gebhart/patrepeval huggingface dataset:
Edytorial: Wokół sporów o suwerenność (2016)

Kategoria suwerenności, pomimo bogatej tradycji, wydaje sie wciąz zagadnieniem na nowo odkrywanym. Wspolczesne wyzwania, z jakimi zmagają sie panstwa, zarowno w wymiarze miedzynarodowym, jak i wewnetrznym, prowadzą do przedefiniowania suwerenności. Na gruncie dyscyplin naukowych, w obrebie ktorych badana jest ta kategoria, rozwijane są interesujące koncepcje, ukazujące niekiedy zupelnie nowe spojrzenie na przedmiot opisywany od przynajmniej kilku stuleci. Pomimo takich nowatorskich ujec, kategoria suwerenności wciąz odnosi sie do stosunkow miedzy panstwami, do ustroju panstwowego, do zorganizowanych spoleczenstw, a niekiedy nawet do poszczegolnych osob. Wciąz warto tez analizowac kilkusetletni dorobek myśli nad suwerennością. Korzystając z niego mozna znaleźc wytlumaczenie takze niektorych aktualnych problemow związanych z rozumieniem suwerenności..,
Crystal Structure of Botulinum Neurotoxin Type G Light Chain:  Serotype Divergence in Substrate Recognition<sup>,</sup> (2005)

The seven serotypes (A-G) of botulinum neurotoxins (BoNTs) block neurotransmitter release through their specific proteolysis of one of the three proteins of the soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) complex. BoNTs have stringent substrate specificities that are unique for metalloprotease in that they require exceptionally long substrates (1). To understand the molecular reasons for the unique specificities of the BoNTs, we determined the crystal structure of the catalytic light chain (LC) of Clostridium botulinum neurotoxin type G (BoNT/G-LC) at 2.35 A resolution. The structure of BoNT/G-LC reveals a C-terminal beta-sheet that is critical for LC oligomerization and is unlike that seen in the other LC structures. Its structural comparison with thermolysin and the available pool of LC structures reveals important serotype differences that are likely to be involved in substrate recognition of the P1' residue. In addition, structural and sequence analyses have identified a potential exosite of BoNT/G-LC that recognizes a SNARE recognition motif of VAMP.
Reverse Two-hybrid Screening Identifies Residues of JNK Required for Interaction with the Kinase Interaction Motif of JNK-interacting Protein-1 (2004)

The development of specific inhibitors for the c-Jun N-terminal kinase (JNK) family of mitogen-activated protein kinases (MAPKs) has been a recent research focus because of the association of JNK with cell death in conditions such as stroke and neurodegeneration. We have demonstrated previously the presence of critical inhibitory residues within an 11-mer peptide (TI-JIP) based on the sequence of JNK-interacting protein-1 (JIP-1). However, the corresponding region of JNK bound by this JIP-1-based peptide was unknown. To identify this region, we used a novel reverse two-hybrid approach with TI-JIP as bait. We screened a library of JNK1 mutants that had been generated by random PCR mutagenesis and found three mutants of JNK1 that failed to interact with TI-JIP. The mutations in JNK1 were L131R, R309W, and Y320H. Of these mutated residues, Leu-131 and Tyr-320 were located on a common face of the JNK protein close to other residues implicated previously in the interactions of MAPKs with substrates, phosphatases, and scaffolds. To test whether these JNK1 mutants were thus affected in their regulation, we evaluated their activation in mammalian cells in response to hyperosmolarity or cotransfection with a constitutively active upstream kinase or their direct phosphorylation by either MAPK kinase (MKK)4 or MKK7. In each situation, all three JNK mutants were not activated or phosphorylated to the same level as wild-type JNK. Therefore, the results of our unbiased reverse two-hybrid screening approach have identified residues of JNK responsible for binding JIP-1-based peptides as well as MKK4 or MKK7.
Reconstruction of Software Component Architectures and Behaviour Models using Static and Dynamic Analysis (2010)

Model-based performance prediction systematically deals with the evaluation of software performance to avoid for example bottlenecks, estimate execution environment sizing, or identify scalability limitations for new usage scenarios. Such performance predictions require up-to-date software performance models. This book describes a new integrated reverse engineering approach for the reconstruction of parameterised software performance models (software component architecture and behaviour).
On the Relation Between Identifiability, Differential Privacy, and Mutual-Information Privacy (2016)

This paper investigates the relation between three different notions of privacy: identifiability, differential privacy, and mutual-information privacy. Under a unified privacydistortion framework, where the distortion is defined to be the expected Hamming distance between the input and output databases, we establish some fundamental connections between these three privacy notions. Given a maximum allowable distortion D, we define the privacy-distortion functions ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> * (D), ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> *(D), and ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> *(D) to be the smallest (most private/best) identifiability level, differential privacy level, and mutual information between the input and the output, respectively. We characterize ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> * (D) and ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> *(D), and prove that ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> * (D) - ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</sub> ≤ ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> *(D) ≤ ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> * (D) for D within certain range, where ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</sub> is a constant determined by the prior distribution of the original database X, and diminishes to zero when X is uniformly distributed. Furthermore, we show that ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> * (D) and ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> *(D) can be achieved by the same mechanism for D within certain range, i.e., there is a mechanism that simultaneously minimizes the identifiability level and achieves the best mutual-information privacy. Based on these two connections, we prove that this mutual-information optimal mechanism satisfies ∈-differential privacy with ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> *(D) ≤ ∈ ≤ ∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> *(D)+2∈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</sub> . The results in this paper reveal some consistency between two worst case notions of privacy, namely, identifiability and differential privacy, and an average notion of privacy, mutual-information privacy.
[Development and evaluation of a modified version of the dietary variety score for community-dwelling older adults]. (2022)

Objectives The dietary variety score (DVS) was developed as an index to assess the variety of food intake among older Japanese adults and has been widely used in epidemiological studies and public health settings. However, this index has not been reviewed since its development in the 1990s and may not adequately reflect the current dietary habits of the older Japanese population. In this study, we developed a modified version of the DVS (MDVS) and examined its validity.Methods We conducted a cross-sectional study of 357 community-dwelling adults aged ≥65 years (mean age: 76.2±4.6, men: 61.1%) who participated in the 2016 survey of the Hatoyama cohort study. The DVS and MDVS were assessed by the number of food groups eaten almost every day based on the weekly frequency of consumption. The DVS was calculated based on ten components: meat, fish/shellfish, eggs, milk, soybean products, green/yellow vegetables, potatoes, fruits, seaweed, and fats/oils. The components of the MDVS were determined by calculating the contribution of each food group to the total and nutrient intakes from the food groups comprising the main dish, side dish, and soup, based on the data from older adults aged ≥65 years who participated in the 2017 National Health and Nutrition Survey in Japan. Based on the contribution of each food group, we added "other vegetables" and "dairy products" in the MDVS. Dietary intake was assessed using a validated, self-administered diet history questionnaire. We calculated the probability of adequacy for each of the fourteen nutrients selected as per the estimated average requirement in the Dietary Reference Intake for Japanese 2020 and the mean probability of adequacy for all fourteen nutrients. In addition, we assessed the correlation between the DVS, MDVS, and each indicator and the significance of the difference between correlation coefficients.Results The MDVS was significantly positively correlated with the energy ratios of protein and fat, dietary fiber, potassium, and the modified diet score based on the Japanese Food Guide Spinning Top (r=0.21-0.45) and negatively correlated with the carbohydrate energy ratio (r=-0.32). The MDVS was also correlated with the mean probability of nutrient adequacy (r=0.41). The correlation coefficients between the MDVS and each indicator were not significantly different from those of the DVS.Conclusions Validity in terms of nutrient intake and diet quality was comparable between the DVS and MDVS. To revise the DVS, it is necessary to conduct nationwide studies based on highly accurate dietary surveys.
Contact interactions between epitheliocytes and fibroblasts: Formation of heterotypic cadherin-containing adhesion sites is accompanied by local cytoskeletal reorganization (2001)

Contact interactions between different cell types play a number of important roles in development, for example in cell sorting, tissue organization, and ordered migration of cells. The nature of such heterocellular interactions, in contrast to interactions between cells of the same type, remains largely unknown. In this report, we present experimental data examining the dynamics of heterocellular interactions between epitheliocytes and fibroblasts, which express different cadherin cell adhesion molecules and possess different actin cytoskeletal organizations. Our analysis revealed two striking features of heterocellular contact. First, the active free edge of an epitheliocyte reorganizes its actin cytoskeleton after making contact with a fibroblast. Upon contact with the leading edge of a fibroblast, epitheliocytes disassemble their marginal bundle of actin filaments and reassemble actin filaments into a geometric organization more typical of a fibroblast lamella. Second, epitheliocytes and fibroblasts form cell--cell adhesion structures that have an irregular organization and are associated with components of cell adhesion complexes. The structural organization of these adhesions is more closely related to the type of contacts formed between fibroblasts rather than to those between epitheliocytes. Heterotypic epithelio-fibroblastic contacts, like homotypic contacts between fibroblasts, are transient and do not lead to formation of stable contact interactions. We suggest that heterocellular contact interactions in culture may be regarded as models of how tissue systems consisting of epithelia and mesenchyme interact and become organized in vivo.
FPGA-based lossless compressors of floating-point data streams to enhance memory bandwidth (2010)

This paper presents an FPGA-based lossless compressor which directly compresses floating-point data streams to enhance the actual memory bandwidth of lattice Boltzmann method (LBM) accelerators. We show that the compression algorithms based on the 1D polynomial prediction are suitable for high-throughput hardware design. Moreover we show that integer operations provide comparable prediction performance to a floating-point predictor, while an integer predictor is expected to have smaller circuits than a floating-point one. We evaluate the compression ratio, the operating frequency and the resource consumption of the compressors with integer-based predictors through their prototype implementation using ALTERA Stratix III FPGA. We demonstrate that the implemented compressors dominate only 0.15 to 0.23 % of the entire logic resources and operate at 95 to 174 MHz to provide the compression ratio of up to 3.5, which means that we can enhance the memory bandwidth by a factor of 3.5 on average.
Structural conservation of druggable hot spots in protein–protein interfaces (2011)

Despite the growing number of examples of small-molecule inhibitors that disrupt protein-protein interactions (PPIs), the origin of druggability of such targets is poorly understood. To identify druggable sites in protein-protein interfaces we combine computational solvent mapping, which explores the protein surface using a variety of small "probe" molecules, with a conformer generator to account for side-chain flexibility. Applications to unliganded structures of 15 PPI target proteins show that the druggable sites comprise a cluster of binding hot spots, distinguishable from other regions of the protein due to their concave topology combined with a pattern of hydrophobic and polar functionality. This combination of properties confers on the hot spots a tendency to bind organic species possessing some polar groups decorating largely hydrophobic scaffolds. Thus, druggable sites at PPI are not simply sites that are complementary to particular organic functionality, but rather possess a general tendency to bind organic compounds with a variety of structures, including key side chains of the partner protein. Results also highlight the importance of conformational adaptivity at the binding site to allow the hot spots to expand to accommodate a ligand of drug-like dimensions. The critical components of this adaptivity are largely local, involving primarily low energy side-chain motions within 6 Å of a hot spot. The structural and physicochemical signature of druggable sites at PPI interfaces is sufficiently robust to be detectable from the structure of the unliganded protein, even when substantial conformational adaptation is required for optimal ligand binding.
Adaptive personalization of multimodal vehicular interfaces using a hybrid recommendation approach with fuzzy preferences (2008)

User-adaptive and situation-aware presentation of information on multimodal interfaces is an important research area for coping with the increasing information load on the driver. This paper describes a comprehensive recommendation approach for inferring vague individual preferences under uncertain conditions by using fuzzy preference relations. The approach was applied to rank internet information on a multimodal driver interface in the vehicle. New information gets successively downloaded to the car by using digital media broadcast and the driver can query information (e.g. press review, cheap petrol stations, snow reports) by using natural language queries. Incoming information elements are gradually matched to ontology categories by a fuzzy membership value based on term frequency. User perferences are learned from interaction and recommendations for content items is based on the resulting preference model. Three different types of fuzzy relations are aggregated to an overall preference score: explicit preferences, implicit preferences, and global preferences. The later influence preference values of one driver based on other drivers in vehicular ad-hoc networks. Therefore, the approach is not solely based on the presence of one kind of interaction data. Furthermore, the situation is modeled using the concept of granules and influences the overall preference score.
Mono-Vision Based Lateral Localization System of Low-Cost Autonomous Vehicles Using Deep Learning Curb Detection (2021)

The localization system of low-cost autonomous vehicles such as autonomous sweeper requires a highly lateral localization accuracy as the vehicle needs to keep a near lateral-distance between the side brush system and the road curb. Existing methods usually rely on a global navigation satellite system that often loses signal in a cluttered environment such as sweeping streets between high buildings and trees. In a GPS-denied environment, map-based methods are often used such as visual and LiDAR odometry systems. Apart from heavy computation costs from feature extractions, they are too expensive to meet the low-price market of the low-cost autonomous vehicles. To address these issues, we propose a mono-vision based lateral localization system of an autonomous sweeper. Our system relies on a fish-eye camera and precisely detects road curbs with a deep curb detection network. Curbs locations are then referred to as straightforward marks to control the lateral motion of the vehicle. With our self-recorded dataset, our curb detection network achieves 93% pixel-level precision. In addition, experiments are performed with an intelligent sweeper to prove the accuracy and robustness of our proposed approach. Results demonstrate that the average lateral distance error and the maximum invalid rate are within 0.035 m and 9.2%, respectively.
FIViz: Forensics Investigation through Visualization for Malware in Internet of Things (2020)

Adoption of the Internet of Things for the realization of smart cities in various domains has been pushed by the advancements in Information Communication and Technology. Transportation, power delivery, environmental monitoring, and medical applications are among the front runners when it comes to leveraging the benefits of IoT for improving services through modern decision support systems. Though with the enormous usage of the Internet of Medical Things, security and privacy become intrinsic issues, thus adversaries can exploit these devices or information on these devices for malicious intents. These devices generate and log large and complex raw data which are used by decision support systems to provide better care to patients. Investigation of these enormous and complicated data from a victim’s device is a daunting and time-consuming task for an investigator. Different feature-based frameworks have been proposed to resolve this problem to detect early and effectively the access logs to better assess the event. But the problem with the existing approaches is that it forces the investigator to manually comb through collected data which can contain a huge amount of irrelevant data. These data are provided normally in textual form to the investigators which are too time-consuming for the investigations even if they can utilize machine learning or natural language processing techniques. In this paper, we proposed a visualization-based approach to tackle the problem of investigating large and complex raw data sets from the Internet of Medical Things. Our contribution in this work is twofold. Firstly, we create a data set through a dynamic behavioral analysis of 400 malware samples. Secondly, the resultant and reduced data set were then visualized most feasibly. This is to investigate an incident easily. The experimental results show that an investigator can investigate large amounts of data in an easy and time-efficient manner through the effective use of visualization techniques.
<title>Optical fiber endface biosensor based on resonances in dielectric waveguide gratings</title> (2000)

A new fiber optic sensor integrating dielectric diffraction gratings and thin films on optical fiber endfaces is prosed for biomedical sensing applications. This device utilizes a resonant dielectric waveguide grating structure fabricated on an optical fiber endface to probe reactions occurring in a sensing layer deposited on its surface. The operation of this sensor is based upon a fundamental resonance effect that occurs in waveguide gratings. An incident broad- spectrum signal is guided within an optical fiber and is filtered to reflect or transmit a desired spectral band by the diffractive thin film structure on its endface. Slight changes in one or more parameters of the waveguide grating, such as refractive index or thickness, can result in a responsive shift of the reflected or transmitted spectral peak that can be detected with spectroscopic instruments. This new sensor concept combines improved sensitivity and accuracy with attractive features found separately in currently available fiber optic sensors, such as large dynamic range, small sensing proximity, real time operation, and remote sensing. Diffractive elements of this type consisting of a photoresist grating on a Si<SUB>3</SUB>N<SUB>4</SUB> waveguide have been fabricated on multimode optical fiber endfaces with 100 micrometers cores. Preliminary experimental tests using a tunable Ti:sapphire laser indicate notches of 18 percent in the transmission spectrum of the fiber endface guided-mode resonance devices. A theoretical analysis of the device performance capabilities is presented and applied to evaluate the feasibility and potential advantages of this bioprobe.
Semiporous MoS2 obtained by the decomposition of thiomolybdate precursors (1998)

The decomposition of three different ammonium thiomolybdates (NH4)2MoS4xH2O, (NH4)2Mo2S12xH2O, and (NH4)2Mo3S13xH2O (x=1–2) have been studied by TG–DSC under argon. While all three thiomolybdates decompose at around 673 K to yield nearly X-ray amorphous MoS2 , the precursor (NH4)2Mo3S13xH2O does so in a manner distinct from the other two precursors displaying a sharp exothermic peak in the DSC trace. We suggest that the unusual thermal behaviour of (NH4)2Mo3S13xH2O might arise from a topochemical relation between the molecular cluster and 2H-MoS2 as proposed previously. The porosity of the X-ray amorphous MoS2 obtained from the decomposition under vacuum of (NH4)2Mo3S13xH2O is unusually large and the material displays interesting sorption behaviour towards small organic molecules. This X-ray amorphous semiporous modification of MoS2 has been characterized in detail by powder X-ray diffraction, high resolution electron microscopy and from its extended X-ray absorption fine structure. An unusual feature of this material is the presence of bent, open-ended lamellae of MoS2 , contrasting fullerene-like MoS2 which forms closed shells.