gebhart/patrepeval huggingface dataset:
A CT-Based Automated Algorithm for Airway Segmentation Using Freeze-and-Grow Propagation and Deep Learning (2020)

Chronic obstructive pulmonary disease (COPD) is a common lung disease, and quantitative CT-based bronchial phenotypes are of increasing interest as a means of exploring COPD sub-phenotypes, establishing disease progression, and evaluating intervention outcomes. Reliable, fully automated, and accurate segmentation of pulmonary airway trees is critical to such exploration. We present a novel approach of multi-parametric freeze-and-grow (FG) propagation which starts with a conservative segmentation parameter and captures finer details through iterative parameter relaxation. First, a CT intensity-based FG algorithm is developed and applied for airway tree segmentation. A more efficient version is produced using deep learning methods generating airway lumen likelihood maps from CT images, which are input to the FG algorithm. Both CT intensity- and deep learning-based algorithms are fully automated, and their performance, in terms of repeat scan reproducibility, accuracy, and leakages, is evaluated and compared with results from several state-of-the-art methods including an industry-standard one, where segmentation results were manually reviewed and corrected. Both new algorithms show a reproducibility of 95% or higher for total lung capacity (TLC) repeat CT scans. Experiments on TLC CT scans from different imaging sites at standard and low radiation dosages show that both new algorithms outperform the other methods in terms of leakages and branch-level accuracy. Considering the performance and execution times, the deep learning-based FG algorithm is a fully automated option for large multi-site studies.
Load balancing in wireless network (2002)

With the growth of wireless subscribers, the service providers face the challenge of how to maximize their network capacity with their existing infrastructure. In a distributed home location register (HLR) wireless network architecture, the mobility of subscribers is a significant factor in resource allocation, and has tremendous impact on network capacity, since the subscriber location must be updated on a regular basis. One approach to maximize the usage of network resources is to balance the subscribers among the MSC (mobile switching center) elements, taking into account their mobility. This paper describes an efficient methodology to solve the load balancing problem by rehoming some of the subscribers in the network, and to maximize network capacity by performing a minimum number of rehoming of subscribers. An algorithm is proposed that balances the load among MSCs with improvement in network capacity.
(<i>N</i>)-Methanocarba 2,<i>N</i><sup>6</sup>-Disubstituted Adenine Nucleosides as Highly Potent and Selective A<sub>3</sub> Adenosine Receptor Agonists (2004)

A series of ring-constrained (N)-methanocarba-5'-uronamide 2,N(6)-disubstituted adenine nucleosides have been synthesized via Mitsunobu condensation of the nucleobase precursor with a pseudosugar ring containing a 5'-ester functionality. Following appropriate functionalization of the adenine ring, the ester group was converted to the 5'-N-methylamide. The compounds, mainly 2-chloro-substituted derivatives, were tested in both binding and functional assays at human adenosine receptors (ARs), and many were found to be highly potent and selective A(3)AR agonists. Selected compounds were compared in binding to the rat A(3)AR to assess their viability for testing in rat disease models. The N(6)-(3-chlorobenzyl) and N(6)-(3-bromobenzyl) analogues displayed K(i) values at the human A(3)AR of 0.29 and 0.38 nM, respectively. Other subnanomolar affinities were observed for the following N(6) derivatives: 2,5-dichlorobenzyl, 5-iodo-2-methoxybenzyl, trans-2-phenyl-1-cyclopropyl, and 2,2-diphenylethyl. Selectivity for the human A(3)AR in comparison to the A(1)AR was the following (fold): the N(6)-(2,2-diphenylethyl) analogue 34 (1900), the N(6)-(2,5-dimethoxybenzyl) analogue 26 (1200), the N(6)-(2,5-dichlorobenzyl) and N(6)-(2-phenyl-1-cyclopropyl) analogues 20 and 33 (1000), and the N(6)-(3-substituted benzyl) analogues 17, 18, 28, and 29 (700-900). Typically, even greater selectivity ratios were obtained in comparison with the A(2A) and A(2B)ARs. The (N)-methanocarba-5'-uronamide analogues were full agonists at the A(3)AR, as indicated by the inhibition of forskolin-stimluated adenylate cyclase at a concentration of 10 microM. The N(6)-(2,2-diphenylethyl) derivative was an A(3)AR agonist in the (N)-methanocarba-5'-uronamide series, although it was an antagonist in the ribose series. Thus, many of the previously known groups that enhance A(3)AR affinity in the 9-riboside series, including those that reduce intrinsic efficacy, may be adapted to the (N)-methanocarba nucleoside series of full agonists.
Data-driven framework for detecting anomalies in field failure data (2011)

This paper discusses the design of a data-driven framework for detecting anomalies in the automotive field failure and repair data. The anomaly detection framework detects anomalies at two levels: 1) It detects anomalies in repair data using system-level fault model (or fault dependency-matrix) and diagnostic reasoner; 2) It detects anomalies in diagnostic trouble code (DTC) data using operating sensory parameter identifiers (PIDs) data mining. The system-level fault model provides a way to capture causal relationships between failures and symptoms of a given system. A repair is declared as anomalous if it does not match the repair recommended by the fault model and diagnostic reasoner. The PIDs data mining detects anomalies in DTC data by detecting patterns in the associated PIDs using various statistical techniques such as scatter plots, clustering and decision trees. The DTC anomalies could be either due to errors in the preconditions under which the DTCs are designed to set or errors while implementing them in the software. The PIDs data mining module provides a focused feedback to engineers for detecting the errors in DTC software algorithms and enhancing the diagnostic design of DTCs during the early stages of vehicle production. We demonstrate the data-driven framework on automobile fuel vapor pressure sensor problem.
Dynamic Understanding of Human-Skin Movement and Strain-Field Analysis (2012)

Understanding the skin's material properties and natural motion is critical to a myriad of applications from tissue engineering to spacesuits. While there is an extensive understanding of human skin properties based on active tensile testing, both in vitro and in vivo, there is a little current knowledge of the strains experienced by skin during natural movements. Using a motion capture system, we have developed a new technique to measure skin movement and strain around the knee during a squatting motion. With these new data, we are also able to calculate the local direction of lines of nonextension, or contours of the skin that remain a constant length during motion, lines of minimum extension, and lines of minimum compression.
Nanocrystalline Manganese-Molybdenum-Tungsten Oxide Anodes for Oxygen Evolution in Acidic Seawater Electrolysis (2005)

In an attempt to tailor new oxygen evolution anodes for acidic seawater electrolysis, manganese-molybdenum-tungsten oxide anodes were prepared by anodic deposition on IrO2/Ti substrate using 0.2 kmol m−3 MnSO4-(0.00–0.006) kmol m−3 Na2MoO4-(0.0–0.03) kmol m−3 Na2WO4 electrolytes at pH −0.1∼+1.0 and 363 K at 600 Am−2. The deposits consist of a nanocrystalline single γ-MnO2 type phase in the form of triple Mn1−x−yMoxWyO2+x+y oxide. Anodic deposition in 0.2 kmol m−3 Mn2+-0.003 kmol m−3 Mo6+-0.006 kmol m−3 W6+ electrolyte at pH 0.0 resulted in the formation of an electrode with 100% and 99.8% oxygen evolution efficiencies before and after electrolysis for 691.2 ks in 0.5 kmol m−3 NaCl solution of pH 2 at 1000 Am−2. Thus, Mn1−x−yMoxWyO2+x+y electrodes were promising oxygen evolving anodes for acidic seawater electrolysis. It has been concluded that additions of both tungsten and molybdenum beneficially bring about an increase in the real electro-catalytic activity along with the formation of deposits with optimum thickness and good adherence to the IrO2/Ti substrate.
<i>Staphylococcus aureus</i> Sortase, an Enzyme that Anchors Surface Proteins to the Cell Wall (1999)

Surface proteins of Gram-positive bacteria are linked to the bacterial cell wall by a mechanism that involves cleavage of a conserved Leu-Pro-X-Thr-Gly (LPXTG) motif and that occurs during assembly of the peptidoglycan cell wall. A Staphylococcus aureus mutant defective in the anchoring of surface proteins was isolated and shown to carry a mutation in the srtA gene. Overexpression of srtA increased the rate of surface protein anchoring, and homologs of srtA were found in other pathogenic Gram-positive bacteria. The protein specified by srtA, sortase, may be a useful target for the development of new antimicrobial drugs.
An All-Dielectric Coaxial Waveguide (2000)

An all-dielectric coaxial waveguide that can overcome problems of polarization rotation and pulse broadening in the transmission of optical light is presented here. It consists of a coaxial waveguiding region with a low index of refraction, bounded by two cylindrical, dielectric, multilayer, omnidirectional reflecting mirrors. The waveguide can be designed to support a single mode whose properties are very similar to the unique transverse electromagnetic mode of a traditional metallic coaxial cable. The new mode has radial symmetry and a point of zero dispersion. Moreover, because the light is not confined by total internal reflection, the waveguide can guide light around very sharp corners.
Epitaxial Ni3FeN thin films: A candidate for spintronic devices and magnetic sensors (2012)

A new type of epitaxial ferromagnetic nitride (Ni3 Fe N = permalloy nitride = “PyN”) compound films were grown on Al2O3(112¯0) substrates using reactive triode magnetron sputtering. The results of electron back-scattering diffraction and x-ray diffraction techniques indicate a high quality epitaxial crystalline structure with growth normal of (100). Magnetization measurements of epitaxial PyN films revealed several unique results. (1) A textbook square hysteresis loop that suggest existence of single magnetic domain in these films. (2) A coercive field is tunable from a few mOe up to a few Oe by changing the film thickness. (3) A magnetization that switches (rotate) over a very small field range of δHC ≤ 0.05 Oe, independent of the film thickness. This small δH indicates a very large resistive sensitivity (δR/δH) of the epitaxial PyN. (4) The epitaxial PyN thermal cycling through several cycles between “2 and 800 K” (−271 °C to +527 °C) shows much less degradation only about 2–5% compared to 40% degradation of a simple Py film. Four-probe transport measurements give an anisotropic magnetoresistance of ≈6%, sufficiently higher than other known ferromagnetic materials. These interesting properties are ideal for a variety of spintronic devices and magnetic sensors.
Secure Authentication using the Ultrafast Response of Chaotic Silicon Photonic Microcavities (2016)

We demonstrate a cryptographic primitive and authentication system based on the ultrafast response of reverberant integrated photonic cavities formed in silicon, which leverage the unpredictability of leaky chaotic systems.
A Broad-Spectrum Microbicide with Virucidal Activity against Sexually Transmitted Viruses (1999)

Sodium dodecyl sulfate (SDS), an alkyl sulfate surfactant derived from an organic alcohol, possesses surfactant properties but also denatures and unfolds both monomeric and subunit proteins. In preliminary experiments, we demonstrated that SDS is a potent inactivator of herpes simplex virus type 2 and human immunodeficiency virus type 1 at concentrations comparable to those used for the surfactant nonoxynol-9. We hypothesized that SDS might be capable of denaturing the capsid proteins of nonenveloped viruses. In this report, we demonstrate inactivation of rabbit, bovine, and human papillomaviruses after brief treatment with dilute solutions of SDS. Effective concentrations were nontoxic to rabbit skin and to split-thickness grafts of human foreskin epithelium. This is the first report of a microbicidal surfactant that will inactivate papillomaviruses. We propose that SDS is now a candidate microbicide for formulation and testing with humans.
Image feature analysis and computer‐aided diagnosis in digital radiography: Automated detection of pneumothorax in chest images (1992)

In order to aid radiologists in the diagnosis of pneumothorax from chest radiographs, an automated method for detection of subtle pneumothorax is being developed. The computerized method is based on the detection of a fine curved-line pattern, which is a unique feature of radiographic findings of pneumothorax. Initially, regions of interest (ROIs) are determined in each upper lung area, where subtle pneumothoraces commonly appear. The pneumothorax pattern is enhanced by the selection of edge gradients within a limited range of orientations. Rib edges included in this edge-enhanced image are removed, based on the locations of posterior ribs that are determined separately. A subtle curved line due to pneumothorax is then detected by means of the Hough transform. The detected pneumothorax pattern is marked on the chest image displayed on a CRT monitor. With the present computer method applied to 50 chest images (28 normals and 22 abnormals with pneumothorax), we were able to detect 77% of pneumothoraces, with 0.44 false-positives per image.
Efficient exon skipping of SGCG mutations mediated by phosphorodiamidate morpholino oligomers (2018)

Exon skipping uses chemically modified antisense oligonucleotides to modulate RNA splicing. Therapeutically, exon skipping can bypass mutations and restore reading frame disruption by generating internally truncated, functional proteins to rescue the loss of native gene expression. Limb-girdle muscular dystrophy type 2C is caused by autosomal recessive mutations in the SGCG gene, which encodes the dystrophin-associated protein γ-sarcoglycan. The most common SGCG mutations disrupt the transcript reading frame abrogating γ-sarcoglycan protein expression. In order to treat most SGCG gene mutations, it is necessary to skip 4 exons in order to restore the SGCG transcript reading frame, creating an internally truncated protein referred to as Mini-Gamma. Using direct reprogramming of human cells with MyoD, myogenic cells were tested with 2 antisense oligonucleotide chemistries, 2'-O-methyl phosphorothioate oligonucleotides and vivo-phosphorodiamidate morpholino oligomers, to induce exon skipping. Treatment with vivo-phosphorodiamidate morpholino oligomers demonstrated efficient skipping of the targeted exons and corrected the mutant reading frame, resulting in the expression of a functional Mini-Gamma protein. Antisense-induced exon skipping of SGCG occurred in normal cells and those with multiple distinct SGCG mutations, including the most common 521ΔT mutation. These findings demonstrate a multiexon-skipping strategy applicable to the majority of limb-girdle muscular dystrophy 2C patients.
Skew Measurements in Clock Distribution Circuits Using an Analytic Signal Method (2004)

This paper presents the application of a new analytic signal method for measuring several different kinds of clock skew in the clock distribution network of microprocessors. First, key terms are defined, and other existing skew measurement methods are reviewed. Then, detailed steps are given for applying the new method for measuring skew between a master and distributed clocks, between two distributed clocks, and between different frequency clocks that are related by frequency division. An indirect procedure for measuring deterministic clock skew is also proposed. Next, the new method is validated with experimental data from a prototype microprocessor test. Performance comparison is performed between the analytic signal method and the two-probe method. Finally, the measurement requirements of the proposed analytic signal method are compared with those of conventional methods.
Depth from motion for smartphone AR (2018)

Augmented reality (AR) for smartphones has matured from a technology for earlier adopters, available only on select high-end phones, to one that is truly available to the general public. One of the key breakthroughs has been in low-compute methods for six degree of freedom (6DoF) tracking on phones using only the existing hardware (camera and inertial sensors). 6DoF tracking is the cornerstone of smartphone AR allowing virtual content to be precisely locked on top of the real world. However, to really give users the impression of believable AR, one requires mobile depth. Without depth, even simple effects such as a virtual object being correctly occluded by the real-world is impossible. However, requiring a mobile depth sensor would severely restrict the access to such features. In this article, we provide a novel pipeline for mobile depth that supports a wide array of mobile phones, and uses only the existing monocular color sensor. Through several technical contributions, we provide the ability to compute low latency dense depth maps using only a single CPU core of a wide range of (medium-high) mobile phones. We demonstrate the capabilities of our approach on high-level AR applications including real-time navigation and shopping.
The road to optogenetics: Microbial rhodopsins (2016)

Optogenetics technology (using light-sensitive microbial proteins to control animal cell physiology) is becoming increasingly popular in laboratories around the world. Among these proteins, particularly important are rhodopsins that transport ions across the membrane and are used in optogenetics to regulate membrane potential by light, mostly in neurons. Although rhodopsin ion pumps transport only one charge per captured photon, channelrhodopsins are capable of more efficient passive transport. In this review, we follow the history of channelrhodopsin discovery in flagellate algae and discuss the latest addition to the channelrhodopsin family, channels with anion, rather than cation, selectivity.
A near-field scanning SQUID microwave microscope (2013)

We developed a scanning DC SQUID microscope with novel readout electronics capable of wideband sensing RF magnetic fields from 50 to 200 MHz and simultaneously providing closed-loop response at kHz frequencies. To overcome the 20 MHz bandwidth limitation of traditional closed-loop SQUIDs, a flux-modulated closed loop simultaneously locks the SQUID quasi-static flux and flux-biases the SQUID for amplification of the RF flux up to $Φ_0/4$ in amplitude. Demodulating the SQUID voltage with a double lock-in technique yields a signal representative of both the amplitude and phase of the RF flux. This provides 80 dB of a linear dynamic range with the flux noise density of 4 $μΦ_0/\sqrt{Hz}$ at 200 MHz for $YBa_2Cu_3O_7$ bi-crystal SQUID at 77 K. We describe the electronics performance and present images for RF magnetic field of the travelling wave in a coplanar waveguide, the standing wave in an open-circuited microstrip, and a surface mounted device antenna.
Quantification of Intracellular HPV E6/E7 mRNA Expression Increases the Positive Predictive Value of Cervical Cancer Screening (2008)

Background: Current methods for HPV screening rely on the detection of L1 DNA from high risk genotypes (HR HPV). These assays have very high negative predictive values (~99%) and as such have been used to triage women to longer screening intervals. The literature has shown that the positive predictive value for pre-cancerous and cancerous lesions is less than 50% for HPV DNA screening. Objectives: The purpose of this study was to combine HPV DNA screening with HPV E6, E7 mRNA detection in an effort to improve the overall performance of cervical cancer screening while potentially reducing the number of women requiring colposcopy.Materials and Methods: Liquid based cervical cytology specimens collected in either PreservCyt or SurePath were submitted for routing cytology, HPV HRDNA detection by Hybrid Capture 2 and HPV E6, E7 mRNA quantification in cells. Results from these three analyses were compared to biopsy in 40 cases.Results: The positive predictive value of HPV E6, E7 mRNA quantification in cells was 86% which was greater than HPV DNA alone. The specificity was 96% based on 142 samples with normal cytology. There was a statistically significant difference in the percent of ectocervical cells expressing E6, E7 mRNA in women with CIN2, CIN3, or cancer (mean 14.7%) compared to women with normal cytology (mean 1.4%) with a p<0.001.
CRP measured by a high sensitivity assay correlates with clinical probability (Wells score) testing for deep venous thrombosis (2004)

CRP measured by a high sensitivity assay correlates with clinical probability (Wells score) testing for deep venous thrombosis -
Experimental validations of the learnable evolution model (2002)

A recently developed approach to evolutionary computation, called Learnable Evolution Model or LEM, employs machine learning to guide processes of generating new populations. The central new idea of LEM is that it generates new individuals not by mutation and/or recombination, but by processes of hypothesis generation and instantiation. The hypotheses are generated by a machine learning system from examples of high and low performance individuals. When applied to problems of function optimization and parameter estimation for nonlinear filters, LEM significantly outperformed the standard evolutionary computation algorithms used in experiments, sometimes achieving two or more orders of magnitude of evolutionary speed-up (in terms of the number of births). An application of LEM to the problem of optimizing heat exchangers has produced designs equal to or exceeding the best human designs. Further research needs to explore trade-offs and determine best areas for LEM application.
A new family of active variable equalizers (1982)

An active version of the Bode-type variable equalizer has been designed. Variable equalizers are widely used for amplitude equalization in wide-band transmission systems because they possess the unique property that the equalization shape does not change as the amount of equalization is varied. Such a property is especially desirable when equalizing cable of varying length. The active variable equalizer to be described here overcomes many of the disadvantages associated with the conventional passive version, which include the need for inductors, a complex design procedure, and incompatibility with modem electronic control elements. This design also has advantages over other active variable equalizer designs. Such an equalizer is especially applicable to precision equalization at frequencies below 10 MHz. As an example, a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\sqrt{f}</tex> equalizer can be built with a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\pm 9-dB</tex> range having only <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\pm 0.05-dB</tex> maximum error. The equalizer is easily built with operational amplifiers and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RC</tex> networks.