gebhart/patrepeval huggingface dataset:
Infrared microscopy studies on high-power InGaAs-GaAs-InGaP lasers with Ga/sub 2/O/sub 3/ facet coatings (1995)

InGaAs-GaAs separate confinement, heterostructure single quantum-well (SCH-SQW) lasers (/spl lambda/=0.98 /spl mu/m) with lattice-matched InGaP cladding layers, using a new Ga/sub 2/O/sub 3/ low reflectivity (LR) front-facet coating, are reported. The CW peak power density (17 MW/cm/sup 2/) of 6 /spl mu/m/spl times/750 /spl mu/m ridge-waveguide lasers is limited by thermal rollover, and repeated cycling beyond thermal rollover produced no change in operating characteristics. The high-power temperature distribution along the active stripe has been measured by high-resolution infrared (3-5 /spl mu/m) imaging microscopy. The temperature profile acquired for a very high optical power density P/sub D/=11 MW/cm/sup 3/ was found to be uniform along the inner active laser stripe, and revealed a local temperature increase at the LR front facet /spl Delta/T/sub f/ of only 9 K above the average stripe temperature /spl Delta/T/sub s/=24 K. An excellent front-facet interface recombination velocity <10/sup 5/ cm/s has been inferred from the measured low local temperature rise in the front facet.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characteristics of 10 mm Multilayer L1-F2Mode Vibrator and Application to a Linear Motor (2003)

In the present paper we discuss a small-sized multilayer L1-F2 mode vibrator and its application to an ultrasonic linear motor. In an attempt to reduce both the size and the driving voltage of an L1-F2 mode vibrator, we constructed a multilayer L1-F2 mode vibrator whose inner electrodes are simply divided into two. Test results clarified that the multilayer L1-F2 mode vibrator exhibits two resonance modes; namely, a first longitudinal mode and a second flexural mode, and that an amplitude of vibration velocity is sufficiently large for application to a linear motor. Specific merits of our multilayer L1-F2 mode vibrator are that the driving voltage is low (5 Vrms), owing to multilayer construction, and that the vibrator is small (10 ×2.5 ×2 mm: W×H×D), owing to the simple construction of the inner electrodes. Additionally, the present study revealed that an ultrasonic linear motor using the multilayer L1-F2 mode vibrator exhibits superior performance in practical application.
Effects of Intermittent Feeding Upon Growth and Life Span in Rats (1982)

From weaning to death, 28 male Wistar rats were maintained on an ad libitum (AL) diet, and 24 counterparts were provided the diet every-other-day (EOD). The mean life span of the EOD group represented an 83% increase over that of the AL group. Furthermore, a Gompertzian analysis of mortality rates suggested that the rate of aging was retarded in the EOD group. While body weight and growth rate were reduced in the EOD group, their growth duration was 75% longer compared to the AL group. Significant positive relationships emerged between life span and growth rate parameters in the AL group; however, no significant relationships were found between life span and body weight parameters in the EOD group. Therefore, in support of the hypothesis that dietary restriction effects prolongevity through retarded development, evidence was produced only in the between-group comparisons of AL- and EOD-fed animals.
Shape from interreflections (2002)

An iterative algorithm is presented that simultaneously recovers the actual shape and the actual reflectance from the pseudo estimates. The recovery algorithm works on Lambertian surfaces of arbitrary shape with possibly varying and unknown reflectance. The general behavior of the algorithm and its convergence properties are discussed. Both simulation and experimental results are included to demonstrate the accuracy and stability of the algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Adjusting the Ground Truth Annotations for Connectivity-Based Learning to Delineate (2021)

Deep learning-based approaches to delineating 3D structure depend on accurate annotations to train the networks. Yet, in practice, people, no matter how conscientious, have trouble precisely delineating in 3D and on a large scale, in part because the data is often hard to interpret visually and in part because the 3D interfaces are awkward to use. In this paper, we introduce a method that explicitly accounts for annotation inaccuracies. To this end, we treat the annotations as active contour models that can deform themselves while preserving their topology. This enables us to jointly train the network and correct potential errors in the original annotations. The result is an approach that boosts performance of deep networks trained with potentially inaccurate annotations. Code has been released at https://github.com/doruk-oner/AdjustingAnnotationswithSnakes.
Challenges and Potential of Intra-Cycle Combustion Control for Direct Injection Diesel Engines (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The injection timing of a Diesel internal combustion engine typically follows a prescribed sequence depending on the operating condition using open loop control. Due to advances in sensors and digital electronics it is now possible to implement closed loop control based on in cylinder pressure values. Typically this control action is slow, and it may take several cycles or at least one cycle (cycle-to-cycle control). Using high speed sensors, it becomes technically possible to measure pressure deviations and correct them within the same cycle (intra-cycle control). For example the in cylinder pressure after the pilot inject can be measured, and the timing of the main injection can be adjusted in timing and duration to compensate any deviations in pressure from the expected reference value.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This level of control can significantly reduce the deviations between cycles and cylinders, and it can also improve the transient behavior of the engine. Reduced variations also mean that a better compromise between emissions and fuel efficiency can be achieved, which promises significant improvement in both.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The paper looks at the technical challenges involved in the implementation of an intra-cycle control scheme. These include the fast computation speed required by the controller, the synchronization of the control algorithm to the engine rotation, and the question at which point in time (or crank angle) the control is most effective. Experimental results are used to assess the levels of pressure deviations usually seen in Diesel engines under different operating conditions, and to discuss potential control strategies to address these. The presented results demonstrate that intra-cycle control is technically feasible, and that it has the potential to reduce pressure variations and to improve both emission and fuel economy. The results also help to understand the nature of the control problem, how to measure and predict the system behavior, and the control authority that can be exercised.&lt;/div&gt;&lt;/div&gt;
Robust error measure for supervised neural network learning with outliers (1996)

Most supervised neural networks (NNs) are trained by minimizing the mean squared error (MSE) of the training set. In the presence of outliers, the resulting NN model can differ significantly from the underlying system that generates the data. Two different approaches are used to study the mechanism by which outliers affect the resulting models: influence function and maximum likelihood. The mean log squared error (MLSE) is proposed as the error criteria that can be easily adapted by most supervised learning algorithms. Simulation results indicate that the proposed method is robust against outliers.
Modeling attention zones on the basis of an analysis of local features of the image texture (2008)

In the basic model developed and published earlier by the authors, the information-content function proposed by Muchnik and Zavalishin is transformed in such a way that the attention zone (AZ) is fixed at the centers of gravity (CGs) of the objects of an image distinguished from the surroundings by the local brightness. This makes it possible to directly recognize images subjected to an affine transformation characteristic of the shapes of distant surfaces projected on the retina. Unlike the basic model described in that article, the expanded model analyzes more general attributes of an image—the local features of its texture. This allows our approach to be used to analyze a broader class of images. The final goal of forming AZs is to automatically decompose and structurally analyze the images of actual three-dimensional scenes.
Transient response during resistance switching in Ag∕Pr0.7Ca0.3MnO3∕Pt thin films (2006)

The transient response during resistance switching in Ag∕Pr0.7Ca0.3MnO3∕Pt thin films is investigated by measurements using pulsed voltage biases. Semiconducting Pr0.7Ca0.3MnO3 (PCMO) films sandwiched by Ag and Pt electrodes show nonvolatile resistance switching (two orders of magnitude) as a result of applying pulsed voltage biases, even at room temperature. The transient responses of the voltage across the PCMO for a set (positive) and a reset (negative) pulse application are consistent with the resistance-switching behavior and show quite fast switching (3–100 ns) for the set pulse application, compared with 60–135 ns for the reset pulse application. The large resistance-switching ratio is saturated after a finite transient time, indicating that the carrier filling of the trap sites into PCMO is completed within quite a short time.
Monomeric selenolato- and tellurolato-aluminium(III) and -gallium(III)[Me3NM(ER)3](E = Se, Te; R = alkyl, aryl), via trimethylamine alane/gallane cleavage of diorgano-dichalcogens (1995)

The reaction of diorgano-dichalcogens (ER)2(E = Se or Te) with trimethylamine adducts of alane or gallane yields trimethylamine adducts of the tris(selenolato- or tellurolato-)metal (III) species [Me3NM(ER)3](M = Al, Ga; E = Se, Te; R = Et, Ph, CH2Ph); two of which have been structurally authenticated as four coordinate, monomeric species in the solid state.
A stochastic FDTD method for statistically varying biological tissues (2011)

An approximate method for determining the statistical properties of an FDTD Analysis has been derived, allowing the determination of the mean and the variance of an FDTD simulation. This stochastic simulator progresses in the same fashion as an FDTD simulation progresses. The variance-wave builds and propagates with reflections occurring at dielectric boundaries. Computer overhead is reduced, i.e. memory and runtime are substantially reduced. Permitting the statistics, i.e. mean and variance to be determined without spending allot of time and computer resources for performing Monte Carlo analysis. This would allow the industry to look at statistical analysis in large 3D model spaces using FDTD, which currently is not being done.
Cover Feature: A Nickel(II)‐Mediated Thiocarbonylation Strategy for Carbon Isotope Labeling of Aliphatic Carboxamides (Chem. Eur. J. 24/2021) (2021)

Like a rocket: An extremely fast nickel-mediated thiocarbonylation reaction yielding 2-pyridyl thioesters provides for a convenient carbon-13 labeling approach to the preparation of structurally elaborate aliphatic carboxamides, including both small molecule and peptide APIs. The methodology could have implications for carbon-11 and carbon-14 labeling of carboxamides. Images created using Mol*: D. Sehnal, A. S. Rose, J. Kovca, S. K. Burley, S. Velankar, 2018, Mol*, Towards a common library and tools for web molecular graphics, MolVA/EuroVis proceedings, https://dl.acm.org/doi/10.5555/3293503.3293509, and RCSB PDB. For insulin degludec: 4AJX, D. B. Steensgaard, G. Schluckebier, H. M. Strauss, M. Norrman, J. K. Thomsen, A. V. Friderichsen, S. Havelund, I. Jonassen, Biochemistry, 2013, 52, 295–309. For Liraglutide: 4APD, S. Ludvigsen, D. B. Steensgaard, J. K. Thomsen, H. Strauss, M. Normann, To be published, DOI: 10.2210/pdb4apd/pdb (see the following links: https://www.rcsb.org/3d-view/4AJX/1 and https://www.rcsb.org/3d-view/4APD/0). More information can be found in the Full Paper by T. Skrydstrup et al. on page 7114.
Robust wideband beamforming (2010)

Robust wideband beamforming with a real-time array testbed will be studied in this paper. For the practical consideration of uncertainty, channel impulse responses or channel transform functions of RF chains can not be obtained exactly due to the limitation of sounding and calibration procedure. Thus robust optimization will be applied to wideband beamforming. It is assumed that the uncertainty will be bounded and the worst case performance can be guaranteed by robust optimization. Finally, the optimal coefficients for a 2-dimensional filter bank to perform wideband beamforming will obtained.
Two dimensional entropy and short time Fourier Transform application on ground penetrating radar data analysis (2013)

Accurate detection of rebar location using Ground Penetrating Radar (GPR) proves to be very useful in assessing roadway/bridge deck concrete structure. Due to large signal processing resource needed to locate and image rebar on a whole road structure, more efficient signal processing method is needed. This paper proposes to combine two-dimensional (2D) entropy algorithm to narrow down the scope of interested data from large radar data set and Short Time Fourier Transform (STFT) algorithm to perform further feature characterization. To validate the analysis, experiments with different rebar setups are conducted.
Stable Matching Algorithm for an Agile Reconfigurable Data Center Interconnect (2016)

This document describes the scheduling algorithm used in the ProjecToR data-center interconnect system. The algorithm assigns bundles to laser-photodetector edges as they arrive online with the goal of minimizing the bundle/flow completion times over all bundles in the system. We compare the performance of the proposed stable-matching algorithm to the optimal performance of a more powerful hindsight optimal algorithm that is aware of all the bundles arriving in the system and can operate offline. We also give an integer linear programming formulation for the problem of maximizing instantaneous throughput.
Combined MEK and ERK inhibition overcomes therapy-mediated pathway reactivation in RAS mutant tumors (2017)

Mitogen-activated protein kinase (MAPK) pathway dysregulation is implicated in >30% of all cancers, rationalizing the development of RAF, MEK and ERK inhibitors. While BRAF and MEK inhibitors improve BRAF mutant melanoma patient outcomes, these inhibitors had limited success in other MAPK dysregulated tumors, with insufficient pathway suppression and likely pathway reactivation. In this study we show that inhibition of either MEK or ERK alone only transiently inhibits the MAPK pathway due to feedback reactivation. Simultaneous targeting of both MEK and ERK nodes results in deeper and more durable suppression of MAPK signaling that is not achievable with any dose of single agent, in tumors where feedback reactivation occurs. Strikingly, combined MEK and ERK inhibition is synergistic in RAS mutant models but only additive in BRAF mutant models where the RAF complex is dissociated from RAS and thus feedback productivity is disabled. We discovered that pathway reactivation in RAS mutant models occurs at the level of CRAF with combination treatment resulting in a markedly more active pool of CRAF. However, distinct from single node targeting, combining MEK and ERK inhibitor treatment effectively blocks the downstream signaling as assessed by transcriptional signatures and phospho-p90RSK. Importantly, these data reveal that MAPK pathway inhibitors whose activity is attenuated due to feedback reactivation can be rescued with sufficient inhibition by using a combination of MEK and ERK inhibitors. The MEK and ERK combination significantly suppresses MAPK pathway output and tumor growth in vivo to a greater extent than the maximum tolerated doses of single agents, and results in improved anti-tumor activity in multiple xenografts as well as in two Kras mutant genetically engineered mouse (GEM) models. Collectively, these data demonstrate that combined MEK and ERK inhibition is functionally unique, yielding greater than additive anti-tumor effects and elucidates a highly effective combination strategy in MAPK-dependent cancer, such as KRAS mutant tumors.
Computational Prediction of Protein–Protein Interactions (2004)

Eukaryotic proteins typically contain one or more modular domains such as kinases, phosphatases, and phoshopeptide-binding domains, as well as characteristic sequence motifs that direct post-translational modifications such as phosphorylation, or mediate binding to specific modular domains. A computational approach to predict protein interactions on a proteome-wide basis would therefore consist of identifying modular domains and sequence motifs from protein primary sequence data, creating sequence specificity-based algorithms to connect a domain in one protein with a motif in another in "interaction space," and then graphically constructing possible interaction networks. Computational methods for predicting modular domains in proteins have been quite successful, but identifying the short sequence motifs these domains recognize has been more difficult. We are developing improved methods to identify these motifs by combining experimental and computational techniques with databases of sequences and binding information. Scansite is a web-accessible program that predicts interactions between proteins using experimental binding data from peptide library and phage display experiments. This program focuses on domains important in cell signaling, but it can, in principle, be used for other interactions if the domains and binding motifs are known. This chapter describes in detail how to use Scansite to predict the binding partners of an input protein, and how to find all proteins that contain a given sequence motif.
The SRI AVEC-2014 Evaluation System (2014)

Though depression is a common mental health problem with significant impact on human society, it often goes undetected. We explore a diverse set of features based only on spoken audio to understand which features correlate with self-reported depression scores according to the Beck depression rating scale. These features, many of which are novel for this task, include (1) estimated articulatory trajectories during speech production, (2) acoustic characteristics, (3) acoustic-phonetic characteristics and (4) prosodic features. Features are modeled using a variety of approaches, including support vector regression, a Gaussian backend and decision trees. We report results on the AVEC-2014 depression dataset and find that individual systems range from 9.18 to 11.87 in root mean squared error (RMSE), and from 7.68 to 9.99 in mean absolute error (MAE). Initial fusion brings further improvement; fusion and feature selection work is still in progress.
Cost-effectiveness and resource implications of aggressive action on tuberculosis in China, India, and South Africa: a combined analysis of nine models (2016)

Bill & Melinda Gates Foundation.
Targeting MLL-AF4 with short interfering RNAs inhibits clonogenicity and engraftment of t(4;11)-positive human leukemic cells (2005)

The chromosomal translocation t(4;11) marks infant acute lymphoblastic leukemia associated with a particularly dismal prognosis. The leukemogenic role of the corresponding fusion gene MLL-AF4 is not well understood. We show that transient inhibition of MLL-AF4 expression with small interfering RNAs impairs the proliferation and clonogenicity of the t(4; 11)-positive human leukemic cell lines SEM and RS4;11. Reduction of mixed-lineage leukemia (MLL)-ALL-1 fused gene from chromosome 4 (AF4) levels induces apoptosis associated with caspase-3 activation and diminished BCL-X(L) expression. Suppression of MLL-AF4 is paralleled by a decreased expression of the homeotic genes HOXA7, HOXA9, and MEIS1. MLL-AF4 depletion inhibits expression of the stem-cell marker CD133, indicating hematopoietic differentiation. Transfection of leukemic cells with MLL-AF4 siRNAs reduces leukemia-associated morbidity and mortality in SCID mice that received a xenotransplant, suggesting that MLL-AF4 depletion negatively affects leukemia-initiating cells. Our findings demonstrate that MLL-AF4 is important for leukemic clonogenicity and engraftment of this highly aggressive leukemia. Targeted inhibition of MLL-AF4 fusion gene expression may lead to an effective and highly specific treatment of this therapy-resistant leukemia.
Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2 (2008)

The target of diphtheria toxin is the diphthamide residue in translation elongation factor 2 (EF-2), which is generated by a three-step post-translational modification of a specific histidine residue in the EF-2 precursor. In the second modification step, an S-adenosylmethionine-dependent methyltransferase, diphthine synthase (DS), catalyzes the trimethylation of the EF-2 precursor. The homodimeric crystal structures of the archaeal diphthine synthases from Pyrococcus horikoshii OT3 and Aeropyrum pernix K1 have been determined. These structures share essentially the same overall fold as the cobalt-precorrin-4 methyltransferase CbiF, confirming that DS belongs to the dimeric class III family of methyltransferases. In the P. horikoshii DS dimer, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine (AdoHcy), while the other active site contains no ligand. This asymmetric AdoHcy binding may be a consequence of intra-domain and inter-domain movements upon binding of AdoHcy at one of the two sites. These movements disrupt the twofold dimeric symmetry of the DS dimer and probably cause lower AdoHcy affinity at the other binding site.
The Effect of Shear on Conditioning: Chemical Requirements during Mechanical Sludge Dewatering (1990)

In this study it is shown that the shear occurring in a sludge cake during dewatering can create an increase in polymer demand. Comparisons between a laboratory mixing unit and a pilot filter press indicate that polymer requirements for mechanical dewatering equipment can be predicted using laboratory procedures.