gebhart/patrepeval huggingface dataset:
Isosurface extraction techniques for Web-based volume visualization (1999)

The reconstruction of isosurfaces from scalar volume data has positioned itself as a fundamental visualization technique in many different applications. But the dramatically increasing size of volumetric data sets often prohibits the handling of these models on affordable low-end single processor architectures. Distributed client-server systems integrating high-bandwidth transmission channels and Web-based visualization tools are one alternative to attack this particular problem, but therefore new approaches to reduce the load of numerical processing and the number of generated primitives are required. In this paper we outline different scenarios for distributed isosurface reconstruction from large-scale volumetric data sets. We demonstrate how to directly generate stripped surface representations and we introduce adaptive and hierarchical concepts to minimize the number of vertices that have to be reconstructed, transmitted and rendered. Furthermore, we propose a novel computation scheme, which allows the user to flexibly exploit locally available resources. The proposed algorithms have been merged together in order to build a platform-independent Web-based application. Extensive use of VRML and Java OpenGL-bindings allows for the exploration of large-scale volume data quite efficiently.
Direct volume visualization of three-dimensional vector fields (1992)

Article Direct volume visualization of three-dimensional vector fields Share on Authors: Roger Crawfis View Profile , Nelson Max View Profile Authors Info & Claims VVS '92: Proceedings of the 1992 workshop on Volume visualizationDecember 1992 Pages 55–60https://doi.org/10.1145/147130.147150Online:01 December 1992Publication History 46citation555DownloadsMetricsTotal Citations46Total Downloads555Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Algorithmic Geometry (1998)

The design and analysis of geometric algorithms have seen remarkable growth in recent years, due to their application in, for example, computer vision, graphics, medical imaging and CAD. The goals of this book are twofold: first to provide a coherent and systematic treatment of the foundations; secondly to present algorithmic solutions that are amenable to rigorous analysis and are efficient in practical situations. When possible, the algorithms are presented in their most general d-dimensional setting. Specific developments are given for the 2- or 3-dimensional cases when this results in significant improvements. The presentation is confined to Euclidean affine geometry, though the authors indicate whenever the treatment can be extended to curves and surfaces. The prerequisites for using the book are few, which will make it ideal for teaching advanced undergraduate or beginning graduate courses in computational geometry.
Soft tissue grafts for dural reconstruction after meningioma surgery (2019)

The meninges are involved in various pathologies and are often directly or indirectly severed during surgical procedures, especially the dura mater. This can pose a real challenge for the surgeon, as a proper reconstruction of the meninges is important to prevent complications such as cerebrospinal fluid leak (CSF). A variety of techniques for dural reconstruction have been described, employing natural and artificial materials. A novel technique for dural reconstruction involves soft tissue grafts in the form of fibrous or fibromuscular flaps, which are placed on the dural defects to seal the gaps. These soft tissue grafts represent an appropriate scaffold for cell ingrowth and fibrosis, thus preventing CSF. In this pilot study, we described the application of soft tissue grafts for dural reconstruction in 10 patients who underwent convexity meningioma surgery.
Characterization of patients referred for non‐specific intellectual disability testing: the importance of autosomal genes for diagnosis (2015)

Genetic testing for non-specific intellectual disability (ID) presents challenges in daily clinical practice. Historically, the focus of the genetic elucidation of non-specific ID has been on genes on the X chromosome, and recent research has brought attention to the growing contribution of autosomal genes. In addition, next-generation sequencing (NGS) has greatly improved the ability to simultaneously analyze multiple genetic loci, making large panel testing a practical approach to testing for non-specific ID. We performed NGS analysis of a total of 90 genes implicated in non-specific ID. The 90 genes included 56 X-linked genes and 34 autosomal genes. Pathogenic variants were identified in 11 of 52 (21%) patient samples. Nine of the eleven cases harbored mutations in autosomal genes including AP4B1, STXB1, SYNGAP1, TCF4 and UBE3A. Our mutation-positive cases provide further evidence supporting the prevalence of autosomal mutations in patients referred for non-specific ID testing and the utility of their inclusion in multi-gene panel analysis.
An auditory model based on the analysis of envelope patterns (2002)

An auditory model incorporating critical band filtering, short time adaptation, and temporal analysis of the auditory nerve responses is presented. Unlike previously proposed synchrony models, this model emphasizes the instantaneous amplitude (i.e. the envelope) of the neural responses rather than the instantaneous frequency as the carrier of perceptually relevant information. It is demonstrated how the auditory speech representation can be used for voiced/unvoiced classification, pitch extraction, phonetic segmentation, and classification of continuous speech.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Metabolic and hepatic effects of liraglutide, obeticholic acid and elafibranor in diet-induced obese mouse models of biopsy-confirmed nonalcoholic steatohepatitis (2018)

DIO-NASH and <i>ob/ob</i>-NASH mouse models show distinct treatment effects of liraglutide, OCA, and elafibranor, being in general agreement with corresponding findings in clinical trials for NASH. The present data therefore further supports the clinical translatability and utility of DIO-NASH and <i>ob/ob</i>-NASH mouse models of NASH for probing the therapeutic efficacy of compounds in preclinical drug development for NASH.
Carbon-Based Solid-State Calcium Ion-Selective Microelectrode and Scanning Electrochemical Microscopy: A Quantitative Study of pH-Dependent Release of Calcium Ions from Bioactive Glass (2016)

Solid-state ion-selective electrodes are used as scanning electrochemical microscope (SECM) probes because of their inherent fast response time and ease of miniaturization. In this study, we report the development of a solid-state, low-poly(vinyl chloride), carbon-based calcium ion-selective microelectrode (Ca(2+)-ISME), 25 μm in diameter, capable of performing an amperometric approach curve and serving as a potentiometric sensor. The Ca(2+)-ISME has a broad linear response range of 5 μM to 200 mM with a near Nernstian slope of 28 mV/log[a(Ca(2+))]. The calculated detection limit for Ca(2+)-ISME is 1 μM. The selectivity coefficients of this Ca(2+)-ISME are log K(Ca(2+),A) = -5.88, -5.54, and -6.31 for Mg(2+), Na(+), and K(+), respectively. We used this new type of Ca(2+)-ISME as an SECM probe to quantitatively map the chemical microenvironment produced by a model substrate, bioactive glass (BAG). In acidic conditions (pH 4.5), BAG was found to increase the calcium ion concentration from 0.7 mM ([Ca(2+)] in artificial saliva) to 1.4 mM at 20 μm above the surface. In addition, a solid-state dual SECM pH probe was used to correlate the release of calcium ions with the change in local pH. Three-dimensional pH and calcium ion distribution mapping were also obtained by using these solid-state probes. The quantitative mapping of pH and Ca(2+) above the BAG elucidates the effectiveness of BAG in neutralizing and releasing calcium ions in acidic conditions.
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling (2011)

Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model.
A transformative route to nanoporous manganese oxides of controlled oxidation states with identical textural properties (2014)

Controlled thermal conversion of Mn-based metal–organic frameworks yielded a series of nanoporous manganese oxides with continuously tuned oxidation states.
MicroRNA167-Directed Regulation of the Auxin Response Factors <i>GmARF8a</i> and <i>GmARF8b</i> Is Required for Soybean Nodulation and Lateral Root Development (2015)

Legume root nodules convert atmospheric nitrogen gas into ammonium through symbiosis with a prokaryotic microsymbiont broadly called rhizobia. Auxin signaling is required for determinant nodule development; however, the molecular mechanism of auxin-mediated nodule formation remains largely unknown. Here, we show in soybean (Glycine max) that the microRNA miR167 acts as a positive regulator of lateral root organs, namely nodules and lateral roots. miR167c expression was up-regulated in the vasculature, pericycle, and cortex of soybean roots following inoculation with Bradyrhizobium japonicum strain USDA110 (the microsymbiont). It was found to positively regulate nodule numbers directly by repressing the target genes GmARF8a and GmARF8b (homologous genes of Arabidopsis [Arabidopsis thaliana] AtARF8 that encode auxin response factors). Moreover, the expression of miR167 and its targets was up- and down-regulated by auxin, respectively. The miR167-GmARF8 module also positively regulated nodulation efficiency under low microsymbiont density, a condition often associated with environmental stress. The regulatory role of miR167 on nodule initiation was dependent on the Nod factor receptor GmNFR1α, and it acts upstream of the nodulation-associated genes nodule inception, nodulation signaling pathway1, early nodulin40-1, NF-YA1 (previously known as HAEM activator protein2-1), and NF-YA2. miR167 also promoted lateral root numbers. Collectively, our findings establish a key role for the miR167-GmARF8 module in auxin-mediated nodule and lateral root formation in soybean.
Effect of Acute Lung Injury on Structure and Function of Pulmonary Surfactant Films (2003)

The structural and functional alterations in pulmonary surfactant that occur during acute lung injury were studied using rat lung surfactant large aggregates (LA) isolated from normal nonventilated lungs (N), and from standard ventilated (V) and injuriously ventilated (IV) excised lungs. N lungs inflated significantly better than IV lungs, with V lungs intermediate. Although IV LA phosphatidylcholine levels were unchanged, cholesterol and protein were elevated. V LA exhibited PC/cholesterol and PC/protein ratios intermediate between N and IV. In contrast to total cholesterol and protein levels, these ratios were not significantly different from IV LA. N and V LA, but not IV LA, adsorbed rapidly and were able to generate surface pressures (pi) near 70 mN/m during surface area reduction at 37 degrees C on a captive bubble tensiometer. Langmuir-Wilhelmy surface balance studies at 23 degrees C showed N LA films consistently attained pi approaching 70 mN/m during ten compression-expansion cycles. IV films were less effective and failed to achieve high pi consistently after the sixth cycle. V films were intermediate. Epifluorescence studies revealed compression of adsorbed N LA films formed well-defined liquid-condensed (LC) domains, but fewer, smaller domains were observed with IV films and, to a lesser extent, V films. Atomic force microscopy on Langmuir-Blodgett N films transferred at pi = 30 mN/m showed high, well-defined LC domains. IV films showed thinner, intermediate height, possibly fluid domains, which contain large numbers of small higher domains with heights corresponding to LC domains. V films were intermediate. We conclude that acute lung injury induced by hyperventilation, and to a lesser extent standard ventilation, of excised lungs alters surfactant surface activity and the ability of natural surfactant to form surface structures at the air-water interface.
Spectrum access system for the citizen broadband radio service (2015)

As a part of the global effort to address the overwhelming demand for wireless broadband capacity, the wireless communities in the United States have undertaken innovative initiatives such as tiered-access to shared spectrum. The Federal Communications Commission has proposed a dynamic spectrum management framework for a Citizen Broadband Radio Service (CBRS) governed by a spectrum access system (SAS). The implementation of a SAS capable of dynamic frequency assignment and interference management is critical for the success of the proposed framework. In this paper we present the efforts toward a spectrum sharing system in the U.S. context by summarizing different interest groups' standpoint on the FCC proposed framework. We also present an example SAS architecture that accommodates the tiered access to shared spectrum and example approaches to achieve important SAS capabilities.
Improving cache utilisation (2021)

Microprocessors have long employed caches to help hide the increasing latency of accessing main memory. The vast majority of previous research has focussed on increasing cache hit rates to improve cache performance, while lately decreasing power consumption has become an equally important issue. This thesis examines the lifetime of cache lines in the memory hierarchy, considering whether they are live (will be referenced again before eviction) or dead (will not be referenced again before eviction). Using these two states, the cache utilisation (proportion of the cache which will be referenced again) can be calculated. This thesis demonstrates that cache utilisation is relatively poor over a wide range of benchmarks and cache configurations. By focussing on techniques to improve cache utilisation, cache hit rates are increased while overall power consumption may also be decreased. Key to improving cache utilisation is an accurate predictor of the state of a cache line. This thesis presents a variety of such predictors, mostly based upon the mature field of branch prediction, and compares them against previously proposed predictors. The most appropriate predictors are then demonstrated in two applications: Improving victim cache performance through filtering, and reducing cache pollution during aggressive prefetching These applications are primarily concerned with improving cache performance and are analysed using a detailed microprocessor simulator. Related applications, including decreasing power consumption, are also discussed, as are the applicability of these techniques to multiprogrammed and multiprocessor systems.
Accuracy of volume measurement by conductance catheter in isolated, ejecting canine hearts. (1985)

We evaluated the accuracy of the recently reported technique of estimating intraventricular volume by measurement of intracavitary electrical conductance in six isolated, ejecting, canine left ventricles. Left ventricular volumes were measured directly by a previously validated servosystem that employed an electroconductive balloon placed in the left ventricular cavity. The volume measured continuously by the balloon method (Vbal) was compared with that estimated by the conductance method (Vcath). For this test, the hearts were made to eject and fill physiologically by the use of a previously described computer-simulated arterial loading system. Complex ejection and filling patterns were created by stimulating the atrium mechanically, which resulted in irregular arrhythmatic contractions spanning a wide range of volumes. We found that there was a highly linear relationship (r2 = .982 +/- .014) between Vbal and Vcath: Vcath = 0.82 (+/- .05) Vbal + 26.7 (+/- 11.8) ml. Despite the wide variation in the offset term of this relationship among the different hearts, the offset within a given heart was predicted within 3.5 ml by a previously detailed "dilution" method that is applicable to the heart in situ within a closed thorax. Thus, since the offset term is obtainable in situ, the conductance method provides a signal that is proportional to the actual volume. To determine whether right ventricular volume influenced the accuracy of left ventricular measurement, we compared the relationship between Vcath and Vbal obtained with right ventricular volumes of 0 and 30 ml. Increasing the right ventricular volume shifted the relationship upward by less than 3 ml in the working range.(ABSTRACT TRUNCATED AT 250 WORDS)
TRK1 encodes a plasma membrane protein required for high-affinity potassium transport in Saccharomyces cerevisiae. (1988)

We identified a 180-kilodalton plasma membrane protein in Saccharomyces cerevisiae required for high-affinity transport (uptake) of potassium. The gene that encodes this putative potassium transporter (TRK1) was cloned by its ability to relieve the potassium transport defect in trk1 cells. TRK1 encodes a protein 1,235 amino acids long that contains 12 potential membrane-spanning domains. Our results demonstrate the physical and functional independence of the yeast potassium and proton transport systems. TRK1 is nonessential in S. cerevisiae and maps to a locus unlinked to PMA1, the gene that encodes the plasma membrane ATPase. Haploid cells that contain a null allele of TRK1 (trk1 delta) rely on a low-affinity transporter for potassium uptake and, under certain conditions, exhibit energy-dependent loss of potassium, directly exposing the activity of a transporter responsible for the efflux of this ion.
Computed Masks in Coronary Subtraction Imaging (1987)

In this paper we propose a method to overcome the effects of cardiac and respiratory motion in coronary subtraction imaging. We present the ideas of retrospective gating of masks, where both cardiac and respiratory phases are measured for a set of masks, and are subsequently used in a functional decomposition of motion. Through retrospective gating of masks, we are able to select appropriate images and to perform temporal and spatial processing on them to produce computed masks, subtraction of which should lead to motion-artifact-free images. The computed masks are built from two components: the first includes the time-variant structures related to respiration, such as ribs and soft tissues of the chest wall, and the second incorporates the time-variant structures related to cardiac motion. A preliminary study of the method in the area of digital subtraction angiography produced images which are comparable to but not better than those produced by techniques in current clinical practice: we discuss the reasons for this.
An Integrated Approach to Maneuver-Based Trajectory Prediction and Criticality Assessment in Arbitrary Road Environments (2016)

This paper describes an integrated Bayesian approach to maneuver-based trajectory prediction and criticality assessment that is not limited to specific driving situations. First, a distribution of high-level driving maneuvers is inferred for each vehicle in the traffic scene via Bayesian inference. For this purpose, the domain is modeled in a Bayesian network with both causal and diagnostic evidences and an additional trash maneuver class, which allows the detection of irrational driving behavior and the seamless application from highly structured to nonstructured environments. Subsequently, maneuver-based probabilistic trajectory prediction models are employed to predict each vehicle's configuration forward in time. Random elements in the designed models consider the uncertainty within the future driving maneuver execution of human drivers. Finally, the criticality time metric time-to-critical-collision-probability (TTCCP) is introduced and estimated via Monte Carlo simulations. The TTCCP is a generalization of the time-to-collision (TTC) in arbitrary uncertain multiobject driving environments and valid for longer prediction horizons. All uncertain predictions of all maneuvers of every vehicle are taken into account. Additionally, the criticality assessment considers arbitrarily shaped static environments, and it is shown how parametric free space (PFS) maps can advantageously be utilized for this purpose.
Automated Femtoliter Droplet-Based Determination of Oil–Water Partition Coefficient (2019)

The oil-water partition coefficient of organic compounds is an essential parameter for the determination of their behaviors in environments, food, drug delivery, and biomedical systems, just to name a few. In this work, we establish a highly efficient approach to quantify the partition/distribution coefficient using surface femtoliter droplets. In our approach, droplets of 1-octanol were produced on the surface of a solid substrate in contact with the flow of an aqueous solution of the analyte. The analyte was rapidly enriched in the droplets from the flow and reached the partition equilibrium in a few seconds. The entire procedure was automated by continuous solvent exchange, and the analyte partition in the droplets was quantified from the in situ UV-vis spectrum collected by a microspectrophotometer. Our approach was validated for several substances with the octanol-water partition/distribution coefficient ranging from -1.5 to 4, where our results were in good agreement with the values reported in the literature. This method took ∼3 min to detect one analyte with the volume of the organic solvent at ∼50 μL. Thus, our surface droplet platform can greatly minimize the consumption of both solvent and analytes and can shorten the time for the determination of the partition of new compounds, which overcomes the drawbacks of the traditional shake-flask method and presents excellent reproducibility, high accuracy, cost-effectiveness, and labor-saving operation. The highly efficient micro/nanoextraction, partition, and real-time detection enabled by the surface droplets has the potential for many other high-throughput applications.