gebhart/patrepeval huggingface dataset:
Robust transformation of middle ear impedance parameters from an intra-aural measuring plane to the eardrum (1986)

In order to eliminate the risk inherent in the insertion of a measuring probe into the ear canal of a subject, a middle ear impedance transducer should be placed a safe distance away from the eardrum. A technique presented in this paper uses a function which represents the area function of the ear canal and transforms impedance parameters from the measurement plane to a plane at the eardrum. The effects of the geometry of the canal on impedance measurements, and the validity of the approximations over a wide frequency range are studied by means of a computer model. The area functions used to transform the impedance parameters are parabolic horns which are found to provide better results than the commonly used cylindrical approximation. The sensitivity of these approximations to errors in the estimation of the parameters defining the horn is also studied. The parabolic horns give a simple and very reliable correction to the interpretation of middle ear impedance data. [Work supported by the Natural Sciences and Engineering Research Council of Canada, CRD-8422.]
A Guided Stochastic Energy-Domain Formulation of the Second Order Møller–Plesset Perturbation Theory (2013)

We develop an alternative formulation in the energy-domain to calculate the second order Møller-Plesset (MP2) perturbation energies. The approach is based on repeatedly choosing four random energies using a nonseparable guiding function, filtering four random orbitals at these energies, and averaging the resulting Coulomb matrix elements to obtain a statistical estimate of the MP2 correlation energy. In contrast to our time-domain formulation, the present approach is useful for both quantum chemistry and real-space/plane wave basis sets. The scaling of the MP2 calculation is roughly linear with system size, providing a useful tool to study dispersion energies in large systems. This is demonstrated on a structure of 64 fullerenes within the SZ basis as well as on silicon nanocrystals using real-space grids.
Cellular electrical impedance to profile SARS-CoV-2 fusion inhibitors and to assess the fusogenic potential of spike mutants (2022)

Abstract Despite the vaccination campaigns for COVID-19, we still cannot control the spread of SARS-CoV-2, as evidenced by the ongoing circulation of the Omicron variants of concern. This highlights the need for broad-spectrum antivirals to further combat COVID-19 and to be prepared for a new pandemic with a (re-)emerging coronavirus. An interesting target for antiviral drug development is the fusion of the viral envelope with host cell membranes, a crucial early step in the replication cycle of enveloped viruses. In this study, we explored the use of cellular electrical impedance (CEI) to quantitatively monitor morphological changes in real time, resulting from cell-cell fusion elicited by SARS-CoV-2 spike. The impedance signal in CEI-quantified cell-cell fusion correlated with the expression level of SARS-CoV-2 spike in transfected HEK293T cells. For antiviral assessment, we validated the CEI assay with the fusion inhibitor EK1 and measured a concentration-dependent inhibition of SARS-CoV-2 spike mediated cell-cell fusion (IC 50 value of 0.13 μM). In addition, CEI was used to confirm the fusion inhibitory activity of the carbohydrate-binding plant lectin UDA against SARS-CoV-2 (IC 50 value of 0.55 μM), which complements prior in-house profiling activities. Finally, we explored the utility of CEI in quantifying the fusogenic potential of mutant spike proteins and in comparing the fusion efficiency of SARS-CoV-2 variants of concern. In summary, we demonstrate that CEI is a powerful and sensitive technology that can be applied to studying the fusion process of SARS-CoV-2 and to screening and characterizing fusion inhibitors in a label-free and non-invasive manner. Importance Despite the success of the vaccines against SARS-CoV-2, new variants of the virus are still emerging and spreading, underlining the need for additional effective antiviral countermeasures. An interesting antiviral target for enveloped viruses is the fusion of the viral envelope with host cell membranes, a crucial early step in the life cycle of coronaviruses like SARS-CoV-2. Here, we present a sensitive impedance-based method to monitor in real-time cell-cell fusion elicited by the SARS-CoV-2 spike protein. With this technique we can profile entry inhibitors and determine the inhibitory potential of fusion inhibitors for SARS-CoV-2. In addition, with cellular electrical impedance we can evaluate the fusogenic properties of new emerging SARS-CoV-2 variants. Overall, the impedance technology adds valuable information on the fusion process of circulating coronaviruses and helps unravel the mode of action of new antivirals, opening new avenues for the development of next generation fusion inhibitors with improved antiviral activity.
Enablers for Transport Layer Protocol Evolution (2015)

In this document we collected requirements for TLP evolution. These
requirements are the consequence of removing obstacles of TLP
evolution. This results in a higher variety of expected TLP
implementations and lower trust level in these. Confidentiality of
communication and security is more and more important. Middleboxes
which today are one of the obstacles of the evolution shall be taken
into account and incentivized to cooperate in the future landscape.
Resulting from the requirements we propose areas for further
investigation.
<title>Segmentation of textured images based on multiple fractal feature combinations</title> (1998)

This paper describes an approach to segmentation of textured grayscale images using a technique based on image filtering and the fractal dimension (FD). Twelve FD features are computed based on twelve filtered versions of the original image using directional Gabor filters. Features are computed in a window and mapped to the central pixel of this window. An iterative K-means-based algorithm which includes feature smoothing and takes into consideration the boundaries between textures is used to segment an image into a desired number of clusters. This approach is partially supervised since the number of clusters has to be predefined. The fractal features are compared to Gabor energy features and the iterative K- means algorithm is compared to the original K-means clustering approach. The performance of segmentation for noisy images is also studied.
Supplementary Figure 7 from RapidCaP, a Novel GEM Model for Metastatic Prostate Cancer Analysis and Therapy, Reveals Myc as a Driver of <i>Pten</i>-Mutant Metastasis (2023)

&lt;p&gt;PDF file 154K, Molecular and pathology analysis of prostate and its spread to other tissues&lt;/p&gt;
New optical correlator technique for header recognition in self-routing networks (1993)

Header or routing-tag processing is an essential function in packet switching. At each switching node the header is decoded and the information in the header is used to route the message data to the desired destination. In this contribution we describe a new technique for header recognition in the optical domain. The technique is based on an optical-loop mirror with a semiconductor laser amplifier (SLA). The SLA in a loop-mirror configuration (SLALOM) was introduced recently.1 As depicted in Fig. 1, the SLALOM consists of a 3-dB coupler with two arms connected to form a loop. The loop contains a SLA and a delay line with delay T. The SLALOM was operated as an optical correlator for picosecond pulses. Two pulses, separated by a time interval of τ, were fed to the input and, at the output, an optical pulse was obtained for τ = T. With a contrast ratio of 13 dB there was no output signal if |τ — T| was larger than the gain recovery time of the SLA.
The shoulder: adaptive motion correction of MR images. (1997)

Adaptive motion correction improved image quality in approximately three-quarters of the examinations in which motion was present.
A Category of Surface-Embedded Graphs (2022)

We introduce a categorical formalism for rewriting surface-embedded graphs. Such graphs can represent string diagrams in a non-symmetric setting where we guarantee that the wires do not intersect each other. The main technical novelty is a new formulation of double pushout rewriting on graphs which explicitly records the boundary of the rewrite. Using this boundary structure we can augment these graphs with a rotation system, allowing the surface topology to be incorporated.
ChemInform Abstract: Identification of Potent, Highly Constrained CGRP Receptor Antagonists. (2010)

Abstract A novel series of potent CGRP receptor antagonists containing a central quinoline ring constraint is identified.
Monolithic Integration of a Micropin-Fin Heat Sink in a 28-nm FPGA (2017)

Microfluidic cooling has been demonstrated as an effective means of cooling microelectronic circuits with a very low convective thermal resistance and potential for integration in close proximity to the area of heat generation. However, microfluidic cooling experiments to date have been limited to silicon with resistive heaters representing the heat generating circuitry. In this paper, a micropin-fin heat sink is etched into the back side of an Altera Stratix V field-programmable gate array (FPGA), built in a 28-nm CMOS process. Thermal and electrical measurements are made running a benchmark pulse compression algorithm on the FPGA. Deionized water is used as a coolant with flow rates ranging from 0.15 to 3.0 mL/s and inlet temperature ranging from 21 °C to 50 °C. An average junction-to-inlet thermal resistance of 0.07 °C/W is achieved.
Development of Thinned Aluminum Flat Heat Pipe Through Inclined Wall and Press Process (2019)

Heat pipes, commonly used for heat dissipation and thermal management in small electronic and communication devices, are regarded as an excellent solution. Heat pipes must be in surface rather than line contact to be applied to the module and system-level heat dissipation package. As such, a round copper heat pipe is transformed into a plate-like shape through a secondary press process. In this study, an extrusion structure is designed to be sloped to solve the difficulty of making it relatively thin compared with the large area of the plate structure. Specifically, substantial partitions separating the working fluid flow space in the plate-type heat pipe are designed to be inclined at 45 deg, and the extruded envelope is developed to obtain the desired total thickness through the secondary press process. The capillary structure is inserted and positioned within the envelope prior to the secondary press process. In this study, an aluminum flat heat pipe (AFHP) with 0.95 mm total thickness, 150 mm total length, and a capillary structure with braided or carbon wire bundles added thereto was designed and manufactured. Performance test results indicated that the heat transfer performance of the AFHP with inclined wall did not show any deterioration characteristic compared with the AFHP with a normal vertical wall. The isothermal characteristics and heat transfer rate of the AFHP with Cu braid wick were superior to those of AFHP with a simple rectangular groove wick. By contrast, when the carbon wire bundle is added in the Cu braid, the isothermal characteristic was enhanced twice, and the heat transfer rate was 15.5 W by improving approximately 42% under the conditions that inclination angle is −90 deg and the evaporator temperature does not exceed 110 °C.
Properties of Glass-Ceramic for Solid Oxide Fuel Cells (2008)

The thermal stability of ‘invert’ glass-ceramics, based on crystalline pyro- and orthosilicate phases, developed for hermetic seals for solid oxide fuel cells (SOFC) are described. The effects of long-term (up to 60 days) high temperature (up to 800°C) heat treatments on the properties of the glass-ceramics in oxidizing and reducing environments were evaluated by dilatometric analyses, x-ray diffraction, weight loss measurements, and impedance spectroscopy. The glass-ceramics have thermal expansion coefficients in the range 9.5-11.5 × 10−6/°C and can be sealed to SOFC materials, including Y2O3-stabilized ZrO2 (YSZ) and Cr-steel interconnect alloys, at or below 900°C. The thermal expansion characteristics of some glassceramics remain essentially unchanged after >40 days at 800°C, and the glass conductivity at 750°C remains constant (in the range 0.3-1.0 × 10−7 S/cm) in forming gas.
An accommodating opto-mechanical model of the aging human eye (2011)

The objective of this paper is to create a new accommodating opto-mechanical model of the aging human eye for basic optical and mechanical simulations. This model can be used for the evaluation and simulation of laser treatments of presbyopia or other diseases of the human eye. The presented eye model contains a lens, structured by cortex and nucleus, which is mechanically simulated by a finite element model (FEM) with the program ANSYS. The model is orientated on physiologically measured values describing the dependences of geometrical lens parameters on age and accommodation. The results of this mechanical simulation are used as input for a complete optical eye model, implemented in the software ZEMAX. The optical performance of the model corresponds with clinical data. The resulting joined opto-mechanical model describes the accommodation of the aging eye. Established optical eye models like those of Koretz et al., Dubbelman et al. and Norrby are used as reference to show the level of correspondence between them and the eye model presented here. Due to a different approach, the presented model makes it possible to explain the changes in the geometric optical parameters during accommodation; for this purpose it uses the changes caused by the stiffness and the effecting forces in the mechanical lens model. The model is suitable for different optical simulations especially for theoretical investigations to develop treatment methods of presbyopia. The state of presbyopia is controlled by the stiffness choice in the mechanical lens model.
Supplementary Figure 4 from A Diverse Array of Cancer-Associated <i>MTOR</i> Mutations Are Hyperactivating and Can Predict Rapamycin Sensitivity (2023)

&lt;p&gt;PDF file 143K, mTOR mutants alter Deptor binding and nutrient deprivation, but not sensitivity to mTOR inhibitors&lt;/p&gt;
Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It (2019)

Rapid sample preparation is one of the leading bottlenecks to low-cost and efficient sample component detection. To overcome this setback, a technology known as Lyse-It has been developed to rapidly (less than 60 seconds) lyse Gram-positive and-negative bacteria alike, while simultaneously fragmenting DNA/RNA and proteins into tunable sizes. This technology has been used with a variety of organisms, but the underlying mechanism behind how the technology actually works to fragment DNA/RNA and proteins has hitherto been studied. It is generally understood how temperature affects cellular lysing, but for DNA/RNA and protein degradation, the temperature and amount of energy introduced by microwave irradiation of the sample, cannot explain the degradation of the biomolecules to the extent that was being observed. Thus, an investigation into the microwave generation of reactive oxygen species, in particular singlet oxygen, hydroxyl radicals, and superoxide anion radicals, was undertaken. Herein, we probe one aspect, the generation of reactive oxygen species (ROS), which is thought to contribute to a non-thermal mechanism behind biomolecule fragmentation with the Lyse-It technology. By utilizing off/on (Photoinduced electron transfer) PET fluorescent-based probes highly specific for reactive oxygen species, it was found that as oxygen concentration in the sample and/or microwave irradiation power increases, more reactive oxygen species are generated and ultimately, more oxidation and biomolecule fragmentation occurs within the microwave cavity.
Static and Modal Topology Optimization of Turbomachinery Components (2016)

The need to be more and more competitive is pushing the complexity of aerodynamic and mechanical design of rotating machines at very high levels. New concepts are required to improve the current machine performances from many points of view: aerodynamics, mechanics, rotordynamics, and manufacturing. Topology optimization is one of the most promising new approaches in the turbomachinery field for mechanical optimization of rotoric and statoric components. It can be a very effective enabler to individuate new paths and strategies, and to go beyond techniques already consolidated in turbomachinery design, such as parametric and shape optimizations. Topology optimization methods improve material distribution within a given design space (for a given set of boundary conditions and loads) to allow the resulting layout to meet a prescribed set of performance targets. Topology optimization allows also to change the topology of the structures (e.g., when a shape splits into two parts or develops holes). This methodology has been applied to a turbine component to reduce the static stress level and the weight of the part and, at the same time, to tune natural frequencies. Thus, the interest of this work is to investigate both static and dynamic/modal aspects of the structural optimization. These objectives can be applied alone or in combination, performing a single analysis or a multiple analysis optimization. It has been possible to improve existing components and to design new concepts with higher performances compared to the traditional ones. This approach could be also applied to other generic components. The research paper has been developed in collaboration with Nuovo Pignone General Electric S.p.A. that has provided all the technical documentation. The developed geometries of the prototypes will be manufactured in the near future with the help of an industrial partner.
WLC32-3: A Distributed Opportunistic Access Scheme for OFDMA Systems (2006)

In this paper, we propose a distributed opportunistic access scheme for uplink OFDMA systems. The sub-carriers are grouped into several sub-channels and users access those sub-channels through a distributed access scheme without requiring extensive information exchange with the access point. Our proposed scheme allows several parallel contention subchannels to exploit multiuser diversity. Using knowledge of all the sub-channels, obtained through a periodically-transmitted beacon signal from the access point, all users contend on their strongest sub-channel(s). The proposed scheme applies a novel backoff mechanism utilizing this sub-channel knowledge to yield further throughput improvement in addition to the throughput gain obtained by the collision reduction design. To a user, the better the sub-channel gain is, the smaller the backoff time on that sub-channel, and hence, the higher the access priority of the user on that sub-channel. Compared with the traditional centralized OFDMA systems, our proposed scheme reduces overhead significantly and achieves a better spectral efficiency as corroborated by the simulation results.
Divide-and-concatenate: an architecture level optimization technique for universal hash functions (2004)

We present an architecture optimization technique called divide-and-concatenate for universal hash functions. The area of a multiplier increases quadratically and its speed increases gradually with the operand size and two universal hash functions are equivalent if they have the same collision probability property. Based on these observations, the divide-and-concatenate approach divides a 2w-bit data path (with collision probability 2-2w) into two w-bit data paths (each with collision probability 2-w), applies one message word to these two w-bit data paths and concatenates their results to construct an equivalent 2w-bit data path (with collision probability 2-2w). We demonstrate this technique on Linear Congruential Hash (LCH) family. When compared to the 100% overhead associated with duplicating a straightforward 32-bit LCH data path, the divide-and-concatenate approach that uses four equivalent 8-bit data paths yields a 101% increase in throughput with only 52% hardware overhead.
Proteome of monoclonal antibody‐purified haustoria from Puccinia triticina Race‐1 (2014)

Puccinia triticina causes leaf rust, a disease that causes annual yield losses in wheat. It is an obligate parasite that invades the host leaf and forms intracellular structures called haustoria, which obtain nutrients and suppress host immunity using secreted proteins called effectors. Since effector proteins act at the frontier between plant and pathogen and help determine the outcome of the interaction, it is critical to understand their functions. Here, we used a direct proteomics approach to identify effector candidates from P. triticina Race 1 haustoria isolated with a specific monoclonal antibody. Haustoria were >95% pure and free of host contaminants. Using high resolution MS we have identified 1192 haustoria proteins. These were quantified using normalized spectral counts and spanned a dynamic range of three orders of magnitude, with unknown proteins and metabolic enzymes as the most highly represented. The dataset contained 140 candidate effector proteins, based on the presence of a signal peptide and the absence of a known function for the protein. Some of these candidates were significantly enriched with cysteine, with up to 13 residues per protein and up to 6.8% cysteine in composition.
Abstract 17158: Patient-Specific Analysis of Pre-Surgical Leaflet Deformations to Predict Outcomes of Surgical Repair for Ischemic Mitral Regurgitation (2020)

Introduction: Ischemic mitral regurgitation (IMR) is a highly prevalent disorder, and current methods of repair have suboptimal rates of failure. Accounting for patient-specific variations in the pre-surgical deformation patterns of the mitral valve (MV) may allow for better prediction of post-surgical outcomes. Methods: Real-time 3D echocardiographic images of the MV were segmented to create geometric representations for 20 patients (10 with and 10 without IMR recurrence) immediately pre- and post-annuloplasty repair as well as for 5 healthy MVs. To build correspondence between the open and closed valve geometries in each state, we morphed the open state geometry to the closed state shape within a finite element framework. Metrics including directional in-plane strains, leaflet area, and orifice dimensions were then computed and compared between the valves with and without recurrent IMR. Results: We found that MVs with IMR had significantly lower magnitudes of compressive circumferential strain in the posterior leaflet and higher radial strains across the whole MV than MVs without IMR (Figure). Patients who would later exhibit MR recurrence were found to have significantly higher circumferential leaflet strain in the anterior commissure prior to surgery than those without recurrence (p = 0.0228). The recurrent MVs also had significantly larger leaflet areas and annuli than the non-recurrent MVs, and their annuli contracted less. Conclusions: Key characteristics of IMR including increased downward leaflet tethering, annular dilation, and reduced ability to contract were most pronounced in MVs with recurrent IMR, suggesting that valves with recurrence may be in a more progressed disease state pre-surgically or may have a different manifestation of the myocardial infarct. Such factors could be used to predict post-surgical IMR recurrence and improve surgical planning.