gebhart/patrepeval huggingface dataset:
Parallel circuit simulation using hierarchical relaxation (1990)

This paper describes a class of parallel algorithms for circuit simulation based on hierarchical relaxation that has been implemented on the Cedar multiprocessor. The Cedar machine is a reconfigurable, general-purpose supercomputer that was designed and implemented at the University of Illinois. A hierarchical circuit simulation scheme was developed to exploit the hierarchical organization of Cedar. The new algorithm and a number of key issues, such as multilevel circuit partitioning, data partitioning, cluster algorithm selection, and cluster algorithm implementation are described in this paper. Performance results on a variety of different configurations of Cedar are also presented that illustrate the benefits of the hierarchical approach over the non-hierarchical approach.
A Xanthocillin-like Alkaloid from the Insect Pathogenic Fungus <i>Cordyceps brunnearubra</i> BCC 1395 (2007)

Cordyformamide (4), the plausible biogenetic precursor of xanthocillin Y2, was isolated from a culture broth of the insect pathogenic fungus Cordyceps brunnearubra BCC 1395. Cordyformamide was found to exhibit activity against the malarial parasite Plasmodium falciparum K1 with an IC50 value of 18 microM, whereas it showed weak or no cytotoxicity.
Improving Butanol Fermentation To Enter the Advanced Biofuel Market (2012)

1-Butanol is a large-volume, intermediate chemical with favorable physical and chemical properties for blending with or directly substituting for gasoline. The per-volume value of butanol, as a chemical, is sufficient for investing into the recommercialization of the classical acetone-butanol-ethanol (ABE) (E. M. Green, Curr. Opin. Biotechnol. 22:337-343, 2011) fermentation process. Furthermore, with modest improvements in three areas of the ABE process, operating costs can be sufficiently decreased to make butanol an economically viable advanced biofuel. The three areas of greatest interest are (i) maximizing yields of butanol on any particular substrate, (ii) expanding substrate utilization capabilities of the host microorganism, and (iii) reducing the energy consumption of the overall production process, in particular the separation and purification operations. In their study in the September/October 2012 issue of mBio, Jang et al. [mBio 3(5):e00314-12, 2012] describe a comprehensive study on driving glucose metabolism in Clostridium acetobutylicum to the production of butanol. Moreover, they execute a metabolic engineering strategy to achieve the highest yet reported yields of butanol on glucose.
Crystal structure of <i>Bacillus licheniformis</i> 1,3‐1,4‐β‐<scp>d</scp>‐glucan 4‐glucanohydrolase at 1.8 Å resolution (1995)

The crystal structure of the 1,3-1,4-beta-D-glucan 4-glucanohydrolase from Bacillus licheniformis is solved at a resolution of 1.8 A and refined to R = 16.5%. The protein has a similar beta-sandwich structure as the homologous enzyme from Bacillus macerans and the hybrid H(A16-M). This demonstrates that the jellyroll fold of these proteins is remarkably rigid and only weakly influenced by crystal contacts. The crystal structure permits to extend mechanistic considerations derived for the B. licheniformis enzyme to the entire class of bacterial 1,3-1,4-beta-D-glucan 4-glucanohydrolases.
Visualizing helicases unwinding DNA at the single molecule level (2010)

DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been developed to follow the unwinding of multiple DNA molecules simultaneously in real time. This was achieved by measuring the accumulation of fluorescent single-stranded DNA-binding protein on the single-stranded DNA product of the helicase, using total internal reflection fluorescence microscopy. By immobilizing either the DNA or helicase, localized increase in fluorescence provides information about the rate of unwinding and the processivity of individual enzymes. In addition, it reveals details of the unwinding process, such as pauses and bursts of activity. The generic and versatile nature of the assay makes it applicable to a variety of DNA helicases and DNA templates. The method is an important addition to the single-molecule toolbox available for studying DNA processing enzymes.
Synthesis of Thiophene‐Substituted Spiropyrans and Spirooxazines, Precursors of Photochromic Polymers (1995)

Abstract The synthesis of spiropyrans 11 and 12 and spirooxazines 13–17 containing a thiophene moiety is described. Two different synthetic approaches were used. The spectrokinetic properties of these new compounds are reported.
Deep Learning Classification of Land Cover and Crop Types Using Remote Sensing Data (2017)

Deep learning (DL) is a powerful state-of-the-art technique for image processing including remote sensing (RS) images. This letter describes a multilevel DL architecture that targets land cover and crop type classification from multitemporal multisource satellite imagery. The pillars of the architecture are unsupervised neural network (NN) that is used for optical imagery segmentation and missing data restoration due to clouds and shadows, and an ensemble of supervised NNs. As basic supervised NN architecture, we use a traditional fully connected multilayer perceptron (MLP) and the most commonly used approach in RS community random forest, and compare them with convolutional NNs (CNNs). Experiments are carried out for the joint experiment of crop assessment and monitoring test site in Ukraine for classification of crops in a heterogeneous environment using nineteen multitemporal scenes acquired by Landsat-8 and Sentinel-1A RS satellites. The architecture with an ensemble of CNNs outperforms the one with MLPs allowing us to better discriminate certain summer crop types, in particular maize and soybeans, and yielding the target accuracies more than 85% for all major crops (wheat, maize, sunflower, soybeans, and sugar beet).
Characteristics of Coaxial Vircator in Three Specific Configurations (2003)

As a novel vircator device, the coaxial vircator can attain much higher efficiency than the common virtual cathode oscillator. In this paper, coaxial vircators in three specific configurations are studied to describe the efficiency and frequency characteristics and their dependence on geometric parameters. The PIC (Particle in Cell) simulation results show that a power efficiency over 11% can be obtained from the coaxial vircator with a finite inner anode conductor, and a narrow-band output can be achieved. A direct-coupled coaxial vircator has a slightly lower efficiency of about 8%, but in this configuration the efficiency is not strongly dependent on the geometry parameters. The introduction of a reflecting cavity can effectively improve the efficiency under certain parameters. Meanwhile, the research results also indicate that improper cavity parameters will countervail some inherent advantages of the configuration with a finite inner conductor, leading to lower efficiency than that of the direct-coupled one. Meanwhile, an experiment was also carried out to testify the simulation results, and a power efficiency over 3% was obtained from the direct-coupled coaxial vircator.
Epistasis in tomato color mutations involves regulation of <i>phytoene synthase 1</i> expression by <i>cis</i> -carotenoids (2012)

Tomato (Solanum lycopersicum) fruit accumulate the red carotenoid pigment lycopene. The recessive mutation yellow-flesh (locus r) in tomato eliminates fruit carotenoids by disrupting the activity of the fruit-specific phytoene synthase (PSY1), the first committed step in the carotenoid biosynthesis pathway. Fruits of the recessive mutation tangerine (t) appear orange due to accumulation of 7,9,7',9'-tetra-cis-lycopene (prolycopene) as a result of a mutation in the carotenoid cis-trans isomerase. It was established 60 y ago that tangerine is epistatic to yellow-flesh. This uncharacteristic epistasis interaction defies a paradigm in biochemical genetics arguing that mutations that disrupt enzymes acting early in a biosynthetic pathway are epistatic to other mutations that block downstream steps in the same pathway. To explain this conundrum, we have investigated the interaction between tangerine and yellow-flesh at the molecular level. Results presented here indicate that allele r(2997) of yellow-flesh eliminates transcription of PSY1 in fruits. In a genetic background of tangerine, transcription of PSY1 is partially restored to a level sufficient for producing phytoene and downstream carotenoids. Our results revealed the molecular mechanism underlying the epistasis of t over r and suggest the involvement of cis-carotenoid metabolites in a feedback regulation of PSY1 gene expression.
I-wlan: intelligent wireless local area networking (2004)

Future wireless networks require intelligent components that can automate, scale and manage the network in order to handle the demand for ubiquitous access. In this dissertation, we first evaluate existing problems, and then we introduce components that improve the performance of existing systems. 
We introduce a new Markov model for Distributed Coordination of Function of IEEE 802.11 with which we formulate the throughput and delay for saturated and non-saturated traffic. We introduce a novel formulation for individual throughput when stations operate with mixed data rates. We introduce an admission control mechanism to maintain the highest achievable throughput by controlling the access. After that we use our throughput formulation to obtain the performance of an indoor network. We introduce a packet size adjustment scheme with respect to data rate so that a slow station sends small packets to prevent throttling of the network. We introduce a frame aggregation scheme for wireless voice over IP We introduce a fast and fair sub-optimal algorithm to allocate sub-carriers and bits adaptively in an OFDMA system for point-to-multipoint communication, and investigate MAC performance of the wireless LAN with adaptive antennas for point-to-point communication. 
We find that ignoring the consecutive transmission probability in the previous Markov models is incomplete. Consequently, our model which takes this into account is closer to the standard. We find that the individual throughput of a station is the same for fast and slow stations, and slow stations throttle the performance, since the CSMA/CA scheme gives equal access but not equal time of channel usage. Our packet size optimization scheme increases the throughput of the total network and the fast station but not that of the slow station. The admission control mechanism can tune the network from random access to controlled access. Network management can monitor the whole network and do real-time adjustments for optimum performance. Our frame aggregation scheme for wireless voice over IP reduces the number of access by concatenating the packets in the accesses point in order to be sent at one time. The results of our resource allocation scheme for adaptive sub-carrier and bit allocation is appealing and can be close to optimal. We find that a directional antenna increases the performance significantly and can provide enhancements for wireless LANs.
Methods for Multi-Category Cancer Diagnosis from Gene Expression Data: A Comprehensive Evaluation to Inform Decision Support System Development (2004)

Cancer diagnosis is a major clinical applications area of gene expression microarray technology. We are seeking to develop a system for cancer diagnostic model creation based on microarray data. In order to equip the system with the optimal combination of data modeling methods, we performed a comprehensive evaluation of several major classification algorithms, gene selection methods, and cross-validation designs using 11 datasets spanning 74 diagnostic categories (41 cancer types and 12 normal tissue types). The Multi-Category Support Vector Machine techniques by Crammer and Singer, Weston and Watkins, and one-versus-rest were found to be the best methods and they outperform other learning algorithms such as K-Nearest Neighbors and Neural Networks often to a remarkable degree. Gene selection techniques are shown to significantly improve classification performance. These results guided the development of a software system that fully automates cancer diagnostic model construction with quality on par with or better than previously published results derived by expert human analysts.
An MR compatible PET scanner based on RatCAP for small animal imaging at 9.4 T (2008)

Combining PET and MRI technology in order to obtain simultaneous functional information with anatomical precision in vivo is of tremendous interest in the field of molecular imaging. PET/MRI imaging provides perfect anatomical and temporal coregistration of PET and MR images, along with clear delineation of tissue boundaries. An MR compatible PET scanner based on Rat Conscious Animal PET (RatCAP) is developed for simultaneous acquisition of PET/MRI images of the rat brain in a 9.4 T microMRI scanner. The PET tomograph is housed in a segmented G10/copper case constructed with a copper coating thickness of 5 microns, to minimize the eddy currents and provide better RF shielding. Special RF coils were designed to fit inside the PET tomograph. A custom made G10 tube assembly was constructed for accurate positioning of the rat bed, RF coil and RatCAP. Simultaneous PET/MRI images of a rat striatum phantom were acquired in the 9.4 T microMRI with minimal interference between PET electronics and MRI. PET compatible RF quadrature coils are being constructed which are capable of providing rat brain images with improved SNR. The preliminary results show the feasibility of performing PET/fMRI studies of rat brain and exploring the possibility of acquiring simultaneous PET/MRI whole body mouse images in the 9.4 T.
Complications of Corneal Collagen Cross-Linking (2011)

Cross-linking of corneal collagen (CXL) is a promising approach for the treatment of keratoconus and secondary ectasia. Several long-term and short-term complications of CXL have been studied and documented. The possibility of a secondary infection after the procedure exists because the patient is subjected to epithelial debridement and the application of a soft contact lens. Formation of temporary corneal haze, permanent scars, endothelial damage, treatment failure, sterile infiltrates, and herpes reactivation are the other reported complications of this procedure. Cross-linking is a low-invasive procedure with low complication and failure rate but it may have direct or primary complications due to incorrect technique application or incorrect patient's inclusion and indirect or secondary complications related to therapeutic soft contact lens, patient's poor hygiene, and undiagnosed concomitant ocular surface diseases.
Intelligent energy management system simulator for PHEVs at municipal parking deck in a smart grid environment (2009)

There is a need for in-depth study of technologies that will affect the utility industry in a time horizon of less than 20 years. One such technology is the plug-in vehicle (PHEV); there is a need for energy management when a large number of plug-in hybrid vehicles penetrate the market. In this paper, we propose an ldquointelligent energy management system (iEMS)rdquo that intelligently allocates power to the vehicle battery chargers through real time monitoring and control, to ensure optimal usage of available power, charging time and grid stability. We begin by conceptualization of the system architecture and description of its operation and provide a theoretical framework for system modeling. A detailed PHEV battery model and state of charge estimation algorithm are also being developed to simulate different PHEVs to be recharged at a municipal parking deck. We will present the simulator we have developed for representing the iEMS using Matlab/Simulink and discuss obtained results and future directions.
Room-Temperature CW Lasing of a GaN-Based Vertical-Cavity Surface-Emitting Laser by Current Injection (2008)

We report the demonstration of CW lasing at room temperature in a GaN-based vertical-cavity surface-emitting laser (VCSEL) by current injection. The active region of the VCSEL consisted of a two-pair InGaN/GaN quantum well active layer. The optical cavity consisted of a 7-λ-thick GaN semiconductor layer and an indium tin oxide layer for p-contact embedded between two SiO2/Nb2O5 dielectric distributed Bragg reflectors. The VCSEL was mounted on a Si substrate by wafer bonding and the sapphire substrate was removed by laser lift-off. Under CW operation for an 8-µm aperture device, the threshold current was 7.0 mA and the emission wavelength was approximately 414 nm.
Contribution of the Kir3.1 Subunit to the Muscarinic-gated Atrial Potassium Channel IKACh (2002)

The muscarinic-gated atrial potassium (I(KACh)) channel contributes to the heart rate decrease triggered by the parasympathetic nervous system. I(KACh) is a heteromultimeric complex formed by Kir3.1 and Kir3.4 subunits, although Kir3.4 homomultimers have also been proposed to contribute to this conductance. While Kir3.4 homomultimers evince many properties of I(KACh), the contribution of Kir3.1 to I(KACh) is less well understood. Here, we explored the significance of Kir3.1 using knock-out mice. Kir3.1 knock-out mice were viable and appeared normal. The loss of Kir3.1 did not affect the level of atrial Kir3.4 protein but was correlated with a loss of carbachol-induced current in atrial myocytes. Low level channel activity resembling recombinant Kir3.4 homomultimers was observed in 40% of the cell-attached patches from Kir3.1 knock-out myocytes. Channel activity typically ran down quickly, however, and was not recovered in the inside-out configuration despite the addition of GTP and ATP to the bath. Both Kir3.1 knock-out and Kir3.4 knock-out mice exhibited mild resting tachycardias and blunted responses to pharmacological manipulation intended to activate I(KACh). We conclude that Kir3.1 confers properties to I(KACh) that enhance channel activity and that Kir3.4 homomultimers do not contribute significantly to the muscarinic-gated potassium current.
Human papillomavirus in head and neck squamous cell carcinoma: are some head and neck cancers a sexually transmitted disease? (1999)

There is abundant epidemiologic and virologic evidence that high-risk human papillomaviruses (HPVs) are tumorigenic in human epithelia, particularly in the cervix, where HPV infection is necessary for cancer development. HPV DNA has been detected in a proportion of head and neck squamous cell carcinomas (HNSCCs) in numerous case series. The mere presence of the virus in tumor specimens, by itself, does not imply a causal relationship. However, recent studies support an etiologic role for HPVs in a subset of HNSCC, particularly poorly differentiated tumors arising from Waldeyer's tonsillar ring. Epidemiologic studies have shown that exposure to HPV increases the risk of HNSCC, and HPV infection may interact with alcohol and tobacco exposure in tumor promotion. Molecular studies indicate that transcriptionally active virus is confined to tumor cells. It will be important to clarify further the role that HPV has in HNSCC development, because HPV-based therapeutic vaccines which are currently being developed for cervical cancer may also be of benefit in the management of HNSCC.
Estrogen Promotes Stress Sensitivity in a Prefrontal Cortex-Amygdala Pathway (2010)

We have recently reported in male rats that medial prefrontal cortex (mPFC) neurons that project to the basolateral nucleus of the amygdala (BLA) are resilient to stress-induced dendritic remodeling. The present study investigated whether this also occurs in female rats. This pathway was identified using the retrograde tracer Fast Blue injected into the BLA of ovariectomized female rats with estrogen replacement (OVX + E) and without (OVX + veh). Animals were exposed for 10 days either to 2-h immobilization stress or to home cage rest, after which layer III mPFC neurons that were either retrogradely labeled by Fast Blue or unlabeled were filled with Lucifer Yellow and analyzed for apical dendritic length and spine density. No dendritic remodeling occurred in unlabeled neurons from OVX + veh or OVX + E animals. In BLA-projecting neurons, however, stress had no effect on length in OVX + veh animals, but stressed OVX + E females showed greater dendritic length than controls at intermediate branches. Stress also caused an increase in spine density in all neurons in OVX + veh animals and a spine density increase in BLA-projecting neurons in OVX + E females. Estrogen also increased spine density on BLA-projecting neurons in unstressed animals. These data demonstrate both independent effects of estrogen on pyramidal cell morphology and effects that are interactive with stress, with the BLA-projecting neurons being sensitive to both kinds of effects.
<title>Solid Fabry-Perot Etalons As High Resolution Infrared Interferometers</title> (1976)

The tilt scanned solid etalon interferometer has very real advantages in resolving power, throughput and sensitivity over other direct detection techniques, particularly for atmospheric and astronomic spectroscopic measurements. This includes many situations where the measuring instrument is detector-noise limited. These advantages can be exploited in a physically compact, stable, electro-optical system, which imposes no severe tolerances on mechanical mounting, optical alignment or angular scan control. Materials and optical fabrication techniques are available at least for the range 1 to 15 µm which allows for etalon bandwidths of ⪅ 0.2 cm-1, finesse of 50, and peak transmission of 65%. The etalon can be fine scanned over a free spectral range (≈ 10 cm-1) at discrete points in its channel transmission spectrum, or over many hundreds of free spectral ranges, depending on the blocking mode. Some practical aspects of the design, evaluation and use of solid etalons in conventional optical systems are discussed, and the characteristics of a number of such etalons fabricated within the past two years are presented.
A radiological and histological analysis of fracture healing using prebending of compression plates. (1979)

The use of an exactly contoured compression plate to the surface of a bone will lead to asymmetrical loading of that fracture line with possible gapping of bone opposite the plate. The stability of fixation can be increased through the use of compression combined with prebending. The present study in 19 sheep demonstrates the biological effects of 3 modes of plating fixation: (1) no compression; (2) compression; and (3) compression after prebending using 2 types of compression plates with different stiffness evaluated radiographically and histologically. Compression together with prebending, especially when using plates of adequate stiffness, can prevent bone resorption at the fragment surfaces even under immediate weight-bearing conditions in the sheep tibia. Prevention of interfragmentary bone resorption lowers the risk of non-union and/or implant failure secondary to motion at the fracture site.