gebhart/patrepeval huggingface dataset:
Detection of Coronaviruses in Bats in Lebanon during 2020 (2023)

Bats are considered the main reservoir of coronaviruses (CoVs), and research evidence suggests the essential role of bats in the emergence of Severe Acute Respiratory Syndrome Coronaviruses (SARS-CoV) and SARS-CoV-2. SARS-CoV-like viruses have been recently detected in bats in different countries. In 2020, we conducted surveillance for CoVs among six different bat species in Lebanon. Of 622 swab specimens taken, 77 tested positive. Alpha- and Beta- CoVs were identified in samples collected from different species. Our results show that SARS-like coronaviruses circulate in bats in this region, and we provide new data on their genetic diversity. The interaction between the spike of the detected SARS-CoV-like viruses and the human angiotensin-converting enzyme 2 (hACE2) receptor could be crucial in understanding the origin of the epidemic. The 3D protein structure analysis revealed that the receptor-binding domains of the SARS-like virus identified in Lebanon bind to the hACE2 protein more efficiently than to the spike of the SARS-CoV-2 strain. The spike of the detected SARS-CoV-like viruses does not contain the recognition site of furin at the cleavage site. Thus, our study highlights the variety of bat coronaviruses in Lebanon and suggests the zoonotic potential for other SARS-CoV-like viruses.
Development of a QA phantom and protocol for proton magnetic resonance spectroscopy (2009)

Abstract The purpose of this study was to develop a special proton magnetic resonance spectroscopy (1H‐MRS) phantom, to establish and verify a quality assurance (QA) protocol, and to perform QA for a MR system. For a complete QA protocol, seven principal quality factors (PQFs) were measured. For evaluation of localization and quantification accuracy, two PQFs which are difficult to measure in commercial phantoms, we developed the layered dumbbell‐shaped phantom. The performance sensitivity of our phantom was determined as a function of the voxel size on three occasions over ∼1 year. All MRS QA factors were optimized on two different MRI/MRS systems. The correlation between the metabolite signal intensity and the metabolite concentration was verified. The seven principal MRS QA factors studied can be used to evaluate MR spectra as well as to measure the stability of MR systems. © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 35B: 168–179, 2009
Functional and biochemical characterization of osteoclast-like cells derived from giant cell tumours of bone. (1992)

Cells harvested from human giant cell tumours of bone were characterized on the basis of morphological features, proliferative capacity, total(AP) and tartrate resistant acid phosphatase (TRAP) activity, and hormonal response. Culture were formed by mononucleated and multinucleated cells. Mononucleated cells showed fibroblastic morphology, whereas multinucleated cells showed osteoclastic phenotype. We conclude that in these cultures mature osteoclasts and their mononuclear precursors are present.
Integrating field and numerical modeling methods for applied urban karst hydrogeology (2009)

Abstract. Infrastructures that are constructed on unstable geologic formations are prone to subsidence. Data have been collected in the context of an upgrading project for a highway located beside a river dam that was constructed on gypsum-containing formations. Surface water infiltrates upstream of the dam, circulates through the gravel deposits and into the weathered bedrock around and beneath the dam, and exfiltrates downstream into the river. As a result, an extended weathering zone within the bedrock and preferential flow paths within voids and conduits developed as part of a rapidly evolving karst system. These processes enhance karstification in the soluble units of the gypsum-containing formations and resulted in the subsidence of the dam and the highway. Since 2006 changes in the hydrogeologic flow regime have been investigated continuously by different methods that also allow the evaluation of the long-term performance of the infrastructures. Geological (outcrops, lithostratigraphic information of boreholes), hydrometrical (extensive groundwater monitoring, dye tracer tests) and hydrogeophysical (Electrical Resistivity Tomography, ERT) field data of varying quality were integrated into high-resolution 3-D hydrogeological and 2-D karst evolution models. The applied investigative methods are validated and the sensitivity of relevant parameters governing the processes determined. It could be demonstrated that the applied methods for karst aquifer characterization complement each other and allow the interpretation of short-term impacts and long-term development on system-dynamics in the context of hydrogeologic flow regimes of karst areas. This includes the description of the transient character of the hydrogeologic flow regime during and after episodic flood events (surface-groundwater interaction, conduit and diffuse model outflow) as well as the evaluation of time scales for karst evolution. Results allow the optimization of investigative methods for similar subsidence problems, leading from general measurements and monitoring technologies to tools with predictive character.
Maximum likelihood reconstruction of attenuation and activity (MLAA) based extended mu-maps for dynamic and gated MR-PET (2013)

97 Objectives Truncation of the arms has been observed in the mu-maps generated by MR/CT, especially for large patients. These truncated mu-maps can cause local artifacts in reconstructed PET images. To reduce the local artifacts, we use the MLAA algorithm to estimate the missing regions of the mu-maps using the untruncated PET emission data combined with the truncated MR image. In this work, we expand the use of the MLAA algorithm for dynamic and gated MR/PET cardiac studies. Methods The MLAA algorithm uses the measured counts emitted from the areas of the patient that are truncated in the MR images to estimate the missing mu-values. MLAA is a joint estimation algorithm that simultaneously estimates the emission as well as attenuation values using an intensity prior that favors mu-values of air and tissue. In gated MR/PET cardiac studies, the PET data is framed into multiple gates and a series of MR based mu-maps corresponding to each gate is generated. The number of PET emission counts detected within each gate is relatively small, resulting in a noisy estimate of the MLAA based extended mu-map. To reduce the noise in the extended mu-map, we combine the PET data from all gates. Once the extended mu-map is generated the central region is replaced with the MR based mu-map corresponding to that particular gate. On the other hand, in dynamic PET studies the uptake in the arms (truncated part of the mu-map) reaches a steady state only after the tracer distributes throughout the body. Hence, for dynamic scans, the projection data of all frames is summed and used to generate the MLAA based extended mu-map for all frames. Results Reconstructed images were evaluated qualitatively for both dynamic and gated cardiac MR/PET studies. The bias in the reconstructed image within the MR FOV was reduced to less than 5% when the MLAA based extended mu-map is used. Conclusions Application of MLAA based extended mu-map to dynamic and gated cardiac studies helps to improve the accuracy of the scatter estimation and reduce the local artifacts present when truncated mu-maps are used.
CT reconstruction from few-views by Anisotropic Total Variation minimization (2012)

Dose reduction is an important factor in medical imaging, One of the key strategies to reduce the dose in CT reconstruction is undersampling, The recently proposed Compressed Sensing (CS) paradigm has shown that nearly exact CT reconstructions can be obtained from highly under-sampled projection sets using e.g. regularized iterative reconstruction algorithms. For the regularization, the standard Total Variation (TV) minimization method is commonly applied. The TV has a sparse setting and can therefore be utilized in the CS framework. It can smooth undesired discontinuities related to noise and preserve edges of the field-of-interest objects. It has developed a de facto standard method in CS based CT reconstructions. Nevertheless, the utilization of the Total Variation method has several drawbacks. One of these is oversmoothing of some fine objects, structures and textures and at the same time great spatial resolution loss. The purpose of this work is to develop a new Anisotropic Total Variation (ATV) method that can overcome these disadvantages and produce strong results in the sparse environment. In this work it will be shown that the usage of ATV regularization leads to edges, objects and fine structures which are sharper and clearer in contrast to the standard TV method. In addition to that the spatial resolution for the ATV method is much higher than for the TV method. The performance of both methods will be evaluated visually by means of digital simulated data, as well as real data scans obtained from an Elekta cone-beam synergy system.
Experimental and theoretical characterization of high frequency polymer ultrasound contrast agents (2012)

Lipid-shelled contrast agents have been the focus of combined experimental and theoretical efforts in order to characterize their dynamics with respect to shell material parameters. The use of independent mechanical measurements such as atomic force microscopy (AFM) for the shell materials has begun to receive attention. Polymer-shelled agents are less understood in terms of behavior and their destruction scenarios are exemplified by complex buckling modes. We present ultra-high frequency (GHz) scanning acoustic microscopy (SAM) measurements of polymers (Philips Healthcare, Best, The Netherlands) with various shell elastic properties and their corresponding thicknesses. Acoustic microscopy offers unique advantages in terms of non-invasive microscale measurements and visualization of the agents. The obtained material parameters are used in numerical simulations to predict pressure thresholds for the onset of the sub-harmonic response.
Supplementary Figure 7 from <i>miR-152</i> Is a Tumor Suppressor microRNA That Is Silenced by DNA Hypermethylation in Endometrial Cancer (2023)

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Metabolic Control of Glia-Mediated Neuroinflammation (2016)

The central nervous system (CNS) shows dynamic immune and inflammatory responses to a variety of insults having crucial implications for reactive gliosis. Glial cells in the CNS serve not only as the source, but also as targets of proinflammatory mediators. Undoubtedly, these cells efficiently work towards the disposal of tissue debris and promotion of wound healing as well as tissue repair. However, these non-neuronal glial cells synthesize and release numerous inflammatory mediators, which can be detrimental to neurons, axons, myelin, and the glia themselves. While an acute insult is typically transient and unlikely to be detrimental to neuronal survival, chronic neuroinflammation is a long-standing and often self-perpetuating response, which persists even long after the initial injury or insult. It can serve as a point of origin for diverse neurological disorders including Alzheimer's disease. Accumulating evidence demonstrates the contribution of metabolic dysfunction and mitochondrial failure to the pathogenesis of neuroinflammatory and neurodegenerative diseases. Neurodegenerative conditions are also characterized by increased oxidative and endoplasmic reticulum stresses and autophagy defects. Furthermore, neuroinflammatory conditions are accompanied by an alteration in glial energy metabolism. Here, we comprehensively review the metabolic hallmarks of glia-mediated neuroinflammation and how the glial metabolic shift orchestrates the neuroinflammatory response and pathophysiology of diverse neurological disorders.
FED-R: a fusion engineering device utilizing resistive magnets (1983)

The principal purpose of the FED-R tokamak facility is to provide a substantial quasi-steady flux of fusion neutrons irradiating a large test area in order to carry out thermal, neutronic, and radiation effects testing of experimental blanket assemblies having a variety of configurations, compositions, and purposes. The design of the FED-R device also suggests potential for an upgrade that could be employed as a full-scale demonstration reactor for some specific fusion-neutron application when required.
Holmium-doped laser materials for eye-safe solid state laser application (2014)

Trivalent holmium has 14 laser channels from 0.55 to 3.9 μm. The laser emission of most interest is the transition <sup>5</sup>I<sub>7</sub>→<sup>5</sup>I<sub>8</sub> near 2 μm because of its potential for use in eye-safe systems and medical applications. In this paper, we present our recent results in the development of Ho<sup>3+</sup> doped laser materials for eye-safe solid state lasers. We report a calorimetric study of non-radiative losses in two micron pumped holmium doped laser host materials such as silica glass, yttrium aluminum garnet (YAG) crystal and Lu<sub>2</sub>O<sub>3</sub> ceramics. Optical, spectral and morphological properties as well as the lasing performance from highly transparent ceramics are presented.
Architecture and CAD for FPGA Clock Networks (2006)

Scaling of process technologies and innovations in FPGA architecture and CAD are allowing increasingly more sophisticated applications to be implemented on FPGAs. These applications include system-level designs consisting of many subcomponents that use separate clocks. To support a wide range of applications with different clocking schemes, commercial devices have incorporated high-speed, low-skew clock networks that supply multiple clock signals to logic, memory, and arithmetic elements in the FPGA. The design of these programmable clock networks and of the CAD tools that support them is of utmost importance. Not only does the clock network itself dissipate a significant amount of power, since it connects to every latch on the FPGA and toggles every cycle. But, the design of clock network also affects how efficiently the rest of the circuit can be implemented, since it imposed constraints on the CAD tools that map applications onto the FPGA.
Low‐frequency electrical response to microbial induced sulfide precipitation (2005)

We investigated the sensitivity of low‐frequency electrical measurements to microbe‐induced metal sulfide precipitation. Three identical sand‐packed monitoring columns were used; a geochemical column, an electrical column and a control column. In the first experiment, continuous upward flow of nutrients and metals in solution was established in each column. Cells of Desulfovibrio vulgaris ( D. vulgaris ) were injected into the center of the geochemical and electrical columns. Geochemical sampling and post‐experiment destructive analysis showed that microbial induced sulfate reduction led to metal precipitation on bacteria cells, forming motile biominerals. Precipitation initially occurred in the injection zone, followed by chemotactic migration of D. vulgaris and ultimate accumulation around the nutrient source at the column base. Results from this experiment conducted with metals show (1) polarization anomalies, up to 14 mrad, develop at the bacteria injection and final accumulation areas, (2) the onset of polarization increase occurs concurrently with the onset of lactate consumption, (3) polarization profiles are similar to calculated profiles of the rate of lactate consumption, and (4) temporal changes in polarization and conduction correlate with a geometrical rearrangement of metal‐coated bacterial cells. In a second experiment, the same biogeochemical conditions were established except that no metals were added to the flow solution. Polarization anomalies were absent when the experiment was replicated without metals in solution. We therefore attribute the polarization increase observed in the first experiment to a metal‐fluid interfacial mechanism that develops as metal sulfides precipitate onto microbial cells and form biominerals. Temporal changes in polarization and conductivity reflect changes in (1) the amount of metal‐fluid interfacial area, and (2) the amount of electronic conduction resulting from microbial growth, chemotactic movement and final coagulation. This polarization is correlated with the rate of microbial activity inferred from the lactate concentration gradient, probably via a common total metal surface area effect.
Covariance shaping least-squares estimation (2003)

A new linear estimator is proposed, which we refer to as the covariance shaping least-squares (CSLS) estimator, for estimating a set of unknown deterministic parameters, x, observed through a known linear transformation H and corrupted by additive noise. The CSLS estimator is a biased estimator directed at improving the performance of the traditional least-squares (LS) estimator by choosing the estimate of x to minimize the (weighted) total error variance in the observations subject to a constraint on the covariance of the estimation error so that we control the dynamic range and spectral shape of the covariance of the estimation error. The presented CSLS estimator is shown to achieve the Cramer-Rao lower bound for biased estimators. Furthermore, analysis of the mean-squared error (MSE) of both the CSLS estimator and the LS estimator demonstrates that the covariance of the estimation error can be chosen such that there is a threshold SNR below which the CSLS estimator yields a lower MSE than the LS estimator for all values of x. As we show, some of the well-known modifications of the LS estimator can be formulated as CSLS estimators. This allows us to interpret these estimators as the estimators that minimize the total error variance in the observations, among all linear estimators with the same covariance.
Multi-Agent Reinforcement-Learning-Based Time-Slotted Channel Hopping Medium Access Control Scheduling Scheme (2020)

Time-slotted channel hopping (TSCH) is a medium access control technology that realizes collision-free wireless network communication by coordinating the media access time and channel of network devices. Although existing TSCH schedulers have suitable application scenarios for each, they are less versatile. Scheduling without collisions inevitably lowers the throughput, whereas contention-based scheduling achieves high-throughput but it may induces to frequent collisions in densely deployed networks. Therefore, a TSCH scheduler that can be used universally, regardless of the topology and data collection characteristics of the application scenario, is required to overcome these shortcomings. To this end, a multi-agent reinforcement learning (RL)-based TSCH scheduling scheme that allows contention but minimizes collisions is proposed in this study. RL is a machine-learning method that gradually improves actions to solve problems. One specific RL method, Q-Learning (QL), was used in the scheme to enable the TSCH scheduler to become a QL agent that learns the best transmission slot. To improve the QL performance, reward functions tailored for the TSCH scheduler were developed. Because the QL agent runs on multiple nodes concurrently, changes in the TSCH schedule of one node also affect the performance of the TSCH schedules of other nodes. The use of action peeking is proposed to overcome this non-stationarity problem in a multi-agent environment. The experimental results indicate that the TSCH scheduler consistently performs well in various types of applications, compared to other schedulers.
Walking With Augmented Reality: A Preliminary Assessment of Visual Feedback With a Cable-Driven Active Leg Exoskeleton (C-ALEX) (2019)

Visual and force feedback are common elements in rehabilitation robotics, but visual feedback is difficult to provide in over-ground mobile exoskeleton systems. This letter aims to provide a method to integrate visual feedback using an augmented reality HoloLens headset with our mobile C-ALEX system. A preliminary study was carried out to assess the effects of providing force-only (Haptic), force and visual (HoloHapt) or visual (Visual) feedback to three independent groups, each containing eight participants. The groups showed an increase in normalized step height, nSH (HoloHapt: 1.10 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 0.13, Haptic: 1.03 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 0.23 Visual: 1.61 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 0.52) and decreased normalized trajectory tracking error, TE (HoloHapt: 42.8% <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 23.4%, Haptic: 47.6% <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 18.4%, <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Visual: 114 .2 % <inline-formula><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 60.0 %</b> ). Visual nSH differed significantly from HoloHapt and Haptic nSH ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$p&lt; 0.005$</tex-math></inline-formula> ). Lap-wise normalized tracking error differed significantly ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$p &lt; 0.005$</tex-math></inline-formula> ) within participants. The results show the feasibility of and differences between each form of feedback for overground gait training. This information is useful for future studies targeted at patients with gait impairments.
Hydrogenated amorphous silicon germanium black‐matrix material for active‐matrix liquid‐crystal displays (1997)

Abstract— Integration of the black matrix (BM) in active‐matrix liquid‐crystal displays (AMLCDs) into the TFT array is desirable to improve display performance. This requires a black‐matrix material that is both an optical absorber and an electrical insulator. Amorphous silicon germanium (a‐SiGe:H) is a candidate material for this application. When deposited by magnetron sputtering, a‐SiGe:H can have both high optical density and high electrical resistivity. Compared to organic materials considered for black‐matrix integration, a‐SiGe:H offers higher optical density at a given film thickness, more‐flexible processing, and better process compatibility with AMLCD fabrication.
Variational (Gradient) Estimate of the Score Function in Energy-based\n Latent Variable Models (2020)

The learning and evaluation of energy-based latent variable models (EBLVMs)\nwithout any structural assumptions are highly challenging, because the true\nposteriors and the partition functions in such models are generally\nintractable. This paper presents variational estimates of the score function\nand its gradient with respect to the model parameters in a general EBLVM,\nreferred to as VaES and VaGES respectively. The variational posterior is\ntrained to minimize a certain divergence to the true model posterior and the\nbias in both estimates can be bounded by the divergence theoretically. With a\nminimal model assumption, VaES and VaGES can be applied to the kernelized Stein\ndiscrepancy (KSD) and score matching (SM)-based methods to learn EBLVMs.\nBesides, VaES can also be used to estimate the exact Fisher divergence between\nthe data and general EBLVMs.\n