gebhart/patrepeval huggingface dataset:
Fatty Acid Remodeling of GPI-anchored Proteins Is Required for Their Raft Association (2007)

Whereas most of the cellular phosphatidylinositol (PI) contain unsaturated fatty chains and are excluded from rafts, GPI-anchored proteins (APs) unusually contain two saturated fatty chains in their PI moiety, and they are typically found within lipid rafts. However, the origin of the saturated chains and whether they are essential for raft association are unclear. Here, we report that GPI-APs, with two saturated fatty chains, are generated from those bearing an unsaturated chain by fatty acid remodeling that occurs most likely in the Golgi and requires post-GPI-attachment to proteins (PGAP)2 and PGAP3. The surface GPI-APs isolated from the PGAP2 and -3 double-mutant Chinese hamster ovary (CHO) cells had unsaturated chains, such as oleic, arachidonic, and docosatetraenoic acids in the sn-2 position, whereas those from wild-type CHO cells had exclusively stearic acid, a saturated chain, indicating that the sn-2 chain is exchanged to a saturated chain. We then assessed the association of GPI-APs with lipid rafts. Recovery of unremodeled GPI-APs from the double-mutant cells in the detergent-resistant membrane fraction was very low, indicating that GPI-APs become competent to be incorporated into lipid rafts by PGAP3- and PGAP2-mediated fatty acid remodeling. We also show that the remodeling requires the preceding PGAP1-mediated deacylation from inositol of GPI-APs in the endoplasmic reticulum.
Deep Learning for Algorithm Portfolios (2016)

It is well established that in many scenarios there is no single solver that will provide optimal performance across a wide range of problem instances. Taking advantage of this observation, research into algorithm selection is designed to help identify the best approach for each problem at hand. This segregation is usually based on carefully constructed features, designed to quickly present the overall structure of the instance as a constant size numeric vector. Based on these features, a plethora of machine learning techniques can be utilized to predict the appropriate solver to execute, leading to significant improvements over relying solely on any one solver. However, being manually constructed, the creation of good features is an arduous task requiring a great deal of knowledge of the problem domain of interest. To alleviate this costly yet crucial step, this paper presents an automated methodology for producing an informative set of features utilizing a deep neural network. We show that the presented approach completely automates the algorithm selection pipeline and is able to achieve significantly better performance than a single best solver across multiple problem domains.
Self-locking Optoelectronic Tweezers for micro-particle manipulation (2014)

We presented a novel Self-Locking Optoelectronic Tweezers (SLOT) for micro-particle manipulation. DEP force generated from ring-shape electrodes is utilized for micro-particle self-locking followed by selectively single particle releasing with lateral phototransistor-based optoelectronic tweezers. Single particle locking and releasing function were demonstrated.
Voltage Correlations in Smart Meter Data (2015)

The connectivity model of a power distribution network can easily become outdated due to system changes occurring in the field. Maintaining and sustaining an accurate connectivity model is a key challenge for distribution utilities worldwide. This work shows that voltage time series measurements collected from customer smart meters exhibit correlations that are consistent with the hierarchical structure of the distribution network. These correlations may be leveraged to cluster customers based on common ancestry and help verify and correct an existing connectivity model. Additionally, customers may be clustered in combination with voltage data from circuit metering points, spatial data from the geographical information system, and any existing but partially accurate connectivity model to infer customer to transformer and phase connectivity relationships with high accuracy.
Identification of the region of a 14-kilodalton protein of Rhodococcus ruber that is responsible for the binding of this phasin to polyhydroxyalkanoic acid granules (1995)

The function of the polyhydroxyalkanoic acid (PHA) granule-associated GA14 protein of Rhodococcus ruber was investigated in Escherichia coli XL1-Blue, which coexpressed this protein with the polyhydroxybutyric acid (PHB) biosynthesis operon of Alcaligenes eutrophus. The GA14 protein had no influence on the biosynthesis rate of PHB in E. coli XL1-Blue(pSKCO7), but this recombinant E. coli strain formed smaller PHB granules than were formed by an E. coli strain that expressed only the PHB operon. Immunoelectron microscopy with GA14-specific antibodies demonstrated the binding of GA14 protein to these mini granules. In a previous study, two hydrophobic domains close to the C terminus of the GA14 protein were analyzed, and a working hypothesis that suggested an anchoring of the GA14 protein in the phospholipid monolayer surrounding the PHA granule core by these hydrophobic domains was developed (U. Pieper-Fürst, M. H. Madkour, F. Mayer, and A. Steinbüchel, J. Bacteriol. 176:4328-4337, 1994). This hypothesis was confirmed by the construction of C-terminally truncated variants of the GA14 protein lacking the second or both hydrophobic domains and by the demonstration of their inability to bind to PHB granules. Further confirmation of the hypothesis was obtained by the construction of a fusion protein composed of the acetaldehyde dehydrogenase II of A. eutrophus and the C terminus of the GA14 protein containing both hydrophobic domains and by its affinity to native and artificial PHB granules.
ICEMS: a platform for advanced condition-based health management (2002)

Health management of a machine, such as a gas turbine engine, offers the potential benefits of efficient operations planning and reduced cost of ownership. It requires a tight integration of major health management functions, such as trending, failure identification, forecasting, life prediction, operations and maintenance planning. Since 1985, the U. S. Air Force has been using a computer program to facilitate the trending and diagnostic functions for its engine fleets. This program is called Comprehensive Engine Trending and Diagnostic System (CETADS). Scientific Monitoring, Inc. (SMI) has been sponsored by the Air Force Research Laboratory to develop a suite of compatible, plug-in tools to enhance CETADS. These tools are configured as software modules, and are collectively called the Intelligent Condition-based Engine Management System (ICEMS). Alternatively, ICEMS modules provide comprehensive platform for equipment or machinery health management. In this implementation, it is a web-based infrastructure for condition monitoring and asset management.
A Rapid Testing Method of Stress Corrosion Cracking of Austenitic Stainless Steels (1974)

A new method was studied to evaluate the stress corrosion susceptibility of austenitic stainless steels from stress-strain curves observed under controlled tensile strain rate in MgCl2 solution boiling at 143°C. The results indicated that when the strain rate was low enough to cause metal dissolution at slip steps, stress corrosion cracking occurred. The fracture strain decreased with the decrease of strain rate. A good relation was obtained between the fracture time in the constant load test and stress corrosion susceptibility parameter, Pc(εc+1)⁄P(ε+1), where ε is the strain at the maximum load P under the strain rate of 0.67×10−2 sec−1, and εc is the strain at the maximum load Pc under the strain rate of 1.67×10−5 sec−1 in MgCl2 solution boiling at 143°C.
Determination of Inlet Transmission and Conversion Efficiencies for in Situ Measurements of the Nocturnal Nitrogen Oxides, NO<sub>3</sub>, N<sub>2</sub>O<sub>5</sub> and NO<sub>2</sub>, via Pulsed Cavity Ring-Down Spectroscopy (2008)

Pulsed cavity ring-down spectroscopy is a highly sensitive method for direct absorption spectroscopy that has been applied to in situ detection of NO3, N2O5 and NO2 in the atmosphere from a variety of platforms, including ships, aircraft, and towers. In this paper, we report the development of schemes to significantly improve the accuracy of these measurements. This includes the following: (1) an overall improvement in the inlet transmission efficiencies (92 +/- 2% for NO3 and 97 +/- 1% for N2O5) achieved primarily through a reduction in the inlet residence time; and (2) the development of a calibration procedure that allows regular determination of these efficiencies in the field by addition of NO3 or N2O5 to the inlet from a portable source followed by conversion of NO3 to NO2. In addition, the dependence of the instrument's sensitivity and accuracy to a variety of conditions encountered in the field, including variations in relative humidity, aerosol loading, and VOC levels, was systematically investigated. The rate of degradation of N2O5 transmission efficiency on the inlet and filter system due to the accumulation of inorganic aerosol was determined, such that the frequency of filter changes required for accurate measurements could be defined. In the absence of aerosol, the presence of varying levels of relative humidity and reactive VOC were found to be unimportant factors in the instrument's performance. The 1 sigma accuracy of the NO3, N2O5, and NO2 measured with this instrument are -9/+12, -8/+11, +/- 6%, respectively, where the -/+ signs indicate that the actual value is low/high relative to the measurement. The largest contribution to the overall uncertainty is now due to the NO3 absorption cross section rather than the inlet transmission efficiency.
Multi-Stage Pricing for Coordination of Thermostatically Controlled\n Loads: A Dynamic Stackelberg Game Approach (2015)

This paper focuses on multi-stage coordination for a population of\nthermostatically controlled loads (TCL). Each load maximizes the individual\nutility in response to an energy price, while the coordinator determines the\nprice to maximize the social welfare subject to a peak energy constraint. The\ncoordination problem is formulated as a dynamic Stackelberg game. The\nStackelberg solution is derived using an indirect approach: we first obtain an\nupper bound of the Stackelberg game, then we prove that this upper bound is\nattainable. Sufficient conditions for the optimal solution are characterized.\nBased on these conditions, a pricing algorithm with guaranteed convergence is\ndeveloped to compute the Stackelberg solution employing the monotonicity of the\nuser responses. Our control strategy is validated using real market data and\nweather information, and realistic simulation results are presented to\ndemonstrate the effectiveness of the proposed control framework.\n
Optical time-domain measurement of Brillouin dynamic grating spectrum in a polarization-maintaining fiber (2009)

We demonstrate the distributed measurement of Brillouin dynamic grating spectra in a polarization-maintaining fiber based on time-domain analysis. Local reflection spectra of the Brillouin dynamic grating are acquired by synchronized propagation of the pump and the probe pulses based on the map of the Brillouin frequency distribution. Large temperature sensitivity as high as -50.9 MHz/ degrees C is observed with 2 m spatial resolution in 100 m range.
Wavelet analysis in virtual colonoscopy (2006)

The computed tomographic colonography (CTC) computer aided detection (CAD) program is a new method in development to detect colon polyps in virtual colonoscopy. While high sensitivity is consistently achieved, additional features are desired to increase specificity. In this paper, a wavelet analysis was applied to CTCCAD outputs in an attempt to filter out false positive detections. 52 CTCCAD detection images were obtained using a screen capture application. 26 of these images were real polyps, confirmed by optical colonoscopy and 26 were false positive detections. A discrete wavelet transform of each image was computed with the MATLAB wavelet toolbox using the Haar wavelet at levels 1-5 in the horizontal, vertical and diagonal directions. From the resulting wavelet coefficients at levels 1-3 for all directions, a 72 feature vector was obtained for each image, consisting of descriptive statistics such as mean, variance, skew, and kurtosis at each level and orientation, as well as error statistics based on a linear predictor of neighboring wavelet coefficients. The vectors for each of the 52 images were then run through a support vector machine (SVM) classifier using ten-fold cross-validation training to determine its efficiency in distinguishing polyps from false positives. The SVM results showed 100% sensitivity and 51% specificity in correctly identifying the status of detections. If this technique were added to the filtering process of the CTCCAD polyp detection scheme, the number of false positive results could be reduced significantly.
Improved resonance technique for materials characterization (1983)

An improved resonance apparatus for materials characterization is described. The apparatus accurately determines the propagation constants of an extensional acoustic wave by exciting a bar of material at one end with a noise source, while the other end is allowed to move freely. Miniature accelerometers measure the acceleration at two locations and their output signals are analyzed by a dual channel FFT spectrum analyzer. At certain frequencies, the acceleration ratio goes through resonant peaks whose amplitudes and frequencies are related to the Young’s moduli and loss factors of the material. The apparatus is capable of measuring the acceleration ratio over a frequency range of 25 Hz to 20 kHz. As illustrations of the technique, Young’s modulus and loss factor were determined on a viscoelastic material; polyurethane (over a temperature range −13.4° to 81 °C) and on two metal matrix composite materials: a silicon carbide–aluminum and a graphite–aluminum. The apparatus was found to be a fast and reliable method to determine dynamic constants.
Acyclic modeling of combinational loops (2005)

This paper presents a method to convert gate-level combinational loop into an acyclic circuit, if the combinational loop is not oscillatory. Combinational loops breach design methodologies, because they can involve undesirable circuit behavior and can possibly lead to oscillations based on the external stimuli to the loops. However, for designs compiled using automated synthesis-compiler, these loops are very likely to appear in the generated gate-level designs. We present a modeling of combinational loops as state holding elements and break non oscillatory loops using a level sensitive latch. Apart from modeling combinational loops consisting of gates, the algorithm also converts the loops through design latches. The increase in design area, due to the loop conversion, has an upper bound of twice the size of the original feedback path. However, in case of multiply nested feedback paths, each path is treated separately. Unlike previous work that converts cyclic combinational logic where the feedback is not exercised, this paper presents an algorithm to identify the stateful latch behavior in a class of feedback logic (non-oscillatory, monotonic). A conversion algorithm replaces such feedback logic by an equivalent circuit comprising explicit latches and acyclic combinational logic. The replacement circuit has an identical behavior as the original stateful feedback logic.
Analytical Validation of a Melanoma Diagnostic Gene Signature Using Formalin-Fixed Paraffin-Embedded Melanocytic Lesions (2015)

These studies indicate this signature is robust and reproducible and is analytically validated on formalin-fixed paraffin-embedded melanocytic lesions.
Restoration of lysosomal acidification rescues autophagy and metabolic dysfunction in non-alcoholic fatty liver disease (2023)

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease in the world. High levels of free fatty acids in the liver impair hepatic lysosomal acidification and reduce autophagic flux. We investigate whether restoration of lysosomal function in NAFLD recovers autophagic flux, mitochondrial function, and insulin sensitivity. Here, we report the synthesis of novel biodegradable acid-activated acidifying nanoparticles (acNPs) as a lysosome targeting treatment to restore lysosomal acidity and autophagy. The acNPs, composed of fluorinated polyesters, remain inactive at plasma pH, and only become activated in lysosomes after endocytosis. Specifically, they degrade at pH of ~6 characteristic of dysfunctional lysosomes, to further acidify and enhance the function of lysosomes. In established in vivo high fat diet mouse models of NAFLD, re-acidification of lysosomes via acNP treatment restores autophagy and mitochondria function to lean, healthy levels. This restoration, concurrent with reversal of fasting hyperglycemia and hepatic steatosis, indicates the potential use of acNPs as a first-in-kind therapeutic for NAFLD.
Phase-Matching Techniques for Coherent Soft X-Ray Generation (2005)

Coherent beams at soft X-ray (SXR) wavelengths can be generated using extreme nonlinear optics by focusing an intense laser into a gas. In this paper, we discuss phase-matching and quasi-phase-matching techniques that use gas-filled modulated waveguides to enhance the frequency conversion process. This leads to the generation of SXR beams that are both spatially and temporally coherent.
Cystic fibrosis gene modifier <i>SLC26A9</i> modulates airway response to CFTR-directed therapeutics (2016)

Cystic fibrosis is realizing the promise of personalized medicine. Recent advances in drug development that target the causal CFTR directly result in lung function improvement, but variability in response is demanding better prediction of outcomes to improve management decisions. The genetic modifier SLC26A9 contributes to disease severity in the CF pancreas and intestine at birth and here we assess its relationship with disease severity and therapeutic response in the airways. SLC26A9 association with lung disease was assessed in individuals from the Canadian and French CF Gene Modifier consortia with CFTR-gating mutations and in those homozygous for the common Phe508del mutation. Variability in response to a CFTR-directed therapy attributed to SLC26A9 genotype was assessed in Canadian patients with gating mutations. A primary airway model system determined if SLC26A9 shows modification of Phe508del CFTR function upon treatment with a CFTR corrector. In those with gating mutations that retain cell surface-localized CFTR we show that SLC26A9 modifies lung function while this is not the case in individuals homozygous for Phe508del where cell surface expression is lacking. Treatment response to ivacaftor, which aims to improve CFTR-channel opening probability in patients with gating mutations, shows substantial variability in response, 28% of which can be explained by rs7512462 in SLC26A9 (P = 0.0006). When homozygous Phe508del primary bronchial cells are treated to restore surface CFTR, SLC26A9 likewise modifies treatment response (P = 0.02). Our findings indicate that SLC26A9 airway modification requires CFTR at the cell surface, and that a common variant in SLC26A9 may predict response to CFTR-directed therapeutics.
Active structural error suppression in MEMS vibratory rate integrating gyroscopes (2003)

Due to restrictive tolerancing in microfabrication, structural imperfections that reduce performance of fabricated micro devices are typical. In microelectromechanical vibratory gyroscopes, feedback control is a common strategy in attempting to correct the imperfections. However, a purely feedback control can be insufficient for compensation of all the errors, requiring post processing in the form of laser trimming to achieve higher levels of performance. In this paper, we explore another alternative: the design and implementation of a dual stage control architecture with self-calibration and feedback capabilities. The self-calibrative portion of the control identifies and electronically "trims" large imperfections, while the feedback control compensates for remaining small nonidealities and in-operation perturbations. Presented here is an algorithm for in-situ imperfection identification based on the dynamic response of the device. A realization of the dual stage control architecture is proposed for a gyroscope using nonlinear electrostatic parallel plate actuators. Modeling and simulation results which demonstrate successful compensation of imperfections with the proposed architecture for a device with 10% fabrication error appearing in the form of stiffness nonidealities and subjected to further 1% in-run perturbations are presented.
SSZ-42: the first high-silica large pore zeolite with an undulating, one-dimensional channel system (1997)

The framework topology of the novel zeolite SSZ-42 is determined from single crystal data (15 × 15 × 35 µm) and refined from powder diffraction data; the crystalline architecture is characterized by an undulating, one-dimensional 12-membered ring channel system.
A spreadsheet approach to information visualization (1997)

In information visualization, as the volume and complexity of the data increases, researchers require more powerful visualization tools that enable them to more effectively explore multidimensional datasets. In this paper, we discuss the general utility of a novelvisualizationspreadsheetframework. Justasa numerical spreadsheetenablesexplorationof numbers,a visualizationspreadsheet enables exploration of visual forms of information. We show that the spreadsheetapproachfacilitates certain information visualization tasks that are more difficult using other approaches. Unlike traditional spreadsheets,which store only simple data elementsand formulasineachcell,avisualizationspreadsheetcellcanholdanentire complex data set, selection criteria, viewing specifications,and other information needed for a full-fledged information visualization. Similarly, inter-cell operations are far more complex, stretching beyond simple arithmetic and string operations to encompassa range of domain-specific operators. We have built two prototype systems that illustrate some of these research issues. The underlying approachin our work allows domain experts to definenew data types and data operations, and enables visualization experts to incorporate new visualizations, viewing parameters, and view operations.
<title>Corneal welding with the hydrogen fluoride laser</title> (1994)

Our current study has looked at the use of a CW hydrogen fluoride laser to weld human cadaver corneas. The laser used was a Helios CL-II laser operating from 2.3 to 2.6 micrometers . A 6-mm full thickness linear incision was made in the center of the cornea. Two 10-0 nylon sutures were placed to hold the corneal stromal edges apposed during welding. Each specimen was mounted on a motorized micrometer stage. The beam was passed over the incision at a rate of between 0.5-2.0 mm per minute. After welding, the specimens were tested for wound strength by increasing intraocular pressure until the wound leaked. Two eyes had corneal welds performed and pressures of up to twice baseline intraocular pressure could be sustained after the stay sutures were removed. Light and electron microscopy demonstrated full thickness welds to be present. Electron micrographic sections demonstrated apparent interdigitation of collagen fibers between adjacent lamellae. Tissue welding may become an alternate means of wound closure in eye surgery.