gebhart/patrepeval huggingface dataset:
Overlap of IGF- and heparin-binding sites in rat IGF-binding protein-5 (2000)

Using site-directed mutagenesis, we have undertaken a study of a potential IGF-binding site in the C-terminal domain of rat IGFBP-5, lying close to or within a previously described heparin-binding domain (residues 201-218) in this protein. After analysis of binding activity using three different methods - ligand blotting, solution phase equilibrium binding and biosensor measurement of real-time on- and off-rates - we report that the mutation of two highly conserved residues within this region (glycine 203 and glutamine 209) reduces the affinity of the binding protein for both IGF-I and IGF-II, while having no effect on heparin binding. In addition, we confirm that mutation of basic residues within the heparin-binding domain (R201L, K202E, K206Q and R214A) results in a protein that has attenuated heparin binding but shows only a small reduction in affinity for IGF-I and -II. Previous findings have described the reduction in affinity of IGFBP-5 for IGFs that occurs after complexation of the binding protein with heparin or other components of the extracellular matrix (ECM) and have postulated that such an interaction may result in conformational changes in protein structure, affecting subsequent IGF interaction. Our data suggesting potential overlap of heparin- and IGF-binding domains argue for a more direct effect of ECM modulation of the affinity of IGFBP-5 for ligand by partial occlusion of the IGF-binding site after interaction with ECM.
Multi axis differential optical absorption spectroscopy (MAX-DOAS) of gas and aerosol distributions (2005)

We present and demonstrate a relatively simple algorithm, which converts a set of slant column density measurements of oxygen dimers (O4) and NO2 at several different elevation angles to determine the atmospheric aerosol extinction and the absolute concentration and mixing ratio of NO2 within the atmospheric boundary layer. In addition the height of the atmospheric boundary layer can usually be derived, also the technique can be readily extended to determine the concentration of several other trace gases including SO2, CH2O, or glyoxal. The algorithm is based on precise radiation transport modelling determination, taking into account the actual aerosol scenario as determined from the O4 measurements. The required hardware is simple encompassing essentially a miniature spectrometer, a small telescope, a pointing mechanism, and a Personal Computer (PC). Effectively the technique combines the simplicity of a passive MAX-DOAS observation with the capability of a much more complex active DOAS instrument to determine path-averaged, absolutely calibrated mixing ratios of atmospheric trace gases at relatively high accuracy.
"Smart" Sensor Module (2007)

An assembly that contains a sensor, sensor-signal-conditioning circuitry, a sensor-readout analog-to-digital converter (ADC), data-storage circuitry, and a microprocessor that runs special-purpose software and communicates with one or more external computer(s) has been developed as a prototype of "smart" sensor modules for monitoring the integrity and functionality (the "health") of engineering systems. Although these modules are now being designed specifically for use on rocket-engine test stands, it is anticipated that they could also readily be designed to be incorporated into health-monitoring subsystems of such diverse engineering systems as spacecraft, aircraft, land vehicles, bridges, buildings, power plants, oilrigs, and defense installations. The figure is a simplified block diagram of the "smart" sensor module. The analog sensor readout signal is processed by the ADC, the digital output of which is fed to the microprocessor. By means of a standard RS-232 cable, the microprocessor is connected to a local personal computer (PC), from which software is downloaded into a randomaccess memory in the microprocessor. The local PC is also used to debug the software. Once the software is running, the local PC is disconnected and the module is controlled by, and all output data from the module are collected by, a remote PC via an Ethernet bus. Several smart sensor modules like this one could be connected to the same Ethernet bus and controlled by the single remote PC. The software running in the microprocessor includes driver programs for operation of the sensor, programs that implement self-assessment algorithms, programs that implement protocols for communication with the external computer( s), and programs that implement evolutionary methodologies to enable the module to improve its performance over time. The design of the module and of the health-monitoring system of which it is a part reflects the understanding that the main purpose of a health-monitoring system is to detect damage and, therefore, the health-monitoring system must be able to function effectively in the presence of damage and should be capable of distinguishing between damage to itself and damage to the system being monitored. A major benefit afforded by the self-assessment algorithms is that in the output of the module, the sensor data indicative of the health of the engineering system being monitored are coupled with a confidence factor that quantifies the degree of reliability of the data. Hence, the output includes information on the health of the sensor module itself in addition to information on the health of the engineering system being monitored.
The complete genome sequence of Pantoea ananatis AJ13355, an organism with great biotechnological potential (2011)

Pantoea ananatis AJ13355 is a newly identified member of the Enterobacteriaceae family with promising biotechnological applications. This bacterium is able to grow at an acidic pH and is resistant to saturating concentrations of L-glutamic acid, making this organism a suitable host for the production of L-glutamate. In the current study, the complete genomic sequence of P. ananatis AJ13355 was determined. The genome was found to consist of a single circular chromosome consisting of 4,555,536 bp [DDBJ: AP012032] and a circular plasmid, pEA320, of 321,744 bp [DDBJ: AP012033]. After automated annotation, 4,071 protein-coding sequences were identified in the P. ananatis AJ13355 genome. For 4,025 of these genes, functions were assigned based on homologies to known proteins. A high level of nucleotide sequence identity (99%) was revealed between the genome of P. ananatis AJ13355 and the previously published genome of P. ananatis LMG 20103. Short colinear regions, which are identical to DNA sequences in the Escherichia coli MG1655 chromosome, were found to be widely dispersed along the P. ananatis AJ13355 genome. Conjugal gene transfer from E. coli to P. ananatis, mediated by homologous recombination between short identical sequences, was also experimentally demonstrated. The determination of the genome sequence has paved the way for the directed metabolic engineering of P. ananatis to produce biotechnologically relevant compounds.
A unified model for binocular fusion and depth perception: Stereo spatial resolution and disparity variance limits (2021)

Recently, we proposed a unified model for binocular fusion and depth perception and tested it with frontoparallel stereograms (Ding & Levi, Vision Research 2021). At each location, the model consists of an array of disparity detectors, each with different preferred position and phase disparities. The phase-disparity detectors compute interocular misalignment and provide phase-disparity energy (binocular fusion energy) to shift the readout of disparity detectors along position disparity space until the misalignment is eliminated; sensory fusion is achieved locally. After sensory fusion, the combination of position and possible residual phase disparity energies is calculated for depth perception. Binocular fusion occurs at multiple scales following a coarse-to-fine process. At a given location, the apparent depth is the weighted sum of sensory readout shifts combined with residual phase disparity in all spatial-frequency channels, and the weights depend on stimulus spatial frequency and contrast. To test the model with more complex depth profiles, we performed experiments using dynamic band-pass noise stereograms (dBNS, central spatial-frequency = 0.75, 1.5, 3 or 6 cpd and one octave bandwidth) with disparity corrugations of 0.094, 0.188, 0.375, 0.75, or 1.5 cpd. Our results, consistent with previous studies using broadband dRDS (Kane et al. 2014, Peterzell et al. 2017), show that stereovision has poor spatial resolution and limited disparity variance; the Dmin corrugation amplitude has a bandpass property and Dmax has a lowpass property. Using narrow-band dBNS, we also revealed that the Dmin amplitude depends on corrugation/carrier spatial-frequency ratio; best performance occurs when corrugation frequency is 4-8 times lower than the carrier frequency. Model simulations show that the unified model without late-stage filters has a lowpass property for depth corrugation perception. After including late-stage bandpass filters, the model predicts band-pass properties for Dmin corrugation amplitude and low-pass properties for Dmax amplitude, consistent with our experimental data.
Tracking Animal Location and Activity with an Automated Radio Telemetry System in a Tropical Rainforest (2011)

How do animals use their habitat? Where do they go and what do they do? These basic questions are key not only to understanding a species’ ecology and evolution, but also for addressing many of the environmental challenges we currently face, including problems posed by invasive species, the spread of zoonotic diseases and declines in wildlife populations due to anthropogenic climate and land-use changes. Monitoring the movements and activities of wild animals can be difficult, especially when the species in question are small, cryptic or move over large areas. In this paper, we describe an Automated Radio-Telemetry System (ARTS) that we designed and built on Barro Colorado Island (BCI), Panama to overcome these challenges. We describe the hardware and software we used to implement the ARTS, and discuss the scientific successes we have had using the system, as well as the logistical challenges we faced in maintaining the system in real-world, rainforest conditions. The ARTS uses automated radio-telemetry receivers mounted on 40-m towers topped with arrays of directional antennas to track the activity and location of radio-collared study animals, 24 h a day, 7 days a week. These receiving units are connected by a wireless network to a server housed in the laboratory on BCI, making these data available in real time to researchers via a web-accessible database. As long as study animals are within the range of the towers, the ARTS system collects data more frequently than typical animal-borne global positioning system collars (∼12 locations/h) with lower accuracy (approximately 50 m) but at much reduced cost per tag (∼10X less expensive). The geographic range of ARTS, like all VHF telemetry, is affected by the size of the radio-tag as well as its position in the forest (e.g. tags in the canopy transmit farther than those on the forest floor). We present a model of signal propagation based on landscape conditions, which quantifies these effects and identifies sources of interference, including weather events and human activity. ARTS has been used to track 374 individual animals from 38 species, including 17 mammal species, 12 birds, 7 reptiles or amphibians, as well as two species of plant seeds. These data elucidate the spatio-temporal dynamics of animal activity and movement at the site and have produced numerous peer-reviewed publications, student theses, magazine articles, educational programs and film documentaries. These data are also relevant to long-term population monitoring and conservation plans. Both the successes and the failures of the ARTS system are applicable to broader sensor network applications and are valuable for advancing sensor network research.
Spectrally-resolved internal quantum efficiency and carrier dynamics of semipolar $(10\bar{1}1)$ core-shell triangular nanostripe GaN/InGaN LEDs (2018)

We investigate the spectrally resolved internal quantum efficiency (IQE) and carrier dynamics in semipolar [Formula: see text] core-shell triangular nanostripe light-emitting diodes (TLEDs) using temperature-dependent photoluminescence (TDPL) and time-resolved photoluminescence (TRPL) at various excitation energy densities. Using electroluminescence, photoluminescence, and cathodoluminescence measurements, we verify the origins of the broad emission spectra from the nanostructures and confirm that localized regions of high-indium-content InGaN exist along the apex of the nanostructures. Spectrally resolved IQE measurements are then performed, with the spectra integrated from 400-450 nm and 450-500 nm to obtain the IQE of the QWs mainly near the sidewalls and apex of the TLEDs, respectively. TDPL and TRPL are used to decouple the radiative and non-radiative carrier lifetimes for different regions of the emission spectra. We observe that the IQE is higher for the spectral region between 450 nm and 500 nm compared to the IQE between 400 and 450 nm. This result is in contrast to the typical observation that the IQE of planar GaN-based LEDs is lower for longer wavelengths (i.e., higher indium contents). We also observe a longer non-radiative recombination lifetime for the longer wavelength portion of the spectrum. Several explanations are proposed for the improved IQE and longer non-radiative lifetime observed near the apex of the nanostructures. The results show that nanostructures may be leveraged to design more efficient green LEDs, potentially addressing a long-standing challenge in GaN-based materials.
A seismic profile of the upper mantle along the southwestern edge of the Philippine Sea plate using short-period array data (1999)

We investigated the structure of the P-wave velocity (Vp) in the upper mantle beneath the southwestern edge of the Philippine Sea plate using traveltimes and waveforms from a dense, short-period seismic array of approximately 75 seismographs in Taiwan. Using the seismograms from 39 shallow-focus earthquakes, a composite seismic profile was constructed for a distance range of up to 4000 km. We picked the traveltimes of the first arrivals to construct a smoothly varying model for Vp which also served as a basis for static corrections. After band-pass filtering and deconvolution to remove effects of source-time functions and attenuation, we modelled the waveforms and triplicated arrivals in order to constrain the nature of the upper-mantle discontinuities. Finally, after slant stacking, the entire observed wavefield was downward continued to obtain a regional model TS.406. This model includes a small low-velocity zone between depths of 105 and 190 km, and then a gradual increase in Vp down to the depth of 406 km. At this discontinuity, Vp increases by 5.5 per cent. The P-wave velocity then varies linearly in the transition zone with a moderate gradient of 0.0027 km s-1 km-1 until the base of the transition zone at 662 km, where Vp increases by 5.4 per cent. When compared with other models for the Philippine Sea region and average global models, model TS.406 has lower velocities above a depth of 300 km and then faster Vp in the upper part of the transition zone. For example, above 300 km the TS.406 model is slower than IASP91 by 1.5 per cent, but in the upper transition zone (406 to 571 km), it is faster by 1.2 per cent. Thus, the moderate-amplitude anomaly of fast Vp in the middle of the transition zone reported by tomographic studies seems to occur at shallower depths. Furthermore, unlike the pronounced Northern Philippine Sea anomaly, Vp near the bottom of the transition zone is close to the global average under the southwestern edge of the Philippine Sea.
Distributed resource allocation for MISO downlink systems via the alternating direction method of multipliers (2014)

We provide distributed algorithms for the radio resource allocation problem in multicell downlink multi-input single-output systems. Specifically, the problems of (1) minimizing total transmit power subject to signal-to-interference-plus-noise ratio (SINR) constraints of each user and (2) SINR balancing subject to total transmit power constraints are considered. We propose a consensus-based distributed algorithm and the fast solution method via alternating the direction method of multipliers. First, we derive a distributed algorithm for minimization of total transmit power. Then, in conjunction with the bracketing method, a distributed algorithm for SINR balancing is derived. Numerical results show that the proposed distributed algorithms achieve the optimal centralized solution.
EFFECT OF ELECTRODE GEOMETRY ON RESISTANCE SPOT WELDING OF AHSS (2006)

The implementation of advanced high strength steels (AHSS) into the automotive industry offers distinct advantages relative to achieving light weighting goals and improved structural performance. The challenge for the automotive industry is a need to develop the processes and know-how to implement these new materials into their product economically. Currently the primary method used to develop spot welding practices for new material involves both extensive and costly laboratory trial and error experimentation. The finite element method was used as a low cost alternative for the fundamental development of joining practices for AHSS. Specifically, the effect of electrode geometry on nugget formation in typical AHSS resistance spot weld applications was investigated. The weld joint chosen for the study was based on an Auto-Steel Partnership (A/SP) state-of-the-art B-Pillar to rocker joint using 1.6 mm GI DP780 to 1.6 mm GI DP780 (B pillar reinforcement to rocker outer reinforcement). The effect of electrode cap geometry was modeled using SORPAS ® resistance spot welding FEA software. The results were verified experimentally at the University of Waterloo Centre for Advanced Materials
Nano-XRF and micro-raman studies of metal impurity decoration around dislocations in multicrystalline silicon (2012)

We push the resolution limits of synchrotron-based nano-X-ray fluorescence mapping below 100 nm to investigate the fundamental differences between benign and deleterious dislocations in multicystalline silicon solar cells. We observe that after processing recombination-active dislocations contain a high degree of nanoscale iron and copper decoration, while recombination-inactive dislocations appear clean. To study the origins of the distinct metal decorations around different dislocations we analyze as-grown samples as well as specimens at different stages of processing. We complement our X-ray studies with micro-Raman mapping to understand the relationship between metallic decoration and stress fields around dislocations.
High-Volume Municipal Solid Waste Incineration Bottom Ash Concrete (2016)

About 50 % of Municipal Solid Waste is incinerated (MSWI) in Europe what represent ca. 50 Mt/a of MSWI bottom ash (BA). Bottom ash contains several marketable components (iron scrap, non-ferrous metals, glass) which can by separated from the main BA stream and placed on the market with secondary sources. The resting material is, by its composition and properties, similar to natural aggregates and can be used in this way. The influence of metals separation form BA on its behavior in concrete was tested by using BA from Praha Malešice Waste-to-Energy plant. particle size fractions 4/8 and 8/16 mm of this BA can be used as aggregates in concrete up to 50 vol. % of given fraction without any significant loss of concrete strength. The combination of valuable component separation form BA and recycling of the rest portion as aggregates feature promising way of BA management reducing the amount of BA to be landfilled to minimum.
An Algorithm for Quantitatively Calculating I/Q Gain and Phase Mismatch (2012)

The in-phase and quadrature modulator (IQ modulator) is a key component in modern wireless transmitter. It provides a convenient method for modulating data bits or symbols onto an RF carrier. It has become the architecture of choice for implementing transmitter signal chains for end applications such as cellular, WiMAX, and wireless point-to-point. However, there are several non-ideal aspects of analog IQ modulator, include IQ gain imbalance, imperfect quadrature, and LO leakage. These imperfections will result in image spectral and degrade MER of the modulator, which in turn degrades bit error rate (BER). Gain matching and phase compensation both affect the total amount of image rejection. Factory calibration can detect the IQ gain and phase mismatch in different frequency and store the correction coefficients in nonvolatile memory. The key issue is how to get the exact mismatch. In this paper, a mathematical model of IQ modulator was established and an analytic solution is obtained about how to get the exact mismatch parameters. DOI:  http://dx.doi.org/10.11591/telkomnika.v10i4.872
Tips and tricks for artifact-free PFA-based fixation of the actin cytoskeleton and its regulatory proteins for single molecule localization super-resolution microscopy (2016)

Tips and tricks for artifact-
Biomimetisches Modell eines pflanzlichen Photosystems bestehend aus einem rekombinanten Lichtsammelkomplex und einem Terrylenfarbstoff (2002)

Ein einfaches Modell eines pflanzlichen Photosystems wurde aus einem rekombinanten Licht sammelnden Chlorophyll-a/b-Protein (LHCIIb) des pflanzlichen Photosyntheseapparats und einem kovalent gebundenen Benzoylterrylen-3,4-dicarboximid(BTI)-Farbstoff als künstlicher Energiefalle konstruiert (siehe Bild). Bis zu 85 % der von LHCIIb absorbierten Energie wurden auf den Acceptor übertragen.
Learning of nonlinear FIR models under uniform distribution (1999)

The PAC learning theory creates a framework to assess the learning properties of a modeling procedure. This paper presents a bound on the size of the training data set required to train a nonlinear FIR model, where the input data are assumed to be generated according to the uniform distribution. The bound is further specified for a family of feedforward neural networks, which utilizes a sigmoid activation function. The learning properties of a neural identification task have been assessed using the aforesaid family of neural networks. Also, using the structural risk minimization algorithm, a learning procedure for the modeling tasks in which the exact number of the hidden neurons is unknown, is introduced.