Identification of genes up-regulated in dedifferentiating Nicotania glauca pith tissue, using an improved method for constructing a subtractive cDNA library (1993)

Pith explants of Nicotiana glauca grown in vitro in synthetic medium supplemented with 2,4 dichlorophenoxyacetic acid (2, 4 D), are induced to dedifferentiate. Treatment with actinomycin D within the first 4-8 h of culture (but not later) is lethal and the explants die, implying a requirement for de novo transcription. The genes expressed during the initial period of culture are presumably critical for subsequent cell survival and proliferation, but so far their identity is unknown. We have constructed a subtractive cDNA library, enriched in sequences more abundant in dedifferentiating tissue than in pith. The subtractive library contains approximately seven major species, two of which, NGSUB7 and NGSUB8, are highly abundant. In Northern blots, these two hybridized to mRNA species whose abundance increased significantly but transiently during the first 4 to 8 h of culture. The sequence of NGSUB7 showed no significant homology at a nucleotide or derived amino acid level with any previously reported sequence. NGSUB8 however, showed significant homology over part of the derived amino acid sequence to several yeast and bacterial proteins with DNA binding function. We propose that the two recombinants represent transcripts from two novel genes edeA and edeB, which are expressed early in dedifferentiation.