gebhart/patrepeval huggingface dataset:
Regulation of Neurotoxin Production and Sporulation by a Putative <i>agrBD</i> Signaling System in Proteolytic <i>Clostridium botulinum</i> (2010)

A significant number of genome sequences of Clostridium botulinum and related species have now been determined. In silico analysis of these data revealed the presence of two distinct agr loci (agr-1 and agr-2) in all group I strains, each encoding putative proteins with similarity to AgrB and AgrD of the well-studied Staphylococcus aureus agr quorum sensing system. In S. aureus, a small diffusible autoinducing peptide is generated from AgrD in a membrane-located processing event that requires AgrB. Here the characterization of both agr loci in the group I strain C. botulinum ATCC 3502 and of their homologues in a close relative, Clostridium sporogenes NCIMB 10696, is reported. In C. sporogenes NCIMB 10696, agr-1 and agr-2 appear to form transcriptional units that consist of agrB, agrD, and flanking genes of unknown function. Several of these flanking genes are conserved in Clostridium perfringens. In agreement with their proposed role in quorum sensing, both loci were maximally expressed during late-exponential-phase growth. Modulation of agrB expression in C. sporogenes was achieved using antisense RNA, whereas in C. botulinum, insertional agrD mutants were generated using ClosTron technology. In comparison to the wild-type strains, these strains exhibited drastically reduced sporulation and, for C. botulinum, also reduced production of neurotoxin, suggesting that both phenotypes are controlled by quorum sensing. Interestingly, while agr-1 appeared to control sporulation, agr-2 appeared to regulate neurotoxin formation.
Immune Modulation in Multiple Sclerosis Patients Treated with the Pregnancy Hormone Estriol (2003)

The protective effect of pregnancy on putative Th1-mediated autoimmune diseases, such as multiple sclerosis and rheumatoid arthritis, is associated with a Th1 to Th2 immune shift during pregnancy. The hormone estriol increases during pregnancy and has been shown to ameliorate experimental autoimmune encephalomyelitis and collagen-induced arthritis. In addition, estrogens induce cytokine changes consistent with a Th1 to Th2 shift when administered in vitro to human immune cells and in vivo to mice. In a pilot trial, oral estriol treatment of relapsing remitting multiple sclerosis patients caused significant decreases in enhancing lesions on brain magnetic resonance imaging. Here, the immunomodulatory effects of oral estriol therapy were assessed. PBMCs collected longitudinally during the trial were stimulated with mitogens, recall Ags, and glatiramer acetate. Cytokine profiles of stimulated PBMCs were determined by intracellular cytokine staining (IL-5, IL-10, IL-12 p40, TNF-alpha, and IFN-gamma) and cytometric bead array (IL-2, IL-4, IL-5, IL-10, TNF-alpha, and IFN-gamma). Significantly increased levels of IL-5 and IL-10 and decreased TNF-alpha were observed in stimulated PBMC isolated during estriol treatment. These changes in cytokines correlated with reductions of enhancing lesions on magnetic resonance imaging in relapsing remitting multiple sclerosis. The increase in IL-5 was primarily due to an increase in CD4(+) and CD8(+) T cells, the increase in IL-10 was primarily due to an increase in CD64(+) monocytes/macrophages with some effect in T cells, while the decrease in TNF-alpha was primarily due to a decrease in CD8(+) T cells. Further study of oral estriol therapy is warranted in Th1-mediated autoimmune diseases with known improvement during pregnancy.
Calda sulfocálcica, óleo mineral e extrato de alho na superação da dormência de quivizeiro (2010)

Este trabalho teve por objetivo testar o efeito da calda sulfocálcica (CS), do óleo mineral (OM) e do extrato de alho (EA) na superação da dormência de quivizeiro 'Bruno'. No experimento com calda sulfocálcica foram testados 16 tratamentos em esquema fatorial 4 x 4 (soluções para superação da dormência x posição das gemas). As soluções foram: OM 6%; OM 6% + CS 10%; OM 6% + CS 20% e OM 6% + CS 30%. No experimento com extrato de alho foram testados 28 tratamentos em esquema fatorial 7 x 4 (soluções para superação da dormência x posição das gemas). As soluções foram: testemunha; OM 4%; OM 4% + EA 2%; OM 4% + EA 4%; OM 4% + EA 6%; OM 4% + EA 8% e OM 4% + EA 10%. Em ambos experimentos foram avaliadas as quatro gemas da porção apical dos ramos em quatro avaliações. Foram consideradas gemas brotadas todas as que se encontravam com uma folha visível ou em estádios fenológicos mais avançados. Em ambos experimentos, a gema apical sempre apresentou a maior porcentagem de brotação, formando um gradiente decrescente até as gemas inferiores. A calda sulfocálcica não apresentou efeito na superação da dormência de gemas de quivizeiro, apresentando-se semelhante ao tratamento apenas com óleo mineral. O extrato de alho apresentou efeito na superação da dormência das gemas do quivizeiro. O tratamento com OM 4% + EA 10% foi superior aos demais, mas não diferiu dos tratamentos com OM 4% + EA 6% e OM 4% + EA 8%. Essa superioridade é consequência da maior brotação das gemas laterais inferiores, já que a brotação das gemas apicais foi praticamente a mesma, em média 93,33%. Conclui-se que, para superação da dormência de gemas de quivizeiro 'Bruno', a calda sulfocálcica até a concentração de 30% em combinação com óleo mineral 6% não é eficiente e o extrato de alho na concentração de 10% em combinação com óleo mineral 4% eleva a porcentagem de brotação das gemas laterais, mas não em níveis satisfatórios.
Ammonia reduction with ornithine phenylacetate restores brain eNOS activity via the DDAH-ADMA pathway in bile duct-ligated cirrhotic rats (2011)

Ammonia is central in the pathogenesis of hepatic encephalopathy, which is associated with dysfunction of the nitric oxide (NO) signaling pathway. Ornithine phenylacetate (OP) reduces hyperammonemia and brain water in cirrhotic animals. This study aimed to determine whether endothelial NO synthase activity is altered in the brain of cirrhotic animals, whether this is associated with changes in the endogenous inhibitor, asymmetric-dimethylarginine (ADMA) and its regulating enzyme, dimethylarginine-dimethylaminohydrolase (DDAH-1), and whether these abnormalities are restored by ammonia reduction using OP. Sprague-Dawley rats were studied 4-wk after bile duct ligation (BDL) (n = 16) or sham operation (n = 8) and treated with placebo or OP (0.6 g/kg). Arterial ammonia, brain water, TNF-α, plasma, and brain ADMA were measured using standard techniques. NOS activity was measured radiometrically, and protein expression for NOS enzymes, ADMA, DDAH-1, 4-hydroxynonenol ((4)HNE), and NADPH oxidase (NOX)-1 were measured by Western blotting. BDL significantly increased arterial ammonia (P < 0.0001), brain water (P < 0.05), and brain TNF-α (P < 0.01). These were reduced significantly by OP treatment. The estimated eNOS component of constitutive NOS activity was significantly lower (P < 0.05) in BDL rat, and this was significantly attenuated in OP-treated animals. Brain ADMA levels were significantly higher and brain DDAH-1 significantly lower in BDL compared with sham (P < 0.01) and restored toward normal following treatment with OP. Brain (4)HNE and NOX-1 protein expression were significantly increased in BDL rat brain, which were significantly decreased following OP administration. We show a marked abnormality of NO regulation in cirrhotic rat brains, which can be restored by reduction in ammonia concentration using OP.
Mono-crystalline silicon strips grown by liquid phase epitaxy for photovoltaic applications (2010)

We have studied epitaxial lateral overgrowth of p-type silicon by Liquid Phase Epitaxy (LPE) on n-type (111) silicon substrates from a Si/In melt. The substrate had a silicon dioxide mask with a set of parallel opening windows for seed lines which were aligned along a [211]direction. The growth parameters, morphology and electrical properties of the grown crystal were studied. Two single crystalline silicon strips were formed on one single seed line, one strip on either side of the seed line, demonstrating that silicon is more likely to deposit near the interface between the silicon and the oxide. All facets of the strips are {111} planes and therefore the bottom surface has a 4 degree angle with the substrate, providing convenience for the epitaxial layer to be peeled off from the substrate and used for potential photovoltaic applications. Monte Carlo random walk model is used to simulate the epitaxial growth of the mono-crystalline strips.
A signaling protocol for complex multimedia services (1991)

The author introduces a signaling protocol for user applications that invokes multimedia services provided by the EXPANSE research prototype, a broadband ISDN testbed. A generic framework that flexibly accommodates a wide variety of services involving multiple parties with heterogeneous terminals is described. The author describes the generic services supported, introduces the EXPANSE call model, discusses syntax and message flow procedures, and relates EXPANSE signaling to the ISDN signaling control part (ISCP) and long-term broadband ISDN signaling work currently under study by CCITT.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Regulation of Protein Quality Control by UBE4B and LSD1 through p53-Mediated Transcription (2015)

Protein quality control is essential for clearing misfolded and aggregated proteins from the cell, and its failure is associated with many neurodegenerative disorders. Here, we identify two genes, ufd-2 and spr-5, that when inactivated, synergistically and robustly suppress neurotoxicity associated with misfolded proteins in Caenorhabditis elegans. Loss of human orthologs ubiquitination factor E4 B (UBE4B) and lysine-specific demethylase 1 (LSD1), respectively encoding a ubiquitin ligase and a lysine-specific demethylase, promotes the clearance of misfolded proteins in mammalian cells by activating both proteasomal and autophagic degradation machineries. An unbiased search in this pathway reveals a downstream effector as the transcription factor p53, a shared substrate of UBE4B and LSD1 that functions as a key regulator of protein quality control to protect against proteotoxicity. These studies identify a new protein quality control pathway via regulation of transcription factors and point to the augmentation of protein quality control as a wide-spectrum antiproteotoxicity strategy.
Context-Aware Channel Coordination for DSRC (2008)

Vehicular communication could be the much anticipated breakthrough against the unabated fatal and near fatal accidents that continue to threaten the public safety on our roads. The same technology is also expected to concurrently support a range of non-safety applications including real-time traffic information, mobile entertainment, and access to the Internet. The standard has specified an explicit multi-channel structure whereby safety and non-safety transmissions will occur at different channels. Consequently, a vehicle with a conventional single-radio transceiver will need to continuously switch between the safety and the non-safety modes of operation. The interval spent in the safety mode (safety interval) at each cycle is a critical parameter that directly limits the availability of the technology for commercial use. Using simulation, we show that the safety interval required to satisfy the reliability of safety applications is a function of traffic density on the road. Given that in most roads traffic density is expected to vary during the day, we propose dynamic adjustment of the safety interval based on the traffic context. To further motivate the concept of traffic aware vehicular communications, we evaluate the performance of three dynamic channel coordination algorithms using empirical traffic data collected from the roads around the city of Sydney, Australia. A key finding is that, the time-of-day is an effective context that can prevent a vehicular radio from keep running in the safety mode unnecessarily, thereby enhancing the commercial opportunity of the technology. We further demonstrate that the use of the location context can dramatically improve the performance of the basic time-of-day algorithms.
A Herpes Simplex Virus Type 1 Human Asymptomatic CD8<sup>+</sup>T-Cell Epitopes-Based Vaccine Protects Against Ocular Herpes in a “Humanized” HLA Transgenic Rabbit Model (2015)

The results of this preclinical trial support the screening strategy used to select the HSV-1 ASYMP CD8+ T-cell epitopes, emphasize their valuable immunogenic and protective efficacy against ocular herpes, and provide a prototype vaccine formulation that may be highly efficacious for preventing ocular herpes in humans.
Quantification of the Composition Dynamics of a Maize Root-associated Simplified Bacterial Community and Evaluation of Its Biological Control Effect (2018)

Besides analyzing the composition and dynamics of microbial communities, plant microbiome research aims to understanding the mechanism of plant microbiota assembly and their biological functions. Here, we describe procedures to investigate the role of bacterial interspecies interactions in root microbiome assembly and the beneficial effects of the root microbiota on hosts by using a maize root-associated simplified seven-species (<i>Stenotrophomonas maltophilia</i>, <i>Ochrobactrum pituitosum</i>, <i>Curtobacterium pusillum</i>, <i>Enterobacter cloacae</i>, <i>Chryseobacterium indologenes</i>, <i>Herbaspirillum frisingense</i> and <i>Pseudomonas putida</i>) synthetic bacterial community described in our previous work. Surface-sterilized maize seeds were grown in a gnotobiotic system based on double-tube growth chambers after being soaked in suspensions containing multiple species of bacteria. The dynamics of the composition of the bacterial communities colonized on maize roots were tracked by a culture-dependent method with a selective medium for each of the seven strains. The impact of bacterial interactions on the community assembly was evaluated by monitoring the changes of community structure. The plant-protection effects of the simplified seven-species community were assessed by quantifying (1) the growth of a fungal phytopathogen, <i>Fusarium verticillioides</i> on the surfaces of the seeds and (2) the severity of seedling blight disease the fungus causes, in the presence and absence of the bacterial community. Our protocol will serve as useful guidance for studying plant-microbial community interactions under the laboratory conditions.
Myrmics: Scalable, Dependency-aware Task Scheduling on Heterogeneous Manycores (2016)

Task-based programming models have become very popular, as they offer an attractive solution to parallelize serial application code with task and data annotations. They usually depend on a runtime system that schedules the tasks to multiple cores in parallel while resolving any data hazards. However, existing runtime system implementations are not ready to scale well on emerging manycore processors, as they often rely on centralized structures and/or locks on shared structures in a cache-coherent memory. We propose design choices, policies and mechanisms to enhance runtime system scalability for single-chip processors with hundreds of cores. Based on these concepts, we create and evaluate Myrmics, a runtime system for a dependency-aware, task-based programming model on a heterogeneous hardware prototype platform that emulates a single-chip processor of 8 latency-optimized and 512 throughput-optimized CPUs. We find that Myrmics scales successfully to hundreds of cores. Compared to MPI versions of the same benchmarks with hand-tuned message passing, Myrmics achieves similar scalability with a 10-30% performance overhead, but with less programming effort. We analyze the scalability of the runtime system in detail and identify the key factors that contribute to it.
Transforming growth factor‐β2 modulates synaptic efficacy and plasticity and induces phosphorylation of CREB in hippocampal neurons (2006)

Transforming growth factor-betas (TGF-betas) are widely expressed and play roles as multifunctional growth factors and regulators of key events in development, disease, and repair. However, it is not known whether TGF-betas affect the plasticity of hippocampal neurons. As a first step to address this issue, we examined whether TGF-beta2 modulated the electrophysiological and biochemical properties of cultured hippocampal neurons. We found that prolonged 24 h treatment with TGF-beta2 induced facilitation of evoked postsynaptic currents (ePSCs). This facilitation was associated with a decrease in short-term synaptic depression of ePSCs and increases in both the amplitude and frequency of spontaneous miniature postsynaptic currents (mPSCs). The long-term changes of ePSCs and mPSCs may be associated with cAMP response element-binding protein (CREB), which has been previously implicated in long-term potentiation. Immunofluorescence techniques and Western blot analysis both revealed that TGF-beta2 enhanced the phosphorylation of CREB. Together, these results suggest that TGF-beta2 may play a role in the cascade of events underlying long-term synaptic facilitation in hippocampus, and that CREB may be an important mediator of these effects.
Security and privacy challenges in industrial internet of things (2015)

Today, embedded, mobile, and cyberphysical systems are ubiquitous and used in many applications, from industrial control systems, modern vehicles, to critical infrastructure. Current trends and initiatives, such as "Industrie 4.0" and Internet of Things (IoT), promise innovative business models and novel user experiences through strong connectivity and effective use of next generation of embedded devices. These systems generate, process, and exchange vast amounts of security-critical and privacy-sensitive data, which makes them attractive targets of attacks. Cyberattacks on IoT systems are very critical since they may cause physical damage and even threaten human lives. The complexity of these systems and the potential impact of cyberattacks bring upon new threats.
The perception of three-dimensional cast-shadow structure is dependent on visual awareness (2014)

In the present study we examined whether the perception of depth from cast shadows is dependent on visual awareness using continuous flash suppression (CFS). As a direct measure of how the visual system infers depth from cast shadows, we examined the cast-shadow motion illusion originally reported by Kersten, Knill, Mamassian, and Bulthoff (1996), in which a moving cast shadow induces illusory motion in depth in a physically stationary object. In Experiment 1, we used a disparity defined probe to determine the stereo motion speed required to match the cast-shadow motion illusion for different cast shadow speeds (0°/s-1.6°/s) and different lighting directions. We found that configurations implying light from above produce more compelling illusory effects. We also found that increasing shadow speed monotonically increased the stereo motion speed required to match the illusory motion, which suggests that quantitative depth can be derived from cast shadows when they are in motion. In Experiment 2, we used CFS to suppress the cast shadow from visual awareness. Visual suppression of the cast shadow from awareness greatly diminished the perception of illusory motion in depth. In Experiment 3 we confirmed that while CFS suppresses the cast-shadow motion from awareness, it continues to be processed by the visual system sufficient to generate a significant motion after effect. The results of the present study suggest that cast shadows can greatly contribute to the perception of scene depth structure, through a process that is dependent on the conscious awareness of the cast shadow.
Chasing cardiac physiology and pathology down the CaMKII cascade (2015)

Calcium dynamics is central in cardiac physiology, as the key event leading to the excitation-contraction coupling (ECC) and relaxation processes. The primary function of Ca(2+) in the heart is the control of mechanical activity developed by the myofibril contractile apparatus. This key role of Ca(2+) signaling explains the subtle and critical control of important events of ECC and relaxation, such as Ca(2+) influx and SR Ca(2+) release and uptake. The multifunctional Ca(2+)-calmodulin-dependent protein kinase II (CaMKII) is a signaling molecule that regulates a diverse array of proteins involved not only in ECC and relaxation but also in cell death, transcriptional activation of hypertrophy, inflammation, and arrhythmias. CaMKII activity is triggered by an increase in intracellular Ca(2+) levels. This activity can be sustained, creating molecular memory after the decline in Ca(2+) concentration, by autophosphorylation of the enzyme, as well as by oxidation, glycosylation, and nitrosylation at different sites of the regulatory domain of the kinase. CaMKII activity is enhanced in several cardiac diseases, altering the signaling pathways by which CaMKII regulates the different fundamental proteins involved in functional and transcriptional cardiac processes. Dysregulation of these pathways constitutes a central mechanism of various cardiac disease phenomena, like apoptosis and necrosis during ischemia/reperfusion injury, digitalis exposure, post-acidosis and heart failure arrhythmias, or cardiac hypertrophy. Here we summarize significant aspects of the molecular physiology of CaMKII and provide a conceptual framework for understanding the role of the CaMKII cascade on Ca(2+) regulation and dysregulation in cardiac health and disease.
Synthesis and structures of neutral and cationic rac-(ethylenebis(tetrahydroindenyl))zirconium(IV) benzyl complexes (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and structures of neutral and cationic rac-(ethylenebis(tetrahydroindenyl))zirconium(IV) benzyl complexesRichard F. Jordan, Robert E. LaPointe, Norman Baenziger, and Garry D. HinchCite this: Organometallics 1990, 9, 5, 1539–1545Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/om00119a028https://doi.org/10.1021/om00119a028research-articleACS PublicationsRequest reuse permissionsArticle Views267Altmetric-Citations86LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts