gebhart/patrepeval huggingface dataset:
More applications of Euler rotation angles (1999)

Discusses various uses of rotation matrices. The author has used rotation matrices to find the patterns with elements in a conformal array that requires one to rotate not only the direction, but the polarization directions, as well. A second useful thing to do with rotation matrices is to analytically rotate objects in space. In computer graphics, it may be neccessary to rotate the object. Many computer graphics texts have useful discussions of object rotations using rotation matrices. A third related use of rotation matrices is to understand antenna positioners. One can describe the rotations of a positioner by rotation matrices, and calculate the effects of rotation not only on the directing of the antenna, but on the polarization directions, as well.
Inflammation and oxygen free radical formation during pulmonary ischemia-reperfusion injury (1992)

In a companion study, we showed that 2 h of warm unilateral lung ischemia followed by reperfusion resulted in bilateral tissue injury, indicated by increases in extravascular density (EVD) and permeability, measured as the pulmonary transcapillary escape rate (PTCER) for radiolabeled transferrin. EVD and PTCER measurements were obtained with the quantitative imaging technique of positron emission tomography (PET). In the current study, we evaluated this increase in EVD histologically and correlated EVD and PTCER with measurements of oxidant-reactive sulfhydryls (RSH) in plasma as a marker of oxygen free radical (OFR) formation. Histologically edema, leukocyte infiltration, and hemorrhage were all present on the ischemic side, but only after reperfusion, whereas only neutrophil infiltration was observed on the nonischemic side. Histology scores correlated with EVD (r = 0.81) and PTCER (r = 0.75), but permeability was abnormal at times even in the absence of neutrophil infiltration. Plasma RSH concentration from the ischemic lung decreased significantly (P less than 0.05) during pulmonary ischemia (i.e., before reperfusion) and returned to baseline on reperfusion. The degree of RSH oxidation did not correlate with the severity of injury as measured by PET or histology. Thus pulmonary ischemia-reperfusion injury is characterized by inflammation, hemorrhage, edema, and OFR formation. Injury occurred after reperfusion, not after ischemia alone. In addition, injury to the contralateral nonischemic lung suggests a neutrophil-independent circulating mediator of injury.
Graded Smad2/3 Activation Is Converted Directly into Levels of Target Gene Expression in Embryonic Stem Cells (2009)

The Transforming Growth Factor (TGF) beta signalling family includes morphogens, such as Nodal and Activin, with important functions in vertebrate development. The concentration of the morphogen is critical for fate decisions in the responding cells. Smad2 and Smad3 are effectors of the Nodal/Activin branch of TGFbeta signalling: they are activated by receptors, enter the nucleus and directly transcribe target genes. However, there have been no studies correlating levels of Smad2/3 activation with expression patterns of endogenous target genes in a developmental context over time. We used mouse Embryonic Stem (ES) cells to create a system whereby levels of activated Smad2/3 can be manipulated by an inducible constitutively active receptor (Alk4*) and an inhibitor (SB-431542) that blocks specifically Smad2/3 activation. The transcriptional responses were analysed by microarrays at different time points during activation and repression. We identified several genes that follow faithfully and reproducibly the Smad2/3 activation profile. Twenty-seven of these were novel and expressed in the early embryo downstream of Smad2/3 signalling. As they responded to Smad2/3 activation in the absence of protein synthesis, they were considered direct. These immediate responsive genes included negative intracellular feedback factors, like SnoN and I-Smad7, which inhibit the transcriptional activity of Smad2/3. However, their activation did not lead to subsequent repression of target genes over time, suggesting that this type of feedback is inefficient in ES cells or it is counteracted by mechanisms such as ubiquitin-mediated degradation by Arkadia. Here we present an ES cell system along with a database containing the expression profile of thousands of genes downstream of Smad2/3 activation patterns, in the presence or absence of protein synthesis. Furthermore, we identify primary target genes that follow proportionately and with high sensitivity changes in Smad2/3 levels over 15-30 hours. The above system and resource provide tools to study morphogen function in development.
Lupus prone (SWR x NZB)F1 mice produce potentially nephritogenic autoantibodies inherited from the normal SWR parent. (1985)

The incidence of nephritis in autoimmune NZB mice is low, but when they are crossed with normal SWR mice, almost 100% of the female F1 hybrids (SNF1) develop lethal glomerulonephritis. To define the contribution of the normal SWR strain to the development of nephritis, we analyzed 65 monoclonal anti-DNA autoantibodies derived from SNF1 mice and compared them with those obtained from the NZB parent. The majority of the SNF1-derived anti-DNA antibodies were IgG and cationic in charge. By contrast, 77% of the NZB-derived antibodies were IgM. Moreover, all three NZB-derived IgG anti-DNA antibodies were anionic. The cationic property of the SNF1-derived IgG autoantibodies was not restricted to any particular antigenic specificity pattern or IgG subclass, nor was there a preference for the allotype of either parent. However, we identified a set of highly cationic (pI at 8.2 to 8.8 pH) IgG2b anti-DNA antibodies from SNF1 hybrids that had the SWR allotype. Isoelectric focusing of intact antibodies and isolated heavy and light chains showed that the highly cationic charge of these antibodies was determined by the variable regions of their heavy chains. Because IgG anti-DNA antibodies with cationic charge are especially pathogenic, those antibodies bearing the allotype of the normal SWR parent may account for the high incidence of severe nephritis in the F1 hybrids. The results indicate that pathogenic autoantibodies, which are encoded by genes of the nonautoimmune SWR parent, are expressed in the SNF1 mice due to some cellular and genetic regulatory influence of the NZB parent.
featureCounts: an efficient general-purpose read summarization program (2013)

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (this http URL) or Rsubread (this http URL) software packages.
A Machine Learning Approach for Locating Acoustic Emission (2010)

This paper reports on the feasibility of locating microcracks using multiple-sensor measurements of the acoustic emissions (AEs) generated by crack inception and propagation. Microcrack localization has obvious application in non-destructive structural health monitoring. Experimental data was obtained by inducing the cracks in rock specimens during a surface instability test, which simulates failure near a free surface such as a tunnel wall. Results are presented on the pair-wise event correlation of the AE waveforms, and these characteristics are used for hierarchical clustering of AEs. By averaging the AE events within each cluster, "super" AEs with higher signal to noise ratio (SNR) are obtained and used in the second step of the analysis for calculating the time of arrival information for localization. Several feature extraction methods, including wavelet packets, autoregressive (AR) parameters, and discrete Fourier transform coefficients, were employed and compared to identify crucial patterns related to P-waves in time and frequency domains. By using the extracted features, an SVM classifier fused with probabilistic output is used to recognize the P-wave arrivals in the presence of noise. Results show that the approach has the capability of identifying the location of AE in noisy environments.
Mortality in Coronary Drug Project Patients During a Nine-Year Posttreatment Period (1985)

JCRP was the first, and remains the only, professional journal dedicated to improving multidisciplinary clinical practice and expanding research evidence specific to both cardiovascular and pulmonary rehabilitation. This includes exercise testing and prescription, behavioral medicine, and cardiopulmonary risk factor management. In 2007, JCRP expanded its scope to include primary prevention of cardiovascular and pulmonary diseases. JCRP publishes scientific and clinical peer-reviewed Original Investigations, Reviews, and Brief or Case Reports focused on the causes, prevention, and treatment of individuals with cardiovascular or pulmonary diseases in both a print and online-only format. Editorial features include Editorials, Invited Commentaries, Literature Updates, and Clinically-relevant Topical Updates. JCRP is the official Journal of the American Association of Cardiovascular and Pulmonary Rehabilitation and the Canadian Association of Cardiac Rehabilitation.
Adaptive quantization by soft thresholding in HEVC (2015)

The High Efficiency Video Coding (HEVC) reference encoder includes a Uniform Reconstruction Quantization (URQ) method. This block level quantization technique does not take into account the importance of transform coefficients in terms of signal reconstruction. In this paper, we present a transform coefficient level quantization technique based on a soft thresholding approach, in which the quantization parameter (QP) of a transform coefficient is altered according to its importance in the signal reconstruction process and according to the overall energy of the corresponding Transform Block (TB). The proposed method attains important coding efficiency performance gains as measured by the Bjøntegaard Delta Bitrate metric (BD-Rate). In comparison with reference encoder HM 16, our technique produces both luma and chroma BD-Rate improvements in all JCT-VC test sequences, particularly for sequences in Class E using the Low Delay B and Low Delay P configurations, with BD-Rate reductions of up to 5.5% (Y), 13.2% (Cb) and 11.7% (Cr).
Metatool 5.0: fast and flexible elementary modes analysis (2006)

The script files and compiled shared libraries can be downloaded from the Metatool website at http://pinguin.biologie.uni-jena.de/bioinformatik/networks/index.html. Metatool consists of script files (m-files) for GNU octave as well as Matlab and shared libraries. The scripts are licensed under the GNU Public License and the use of the shared libraries is free for academic users and testing purposes. Commercial use of Metatool requires a special contract.
Huh-7 or HepG2 cells: which is the better model for studying human apolipoprotein-B100 assembly and secretion? (2010)

Apolipoprotein-B100 (apoB100) is the essential protein for the assembly and secretion of very low density lipoproteins (VLDL) from liver. The hepatoma HepG2 cell line has been the cell line of choice for the study of synthesis and secretion of human apoB-100. Despite the general use of HepG2 cells to study apoB100 metabolism, they secrete relatively dense, lipid-poor particles compared with VLDL secreted in vivo. Recently, Huh-7 cells were adopted as an alternative model to HepG2 cells, with the implicit assumption that Huh-7 cells were superior in some respects of lipoprotein metabolism, including VLDL secretion. In this study we addressed the hypothesis that the spectrum of apoB100 lipoprotein particles secreted by Huh-7 cells more closely resembles the native state in human liver. We find that Huh-7 cells resemble HepG2 cells in the effects of exogenous lipids, microsomal triglyceride transfer protein (MTP)-inhibition, and proteasome inhibitors of apoB100 secretion, recovery, and degradation. In contrast to HepG2 cells, however, MEK-ERK inhibition does not correct the defect in VLDL secretion. Huh-7 cells do not appear to offer any advantages over HepG2 cells as a general model of human apoB100-lipoprotein metabolism.
Non-rigid surface shape registration to monitor change in back surface topography. (2010)

Measured back surface topographies can be useful to monitor the external manifestation of scoliosis to avoid exposure to large doses of radiation. Manual shape fitting of back surface topographies from successive clinical visits can then be used to detect differences. Automated matching of the measured topographies has been seen as a possible improvement on manual comparisons. Recognizing that two changed surface cannot be expected to be simple rigid replicas of each other, the goal of this research has been to develop a new algorithm based on a non-rigid surface matching algorithm, suited to matching the surfaces into same reference frame while also estimating the parameters of the scoliosis deformities, and eliminating noise due to normal body change caused by growth. Back surface topography data from laser optical scanning have been automatically matched by a least squares non-rigid matching algorithm. The algorithm includes new parameters able to model shape changes caused by normal growth and scoliosis deformation. This non-rigid matching algorithm returned r.m.s. values for surface closeness which were improved by at least 10% over rigid matching. Experiments on various scoliosis data demonstrate that the non-rigid matching algorithm is able to accurately match the surfaces while simultaneously extracting parameters representing patient shape change. The non-rigid algorithm has proven to be an improvement on the classical rigid surface matching approach which allows positional fit rather than shape fit. Measured back surface topographies can be closely matched to monitor the external manifestation of scoliosis.
The Year in Scotland Activities of the Scottish Division (1980)

There are 352 College members north of the Border, a number close to the ideal village community—too small for impersonality, too large for boredom—and the activities of the Scottish Division are in consequence lively. About 50 members managed to attend each quarterly meeting during the 1979/80 season, with attendance rising to around 100 at our annual dinner in December.
Pseudoranges Error Correction in Partial GPS Outages for a Nonlinear Tightly Coupled Integrated System (2013)

Integrated navigation systems based on a tightly coupled integration scheme utilize pseudoranges and pseudorange rates from Global Positioning System (GPS) satellites measured by the receiver. The positioning accuracy is highly dependent on the accuracy of the pseudoranges whose residual errors can deteriorate the overall positioning accuracy. The integrated system can be improved by the provision of more accurate pseudoranges through modeling the residual correlated errors. This paper utilizes parallel cascade identification (PCI), which is a nonlinear system identification technique, to model these correlated errors. To address the nonlinear error characteristics in the whole integrated navigation system, a nonlinear filter, i.e., mixture particle filter (M-PF), is employed to perform tightly coupled integration of a 3-D reduced inertial sensor system (RISS) with a GPS. The M-PF can accommodate the PCI models of the pseudorange errors in the measurement model. The results demonstrate the advantages of using M-PF-PCI for correcting the pseudoranges and enhancing the positioning solution as compared with M-PF-only, Kalman filter (KF)-PCI, and KF-only solutions.
Prospective use of DNA microarrays for evaluating renal function and disease (2000)

At the forefront of the revolution in human genomics is DNA microarray technology, which evaluates expression levels or genotypes of thousands of genes simultaneously, by means of miniaturization and parallel processing. Furthermore, advances in bioinformatics will result in the creation of large databases, which will require complex software programming for structural analysis. Over the next decade, DNA microarrays, combined with sophisticated informatics and genomic databases, will provide molecular fingerprints of disease processes and prognoses. This review provides an update on DNA microarray technology and its application to renal diseases.
Capacity of human subjects to utilize keto analogues of valine and phenylalanine (1971)

Three adult human subjects were maintained for 7 days (period I) on a protein-free formula diet containing the minimum daily requirements of the eight essential amino acids plus 40 g glycine. During the last 5 days of this period, the average daily nitrogen balances for the three subjects were +0.52, +0.71, and +0.30 g, respectively. During the next 7 days (period II), valine was withdrawn from the diet, and the glycine ration increased by an equimolar amount. During the last 5 days of period II, average daily nitrogen balances declined to -1.82, -1.61, and -1.87 g, respectively. In the final period of 7 days (period III), the keto analogue of valine, alpha-ketoisovaleric acid, was added to the diet in a quantity equimolar to the minimum daily requirement of valine. During the last 5 days of this period, average daily nitrogen balances improved to -0.02, -0.18, and -0.83 g, respectively. Analogous experiments in three subjects involved the withdrawal from the diet of phenylalanine (period II) and replacement by its keto analogue, phenylpyruvic acid (period III). The average daily nitrogen balances were as follows: period I: +1.04, +0.96, and +0.53 g; period II: -1.45, -1.83, and -1.94 g; period III: +0.07, +0.11, and -0.52 g. The data demonstrate that man can convert alpha-ketoisovaleric acid and phenylpyruvic acid to the corresponding essential amino acids, valine and phenylalanine. The efficiency of these conversions is considerably less than 100%.
<title>FUSE attitude control: target recognition and fine guidance performance</title> (2000)

The FUSE satellite employs innovative techniques for autonomous target acquisitions and fine pointing control. One of two Fine Error Sensors, incorporated in the optical path of the science instrument, provide the Instrument Data System computer with images, for target identification, and field star centroids, for fine pointing information to the spacecraft attitude control system. A suite of 'toolbox' functions has been developed to locate stars, selected and track on 'unknown' guide stars from the image, identify the star field, track preselected 'known' guide stars, follow moving targets, and provide pointing optimizations to fine- tune the centering of a target. After a maneuver to a new field, initial attitude is determined by identifying stars found in a 20' X 20' image. Identification is done by matching stars with an uploaded table of up to 200 objects selected from the Hubble Space Telescope (HST) Guide Star Catalog (GSC), ranging from V equals 9 to 13.5 mag., and typically covering a one degree field around the target. During identification, tracking is performed on unidentified stars in the image to prevent the satellite from drifting. A corrective slew is then commanded to place the target at the desired position. Tracking is then resumed on preselected guide stars. If desired, further fine alignment of the science apertures is performed by a target peakup using the FUV detectors. We discuss the target acquisition process; end-to- end performance; and problems encountered due to the limitations of the small field of view of the FES, HST GSC errors, and stray light in the telescope baffles.
Structural curvature versus amplitude curvature (2013)

Because they are second-order derivatives, seismic curvature attributes can enhance subtle information that may be difficult to see using first-order derivatives such as the dip magnitude and the dip-azimuth attributes. As a result, these attributes form an integral part of most seismic interpretation projects. This conventional computation of curvature may be termed as structural curvature, as lateral second-order derivatives of the structural component of seismic time or depth of reflection events are used to generate them. In this study, we explore the case of applying lateral second-order derivatives on the amplitudes of seismic data along the reflectors. We refer to such computation as amplitude curvature. For volumetric structural curvature we compute first derivatives in the inline and crossline components of structural dip. For amplitude curvature, we apply a similar computation to the inline and crossline components of the energy-weighted amplitude gradients, which represent the directional measures of amplitude variability. Because of limits to lateral resolution, application of amplitude curvature computation to real seismic data results in greater lateral resolution than structural curvature. The images are mathematically independent of each other and thus highlight different features in the subsurface, but are often correlated through the underlying geology.
Geometric constraint solver using multivariate rational spline functions (2001)

We present a new approach to building a solver for a set of geometric constraints represented by multivariate rational functions. The constraints are formulated using inequalities as well as equalities. When the solution set has dimension larger than zero, we approximate it by fitting a hypersurface to discrete solution points. We also consider a variety of constraint solving problems common in geometric modeling. These include computing ray-traps, bisectors, sweep envelopes, and regions accessible during 5-axis machining.
The change of spherical aberration during accommodation and its effect on the accommodation response (2010)

Theoretical and ray-tracing calculations on an accommodative eye model based on published anatomical data, together with wave-front experimental results on 15 eyes, are computed to study the change of spherical aberration during accommodation and its influence on the accommodation response. The three methodologies show that primary spherical aberration should decrease during accommodation, while secondary spherical aberration should increase. The hyperbolic shape of the lens' surfaces is the main factor responsible for the change of those aberrations during accommodation. Assuming that the eye accommodated to optimize image quality by minimizing the RMS of the wave front, it is shown that primary spherical aberration decreases the accommodation response, while secondary spherical aberration slightly increases it. The total effect of the spherical aberration is a reduction of around 1/7 D per diopter of stimulus approximation, although that value depends on the pupil size and its reduction during accommodation. The apparent accommodation error (lead and lag), typically present in the accommodation/response curve, could then be explained as a consequence of the strategy used by the visual system, and the apparatus of measurement, to select the best image plane that can be affected by the change of the spherical aberration during accommodation.