gebhart/patrepeval huggingface dataset:
Expression of a pertussis toxin S1 fragment by inducible promoters in oralStreptococcusand the induction of immune responses during oral colonization in mice (2006)

Previous work aimed at developing a live oral vaccine expressing pertussis toxin S1 fragment on the surface of the bacterium Streptococcus gordonii elicited a lower than expected antibody response, perhaps because of low antigen expression. In this study, in-frame promoter fusions were constructed to investigate whether an increase in antigen production by the streptococcal vaccine strain results in a better antibody response. The promoters tested were (i) the Streptococcus mutans sucrose-inducible fructosyltransferase (ftf) promoter and (ii) the Bacillus subtilis/Escherichia coli chimeric tetracycline-inducible xyl/tetO promoter. Each of these two promoters was placed upstream of the spaP/s1 fusion gene to drive its expression. The constructs were introduced into S. gordonii DL1 and S. mutans 834. The inducibility of the promoters was confirmed through the determination of SpaP/S1 production via Western blottings. Induced production of SpaP/S1 was observed in S. gordonii and S. mutans with each of the promoters, but the level of expression was the highest in S. mutans, using the xyl/tetO promoter. Thus, S. mutans carrying the xyl/tetO/spaP/s1 construct (S. mutans PM14) was used in oral colonization studies in BALB/c mice. Streptococccus mutans PM14 was able to colonize the animals for the 14-week duration of experimentation. A mucosal IgA response was observed in all the treatment groups but was highest in mice receiving tetracycline induction. In the mouse model of Bordetella pertussis respiratory infection, animals colonized with S. mutans PM14 showed a decreased in B. pertussis lung colony count (P = 0.03) on day 3 compared with control mice colonized by the parent S. mutans 834.
Ganglioside-mediated modulation of cell growth. Specific effects of GM3 on tyrosine phosphorylation of the epidermal growth factor receptor. (1986)

Epidermal growth factor- (EGF) dependent tyrosine phosphorylation of the EGF receptor was inhibited by the exogenous addition of GM3 to a membrane preparation and to purified EGF receptor adsorbed to antireceptor-antibody-Sepharose (Bremer, E. G., Schlessinger, J., and Hakomori, S. (1986) J. Biol. Chem. 261, 2434-2440). A specific functional correlation between GM3 and EGF receptor function has been further assessed in this study, employing two variant clones of A431 cells showing completely different growth responses to EGF. The A1S clone showed EGF cell growth stimulation and contained GM3 whereas the A5I clone, whose growth was completely inhibited by EGF addition, lacked detectable GM3. Both the endogenous and EGF-dependent receptor tyrosine-kinase activities were low in the A1S clone and were only minimally inhibited by the exogenous addition of GM3. In contrast the EGF receptor kinase activity in A5I cells was much higher and was more strongly inhibited by GM3 than it was in A1S cells. The EGF receptor fraction prepared from A1S cells, eluted from an anti-EGF receptor antibody-Sepharose column, contained GM3, in contrast to the fraction prepared from A5I cells, which lacked detectable GM3. The receptor kinase activity in vitro was greatly influenced by detergent and ATP concentration. GM3 affected the receptor kinase in a biphasic manner, i.e. GM3 was inhibitory at a low concentration of detergent under a physiological concentration of ATP and stimulatory at a high concentration of detergent. In contrast lyso-GM3 displayed a monophasic inhibitory effect under a wide range of detergent concentrations. Lyso-CDH (lactosylsphingosine) had no detectable effect on the receptor kinase activity. The presence of a small quantity of lyso-GM3 in A431 cells was detected after DEAE-Sepharose chromatography followed by high performance liquid chromatography in a n-propanolyl alcohol-ammonia system. It is possible that de-N-fatty acylation of gangliosides could be an effective means to modulate EGF receptor function in membranes.
Cell-Less Network for Handover-Free Communications to High-Speed Trains Using a Switched WDM Fiber-Wireless Backhaul (2018)

A cell-less network for high-speed and non-interrupted communications to high-speed trains is proposed and demonstrated using a switched WDM fiber-wireless backhaul system. More than 10 Gb/s signal transmission with an ultra-fast cell switching is experimentally demonstrated in the uplink.
Topological Mimicry of Cross-reacting Enantiomeric Peptide Antigens (1995)

Rabbit polyclonal antibodies against multimeric peptide antigens were found to cross-react to a significant extent with topologically related variants of the parent antigen, where the chirality of each amino acid residue (inverso derivatives), or the peptide sequence orientation (retro derivatives), was inverted or where both modifications were simultaneously introduced (retro-inverso derivatives). All peptide variants displayed similar recognition properties for antibodies and similar dose-dependent inhibitory effects on the interaction between immobilized parent antigen and corresponding antibodies. Importance of peptide side chain topology on antigenicity was evaluated analyzing the recognition properties of two sequence-simplified parent peptide variants, one lacking of the side chains in the sequence odd position and the other in even position. These two variants, prepared introducing glycine residues alternatively in the parent peptide sequence, were found to cross-react to a significant extent with the original antibody raised against the parent peptide. Analysis of molecular models of peptide enantiomeric variants in the elongated all-trans configuration suggested that the topological equivalence of alternating side chains could lead to the formation of similar recognition surfaces, thus mimicking the parent peptide antigenic structure.
The Reduced Quantity and Functionality of Mesenchymal Stem Cells in the Synovium of Charcot Neuroarthropathy (2016)

Category: Basic Sciences/Biologics Introduction/Purpose: Managing Charcot Neuroarthropathy (CNA) remains a challenge facing the foot and ankle surgeons. Lack of understanding the pathogenesis of the disease prevents the development of novel therapies. Our previous studies revealed the involvement of fibroblast-like synoviocytes in the pathology of CNA. Residing in the synovium are also mesenchymal stem cells (MSCs), which maintain tissue homeostasis. In this study, MSCs isolated from the synovium of CNA and non-CNA patients were comparatively analyzed for their potential role in the pathology of CNA. Methods: Synovial samples were collected from CNA patients (n=7) and patients with osteoarthritis or intraarticular fracture (non-CNA; n=7), during foot and ankle procedures (approved by IRB). The synovial samples were minced and digested with 0.1% collagenase to isolate MSCs. The cells were plated and cultured in low density for counting colony-forming units-fibroblast (CFU- F), which is indicative of the number of MSCs. The colonies formed by CNA-MSCs and non-CNA MSCs were further characterized by size and imaging density. CNA-MSCs and non-CNA MSCs were cultured in adipogenic, osteogenic and chondrogenic differentiation media. The differentiation potentials of CNA-MSCs and non-CNA MSCs were assessed with histochemical staining and quantitative gene expression. Results: CFU-F: The number of colonies formed by CNA-MSCs was 6 ± 3.5 per (1/2) plate, while it was 43 ± 21.6 by the non- CNA MSCs (p &lt; 0.05; Fig 1). The average size (pixels) of colonies was smaller in the CNA-MSCs than the non-CNA MSCs (4780 vs. 7960). When the colonies were stratified into high, medium and low density subgroups, colonies formed by the CNA-MSCs had a reduced density compared with the non-CNA MSCs (30±6 vs. 35±10) in the high density subgroup. Differentiation: Expression of adipogenic marker gene PPAR-γ by CNA-MSCs was less than half of that by non-CNA MSCs. The expression of osteogenic marker gene RUNX2 by CNA-MSCs was a third of that by the non-CNA MSCs. Similarly, the expression of chondrogenic marker genes, including SOX9 and type II collagen, by the CNA-MSCs declined as compared with the non- CNA MSCs. Conclusion: The synovium in CNA joints had fewer MSCs and that may impact joint’s response to inflammation and tissue repair. Furthermore, CNA-MSCs were declined in differentiation potentials. Analyses of the size and density of the colonies formed by CNA-MSCs showed that a subpopulation of MSCs was particularly affected. Further study will focus on the pathological role of the high-density subpopulation of MSCs in the development of CNA.
Bibliography Of Optical Polarization Papers (1990)

This paper contains a database of references on polarization related topics. The database will facilitate the search for papers dealing with a specific topic, author, etc., and aid in compiling lists of references.
A prototype paediatric venous cannula with shape change in situ (2003)

During cardiopulmonary bypass (CPB), venous drainage may be impeded due to small vessel and cannula size or chattering, thus, blood return to the heart-lung machine is reduced. We designed a self-expandable prototype cannula, which is able to maintain the vein open and overcome this problem and analysed its performance capability. This prototype and several other cannulae were tested using an access vessel diameter of 7 mm. An in vitro circuit was set up with a 10 mm penrose latex tube simulating the patient's vein placed between the patient preload reservoir and the cannula, encasing the cannula's inlet(s). Maximum flow rate was determined for passive venous drainage (PVD) at preloads (P) of 2 and 4 mmHg. We compared these results to three classic single-stage venous cannulae: basket tip, thoracic drain and percutaneous tip. By comparing the other cannulae to the prototype, under PVD conditions and a central venous pressure (CVP) of 2 mmHg, the prototype cannula's flow rate (1.32 +/- 0.04 L/min) outperformed the basket type (the best performing comparator) (1.02 +/- 0.08 L/min) by 23% (p < 0.005). When the preload was increased to 4 mmHg under PVD conditions, the same trend was noted with the prototype cannula (1.65 +/- 0.05 L/min), outperforming the basket cannula's value (1.26 +/- 0.05 L/min) by 24% (p < 0.001). This new cannula design provides superior flow characteristics, under all test conditions, compared to the classic single-stage venous cannulae used for paediatric CPB surgery.
Adaptive Loop Filter with a CNN-Based Classification (2022)

In this paper, a data-driven generalization of the adaptive loop filter (ALF) of Versatile Video Coding (VVC) is presented. It is shown how the conventional ALF process of classification and FIR filtering can be generalized to define a natural model architecture for convolutional neural network (CNN) based in-loop filters. Experimental results show that over VVC, average bit-rate savings of 3.85%/4.75% and 4.39%/4.33% can be achieved for the all intra and random access configurations in the low- and high-QP settings.
The synthesis of novel core-substituted naphthalene diimides via Suzuki cross-coupling and their properties (2009)

This paper reports the efficient core-substitution of halogenated naphthalene diimides utilizing the Suzuki cross-coupling reaction to install various aryl substituents at the 2,6 positions. The UV-visible spectra of these compounds show a clear absorbance red shift and an enhanced fluorescence output, making them potential candidates for solar-cell dyes and electroactive elements for supramolecular materials.
<title>Control system design for the SPICES smart structure demonstrations</title> (1995)

In this paper we focus on topics related to the control system design to the control system design for the SPICES demonstrations: (1) The hierarchical control system, its motivation and design; (2) SRI's SWAPS (neutralized feedforward) design methodology, its necessity in the SPICES high frequency demonstration, and its properties; and (3) simulated performance of preliminary designs of the vibration control loop for the demonstrations.
The proSAAS chaperone provides neuroprotection and attenuates transsynaptic α–synuclein spread in rodent models of Parkinson’s disease (2021)

ABSTRACT Parkinson’s disease is a devastating motor disorder involving the aberrant aggregation of the synaptic protein synuclein (aSyn) and degeneration of the nigrostriatal dopaminergic tract. We previously showed that proSAAS, a small secreted chaperone protein widely expressed in neurons within the brain, is able to block aSyn-induced dopaminergic cytotoxicity in primary nigral neuron cultures. We show here that coinjection of proSAAS-encoding lentivirus profoundly reduced the motor asymmetry caused by unilateral nigral AAV-mediated human aSyn overexpression. This positive functional outcome was accompanied by significant amelioration of the human aSyn-induced loss of both nigral tyrosine hydroxylase-positive cells and striatal tyrosine hydroxylase-positive terminals, demonstrating clear proSAAS-mediated protection of the nigro-striatal tract. ProSAAS overexpression also reduced the content of human aSyn protein in both the nigra and striatum and reduced the loss of tyrosine hydroxylase protein in both regions. Since proSAAS is a secreted protein, we tested the possibility that proSAAS is able to block the transsynaptic spread of aSyn from the periphery to the central nervous system, increasingly recognized as a potentially significant pathological mechanism. The number of human aSyn-positive neurites in the pons and caudal midbrain of mice following administration of human aSyn-encoding AAV into the vagus nerve was considerably reduced in mice coinjected with proSAAS-encoding AAV, supporting proSAAS-mediated blockade of transsynaptic aSyn transmission. We suggest that proSAAS may represent a promising target for therapeutic development in Parkinson’s disease. Significance This paper describes two independent avenues of research that both provide support for the in vivo neuroprotective function of this small chaperone protein. In the first approach, we show that proSAAS overexpression provides remarkably effective protection against dopaminergic neurotoxicity in a rat model of Parkinson’s disease. This conclusion is supported both by three independent assays of motor function as well as by quantitative analysis of surviving dopaminergic neurons in brain areas involved in the control of motor function. In the second line of research, we show that in mice, the spread of human synuclein across synapses can be blunted by proSAAS overexpression.
Distinct resistance mechanisms arise to allosteric vs. ATP-competitive AKT inhibitors (2022)

The AKT kinases have emerged as promising therapeutic targets in oncology and both allosteric and ATP-competitive AKT inhibitors have entered clinical investigation. However, long-term efficacy of such inhibitors will likely be challenged by the development of resistance. We have established prostate cancer models of acquired resistance to the allosteric inhibitor MK-2206 or the ATP-competitive inhibitor ipatasertib following prolonged exposure. While alterations in AKT are associated with acquired resistance to MK-2206, ipatasertib resistance is driven by rewired compensatory activity of parallel signaling pathways. Importantly, MK-2206 resistance can be overcome by treatment with ipatasertib, while ipatasertib resistance can be reversed by co-treatment with inhibitors of pathways including PIM signaling. These findings demonstrate that distinct resistance mechanisms arise to the two classes of AKT inhibitors and that combination approaches may reverse resistance to ATP-competitive inhibition.
Identification of Inhibitors of NOD1-Induced Nuclear Factor-κB Activation (2011)

NOD1 (nucleotide-binding oligomerization domain 1) protein is a member of the NLR (NACHT and leucine rich repeat domain containing proteins) protein family, which plays a key role in innate immunity as a sensor of specific microbial components derived from bacterial peptidoglycans and induction of inflammatory responses. Mutations in NOD proteins have been associated with various inflammatory diseases that affect NF-κB (nuclear factor κB) activity, a major signaling pathway involved in apoptosis, inflammation, and immune response. A luciferase-based reporter gene assay was utilized in a high-throughput screening program conducted under the NIH-sponsored Molecular Libraries Probe Production Center Network program to identify the active scaffolds. Herein, we report the chemical synthesis, structure-activity relationship studies, downstream counterscreens, secondary assay data, and pharmacological profiling of the 2-aminobenzimidazole lead (compound 1c, ML130) as a potent and selective inhibitor of NOD1-induced NF-κB activation.
Secondary structure of the circular intervening sequence: A technique using chemical probes and reverse (RNA splicing/RNA catalysis/base modification/base methylation/R) (2016)

The structure of the intervening sequence (IVS) of the Tetrahymena rRNA precursor mediates cleavage- ligation reactions that result in pre-rRNA splicing and IVS cy- clization. We have developed a method for RNA structure analysis and applied it to the circular form of the IVS RNA. The native RNA was treated with dimethyl sulfate or diethyl pyrocarbonate to modify bases not involved in secondary or tertiary interactions. The RNA was then used as a template for reverse transcription. Elongation of synthetic oligodeoxynu- cleotide primers was found to stop (or pause) one nucleotide prior to 1-methyladenosine, 3-methylcytidine, and 7-ethoxy- carbonyladenosine residues. The detection of l-methyladeno- sine is particularly useful for locating single-stranded regions. After chemical cleavage of the RNA, 7-methylguanosine also could be detected. In general, the sites of modification were consistent with a previous model of the secondary structure of the linear form of the IVS RNA, a model based on enzymatic cleavage data, free energy calculations, and phylogenetic com- parison. Thus, IVS RNA autocyclization does not involve ma- jor rearrangements of the secondary structure, although there is evidence for a conformational change in one region of the molecule. The methods described here should be of general use for obtaining information about structure far from the ends of RNA molecules.
The Measurement of Full-Surface Internal Heat Transfer Coefficients for Turbine Airfoils Using a Non-Destructive Thermal Inertia Technique (2002)

A new method has been developed and demonstrated for the non-destructive, quantitative assessment of internal heat transfer coefficient distributions of cooled metallic turbine airfoils. The technique employs the acquisition of full-surface external surface temperature data in response to a thermal transient induced by internal heating/cooling, in conjunction with knowledge of the part wall thickness and geometry, material properties, and internal fluid temperatures. An imaging Infrared camera system is used to record the complete time history of the external surface temperature response during a transient initiated by the introduction of a convecting fluid through the cooling circuit of the part. The transient data obtained is combined with the cooling fluid network model to provide the boundary conditions for a finite element model representing the complete part geometry. A simple 1D lumped thermal capacitance model for each local wall position is used to provide a first estimate of the internal surface heat transfer coefficient distribution. A 3D inverse transient conduction model of the part is then executed with updated internal heat transfer coefficients until convergence is reached with the experimentally measured external wall temperatures as a function of time. This new technique makes possible the accurate quantification of full-surface internal heat transfer coefficient distributions for prototype and production metallic airfoils in a totally non-destructive and non-intrusive manner. The technique is equally applicable to other material types and other cooled/heated components.
Dynamic comparisons of high-resolution expression profiles highlighting mitochondria-related genes betweenin vivoandin vitrofertilized early mouse embryos (2015)

The present study provides a new insight in understanding the mechanism of IVF-induced aberrations during embryonic development and the increased health risks in the offspring. In addition, we highlighted the possibility of improving existing IVF systems by modulating mitochondrial functions.
Generalised twin‐box model for compensation of transmitters radio frequency impairments (2014)

A novel generalised twin‐box model is proposed for the mutual compensation of modulator imperfections and power amplifier (PA) distortion. It is composed of two cascaded boxes, a dual branch of simplified Volterra filters for the joint characterisation of the mild non‐linear dynamic memory effects of the PA and modulator imperfections. The second box is a look‐up table for characterising the highly non‐linear static distortion exhibited by the PA. Hence, the proposed model has reduced complexity in comparison with the state‐of‐the‐art models, owing to the separate identification of the dynamic and static effects of the PA. The model validation is carried out using a Class AB PA, and the proposed model showed significant improvement in performance as well as reducing the computational complexity of the model.
Figure S6 and S7 from RAS–MAPK Reactivation Facilitates Acquired Resistance in <i>FGFR1</i>-Amplified Lung Cancer and Underlies a Rationale for Upfront FGFR–MEK Blockade (2023)

&lt;p&gt;Figure S6 describes genomic analysis of resistant NCI-H2077 cells and Figure S7 shows weight of animals of xenograft studies.&lt;/p&gt;
Demonstration of laser-diode-pumped ultrafast all-optical switching in a nonlinear Sagnac interferometer (1991)

Ultrafast all-optical switching in a nonlinear Sagnac interferometer using picosecond pulses from a laser diode is reported. The key technologies are a highly stable fibre Sagnac interferometer with a long interaction length of 1600 m, and high-intensity 14 ps control pulses provided by a gain switched DFB-LD coupled with an erbium-doped fibre amplifier.
The Spectrum of Fungi That Infects Humans (2014)

Few among the millions of fungal species fulfill four basic conditions necessary to infect humans: high temperature tolerance, ability to invade the human host, lysis and absorption of human tissue, and resistance to the human immune system. In previously healthy individuals, invasive fungal disease is rare because animals' sophisticated immune systems evolved in constant response to fungal challenges. In contrast, fungal diseases occur frequently in immunocompromised patients. Paradoxically, successes of modern medicine have put increasing numbers of patients at risk for invasive fungal infections. Uncontrolled HIV infection additionally makes millions vulnerable to lethal fungal diseases. A concerted scientific and social effort is needed to meet these challenges.
Strand specific RNA sequencing of L.monocytogenes 10403S under UV irradiation conditions in comparison to bacteria grown in BHI (2020)

Part1. Bacteria were grown in BHI medium without UV irradiation for ssRNA-Seq analysis.