gebhart/patrepeval huggingface dataset:
Transmission reconstruction using an ordered-subset algorithm for single photon transmission tomography in PET (2002)

The authors have implemented the penalized ordered-subset transmission reconstruction algorithm (OSTR) for the ECAT ART PET scanner, which uses single photon transmission sources rather then positron sources. The OSTR algorithm of Erdogan and Fessler (1999) uses separable surrogates for fast convergence and a more accurate system model for transmission tomography than OSEM. The OSTR algorithm is directly applicable to post-injection transmission scanning with a single photon source, as emission contamination from the patient mimics the effect, in the original derivation of OSTR, of random coincidence contamination in a positron source transmission scan. Multiple noise realizations of simulated post-injection transmission data were reconstructed using OSTR, FBP, and OSEM algorithms. The image noise, contrast, uniformity, and signal-to-noise ratios (SNRs) of the reconstructed images were then calculated. The authors show: (1) the use of a 3D regularizing image roughness penalty with OSTR improves SNR relative to the use of a 2D penalty. (2) OSTR with an 3D penalty has higher SNR than FBP or OSEM. (3) The use of image uniformity (std. dev. from a single realization) to estimate the true SNR can be particularly misleading in the case of OSEM. It is concluded that using OSTR with a 3D penalty allows for shorter transmission scans in single photon transmission tomography in PET, relative to FBP or OSEM reconstructed images with the same image SNR.
Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA (2017)

Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with many nearly matched targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear. Here we consider a kinetic system, inspired by homology dependent pairing between double stranded DNA in bacteria. By considering a simplified tractable model, we identify different homology testing stages that naturally occur in the system. In particular, we first model dsDNA molecules as short rigid rods containing periodically spaced binding sites. The interaction begins when the centers of two rods collide at a random angle. For most collision angles, the interaction energy is weak because only a few binding sites near the collision point contribute significantly to the binding energy. We show that most incorrect pairings are rapidly rejected at this stage. In rare cases, the two rods enter a second stage by rotating into parallel alignment. While rotation increases the stability of matched and nearly matched pairings, subsequent rotational fluctuations reduce kinetic trapping. Finally, in vivo chromosome are much longer than the persistence length of dsDNA, so we extended the model to include multiple parallel collisions between long dsDNA molecules, and find that those additional interactions can greatly accelerate the searching.
Basal Plane Stacking-Fault Related Anisotropy in X-ray Rocking Curve Widths of m-Plane GaN (2008)

A model of basal plane stacking faults as boundaries between incoherently scattering domains in m-plane GaN films is reviewed. m-Plane GaN films are analyzed with a modified version of the Williamson–Hall analysis in order to determine the length-scale of coherent scattering and tilt-mosaic contribution to X-ray rocking curve widths for the primary in-plane directions. This analysis shows that basal plane stacking faults are the predominant source of rocking-curve width anisotropy in the m-plane films, and indicate that the modified Williamson–Hall analysis can be used as a non-destructive technique for measuring basal plane stacking fault densities in m-GaN films.
Paper #176: The Effect of Anterolateral Complex Sectioning and a Macintosh Tenodesis on Patellofemoral Joint Contact Pressures and Kinematics (2017)

In knees with injury to the anterolateral complex a MacIntosh tenodesis did not affect patellofemoral contact pressures or patellar kinematics as compared to the intact knees as long as 20 N graft tension was used - but with 80 N graft tension, and the tibia free to rotate into external rotation, increased lateral contact pressures and increased patellar tilt was seen.
Lung function testing in preschool‐aged children with cystic fibrosis in the clinical setting (2010)

In cystic fibrosis (CF) lung function testing is a means of monitoring progression of lung disease. The preschool years have often been referred to as the "silent years" due to the previous lack suitable measures of lung function testing in this age group. This review outlines the various techniques of lung function testing in preschool children with CF in the clinical setting. This includes measures requiring tidal breathing including the forced oscillation technique, the interrupter technique, plethysmography, and multiple breath washout, as well as spirometry that requires respiratory maneuvers. We describe the feasibility and variability of different lung function methods used in preschoolers and report measurements made during tidal breathing have greater feasibility, although greater variability compared to spirometry. We also report associations with lung function and markers of CF lung disease. In the preschool age group measurements made during tidal breathing may be more appropriate in the clinic setting than those that require a higher degree of cooperation and specific respiratory maneuvers.maneuvers.
Do altered energy metabolism or spontaneous locomotion ‘mediate’ decelerated senescence? (2015)

That one or multiple measures of metabolic rate may be robustly associated with, or possibly even causative of, the progression of aging-resultant phenotypes such as lifespan is a long-standing, well-known mechanistic hypothesis. To broach this hypothesis, we assessed metabolic function and spontaneous locomotion in two genetic and one dietary mouse models for retarded aging, and subjected the data to mediation analyses to determine whether any metabolic or locomotor trait could be identified as a mediator of the effect of any of the interventions on senescence. We do not test the hypothesis of causality (which would require some experiments), but instead test whether the correlation structure of certain variables is consistent with one possible pathway model in which a proposed mediating variable has a causal role. Results for metabolic measures, including oxygen consumption and respiratory quotient, failed to support this hypothesis; similar negative results were obtained for three behavioral motion metrics. Therefore, our mediation analyses did not find support that any of these correlates of decelerated senescence was a substantial mediator of the effect of either of these genetic alterations (with or without caloric restriction) on longevity. Further studies are needed to relate the examined phenotypic characteristics to mechanisms of aging and control of longevity.
Humanoid Head Prototype with Uncoupled Eyes and Vestibular Sensors (2006)

This paper deals with the biomimetic design of a humanoid head prototype. This prototype is developed in order to offer some mechanical device for multimodality objectives, and to demonstrate the importance of uncoupled eyes mechanism in humanoid head function. Indeed, the prototype development is based on our understanding of the humans head properties in the filed of visual and vestibular capabilities. The final prototype will have 3 DOF for each eye and 2 DOF for the neck. The developed device based as on one dof for each eye and one dof for the neck is able to show the vestibular ocular reflex (VOR) and the target tracking (TT) in real time. To carry out all these capabilities, a generic visual perception processor is developed and used. The first experiments on 3 DOF mechanism are given
Reduced synaptic activity and dysregulated extracellular matrix pathways are common phenotypes in midbrain neurons derived from sporadic and mutation-associated Parkinson’s disease patients (2022)

Abstract Several mutations that cause Parkinson’s disease (PD) have been identified over the past decade. These account for 15-25% of PD cases; the rest of the cases are considered sporadic. Currently, it is accepted that PD is not a single monolithic disease but rather a constellation of diseases with some common phenotypes. While rodent models exist for some of the PD-causing mutations, research on the sporadic forms of PD is lagging due to a lack of cellular models. In our study, we differentiated PD patient-derived dopaminergic (DA) neurons from induced pluripotent stem cells (iPSCs) of several PD-causing mutations as well as from sporadic PD patients. Strikingly, we observed a common neurophysiological phenotype: Neurons derived from PD patients had a severe reduction in the rate of synaptic currents compared to those derived from healthy controls. While the relationship between mutations in genes such as the SNCA and LRRK2 and a reduction in synaptic transmission has been investigated before, here we show evidence that the pathogenesis of the synapses in neurons is a general phenotype in PD. Analysis of RNA sequencing results displayed changes in gene expression in different synaptic mechanisms as well as other affected pathways such as extracellular matrix-related pathways. Some of these dysregulated pathways are common to all PD patients (monogenic or idiopathic). Our data, therefore, shows changes that are central and convergent to PD and suggests a strong involvement of the tetra-partite synapse in PD pathophysiology.
RNA of simian sarcoma-associated virus type 1 produced in human tumor cells (1975)

Simian sarcoma-associated virus type 1 propagated in human rhabdomyosarcoma cells exhibited characteristics typical of oncornaviruses but seemed to have several aberrant properties. It had a buoyant density of 1.14 g/cm3, had RNA-dependent DNA polymerase activity, seemed to be labile to high salt concentrations, and contained little 50 to 60S RNA but relatively large amounts of human ribosomal RNA. In addition to 50 to 60S RNA, purified virions contained smaller RNA molecules with sedimentation coefficients of 28 to 30S, 18 TO 20S, and 4 to 10S. Unlike the 50 to 60S RNA species, the smaller virion-associated RNAs lacked polyadenylic acid, and the 28 to 30S RNA had an average base composition similar to that of human ribosomal RNA. Upon heat denaturation, the native 50 to 60S RNA genome yielded polyadenylic acid-containing 28 to 30S subunits that degraded in to 18 to 20S molecules upon further heat treatment. The 50 to 60S viral RNA had a guanine plus cytosine content of 56%.
Experimental use of electronic nose for analysis of volatile organic compound (VOC) (2009)

An electronic nose is an instrument intended to mimic the human sense of smell. Electronic noses (e-nose) employ an array of chemical gas sensors, a sample handling system and a pattern recognition system. Pattern recognition provides a higher degree of selectivity and reversibility to the system leading to an extensive range of applications. These ranges from the food and medical industries to environmental monitoring and process control. Many other types of different gas sensors available. These include conducting polymers (CP), metal oxide semiconductors (MOS), piezoelectric, optical fluorescence, quartz crystal microbalance (QCM) and amperometric gas sensors. The ideal gas sensor would exhibit reliability, robustness, sensitivity, selectivity and reversibility. High selectivity with high reversibility is difficult to attain. After signal processing and feature extraction the output of the sensors provide a unique ldquosmellprintrdquo for that substances which can be used to classify, measure concentration, or verify quality. The present paper illustrates the function of electronic nose, its application and investigates the effective use of e-nose in detecting gases that have some smell developed by the volatile organic compounds (VOC) like ethanol, acetone and benzene at different concentrations. The response and characteristics prove that the Electronic nose is a reliable instrument which can be used for environment control (air quality, pollutants, and gas emission levels), medical science (urine, skin and breath odour etc.), food industry (coffee, milk, soft drink fish, meat etc.), pharmaceutics, chemical industry, Defence and security industries (detecting humanitarian land mines etc.) and semiconductor industrial processes.
The Orthonormalized Volume Magnetic Source Model for Discrimination of Unexploded Ordnance (2014)

We introduce a fast and accurate numerical technique for the solution of electromagnetic induction sensing problems called the orthonormalized volume magnetic source model. The model assumes that the secondary magnetic field measured by a sensor originates from a set of magnetic dipole sources distributed over a volume that coincides with the interrogated area. The Green functions associated with the responding sources are turned into an orthonormal basis using a generalization of the Gram-Schmidt method, enabling one to determine the sources' strengths directly from measured data without having to invert large and potentially ill-conditioned matrices. The method treats multitarget cases naturally and robustly. Several examples are presented to illustrate the applicability of the method in the discrimination of unexploded ordnance (UXO). In particular, we analyze data taken by the Time-Domain Electromagnetic Multisensor Towed Array Detection System sensor array at a test stand and during a blind test administered at a UXO live site. The method is highly successful in distinguishing UXO from among other UXO and from accompanying clutter.
Molecular basis for the irreversible inhibition of 4-aminobutyric acid:2-oxoglutarate and L-ornithine:2-oxoacid aminotransferases by 3-amino-1,5-cyclohexadienyl carboxylic acid (isogabaculline). (1979)

Isogabaculine reacts with pyridoxal phosphate to form N-meta-carboxyphenylpyridoxamine phosphate as does its natural isomer gabaculine. The two compounds are almost equipotent in vitro and in vivo in inhibiting 4-amino-butyrate (GABA) aminotransferase and L-ornithine aminotransferase and in elevating brain GABA levels.
Clinical parameters before and after the transition to dialysis (2017)

This study uniquely demonstrates the trajectories of key parameters though the transition from pre-dialysis to post-dialysis start. Significant differences are noted in the pre-dialysis period for patients who survive vs. those who do not survive the first year of dialysis. Early recognition of adverse trends in the pre-dialysis period may create opportunity to intervene to improve early dialysis outcomes.
Mesoporous silica as a membrane for ultra-thin implantable direct glucose fuel cells (2011)

The design, fabrication and characterization of an inorganic catalyst based direct glucose fuel cell using mesoporous silica coating as a functional membrane is reported. The desired use of mesoporous silica based direct glucose fuel cell is for a blood vessel implantable device. Blood vessel implantable direct glucose fuel cells have access to higher continuous glucose concentrations. However, reduction in the implant thickness is required for application in the venous system as part of a stent. We report development of an implantable device with a platinum thin-film (thickness: 25 nm) deposited on silicon substrate (500 μm) to serve as the anode, and graphene pressed on a stainless steel mesh (175 μm) to serve as the cathode. Control experiments involved the use of a surfactant-coated polypropylene membrane (50 μm) with activated carbon (198 μm) electrodes. We demonstrate that a mesoporous silica thin film (270 nm) is capable of replacing the conventional polymer based membranes with an improvement in the power generated over conventional direct glucose fuel cells.
Cascaded silicon micro-ring modulators for WDM optical interconnection (2006)

We experimentally demonstrate cascaded silicon micro-ring modulators as the key component of a WDM interconnection system. We show clean eye-diagrams when each of the four micro-ring modulators is modulated at 4 Gbit/s. We show that optical inter-channel crosstalk is negligible with 1.3-nm channel spacing.
Why the State of the Art Matters: The Importance of Functional Abstraction in Robot Hand Design (2014)

Despite 40 years of research in the field of robotic hands, the reproduction of human capabilities for dexterous manipulation still seems far to be achieved by state-of-the-art technologies. From a design perspective, even defining what are the “optimal functionalities” of a robotic hand is a very challenging task due to the number of different requirements in terms of degrees of freedom, force, speed, compactness, robustness and so on.&#13;\n&#13;\nIn the specific fields of humanoid robotics and prosthetics, the robotic hand is expected to provide high flexibility and adaptability, ideally replicating the overall functionality of the human hand. The general perception, however, is that current robotic hands able to provide (even limited) human-like dexterity and functionalities are either too complex and expensive or too bulky and unreliable to truly represent effective solutions for the market, limiting their usage to research labs.&#13;\n&#13;\nA closer look to the specific aspects involved in the development of a robotic hand shows that, even if the mechanical structure of the device is somehow inspired by the biological counterpart, a large range of solutions can be found for the implementation of joints, actuators and sensors, but none of those represents “the” solution to the specific problem.&#13;\n&#13;\nAlso from the point of view of control algorithms and user interfaces, the actual scenario is quite controversial, since the use of current robotic hands is in some way largely limited by the difficulties in task planning, problem that is sometimes amplified by the limited portability of the solutions developed for a specific hand to the others. The result is that only very specialized and well-trained experts can effectively use a specific robotic hand exploiting its full potential, while the generalization and the standardization of the robotic hand control problem is still a serious issue.
Semidefinite relaxation for detection of 16-QAM signaling in MIMO channels (2005)

We develop a computationally efficient approximation of the maximum likelihood (ML) detector for 16 quadrature amplitude modulation (16-QAM) in multiple-input multiple-output (MIMO) systems. The detector is based on a convex relaxation of the ML problem. The resulting optimization is a semidefinite program that can be solved in polynomial time with respect to the number of inputs in the system. Simulation results in a random MIMO system show that the proposed algorithm outperforms the conventional decorrelator detector by about 2.5 dB at high signal-to-noise ratios.
Heart of glass anchors Rasip1 at endothelial cell-cell junctions to support vascular integrity (2016)

Heart of Glass (HEG1), a transmembrane receptor, and Rasip1, an endothelial-specific Rap1-binding protein, are both essential for cardiovascular development. Here we performed a proteomic screen for novel HEG1 interactors and report that HEG1 binds directly to Rasip1. Rasip1 localizes to forming endothelial cell (EC) cell-cell junctions and silencing HEG1 prevents this localization. Conversely, mitochondria-targeted HEG1 relocalizes Rasip1 to mitochondria in cells. The Rasip1-binding site in HEG1 contains a 9 residue sequence, deletion of which abrogates HEG1's ability to recruit Rasip1. HEG1 binds to a central region of Rasip1 and deletion of this domain eliminates Rasip1's ability to bind HEG1, to translocate to EC junctions, to inhibit ROCK activity, and to maintain EC junctional integrity. These studies establish that the binding of HEG1 to Rasip1 mediates Rap1-dependent recruitment of Rasip1 to and stabilization of EC cell-cell junctions.
Molecular Dynamics Prediction of the Mechanism of Ester Hydrolysis in Water (2008)

Hydrolysis reactions of the basic units of biological polymers with water, or the reverse reaction, the formation of ester, amide, ketal, or phosphate bonds, occur with very high activation barriers in the gas phase but occur much more rapidly in pure water. Car-Parrinello molecular dynamics simulations reported here show that the rate of hydrolysis of methyl formate in pure water is consistent with mechanisms involving cooperative catalysis by autoionization-generated hydroxide and hydronium, a process known to have an activation free energy of 23.8 kcal/mol. In this mechanism, autoionization is followed by rapid simultaneous acid-base catalysis.
Real-Time Haar-like Feature Extraction Coprocessor with Pixel-Based Pipelined Hardware Architecture for Flexible Low-Power Object Detection and Recognition (2016)

2016 International Conference on Solid State Devices and Materials,Real-Time Haar-like Feature Extraction Coprocessor with Pixel-Based Pipelined Hardware Architecture for Flexible Low-Power Object Detection and Recognition
QUANTITATIVE ANALYSIS OFRANDOMTELEGRAPH SIGNALS AS FLUCTUATIONS OFTHRESHOLD VOLTAGESINSCALEDFLASHMEMORYCELLS (2007)

Randomtelegraph signals (RTS)influctuations ofthreshold voltage are analyzed usingmassive readout datainscaled flash memories. A novelquantitative analytical methodisproposed to evaluate parameters oftheRTS,suchasamplitudes andmean time spentinindividual states. Thisevaluation gives us a statistical view ofparameters oftheRTS aswellas their correlations. Allofthe parameters were found tofollow log-normal distribution andtoshow weakmutual dependences. Possible origins ofthedistributions are discussed. We alsostudied evolution ofRTSduring program/erase operations offlash memories andpoint outitspotential similarity withbreakdown phenomena ingateoxide. [Keywords: random telegraph signal, RTS,flash memories, Vthfluctuation, oxide breakdown, percolation]
Photocatalytic growth of dendritic silver nanostructures as SERS substrates (2011)

We report a one-step photocatalytic synthesis method of dendritic silver nanostructures. These self-organised structures show an excellent Raman enhancement enabling the detection of analytes from dilute solutions by surface-enhanced Raman spectroscopy.
Force Requirements for Artificial Muscle to Create an Eyelid Blink With Eyelid Sling (2010)

The force and stroke required to close an eyelid with the eyelid sling are well within the attainable range of the electroactive polymer artificial muscle (EPAM). This may allow the creation of a realistic and functional eyelid blink that is symmetric and synchronous with the contralateral, normally functioning blink. Future aims include consideration of different sling materials and development of both the EPAM device and an articulation between the EPAM and sling. The biocompatibility and durability studies of EPAM in a gerbil model are under way. The successful application of artificial muscle technology to create an eyelid blink would be the first of many potential applications.
Improving tungstate crystal laser performance by optimization of Yb concentration (2000)

We investigate laser performance of Yb:KGW and Yb:KYW crystals with the goal to optimize Yb concentration while reducing crystal thickness. We also report the first room temperature laser operation of 20% Yb: KYW.