gebhart/patrepeval huggingface dataset:
Pin1: A Promising Novel Diagnostic and Therapeutic Target that Acts on Numerous Cancer-Driving Pathways (2013)

Proline-directed phosphorylation is a common and central regulatory mechanism in cell proliferation and oncogenic transformation. In fact, numerous oncogenes and tumor suppressors themselves are directly regulated by proline-directed phosphorylation and/or can trigger signaling pathways involving proline-directed phosphorylation. Our recent identification of the phosphorylation dependent prolyl isomerase Pin1 has uncovered a novel signaling mechanism controlling protein function after phosphorylation via conformational changes. Importantly, Pin1 deregulation plays a pivotal role in the development of some diseases, providing a new therapeutic option, most notably for cancers. Pin1 is prevalently overexpressed and its levels correlate with poor clinical outcome in human cancers. Significantly, Pin1 is required for activation of multiple oncogenic pathways by acting on numeroous oncogenes and tumor suppressors. Moreover, Pin1 knockdown or knockout inhibits cancer cell growth and prevents cell transformation and tumorigenesis induced either by oncogenes or tumor suppressors in vitro and in vivo. Pin1-mediated post-phosphorylation isomerisation represents a unique regulatory mechanism in cell signalling whose upregulation during tumorigenesis promotes the pro-proliferative capacity of tumour cells. Accumulating evidences indicate that Pin1 may represent a novel tumour marker and potential therapeutic target. Therefore, there is an urgent need to develop Pin1-specific inhibitors because they may have the desired property to suppress numerous oncogenic pathways, which are often activated simultaneously in cancers, especially in those aggressive and drug-resistant ones.
Form2Seq : A Framework for Higher-Order Form Structure Extraction (2020)

Document structure extraction has been a widely researched area for decades with recent works performing it as a semantic segmentation task over document images using fullyconvolution networks. Such methods are limited by image resolution due to which they fail to disambiguate structures in dense regions which appear commonly in forms. To mitigate this, we propose Form2Seq, a novel sequenceto-sequence (Seq2Seq) inspired framework for structure extraction using text, with a specific focus on forms, which leverages relative spatial arrangement of structures. We discuss two tasks; 1) Classification of low-level constituent elements (TextBlock and empty fillable Widget) into ten types such as field captions, list items, and others; 2) Grouping lower-level elements into higher-order constructs, such as Text Fields, ChoiceFields and ChoiceGroups, used as information collection mechanism in forms. To achieve this, we arrange the constituent elements linearly in natural reading order, feed their spatial and textual representations to Seq2Seq framework, which sequentially outputs prediction of each element depending on the final task. We modify Seq2Seq for grouping task and discuss improvements obtained through cascaded end-to-end training of two tasks versus training in isolation. Experimental results show the effectiveness of our text-based approach achieving an accuracy of 90% on classification task and an F1 of 75.82, 86.01, 61.63 on groups discussed above respectively, outperforming segmentation baselines. Further we show our framework achieves state of the results for table structure recognition on ICDAR 2013 dataset.
Evolution of an Electrohydraulic Ventricular Assist Device Through In Vivo Testing (1996)

A totally implantable intrathoracic electrohydraulic ventricular assist device has been developed at the University of Ottawa Heart Institute. In vivo testing has been instrumental in its progressive development. A total of 15 experiments (4 acute, 11 performance) have been performed using male calves (62-117 kg). Data from the acute experiments, human fit trials, fluid dynamic studies, and hydraulic/energy efficiency analyses formed the basis for the development of a compact, single piece ventricular assist device called the Unified System in which the volume displacement chamber, motor, and blood chamber are housed within a compact 600 cc, 740 g unit. The performance experiments indicated that the unified system could support calves for periods up to 96 hr. The mean postoperative cardiac output was 7.1 +/- 0.7 L/ min (range = 4.9-11), mean blood pressure was 99.7 +/- 5.8 mmHg, and mean pulmonary artery pressure was 32.1 +/- 1.2 mmHg. The operative technique for intrathoracic implantation has been developed. The major problems encountered were of respiratory failure, improved by device repositioning in the calf; decreased blood inflow to the device that was improved by cannula redesign; circuit board fracture corrected by design modification; and a power supply problem that was limited to a single unit. The preliminary experiments have helped in the design modifications of the Unified System. The improved version of the system will undergo formal performance, reliability, and chronic in vivo testing before human implantation.
Full-Flat keyboard light optimized for Edge-to-Edge flat glass screen (2012)

Conventional Keyboard-Light which is implemented at upper LCD area, has overhanging shape in order to light keyboard effectively, but the overhanging shape is not suitable for Edge-to-Edge flat glass surface screen which is adopted for recent Design-Centric Notebook PC. We developed Keyboard-Light which is optimized optically for Edge-to-Edge flat glass surface screen, and has Full-Flat shape which is unified physically with glass surface screen.
An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments (2016)

We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex.
High-Pressure Ion Mobility Spectrometry (2009)

The effects of above-ambient pressure on ion mobility on resolving power, resolution, and ion current were investigated using a small, stand-alone ion mobility spectrometer (IMS). This work demonstrates the first example of ion mobility spectrometry at pressures above ambient. Ion mobility spectra of chemical warfare agent (CWA) stimulant dimethyl methylphosphonate (DMMP) and several other standard compounds are shown for superambient conditions. The IMS was operated at pressures from 700 to 4560 Torr. An optimal resolving power was obtained at a specific voltage as a function of pressure, with higher optimal resolving powers obtained at higher voltages, as predicted from standard IMS theory. At high pressures, however, resolving power did not increase as much as theory predicted, presumably due to ion clustering. Nevertheless, an increase in pressure was found to improve resolution in IMS. One example where high pressure improved resolution was the separation of cyclohexylamine (K(0) = 1.83) and 2-hexanone (K(0) = 1.86) (where K(0) is the reduced mobility value). The product ions of these two compounds could not be separated at ambient pressure but could be nearly baseline separated when the pressure of the buffer gas was raised to 2280 Torr. Total ion current was also examined at pressures from ambient up to 4560 Torr. Total ion current, when investigated with pressure, was found to reach a maximum, initially rising with increased pressure.
Graft copolymer directed synthesis of micron-thick organized mesoporous TiO2 films for solid-state dye-sensitized solar cells (2011)

Micron thick, well-organized mesoporous TiO(2) films with high porosity and good connectivity were synthesized by templating an amphiphilic graft copolymer for solid-state dye-sensitized solar cells.
Language-independent sandboxing of just-in-time compilation and self-modifying code (2011)

When dealing with dynamic, untrusted content, such as on the Web, software behavior must be sandboxed, typically through use of a language like JavaScript. However, even for such specially-designed languages, it is difficult to ensure the safety of highly-optimized, dynamic language runtimes which, for efficiency, rely on advanced techniques such as Just-In-Time (JIT) compilation, large libraries of native-code support routines, and intricate mechanisms for multi-threading and garbage collection. Each new runtime provides a new potential attack surface and this security risk raises a barrier to the adoption of new languages for creating untrusted content. Removing this limitation, this paper introduces general mechanisms for safely and efficiently sandboxing software, such as dynamic language runtimes, that make use of advanced, low-level techniques like runtime code modification. Our language-independent sandboxing builds on Software-based Fault Isolation (SFI), a traditionally static technique. We provide a more flexible form of SFI by adding new constraints and mechanisms that allow safety to be guaranteed despite runtime code modifications. We have added our extensions to both the x86-32 and x86-64 variants of a production-quality, SFI-based sandboxing platform; on those two architectures SFI mechanisms face different challenges. We have also ported two representative language platforms to our extended sandbox: the Mono common language runtime and the V8 JavaScript engine. In detailed evaluations, we find that sandboxing slowdown varies between different benchmarks, languages, and hardware platforms. Overheads are generally moderate and they are close to zero for some important benchmark/platform combinations.
Strip Histogram Grid for efficient LIDAR segmentation from urban environments (2011)

As part of a large-scale 3D recognition system for LIDAR data from urban scenes, we describe an approach for segmenting millions of points into coherent regions that ideally belong to a single real-world object. Segmentation is crucial because it allows further tasks such as recognition, navigation, and data compression to exploit contextual information. A key contribution is our novel Strip Histogram Grid representation that encodes the scene as a grid of vertical 3D population histograms rising up from the locally detected ground. This scheme captures the nature of the real world, thereby making segmentation tasks intuitive and efficient. Our algorithms work across a large spectrum of urban objects ranging from buildings and forested areas to cars and other small street side objects. The methods have been applied to areas spanning several kilometers in multiple cities with data collected from both aerial and ground sensors exhibiting different properties. We processed almost a billion points spanning an area of 3.3 km <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in less than an hour on a regular desktop.
Optimization of white matter fiber tractography with diffusional kurtosis imaging (2015)

Diffusional kurtosis imaging (DKI) is a clinically feasible diffusion MRI technique for white matter (WM) fiber tractography (FT) with the ability to directly resolve intra-voxel crossing fibers by means of the kurtosis diffusion orientation distribution function (dODF). Here we expand on previous work by exploring properties of the kurtosis dODF and their subsequent effects on WM FT for in vivo human data. For comparison, the results are contrasted with fiber bundle orientation estimates provided by the diffusion tensor, which is the primary quantity obtained from diffusion tensor imaging. We also outline an efficient method for performing DKI-based WM FT that can substantially decrease the computational requirements. The recommended method for implementing the kurtosis ODF is demonstrated to optimize the reproducibility and sensitivity of DKI for detecting crossing fibers while reducing the occurrence of non-physically-meaningful, negative values in the kurtosis dODF approximation. In addition, DKI-based WM FT is illustrated for different protocols differing in image acquisition times from 48 to 5.3 min.
The Magnetic Stability of Spin-Dependent Tunneling Devices (1998)

The tunneling resistance between two ferromagnetic metal layers that are separated by a thin insulator depends on the relative orientation of the magnetization M of each layer. In a memory device, independent switching of the magnetically soft layer is achieved by making the other layer either exchange-biased or magnetically hard. The repeated reversal of M of the soft layer by field cycling can demagnetize the other magnetically hard layer and thus erase the tunnel junction's memory. The M of exchange-biased structures was stable at least to 10(7) cycles, whereas in hard structures, M generally decayed logarithmically with the number of field cycles. The decay was very sensitive to the thickness of the hard layer and the composition of the soft layer. However, no decay was observed when the moment reversal was accomplished by coherent rotation, establishing that demagnetization results from the formation and motion of domain walls in the soft layer during field cycling.
KGF Receptor: Transforming Potential on Fibroblasts and Epithelial Cell-Specific Expression by Alternative Splicing (1992)

The mouse keratinocyte growth factor (KGF) receptor (KGFR) cDNA was isolated by an expression cDNA cloning strategy involving creation of a transforming autocrine loop. Characterization of the cloned 4.2 kb cDNA revealed a predicted membrane-spanning tyrosine kinase structurally related to the FGF receptor (FGFR). Structural analysis of the human KGFR cloned by the analogous procedure revealed identity with one of the fibroblast growth factor (FGF) receptors (bek/FGFR-2) except for a divergent stretch of 49 amino acids in their extracellular domains. Binding assays demonstrated that the KGFR was a high affinity receptor for both KGF and acidic FGF, while FGFR-2 showed high affinity for basic FGF and acidic FGF but no detectable binding by KGF. Analysis of the bek gene revealed two alternative exons responsible for the region of divergence between the two receptors. The KGFR transcript was specific to epithelial cells, and it appeared to be differentially regulated with respect to the alternative FGFR-2 transcript.
Lossless Multiway Power Combining and Outphasing for High-Frequency Resonant Inverters (2013)

A lossless multi-way power combining and outphasing system have recently been proposed for high-frequency inverters and power amplifiers that offers major performance advantages over traditional approaches. This paper presents outphasing control strategies for the proposed power combining system that enable output power control through effective load modulation of the inverters. It describes a straightforward power combiner design methodology and enumerates various possible topological combiner implementations. Moreover, this study presents the first-ever experimental demonstration of the proposed outphasing system. The design of a 27.12 MHz, four-way power combining and outphasing system is described and used to experimentally verify the power combiner's characteristics. The proposed outphasing law is shown to be effective in controlling the output power over a 10-100 W (10:1) power range.
A proximity-coupled circularly polarized slotted-circular patch antenna for RF energy harvesting applications (2016)

A proximity-coupled (electromagnetic coupling feed) circularly polarized slotted-circular microstrip antenna is proposed for RF energy harvesting applications. The antenna consists of an asymmetric-slotted-circular-patch radiator with a proximity-coupled feed. Two asymmetric-circular slots are cut diagonally onto a circular-patch antenna to generate two orthogonal modes with a 90° phase-shift for requirements of circularly polarized radiation. The proposed designed antenna is achieved gain of more than 6.0 dBic across the 3-dB axial ratio (AR) bandwidth (2.36 GHz–2.40 GHz). An overall antenna volume is 60 mm × 60 mm × 3.2 mm.
Proton Radiation-Induced Void Formation in Ni/Au-Gated AlGaN/GaN HEMTs (2014)

AlGaN/GaN high-electron mobility transistors (HEMTs) were exposed to 2-MeV protons irradiation, at room temperature, up to a fluence of 6 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> /cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Aside from degradation resulting from radiation-induced charge trapping, transmission electron microscopy and electrical measurements reveal a radiation-induced defect located at the edges of the Ni/Au Schottky gate in the proton-irradiated devices. At the edges of the Ni/Au gate, the Ni of the Ni/Au gate diffused up into the Au layer and migrated into the AlGaN barrier, leaving voids in the Ni layer at the gate edges after irradiation. These radiation-induced voids are caused by diffusion of Ni through vacancy exchange, known as the Kirkendall effect, resulting in reduced gate area and degrading the HEMT performance.
Defect Microchemistry at the Si<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>/Si Interface (1987)

The intrinsic oxide decomposition reaction Si+Si${\mathrm{O}}_{2}$\ensuremath{\rightarrow}2SiO\ensuremath{\uparrow} at the Si${\mathrm{O}}_{2}$/Si interface is shown to be nucleated at existing defect sites prior to the growth of physical oxide voids. At lower temperatures than needed for void formation, these defects become electrically active, leading to low-field dielectric break-down unless sufficient ${\mathrm{O}}_{2}$ is available (low concentrations). The systematics of the required ${\mathrm{O}}_{2}$ suggests strongly that it reverses the initial decomposition by reoxidizing the SiO product at the interface.
Influence of the Triel Elements (<i>M</i> = Al, Ga, In) on the Transport Properties of Ca<sub>5</sub><i>M</i><sub>2</sub>Sb<sub>6</sub> Zintl Compounds (2012)

The Zintl compound Ca_5Al_2Sb_6 has extremely low lattice thermal conductivity (<0.6 W/mK at 1000 K) and tunable electronic properties, making it a promising thermoelectric material for high temperature waste-heat recovery. The current study investigates trends in the chemical and transport properties of the Ca_5M_2Sb_6 compounds (M = Al, Ga, or In), revealing potential routes toward improved thermoelectric properties in this system. Here, we show that isoelectronic M-site substitutions can be used to “fine-tune” the electronic properties of the Ca_5M_2Sb_6 system, without inducing electronic doping effects. Electronic structure calculations reveal that the electronegativity of the M element is a good indicator for the energy level of M electronic states. The effects of M-site substitutions on the effective mass and band gap are reflected in measurements of the high temperature electronic properties of Ca_5M_2Sb_6 samples (M = Al, Ga, and In) which reveal increased hole mobility as well as a smaller thermal band gap in the Ga analogue, relative to Ca_5Al_2Sb_6 and Ca_5In_2Sb_6. Optical absorption measurements reveal a trend in the direct band gaps consistent with both calculations and transport measurements. Additionally, a direct benefit of substituting heavier elements on the Al site arises from the increased density and softer lattice, which leads to reduced sound velocity and lattice thermal conductivity.
Automatic jump detection in skiing/snowboarding using head-mounted MEMS inertial and pressure sensors (2015)

With advancing technology in the miniature microelectromechanical systems (MEMS) sensors, wearable devices are becoming increasingly popular, facilitating convenient activity detection. One particular application is in sports performance monitoring. This article presents a novel real-time jump detection algorithm in skiing and snowboarding using a microelectromechanical systems–based inertial measurement unit, which is integrated with a barometric pressure sensor. The key performance variables of the jump can be extracted and evaluated for training and/or entertainment purposes. In contrast to the existing jump detection algorithms based on acceleration signals, the proposed algorithm uses vertical velocity and air time in addition to acceleration in the vertical direction. The experimental results show that by incorporating the velocity and air time into the detection algorithm, the sensitivity and specificity increase dramatically to 92% and 93%, respectively.
Attenuation measuring ultrasound shearwave elastography and<i>in vivo</i>application in post-transplant liver patients (2016)

Ultrasound and magnetic resonance elastography techniques are used to assess mechanical properties of soft tissues. Tissue stiffness is related to various pathologies such as fibrosis, loss of compliance, and cancer. One way to perform elastography is measuring shear wave velocity of propagating waves in tissue induced by intrinsic motion or an external source of vibration, and relating the shear wave velocity to tissue elasticity. All tissues are inherently viscoelastic and ignoring viscosity biases the velocity-based estimates of elasticity and ignores a potentially important parameter of tissue health. We present attenuation measuring ultrasound shearwave elastography (AMUSE), a technique that independently measures both shear wave velocity and attenuation in tissue and therefore allows characterization of viscoelasticity without using a rheological model. The theoretical basis for AMUSE is first derived and validated in finite element simulations. AMUSE is validated against the traditional methods for assessing shear wave velocity (phase gradient) and attenuation (amplitude decay) in tissue mimicking phantoms and excised tissue. The results agreed within one standard deviation. AMUSE was used to measure shear wave velocity and attenuation in 15 transplanted livers in patients with potential acute rejection, and the results were compared with the biopsy findings in a preliminary study. The comparison showed excellent agreement and suggests that AMUSE can be used to separate transplanted livers with acute rejection from livers with no rejection.