gebhart/patrepeval huggingface dataset:
Gene Expression Correlates with Process Rates Quantified for Sulfate- and Fe(III)-Reducing Bacteria in U(VI)-Contaminated Sediments (2012)

Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI) reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III) and sulfate reduction pathways in order to monitor these processes during in situ U(VI) remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA) and the dissimilatory (bi)sulfite reductase gene (dsrA), were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC) site at Oak Ridge, TN, USA. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.
Interleukin-18 in Pulmonary Inflammatory Diseases (2012)

The proinflammatory cytokine interleukin (IL)-18 was originally discovered as an interferon-γ-inducing factor in 1995. IL-18 is known to play an important role in Th1/Tc1 polarization and promoting the production of Th2 cytokines (e.g., IL-4, IL-5, IL-9, and IL-13) by T cells, NK cells, basophils, and mast cells. IL-18 can act as a cofactor for Th2 cell development and IgE production, and also plays an important role in the differentiation of Th17 cells. IL-18 is a key player in the pathogenesis of inflammatory diseases such as atopic dermatitis, rheumatoid arthritis, adult-onset Still's disease, Sjögren's syndrome, and inflammatory bowel diseases. Furthermore, many lines of evidence suggest that IL-18 plays a key role in the pathogenesis of pulmonary inflammatory diseases, including bronchial asthma and chronic obstructive pulmonary disease. Here, we review the pathological roles of IL-18 in pulmonary inflammatory diseases.
Early Ametropia and Rod Photoreceptor Function in Retinopathy of Prematurity (2005)

Purpose. When performing perimetry, refracting subjects with central visual field loss, and in emmetropization studies, it is important to accurately measure peripheral refractive errors. Traditional methods for foveal refraction often give uncertain results in eccentric angles as a result of the large aberrations and the reduced retinal function. The aim of this study is therefore to compare and evaluate four methods for eccentric refraction. Methods. Four eccentric methods were tested on 50 healthy subjects: one novel subjective procedure, optimizing the detection contrast sensitivity with different trial lenses, and three objective ones: photorefraction with a PowerRefractor, wavefront measurements with a Hartmann-Shack sensor, and retinoscopy. The peripheral refractive error in the horizontal nasal visual field of the right eye was measured in 20° and 30°. Results. In general, the eccentric refraction methods compared reasonably well. However, the following differences were noted. Retinoscopy showed a significant difference from the other methods in the axis of astigmatism. In 30° eccentric angle, it was not possible to measure 15 of the subjects with the PowerRefractor and the instrument also tended to underestimate high myopia (<-6 D). The Hartmann-Shack sensor showed a myopic shift of approximately 0.5 D in both eccentricities. The subjective method had a relatively larger spread. Conclusions. This study indicates that it is possible to assess the eccentric refraction with all methods. However, the Hartmann-Shack technique was found to be the most useful method. The agreement between the objective methods and the subjective eccentric refraction shows that detection contrast sensitivity in the periphery is affected by relatively small amounts of defocus.
Fabrication of a surface acoustic wave-based correlator using step-and-flash imprint lithography (2004)

We report the surface acoustic wave (SAW) correlator devices fabricated using nanoimprint lithography. Using step-and-flash imprint lithography (S-FIL), we produced SAW correlator devices on 100mm diameter z-cut LiNbO3 devices and an aluminum metal etch process. On the same chip layout, we fabricated SAW filters and compared both the filters and correlators to similar devices fabricated using electron-beam lithography (EBL). Both S-FIL- and EBL-patterned correlators and SAW filters were analyzed using a bit-error rate tester to generate the signal and a parametric signal analyzer to evaluate the output. The NIL filters had an average center frequency of 2.38GHz with a standard deviation of 10MHz. The measured insertion loss averaged −31dB. In comparison, SAW filters fabricated using EBL exhibited a center frequency of 2.39GHz and a standard deviation of 100kHz. Based on our preliminary results, we believe that S-FIL is an efficient and entirely viable fabrication method to produce quality SAW filters and correlators.
First Observation of Polygyny in Fire Ants,Solenopsis SPP., in South America (1989)

Polygyny, the coexistence of two or more egg-laying queens in a single colony of a social insect, occurs in several subfamilies of ants (Wilson 1971). The species of Solenopsis, however, were considered to be monogynous until Banks et al. (1973), and Glancey et al. (1973) observed polygyny in Solenopsis geminata (F.) and Solenop- sis invicta Buren, respectively. Subsequently, Summerlin (1976) found a single polygynous colony of Solenopsis xyloni McCook. The existence of a spectrum from monogyny to extreme polygyny in the North American S. invicta population was substantiated by Fletcher et al. (1980). Populations of polygynous S. invicta are now known from Florida, Georgia, Mississippi, Louisiana, Texas (Lofgren and Williams 1984), Alabama, Arkansas, and Oklahoma (Banks and Wojcik unpublished). These populations are spreading, Dealates Escobar S. quinquecuspis 2 (2) 3 Campana S. richteri 16 (0) 0 Mercedes S. richteri 2 (2) 0 Suipacha S. richteri 3 (3) 0 S. richteri 9 (9) 0 S. quinquecuspis 3 (0) 0 Corbet S. richteri 11 (0) 0 S. richteri 4 (4) 3 Del Carril S. richteri 21 (2) 2 S. richteri 2 (2) 0 S. richteri 4 (0) 0 S. richteri
Synergistic Induction of Adaptive Antitumor Immunity by Codelivery of Antigen with α-Galactosylceramide on Exosomes (2013)

Exosomes and the invariant NKT (iNKT) immune cell ligand α-galactosylceramide (αGC) may offer novel tools for cancer immunotherapy. In this study, we investigated whether exosomes loaded with αGC can activate iNKT cells and potentiate a cancer-specific adaptive immune response. αGC loaded exosomes readily activated iNKT cells both in vitro and in vivo. Exosomes loaded with αGC plus the model antigen ovalbumin (OVA) induced potent NK and γδ T-cell innate immune responses, and they also synergistically amplified T- and B-cell responses that were OVA specific. In contrast to soluble αGC, which anergizes iNKT cells, we found that αGC/OVA-loaded exosomes did not induce iNKT cell anergy but were more potent than soluble αGC + OVA in inducing adaptive immune responses. In an OVA-expressing mouse model of melanoma, treatment of tumor-bearing mice with αGC/OVA-loaded exosomes decreased tumor growth, increased antigen-specific CD8(+) T-cell tumor infiltration, and increased median survival, relative to control mice immunized with soluble αGC + OVA alone. Notably, an additional injection of αGC/OVA-loaded exosomes further augmented the treatment effects. Our findings show that exosomes loaded with protein antigen and αGC will activate adaptive immunity in the absence of triggering iNKT-cell anergy, supporting their application in the design of a broad variety of cancer immunotherapy trials.
When more is less: Excess and deficiency of autophagy coexist in skeletal muscle in Pompe disease (2009)

The role of autophagy, a catabolic lysosome-dependent pathway, has recently been recognized in a variety of disorders, including Pompe disease, which results from a deficiency of the glycogen-degrading lysosomal hydrolase acid-alpha glucosidase (GAA). Skeletal and cardiac muscle are most severely affected by the progressive expansion of glycogen-filled lysosomes. In both humans and an animal model of the disease (GAA KO), skeletal muscle pathology also involves massive accumulation of autophagic vesicles and autophagic buildup in the core of myofibers, suggesting an induction of autophagy. Only when we suppressed autophagy in the skeletal muscle of the GAA KO mice did we realize that the excess of autophagy manifests as a functional deficiency. This failure of productive autophagy is responsible for the accumulation of potentially toxic aggregate-prone ubiquitinated proteins, which likely cause profound muscle damage in Pompe mice. Also, by generating muscle-specific autophagy-deficient wild-type mice, we were able to analyze the role of autophagy in healthy skeletal muscle.
Change From the CYP2D6 Extensive Metabolizer to the Poor Metabolizer Phenotype During Treatment With Bupropion (2002)

Some data indicate that bupropion inhibits the cytochrome P-450 enzyme CYP2D6, but very little published data is available on the extent of this inhibition. The objective of the present study was to quantify this inhibition in a subject treated with bupropion for smoking cessation. Genotypically, the patient was a CYP2D6 homozygous extensive metabolizer (EM). His CYP2D6 phenotype was assessed using the test drug dextromethorphan before, during, and after treatment with bupropion. During treatment with bupropion, he clearly changed from the EM to the poor metabolizer (PM) phenotype. Although the results from a single patient should be interpreted with great caution, the extent of the interaction indicates that bupropion might be a CYP2D6 inhibitor as potent as the most powerful CYP2D6 inhibitors known, such as quinidine and paroxetine.
JSS FOCUS ISSUE ON PRINTABLE FUNCTIONAL MATERIALS FOR ELECTRONICS AND ENERGY APPLICATIONS Fabrication of a Flexible Amperometric Glucose Sensor Using Additive Processes (2015)

This study details the use of printing and other additive processes to fabricate a novel amperometric glucose sensor. The sensor was fabricated using a Au coated 12.7 μm thick polyimide substrate as a starting material, where micro-contact printing, electrochemical plating, chloridization, electrohydrodynamic jet (e-jet) printing, and spin coating were used to pattern, deposit, chloridize, print, and coat functional materials, respectively. We have found that e-jet printing was effective for the deposition and patterning of glucose oxidase inks with lateral feature sizes between ∼5 to 1000 μm in width, and that the glucose oxidase was still active after printing. The thickness of the permselective layer was optimized to obtain a linear response for glucose concentrations up to 32 mM and no response to acetaminophen, a common interfering compound, was observed. The use of such thin polyimide substrates allow wrapping of the sensors around catheters with high radius of curvature ∼250 μm, where additive and microfabrication methods may allow significant cost reductions.
A Computer Simulation of Marine Traffic Using Domains and Arenas (1980)

This paper outlines the concept of a domain and an evasion area, called an arena, around a ship which are then applied to produce a computer model of ship behaviour. The arena determines when a ship takes avoiding action, as does the land arena which reacts with a discrete series of coastal points to prevent the ship running aground. The increase in the number and size of ships has resulted in the introduction of traffic routing schemes and the need to understand ship behaviour more thoroughly. The concept of ‘the effective area around a ship which a navigator would like to keep clear with respect to other ships and stationary objects’ has been used by various authors including Goodwin, Fujii and Lewison with varying names such as domain, collision diameters and encounter area. There has been no fixed shape for these areas. Some are circular, others elliptical, while Goodwin's has three segments each with its own portion of a circle. By developing the theory of the domain, it was hoped to be able to produce a model of traffic behaviour which could be used to simulate traffic flows, or specific incidents, in order to study them more fully.
Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality (2016)

The data presented here highlight the small number of protein coding genes for which we have strong evidence that their essentiality status differs between the closely related bacterial taxa E. coli and Shigella. A set of genes involved in acetate utilization provides a canonical example. These results leave open the possibility of developing strain-specific antibiotic treatments targeting such differentially essential genes, but suggest that such opportunities may be rare in closely related bacteria.
Role of Flagellin and the Two-Component CheA/CheY System of Listeria monocytogenes in Host Cell Invasion and Virulence (2004)

The flagellum protein flagellin of Listeria monocytogenes is encoded by the flaA gene. Immediately downstream of flaA, two genes, cheY and cheA, encoding products with homology to chemotaxis proteins of other bacteria, are located. In this study we constructed deletion mutants with mutations in flaA. cheY, and cheA to elucidate their role in the biology of infection with L. monocytogenes. The DeltacheY, DeltacheA, and double-mutant DeltacheYA mutants, but not DeltaflaA mutant, were motile in liquid media. However, the DeltacheA mutant had impaired swarming and the DeltacheY and DeltacheYA mutants were unable to swarm on soft agar plates, suggesting that cheY and cheA genes encode proteins involved in chemotaxis. The DeltaflaA, DeltacheY, DeltacheA, and DeltacheYA mutants (grown at 24 degrees C) showed reduced association with and invasion of Caco-2 cells compared to the wild-type strain. However, spleens from intragastrically infected BALB/c and C57BL/6 mice showed larger and similar numbers of the DeltaflaA and DeltacheYA mutants, respectively, compared to the wild-type controls. Such a discrepancy could be explained by the fact that tumor necrosis factor receptor p55 deficient mice showed dramatically exacerbated susceptibility to the wild-type but unchanged or only slightly increased levels of the DeltaflaA or DeltacheYA mutant. In summary, we show that listerial flaA. cheY, and cheA gene products facilitate the initial contact with epithelial cells and contribute to effective invasion but that flaA could also be involved in the triggering of immune responses.
Growth Performance of Rats Fed Jojoba Proteins. Possible Correlations with Trypsin Inhibitory Activity in Jojoba Proteins (1997)

The effects of the water-soluble protein fraction of jojoba meal on growth and relative organ weight in rats were tested. Trypsin inhibitory activity (TIA) was measured in the untreated water-soluble jojoba proteins and in preparations after dry-heating (100 °C, 2 h) or methanol extraction (Soxhlet, 6 h). TIA was found in the jojoba protein fraction and could not be destroyed by dry-heating or methanol extraction of the jojoba proteins. In the first feeding experiment, growth performance and relative organ weight were compared of young rats fed ad libitum a diet containing either 18% soybean proteins (C), 6% soybean proteins (P6), or 6% soybean proteins supplemented with 12% jojoba proteins (JJ) or 12% toasted jojoba proteins (JJT). In a second 3 week experiment, growth and relative organ weight of young rats receiving a diet containing 6% soybean proteins supplemented with 12% methanol-extracted jojoba proteins (JJM) were compared for rats pair-fed with JJM with a diet containing 18% soybean proteins (PF). Although food intakes of C, JJ, and JJT rats were similar and P6 rats ate more than C rats, P6, JJ, and JJT rats showed growth retardation compared to C rats. JJM rats and PF rats showed a similar growth. The pancreas was hypertrophied in JJ and JJT rats, compared to C rats, and in JJM rats, compared to PF rats. Interscapular brown adipose tissue (BAT) was hypertrophied in P6, JJ, and JJT rats but normal in the JJM group. Jojoba proteins induce growth retardation. This is accompanied by pancreatic and BAT hypertrophy. As trypsin inhibition does not change but growth does ameliorate and BAT hypertrophy is abolished after methanol extraction, trypsin inhibition has no major influence on growth in the present experiments, while BAT hypertrophy is accompanied by growth reduction. Keywords: Simmondsia chinensis; jojoba meal; jojoba protein concentrate; rat
Identifying a Deletion Affecting Total Lung Capacity Among Subjects in the COPDGene Study Cohort (2015)

Chronic obstructive pulmonary disease (COPD) is a progressive disease with both environmental and genetic risk factors. Genome-wide association studies (GWAS) have identified multiple genomic regions influencing risk of COPD. To thoroughly investigate the genetic etiology of COPD, however, it is also important to explore the role of copy number variants (CNVs) because the presence of structural variants can alter gene expression and can be causal for some diseases. Here, we investigated effects of polymorphic CNVs on quantitative measures of pulmonary function and chest computed tomography (CT) phenotypes among subjects enrolled in COPDGene, a multisite study. COPDGene subjects consist of roughly one-third African American (AA) and two-thirds non-Hispanic white adult smokers (with or without COPD). We estimated CNVs using PennCNV on 9,076 COPDGene subjects using Illumina's Omni-Express genome-wide marker array. We tested for association between polymorphic CNV components (defined as disjoint intervals of copy number regions) for several quantitative phenotypes associated with COPD within each racial group. Among the AAs, we identified a polymorphic CNV on chromosome 5q35.2 located between two genes (FAM153B and SIMK1, but also harboring several pseudo-genes) giving genome-wide significance in tests of association with total lung capacity (TLCCT ) as measured by chest CT scans. This is the first study of genome-wide association tests of polymorphic CNVs and TLCCT . Although the ARIC cohort did not have the phenotype of TLCCT , we found similar counts of CNV deletions and amplifications among AA and European subjects in this second cohort.
Surgical Approaches to Brain Stem Cavernous Malformations (1997)

Introduction: Brain stem cavernous malformations are rare intracranial vascular lesions. They account for 9 to 35% of all cavernous malformations. Their natural history is poorly defined, and surgical series to date have been small. Methods: We reviewed our clinical experience from 1988 to 1996 with 78 patients with brain stem cavernous malformations and attempted to determine the hemorrhage rate and factors that influence outcome. There were 30 males and 48 females (mean age, 37 years). The lesions were located throughout the brain stem: the pons (27), pontomesencephalic (17), medulla (13), midbrain (11), pontomedullary function (8), and midbrain-pons-medulla (2). We also evaluated their neurological morbidity and mortality. Results: The prospective annual rehemorrhage rate was 33% per lesion per year. All patients had associated venous malformations. Standard skull base approaches were used to resect 72 of the 78 lesions. Of the 72 operated patients, 60 were the same or better after surgical...
Combustible hydrogène - Production (2013)

L'hydrogène est un combustible qui n'émet aucun gaz à effet de serre. Il peut être produit en dissociant l'eau par électrolyse ou par thermochimie à haute température. D'autres possibilités existent à partir d'hydrocarbures, d'alcools ou de biomasse, ce sont le reformage, l'oxydation partielle et la gazéification. Le CO2 émis par ces méthodes peut être capté et stocké. L'hydrogène obtenu par dissociation de l'eau est «vert» si l'énergie nécessaire est d'origine renouvelable, il devient alors un auxiliaire de ce type d'énergie qu'il permet de stocker.
Final Technical Report (2005)

This variable length wind turbine blade project met the project objectives by successfully completing the task schedule. A set of variable length blades (8 to 12 meters in length) is now flying, in a configuration that is representative of a commercial blade designed to replace a standard 9 meter blade. Static testing and operations show that the blades are durable and stiff enough to prevent tower strikes. Power curve testing shows significant gains in low wind speed power production. An improved controller and drive mechanism have now been working for six months. Moving forward, we continue to monitor power curve, controller performance, and durability data. The project has made good progress towards understanding the costs and challenges associated with commercial production of variable length blades. Items that will require further study are: tip airfoil; blade pitching, tip and root interface design; jigs for more efficient construction, and optimization of subsystems