gebhart/patrepeval huggingface dataset:
Chondroitin Sulfates Are Required for Fibroblast Growth Factor-2-Dependent Proliferation and Maintenance in Neural Stem Cells and for Epidermal Growth Factor-Dependent Migration of Their Progeny (2010)

The neural stem cell niche of the embryonic and adult forebrain is rich in chondroitin sulfate glycosaminoglycans (CS-GAGs) that represent complex linear carbohydrate structures on the cell surface of neural stem/progenitor cells or in their intimate environment. We reported earlier that the removal of CS-GAGs with the bacterial enzyme chondroitinase ABC (ChABC) reduced neural stem/progenitor cell proliferation and self-renewal, whereas this treatment favored astroglia formation at the expense of neurogenesis. Here, we studied the consequences of CS-deglycanation further and revealed that CS-GAGs are selectively required for neurosphere formation, proliferation, and self-renewal of embryonic cortical neural stem/progenitor cells in response to fibroblast growth factor (FGF)-2. Consistently, the FGF-2-dependent activation of the MAPKinase in neural stem/progenitor cells was diminished after ChABC treatment, but unaltered after epidermal growth factor (EGF) stimulation. Upon EGF treatment, fewer radial glia were brain lipid-binding protein (BLBP)-positive, whereas more were glutamate aspartate transporter (GLAST)-positive after CS-GAG removal. Only in this latter situation, GLAST-positive radial glia cells extended processes that supported neuronal migration from differentiating neurospheres. CS-deglycanation also selectively increased astrocyte numbers and their migration in response to EGF. Thus, our approach revealed that CS-GAGs are essential for FGF-2-mediated proliferation and maintenance of neuron-generating neural stem/progenitor cells. Simultaneously, CS-GAGs act as a brake on the EGF-dependent maturation, migration, and gliogenesis of neural stem/progenitor cells. We conclude that neural stem/progenitor cell subpopulations reside in neurospheres that are distinguishable by their responsiveness to FGF-2 and EGF which is differentially regulated by CS-carbohydrate structures.
Inhibition of Vascular Permeability Increase in Mice (1988)

Effects of glucocorticoids on IgE antibody-mediated 48-hour homologous passive cutaneous anaphylaxis (PCA) and skin reactions caused by mediator releasers and vascular permeability increasing factors were investigated comparatively. Both PCA and skin reactions were evoked in the mouse ear and these reactions were quantitatively evaluated by measuring the amount of dye extravasated into the ear. The glucocorticoids hydrocortisone, prednisolone and dexamethasone inhibited the PCA significantly. The maximum inhibitory effects of these glucocorticoids were obtained when administered 8 h prior to the antigenic challenge. Dexamethasone significantly inhibited the skin reactions caused by compound 48/80, Ca ionophore A 23187 and hypotonic salt solution. Dexamethasone also significantly inhibited the skin reactions caused by histamine, serotonin, platelet-activating factor, leukotrienes C4 and D4, and bradykinin. The maximum inhibitory effects of dexamethasone on these skin reactions were observed when administered 12-6 h before. These results support the previous observations that glucocorticoids inhibit the increase of vascular permeability caused by various stimuli, and indicate that the inhibition of vascular permeability increase contributes at least in part to the inhibitory effects on the PCA and the mediator releaser-induced skin reactions. Furthermore, the inhibition of vascular permeability increase by glucocorticoids might play an important role in their anti-allergic actions.
Bounding the Number of Self-Blocking Occurrences of SIRAP (2010)

This paper presents a new schedulability analysis for hierarchically scheduled real-time systems executing on a single processor using SIRAP, a synchronization protocol for inter subsystem task synchronization. We show that it is possible to bound the number of self-blocking occurrences that should be taken into consideration in the schedulability analysis of subsystems. Correspondingly, we present two novel schedulability analysis approaches with proof of correctness for SIRAP. An evaluation suggests that this new schedulability analysis can decrease the analytical subsystem utilization significantly.
Restructuring multi-level networks by using function approximations (2003)

In Alzheimer's disease (AD), Aβ deposits form slowly, several decades before further pathological events trigger neurodegeneration and dementia. However, a substantial proportion of affected individuals remains non-demented despite AD pathology, raising questions about the underlying factors that determine the transition to clinical disease. Here, we emphasize the critical function of resilience and resistance factors, which we extend beyond the concept of cognitive reserve to include the glial, immune, and vascular system. We review the evidence and use the metaphor of "tipping points" to illustrate how gradually forming AD neuropathology in the preclinical stage can transition to dementia once adaptive functions of the glial, immune, and vascular system are lost and self-reinforcing pathological cascades are unleashed. Thus, we propose an expanded framework for pathomechanistic research that focuses on tipping points and non-neuronal resilience mechanisms, which may represent previously untapped therapeutic targets in preclinical AD.
<i>Haemophilus influenzae</i>and<i>Vibrio cholerae</i>genes for<i>mutH</i>are able to fully complement a<i>mutH</i>defect in<i>Escherichia coli</i> (2002)

MutH, MutL and MutS are essential components of the mismatch repair system in Escherichia coli. Whereas mutS and mutL genes are found in most organisms, the mutH gene is limited to some proteobacteria. We show here that the cloned genes of MutH from Vibrio cholerae and Haemophilus influenzae are able to fully complement a mutH defect in E. coli. Moreover, the purified proteins were shown to be dam methylation sensitive endonucleases, which can be activated by the E. coli MutL protein. These results allow to narrow down regions that are important for the interaction of MutH with MutL.
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL (2020)

The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative analyses, combining information from multiple data sources. However, analyzing evolutionary data in RDF is not trivial, due to the steep learning curve required to understand both the data models adopted by different RDF data sources, as well as the equivalent SPARQL constructs required to benefit from this data - in particular, recursive property paths. In this article, we provide a hands-on introduction to querying evolutionary data across several data sources that publish orthology information in RDF, namely: The Orthologous MAtrix (OMA), the European Bioinformatics Institute (EBI) RDF platform, the Database of Orthologous Groups (OrthoDB) and the Microbial Genome Database (MBGD). We present four protocols in increasing order of complexity. In these protocols, we demonstrate through SPARQL queries how to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups. Finally, we show how orthology information in different data sources can be compared, through the use of federated SPARQL queries.
Investigation of the wake of low aspect ratio cylinders by tomographic PIV (2011)

The wakes of wall mounted circular cylinders of very low aspect ratio have been investigated in a wind tunnel. Besides planar PIV, also high resolution tomographic PIV was used to capture the flow phenomena downstream of the cylinder. By changing the velocity U_inf and the cylinder height h at a constant aspect ratio h/D, a wide database of different flow conditions was obtained. The resulting relative height of the boundary layer thickness was between h/delta=0.6 and h/delta=2.5, while the Reynolds number based on the length l between leading edge and cylinder centre Re_l was between Re_l=57,000 and Re_l=188,000. A pair of counter-rotating vortices was found in the wake of the cylinder. The rotation sense is such, that in the center of the wake a positive vertical velocity component results. Also horseshoe vortices were found next to these trailing vortices. The relative height of the incoming boundary layer has a large impact on the development, strength and dissipation of the vortex system.
Pretreatment of Biological Samples for Microchip Analysis (2006)

A number of analytical processes have been developed on microchips for genomic and proteomic analysis, but reaching the analytical step often requires significant preprocessing before the sample reaches the microchip. Development of microchips that perform these sample processing steps is now underway to take advantage of the speed and cost benefits that microchips provide the analytical processes. In both the genomic and proteomic arenas, proof of principle has been shown for a number of microchip sample preparation steps, with application to real samples already reported for some of these processes. At present, many of the microchips are being designed for individual processing steps, but integration of multiple sample preparation steps has been shown, along with integration of sample processing and analytical procedures on single microchips.
An enhanced on-wafer millimeter-wave noise parameter measurement system (1999)

A novel on-wafer resistive noise source, useful for noise characterization of microwave devices with the cold noise power measurement technique, is described. The noise source enhances measurement accuracy by providing a calibrated noise temperature directly at the device reference plane. A procedure for determining the excess noise ratio of the noise source is presented and validated up to 40 GHz. The noise source is employed in an on-wafer measurement system, allowing the noise parameters of two-port devices to be extracted. Following a description of the apparatus and measurement procedure, an example of a high-electron-mobility transistor noise parameter measurement at millimeter-wave frequencies is presented.
Purification and Properties of a Bacterial Enzyme Catalyzing Purine Nucleoside Transribosylation (1963)

An enzyme catalyzing the ribosyl group transfer from inosine to adenine was purified from Aerobacter cloacae No. 172–1 by means of ammonium sulfate fractionation and DEAE-cellulose and hydroxylapatite column chromatographies. A. cloacae was found to have much activities of this enzyme in its cell free extract. The enzyme activity was increased about 90-fold. By using the purified enzyme, some properties of the reaction were investigated. The enzyme was considerably stable and essentially required inorganic orthophosphate for the reaction. It was suggested that the enzyme might be a purine nucleoside phosphorylase and that the reaction might be a coupled reaction with ribose-1-phosphate as an intermediate. The enzyme could not transfer the ribosyl group between purine and pyrimidine bases.
Soundscape Assessment of Aircraft Height and Size (2018)

It is accepted knowledge that, for a given equivalent sound pressure level, sounds produced by planes are worse received from local communities than other sources related to transportation. Very little is known on the reasons for this special status, including any interactions that non-acoustical factors may have in listener assessments. Here we focus on one of such factors, the multisensory aspect of aircraft events. We propose a method to assess the visual impact of perceived aircraft height and size, beyond the objective increase in sound pressure level for a plane flying lower than another. We utilize a soundscape approach, based on acoustical indicators (dBs, <i>L</i> <sub>A, max</sub>, background sound pressure level) and social surveys: a combination of postal questionnaires (related to long-term exposure) and field interviews (related to the contextual perception), complementing well-established questions with others designed to capture new multisensory relationships. For the first time, we report how the perceived visual height of airplanes can be established using a combination of visual size, airplane size, reading distance, and airplane distance. Visual and acoustic assessments are complemented and contextualized by additional questions probing the subjective, objective, and descriptive assessments made by observers as well as how changes in airplane height over time may have influenced these perceptions. The flexibility of the proposed method allows a comparison of how participant reporting can vary across live viewing and memory recall conditions, allowing an examination of listeners' acoustic memory and expectations. The compresence of different assessment methods allows a comparison between the "objective" and the "perceptual" sphere and helps underscore the multisensory nature of observers' perceptual and emotive evaluations. In this study, we discuss pro and cons of our method, as assessed during a community survey conducted in the summer 2017 around Gatwick airport, and compare the different assessments of the community perception.
CLINICAL STUDY OF OPERATED CASES OF ACUTE CHOLECYSTITIS WITH SPECIAL REFERENCE TO THE CLINICAL CHARACTERISTICS AND THERAPEUTIC PROBLEMS IN AGED PATIENTS (1993)

For the purpose of making clear the clinical characteristics and therapeutic problems in aged patients over 70 years old undergoing surgery for acute cholecystitis, 64 patients treated at the department during a recent fiveyear.1986-1990 were retrospectively studied by comparing with younger age group (under 69 years old). In the aged group 52.6% (30 cases) of all patients undergoing cholecystectomy had acute cholecystitis. Stones in the choledocus were found in 46.7% of the aged patients. It was 1.8 times higher than that of the youngers. Only 4 cases of the aged group had sepsis. Patients in the aged group had some underlying disease preoperatively in a significantly high rate compared to that of younger patients. The longest delay from the onset to the operation was noted in aged patients with preoperative underlying disease. There was no significant difference in operating time between both groups, however, aged patients tended to show more operative bleeding amount. The degree of inflammation was also severer in aged patients than the others. No significant difference in the frequency of postoperative complications was noted between both groups, but gastrointestinal bleeding was observed in only aged patients. There was no significant difference in postoperative hospital stay between them. No deaths were noted. Further efforts to make inflammation disappear as soon as possible, to perform safe and early operation under an appropriate control of the underlying disease, and to shorten the hospital stay are important.
Interaction Between the <i>μ</i>‐Opioid Receptor Gene and the Number of Heavy‐Drinking Peers on Alcohol Use (2017)

Findings suggest no OPRM1-based susceptibility to the number of heavy-drinking peers, adding to the existing mixed findings from correlational studies. Future research on OPRM1-related susceptibility to alcohol-promoting peer environments through meta-analytic synthesis and both experimental and prospective, multiwave designs is needed to resolve these mixed findings.
Design of a nested SPECT-CT system with fully suspended CT sub-system for dedicated breast imaging (2014)

A fully suspended, stand-alone cone beam CT system capable of complex trajectories, in addition to a simple circular trajectory, has previously been developed and shown to minimize cone beam sampling insufficiencies and have better sampling close to the chest wall for pendant breast CT imaging. A hybrid SPECT-CT system with SPECT capable of complex 3D trajectories has already been implemented and is currently in use. Here, the individual systems are redesigned into one hybrid system where each individual component is capable of traversing independent, arbitrary trajectories around a pendant breast and anterior chest wall in a common field of view. The integration also involves key hardware upgrades: a new high resolution 40x30cm2 flat panel CT imager with an 8mm bezel on two sides for closer chest wall access, a new x-ray source, and a unique tilting mechanism to enable the spherical trajectories for CT. A novel method to tilt the CT gantry about a 3D center of rotation is developed and included in the new gantry, while preserving the fully-3D SPECT system nested within the larger CT gantry. The flexibility of the integrated system is illustrated.
Performance analysis and material dependence of micro holographic optical elements as couplers for fiber optic communication (2005)

Holographic Optical Elements (HOEs) are gaining much importance and finding newer and better applications in areas of optical fiber communication and optical information processing systems. In contrast to conventional HOEs, optical communication and information systems require smaller and efficient elements of desired characteristics and transfer functions. Such Micro Holographic Optical Elements (MHOEs) can either be an HOE, recorded with two narrow beams of laser light or a segment cut from a larger HOE (SHOEs), and recorded in the conventional manner. In this study, micro holographic couplers, having specific focusing and diffraction characteristics were recorded in different holographic recording media such as silver halide and dichromated gelatin. Wavelength response of the elements was tested at 633 nm and 442 nm. Variation in diffraction efficiency/coupling factor, and insertion loss of the elements were studied. The paper reports in detail about the above results and related design considerations.
Differential Regulation of Cytokine Gene Expression by Avian Heterophils During Receptor-Mediated Phagocytosis of Opsonized and Nonopsonized <i>Salmonella enteritidis</i> (2003)

Internalization of pathogens by phagocytic cells triggers the innate immune response, which in turn regulates the acquired response. Phagocytes express a variety of receptors that are involved in recognition of pathogens, including (1) pattern recognition receptors (PRR), which recognize conserved motifs, (2) complement receptors (CR), which recognize complement-opsonized pathogens, and (3) Fc receptors (FcR), which recognize antibody-opsonized pathogens. Recognition of microbes is accompanied by the induction of multiple cell processes, including the production of proinflammatory and anti-inflammatory cytokines and chemokines. The objective of the present experiments was to use probes to known avian proinflammatory and anti-inflammatory cytokines and TaqMan technology to ascertain levels of cytokine gene expression in avian heterophils following receptor-mediated phagocytosis of either nonopsonized Salmonella enteritidis (SE), serum-opsonized SE, or IgG-opsonized SE. Expression of interleukin-6 (IL-6) and IL-8, considered in mammals as a proinflammatory chemokine, were upregulated following exposure to the nonopsonized or the opsonized SE. However, mRNA expression for IL-18 and interferon-gamma (IFN-gamma) was downregulated, and the expression of mRNA for the anti-inflammatory cytokine transforming growth factor-beta4 (TGF-beta 4) was upregulated. Interestingly, IL-1beta mRNA expression was significantly upregulated in heterophils that phagocytized either the nonopsonized SE via PRRs or IgG-opsonized SE via FcRs, whereas serum-opsonized SE phagocytized by CRs induced a downregulation of IL-1beta mRNA. These results suggest that signaling interactions initiated by receptor recognition of the microbe surface differentially regulate the induction of inflammatory cytokines in avian heterophils.
Identification of a new Leu354Pro mutation responsible for factor XIII deficiency (2001)

Abstract: We report a new homozygous C T G→C C G (Leu→Pro) mutation at codon 354 in the factor XIIIA gene of a patient suffering from FXIII deficiency. Leu354 lies in a pocket within the core domain of the FXIIIA molecule, with its side chain pointing into the structure of the barrel 1 domain. Replacement of leucine with a proline residue gives rise to steric hindrance between the proline ring and the surrounding residues, and rearrangement of these residues would be necessary for proline to be accommodated at this position. Using PCR‐RFLP, we have demonstrated the absence of this mutation from 220 normal alleles. Together, these data suggest that Leu354Pro is likely to be the disease‐causing mutation in this factor XIII deficient family.
NMDA Receptor-Mediated Refinement of a Transient Retinotectal Projection during Development Requires Nitric Oxide (1999)

A transient ipsilateral retinotectal projection is normally eliminated during embryonic development of the chick visual system. Administration of the NMDA receptor antagonist 5-methyl-10, 11-dihydro-5H-dibenzo[a,d]cyclohepten-5,10-imine (MK-801) during the developmental period in which this projection normally disappears prevented its complete elimination. Previous studies showed that tectal cells express nitric oxide synthase during development, and blocking synthesis of nitric oxide also prevented elimination of the ipsilateral retinotectal projection. The effect of NMDA receptor blockade on nitric oxide synthase activity in tectal cells was assessed biochemically in chick embryos. Increasing concentrations of MK-801 resulted in a dose-dependent decrease in nitric oxide synthase activity. This result suggests that NMDA receptor activation can regulate nitric oxide synthase activity in the tectum. The degree of rescue of the ipsilateral retinotectal projection was compared in embryos treated either with MK-801 or with an inhibitor of nitric oxide synthesis, Nomega-nitro-L-arginine (L-NoArg). At comparable levels of inhibition of nitric oxide synthesis, no significant difference was observed in the degree of rescue mediated by NMDA receptor blockade or nitric oxide synthesis blockade. These results suggest that NMDA receptor-mediated elimination of the ipsilateral retinotectal projection is completely mediated via nitric oxide.