gebhart/patrepeval huggingface dataset:
Photosynthesis and Inorganic Carbon Usage by the Marine Cyanobacterium, <i>Synechococcus</i> sp (1982)

The marine cyanobacterium, Synechococcus sp. Nägeli (strain RRIMP N1) changes its affinity for external inorganic carbon used in photosynthesis, depending on the concentration of CO(2) provided during growth. The high affinity for CO(2) + HCO(3) (-) of air-grown cells (K((1/2)) < 80 nanomoles [pH 8.2]) would seem to be the result of the presence of an inducible mechanism which concentrates inorganic carbon (and thus CO(2)) within the cells. Silicone-oil centrifugation experiments indicate that the inorganic carbon concentration inside suitably induced cells may be in excess of 1,000-fold greater than that in the surrounding medium, and that this accumulation is dependent upon light energy. The quantum requirements for O(2) evolution appear to be some 2-fold greater for low CO(2)-grown cells, compared with high CO(2)-grown cells. This presumably is due to the diversion of greater amounts of light energy into inorganic carbon transport in these cells.A number of experimental approaches to the question of whether CO(2) or HCO(3) (-) is primarily utilized by the inorganic carbon transport system in these cells show that in fact both species are capable of acting as substrate. CO(2), however, is more readily taken up when provided at an equivalent concentration to HCO(3) (-). This discovery suggests that the mechanistic basis for the inorganic carbon concentrating system may not be a simple HCO(3) (-) pump as has been suggested. It is clear, however, that during steady-state photosynthesis in seawater equilibrated with air, HCO(3) (-) uptake into the cell is the primary source of internal inorganic carbon.
PTEN Depletion Decreases Disease Severity and Modestly Prolongs Survival in a Mouse Model of Spinal Muscular Atrophy (2014)

Spinal muscular atrophy (SMA) is the second most common genetic cause of death in childhood. However, no effective treatment is available to halt disease progression. SMA is caused by mutations in the survival motor neuron 1 (SMN1) gene. We previously reported that PTEN depletion leads to an increase in survival of SMN-deficient motor neurons. Here, we aimed to establish the impact of PTEN modulation in an SMA mouse model in vivo. Initial experiments using intramuscular delivery of adeno-associated vector serotype 6 (AAV6) expressing shRNA against PTEN in an established mouse model of severe SMA (SMNΔ7) demonstrated the ability to ameliorate the severity of neuromuscular junction pathology. Subsequently, we developed self-complementary AAV9 expressing siPTEN (scAAV9-siPTEN) to allow evaluation of the effect of systemic suppression of PTEN on the disease course of SMA in vivo. Treatment with a single injection of scAAV9-siPTEN at postnatal day 1 resulted in a modest threefold extension of the lifespan of SMNΔ7 mice, increasing mean survival to 30 days, compared to 10 days in untreated mice. Our data revealed that systemic PTEN depletion is an important disease modifier in SMNΔ7 mice, and therapies aimed at lowering PTEN expression may therefore offer a potential therapeutic strategy for SMA.
Correction: Mutation Scanning Using MUT-MAP, a High-Throughput, Microfluidic Chip-Based, Multi-Analyte Panel (2013)

Targeted anticancer therapies rely on the identification of patient subgroups most likely to respond to treatment. Predictive biomarkers play a key role in patient selection, while diagnostic and prognostic biomarkers expand our understanding of tumor biology, suggest treatment combinations, and facilitate discovery of novel drug targets. We have developed a highthroughput microfluidics method for mutation detection (MUT-MAP, mutation multi-analyte panel) based on TaqMan or allele-specific PCR (AS-PCR) assays. We analyzed a set of 71 mutations across six genes of therapeutic interest. The six-gene mutation panel was designed to detect the most common mutations in the EGFR, KRAS, PIK3CA, NRAS, BRAF, and AKT1 oncogenes. The DNA was preamplified using custom-designed primer sets before the TaqMan/AS-PCR assays were carried out using the Biomark microfluidics system (Fluidigm; South San Francisco, CA). A cross-reactivity analysis enabled the generation of a robust automated mutation-calling algorithm which was then validated in a series of 51 cell lines and 33 FFPE clinical samples. All detected mutations were confirmed by other means. Sample input titrations confirmed the assay sensitivity with as little as 2 ng gDNA, and demonstrated excellent inter-and intra-chip reproducibility. Parallel analysis of 92 clinical trial samples was carried out using 2-100 ng genomic DNA (gDNA), allowing the simultaneous detection of multiple mutations. DNA prepared from both fresh frozen and formalin-fixed, paraffin-embedded (FFPE) samples were used, and the analysis was routinely completed in 2-3 days: traditional assays require 0.5-1 mg high-quality DNA, and take significantly longer to analyze. This assay can detect a wide range of mutations in therapeutically relevant genes from very small amounts of sample DNA. As such, the mutation assay developed is a valuable tool for high-throughput biomarker discovery and validation in personalized medicine and cancer drug development.
Influence of small additions of copper and niekel on hot ductility of steels (1995)

AbstractAbstractThe influence of small additions of Cu and Ni on the hot ductility of C–Mn–Al–Nb and C–Mn–Al steels has been examined by tensile testing specimens in the temperature range 750–1000°C at a low strain rate (~10−3 S−l). On solution treating at 1330°C and cooling to the test temperature, no significant influence ofCu could befound on ductility, independent of whether or not testing was carried out in air or in a protective atmosphere of Ar. However, samples tested in an Ar atmosphere gave improved ductility over samples tested in air. Tensile samples cast directly after melting and tested in a protective Ar atmosphere were again found to be uninfluenced by compositional changes. In contrast, samples melted and tested in air showed a deterioration in ductility on the addition of Cu, but the deleterious effect on ductility of Cu could be prevented by a similar addition of Ni. No evidence for thin films of Cu rich phases penetrating along the intergranular boundaries taken by surface cracks could be found, as in conventional hot shortness. It is suggested that the observed behaviour is due to the formation of fine copper sulphide or possibily oxysulphide precipitates as a result of oxidation and the presence of Cu.MST/3014
PIV and WPIV: Two New Performance Indices for Heterogeneous Systems Evaluation (2006)

Two new performance indices (PIV - Performance Index Vector and WPIV – Weighted Performance Index Vector) are presented in this article. Those indices to evaluate heterogeneous computing systems are based on a Euclidian metric. Aiming to maximize the use of the machines, the proposed indices are a combination of several usual indices and the results of their evaluation through a simulator show an appropriate behavior for different kinds of applications.
RDL: A novel approach for passive object localization in WSN based on RSSI (2012)

The Radio Signal Strength Indicator (RSSI)-based localization algorithm is an effective solution for passive object localization. However, the localization accuracy of the existing methods highly depends on the transceiver distance and deployment density. Generally speaking, to obtain higher accuracy, we need a denser sensor node deployment, which results in a higher deployment cost and more communication overheads. In this paper, we investigate this problem based on extensive measurements. According to the measurement results, we propose to localize objects using an RSSI distribution based localization (RDL) model to identify the object location by different RSSI distributions of the communicating links. Experimental results show that the RDL method can achieve higher localization accuracy with less sensor nodes.
Migration of Bone Marrow and Cord Blood Mesenchymal Stem Cells In Vitro Is Regulated by Stromal‐Derived Factor‐1‐CXCR4 and Hepatocyte Growth Factor‐c‐met Axes and Involves Matrix Metalloproteinases (2006)

Human mesenchymal stem cells (MSCs) are increasingly being considered in cell-based therapeutic strategies for regeneration of various organs/tissues. However, the signals required for their homing and recruitment to injured sites are not yet fully understood. Because stromal-derived factor (SDF)-1 and hepatocyte growth factor (HGF) become up-regulated during tissue/organ damage, in this study we examined whether these factors chemoattract ex vivo-expanded MSCs derived from bone marrow (BM) and umbilical cord blood (CB). Specifically, we investigated the expression by MSCs of CXCR4 and c-met, the cognate receptors of SDF-1 and HGF, and their functionality after early and late passages of MSCs. We also determined whether MSCs express matrix metalloproteinases (MMPs), including membrane type 1 (MT1)-MMP, matrix-degrading enzymes that facilitate the trafficking of hematopoietic stem cells. We maintained expanded BM- or CB-derived MSCs for up to 15-18 passages with monitoring of the expression of 1) various tissue markers (cardiac and skeletal muscle, neural, liver, and endothelial cells), 2) functional CXCR4 and c-met, and 3) MMPs. We found that for up to 15-18 passages, both BM- and CB-derived MSCs 1) express mRNA for cardiac, muscle, neural, and liver markers, as well as the vascular endothelial (VE) marker VE-cadherin; 2) express CXCR4 and c-met receptors and are strongly attracted by SDF-1 and HGF gradients; 3) express MMP-2 and MT1-MMP transcripts and proteins; and 4) are chemo-invasive across the reconstituted basement membrane Matrigel. These in vitro results suggest that the SDF-1-CXCR4 and HGF-c-met axes, along with MMPs, may be involved in recruitment of expanded MSCs to damaged tissues.
Wind Tunnel Pulsations and their Active Suppression (2000)

<div class="htmlview paragraph">Low-frequency pressure fluctuations which occur at certain flow speeds are an undesired feature in many open jet wind tunnels. This so called ‘wind tunnel pumping’ affects the aerodynamic quality of the flow and thus the quality of the measured data. In this paper a novel approach is presented to control the pulsation phenomenon by active damping of the acoustic resonant modes of the wind tunnel circuit. The acoustic mechanism of the resonance effect was investigated using a 1/20 scale pilot wind tunnel with a complete and detailed representation of test section, ducting, turning vanes and fan. The newly devised Active Resonance Control (ARC) System essentially consists of a microphone which picks up the pressure fluctuations in the plenum, a loudspeaker which is mounted in the tunnel wall and a time delay to adjust the phase relation between the microphone signal and the loudspeaker output. The ARC system reduces the periodic pressure fluctuations by 20 dB and completely eliminates the periodic velocity fluctuations. Based on the experiences with the pilot wind tunnel an ARC System was implemented in the new Audi aeroacoustic wind tunnel. The ARC System eliminates the low-frequency flow fluctuations without introducing additional noise into the wind tunnel and thus allows high-quality aerodynamic and acoustic measurements over the entire velocity range.</div>
Halogen and Hydrogen Bond Architectures in Switchable Chains of Di- and Trihaloimidazoles (2015)

Halogen bonds have been employed for controlling the structure of NH···N hydrogen-bonded chains in halogenated imidazoles; the CH···halogen contacts stabilize the coplanar arrangement of molecules, whereas the halogen···halogen contacts twist the molecules around the NH···N bonds and stretch their N···N distances. The interplay of halogen···halogen and NH···N hydrogen bonds leads to isostructural relations of 4,5-dihaloimidazoles as well as between trichloro- and tribromoimidazole. However, the increasing steric hindrance excludes the triiodoimidazole from this isostructural series, and the triiodo derivative forms an unusual structure with three symmetry-independent molecules. All symmetrically substituted 4,5-dichloro-, dibromo-, and diiodoimidazoles as well as trichloro-, tribromo-, and triiodoimidazoles have been synthesized and crystallized and their structures determined. The derived rules also apply to the co-crystal structures of 4,5-diiodoimidazole:2,4,5-triiodoimidazole as well as to 4-iodoimidazole:2,4-diiodoimidazole. The halogen interactions prove an efficient means for engineering and tuning new materials with desired dielectric properties relying on highly polarizable NH···N hydrogen bonds.
Geometrical multiscale model of an idealized left ventricle with fluid-structure interaction effects coupled to a one-dimensional viscoelastic arterial network (2011)

A geometrical multiscale model for blood flow through an ideal left ventricle and the main arteries is presented. The blood flow in the three-dimensional idealized left ventricle is solved through a monolithic fluid-structure interaction solver. To account for the interaction between the heart and the circulatory system the heart flow is coupled through an ideal valve with a network of viscoelastic one-dimensional models representing the arterial network. The geometrical multiscale approach used in this work is based on the exchange of averaged/integrated quantities between the fluid problems. The peripheral circulation is modelled by zero-dimensional windkessel terminals. We demonstrate that the geometrical multiscale model is (i) highly modular in that component models can be easily replaced with higher-fidelity ones whenever the user has a specific interest in modelling a particular part of the system, (ii) passive in that it reaches a stable limit cycle of flow rate and pressure in a few heartbeat cycles when driven by a periodic force acting on the epicardium, and (iii) capable of operating at physiological regimes.
Collagen‐Hydroxyapatite/Tricalcium Phosphate Microspheres as a Delivery System for Recombinant Human Transforming Growth Factor‐β 1 (2003)

The purpose of this study is to evaluate the carrier capability of collagen-hydroxyapatite/tricalcium phosphate (Col-HA/TCP) microspheres to the rhTGF-beta 1 (recombinant human transforming growth factor-beta 1). After anesthesia, a bone defect (7.0 mm in diameter and 10.0 mm in depth) was created at the distal femoral condyles of New Zealand white rabbits. These defects were then completely filled with the implant materials. After 5, 7, 9, 11, 13, and 15 weeks, the animals were sacrificed and histological evaluations were performed. The results showed that when the defects were treated with Col-HA/TCP microspheres without rhTGF-beta 1, there was only spotty new bone formation during the 15 week experimental period and most of the defect was filled with fibrous tissue and inflammatory cells, whereas active bone formation with mature marrow tissue formation was evident in the defect treated with Col-HA/TCP microspheres containing rhTGF-beta 1. Collagen-hydroxyapatite/tricalcium phosphate microspheres were expected to be replaced by the regenerated bone structure as the bone reconstruction and bone-remodeling process occurred. It was apparent that bone regeneration was influenced by the addition of rhTGF-beta 1. Collagen-hydroxyapatite/tricalcium phosphate microspheres were a good carrier for rhTGF-beta 1.
Naturally Acquired Simian Varicella Virus Infection in African Green Monkeys (2002)

Simian varicella virus (SVV) infection of primates shares clinical, pathological, immunological, and virological features with varicella-zoster virus infection of humans. Natural varicella infection was simulated by exposing four SVV-seronegative monkeys to monkeys inoculated intratracheally with SVV, in which viral DNA and RNA persist in multiple tissues for more than 1 year (T. M. White, R. Mahalingam, V. Traina-Dorge, and D. H. Gilden, J. Neurovirol. 8:191-205, 2002). The four naturally exposed monkeys developed mild varicella 10 to 14 days later, and skin scrapings taken at the time of the rash contained SVV DNA. Analysis of multiple ganglia, liver, and lung tissues from the four naturally exposed monkeys sacrificed 6 to 8 weeks after resolution of the rash revealed SVV DNA in ganglia at multiple levels of the neuraxis but not in the lung or liver tissue of any of the four monkeys. This animal model provides an experimental system to gain information about varicella latency with direct relevance to the human disease.
Membrane Association of Lipoprotein Lipase and a cAMP-Binding Ectoprotein in Rat Adipocytes (1994)

cAMP-binding ectoprotein (Gce1) and lipoprotein lipase (LPL) are anchored to plasma membranes of rat adipocytes by glycosylphosphatidylinositol (GPI) moieties as demonstrated by cleavage by bacterial phosphatidylinositol-specific phospholipase C (PI-PLC), reactivity with anti-crossreacting determinant antibodies (anti-CRD), and metabolic labeling with radiolabeled palmitic acid and myo-inositol. Quantitative release from the membrane of LPL and Gce1 requires both lipolytic removal of their GPI anchors and the presence of either 2 M NaCl or 1 mM inositol 1,2-cyclic monophosphate or inositol 1-monophosphate. PI-PLC-cleaved and released LPL or Gce1 reassociates with isolated plasma membranes of rat adipocytes and, less efficiently, with membranes of 3T3 fibroblasts. The specificity of the reassociation is demonstrated (i) by its inhibition after pretreatment of the membranes with trypsin, (ii) by its competition with inositol 1,2-cyclic monophosphate and inositol 1-monophosphate in a concentration-dependent manner, and (iii) by the limited number of binding sites. Enzymic or chemical removal as well as masking with anti-CRD antibodies of the terminal inositol (cyclic) monophosphate moiety of hydrophilic Gce1 and LPL significantly impairs the reassociation. These data suggest that in rat adipocytes GPI-proteins are not readily released from the cell surface upon lipolytic cleavage, but remain associated through a receptor which specifically recognizes the terminal inositol (cyclic) monophosphate epitope of the (G)PI-PLC-cleaved GPI moiety. This interaction may have implications for the regulated membrane release of GPI-proteins and for their possible internalization.
Fraud in the ‘outback’: Capable guardianship in preventing financial crime in regional and remote communities (2011)

The Australian Institute of Criminology previously estimated the cost of fraud in Australia in 2005 to be approximately $8.5b (Rollings 2008). Fraud risks affect all sectors of society extending from those who provide government services, to those who receive benefits, as well as private sector businesses such as primary producers, and those who buy and sell goods and services online. In this paper, the specific risks of financial crime that arise in and subsequently affect those in remote and regional communities in Australia are explored. The risk of fraud is increased because of the difficulties that arise in ensuring adequate levels of ‘capable guardianship’ in non-urban locations which are often disadvantaged in terms of money and knowledge of fraud risks, as well as the ability to avoid them. Examples of recent fraud cases from regional and remote Australia are used to highlight the risks associated with fraud in these places and to indicate where the absence of guardianship may have increased risks. It is concluded that capable guardianship, as a whole, needs to be enhanced outside major cities in order to reduce the level of fraud experienced by government, businesses and individuals each year.
A secreted<i>Salmonella</i>protein induces a proinflammatory response in epithelial cells, which promotes neutrophil migration (2000)

In response to Salmonella typhimurium, the intestinal epithelium generates an intense inflammatory response consisting largely of polymorphonuclear leukocytes (neutrophils, PMN) migrating toward and ultimately across the epithelial monolayer into the intestinal lumen. It has been shown that bacterial-epithelial cell interactions elicit the production of inflammatory regulators that promote transepithelial PMN migration. Although S. typhimurium can enter intestinal epithelial cells, bacterial internalization is not required for the signaling mechanisms that induce PMN movement. Here, we sought to determine which S. typhimurium factors and intestinal epithelial signaling pathways elicit the production of PMN chemoattractants by enterocytes. Our results suggest that S. typhimurium activates a protein kinase C-dependent signal transduction pathway that orchestrates transepithelial PMN movement. We show that the type III effector protein, SipA, is not only necessary but is sufficient to induce this proinflammatory response in epithelial cells. Our results force us to reconsider the long-held view that Salmonella effector proteins must be directly delivered into host cells from bacterial cells.
Ultrasensitive CRISPR-based diagnostic for field-applicable detection of <i>Plasmodium</i> species in symptomatic and asymptomatic malaria (2020)

Asymptomatic carriers of <i>Plasmodium</i> parasites hamper malaria control and eradication. Achieving malaria eradication requires ultrasensitive diagnostics for low parasite density infections (<100 parasites per microliter blood) that work in resource-limited settings (RLS). Sensitive point-of-care diagnostics are also lacking for nonfalciparum malaria, which is characterized by lower density infections and may require additional therapy for radical cure. Molecular methods, such as PCR, have high sensitivity and specificity, but remain high-complexity technologies impractical for RLS. Here we describe a CRISPR-based diagnostic for ultrasensitive detection and differentiation of <i>Plasmodium falciparum</i>, <i>Plasmodium vivax</i>, <i>Plasmodium ovale</i>, and <i>Plasmodium malariae</i>, using the nucleic acid detection platform SHERLOCK (specific high-sensitivity enzymatic reporter unlocking). We present a streamlined, field-applicable, diagnostic comprised of a 10-min SHERLOCK parasite rapid extraction protocol, followed by SHERLOCK for 60 min for <i>Plasmodium</i> species-specific detection via fluorescent or lateral flow strip readout. We optimized one-pot, lyophilized, isothermal assays with a simplified sample preparation method independent of nucleic acid extraction, and showed that these assays are capable of detection below two parasites per microliter blood, a limit of detection suggested by the World Health Organization. Our <i>P. falciparum</i> and <i>P. vivax</i> assays exhibited 100% sensitivity and specificity on clinical samples (5 <i>P. falciparum</i> and 10 <i>P. vivax</i> samples). This work establishes a field-applicable diagnostic for ultrasensitive detection of asymptomatic carriers as well as a rapid point-of-care clinical diagnostic for nonfalciparum malaria species and low parasite density <i>P. falciparum</i> infections.