gebhart/patrepeval huggingface dataset:
Relationship of alveolar epithelial injury and repair to the induction of pulmonary fibrosis. (1988)

Explants of mouse lung were cultured at various stages of injury after exposure to hyperoxia for determination of whether endothelial or epithelial injury alone could stimulate fibrosis in a blood-free environment. Mice were exposed to 95% O2 for periods up to 6 days. Then one lobe of lung was prepared for organ culture, and others were used for assessment of lung damage by morphologic studies and by the protein and cellular content of bronchoalveolar lavage (BAL) fluid. Explants cultured when the lung showed endothelial injury only were not different from air-exposed controls. As alveolar damage, particularly to Type 1 epithelial cells, increased at 6 days, more protein was found by lavage; and after culture, overall DNA synthesis in explants was reduced. Autoradiography showed that epithelial cell proliferation was preferentially retarded while fibroblast growth became predominant. Collagen production was also significantly increased after 3 and 6 days of culture. In these explants there were few macrophages and no white blood cells or other blood components. Some mice, returned to air after hyperoxia, showed prompt epithelial repair, and cultures of these lungs were not different from controls. The results suggest that severe injury and retarded repair of the alveolar epithelium disturbs normal epithelial-fibroblast interactions and is sufficient to promote the fibrotic process. Less severe injury involving the endothelium only is not associated with fibrosis.
Critical and optimal Ig domains for promotion of neurite outgrowth by L1/Ng-CAM (2000)

Mammalian L1 and avian Ng-CAM are homologous neural cell adhesion molecules (CAMs) that promote neurite outgrowth and cell adhesion in most neurons. Previous attempts to map these activities to discrete regions in the CAMs have suggested the involvement of a variety of different domains. However, these studies mainly used bacterially expressed proteins that were much less active on a molar basis than the native molecules. To define regions that are critical for maximal neurite outgrowth, we constructed and tested a panel of eukaryotically expressed proteins containing various extracellular segments of human L1 (hL1) or Ng-CAM. Our results indicate that Ig domains 1–4 of hL1 are critical for homophilic binding and neurite outgrowth; however this segment is less potent than the entire extracellular region. Optimal neurite outgrowth activity was seen with proteins containing all six Ig domains of hL1 or Ng-CAM. The adhesive properties of hL1 fragments correlated tightly with their neurite outgrowth activities, suggesting that these two processes are closely linked. These results suggest that Ig domains 1–4 form a structural cassette responsible for hL1 homophilic binding, while Ig domains 1–6 represent a functional region for optimal promotion of neurite outgrowth in vitro and possibly in vivo. © 2000 John Wiley & Sons, Inc. J Neurobiol 42: 287–302, 2000
Net energy of cellulosic ethanol from switchgrass (2008)

Perennial herbaceous plants such as switchgrass (Panicum virgatum L.) are being evaluated as cellulosic bioenergy crops. Two major concerns have been the net energy efficiency and economic feasibility of switchgrass and similar crops. All previous energy analyses have been based on data from research plots (<5 m2) and estimated inputs. We managed switchgrass as a biomass energy crop in field trials of 3-9 ha (1 ha = 10,000 m2) on marginal cropland on 10 farms across a wide precipitation and temperature gradient in the midcontinental U.S. to determine net energy and economic costs based on known farm inputs and harvested yields. In this report, we summarize the agricultural energy input costs, biomass yield, estimated ethanol output, greenhouse gas emissions, and net energy results. Annual biomass yields of established fields averaged 5.2-11.1 Mg x ha(-1) with a resulting average estimated net energy yield (NEY) of 60 GJ x ha(-1) x y(-1). Switchgrass produced 540% more renewable than nonrenewable energy consumed. Switchgrass monocultures managed for high yield produced 93% more biomass yield and an equivalent estimated NEY than previous estimates from human-made prairies that received low agricultural inputs. Estimated average greenhouse gas (GHG) emissions from cellulosic ethanol derived from switchgrass were 94% lower than estimated GHG from gasoline. This is a baseline study that represents the genetic material and agronomic technology available for switchgrass production in 2000 and 2001, when the fields were planted. Improved genetics and agronomics may further enhance energy sustainability and biofuel yield of switchgrass.
SGML as a message interchange format in healthcare. (1997)

SGML compares favorably with other syntaxes investigated by CEN. None of the interchange formats support all functional requirements. Optimal and standard mechanisms of combining different formats through a modular approach to achieve greater overall functionality requires further study.
Design, validation and FPGA implementation of a brushless DC motor speed controller (2010)

The brushless DC (BLDC) motors have become the common choice in low power, high speed, high accuracy applications and this imposed the need for efficient and low cost motor control drives. In this paper, a design method for a digital controller implemented in a low cost field programmable gate array (FPGA) is presented. The design is done by schematic capture and Simulink block diagram capture. The developed design is validated in a modular fashion by Simulink-HDL (hardware description language) co-simulation and experimental results are provided. The main contribution is the presented controller design method for FPGA implementation, with special emphasis on simulation validation and FPGA debugging tools usage for signals extraction and analysis.
A Data-reversible Hiding Algorithm in WSNs (2013)

In view of the phenomenon that data-hiding algorithm is easy to be detected by inspecting tool SPAM when carrying information, random insertion and histogram modification are adapted in the data hiding. A data-reversible hiding algorithm in WSNs is put forward. By collecting and referring sub-graph, calculating data fusion algorithm that can protect the data’s completion and privacy and analyzing the reversible hiding data algorithm research, the inspection of SPAM. Finally MATLAB7.0 exploitation is adopted to stimulate the analysis of experiment. The result shows that compared with Kim algorithm, the algorithm is safer to prevent the SPAM inspection and is more suitable for information transfer.
Three-dimensional computation of reduction in Radar cross section using plasma shielding (2005)

We have performed three-dimensional (3-D) finite-difference time-domain (FDTD) simulations for calculating microwave scattering from metallic objects shielded by a plasma shroud. Such simulations are of interest for plasma-based stealth technology. The simulations yield a reasonable match with experimental measurements. A physical interpretation has also been provided for these results, in terms of the flow of electromagnetic power. Such an analysis is only possible using the detailed spatio-temporal evolution of electromagnetic fields that is provided by the FDTD method. We find that apart from absorption, the bending of waves toward regions of lower plasma density plays an important role in determining the extent of backscatter. This has major implications for plasma stealth applications, which have heretofore assumed that plasma absorption is the main mechanism. Also, bending could actually enhance radar scattering in directions oblique to the incident direction. We have also identified situations where 3-D simulations become necessary, and other situations where a composite one-dimensional simulation may be enough. This has practical relevance since it could help reduce the demand for computational resources while modeling large objects like aircraft.
Automatic Speech Recognition for Under-Resourced Languages: Application to Vietnamese Language (2009)

This paper presents our work in automatic speech recognition (ASR) in the context of under-resourced languages with application to Vietnamese. Different techniques for bootstrapping acoustic models are presented. First, we present the use of acoustic-phonetic unit distances and the potential of crosslingual acoustic modeling for under-resourced languages. Experimental results on Vietnamese showed that with only a few hours of target language speech data, crosslingual context independent modeling worked better than crosslingual context dependent modeling. However, it was outperformed by the latter one, when more speech data were available. We concluded, therefore, that in both cases, crosslingual systems are better than monolingual baseline systems. The proposal of grapheme-based acoustic modeling, which avoids building a phonetic dictionary, is also investigated in our work. Finally, since the use of sub-word units (morphemes, syllables, characters, etc.) can reduce the high out-of-vocabulary rate and improve the lack of text resources in statistical language modeling for under-resourced languages, we propose several methods to decompose, normalize and combine word and sub-word lattices generated from different ASR systems. The proposed lattice combination scheme results in a relative syllable error rate reduction of 6.6% over the sentence MAP baseline method for a Vietnamese ASR task.
Ordinal Classification of Imbalanced Data with Application in Emergency and Disaster Information Services (2016)

Previous ordinal classification methods implicitly assume that the class distribution within a dataset is balanced, which is often not the case for real-world datasets. If the dataset is imbalanced, the previous methods tend to be biased toward the majority class. The authors propose a new method for ordinal classification that attempts to mitigate the impact of imbalanced datasets. They propose a modified version of the weighted k-nearest neighbors method that determines the class membership using the Î±th quantile of the estimated class probability distribution and thus mitigates the impact of the class imbalance.
Reaching Out Locating and Lengthening the Interdomain Linker in AraC Protein (1994)

A genetic method was developed to determine, in proteins, areas which are tolerant of insertions and deletions. Attractive candidates for these areas are linker regions. Such a region was found to include positions 171 to 178 in the Escherichia coli regulatory protein AraC. Independent biochemical methods identified amino acid residues 11 to 170 as the minimal dimerization domain of AraC, and amino acid residues 178 to 286 out of the 291 residue protein as the minimal DNA-binding domain. Hence, by both the genetic and biochemical approaches, the interdomain linking region was determined to include amino acid residues 171 to 177. The properties of altered proteins were examined using templates with AraC half-sites more widely separated than in the wild-type case. Both AraC protein containing an insertion in the interdomain linker region and a protein consisting of the minimal functional dimerization and DNA-binding domains separated by a 39 amino acid residue linker were able to bind to and function on such a DNA site. In vitro, the proteins with longer linkers bound substantially more stably than wild-type AraC to the DNA containing half-sites for AraC separated by an extra two helical turns of DNA. In vivo on an ara promoter with the more widely separated AraC half-sites, the proteins could activate transcription much better than wild-type AraC.
Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing (2012)

This approach, which leverages the advantages of RNA-seq approaches, enabled rapid generation of gene-linked SNP and haplotype markers. The general approach presented in this study can be easily applied to other non-model eukaryotes irrespective of the ploidy level to identify gene-linked polymorphisms that are expected to facilitate efficient Gene Assisted Breeding (GAB), genotyping and population genetics studies. The identified SNP haplotypes reveal some of the allelic differences in the two sweet cherry cultivars analyzed. The identification of these SNP and haplotype markers is expected to significantly improve the genomic resources for sweet cherry and facilitate efficient GAB in this non-model crop.
TNF-α modulates expression of the tissue transglutaminase gene in liver cells (1998)

One of several postulated roles for tissue transglutaminase (tTG) is the stabilization and assembly of extracellular matrix via peptide cross-linking. We previously determined that tTG activity increased in an animal model of hepatic fibrogenesis and in human liver disease. To further study the role of tTG in liver disease, we initiated investigations into the effect of a proinflammatory mediator, tumor necrosis factor (TNF)-alpha, on tTG activity in cultured liver cells. Treatment of human Hep G2 cells with 1 ng/ml TNF-alpha increased [14C]putrescine cross-linking to cellular proteins. An increase in tTG mRNA content was observed 1 h after addition of TNF-alpha, and levels of tTG mRNA remained elevated after 24 h. Hep G2 cells, transiently transfected with a luciferase reporter containing 1.67 kb of the human tTG promoter, showed an increase in reporter activity after addition of TNF-alpha. Gel shift experiments using nuclear extracts from TNF-alpha-treated cells and oligonucleotides containing the tTG nuclear factor (NF)-kappa B motif revealed increased binding, concordant with mRNA data. Transient transfections with a truncated reporter construct lacking the tTG NF-kappa B sequence showed an attenuated response to TNF-alpha treatment. Similar responses were seen in stably transfected HeLa cells. Primary hepatocytes isolated from a transgenic mouse line containing the mouse tTG promoter driving the beta-galactosidase reporter, show similar time-dependent increases in promoter activity when treated with TNF-alpha. Furthermore, Hep G2 cells are incapable of upmodulating tTG promoter reporter activity in the presence of TNF-alpha when those cells overexpress a transdominant, negative mutant NF-kappa B subunit. Because TNF-alpha expression is upregulated in hepatic inflammation, the data suggest TNF-alpha-mediated increases in tTG expression may play an important role in the process of hepatic fibrogenesis.
Long-Range Order in a Two-Dimensional Dynamical<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>XY</mml:mi></mml:math>Model: How Birds Fly Together (1995)

We propose a nonequilibrium continuum dynamical model for the collective motion of large groups of biological organisms (e.g., flocks of birds, slime molds, etc.) Our model becomes highly nontrivial, and different from the equilibrium model, for $d<{d}_{c}=4$; nonetheless, we are able to determine its scaling exponents exactly in $d=2$ and show that, unlike equilibrium systems, our model exhibits a broken continuous symmetry even in $d=2$. Our model describes a large universality class of microscopic rules, including those recently simulated by Vicsek et al.
Surface mode coupling in GaAs/AlGaAs laser diodes—A novel concept for a single laser mode emission (1995)

We demonstrate a novel concept for a mode selection mechanism in surface emitting laser diodes. This concept is based on a strong coupling process between the laser mode and a surface mode on top of the laser diode. The mode selection mechanism is the result of a strong feedback from the surface mode into the laser diode. Nearly single-modelike emission spectra are achieved from surface emitting GaAs/AlGaAs laser diodes and qualitatively explained by a model based on ray optics. The main advantage of this type of laser diode is its simple fabrication and the possibility of adjusting the desired wavelength independent of the growth process by external technological parameters.
Syntheses of 9-deazatheophyllines and 6-deoxy-9-deazatheophyllines. (1980)

The reaction of 1, 3-dimethyl-5-nitro-6-styryluracils (IIa-e) with sodium dithionite in formic acid afforded the corresponding 8-aryl-9-deazatheophyllines (IVa-e). The reaction of IVa with phosphorus oxychloride gave 6-chloro-6-deoxy-8-phenyl-9-deazatheophylline (XIII), while the reaction of IVa with phosphorus oxychloride in the presence of arylamines provided the corresponding 6-arylamino-6-deoxy-8-phenyl-9-deazatheophyllines (XIV-XVI) in a single step.
MOBILE INTERNET TECHNOLOGIES AND THEIR APPLICATION TO INTELLIGENT TRANSPORTATION SYSTEMS (2003)

The worlds of mobile communication and the Internet are rapidly converging. This new domain, which is being touted as the Wireless Web or Mobile Internet, is in its infancy and will require a number of complex technologies to mature and converge before it becomes as prevalent and as functional as its wired counterpart. While being developed to extend the reach of Internet users, these new technologies can also be used to support various ITS operations. This report introduces the new mobile Internet technologies and describes how they could be applied to ITS; it also presents some of the technical and institutional considerations when using such technologies to support agency operations
John Russell: Australia's Unknown Artist (1956)

A biography of the little known Australian artist John P. Russell. He is rarely represented in Australian art collections as he mostly lived outside Australia and did not hold exhibitions of his work even after he returned to live in the country.
Effect of Organic Complex Compounds on <i>Bacillus thermoamylovorans</i> Growth and Glucose Fermentation (1999)

The effect of the concentration of a mixture (1/1 [wt/wt]) of yeast extract and bioTrypcase (YE+bT) on the growth and physiology of a new species, Bacillus thermoamylovorans, a moderately thermophilic, non-spore-forming, lactic acid-producing bacterium isolated from palm wine, was studied. At an initial glucose concentration of 100 mM, B. thermoamylovorans growth was limited when the concentration of YE+bT was lower than 5.0 g liter(-1); under these conditions, cellular yield reached a maximum value of 0.4 g of cells per g of YE+bT. Growth limitation due to deficiency in growth factors led to a significant shift in glucose metabolism towards lactate production. Lactate constituted 27.5 and 76% of the end products of glucose fermentation in media containing YE+bT at 20.0 and 1.0 g liter(-1), respectively. This result markedly differed from published data for lactic bacteria, which indicated that fermentative metabolism remained homolactic regardless of the concentration of YE. Our results showed that the ratio between cellular synthesis and energy production increased with the concentration of YE+bT in the culture medium. They indicate that the industrial production of lactic acid through glucose fermentation by B. thermoamylovorans can be optimized by using a medium where glucose is present in excess and the organic additives are limiting.
Progress in breeding perennial forage grasses for temperate agriculture (2003)

Breeding of temperate forage grasses is aimed at improving the economic and environmental sustainability of production from cattle and sheep. The primary objective is to ensure that forage can be the main source of feed for ruminants. This requires consistent production of herbage with a high feeding value, usually under nitrogen-limiting conditions. The most important traits affecting the feeding value of herbage are in vitro dry matter digestibility (DMD), the ratios of crude protein, water-soluble carbohydrate and fibre, and the concentration of alkaloid toxins. Improvements in these primary quality traits must be combined with good plant persistency, adequate tolerance to a range of environmental stresses, adequate resistance to a large number of different pathogens and invertebrate pests, and adequate seed yield. Forage grasses also have considerable potential to produce material for refining, to provide protein extracts for feeding to monogastric animals and carbohydrate for fermentation into fuel or into feedstocks for other industries.
Modelling and Rendering Graphics Scenes Composed of Multiple Volumetric Datasets (1999)

This paper presents a method for modelling graphics scenes consisting of multiple volumetric objects. A two‐level hierarchical representation is employed, which enables the reduction of the overall storage consumption as well as rendering time. With this approach, different objects can be derived from the same volumetric dataset, and 2D images can be trivially integrated into a scene. The paper also describes an efficient algorithm for rendering such scenes on ordinary workstations, and addresses issues concerning memory requirements and disk swapping.
Microfluidic Synthesis of Biodegradable Polyethylene-Glycol Microspheres for Controlled Delivery of Proteins and DNA Nanoparticles (2015)

Polymeric microspheres represent an injectable platform for controlling the release of a variety of biologics; microspheres may be combined in a modular fashion to achieve temporal release of two or more biomolecules. Microfluidics offers a versatile platform for synthesizing uniform polymeric microspheres harboring a variety of biologics under relatively mild conditions. Poly(ethylene glycol) (PEG) is a bioinert polymer that can be easily tailored to encapsulate and control the release of biologics. In this study, we report the microfluidic synthesis of biodegradable PEG-based microparticles for controlled release of growth factors or DNA nanoparticles. Simple changes in microfluidic design increased the rate of microparticle formation and controlled the size of the microspheres. Mesh size and degradation rate were controlled by varying the PEG polymer weight percent from 7.5 to 15% (w/v), thus tuning the release of growth factors and DNA nanoparticles, which retained their bioactivity in assays of cell proliferation and DNA transfection, respectively. This platform may provide a useful tool for synthesizing microspheres for use as injectable carriers to achieve coordinated growth-factor or DNA nanoparticle release in therapeutic applications.