gebhart/patrepeval huggingface dataset:
Prediction of Protein Interdomain Linker Regions by a Nonstationary Hidden Markov Model (2008)

Proteins have two types of regions: linker regions that connect active domains and nonlinker regions, which include domains and terminal residues. It is important to try to distinguish these regions using information in the sequence of amino acids that, when folded, form the protein. In this article we develop a nonstationary hidden Markov model to infer region boundaries. The approach is based on a latent variable defined on the sequence; this variable is a continuous index of the region type and affects the probabilities that specific amino acids will appear. We develop an efficient Bayesian estimate of the model using Markov chain Monte Carlo methods, particularly Gibbs sampling, to simulate the parameters from the posteriors. We apply our method to protein sequences with domains and interdomain linkers delineated using the Pfam-A database. The prediction results are superior to simpler methods. Importantly, our method estimates the probability that each amino acid belongs to a linker region, giving insight into the properties of interdomain linkers.
Endophthalmitis After Intravitreal Injections (2009)

Endophthalmitis following intravitreal injection is an infrequent but serious clinical problem. Infectious endophthalmitis must be differentiated from noninfectious inflammation. Depending on the series, the risk of endophthalmitis is very low. The use of a standardized injection protocol can reduce the risk of infection.
Independent vs. Axle Suspension for On/Off Road Vehicles (1992)

<div class="htmlview paragraph">The conflicting suspension requirements of vehicles which are designed for both on and off-road operation are examined. The example vehicle used throughout the calculations is a six-wheel truck of 24 tonne GVW and is based on an existing crash tender design. Using the Vehicle Dynamics Analysis Software (VDAS) package, the ride and handling behaviour of the truck is analysed for two versions of the vehicle; one with three axles suspended on leaf springs with a bogie arrangement at the rear, and another with independent wheel suspension throughout.</div> <div class="htmlview paragraph">The overall conclusion drawn is that axle designs have significant advantages for off-road vehicle applications; they maintain good ground clearance, they are based on inexpensive, well proven technology and, with attention to detail design, offer vehicle dynamic performance comparable with independent designs. On the other hand, if the optimum ride and handling compromise for on-road conditions is a priority, then the independent suspension may be worth the additional investment.</div>
Multilevel inverter modulation schemes to eliminate common-mode voltages (2000)

It is well known that conventional two-level pulsewidth modulated (PWM) inverters generate high-frequency common-mode voltages with high dv/dt. Similarly, commonly used multilevel inverter modulation schemes generate common-mode voltages. Common-mode voltages may cause motor shaft voltages and bearing currents and conducted electromagnetic interference (EMI). Premature motor bearing failures and electronic equipment malfunctions have been reported to be directly related to bearing currents and EMI. In this paper, approaches to eliminating common-mode voltage when using multilevel PWM inverters are presented. It is shown that inverters, which have an odd number of levels, will generate zero common-mode voltage by switching among certain states. Therefore, motor bearing currents will be eliminated and conducted EMI will be reduced. Both sinusoidal PWM and space-vector modulation (SVM) schemes are discussed and detailed comparative simulation results between conventional and novel modulation schemes are provided. The value of the proposed technique is demonstrated experimentally by applying the novel SVM approach to a conventional multilevel inverter.
A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes (2014)

The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing.
New adaptive partial distortion search using clustered pixel matching error Characteristic (2005)

In order to reduce the computation load, many conventional fast block-matching algorithms have been developed to reduce the set of possible searching points in the search window. All of these algorithms produce some quality degradation of a predicted image. Alternatively, another kind of fast block-matching algorithms which do not introduce any prediction error as compared with the full-search algorithm is to reduce the number of necessary matching evaluations for every searching point in the search window. The partial distortion search (PDS) is a well-known technique of the second kind of algorithms. In the literature, many researches tried to improve both lossy and lossless block-matching algorithms by making use of an assumption that pixels with larger gradient magnitudes have larger matching errors on average. Based on a simple analysis, it is found that, on average, pixel matching errors with similar magnitudes tend to appear in clusters for natural video sequences. By using this clustering characteristic, we propose an adaptive PDS algorithm which significantly improves the computation efficiency of the original PDS. This approach is much better than other algorithms which make use of the pixel gradients. Furthermore, the proposed algorithm is most suitable for motion estimation of both opaque and boundary macroblocks of an arbitrary-shaped object in MPEG-4 coding.
MatConvNet (2015)

MatConvNet is an open source implementation of Convolutional Neural Networks (CNNs) with a deep integration in the MATLAB environment. The toolbox is designed with an emphasis on simplicity and flexibility. It exposes the building blocks of CNNs as easy-to-use MATLAB functions, providing routines for computing convolutions with filter banks, feature pooling, normalisation, and much more. MatConvNet can be easily extended, often using only MATLAB code, allowing fast prototyping of new CNN architectures. At the same time, it supports efficient computation on CPU and GPU, allowing to train complex models on large datasets such as ImageNet ILSVRC containing millions of training examples
RBF Networks-Based Adaptive Inverse Model Control System for Electronic Throttle (2009)

An electronic throttle is a dc-motor-driven valve that regulates air inflow into the combustion system of the engine. An effective controller for electronic throttle is not easy to accomplish since the plant is burdened with strong nonlinear effects of stick-slip friction, spring, and gear backlash. In this brief, an adaptive inverse model control system (AIMCS) is designed for the plant, and two radial basis function (RBF) neural networks are utilized in the AIMCS. The plant is identified by a RBF networks identifier, which provides the sensitivity information of the plant to the control input. And another RBF networks is utilized as inverse model controller established by inverse system method. The RBF networks are offline learned firstly and are online trained using back propagation algorithms. To guarantee convergence and for faster learning, adaptive learning rates are developed. Simulation and experiment results show the effectiveness of the AIMCS.
Automated Defect and Correlation Length Analysis of Block Copolymer Thin Film Nanopatterns (2015)

Line patterns produced by lamellae- and cylinder-forming block copolymer (BCP) thin films are of widespread interest for their potential to enable nanoscale patterning over large areas. In order for such patterning methods to effectively integrate with current technologies, the resulting patterns need to have low defect densities, and be produced in a short timescale. To understand whether a given polymer or annealing method might potentially meet such challenges, it is necessary to examine the evolution of defects. Unfortunately, few tools are readily available to researchers, particularly those engaged in the synthesis and design of new polymeric systems with the potential for patterning, to measure defects in such line patterns. To this end, we present an image analysis tool, which we have developed and made available, to measure the characteristics of such patterns in an automated fashion. Additionally we apply the tool to six cylinder-forming polystyrene-block-poly(2-vinylpyridine) polymers thermally annealed to explore the relationship between the size of each polymer and measured characteristics including line period, line-width, defect density, line-edge roughness (LER), line-width roughness (LWR), and correlation length. Finally, we explore the line-edge roughness, line-width roughness, defect density, and correlation length as a function of the image area sampled to determine each in a more rigorous fashion.
The effect of surface-electrode resistance on the performance of ionic polymer-metal composite (IPMC) artificial muscles (2000)

Reported in this study are the effects of the surface-electrode resistance on the performance of ionic polymer-metal composite (IPMC) artificial muscles. The IPMC artificial muscles manufactured in this study is composed of a perfluorinated ion-exchange membrane, platinum composited by using a chemical processing technique that employs a platinum salt and appropriate reducing agents. Furthermore, the IPMC artificial muscles were optimized for producing improved forces by changing multiple process parameters including the time-dependent concentrations of the salt and reducing agents. However, the analytical results confirmed that the platinum electrode is successfully deposited on the surface of the material where platinum particles stay in a dense form that appears to introduce a significant level of surface-electrode resistance. In order to address this problem, a thin layer of silver (or copper) was electrochemically deposited on top of the platinum electrode to reduce the surface-electrode resistance. Actuation tests were performed for such IPMC artificial muscles under a low voltage. The test results show that the lower surface-electrode resistance generates higher actuation capability in the IPMC artificial muscles. This observation is briefly discussed based on the role that the equivalent circuit for the IPMC plays and a possible electrophoretic cation-transport phenomenon under the influence of an electric field.
Detection of the Bean Common Blight Bacteria,<i>Xanthomonas campestris</i>pv.<i>phaseoli</i>and<i>X. c. phaseoli</i>var.<i>fuscans,</i>Using the Polymerase Chain Reaction (1994)

A 3.4-kb plasmid DNA fragment (p7) of Xanthomonas campestris pv. phaseoli that hybridizes specifically to X. c. phaseoli was subcloned and partially sequenced to design primers for a polymerase chain reaction (PCR) assay for the detection of bacteria causing common blight in bean. In Southern hybridization experiments, p7X3 and p7X4 subfragments showed high specificity for total genomic DNA of pathogenic X. c. phaseoli, whereas the p7X2 segment also weakly hybridized to DNA extracted from some strains belonging to other X. campestris pathovars. For each of these p7 fragments, a set of G + C-rich oligonucleotide primers was devised and tested under high-stringency conditions in PCR assays
Preparation and Sorption Properties of Spherical Polyacrylamide-Zirconium Phosphate Ion-Exchanger (1983)

Abstract Spherical particles of polyacrylamide-zirconium phosphate (PZP) ion-exchanger have been prepared by the conversion of hydrous zirconia with the sol-gel technique using acrylamide and N,N'-methylenebisacrylamide copolymer as binders. Some chemical properties, stabilities, and sorptions of 1–2 valent cations have been studied. An elution curve of 137Cs is reported, and the effective separation of Cs+, Co2+, and Ce3+ has been achieved with a small column of PZP.
Development of pervasive compaction monitoring interface for soil compactor &#x2014; A GPS/GSM based approach (2013)

Pervasive computing provides an attractive visionfor the future. Mobile and stationary devices will dynamically connect and coordinate to seamlessly help people to implement their tasks. However, in reality still there are practices which require pervasive monitoring especially in the domain of geo vehicle monitoring. To make the vision of pervasive computing technologies for the geo vehicle monitoring we are integrating technologies like GPS (Global Positioning Technology), GSM (Global System for Mobile) for compaction monitoring. GPS is recently used for wide applications like orbit identification and positioning. GPS need some compatible receivers which support location-awareness using positioning technique like LBS (Location Based System). Soil compaction is a form of physical degradation resulting in densification and distortion of the soil where biological activity, porosity and permeability were reduced, soil strength is increased and soil structure partly destroyed. Monitoring the soil compaction manually in the workspace is not reliable and continuous monitoring by a single person may not be feasible. This would be the motivation to choose wireless communication. The compaction data and the location data will be sent to the server for remote monitoring. GSM will allow us to transmit the data to the remote server. The objective of this paper is to provide better accuracy with low cost GPS receiver's positioning results. This paper makes use of GPS, ARM7/TDMI (LPC2378) family and GSM. NMEA (National Marine Electronics Association) data acquisition from GPS is monitored. Compaction input is interfaced with GPS coordinates. Alerts can be sent from the vehicle to the user mobile phone through GSM communication using AT commands.
Arterial Stiffness and Endothelial Function in Patients With β-Thalassemia Major (2002)

Increased arterial stiffness, endothelial dysfunction, and LV hypertrophy occur in patients with beta-thalassemia major, which may result in reduction of mechanical efficiency of the heart.
Expression of Functional Gap Junctions and Regulation by Fluid Flow in Osteocyte-Like MLO-Y4 Cells (2001)

Osteocytes are thought to be mechanosensory cells that respond to mechanical stress by sending signals to other bone cells to initiate bone remodeling. An osteocyte-like cell line MLO-Y4 provides a model system to examine whether gap junctions participate in the regulation of osteocyte function and signaling by mechanical stress. In this study, we show that MLO-Y4 cells are coupled and that gap junction channels mediate this coupling. Biochemical analyses show that connexin 43 (Cx43) is a major gap junction protein expressed in MLO-Y4 cells and approximately 5% of Cx43 protein is phosphorylated. MLO-Y4 cells were exposed to mechanical stress using a parallel plate flow chamber to model bone fluid flow shear stress. Fluid flow increased significantly the length of the dendritic processes, a morphological characteristic of osteocytes. A redistribution of the gap junction protein, Cx43 also was observed from a location circling the nucleus to punctate spots in the cytoplasm and in the dendritic processes. "Scrape-loading" dye transfer analyses showed that fluid flow increased intercellular coupling and increased the number of cells coupled immediately after fluid flow treatment, in direct proportion to shear stress magnitude. Although intercellular coupling continued to increase, stimulation of Cx43 protein expression during the poststress period was found to be biphasic. Cx43 protein was elevated 30 minutes after application of stress but decreased at 24 h poststress. Pulsating fluid flow had a similar stimulatory effect as steady fluid flow on gap junctions. However, this stimulatory effect in osteocyte-like cells was not observed in osteoblast-like 2T3 cells. Together, these results show that fluid flow has stimulatory effects on osteocyte-like MLO-Y4 cells with early effects on cellular morphology, opening of gap junctions, and redistribution of Cx43 protein and delayed effects on Cx43 protein expression. The high expression of Cx43 and its location in the cytoplasm also suggest that Cx43 may have unknown functions in addition to forming gap junctions. These studies indicate that gap junctions may serve as channels for signals generated by osteocytes in response to mechanical loading.
Clickable Multifunctional Dumbbell Particles for in Situ Multiplex Single-Cell Cytokine Detection (2017)

We report a novel strategy for fabrication of multifunctional dumbbell particles (DPs) through click chemistry for monitoring single-cell cytokine releasing. Two different types of DPs were prepared on a large scale through covalent bioorthogonal reaction between methyltetrazine and trans-cyclooctene on a microchip under a magnetic field. After collection of the DPs, the two sides of each particle were further functionalized with different antibodies for cell capturing and cytokine detection, respectively. These DPs labeled with different fluorescent dyes have been used for multiplex detection and analysis of cytokines secreted by single live cells. Our results show that this new type of DPs are promising for applications in cell sorting, bioimaging, single-cell analysis, and biomedical diagnostics.
Malware Forensics: Investigating and Analyzing Malicious Code (2008)

Malware Forensics: Investigating and Analyzing Malicious Code covers the emerging and evolving field of forensics, where investigators examine a computer system to collect and preserve critical live data that may be lost if the system is shut down. Unlike other texts that discuss on a particular operating system, or in a generic context, this book emphasizes a live forensics and evidence collection methodology on both Windows and Linux operating systems in the context of identifying and capturing malicious code and evidence of its effect on the compromised system. Malware Forensics: Investigating and Analyzing Malicious Code also devotes extensive coverage of the burgeoning field of physical and process memory analysis on both Windows and Linux platforms. This book provides clear and concise guidance as to how to forensically capture and examine physical and process memory as a key investigative step in malicious code forensics. Prior to this book, competing texts have described malicious code, accounted for its evolutionary history, and in some instances, dedicated a mere chapter or two to analyzing malicious code. Conversely, Malware Forensics: Investigating and Analyzing Malicious Code emphasizes the practical how-to aspect of malicious code investigation, giving deep coverage on the tools and techniques of conducting runtime behavioral malware analysis (such as file, registry, network and port monitoring) and static code analysis (such as file identification and profiling, strings discovery, armoring/packing detection, disassembling, debugging), and more. * Winner of Best Book Bejtlich read in 2008!* http://taosecurity.blogspot.com/2008/12/best-book-bejtlich-read-in-2008.html* Authors have investigated and prosecuted federal malware cases, which allows them to provide unparalleled insight to the reader.* First book to detail how to perform forensic techniques on malicous code.* In addition to the technical topics discussed, this book also offers critical legal considerations addressing the legal ramifications and requirements governing the subject matter
Poly(2‐ethyl‐2‐oxazoline) as Alternative for the Stealth Polymer Poly(ethylene glycol): Comparison of in vitro Cytotoxicity and Hemocompatibility (2012)

Limitations of PEG in drug delivery have been reported from clinical trials. PEtOx (0.4-40 kDa) as alternative is synthesized by a living, microwave-assisted polymerization, and is directly compared to PEG of similar molar mass regarding cytotoxicity and hemocompatibility. In short-term treatments, both types of polymers are well tolerated even at high concentrations. Moderate concentration and molar mass dependent cytotoxic effects occurred only after long-term incubation at concentrations higher than therapeutic doses. PEtOx possesses not only an easy route of synthesis and beneficial physicochemical characteristics such as low viscosity and high stability, which are advantageous over PEG, but additionally in vitro toxicology comparable to PEG.
Size-selected agglomerates of SnO2 nanoparticles as gas sensors (2009)

The effect of nanoparticle structure on gas sensing performance is investigated. Size-selected nanostructured SnO2 agglomerate particles for gas sensors were made by scalable flame spray pyrolysis. These particles were polydisperse (up to 12μm in diameter) and consisted of primary particles of 10nm in grain and crystal size as measured by transmission electron microscopy, x-ray diffraction, and Berner low pressure impactor (BLPI). The effect of agglomerate size on thermal stability and sensing of ethanol vapor (4–100ppm) and CO (4–50ppm) was investigated by selecting nearly monodisperse fractions of these agglomerates by the BLPI. Sensor layers made with these size-fractionated agglomerates exhibited higher thermal stability and dramatically enhanced sensitivity for both analytes than layers made with polydisperse agglomerates. This is attributed to their aggregate (or hard agglomerate) structure exhibiting small sinter necks between their constituent primary particles of tin dioxide that had also a narrow size distribution as expected for particles generated in flames. Upon further sintering of these optimally sized, nanostructured agglomerates, grain and neck growth degraded their superior sensitivity, supporting the proposed mechanism of their enhanced sensitivity: optimal primary particle necking.