gebhart/patrepeval huggingface dataset:
Molecular and Physiological Analysis of Aluminum Tolerance in Maize Recombinant Inbreds (2009)

Aluminum (Al) toxicity is a major constraint for crop production on acid, Al toxic soils, that occupy over 50% of the potentially arable lands in the world. Aluminum is ubiquitous in soils and when solubilized at pH values below 5.0, becomes highly phytotoxic as Al3+, causing severe yield reduction to sensitive crops. Al tolerance in species such as wheat, barley and sorghum appears to rely largely on a small number of genes within each species. However, quantitative inheritance for Al tolerance appears to be the general pattern observed in rice and maize. In maize, citrate exudation has been suggested as an important tolerance mechanism. However, lack of correlation between citrate exudation and differential Al tolerance observed in some maize lines suggests that other Al tolerance mechanisms may take place in maize. In this study, we undertook a physiological study of Al tolerance mechanisms focusing on citrate exudation in selected maize recombinant inbred lines for which a QTL map had been previously developed. Our results are being assessed in light of the genetic constitution of these RILs for the major Al tolerance QTLs segregating in the population. Our results support the role of citrate exudation as a major Al tolerance mechanism in maize but suggest that other mechanisms probably take place in this population.
A phosphonate monoester hydrolase from <i>Burkholderia caryophilli</i> PG2982 is useful as a conditional lethal gene in plants (1996)

A bacterial phosphonate monoester hydrolase was evaluated in plants as a conditional lethal gene useful for cell ablation and negative selection. Glyphosate is a potent herbicide whereas its phosphonate monoester derivative, glyceryl glyphosate, is approximately 50-fold less active. A phosphonate monoesterase gene (pehA) encoding an enzyme that hydrolyzes phosphonate esters including glyceryl glyphosate to glyphosate and glycerol was cloned from the glyphosate metabolizing bacterium, Burkholderia caryophilli PG2982. Constitutive expression of the pehA gene in Escherichia coli and Arabidopsis thaliana RLD had no observable phenotypic effects on growth and development. However, cells and plants expressing the pehA gene were killed when treated with glyceryl glyphosate. The phytotoxicity resulted from the hydrolysis of glyceryl glyphosate to glyphosate and subsequent inhibition of aromatic amino acid biosynthesis. As an example of tissue-specific cell ablation, floral sterility without vegetative toxicity was demonstrated by expressing the pehA gene using a tapetal-specific promoter and treating the mature plants with glyceryl glyphosate. A chromogenic phosphonate ester substrate, 5-bromo-4-chloro-indolyl phenylphosphonate, was used to monitor in situ expression of the pehA gene. The general utility of the pehA gene as a heterologous conditional lethal gene in plants is discussed.
Susceptibility of low-density lipoprotein particles to aggregate depends on particle lipidome, is modifiable, and associates with future cardiovascular deaths (2018)

Aims\nLow-density lipoprotein (LDL) particles cause atherosclerotic cardiovascular disease (ASCVD) through their retention, modification, and accumulation within the arterial intima. High plasma concentrations of LDL drive this disease, but LDL quality may also contribute. Here, we focused on the intrinsic propensity of LDL to aggregate upon modification. We examined whether inter-individual differences in this quality are linked with LDL lipid composition and coronary artery disease (CAD) death, and basic mechanisms for plaque growth and destabilization.\n\nMethods and results\nWe developed a novel, reproducible method to assess the susceptibility of LDL particles to aggregate during lipolysis induced ex vivo by human recombinant secretory sphingomyelinase. Among patients with an established CAD, we found that the presence of aggregation-prone LDL was predictive of future cardiovascular deaths, independently of conventional risk factors. Aggregation-prone LDL contained more sphingolipids and less phosphatidylcholines than did aggregation-resistant LDL. Three interventions in animal models to rationally alter LDL composition lowered its susceptibility to aggregate and slowed atherosclerosis. Similar compositional changes induced in humans by PCSK9 inhibition or healthy diet also lowered LDL aggregation susceptibility. Aggregated LDL in vitro activated macrophages and T cells, two key cell types involved in plaque progression and rupture.\n\nConclusion\nOur results identify the susceptibility of LDL to aggregate as a novel measurable and modifiable factor in the progression of human ASCVD.
Persistent secretion of IL-18 in the skin contributes to IgE response in mice (2003)

After exposure of the skin to microbes, the host develops skin-specific inflammation and an acquired immune response, in which keratinocytes (KC) and Langerhans cells play critical roles respectively. We established two animal models. (i) We examined the importance of KC-derived IL-18 for the systemic IgE response by using a skin transplantation model. As previously reported, transgenic mice (KCASP1Tg), that over-express caspase-1 in their KC, display high serum levels of IgE, and spontaneously develop chronic dermatitis by production of IL-18 and IL-1beta. We examined the capacity of transplantation of cutaneous lesions from KCASP1Tg to induce IgE production in wild-type or mutant mice with a syngeneic background. Transplantation of active cutaneous lesions, that expressed high levels of IL-18 and IL-1beta, induced long-lasting IgE production in wild-type mice without elevation of circulating IL-18 and IL-1beta. Furthermore, IL-18R-, CD4- or stat6-deficient mice transplanted with the lesions did not produce IgE, indicating that this IgE response is initiated by IL-18, and dependent on host-derived CD4(+) T cells and stat6. (ii) We investigated IL-18 secretion from KC upon stimulation with microbe products. Freshly isolated KC from wild-type mice secreted IL-18 in response to Protein A purified from Cowan 1 strain of Staphylococcus aureus (SpA), which often exacerbates human skin diseases, including atopic dermatitis. Cutaneous application of SpA increased serum levels of IL-18 and IgE. These results indicate that local accumulation of IL-18 triggers systemic IgE responses without exposure to antigen.
The role of the eosinophil-selective chemokine, eotaxin, in allergic and non-allergic airways inflammation (1997)

Blood eosinophilia and tissue infiltration by eosinophils are frequently observed in allergic inflammation and parasitic infections. This selective accumulation of eosinophils suggested the existence of endogenous eosinophil-selective chemoattractants. We have discovered a novel eosinophil-selective chemoattractant which we called eotaxin in an animal model of allergic airways disease. Eotaxin is generated in both allergic and non-allergic bronchopulmonary inflammation. The early increase in eotaxin paralleled eosinophil infiltration in the lung tissue in both models. An antibody to IL-5 suppressed lung eosinophilia, correlating with an inhibition of eosinophil release from bone marrow, without affecting eotaxin generation. This suggests that endogenous IL-5 is important for eosinophil migration but does not appear to be a stimulus for eotaxin production. Constitutive levels of eotaxin observed in guinea-pig lung may be responsible for the basal lung eosinophilia observed in this species. Allergen-induced eotaxin was present mainly in the epithelium and alveolar macrophages, as detected by immunostaining. In contrast there was no upregulation of eotaxin by the epithelial cells following the injection of sephadex beads and the alveolar macrophage and mononuclear cells surrounding the granuloma were the predominant positive staining cells. Eotaxin and related chemokines acting through the CCR3 receptor may play a major role in eosinophil recruitment in allergic inflammation and parasitic diseases and thus offer and attractive target for therapeutic intervention.
Molecular analysis of rabies-related viruses from Ethiopia. (1993)

From brain samples collected from domestic animals in Ethiopia, two rabies-related viruses were isolated. According to their reactivity pattern with anti-nucleocapsid monoclonal antibodies, they were characterized as Lagos bat virus (isolate Eth-58) and Mokola virus (isolate Eth-16). This classification was confirmed by neutralization experiments with Mokola and Lagos bat specific antisera. Two potent anti-rabies vaccines were unable to protect mice against the two rabies-related viruses. In order to investigate molecular relationships to classical rabies virus, cDNA cloning and sequencing was performed. The RNA genome of both viruses comprises 12 kilobases (kb) and has an organization similar to that of rabies virus with the gene order 3'-N-P-M-G-L-5'. Using virus-specific cDNA as probes in heterologous hybridization experiments, the RNAs of other members of lyssavirus serotypes 2 and 3 were detected. From hybridization experiments and sequence analysis of the 3' terminal 5,5 kb of the genomes, Eth-16 and Eth-58 viruses were shown to be equally genetically distant from rabies virus with 60% nucleotide identity; Eth-16 and Eth-58 had 68% homology.
Effect of Dietary Lactose and Cell Concentration on the Ability of a Continuous-Flow-Derived Bacterial Culture to Control Salmonella Cecal Colonization in Broiler Chickens (1994)

The effect of dietary lactose and of cell concentration of a continuous-flow (CF) derived bacterial culture on Salmonella typhimurium cecal colonization in 10-d-old broiler chickens was examined. One-day-old chicks were provided 1) no CF culture and the control diet; 2) no culture and a 2% lactose diet; 3) CF culture (10(8) or 10(11) anaerobic cfu) and control diet; or 4) CF culture (10(8) or 10(11) anaerobic cfu) and 2 to 4% lactose diet. All groups were challenged orally with 10(4) S. typhimurium at 3 d of age. Salmonella typhimurium growth in cecal contents was significantly decreased (P < .05) at 10 d of age when 2% lactose was used in combination with CF culture containing 10(8) or 10(11) anaerobic cfu. The protection factor (log10 Salmonella control diet divided by log10 Salmonella treatment group) for these treatment groups was 2.49 and 9.26, respectively. Results indicate that birds treated with CF culture and maintained on 2% dietary lactose are protected against S. typhimurium colonization. Additionally, inoculating birds with CF culture containing a higher concentration of anaerobic colony-forming units resulted in a substantially higher protection factor.
Chemical ordering and large tunnel magnetoresistance in Co<sub>2</sub>FeAl/MgAl<sub>2</sub>O<sub>4</sub>/Co<sub>2</sub>FeAl(001) junctions (2016)

Epitaxial magnetic tunnel junctions (MTJs) with a Co2FeAl/CoFe (0.5 nm)/MgAl2O4/Co2FeAl(001) structure were fabricated by magnetron sputtering. High-temperature in situ annealing led to a high degree of B2-order in the Co2FeAl layers and cation order of the MgAl2O4 barrier. Large tunnel magnetoresistance (TMR) of up to 342% was obtained at room temperature (616% at 4 K), in contrast to the TMR ratio (%) suppressed by the band-folding effect in Fe/cation-ordered MgAl2O4/Fe MTJs. The present study reveals that the high degree of B2-order and the resulting high spin polarization in the Co2FeAl electrodes enable us to bypass the band-folding problem in spinel barriers.
A methodology for minimizing power dissipation of embedded systems through hardware/software partitioning (2003)

We present a novel approach that minimizes the power dissipation of embedded core-based systems through hardware/software partitioning. Our approach is based on the idea of mapping clusters of operations/instructions to a core that yields a high utilization rate of the involved resources (ALUs, multipliers, shifters etc.) and thus minimizing power dissipation. Our approach is comprehensive since it takes into consideration the power dissipation of a whole embedded system comprising a microprocessor core, application specific (ASIC) core(s), cache cores and a memory core. We report high reductions of power dissipation between 35% and 94% at the cost of a relatively small additional hardware overhead of less than 16 k cells while maintaining or even slightly increasing the performance compared to the initial design.
Engineered neural tissue for peripheral nerve repair (2013)

A new combination of tissue engineering techniques provides a simple and effective method for building aligned cellular biomaterials. Self-alignment of Schwann cells within a tethered type-1 collagen matrix, followed by removal of interstitial fluid produces a stable tissue-like biomaterial that recreates the aligned cellular and extracellular matrix architecture associated with nerve grafts. Sheets of this engineered neural tissue supported and directed neuronal growth in a co-culture model, and initial in vivo tests showed that a device containing rods of rolled-up sheets could support neuronal growth during rat sciatic nerve repair (5 mm gap). Further testing of this device for repair of a critical-sized 15 mm gap showed that, at 8 weeks, engineered neural tissue had supported robust neuronal regeneration across the gap. This is, therefore, a useful new approach for generating anisotropic engineered tissues, and it can be used with Schwann cells to fabricate artificial neural tissue for peripheral nerve repair.
Reconstitution of a Thermostable Xylan-Degrading Enzyme Mixture from the Bacterium Caldicellulosiruptor bescii (2012)

Xylose, the major constituent of xylans, as well as the side chain sugars, such as arabinose, can be metabolized by engineered yeasts into ethanol. Therefore, xylan-degrading enzymes that efficiently hydrolyze xylans will add value to cellulases used in hydrolysis of plant cell wall polysaccharides for conversion to biofuels. Heterogeneous xylan is a complex substrate, and it requires multiple enzymes to release its constituent sugars. However, the components of xylan-degrading enzymes are often individually characterized, leading to a dearth of research that analyzes synergistic actions of the components of xylan-degrading enzymes. In the present report, six genes predicted to encode components of the xylan-degrading enzymes of the thermophilic bacterium Caldicellulosiruptor bescii were expressed in Escherichia coli, and the recombinant proteins were investigated as individual enzymes and also as a xylan-degrading enzyme cocktail. Most of the component enzymes of the xylan-degrading enzyme mixture had similar optimal pH (5.5 to ∼6.5) and temperature (75 to ∼90°C), and this facilitated their investigation as an enzyme cocktail for deconstruction of xylans. The core enzymes (two endoxylanases and a β-xylosidase) exhibited high turnover numbers during catalysis, with the two endoxylanases yielding estimated k(cat) values of ∼8,000 and ∼4,500 s(-1), respectively, on soluble wheat arabinoxylan. Addition of side chain-cleaving enzymes to the core enzymes increased depolymerization of a more complex model substrate, oat spelt xylan. The C. bescii xylan-degrading enzyme mixture effectively hydrolyzes xylan at 65 to 80°C and can serve as a basal mixture for deconstruction of xylans in bioenergy feedstock at high temperatures.
Engineered symbionts activate honey bee immunity and limit pathogens (2020)

Honey bees are essential pollinators threatened by colony losses linked to the spread of parasites and pathogens. Here, we report a new approach for manipulating bee gene expression and protecting bee health. We engineered a symbiotic bee gut bacterium, <i>Snodgrassella alvi</i>, to induce eukaryotic RNA interference (RNAi) immune responses. We show that engineered <i>S. alvi</i> can stably recolonize bees and produce double-stranded RNA to activate RNAi and repress host gene expression, thereby altering bee physiology, behavior, and growth. We used this approach to improve bee survival after a viral challenge, and we show that engineered <i>S. alvi</i> can kill parasitic <i>Varroa</i> mites by triggering the mite RNAi response. This symbiont-mediated RNAi approach is a tool for studying bee functional genomics and potentially for safeguarding bee health.
Phytosterols in the seeds of wild sunflower species (2011)

Ingestion of phytosterols prevents intestinal absorption of cholesterol in humans and results in a lowering of serum cholesterol, which has stimulated the use of phytosterols as enriched food ingredients in functional foods. Sunflower seeds and oils are rich sources of phytosterols. The variation reported for these compounds in cultivated sunflower germplasm is low. As for many other traits, wild sunflower species may contain valuable unexplored variation for phytosterol content and profile. The objective of this research was to evaluate the variation for seed phytosterols in a set of 47 wild Helianthus species from the USDA-ARS collection. An impressive variation was identified for total phytosterol content (1017 to 4308 mg kg -1 seed) and proportion of individual phytosterols, particularly campesterol (5.1 to 16.3%), stigmasterol (3.1 to 23.9%), beta-sitosterol (35.1 to 72.3%), delta-5-avenasterol (1.9 to 20.5%), delta-7-stigmastenol (1.1 to 20.3%), and delta-7-avenasterol (0.3 to 10.6%). Some of the extremes of these ranges of variation have not been identified in cultivated sunflower. The feasibility of transferring genes determining interesting phytosterol traits to cultivated sunflower should be investigated.
Mechanistic Principles of Antisense Targets for the Treatment of Spinal Muscular Atrophy (2015)

Spinal muscular atrophy (SMA) is a major neurodegenerative disorder of children and infants. SMA is primarily caused by low levels of SMN protein owing to deletions or mutations of the SMN1 gene. SMN2, a nearly identical copy of SMN1, fails to compensate for the loss of the production of the functional SMN protein due to predominant skipping of exon 7. Several compounds, including antisense oligonucleotides (ASOs) that elevate SMN protein from SMN2 hold the promise for treatment. An ASO-based drug currently under Phase III clinical trial employs intronic splicing silencer N1 (ISS-N1) as its target. Cumulative studies on ISS-N1 reveal a wealth of information with significance to the overall therapeutic development for SMA. Here, the authors summarize the mechanistic principles behind various antisense targets currently available for SMA therapy.
Elastomer degradation sensor (1989)

This document describes the present invention which is method and apparatus using piezoelectric oscillators as elastomer degradation sensors, particularly as in situ sensors. A piezoelectric material is placed in contact with an elastomer to form an oscillating system. The piezoelectric may contact a surface of the elastomer or be embedded therein. The elastomer can be in situ in a piece of equipment or vehicle. The characteristics of the piezoelectric material, such as size, shape, and composition, and the elasticity of the elastomer determine the resonant frequency and other properties or parameters of the oscillating system. The resonant oscillation of the oscillating system is used to drive a simple electric oscillator circuit. The frequency of this oscillator circuit, and hence the resonant frequency of the oscillating system, is measured with standard frequency counting electronics. Changes in the resonance frequency of the oscillating system indicate changes in the elastic properties of the elastomer. 7 figs.
Dependence of radiation induced buried oxide charge on silicon-on-insulator fabrication technology (1996)

X-rays have been used to irradiate material fabricated using various Silicon-on-Insulator (SOI) technologies, including the Bond and Etchback SOI (BESOI) process and several different Separation-by-Implantation-of-Oxygen (SIMOX) processes. The thickness of the buried oxide (BOX) in these samples ranged from 80 nm to 400 nm. The irradiations were done under high field (1 MV/cm) bias conditions. For each of these materials the net number of occupied traps in the buried oxide and the location of the charge centroid was determined. It was found that the location of the charge centroid depends on the density of the BOX, and on the radiation dose. It was also found that for buried oxides which have densities similar to that of fused silica, the net number of occupied traps in the BOX saturates at approximately 1.1/spl times/10/sup 13/ cm/sup -2/, and does not depend on the BOX thickness or fabrication technique. Both of these findings are important in device design, especially for substrates with thin buried oxides.
Multivalent display of minimal Clostridium difficile glycan epitopes mimics antigenic properties of larger glycans (2016)

Synthetic cell-surface glycans are promising vaccine candidates against Clostridium difficile. The complexity of large, highly antigenic and immunogenic glycans is a synthetic challenge. Less complex antigens providing similar immune responses are desirable for vaccine development. Based on molecular-level glycan-antibody interaction analyses, we here demonstrate that the C. difficile surface polysaccharide-I (PS-I) can be resembled by multivalent display of minimal disaccharide epitopes on a synthetic scaffold that does not participate in binding. We show that antibody avidity as a measure of antigenicity increases by about five orders of magnitude when disaccharides are compared with constructs containing five disaccharides. The synthetic, pentavalent vaccine candidate containing a peptide T-cell epitope elicits weak but highly specific antibody responses to larger PS-I glycans in mice. This study highlights the potential of multivalently displaying small oligosaccharides to achieve antigenicity characteristic of larger glycans. The approach may result in more cost-efficient carbohydrate vaccines with reduced synthetic effort.
Equalization: a technique to improve the accuracy of antenna radiation pattern measurements (2003)

The paper describes a novel system that overcomes inaccuracies in antenna radiation pattern measurements caused by multipath propagation. The system operates by specifically correcting for the effects of unwanted signals rather than by attempting to remove, or minimize, them through the use of screens or baffles or an anechoic chamber. An equalization technique is used, the parameters of the equalizer(s) being determined from a special measurement of the antenna range under consideration. The technique is generally applicable; it may be implemented ab initio in new indoor or outdoor ranges, or retrofitted to existing ranges to improve accuracy. Most importantly, however, the basic idea leads to the design of a completely new type of real-time 3-dimensional range in which sensors are placed on the surface of an imaginary sphere surrounding the antenna under test (AUT), and an anechoic chamber is not required.
Analysis of high-order surface etched gratings for longitudinal mode selection in DFB lasers (2010)

A model to analyze longitudinal mode selection in high-order laterally coupled DFB lasers is developed and used to verify an ability to control the complex coupling resulting in a single-frequency lasing by manipulating the grating shape.
Studies Directed toward the Elucidation of the Pharmacophore of Steroid-Based Sonic Hedgehog Signaling Inhibitors (2011)

Previous work from our laboratory has established that the readily available steroid-based analog 2 of cyclopamine 1 is, like 1, a highly potent inhibitor of Hedgehog signaling. The first structure-activity relationship studies on 2, i.e., the synthesis and biological evaluation of both the C-17 epi analog 4 and the C-3 deoxy analog 11, both of which are more potent than cyclopamine 1, are described. The implications of these results for the emerging pharmacophore of these Sonic Hedgehog signaling inhibitors are discussed.