gebhart/patrepeval huggingface dataset:
Comparative Analysis of <i>Salmonella</i> Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut (2014)

The Salmonella genus comprises a group of pathogens associated with illnesses ranging from gastroenteritis to typhoid fever. We performed an in silico analysis of comparatively reannotated Salmonella genomes to identify genomic signatures indicative of disease potential. By removing numerous annotation inconsistencies and inaccuracies, the process of reannotation identified a network of 469 genes involved in central anaerobic metabolism, which was intact in genomes of gastrointestinal pathogens but degrading in genomes of extraintestinal pathogens. This large network contained pathways that enable gastrointestinal pathogens to utilize inflammation-derived nutrients as well as many of the biochemical reactions used for the enrichment and biochemical discrimination of Salmonella serovars. Thus, comparative genome analysis identifies a metabolic network that provides clues about the strategies for nutrient acquisition and utilization that are characteristic of gastrointestinal pathogens. IMPORTANCE While some Salmonella serovars cause infections that remain localized to the gut, others disseminate throughout the body. Here, we compared Salmonella genomes to identify characteristics that distinguish gastrointestinal from extraintestinal pathogens. We identified a large metabolic network that is functional in gastrointestinal pathogens but decaying in extraintestinal pathogens. While taxonomists have used traits from this network empirically for many decades for the enrichment and biochemical discrimination of Salmonella serovars, our findings suggest that it is part of a "business plan" for growth in the inflamed gastrointestinal tract. By identifying a large metabolic network characteristic of Salmonella serovars associated with gastroenteritis, our in silico analysis provides a blueprint for potential strategies to utilize inflammation-derived nutrients and edge out competing gut microbes.
Fluid power systems and technology 1997 collected papers : presented at 1997 ASME International Mechanical Engineering Congress and Exposition, November 16-21, 1997, Dallas, Texas (1997)

The 31 papers are concerned with such areas as pumps and motors, hydraulic pipes, hoses and fluid, pneumatic and electric drives, hydraulic and electrohydraulic systems, and intelligent techniques in fluid power systems. Among the topics are a real- time adaptive control algorithm for a VVVF hydraul
A Unified Neural Network Approach for Estimating Travel Time and Distance for a Taxi Trip (2017)

In building intelligent transportation systems such as taxi or rideshare services, accurate prediction of travel time and distance is crucial for customer experience and resource management. Using the NYC taxi dataset, which contains taxi trips data collected from GPS-enabled taxis [23], this paper investigates the use of deep neural networks to jointly predict taxi trip time and distance. We propose a model, called ST-NN (Spatio-Temporal Neural Network), which first predicts the travel distance between an origin and a destination GPS coordinate, then combines this prediction with the time of day to predict the travel time. The beauty of ST-NN is that it uses only the raw trips data without requiring further feature engineering and provides a joint estimate of travel time and distance. We compare the performance of ST-NN to that of state-of-the-art travel time estimation methods, and we observe that the proposed approach generalizes better than state-of-the-art methods. We show that ST-NN approach significantly reduces the mean absolute error for both predicted travel time and distance, about 17% for travel time prediction. We also observe that the proposed approach is more robust to outliers present in the dataset by testing the performance of ST-NN on the datasets with and without outliers.
Hypoxia response elements. (1997)

Hypoxia-inducible factor-1 (HIF-1) has been shown to mediate the transcriptional activation of its target genes in response to oxygen concentration, most likely via a pathway involving a specific oxygen sensor. Molecular cloning of HIF-1 has shown that this widely expressed, DNA binding transcription factor is a heterodimer of two proteins, HIF-1 alpha and HIF-1 beta. A major control of HIF-1 activity by oxygen tension is achieved by changes in the level of the HIF-1 alpha subunit, which complexes with the constitutively expressed HIF-1 beta subunit. Such changes in HIF-1 alpha abundance occur via regulated stability, probably involving proteolysis, rather than at the level of transcription or translation. Further analysis has shown the existence of two separate regulatory domains in the C-terminus of the alpha subunit. Thus, a mechanism of oxygen-regulated HIF-1 activation is proposed, which involves the operation of one inducible domain being amplified by changes in protein level conferred by a second regulatory domain. Evidence for a critical role of HIF-1 in the response of diverse target genes involved in cellular growth and metabolism comes from studies on cultured, mutant mouse cells that lack a functional HIF-1 beta subunit. Furthermore, studies on tumor xenografts derived from the mutant and wild-type cells show that HIF-1 is activated in vivo, and has major effects on gene expression in response to tumor hypoxia. Thus, HIF-1 is a critical component of the oxygen-signaling pathway, and is a prime candidate regulator molecule for the role of coordinating vascular oxygen supply with cellular growth and energy metabolism.
Microphone array calibration for robust adaptive processing (1995)

Significant interest exists in the use of microphone arrays for enhancing audio and speech signals. Various combinations of fixed array, adaptive array, time-domain and frequency domain processing approaches are being considered. Any well-designed sensor array processing system needs (either explicitly or implicitly) accurate modeling or measurement of the sensor responses to allow robust and effective signal enhancement. The article explores the limits that microphone array calibration places on robust speech enhancement. Modelled microphone array data is used to examine the effect of variations in array parameters on processing algorithms.
ROOTCAP STRUCTURE IN WILD TYPE AND IN A STARCHLESS MUTANT OF ARABIDOPSIS (1989)

Rootcaps of the wild type (WT) and of a starchless, gravitropic mutant (TC7) of Arabidopsis thaliana L. were examined by electron microscopy to identify cellular polarities with respect to gravity. In columella cells, nuclei are located proximally, and the nuclear envelope is continuous with endoplasmic reticulum (ER) that is in turn connected to nearby plasmodesmata. Impregnation of ER with osmium ferricyanide revealed numerous contacts between columella plastids and ER in both genotypes. ER is present mostly in the outer regions of the columella protoplast except in older columella cells that are developing into peripheral cells. In vertical roots, only columella cells that are intermediate in development (story 2 cells) have a higher surface density (S) of ER in the distal compared to proximal regions of the cell. The distal but not the proximal S of the ER is constant throughout columella development. Plastids are less sedimented in TC7 columella cells compared to those of the WT. It is hypothesized that plastid contact with the ER plays a role in gravity perception in both genotypes.
Direct extraction of the mean particle size from a digital hologram (2006)

Digital holography, which consists of both acquiring the hologram image in a digital camera and numerically reconstructing the information, offers new and faster ways to make the most of a hologram. We describe a new method to determine the rough size of particles in an in-line hologram. This method relies on a property that is specific to interference patterns in Fresnel holograms: Self-correlation of a hologram provides access to size information. The proposed method is both simple and fast and gives results with acceptable precision. It suppresses all the problems related to the numerical depth of focus when large depth volumes are analyzed.
Inability to sustain intraphagolysosomal killing of<i><scp>Staphylococcus aureus</scp></i>predisposes to bacterial persistence in macrophages (2015)

Macrophages are critical effectors of the early innate response to bacteria in tissues. Phagocytosis and killing of bacteria are interrelated functions essential for bacterial clearance but the rate-limiting step when macrophages are challenged with large numbers of the major medical pathogen Staphylococcus aureus is unknown. We show that macrophages have a finite capacity for intracellular killing and fail to match sustained phagocytosis with sustained microbial killing when exposed to large inocula of S. aureus (Newman, SH1000 and USA300 strains). S. aureus ingestion by macrophages is associated with a rapid decline in bacterial viability immediately after phagocytosis. However, not all bacteria are killed in the phagolysosome, and we demonstrate reduced acidification of the phagolysosome, associated with failure of phagolysosomal maturation and reduced activation of cathepsin D. This results in accumulation of viable intracellular bacteria in macrophages. We show macrophages fail to engage apoptosis-associated bacterial killing. Ultittop mately macrophages with viable bacteria undergo cell lysis, and viable bacteria are released and can be internalized by other macrophages. We show that cycles of lysis and reuptake maintain a pool of viable intracellular bacteria over time when killing is overwhelmed and demonstrate intracellular persistence in alveolar macrophages in the lungs in a murine model.
Nicotine and Pemphigus (2000)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Dermatology journal
Color impression factor: an image understanding method for outdoor mobile robots (2002)

The color vision in the outdoor environment has two problems. The first is the hue shift of the object under the changes of the season, weather, the hour and the view position. The second is the hue shift of the object between in the sunny place and in the shaded place. We propose the color impression factor to memory the hue of the object. The color impression factor is defined as R-B. It is the function of the sunlight condition (sunny/shaded) and the hour. We show this factor is useful to discriminate objects from the shadows in the asphalt paved road-yellow tactile blocks from the asphalt paved road.
Hyperbolic Metamaterials: Hyperbolic Metamaterials and Metasurfaces: Fundamentals and Applications (Advanced Optical Materials 14/2019) (2019)

Hyperbolic media are very attractive for the application of light field manipulation due to their unique optical properties. In article number 1801616, Ting Xu and coworkers comprehensively discuss the working principle, realization and practical applications of two types of hyperbolic media, including three-dimensional bulk hyperbolic metamaterials and two-dimensional planar hyperbolic metasurfaces.
A novel single-fluorophore-based ratiometric fluorescent probe for direct detection of isocyanates in air (2017)

A ratiometric fluorescent probe based on anthracene carboximide was developed for direct detection of isocyanates in air. The sensing mechanism was illustrated to be variation in the photophysical properties caused by the nucleophilic reaction of the probe molecule. A number of isocyanates were conveniently detected by a test paper.
Potent Immunoregulatory Effects of<i>Salmonella typhi</i>Flagella on Antigenic Stimulation of Human Peripheral Blood Mononuclear Cells (1999)

A key function of monocytes/macrophages (Mphi) is to present antigens to T cells. However, upon interaction with bacteria, Mphi lose their ability to effectively present soluble antigens. This functional loss was associated with alterations in the expression of adhesion molecules and CD14 and a reduction in the uptake of soluble antigen. Recently, we have demonstrated that Salmonella typhi flagella (STF) markedly decrease CD14 expression and are potent inducers of proinflammatory cytokine production by human peripheral blood mononuclear cells (hPBMC). In order to determine whether S. typhi and soluble STF also alter the ability of Mphi to activate T cells to proliferate to antigens and mitogens, hPBMC were cultured in the presence of tetanus toxoid (TT) or phytohemagglutinin (PHA) and either killed whole-cell S. typhi or purified STF protein. Both whole-cell S. typhi and STF suppressed proliferation to PHA and TT. This decreased proliferation was not a result of increased Mphi production of nitric oxide, prostaglandin E2, or oxygen radicals or the release of interleukin-1beta, tumor necrosis factor alpha, interleukin-6, or interleukin-10 following exposure to STF. However, the ability to take up soluble antigen, as determined by fluorescein isothiocyanate-labeled dextran uptake, was reduced in cells cultured with STF. Moreover, there was a dramatic reduction in the expression of CD54 on Mphi after exposure to STF. These results indicate that whole-cell S. typhi and STF have the ability to alter in vitro proliferation to soluble antigens and mitogens by affecting Mphi function.
Motoneurons deprived of trophic support <i>in vitro</i> require new gene expression to undergo programmed cell death (1994)

During normal development, large numbers of neurons die by programmed cell death. This phenomena has been extensively studied in the lateral motor column of chick embryos, where approximately 50% of the motoneurons that are initially produced, subsequently die due in part to competition for a limited supply of target-derived trophic support. Inhibitors of RNA and protein synthesis block this cell loss in vivo, indicating a requirement for new gene expression (Oppenheim et al., 1990). Prior to their commitment to death, motoneurons can be isolated as a relatively pure population from chick spinal cord for in vitro study. Cells plated with muscle extract, a potent source of target-derived trophic support, survive, and have large, phase-bright cell bodies and extensive neurite outgrowth. In contrast, motoneurons cultured in the absence of muscle extract die within 48 h. This death can be blocked by the RNA synthesis inhibitor actinomycin D, at the time when the cells become committed to die, suggesting that new gene expression is required for cell death. DNA fragmentation and nuclear condensation indicate that some of these cells die by apoptosis. Therefore, it appears that many aspects of motoneuron development observed in vivo can be reconstituted in vitro. These cultures can be used as a model system for studying neuronal death and may contribute to an understanding of the molecular mechanisms that mediate programmed cell death during neuronal development.
Thermally stable, sub-nanometer equivalent oxide thickness gate stack for gate-first In0.53Ga0.47As metal-oxide-semiconductor field-effect-transistors (2012)

Metal-oxide-semiconductor (MOS) capacitors were fabricated by depositing composite 2 nm HfO2/1 nm Al2O3/1 nm a-Si gate stacks on p-In0.53Ga0.47As/InP (001) substrates. Thanks to the presence of the Al2O3 barrier layer, a minimum amount of the a-Si passivating layer is oxidized during the whole fabrication process. The capacitors exhibit excellent electrical characteristics with scaled equivalent oxide thickness (EOT) of 0.89 nm and mid-gap interface state density of 5 × 1011 eV−1 cm−2 upon post-metallization anneal up to 550 °C. Gate-first, self-aligned MOS field-effect-transistors were fabricated with a similar 5 nm HfO2/1 nm Al2O3/1 nm a-Si gate stack and raised source and drain (600 °C for 30 min). Owing to the excellent thermal stability of the stack, no degradation of the gate stack/semiconductor interface is observed, as demonstrated by the excellent capacitance vs voltage characteristics and the good mobility values (peak at 1030 cm2 V−1 s−1 and 740 cm2 V−1 s−1 at carrier density of 6.5 × 1012 cm−2) for a 1.3 nm EOT.
Interaction of Tea Catechins with Lipid Bilayers Investigated with Liposome Systems (1999)

Interaction of tea catechins with lipid bilayers was investigated with liposome systems, which enabled us to separate liposomes from the external medium by centrifugation. We found that epicatechin gallate had the highest affinity for lipid bilayers, followed by epigallocatechin gallate, epicatechin, and epigallocatechin. Epicatechin gallate and epigallocatechin gallate in the surface of lipid bilayer perturbed the membrane structure.
Integration of Internal and External Clock Synchronization by the Combination of Clock-State and Clock-Rate Correction in Fault-Tolerant Distributed Systems (2005)

This paper proposes the integration of internal and external clock synchronization by a combination of a fault-tolerant distributed algorithm for clock state correction with a central algorithm for clock rate correction. By means of hardware and simulation experiments it is shown that this combination improves the precision of the global time base in a distributed single cluster system while reducing the need for high-quality oscillators. Simulation results have shown that the rate-correction algorithm contributes not only in the internal clock synchronization of a single cluster system, but it can be used for external clock synchronization of a multi-cluster system with a reference clock. Therefore, deployment of the rate-correction algorithm integrates internal and external clock synchronization in one mechanism. Experimental results show that a failure in the clock rate correction does not hinder the distributed fault-tolerant clock state synchronization algorithm, since the state correction operates independently from the rate correction. The paper introduces new algorithms and presents experimental results on the achieved improvements in the precision measured in a time-triggered system. Results of simulation experiments of the new algorithms in single-cluster and multi-cluster configurations are also presented.
Universal tunneling behavior in technologically relevant P/N junction diodes (2004)

Band-to-band tunneling was studied in ion-implanted P/N junction diodes with profiles representative of present and future silicon complementary metal–oxide–silicon (CMOS) field effect transistors. Measurements were done over a wide range of temperatures and implant parameters. Profile parameters were derived from analysis of capacitance versus voltage characteristics, and compared to secondary-ion mass spectroscopy analysis. When the tunneling current was plotted against the effective tunneling distance (tunneling distance corrected for band curvature) a quasi-universal exponential reduction of tunneling current versus, tunneling distance was found with an attenuation length of 0.38 nm, corresponding to a tunneling effective mass of 0.29 times the free electron mass (m0), and an extrapolated tunneling current at zero tunnel distance of 5.3×107 A/cm2 at 300 K. These results are directly applicable for predicting drain to substrate currents in CMOS transistors on bulk silicon, and body currents in CMOS transistors in silicon-on-insulator.
Correction: Systematic Analysis of Immune Infiltrates in High-Grade Serous Ovarian Cancer Reveals CD20, FoxP3 and TIA-1 as Positive Prognostic Factors (2013)

Background: Tumor-infiltrating T cells are associated with survival in epithelial ovarian cancer (EOC), but their functional status is poorly understood, especially relative to the different risk categories and histological subtypes of EOC.
Designing Cytokine Variants by Phage-Display (2005)

Cytokines are important mediators of many cellular functions including coordination of the immune system and regulation of regenerative processes. Therefore, cytokines can be exploited for therapeutic strategies. Cytokines can be altered in a way that their biologic activity is enhanced or antagonized. This can be accomplished by changing the interaction of cytokines with their cognate cytokine receptor complexes. Therefore, many research groups tried to design cytokines, which bind with higher affinity to their receptors. Alternatively, cytokine variants have been created which do bind to their receptors but do not elicit a signal. Such strategies have been followed using high throughput techniques like error-prone polymerase chain reaction and phage display. Designer cytokines can be used to specifically inhibit cytokine functions. Moreover, peptides have been generated with the help of phage display techniques, which exhibit cytokine activity. Surprisingly, such mimetic peptides do not show any sequence similarity to the parental cytokines. Such peptide mimetics can be used as lead structures for the generation of non-peptidic chemical compounds with cytokine activity.
Design and implementation of an OGSI-compliant grid broker service (2004)

Grid computing promises the ability to share geographically and organizationally distributed resources to increase effective computational power and resource utilization. However, for the Grid computing to be successful, it is very important to provide middleware services that assist Grid users to easily interact with Grid environments. In this paper, we have designed and implemented a new general-purpose OGSI-compliant Grid resource broker service to hide the underlying complexity of the Grid resources from Grid users and to meet not only Grid user requirements but also resource owner policies. It focuses on discovering and scheduling dynamic resources scattered across multiple organizations. Furthermore, it can be integrated with various scheduling services. We also present experimental results and demonstrate the effectiveness of our Grid broker service.
Enhancement of photocatalytic performance via a P3HT-g-C<sub>3</sub>N<sub>4</sub> heterojunction (2014)

Schematic illustration of charge separation and photocatalytic processes over <italic>g</italic>-C<sub>3</sub>N<sub>4</sub> and P3HT-<italic>g</italic>-C<sub>3</sub>N<sub>4</sub> photocatalysts under visible light irradiation.
Aloeresin I, an Anti-Inflammatory 5-Methylchromone from Cape Aloe (2005)

A new diglucoside having a 5-methylchromone moiety was isolated from a commercial sample of Cape aloe, the dried exudate from Aloe ferox Miller, and named aloeresin I. Its structure was established as 1 on the basis of spectral and chemical evidence. Aloeresin I (1) (1 micromol/cm2) reduces in vivo the oedematous response (39 %) induced by Croton oil in the mouse ear with the same potency as aloesin, one of the most abundant Cape aloe constituents, and to a higher extent than aloeresin H (2). Indomethacin (0.3 micromol/cm2), the reference anti-inflammatory compound, provokes 61 % oedema inhibition.