gebhart/patrepeval huggingface dataset:
Complete Nucleotide Sequence and Organization of the Atrazine Catabolic Plasmid pADP-1 from <i>Pseudomonas</i> sp <i>.</i> Strain ADP (2001)

The complete 108,845-nucleotide sequence of catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP was determined. Plasmid pADP-1 was previously shown to encode AtzA, AtzB, and AtzC, which catalyze the sequential hydrolytic removal of s-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. Computational analyses indicated that pADP-1 encodes 104 putative open reading frames (ORFs), which are predicted to function in catabolism, transposition, and plasmid maintenance, transfer, and replication. Regions encoding transfer and replication functions of pADP-1 had 80 to 100% amino acid sequence identity to pR751, an IncPbeta plasmid previously isolated from Enterobacter aerogenes. pADP-1 was shown to contain a functional mercury resistance operon with 99% identity to Tn5053. Complete copies of transposases with 99% amino acid sequence identity to TnpA from IS1071 and TnpA from Pseudomonas pseudoalcaligenes were identified and flank each of the atzA, atzB, and atzC genes, forming structures resembling nested catabolic transposons. Functional analyses identified three new catabolic genes, atzD, atzE, and atzF, which participate in atrazine catabolism. Crude extracts from Escherichia coli expressing AtzD hydrolyzed cyanuric acid to biuret. AtzD showed 58% amino acid sequence identity to TrzD, a cyanuric acid amidohydrolase, from Pseudomonas sp. strain NRRLB-12227. Two other genes encoding the further catabolism of cyanuric acid, atzE and atzF, reside in a contiguous cluster adjacent to a potential LysR-type transcriptional regulator. E. coli strains bearing atzE and atzF were shown to encode a biuret hydrolase and allophanate hydrolase, respectively. atzDEF are cotranscribed. AtzE and AtzF are members of a common amidase protein family. These data reveal the complete structure of a catabolic plasmid and show that the atrazine catabolic genes are dispersed on three disparate regions of the plasmid. These results begin to provide insight into how plasmids are structured, and thus evolve, to encode the catabolism of compounds recently added to the biosphere.
Two-year efficacy and tolerability of once-monthly oral ibandronate in postmenopausal osteoporosis: the MOBILE study (2005)

peer reviewed
GPU acceleration of a fully 3D Iterative Reconstruction Software for PET using CUDA (2009)

A CUDA implementation of the existing software FIRST (Fast Iterative Reconstruction Software for (PET) Tomography) is presented. This implementation uses consumer graphics processing units (GPUs) to accelerate the compute-intensive parts of the reconstruction: forward and backward projection. FIRST was originally developed in FORTRAN, and it has been migrated to C language to be used with NVIDIA C for CUDA, as well as for a straightforward implementation and performance comparison between the C versions of the code running on the CPU and on the GPU. We measured the execution time of the CUDA version compared to the fastest available CPU. The CUDA implementation includes a loop re-ordering and an optimized memory allocation, which improves even more the performance of the reconstruction on the GPUs.
Bi-LSTM Model to Increase Accuracy in Text Classification: Combining Word2vec CNN and Attention Mechanism (2020)

There is a need to extract meaningful information from big data, classify it into different categories, and predict end-user behavior or emotions. Large amounts of data are generated from various sources such as social media and websites. Text classification is a representative research topic in the field of natural-language processing that categorizes unstructured text data into meaningful categorical classes. The long short-term memory (LSTM) model and the convolutional neural network for sentence classification produce accurate results and have been recently used in various natural-language processing (NLP) tasks. Convolutional neural network (CNN) models use convolutional layers and maximum pooling or max-overtime pooling layers to extract higher-level features, while LSTM models can capture long-term dependencies between word sequences hence are better used for text classification. However, even with the hybrid approach that leverages the powers of these two deep-learning models, the number of features to remember for classification remains huge, hence hindering the training process. In this study, we propose an attention-based Bi-LSTM+CNN hybrid model that capitalize on the advantages of LSTM and CNN with an additional attention mechanism. We trained the model using the Internet Movie Database (IMDB) movie review data to evaluate the performance of the proposed model, and the test results showed that the proposed hybrid attention Bi-LSTM+CNN model produces more accurate classification results, as well as higher recall and F1 scores, than individual multi-layer perceptron (MLP), CNN or LSTM models as well as the hybrid models.
Cell Therapy for the Treatnent of Malignant Pleural Mesothelioma (2013)

Malignant pleural mesothelioma (MPM) is a devastating malignancy of the pleural lining. It presents insidiously and at the time of presentation the disease is often diffusely spread throughout the chest cavity. There are few effective therapies available, the average survival is 9-12 months from diagnosis and 5-year survival rates are only 2%. Novel therapies are desperately needed. There is increasing interest in combined gene and cell therapy approaches and for a malignant disease this is particularly appealing. Mesenchymal stem cells (MSCs) are known to home to tumours and are readily transduced with viral vectors making them ideal cells for delivering targeted therapy. TNF-related apoptosis inducing ligand (TRAIL) is an exciting anti-cancer therapy as it selectively causes apoptosis in cancer cells without affecting healthy cells. This makes the combination of MSCs carrying TRAIL (MSCTRAIL) a viable prospect for the targeted treatment of MPM. Lentiviral vectors expressing TRAIL were used to transduce human bone marrow-derived MSCs (MSCTRAIL) which induced apoptosis and cell death in multiple human MPM cell lines. MPM cells were transduced with a luciferase-expressing lentiviral vector (MPMLuc) and were used to establish a murine model of MPM allowing me to track tumour growth in vivo using bioluminescent imaging. Systemic delivery of MSCTRAIL to MPM tumours resulted in a significant reduction in tumour growth but topical delivery was not effective. Using dual bioluminescent and fluorescent imaging I showed that MSCs home to tumours when delivered both systemically and topically but that they engraft in greater numbers following systemic delivery. Combining chemotherapy with MSCTRAIL showed promising effects in vitro but was not effective in reducing tumour burden in vivo. In summary, human bone marrow derived MSCs were shown to localise to areas of MPM and when modified to express TRAIL and delivered systemically they significantly reduced tumour burden.
Conjugated “<i>B</i>-Entacenes”: Polycyclic Aromatics Containing Two Borepin Rings (2011)

The synthesis and characterization of functionalized bora-acenes (B-entacenes) where Stille and Sonogashira cross-couplings were used to attach a series of electron-donating and -withdrawing substituents is reported. Photophysical, electrochemical, and computational analyses revealed that the LUMO level can be tuned by changing the para-conjugated substituent. Furthermore, the dimethylamino-functionalized molecule exhibited intense solvatochromism due to the intramolecular charge-transfer interaction.
Bone marrow derived elements and resident microglia in brain inflammation (1993)

Infection of the central nervous (CNS) system by the human immunodeficiency virus (HIV) depends on the migration of infected hematogenous cells into the brain. We thus used quantitative light and electron microscopic immunocytochemistry to study the homing and turnover of bone marrow derived cells in the CNS in radiation bone marrow chimeras under normal conditions and in experimental autoimmune encephalomyelitis (EAE) as an experimental model of brain inflammation. Our studies suggest the following conclusions. First, the central nervous system is continuously patrolled by a small number of T-lymphocytes and monocytes. Meningeal and perivascular monocytes are slowly replaced by hematogenous cells under normal conditions, and this turnover is accelerated in the course of inflammation. In contrast, resident microglia represent a very stable cell pool, which in adult animals is only exceptionally replaced by hematogenous cells, even after recovery from severe brain inflammation. Second, although in bone-marrow-chimeric animals resident microglia, astrocytes, and ependymal cells are not able to present antigen to Lewis T-lymphocytes, the inflammatory reaction in EAE is qualitatively and quantitatively similar in these animals compared to fully histocompatible Lewis rats. Finally, resident microglia express the macrophage activation antigen ED1. Thus, microglia cells appear to function as effector cells in EAE lesions.
Phase Identification in Electric Power Distribution Systems by Clustering of Smart Meter Data (2016)

Accurate network and phase connectivity models are crucial to distribution system analytics, operations and planning. Although network connectivity information is mostly reliable, phase connectivity data is typically missing or erroneous. In this paper, an innovative phase identification algorithm is developed by clustering of voltage time series gathered from smart meters. The feature-based clustering approach is adopted where principal component analysis is first carried out to extract feature vectors from the raw time series. A constrained k-means clustering algorithm is then executed to separate customers/smart meters into various phase connectivity groups. The algorithm is applied on a real distribution feeder in Southern California Edison's service territory. The accuracy of the proposed algorithm is over 90%.
High-throughput detection of immobilized plasmonic nanoparticles by a hyperspectral imaging system based on Fourier transform spectrometry (2011)

To facilitate the application of plasmonic nanoparticles (PNPs) in high-throughput detection, we develop a hyperspectral imaging system (HSIS) combining dark-filed microscopy and imaging Fourier transform spectrometry to measure scattering spectra from immobilized PNPs. The current setup has acquisition time of 5 seconds and spectral resolution of 21.4 nm at 532.1 nm. We demonstrate the applicability of the HSIS in conjunction with spectral data analysis to quantify multiple types of PNPs and detect small changes in localized surface plasmon resonance wavelengths of PNPs due to changes in the environmental refractive index.
Estimating the minimum delay optimal cycle length based on a time-dependent delay formula (2016)

For fixed time traffic signal control, the well-known Webster’s formula is widely used to estimate the minimum delay optimal cycle length. However, this formula overestimates the cycle length for high degrees of saturation. In this paper, we propose two regression formulas for estimating the minimum delay optimal cycle length based on a time-dependent delay formula as used in the Canadian Capacity Guide and the Highway Capacity Manual (HCM). For this purpose, we develop a search algorithm to determine the minimum delay optimal cycle length required for the regression analysis. Numerical results show that the proposed formulas give a better estimation for the optimal cycle length at high intersection flow ratios compared to Webster’s formula.
The effect of wrist force sensor stiffness on the control of robot manipulators (2005)

This paper analyzes the effects of the mechanical stiffness of end effector force sensors on the control of robot manipulators. Modeling of the general manipulator-sensor system is presented, along with a detailed investigation of a single joint case. Analytical and experimental results indicate that the use of a mechanically compliant sensor permits a more responsive force controlled system to be realized. In addition, an active compensator for sensor deflections was developed to recover the static positional stiffness of the manipulator.
Automated Indent Scanning: Artificial intelligence assisted scanning of large regular and irregular nanoindentation arrays in scanning electron microscopes (2024)

Recording larger arrays of indents is a tedious and time intensive task. This project aims to automate this process through the use of the Python API provided by the Tescan microscope (SharkSEM), simple automation scripts, and the use of object detection techniques (YOLO).
System Identification and Estimation Framework for Pivotal Automotive Battery Management System Characteristics (2011)

The battery management system (BMS) is an integral part of an automobile. It protects the battery from damage, predicts battery life, and maintains the battery in an operational condition. The BMS performs these tasks by integrating one or more of the functions, such as protecting the cell, thermal management, controlling the charge-discharge, determining the state of charge (SOC), state of health (SOH), and remaining useful life (RUL) of the battery, cell balancing, data acquisition, communication with on-board and off-board modules, as well as monitoring and storing historical data. In this paper, we propose a BMS that estimates the critical characteristics of the battery (such as SOC, SOH, and RUL) using a data-driven approach. Our estimation procedure is based on a modified Randles circuit model consisting of resistors, a capacitor, the Warburg impedance for electrochemical impedance spectroscopy test data, and a lumped parameter model for hybrid pulse power characterization test data. The resistors in a Randles circuit model usually characterize the self-discharge and internal resistance of the battery, the capacitor generally represents the charge stored in the battery, and the Warburg impedance represents the diffusion phenomenon. The Randles circuit parameters are estimated using a frequency-selective nonlinear least squares estimation technique, while the lumped parameter model parameters are estimated by the prediction error minimization method. We investigate the use of support vector machines (SVMs) to predict the capacity fade and power fade, which characterize the SOH of a battery, as well as estimate the SOC of the battery. An alternate procedure for estimating the power fade and energy fade from low-current Hybrid Pulse Power characterization (L-HPPC) test data using the lumped parameter battery model has been proposed. Predictions of RUL of the battery are obtained by support vector regression of the power fade and capacity fade estimates. Survival function estimates for reliability analysis of the battery are obtained using a hidden Markov model (HMM) trained using time-dependent estimates of capacity fade and power fade as observations. The proposed framework provides a systematic way for estimating relevant battery characteristics with a high-degree of accuracy.
The Association of Circulating Endotoxin with the Development of the Adult Respiratory Distress Syndrome (1989)

Despite extensive investigation, the pathogenesis of the adult respiratory distress syndrome (ARDS) remains uncertain. As yet, there is no clear explanation of why some patients at risk for ARDS develop the syndrome, whereas others do not. Neutrophils and complement fragments have been implicated in the acute lung injury, but it is clear from published data that evidence of complement activation alone predicts neither the development nor the severity of ARDS. We investigated whether the combination of endotoxin, a leukocyte-priming agent, and complement fragments, leukocyte-stimulating agents, was associated with the development of ARDS. Ninety-eight patients were identified as being either at risk for the development of ARDS or having ARDS, and serial blood samples were obtained. There was no correlation between C5 fragments and the development of ARDS. C3 fragment levels were increased in 89% of the patients with ARDS, but they were also increased in 62% of patients at risk. Endotoxin was detected in 74% of the plasma samples obtained from patients at risk who subsequent developed ARDS and in 64% of the plasma samples obtained from the patients with ARDS. In contrast, only 22% of the plasma samples obtained from the patients at risk who did not develop ARDS had measurable endotoxin. We suggest that the combination of endotoxin and complement fragments may be one mechanism involved in the development of ARDS.
Analysis of H.264 Bitstream Prioritization for Dual TCP/UDP Streaming of HD video over WLANs (2015)

Flexible Dual-TCP/UDP Streaming Protocol (FDSP) is a new method for streaming H.264-encoded HD video over wireless networks. The method takes advantage of the hierarchical structure of H.264/AVC syntax and uses TCP to transmit important syntax elements of H.264/AVC video and UDP to transmit less important elements. FDSP was shown to outperform pure-UDP streaming in visual quality and pure-TCP streaming in delay. In this work, FDSP is expanded to include a new parameter called Bitstream Prioritization (BP). The newly modified algorithm, FDSP-BP, is analyzed to measure the impact of BP on the quality of streaming for partially and fully congested networks. Our analysis shows that FDSP-BP is superior to pure-TCP streaming methods with respect to rebuffering instances, while still maintaining high visual quality.
An alternative interpretation of hot electron interface degradation in NMOSFETs: isotope results irreconcilable with major defect generation by holes? (1999)

The giant deuterium isotope effect found previously for NMOS hot electron degradation is applied to study defect generation at the Si-SiO/sub 2/ interface. The data suggest that interface defects related to hydrogen depassivation may be generated directly by channel hot electrons bombarding the interface without the necessity of injection into the oxide. This is in contrast to the standard teaching that energetic holes, created by impact ionization, and injected into the oxide are the main cause for hydrogen-related defect generation at the Si-SiO/sub 2/ interfaces.
Polymers, Biodegradable (2009)

Abstract The article contains sections titled: 1. Glossary and Abbreviations 2. Introduction 3. Biodegradability and Toxicology 3.1. Mechanism of Biodegradation 3.2. Toxicity of Biodegradable Polymers 3.3. Standards for Biodegradable Polymers 3.3.1. Controlled Composting Test 3.3.2. Standard Assessment of Biodegradable Polymers 4. Biodegradable Polymers: Synthesis, Properties, and Suppliers 4.1. Raw Materials 4.2. Starch 4.3. Poly(lactic acid) (Polylactide, PLA) 4.4. Polyhydroxyalkanoates (PHA) 4.5. Synthetic Polyesters 4.5.1. Aliphatic Polyesters 4.5.2. Aliphatic/Aromatic Polyesters 4.6. Other Synthetic Polymers 4.7. Compounds 4.7.1. Compounds of Starch and Biodegradable Polyesters 4.7.2. Compounds of PLA and Biodegradable Polyesters 4.8. Cellulose Derivatives 5. Processing and Additives 5.1. Introduction 5.2. Extrusion 5.3. Blown‐Film Extrusion 5.4. Cast‐Film Extrusion 5.5. Modification of Biodegradable Films 5.6. Extrusion Coating 5.7. Sheet Extrusion and Thermoforming 5.8. Injection Molding 5.9. Blow Molding 6. Market Overview and Growth Drivers 7. Value of Biodegradability—Life‐Cycle Assessment (LCA) 8. Applications 8.1. Organic Waste Bags 8.2. Shopping (Carrier) Bags 8.3. Mulch Film 8.4. Horticulture 8.5. Packaging 8.5.1. Food Packaging 8.5.2. Nonfood Packaging 9. Production Capacity 10. Outlook 11. References
Laser-Plasma Extreme Ultraviolet Source Incorporating a Cryogenic Xe Target (2011)

Optical lithography is a core technique used in the industrial mass production of semiconductor memory chips. To increase the memory size per chip, shorter wavelength light is required for the light source. ArF excimer laser light (193 nm) is used at present and extreme ultraviolet (EUV) light (13.5 nm) is proposed in next-generation optical lithography. There is currently worldwide research and development for lithography using EUV light (Bakshi, 2005). EUV lithography (EUVL) was first demonstrated by Kinoshita et al. in 1984 at NTT, Japan (Kinoshita et al., 1989). He joined our laboratory in 1995 and has since been actively developing EUVL technology using our synchrotron facility NewSUBARU. Today, EUVL is one of the major themes studied at our laboratory. To use EUVL in industry, however, a small and strong light source instead of a synchrotron is required. Our group began developing laser-produced plasma (LPP) sources for EUVL in the mid-1990s (Amano et al., 1997). LPP radiation from high-density, high-temperature plasma, which is achieved by illuminating a target with high-peak-power laser irradiation, constitutes an attractive, high-brightness point source for producing radiation from EUV light to x-rays. Light at a wavelength of 13.5 nm with 2% bandwidth is required for the EUV light source, which is limited by the reflectivity of Mo/Si mirrors in a projection lithography system. Xe and Sn are known well as plasma targets with strong emission around 13.5 nm. Xe was mainly studied initially because of the debris problem, in which debris emitted from plasma with EUV light damages mirrors near the plasma, quickly degrading their reflectivity. This problem was of particular concern in the case of a metal target such as Sn because the metal would deposit and remain on the mirrors. On the other hand, Xe is an inert gas and does not deposit on mirrors, and thus has been studied as a deposition-free target. Because of this advantage, researchers initially studied Xe. To provide a continuous supply of Xe at the laser focal point, several possible approaches have been investigated: employing a Xe gas puff target (Fiedrowicz et al., 1999), Xe cluster jet (Kubiak et al., 1996), Xe liquid jet (Anderson et al., 2004; Hansson et al., 2004), Xe capillary jet (Inoue et al., 2007), stream of liquid Xe droplets (Soumagne et al., 2005), and solid Xe pellets (Kubiak et al., 1995). Here, there are solid and liquid states, and their cryogenic Xe targets were expected to provide higher laser-to-EUV power conversion efficiency (CE) owing to their higher density compared with the gas state. In addition, a smaller gas load to be evacuated by the exhaust pump system was expected.
Synthesis of water-soluble ZnS : Mn2+ nanocrystals by using mercaptopropionic acid as stabilizer (2003)

The synthesis of water-soluble Mn doped ZnS nanocrystals with MPA (3-mercaptopropionic acid) as stabilizer is described. The coordination of Zn ion with MPA helps efficient doping of Mn and thus makes the process reproducible as compared to the common co-precipitation method. To obtain a high luminescent intensity, post-preparative treatments are performed. It is found that the surface states of the nanocrystals, such as the adsorption of oxygen and the coordination of MPA, play important roles in the enhancement of the luminescent intensity.
Electrospun PGA/gelatin nanofibrous scaffolds and their potential application in vascular tissue engineering (2011)

Incorporation of gelatin improves the biological and mechanical properties of PGA, making promising scaffolds for vascular tissue engineering.
Scheduling Interval-Ordered Tasks (1979)

We show that unit execution time jobs subject to a precedence constraint whose complement is chordal can be scheduled in linear time on m processors. Generalizations to arbitrary execution times are NP-complete.