gebhart/patrepeval huggingface dataset:
Protein Dynamics in the Solid State from2H NMR Line Shape Analysis: A Consistent Perspective (2015)

Deuterium line shape analysis of CD3 groups has emerged as a particularly useful tool for studying microsecond-millisecond protein motions in the solid state. The models devised so far consist of several independently conceived simple jump-type motions. They are comprised of physical quantities encoded in their simplest form; improvements are only possible by adding yet another simple motion, thereby changing the model. The various treatments developed are case-specific; hence comparison among the different systems is not possible. Here we develop a new methodology for (2)H NMR line shape analysis free of these limitations. It is based on the microscopic-order-macroscopic-disorder (MOMD) approach. In MOMD motions are described by diffusion tensors, spatial restrictions by potentials/ordering tensors, and geometric features by relative tensor orientations. Jump-type motions are recovered in the limit of large orientational potentials. Model improvement is accomplished by monitoring the magnitude, symmetry, and orientation of the various tensors. The generality of MOMD makes possible comparison among different scenarios. CD3 line shapes from the Chicken Villin Headpiece Subdomain and the Streptomyces Subtilisin Inhibitor are used as experimental examples. All of these spectra are reproduced by using rhombic local potentials constrained for simplicity to be given by the L = 2 spherical harmonics, and by axial diffusion tensors. Potential strength and rhombicity are found to be ca. 2-3 k(B)T. The diffusion tensor is tilted at 120° from the C-CD3 axis. The perpendicular (parallel) correlation times for local motion are 0.1-1.0 ms (3.3-30 μs). Activation energies in the 1.1-8.0 kcal/mol range are estimated. Future prospects include extension to the (2)H relaxation limit, application to the (15)N and (13)C NMR nuclei, and accounting for collective motions and anisotropic media.
Eliminating antibody polyreactivity through addition of N‐linked glycosylation (2015)

Antibody polyreactivity can be an obstacle to translating a candidate antibody into a clinical product. Standard tests such as antibody binding to cardiolipin, HEp-2 cells, or nuclear antigens provide measures of polyreactivity, but its causes and the means to resolve are often unclear. Here we present a method for eliminating antibody polyreactivity through the computational design and genetic addition of N-linked glycosylation near known sites of polyreactivity. We used the HIV-1-neutralizing antibody, VRC07, as a test case, since efforts to increase VRC07 potency at three spatially distinct sites resulted in enhanced polyreactivity. The addition of N-linked glycans proximal to the polyreactivity-enhancing mutations at each of the spatially distinct sites resulted in reduced antibody polyreactivity as measured by (i) anti-cardiolipin ELISA, (ii) Luminex AtheNA Multi-Lyte ANA binding, and (iii) HEp-2 cell staining. The reduced polyreactivity trended with increased antibody concentration over time in mice, but not with improved overall protein stability as measured by differential scanning calorimetry. Moreover, glycan proximity to the site of polyreactivity appeared to be a critical factor. The results provide evidence that antibody polyreactivity can result from local, rather than global, features of an antibody and that addition of N-linked glycosylation can be an effective approach to reducing antibody polyreactivity.
Longitudinal imaging and deterioration in word comprehension in primary progressive aphasia: Potential clinical significance (2014)

Progressive atrophy in focal areas surrounding left temporal pole and left inferior temporal cortex, and right homologous area is closely related to progressive decline in auditory word comprehension. These correlations likely reflect areas that help support auditory word comprehension, effectively compensating for subtle deficits in some individuals early in the course of semantic variant PPA, as well as areas that are critical for auditory word comprehension that eventually atrophy in individuals with other variants of PPA. Individual patterns of atrophy also help us understand and predict the clinical course of individuals, such as associated behavioral or motor deficits.
Binary Image Algebra and Digital Optical Cellular Image Processors (1987)

Image processing and image analysis tasks have large data processing requirements and inherent parallelism and are well suited to implementation on digital optical processors because of the parallelism and free interconnection capabilities of optical systems [1][2]. Recently, several techniques for constructing optical cellular logic processors for image processing have been proposed [2]-[5]. Through parallel studies of architectures, algorithms, mathematical structures, and optics we have found that: 1) cellular automata are appropriate models for parallel image processing machines [6]; 2) an image algebra extending from mathematical morphology [7] [8] can lead to a formal parallel language approach to the design of image processing algorithms; 3) the algebraic structure serves as a framework for both algorithms and architectures of parallel image processing; and 4) optical computing techniques are able to efficiently implement image algebra based on cellular logic architectures (e.g. cellular array, cellular hypercube etc.). Here we will first discuss image algebra and then architectures for its implementation.
A physically-based human skin reflection model (2009)

A theoretical reflection model for human skin is presented. A layer of sebum has been included in the three-layer skin reflection model, since it is found over most parts of the body and contributes significantly to the specularity of human skin appearance. The Monte Carlo method is used to simulate the propagation of light in skin tissues. Optical and geometric properties are used as control parameters to influence the surface reflection and subsurface scattering of light within the sebum-covered skin layers. The bi-directional reflectance distribution function (BRDF) obtained from the simulation is used to render the appearance of human skin. Comparisons between the simulated BRDF results and experimental measurements show that the physical simulation is highly realistic.A theoretical reflection model for human skin is presented. A layer of sebum has been included in the three-layer skin reflection model, since it is found over most parts of the body and contributes significantly to the specularity of human skin appearance. The Monte Carlo method is used to simulate the propagation of light in skin tissues. Optical and geometric properties are used as control parameters to influence the surface reflection and subsurface scattering of light within the sebum-covered skin layers. The bi-directional reflectance distribution function (BRDF) obtained from the simulation is used to render the appearance of human skin. Comparisons between the simulated BRDF results and experimental measurements show that the physical simulation is highly realistic.
Benchmarking Machine Learning Technologies for Software Defect Detection (2015)

Machine Learning approaches are good in solving problems that have less information. In most cases, the software domain problems characterize as a process of learning that depend on the various circumstances and changes accordingly. A predictive model is constructed by using machine learning approaches and classified them into defective and non-defective modules. Machine learning techniques help developers to retrieve useful information after the classification and enable them to analyse data from different perspectives. Machine learning techniques are proven to be useful in terms of software bug prediction. This study used public available data sets of software modules and provides comparative performance analysis of different machine learning techniques for software bug prediction. Results showed most of the machine learning methods performed well on software bug datasets.
Matching colonic polyps from prone and supine CT colonography scans based on statistical curvature information (2008)

Computed tomographic colonography (CTC) provides a feasible way for the detection of colorectal polyps and cancer screening. In the clinical practice of CTC, a true colonic polyp will be confirmed with high confidence if a radiologist can find it in both the supine and prone scans. To assist radiologists in CTC reading, we propose a new colonic polyp matching method based on statistical curvature information of polyp candidates. We first extract histograms of curvature-related features (HCF) from each polyp candidate, then use diffusion map to embed the original high dimensional data into a low-dimensional space. Experimental results show that by using our HCF method, we can improve the sensitivity from 0.58 to 0.74 at false positive rate 0.1 compared with a traditional method that uses only means of curvature-related features.
Digital Hydraulic System Using Pumps and On/Off Valves Controlling the Actuator (2014)

Hydraulic systems employed in several industrial and mobile applications present significant advantages, such as a high power-to-weight ratio and fast dynamic response. However, these systems have low efficiency due to high power dissipation. A recent concept called “digital hydraulics” comprises particularities that create opportunities for a reduction in load loss. This paper proposes a configuration and control method for actuator speed control based on the principles of digital hydraulics. In this context, several fixed displacement units and on/off valves are connected directly to the actuators without throttling valves. The system studied here presents three operation methods (pump mode, motor mode and idle mode), which allows discrete valves to replace continuous or flow control valves in order to control the actuator. Furthermore, a fixed or variable displacement pump with large displacement is replaced by several small, fixed displacement units. Simulations are performed with a co-simulation technique using AMESim and MATLAB. The actuator speed, inlet and outlet pressures on the fixed displacement units and flow rate in the circuit lines are analysed. Preliminary simulation results exhibit smooth transitions between speed levels, adequate dynamic performance, low power dissipation and high energy-storage capacity. A specific limitation of this technology is the obtained actuator discrete speed. The main contributions of this research are the development of a digital hydraulic system configuration and its control strategy, which allows speed control of hydraulic actuators and provides the capacity to store energy.
IDNet: Framework de conexión P2P de bases de datos distribuidas e independientes (2018)

“IDNet” es un framework consistente en la creacion de una red de conexion Peer-to-Peer (P2P) para conectar bases de datos independientes y distribuidas, es decir, sin necesidad de discriminar la estructura interna de la misma y sin estar centralizadas las bases de datos.
El prototipo esta disenado con el objetivo de soportar la creacion de Organizaciones Virtuales, en las cuales los usuarios pueden obtener informacion de las bases de datos de sus vecinos, pudiendo realizar consultas a la base de datos vecina. La informacion sensible transmitida entre los vecinos se encuentra securizada mediante una capa de seguridad inherente al framework.
 La red P2P esta implementada mediante contenedores Docker en Cloud mediante el proveedor Amazon Web Services, aportandonos elasticidad y capacidad de respuesta a la misma.
Vehicle authentication scheme based on random permutation for VANET (2011)

Security is a key aspect in networks that circulate critical information. Vehicular Ad Hoc Network (VANET) is one such network where vehicles transmit and receive traffic information and emergency alerts. It is imperative to ensure only legitimate nodes join the network, since VANET thrives on authentic and accurate information. This paper proposes a vehicle authentication scheme based on weak encryption. Weak encryption in this context means encryption is not used as a means to realize confidentiality but to achieve a less obvious goal of authentication. We present the scheme in a detailed manner, followed by a brief discussion. Our future work includes simulation studies to estimate overheads and exploring possibilities of integrating our scheme with others.
Continuous coronary sinus and arterial pH monitoring during pacing-induced ischaemia in coronary artery disease. (1982)

Catheter tip pH electrodes were used for continuous recording of coronary sinus and arterial pH during atrial pacing in 20 patients undergoing coronary arteriography for chest pain. An ischaemic response to atrial pacing was identified by the onset of angina and/or electrocardiographic abnormalities. Technically satisfactory coronary sinus recordings were obtained in 18 patients. Mean coronary sinus pH at the peak pacing rate fell by 0.021 +/- 0.006 units (n = 9) in the ischaemic group, while there was no significant change in the non-ischaemic group. A larger fall in coronary sinus pH (-0.052 +/- 0.009) was found in the ischaemic group in the 30 seconds after the end of atrial pacing, the maximum change occurring after 16.1 +/- 1.5 seconds. A maximum fall of coronary sinus pH greater then 0.02 units identified patients with an ischaemic response. Changes in arterial pH did not account for these results. The sensitivity of coronary sinus pH recording for the detection of ischaemic heart disease is enhanced by sampling during the "washout" phase after the end of pacing.
DOTS: A Propagation Delay-Aware Opportunistic MAC Protocol for Mobile Underwater Networks (2014)

Mobile underwater networks with acoustic communications are confronted with several unique challenges such as long propagation delays, high transmission power consumption, and node mobility. In particular, slow signal propagation permits multiple packets to concurrently travel in the underwater channel, which must be exploited to improve the overall throughput. To this end, we propose the delay-aware opportunistic transmission scheduling (DOTS) protocol that uses passively obtained local information (i.e., neighboring nodes' propagation delay map and their expected transmission schedules) to increase the chances of concurrent transmissions while reducing the likelihood of collisions. Our extensive simulation results document that DOTS outperforms existing solutions and provides fair medium access even with node mobility.
Third A.S. Geyser Commemorative Lecture on 30 March 2017: Welcoming address by the moderator of the executive of the General Assembly of the Netherdutch Reformed Church of Africa (2017)

With the wisdom of hindsight, I briefly want to reflect on some events in the past. Of course, there are many good things to say about the past, but given that the lecture of Dr Wim Dreyer is about Albert Geyser, it is also necessary to reflect on some regrettable actions of the Hervormde Kerk [Netherdutch Reformed Church] in this regard. The Hervormde Kerk is the Church I have known from childhood and the Church I love dearly in spite of her shortcomings.
Distributed Riemannian Optimization with Lazy Communication for Collaborative Geometric Estimation (2022)

We present the first distributed optimization algorithm with lazy communication for collaborative geometric estimation, the backbone of modern collaborative simultaneous localization and mapping (SLAM) and structure-from-motion (SfM) applications. Our method allows agents to cooperatively reconstruct a shared geometric model on a central server by fusing individual observations, but without the need to transmit potentially sensitive information about the agents themselves (such as their locations). Furthermore, to alleviate the burden of communication during iterative optimization, we design a set of communication triggering conditions that enable agents to selectively upload a targeted subset of local information that is useful to global optimization. Our approach thus achieves significant communication reduction with minimal impact on optimization performance. As our main theoretical contribution, we prove that our method converges to first-order critical points with a global sublinear convergence rate. Numerical evaluations on bundle adjustment problems from collaborative SLAM and SfM datasets show that our method performs competitively against existing distributed techniques, while achieving up to 78% total communication reduction.
Susceptibility Testing of Common and Uncommon Aspergillus Species against Posaconazole and Other Mold-Active Antifungal Azoles Using the Sensititre Method (2017)

We tested 59 common and 27 uncommon <i>Aspergillus</i> species isolates for susceptibility to the mold-active azole antifungal agents itraconazole, voriconazole, and posaconazole using the Sensititre method. The overall essential agreement with the CLSI reference method was 96.5% for itraconazole and posaconazole and was 100% for voriconazole. By the Sensititre method as well as the CLSI reference method, all of 10 <i>A. fumigatus</i> isolates with a <i>cyp51</i> mutant genotype were classified as being non-wild-type isolates (MIC > epidemiological cutoff value [ECV]) with respect to triazole susceptibility.
Reflected scatterometry for noninvasive interrogation of bacterial colonies (2016)

A phenotyping of bacterial colonies on agar plates using forward-scattering diffraction-pattern analysis provided promising classification of several different bacteria such as Salmonella, Vibrio, Listeria, and E. coli. Since the technique is based on forward-scattering phenomena, light transmittance of both the colony and the medium is critical to ensure quality data. However, numerous microorganisms and their growth media allow only limited light penetration and render the forward-scattering measurement a challenging task. For example, yeast, Lactobacillus, mold, and several soil bacteria form colorful and dense colonies that obstruct most of the incoming light passing through them. Moreover, blood agar, which is widely utilized in the clinical field, completely blocks the incident coherent light source used in forward scatterometry. We present a newly designed reflection scatterometer and validation of the resolving power of the instrument. The reflectance-type instrument can acquire backward elastic scatter patterns for both highly opaque media and colonies and has been tested with three different bacterial genera grown on blood agar plates. Cross-validation results show a classification rate above 90% for four genera.
Reduced Depth and Visual Hulls of Complex 3D Scenes (2008)

Abstract Depth and visual hulls are useful for quick reconstruction and rendering of a 3D object based on a number of reference views. However, for many scenes, especially multi‐object, these hulls may contain significant artifacts known as phantom geometry. In depth hulls the phantom geometry appears behind the scene objects in regions occluded from all the reference views. In visual hulls the phantom geometry may also appear in front of the objects because there is not enough information to unambiguously imply the object positions. In this work we identify which parts of the depth and visual hull might constitute phantom geometry. We define the notion of reduced depth hull and reduced visual hull as the parts of the corresponding hull that are phantom‐free. We analyze the role of the depth information in identification of the phantom geometry. Based on this, we provide an algorithm for rendering the reduced depth hull at interactive frame‐rates and suggest an approach for rendering the reduced visual hull. The rendering algorithms take advantage of modern GPU programming techniques. Our techniques bypass explicit reconstruction of the hulls, rendering the reduced depth or visual hull directly from the reference views.
Agrobacterium-Mediated Maize Transformation: Immature Embryos Versus Callus (2009)

Transformation with Agrobacterium tumefaciens is the preferred method for delivery of transgenes into a wide range of plant species including maize. Optimized protocols for the Agrobacterium-mediated transformation of freshly isolated immature embryos and embryogenic Type I callus derived from plant seedlings are described. These protocols are suitable for the transformation of a wide variety of corn genotypes including commercial inbred lines. Agrobacterium harboring a binary vector containing the neomycin phosphotransferase (nptII) or the glyphosate resistant 5-enolpyruvylshikimate-3-phosphate (EPSPS) as selectable marker genes and also the green fluorescence protein gene (gfp) have been used. GFP is a visual screening marker which allows tracking of transformation during different selection and regeneration steps. The described protocols provide double digit transformation frequencies and can be routinely used for the production of a large numbers of transgenic plants.
The vibrational distribution of O2(X 3Σg−) produced in the photodissociation of ozone between 226 and 240 and at 266 nm (2000)

Resonance-enhanced multiphoton ionization coupled with time-of-flight product imaging has been used to study the O3(X 1A1)+hν→O(2p 3PJ)+O2(X 3Σg−) product channel in the UV (ultraviolet) photodissociation of ozone at photolysis wavelengths of 226, 230, 233, 234, 240, and 266 nm. These imaging experiments, together with a measurement of the branching ratio into the different spin orbit states of the O atom, allowed the determination of the yields of the O2 product in vibrational states greater than or equal to 26 as a function of wavelength. It was found that at 226, 230, 233, 234, and 240 nm, the yield was 11.8±1.9%, 11.5±1.2%, 8.2±2.0%, 4.7±1.8%, and 0.6±0.1%, respectively.
Civitas: The Smart City Middleware, from Sensors to Big Data (2013)

Software development for smart cities bring into light new concerns, such as how to deal with scalability, heterogeneity (sensors, actuators, high performance computing devices, etc.), geolocation information or privacy issues, among some. Traditional approaches to distributed systems fail to address these challenges, because they were mainly devoted to enterprise IT environments. This paper proposes a middleware framework, called Civitas, specially devoted to support the task of service development for the Smart City paradigm. This paper also analyzes the main drawbacks of traditional approaches to middleware service development and how these are overcome in the middleware framework proposed here.