gebhart/patrepeval huggingface dataset:
Partial volume correction in arterial spin labeling perfusion MRI: A method to disentangle anatomy from physiology or an analysis step too far? (2021)

The mismatch in the spatial resolution of Arterial Spin Labeling (ASL) MRI perfusion images and the anatomy of functionally distinct tissues in the brain leads to a partial volume effect (PVE), which in turn confounds the estimation of perfusion into a specific tissue of interest such as gray or white matter. This confound occurs because the image voxels contain a mixture of tissues with disparate perfusion properties, leading to estimated perfusion values that reflect primarily the volume proportions of tissues in the voxel rather than the perfusion of any particular tissue of interest within that volume. It is already recognized that PVE influences studies of brain perfusion, and that its effect might be even more evident in studies where changes in perfusion are co-incident with alterations in brain structure, such as studies involving a comparison between an atrophic patient population vs control subjects, or studies comparing subjects over a wide range of ages. However, the application of PVE correction (PVEc) is currently limited and the employed methodologies remain inconsistent. In this article, we outline the influence of PVE in ASL measurements of perfusion, explain the main principles of PVEc, and provide a critique of the current state of the art for the use of such methods. Furthermore, we examine the current use of PVEc in perfusion studies and whether there is evidence to support its wider adoption. We conclude that there is sound theoretical motivation for the use of PVEc alongside conventional, 'uncorrected', images, and encourage such combined reporting. Methods for PVEc are now available within standard neuroimaging toolboxes, which makes our recommendation straightforward to implement. However, there is still more work to be done to establish the value of PVEc as well as the efficacy and robustness of existing PVEc methods.
Mousse (2020)

Selective symbolic execution (SSE) is a powerful program analysis technique for exploring multiple execution paths of a program. However, it faces a challenge in analyzing programs with environments that cannot be modeled nor virtualized. Examples include OS services managing I/O devices, software frameworks for accelerators, and specialized applications. We introduce Mousse, a system for analyzing such programs using SSE. Mousse uses novel solutions to overcome the above challenge. These include a novel process-level SSE design, environment-aware concurrent execution, and distributed execution of program paths. We use Mousse to comprehensively analyze five OS services in three smartphones. We perform bug and vulnerability detection, taint analysis, and performance profiling. Our evaluation shows that Mousse outperforms alternative solutions in terms of performance and coverage.
Data Information Fusion From Multiple Access Points for WiFi-Based Self-localization (2018)

In this letter, we propose a novel approach for fusing information from multiple access points in order to enhance WiFi-based self-localization. A common approach for designing WiFi-based localization systems is to learn location-to-signal strength mappings for each access point in an environment. Each mapping is then used to compute the likelihood of the robot's location conditioned on sensed signal strength data, yielding as many likelihood functions as mappings are available. Office buildings typically have from several tens to a few hundreds of access points, making it essential to properly combine all available likelihoods into a single, coherent, joint likelihood that yields precise likelihoods, yet is not overconfident. While most research has focused on techniques for learning these mappings and improving data acquisition; research on techniques to adequately fuse them has been neglected. Our approach for data information fusion is based on information theory and yields considerably better joint distributions than previous approaches. Furthermore, through extensive testing, we show that these joint likelihoods considerably increase the system's localization performance.
Demonstration of Both Mode and Space Diversity in a 100-Gbit/s QPSK Free-Space Optical Link to Increase System Tolerance to Turbulence (2019)

We experimentally demonstrate the use of mode and space diversity with 2 modes and 2 aperture pairs to enhance system reliability under turbulence for a 100-Gbit/s QPSK FSO link, achieving BERs of <3.8× 10−3 under various emulated turbulence realizations.
Milk protein‐derived opioid receptor ligands (1997)

Milk is a mammalian characteristic and is of particular importance for humans: Mother's milk or its substitutes from cows' milk are absolutely essential nutriments for the neonate and cows' milk also represents a basic foodstuff for adults. However, in addition to their well-known nutritive role, milk constituents apparently are also able to carry specific information from the milk producer's to the milk receiver's organism: Thus, a number of milk protein fragments has been shown to behave like opioid receptor ligands able to address opioidergic systems in the adult's or in the neonate's organism. With respect to the proteins, which they are derived off, these peptides have been named α-casein exorphins or casoxin D (α-casein), β-casomorphins or β-casorphin (β-casein), casoxin or casoxin A, B, or C (κ-casein), α-lactorphins (α-lactalbumin), β-lactorphin (β-lactoglobulin) or lactoferroxins (lactoferrin). Only casoxins and lactoferroxins display antagonistic properties; the other peptides behave like opioid receptor agonists. Most of the information available so far has been collected about β-casomorphins. These peptides obviously can be released from β-casein in the adult's or in the neonate's organism, where they might elicit opioid effects in the frame of a regulatory role as “food hormones”. Several synthetic β-casomorphin derivatives have been shown to be highly specific and potent μ-type opioid receptor ligands which frequently have been used as standard tools in opioid research. © 1997 John Wiley & Sons, Inc. Biopoly 43: 99–117, 1997
Analysis of Water and Solute Transport Away from a Surface Point Source (1995)

Abstract Mathematical theories describing the movement of water and solute away from sources of limited spatial extent mostly assume some form of three‐dimensional flow domain, but few have been rigorously tested, mainly because of the lack of experimental data. The objectives of this study were to obtain water flow and solute transport measurements during three‐dimensional, axially symmetric water flow, using time domain reflectometry (TDR), and to test some of the existing theories of three‐dimensional flow and transport using the measured data. A sandy soil was packed into a Plexiglas box fitted with curved TDR probes at different radial distances from one corner. A constant flux of water was applied at the corner of the box, and a pulse of KCl added as a tracer. Measurements of volumetric water content, θ, and resident solute concentration, C R , as a function of time and radial distance were made along four flowlines. The utility of a quasilinear solution was evaluated by comparing measured and predicted profiles of θ at steady state, and the distribution of solute travel times along various transects. Along the various streamlines, nonlinear least‐squares analysis of measured solute travel times ( t *) produced estimates of the slope (α) of the exponential hydraulic conductivity function that were comparable to independently determined values. Estimation of α from t * along a single flowline, using a quasilinear solution, offers potential for field application. This technique could be used as a first step in the investigation of contaminant migration from point sources, or used in trickle‐irrigation design.
Orbit determination of geosynchronous satellites by VLBI and differential VLBI (1982)

Four approaches to radio interferometric tracking of geosynchronous satellites are analyzed and compared. Quasar-based differential very-long-baseline interferometry, which requires a very sensitive receiver, can achieve meter-level position accuracy with a two-baseline system. Satellite-based differential VLBI gives somewhat lower accuracy with a compact, inexpensive receiver. Nondifferential VLBI, using less precise media and clock calibrations obtained by observing the GPS satellites, still gives 5-10 m position accuracy with two baselines. For a sufficiently inclined orbit, all interferometric approaches can yield six-component satellite state from a single baseline.
Cells activated for wound repair have the potential to direct collective invasion of an epithelium (2015)

Mechanisms regulating how groups of cells are signaled to move collectively from their original site and invade surrounding matrix are poorly understood. Here we develop a clinically relevant ex vivo injury invasion model to determine whether cells involved in directing wound healing have invasive function and whether they can act as leader cells to direct movement of a wounded epithelium through a three-dimensional (3D) extracellular matrix (ECM) environment. Similar to cancer invasion, we found that the injured cells invade into the ECM as cords, involving heterotypical cell-cell interactions. Mesenchymal cells with properties of activated repair cells that typically locate to a wound edge are present in leader positions at the front of ZO-1-rich invading cords of cells, where they extend vimentin intermediate filament-enriched protrusions into the 3D ECM. Injury-induced invasion depends on both vimentin cytoskeletal function and MMP-2/9 matrix remodeling, because inhibiting either of these suppressed invasion. Potential push and pull forces at the tips of the invading cords were revealed by time-lapse imaging, which showed cells actively extending and retracting protrusions into the ECM. This 3D injury invasion model can be used to investigate mechanisms of leader cell-directed invasion and understand how mechanisms of wound healing are hijacked to cause disease.
Towards visualising early-stage osteonecrosis using intraoperative imaging modalities (2022)

Osteonecrosis of the Femoral Head (ONFH) is a progressive disease characterized by the death of bone cells due to the loss of blood supply. Early detection and treatment of this disease are vital in avoiding Total Hip Replacement. Early stages of ONFH can be diagnosed using Magnetic Resonance Imaging (MRI), commonly used intra-operative imaging modalities such as fluoroscopy frequently fail to depict the lesion. Therefore, increasing the difficulty of intra-operative localization of osteonecrosis. This work introduces a novel framework that enables the localization of necrotic lesions in Computed Tomography (CT) as a step toward localizing and visualizing necrotic lesions in intra-operative images. The proposed framework uses Deep Learning algorithms to enable automatic segmentation of femur, pelvis, and necrotic lesions in MRI. An additional step performs semi-automatic segmentation of these anatomies, excluding the necrotic lesions, in CT. A final step performs pairwise registration of the corresponding anatomies, allowing for the localization and visualization of the necrosis in CT. To investigate the feasibility of integrating the proposed framework in the surgical workflow, we conducted experiments on MRIs and CTs containing early-stage ONFH. Our results indicate that the proposed framework is able to segment the anatomical structures of interest and accurately register the femurs and pelvis of the corresponding volumes, allowing for the visualization and localization of the ONFH in CT and generated X-rays, which could enable intra-operative visualization of the necrotic lesions for surgical procedures such as core decompression of the femur.
Data from <i>In Vivo</i> Quantification of Hypoxic and Metabolic Status of NSCLC Tumors Using [<sup>18</sup>F]HX4 and [<sup>18</sup>F]FDG-PET/CT Imaging (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Increased tumor metabolism and hypoxia are related to poor prognosis in solid tumors, including non–small cell lung cancer (NSCLC). PET imaging is a noninvasive technique that is frequently used to visualize and quantify tumor metabolism and hypoxia. The aim of this study was to perform an extensive comparison of tumor metabolism using 2[&lt;sup&gt;18&lt;/sup&gt;F]fluoro-2-deoxy-d-glucose (FDG)-PET and hypoxia using HX4-PET imaging.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; FDG- and HX4-PET/CT images of 25 patients with NSCLC were coregistered. At a global tumor level, HX4 and FDG parameters were extracted from the gross tumor volume (GTV). The HX4 high-fraction (HX4-HF) and HX4 high-volume (HX4-HV) were defined using a tumor-to-blood ratio &gt; 1.4. For FDG high-fraction (FDG-HF) and FDG high-volume (FDG-HV), a standardized uptake value (SUV) &gt; 50% of SUV&lt;sub&gt;max&lt;/sub&gt; was used. We evaluated the spatial correlation between HX4 and FDG uptake within the tumor, to quantify the (mis)match between volumes with a high FDG and high HX4 uptake.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; At a tumor level, significant correlations were observed between FDG and HX4 parameters. For the primary GTV, the HX4-HF was three times smaller compared with the FDG-HF. In 53% of the primary lesions, less than 1 cm&lt;sup&gt;3&lt;/sup&gt; of the HX4-HV was outside the FDG–HV; for 37%, this volume was 1.9 to 12 cm&lt;sup&gt;3&lt;/sup&gt;. Remarkably, a distinct uptake pattern was observed in 11%, with large hypoxic volumes localized outside the FDG-HV.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Hypoxic tumor volumes are smaller than metabolic active volumes. Approximately half of the lesions showed a good spatial correlation between the PET tracers. In the other cases, a (partial) mismatch was observed. The addition of HX4-PET imaging has the potential to individualize patient treatment. &lt;i&gt;Clin Cancer Res; 20(24); 6389–97. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Tenascin-C knockout mouse has no detectable tenascin-C protein (1997)

A recent study by Mitrovic and Schachner (J Neurosci Res 42:710-717, 1995) reported the detection of a small amount of truncated tensacin-C (TN-C) in the nervous system of the TN-C knockout mice created by Saga et al. (Genes Dev 6:1821-1831, 1992). The authors suggested that the truncated protein might be responsible for the failure to detect any phenotypic abnormalities in the knockout mice. We have reexamined the knockout mice in our laboratories by Western blot and immunocytochemistry, and have not detected any full-length or truncated TN-C protein. In addition, we note that the construction of the knockout gene deleted the signal sequence, so if any residual truncated protein were produced it would be trapped in the cytoplasm, and therefore inaccessible to extracellular ligands or receptors. We therefore conclude that the TN-C knockout created by Saga et al. is a valid TN-C null.
MediSyn (2003)

Currently, Internet hosting centers and content distribution networks leverage statistical multiplexing to meet the performance requirements of a number of competing hosted network services. Developing efficient resource allocation mechanisms for such services requires an understanding of both the short-term and long-term behavior of client access patterns to these competing services. At the same time, streaming media services are becoming increasingly popular, presenting new challenges for designers of shared hosting services. These new challenges result from fundamentally new characteristics of streaming media relative to traditional web objects, principally different client access patterns and significantly larger computational and bandwidth overhead associated with a streaming request. To understand the characteristics of these new workloads we use two long-term traces of streaming media services to develop MediSyn, a publicly available streaming media workload generator. In summary, this paper makes the following contributions: i) we model the long-term behavior of network services capturing the process of file introduction and changing file popularity, ii) we present a novel generalized Zipf-like distribution that captures recently-observed popularity of both web objects and streaming media not captured by existing Zipf-like distributions, and iii) we capture a number of characteristics unique to streaming media services, including file duration, encoding bit rate, session duration and non-stationary popularity of media accesses.
How to find the sensitivity limit for DNA sequencing based on laser-induced fluorescence (1993)

The sensitivity limit for one-lane DNA sequencing based on laser-induced fluorescence is derived by statistical means. A closed-form expression for the sequencing error probability as a function of the signal strength and of the differences in the fluorescence properties of the labels is given. Fluctuations of the signal caused by photodestruction of the molecules cannot be neglected. The expected sequencing error probability is expressed in terms of the number of molecules and the physical parameters of the measurement. This equation can be used in many ways to design and optimize sequencing experiments.
Reconstructing while registering: a novel approach for markerless augmented reality (2003)

This paper addresses the registration problem for unprepared multi-planar scenes. An interactive process is proposed to obtain accurate results using only the texture information of planes. In particular, classical preparation steps (camera calibration, scene acquisition) are greatly simplified, since they are included in the on-line registration process. Results are shown on indoor and outdoor scenes. Videos are available at url http://www.loria.fr//spl tilde/gsimon/Ismar.
Wave tracing: Ray tracing for the propagation of band-limited signals: Part 2 — Applications (2008)

Abstract Modeling seismic propagation is critically important to our work; unfortunately, we often must trade simulation accuracy for reduced computational expense. We present a new seismic-modeling method that is as simple and computationally efficient as Snell's law ray tracing but provides propagation paths and arrival times more consistent with finite-bandwidth data. We refer to this modeling method as wave tracing and apply it to nonlinear traveltime tomography and depth imaging. By replacing Snell's law ray tracing with wave tracing, we get better ray coverage, more robust and faster ray bending (fewer iterations), and a much more robust and faster algorithm for nonlinear tomography (fewer iterations, too). A very significant benefit is increased stability and robustness of tomographic inversion with respect to small changes in model parameterization and regularization. A related benefit is the increased stability of depth images with respect to small changes in velocity, which can increase confidence in interpretation. The velocity models that result from wave tracing match picked arrival times in band-limited data better and generate improved depth images. These advantages of wave tracing relative to conventional Snell's law ray tracing have been tested on both synthetic and real data examples for crosswell seismic geometry.
Lack of strong immune selection pressure by the immunodominant, HLA-A*0201-restricted cytotoxic T lymphocyte response in chronic human immunodeficiency virus-1 infection. (1998)

Despite detailed analysis of the HIV-1-specific cytotoxic T lymphocyte response by various groups, its relation to viral load and viral sequence variation remains controversial. We analyzed HLA-A*0201 restricted cytotoxic T lymphocyte responses in 17 HIV-1-infected individuals with viral loads ranging from < 400 to 221,000 HIV RNA molecules per milliliter of plasma. In 13 out of 17 infected subjects, CTL responses against the SLYNTVATL epitope (p17 Gag; aa 77-85) were detectable, whereas two other HLA-A*0201 restricted epitopes (ILKEPVHGV, IV9; and VIYQYMDDL, VL9) were only recognized by six and five individuals out of 17 individuals tested, respectively. Naturally occurring variants of the SL9 epitope were tested for binding to HLA-A*0201 and for recognition by specific T cell clones generated from five individuals. Although these variants were widely recognized, they differed by up to 10,000-fold in terms of variant peptide concentrations required for lysis of target cells. A comparison of viral sequences derived from 10 HLA-A*0201-positive individuals to sequences obtained from 11 HLA-A*0201-negative individuals demonstrated only weak evidence for immune selective pressure and thus question the in vivo efficacy of immunodominant CTL responses present during chronic HIV-1 infection.
Improved Processing of Titanium Alloys by Metal Injection Moulding (2011)

The commercially pure (CP-Ti) and Ti6Al4V (Ti-64) powders with powder size of sub 45-micron were mixed with a water soluble binder consisting of a major fraction of Polyethylene Glycol (PEG), a minor fraction of Polymethylmethacrylate (PMMA) and some stearic acid as surfactant. The pelletised mix was injection-moulded into standard tensile bar specimens and then subjected solvent debinding by water leaching and thermal debinding in an argon atmosphere. The titanium compacts were then subjected to sintering studies using the Taguchi method. The results of the oxygen impurity levels of the sintered parts are presented in this paper. Titanium parts conforming to Grade 2 requirements were achieved for CP-Ti whilst those conforming to Grade 5 were achieved for Ti-64.
Tunable Dual Semiconductor Laser (1987)

Parallel lasers interact in shared space to alter output wavelength. New device consists of two stripe lasers in aluminum gallium arsenide chip. Parallel stripes close enough so light from lower laser coupled into upper laser and vice versa. Lasers operated by low-duty-cycle current pulses. Lasing threshold of each about 100 mA. Currents controlled independently. Useful in optical communications systems employing wavelength-division multiplexing.
Mitral Ring Motion in Assessment of Left Ventricular Function (1998)

The motion of the mitral ring was studied with M-mode echocardiography using the apical four- and two-chamber views.With the purpose of obtaining adequate reference materials for mitral ring motion ...
Unsupervised Particle Picking and Clustering in Cryo-EM Micrographs (2023)

Journal Article Unsupervised Particle Picking and Clustering in Cryo-EM Micrographs Get access Alireza Nasiri, Alireza Nasiri Simons Machine Learning Center, New York Structural Biology Center, New York, NY, United States Search for other works by this author on: Oxford Academic Google Scholar Darnell Granberry, Darnell Granberry Simons Machine Learning Center, New York Structural Biology Center, New York, NY, United States Search for other works by this author on: Oxford Academic Google Scholar Tristan Bepler Tristan Bepler Simons Machine Learning Center, New York Structural Biology Center, New York, NY, United States Corresponding author: tbepler@nysbc.org Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Pages 965–966, https://doi.org/10.1093/micmic/ozad067.482 Published: 22 July 2023