gebhart/patrepeval huggingface dataset:
Measurement of granule strength in particle beds using ultrasonic velocity (2009)

It is proposed in this work that the mean "strength" of the individual particles or pellets can be determined ultrasonically by measuring the longitudinal or shear sound speed of a sample of powder or pellets placed under pressure and calculating from this the average sound speed of the particles themselves. These measurements then can be compared to the standard "strength" measurements in use to determine whether in those particular cases the sound speed measurement is a feasible alternative. The sound measurement, if demonstrated to be feasible, may well have extensive practical advantages over the old techniques in terms of repeatability, ease of use and having a direct relationship with a well known physical parameter.
Binding Specificity of a New Artificial β-Glucan Recognition Protein and Its Application to β-Glucan Detection in Mushroom Extracts (2021)

β-1,3-D-glucan (BG) activates innate immunity and enhances immune responses. Fungi, such as mushrooms, produce a relatively large amount of BG, the structure and molecular weight of which varies depending on the species of fungi. This study was conducted to develop a detection probe for quantifying or detecting BG from fungi using BG-binding proteins. The binding properties of a new β-glucan recognition protein (BGRP) against various BGs were compared. With reference to the amino acid sequences of BGRP in insects, an artificial BGRP (supBGRP) was designed with higher production efficiency using gene recombination technology. SupBGRP was produced in Escherichia coli with high efficiency, and its reactivity with BG from fungi was the highest among the BG-binding proteins examined. SupBGRP exhibited high reactivity with 1,6-branched BG and will be useful for the quantification and detection of fungal BG.
A software-only scheme for managing heap data on limited local memory(LLM) multicore processors (2013)

This article presents a scheme for managing heap data in the local memory present in each core of a limited local memory (LLM) multicore architecture. Although managing heap data semi-automatically with software cache is feasible, it may require modifications of other thread codes. Crossthread modifications are very difficult to code and debug, and will become more complex and challenging as we increase the number of cores. In this article, we propose an intuitive programming interface, which is an automatic and scalable scheme for heap data management. Besides, for embedded applications, where the maximum heap size can be profiled, we propose several optimizations on our heap management to significantly decrease the library overheads. Our experiments on several benchmarks from MiBench executing on the Sony Playstation 3 show that our scheme is natural to use, and if we know the maximum size of heap data, our optimizations can improve application performance by an average of 14%.
Novel Split Intein for trans-Splicing Synthetic Peptide onto C Terminus of Protein (2009)

Conventional split inteins have been useful for trans-splicing between recombinant proteins, and an artificial S1 split intein is useful for adding synthetic peptide onto the N terminus of recombinant proteins. Here we have engineered a novel S11 split intein for trans-splicing synthetic peptide onto the C terminus of recombinant proteins. The C-intein of the S11 split intein is extremely small (6 amino acids (aa)); thus it can easily be produced together with a synthetic C-extein to be added to the C terminus of target proteins. The S11 intein was derived from the Ssp GyrB intein after deleting the homing endonuclease domain and splitting the remaining intein sequence near the C terminus, producing a 150-aa N-intein (IN) and a 6-aa C-intein (IC). Its trans-splicing activity was demonstrated first in Escherichia coli cells and then in vitro for trans-splicing between a synthetic peptide and a recombinant protein. The in vitro trans-splicing reaction exhibited a typical rate constant of (6.9+/-2.2)x10(-5) s(-1) and reached a high efficiency of approximately 80%. This S11 split intein can be useful for adding any desirable chemical groups to the C terminus of a protein of interest, which may include modified and unnatural amino acids, biotin and fluorescent labels, and even drug molecules.
Digital halftoning algorithms for high-quality and high-speed electro-photographic printing (2002)

The objective of this research is to develop new digital halftoning algorithms targeting high-quality, high-speed electro-photographic (EP) printing for scan-to-print applications. Conventionally, AM halftoning modulates the size of printed dots. It has very low computation load, good print stability for EP printing, but poor spatial resolution and Moire resistance. Alternatively, FM halftoning modulates the density of printed dots. It can achieve high spatial resolution and is free of Moire artifacts; but it may lack the required print stability needed for EP printing. To combine the advantages of both AM and FM halftoning methods, we first developed an algorithm called AM/FM halftoning, which simultaneously modulates dot size and dot density to render gray levels. AM/FM halftoning first determines the position of each dot using a dispersed dot halftoning algorithm and a dot density curve. The size of each dot is then modulated according to a dot size curve. A measurement-based parameter design system is developed to optimize both the dot size and dot density curves. A specific implementation of AM/FM halftoning is developed for electro-photographic printers having subpixel modulation ability such as Hewlett-Packard's pulse width modulation (PWM) technology. Dot size diffusion (DSD) and dot size screening (DSS) techniques are also developed for use when the quantization levels of PWM are insufficient. For parallel hardware implementation of AM/FM halftoning, a boundary-stitching algorithm is developed to reduce the halftone texture artifacts across the stripe boundary. AM/FM halftoning is also developed for color printing. To further improve the print stability and image quality, we generalize AM/FM halftoning to an algorithm called clustered AM/FM halftoning. Similar to AM/FM halftoning, it still simultaneously modulates dot size and dot density. Moreover, with tone-dependent optimal cluster control, the algorithm achieves even better print stability and image quality than can be achieved with AM/FM halftoning. Clustered AM/FM halftoning is also extended to color printing.
Carboxyl-Terminal Protease Regulates<i>Brucella suis</i>Morphology in Culture and Persistence in Macrophages and Mice (2005)

The putative carboxyl-terminal processing protease (CtpA) of Brucella suis 1330 is a member of a novel family of endoproteases involved in the maturation of proteins destined for the cell envelope. The B. suis CtpA protein shared up to 77% homology with CtpA proteins of other bacteria. A CtpA-deficient Brucella strain (1330DeltactpA), generated by allelic exchange, produced smaller colonies on enriched agar plates and exhibited a 50% decrease in growth rate in enriched liquid medium and no growth in salt-free enriched medium compared to the wild-type strain 1330 or the ctpA-complemented strain 1330DeltactpA[pBBctpA]. Electron microscopy revealed that in contrast to the native coccobacillus shape of wild-type strain 1330, strain 1330DeltactpA possessed a spherical shape, an increased cell diameter, and cell membranes partially dissociated from the cell envelope. In the J774 mouse macrophage cell line, 24 h after infection, the CFU of the strain 1330DeltactpA declined by approximately 3 log(10) CFU relative to wild-type strain 1330. Nine weeks after intraperitoneal inoculation of BALB/c mice, strain 1330DeltactpA had cleared from spleens but strain 1330 was still present. These observations suggest that the CtpA activity is necessary for the intracellular survival of B. suis. Relative to the saline-injected mice, strain 1330DeltactpA-vaccinated mice exhibited 4 to 5 log(10) CFU of protection against challenge with virulent B. abortus strain 2308 or B. suis strain 1330 but no protection against B. melitensis strain 16 M. This is the first report correlating a CtpA deficiency with cell morphology and attenuation of B. suis.
<i>N</i>-Acyl <scp>l</scp>-Homocysteine Thiolactones Are Potent and Stable Synthetic Modulators of the RhlR Quorum Sensing Receptor in <i>Pseudomonas aeruginosa</i> (2019)

The RhlR quorum sensing (QS) receptor in the pathogen Pseudomonas aeruginosa plays a prominent role in infection, and both antagonism and agonism of RhlR have been shown to negatively regulate important virulence phenotypes. Non-native lactone ligands are known to modulate RhlR activity, but their utility as chemical probes is relatively limited due to hydrolytic instability. Herein, we report our design and biological evaluation of a suite of hybrid AHL analogs with structures merging (1) features of reported lead RhlR ligands and (2) head groups with improved hydrolytic stabilities. The most promising compounds identified were N-acyl l-homocysteine thiolactones, which displayed enhanced stabilities relative to lactones. Moreover, they were highly selective for RhlR over another key QS receptor in P. aeruginosa, LasR. These compounds are among the most potent RhlR modulators known and represent robust chemical tools to dissect the complex roles of RhlR in the P. aeruginosa QS circuitry.
Ureteroscopic ultrasound technology to size kidney stone fragments: Proof of principal using a miniaturized probe in a porcine model. (2009)

Background: the ability to measure stone fragment size could help prevent attempting to extract too large a stone fragment. We evaluated the ability of a 1.2 mm (3.6 French) ultrasound probe to measure stone fragments in a porcine kidney. Methods: 15 human stones of three types (five each calcium oxalate, cystine, calcium phosphate) sized 3–7 mm were placed deep in a porcine kidney collecting system. The sound speed of each stone type was determined using a separate reference stone. A 2 MHz, 1.2 mm needle hydrophone was used to send and receive ultrasound pulses. Stone thickness was calculated as d=c*t/2 by determining the signal transit time through the stone, t, and the stone sound speed, c. Calculated stone thicknesses were compared to digital caliper measurements. Results: Stone size was determined for all 15 stones. Correlation between ultrasound-determined thickness and caliper measurements was excellent (r2=0.90, p&lt;0.0001) with ultrasound performing well in all three stone types. All stone measurements were accurate within 1 mm, and ten (66%) stone measurements were accurate within 0.5 mm. Conclusions: Ultrasound-based measurements are accurate and precise using a 3.6 French probe with stone fragments placed deep in a porcine kidney. [Work supported by Grants NIH DK43881 and NSBRI SMST01601.]
Uncovering the active sites and demonstrating stable catalyst for the cost-effective conversion of ethanol to 1-butanol (2021)

The emergence of a renewable ethanol industry has provided a sustainable platform molecule to produce value-added chemicals and fuels; what is lacking now are viable conversion processes from ethanol that can displace non-renewable pathways.
An Integrated Fault Isolation and Prognosis Method for Electric Drive Systems of Battery Electric Vehicles (2020)

The electric drive system is a key subsystem of battery electric vehicles (BEVs). Abnormalities in the electric drive system components may lead to performance degradation in the drive system and, more severely, loss of power in the vehicle. This article presents an integrated prognosis system for early detection and isolation of the electric drive system and component faults. The system first calculates multiple health features, known as health indicators derived from the available onboard sensor signals. Then, an integrated prognostic and fault isolation strategy is used to isolate the root cause of electric drive faults by monitoring the performance of the multiple health indicators. The prognostic system uses a hierarchical approach: it first determines if there is a degradation in the electric drive system by comparing the system achieved torque with the estimated torque and, then, goes further to check multiple component-level health indicators for the various components comprising an electric drive system, including motor stator winding, three-phase current sensors, and resolver. After a component has been detected to degrade to a certain level, the prognosis system sends out an alert before the severe performance reduction of the drive system occurs, thus protecting the customers from loss of propulsion and walk home situations.
INTEGRATION OF RELAY PROTECTION FUNCTIONS (2011)

This paper presents a novel solution that integrates protection of power transformers and power cables based on differential protection principles. Primary currents are measured by Rogowski Coil current sensors. In this solution, one Rogowski Coil set shares signals for two protection functions, simplifying the protection installation and reducing the project cost. This solution has been designed for all power transformer and cable/line installations.
Augmented video calls on mobile devices (2013)

We present a system and a method to segment the head-shoulder image of participants in a video call using mobile devices such as a smartphone or a tablet. Participants can choose to send only the segmented head-shoulder foreground image and overlay it on top of a static background image or a background video on the receiver side of the video call, as well as to replace the background of the caller himself/herself during the video call. Our proposed method extracts the head-shoulder area of each video frame based on detected face region, superpixel clustering, and efficient label propagation.
Following Passive DNS Traces to Detect Stealthy Malicious Domains Via Graph Inference (2020)

Malicious domains, including phishing websites, spam servers, and command and control servers, are the reason for many of the cyber attacks nowadays. Thus, detecting them in a timely manner is important to not only identify cyber attacks but also take preventive measures. There has been a plethora of techniques proposed to detect malicious domains by analyzing Domain Name System (DNS) traffic data. Traditionally, DNS acts as an Internet miscreant’s best friend, but we observe that the subtle traces in DNS logs left by such miscreants can be used against them to detect malicious domains. Our approach is to build a set of domain graphs by connecting “related” domains together and injecting known malicious and benign domains into these graphs so that we can make inferences about the other domains in the domain graphs. A key challenge in building these graphs is how to accurately identify related domains so that incorrect associations are minimized and the number of domains connected from the dataset is maximized. Based on our observations, we first train two classifiers and then devise a set of association rules that assist in linking domains together. We perform an in-depth empirical analysis of the graphs built using these association rules on passive DNS data and show that our techniques can detect many more malicious domains than the state-of-the-art.
Effect of Molecular Weight of Methylphenylsiloxy‐Containing Vinyl‐Functionalized Terpolysiloxanes on Their UV‐Activated Crosslinking by Hydrosilylation and Mechanical Properties of Crosslinked Elastomers (2021)

Effects of molecular weight of methylphenyl-containing vinylsiloxy-functionalized terpolysiloxanes on their UV-activated crosslinking by hydrosilylation at room temperature in air, shelf life stability of "all-in-one" pastes prepared from them for additive manufacturing, and mechanical properties of the resulting crosslinked elastomers, are investigated. It is found that while rheology of pastes containing base polymers, trimethylsilylated silica fillers, and thixotropic additives is not significantly affected by the base polymer molecular weight but is dominated by the filler concentration, the pastes based on higher molecular weight polymers exhibit faster crosslinking (corresponding to higher catalyst turnover numbers) and their crosslinked elastomers show transient strain-induced crystallization. The latter appears in networks from terpolymers with degrees of polymerization (DP) of 240 and above (corresponding to about one half of the critical polydimethylsiloxane chain length for entanglement formation of DP = 460), within the temperature range of -80 to -30 °C, characteristic for polydimethylsiloxane melting transition. It is believed that this is the first time an observation of this chain length effect is reported for polysiloxane elastomers and that the properties reported herein can be expected to have major implications on the application potential of these polymers in both additive manufacturing and performance of their elastomers at sub-ambient temperatures.
Structure and Function of RNA Polymerase II Elongation Factor ELL (1997)

The human ELL gene on chromosome 19p13.1 undergoes frequent translocations with the trithorax-like MLL gene on chromosome 11q23 in acute myeloid leukemia. Recently, the human ELL gene was shown to encode an RNA polymerase II elongation factor that activates elongation by suppressing transient pausing by polymerase at many sites along the DNA. In this report, we identify and characterize two overlapping ELL functional domains that govern its interaction with RNA polymerase II and the ternary elongation complex. Our findings reveal that, in addition to its elongation activation domain, ELL contains a novel type of RNA polymerase II interaction domain that is capable of negatively regulating polymerase activity in promoter-specific transcription initiation in vitro. Notably, the MLL-ELL translocation results in deletion of a portion of this functional domain, and ELL mutants lacking sequences deleted by the translocation bind RNA polymerase II and are fully active in elongation, but fail to inhibit initiation. Taken together, these results raise the possibility that the MLL-ELL translocation could alter ELL-RNA polymerase II interactions that are not involved in regulation of elongation.
An Optimization Approach to Services Sales Forecasting in a Multi-staged Sales Pipeline (2016)

Services organization manage a pipeline of sales opportunities with variable enterprise sales engagement lifespan, maturity levels (belonging to progressive sales stages), and contract values at any given point in time. Accurate forecasting of contract signings by the end of a time period (e.g., a quarter) is a desire for many services organizations in order to get an accurate projection of incoming revenues, and to provide support for delivery planning, resource allocation, budgeting, and effective sales opportunity management. While the problem of sales forecasting has been investigated in its generic context, sales forecasting for services organizations entails the consideration of additional complexities, which has not been thoroughly investigated: (i) considering opportunities in multi-staged sales pipeline, which means providing stage-specific treatment of sales opportunities in each group, and (ii) using the information of the current pipeline build-up, as well as the projection of the pipeline growth over the remaining time period before the end of the target time period in order to make predictions. In this paper, we formulate this problem, considering the service-specific context, as a machine learning problem over the set of historical services sales data. We introduce a novel optimization approach for finding the optimized weights of a sales forecasting function. The objective value of our optimization model minimizes the average error rates for predicting sales based on two factors of conversion rates and growth factors for any given point in time in a sales period over historical data. Our model also optimally determines the number of historical periods that should be used in the machine learning framework to predict the future revenue. We have evaluated the presented method, and the results demonstrate superior performance (in terms of absolute and relative errors) compared to a baseline state of the art method.
Cloning and expression of superoxide dismutase from <i>Aquifex pyrophilus</i>, a hyperthermophilic bacterium (1997)

A superoxide dismutase (SOD) gene of Aquifex pyrophilus, a marine hyperthermophilic bacterium, was cloned, sequenced, expressed in Escherichia coli, and its gene product characterized. This is the first SOD from a hyperthermophilic bacterium that has been cloned. It is an iron-containing homo-oligomeric protein with a monomeric molecular mass of 24.2 kDa. The DNA-derived amino acid sequence is more similar to those of known Mn- and Fe-SODs from thermophilic archaea than of Cu, Zn-SODs. The metal binding residues found in all SOD sequences from different species are also conserved in A. pyrophilus SOD. The protein is biochemically active only as an oligomer and is resistant to thermal denaturation.
Multidimensional information visualization through sliding rods (2000)

In this paper we propose new visual interface technology to address multidimensional data exploration and browsing tasks. MultiNav, a prototype from GTE Laboratories, is based upon a multidimensional information model that affords new data exploration and semantically structured browsing interactions. The primary visual metaphor is based on sliding rods, each of which is associated with an information dimension from the underlying model. Users can interactively select value ranges along the rods in order to reveal hidden relationships as well as query and restrict the set through direct manipulation. A novel focus+context view is afforded in which detail about individual items is revealed within the context of the global multidimensional attribute space. We propose a novel interaction technique to change focus, which is based on dragging rods from side to side. We relate this work on multidimensional information visualization to other research in the area, including Parallel Coordinates, Dynamic Histograms, Dynamic Queries, and focus+context tables.*.
PROSTHESIS-GUIDED TRAINING INCREASES FUNCTIONAL WEAR TIME AND IMPROVES TOLERANCE TO MALFUNCTIONING INPUTS OF PATTERN RECOGNITION-CONTROLLED PROSTHESES (2011)

A remaining barrier to the clinical accessibility of pattern recognition systems is the lack of practical methods to acquire the myoelectric signals required to train the system. Many current methods involve screen-guided training (SGT), where wearers connected to an external computer perform muscle contractions synchronized with a sequence of visual cues. The system complexity prevents easy retraining when signal conditions change. We have developed a method called prosthesis-guided training (PGT), where the prosthesis itself provides the cues by moving through a sequence of preprogrammed motions; screen prompting and external connections are eliminated. Five prosthesis wearers performed a repetitive clothespin placement task using pattern recognition control. Wearers demonstrated similar baseline functionality between systems trained with PGT (10 ± 4 clothespins) and SGT (12 ± 7 clothespins) (p = 0.56). To investigate the efficacy of PGT retraining, real-world issues (e.g. broken wires, external noise) were simulated to accelerate control degradation. Sessions ended when wearers indicated loss of functional control. On average, wearers maintained function through two malfunctioning inputs, placing 48 ± 17 clothespins in 31.6 ± 16.2 minutes when allowed to retrain using PGT. These results suggest that PGT acquires adequate training data and may enable longer-lasting functional use, potentially increasing prosthesis wear time and reducing device rejection.