gebhart/patrepeval huggingface dataset:
Cellular vacuoles induced by Helicobacter pylori originate from late endosomal compartments. (1994)

Pathogenic strains of Helicobacter pylori cause progressive vacuolation and death of epithelial cells. To identify the nature of vacuoles, the distribution of markers of various membrane traffic compartments was studied. Vacuoles derive from the endocytic pathway since they include the fluid-phase marker Lucifer yellow. Early endosome markers such as rab5, transferrin, and transferrin receptor, as well as the lysosomal hydrolase cathepsin D, are excluded from these structures. In contrast, the vacuolar membrane is specifically stained by affinity-purified antibodies against rab7, a small GTPase, localized to late endosomal compartments. The labeling of rab7 on vacuolar membranes increases as vacuolation progresses, without a concomitant increase of cellular rab7. Cell vacuolation is inhibited by the microtubule-depolymerizing agents nocodazole and colchicine. Taken together, these findings indicate that the vacuoles specifically originate from late endosomal compartments.
Tomographic magnetic particle imaging of cancer targeted nanoparticles (2017)

Magnetic Particle Imaging (MPI) is an emerging, whole body biomedical imaging technique, with sub-millimeter spatial resolution and high sensitivity to a biocompatible contrast agent consisting of an iron oxide nanoparticle core and a biofunctionalized shell. Successful application of MPI for imaging of cancer depends on the nanoparticles (NPs) accumulating at tumors at sufficient levels relative to other sites. NPs' physiochemical properties such as size, crystallographic structure and uniformity, surface coating, stability, blood circulation time and magnetization determine the efficacy of their tumor accumulation and MPI signal generation. Here, we address these criteria by presenting strategies for the synthesis and surface functionalization of efficient MPI tracers, that can target a typical murine brain cancer model and generate three dimensional images of these tumors with very high signal-to-noise ratios (SNR). Our results showed high contrast agent sensitivities that enabled us to detect 1.1 ng of iron (SNR ∼ 3.9) and enhance the spatial resolution to about 600 μm. The biodistribution of these NPs was also studied using near-infrared fluorescence (NIRF) and single-photon emission computed tomography (SPECT) imaging. NPs were mainly accumulated in the liver and spleen and did not show any renal clearance. This first pre-clinical study of cancer targeted NPs imaged using a tomographic MPI system in an animal model paves the way to explore new nanomedicine strategies for cancer diagnosis and therapy, using clinically safe magnetic iron oxide nanoparticles and MPI.
Selection and Application of Bacteriophages for Treating Salmonella enteritidis Infections in Poultry (2007)

The objective of this study was to select appropriate bacteriophages that survive in the gastrointestinal tract of neonatal poultry and utilize those bacteriophages to reduce intestinal colonization of Salmonella enteritidis phage type 13A (SE) in challenged birds. Broiler chicks served as an in vivo biological filter to preferentially select bacteriophages from our bacteriophage library capable of surviving the gastrointestinal environment. A mixture of bacteriophage isolates designated PHL 1-71 was administered orally to three SE challenged chicks on three consecutive days. Each day, bacteriophages were recovered from the ileum, ileocecal junction and ceca for sequential administration the following day. The recovered bacteriophages were then administered to SE-infected turkey poults. In the first experiment, two-day old poults were challenged with 10 cfu SE and treated 48 h later with 5mM Mg (OH) followed by 2.5×10 plaque 4 9 2 forming units (pfu) of bacteriophages in 1mM Mg (OH) solution. This treatment numerically reduced SE 2 recovered from cecal contents at 12 and 24 h after treatment as compared to untreated controls. In a second experiment, two-day old poults were challenged with 1.6×10 cfu SE and treated with 5mM Mg (OH) followed 4 2 by 7.5×10 pfu phage in 1mM Mg (OH) solution 48 h post-challenge. We recovered 79,728 cfu of SE per g 9 2 of cecal contents in the control group and 11,224 cfu/g in the phage treated group 24 h post treatment. These data were not significantly different, but they suggest that bacteriophages can be preferentially selected in vivo to increase survival in the avian gastrointestinal tract. However, improved efficacy is required prior to useful application of the approach for reducing Salmonella infection.
Planar Microparticle Assembly and Photopolymerized Joining with Holographic Optical Tweezers (2016)

Holographic optical tweezers are able to assemble and permanently join polystyrene microspheres into planar patterns using an acrylamide-based photopolymerization reaction. This approach holds potential as a new method for additive fabrication of multi-material microstructures.
Forward-Backward (1987)

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Virtual sensing techniques and their applications (2009)

Developing new sensing technologies to obtain desired and accurate information more effectively from the limited sensor positions is one of the critical challenges that scientists and engineers aspire to undertake in the 21st century. This paper surveys applications of virtual sensing in different fields, e.g., transportation, wireless communication, sensor networks and active noise control. It reviews the existing methods used to infer virtual sensing information. The virtual sensing techniques and their application in active noise control are especially discussed.
Characterization of Antibody Bipolar Bridging Mediated by the Human Cytomegalovirus Fc Receptor gp68 (2016)

The human cytomegalovirus glycoprotein gp68 functions as an Fc receptor for host IgGs and can form antibody bipolar bridging (ABB) complexes in which gp68 binds the Fc region of an antigen-bound IgG. Here we show that gp68-mediated endocytosis transports ABB complexes into endosomes, after which the complex is routed to lysosomes, presumably for degradation. These results suggest gp68 contributes to evasion of IgG-mediated immune responses by mediating destruction of host IgG and viral antigens.
Radiographically Determined Lung Volumes at Full Inspiration and During Dynamic Forced Expiration in Normal Subjects (1975)

Posteroanterior and lateral radiographs of the lungs of 30 normal adults were obtained at total lung capacity (TLC) and 1 sec after initiation of forced expiration from ttlc. simultaneous spirographic recording of the volume expired (FEV-1) and independent plethysmographic recording of TLC were obtained. Two types of measurements were made from the radiographs: 1) surface areas of the lung fields, measured planimetrically; and 2) combinations of linear distances between selected points. These radiographic measurements and the measured lung volumes were subjected to computer analysis to develop reliable formulas for determining lung volumes solely from radiographs. Formulas derived using planimetry produced multiple correlation coefficients of 0.95 for TLC and 0.89 for volume during forced expiration. Use of linear measurements produced multiple correlation coefficients of 0.92 for TLC and 0.84 for dynamic volume. Thus, in normal subjects, static lung volumes and lung volumes during dynamic forced expiration can be determined from radiographs.
Simulation of materials processing: Fantasy or reality? (1994)

This experiment introduces students to the application of computer-aided design (CAD) and analysis of materials processing in the context of integrated circuit (IC) fabrication. The fabrication of modern IC's is a complex process which consists of several sequential steps. These steps involve the precise control of processing variables such as temperature, humidity, and ambient gas composition. In essence, the particular process employed during the fabrication becomes a 'recipe'. Due to economic and other considerations, CAD is becoming an indispensable part of the development of new recipes for IC fabrication. In particular, this experiment permits the students to explore the CAD of the thermal oxidation of silicon.
Study of the mechanism of insulin encapsulation in poly(isobutylcyanoacrylate) nanocapsules obtained by interfacial polymerization (1999)

In previous studies, insulin-loaded poly(alkylcyanoacrylate) nanocapsules were found to reduce the blood glucose level after oral administration to diabetic rats and dogs. The reduction of the glycemia induced by the nanocapsules was the same regardless of the insulin doses administered, but the effect appeared only after a delay of a few days. The purpose of this study was to investigate the mechanism of insulin encapsulation and the type of interactions that may exist between the polymer forming the nanocapsule wall and the insulin. The results of this study showed, based on the interfacial polymerization of isobutylcyanoacrylate, that the insulin molecule is not chemically modified during the nanoencapsulation process. In addition, no interaction between the poly(isobutylcyanoacrylate) and the insulin could be observed. The observed high encapsulation efficiency of intact insulin may be explained by the fact that the ethanol used in the preparation of the nanocapsules is responsible for the initiation of the interfacial polymerization of isobutylcyanoacrylate instead of the insulin. The zeta potential measurements suggest that insulin is located within the core of the nanocapsules. Thus the biological activity of the nanoencapsulated peptide and the high efficiency of insulin encapsulation achieved with this nanoencapsulation process cannot be explained by a specific interaction of the insulin with the polymer forming the nanocapsule's wall. It may be due, however, to the fact that the encapsulated insulin molecule is chemically intact and located within the oily core of the nanocapsules. © 1999 John Wiley & Sons, Inc. J Biomed Mater Res, 47, 568–576, 1999.
Interpretation of the depths of maximum of extensive air showers measured by the Pierre Auger Observatory (2013)

Collaboration members: K.B. Barber, J.A. Bellido, R.W. Clay, M.J. Cooper, B.R. Dawson, T.D. Grubb, T.A. Harrison, A.E. Herve, G.C. Hill, V.C. Holmes, M. Malacari, S.J. Saffi, and P. Wahrlich of the University of Adelaide, Adelaide, South Australia, Australia
DC Bus Capacitor Discharge of Permanent-Magnet Synchronous Machine Drive Systems for Hybrid Electric Vehicles (2016)

This paper investigates control methods to quickly and safely discharge the high-voltage dc bus capacitor for the permanent-magnet synchronous machine drive systems of hybrid electric vehicles during emergency situations such as a crash event. The published dc bus capacitor discharge strategies either need impractically heavy and bulky hardware or are only effective for low machine speeds. Applying the existing methods under high speeds will lead to loss of the current control and a system shutdown, followed by the bus voltage recharging again. The proposed new control method applies a modulation index controller together with a bus voltage regulator to quickly discharge the bus voltage and avoid any bus recharge regardless of the electric machine speed. Simulation and experimental results are presented to verify the effectiveness of the proposed control algorithm.
Renal Ischemia-Reperfusion Injury and Adenosine 2A Receptor-Mediated Tissue Protection: The Role of CD4+ T Cells and IFN-γ (2006)

A(2A) adenosine receptor (A(2A)R)-expressing bone marrow (BM)-derived cells contribute to the renal protective effect of A(2A) agonists in renal ischemia-reperfusion injury (IRI). We performed IRI in mice lacking T and B cells to determine whether A(2A)R expressed in CD4+ cells mediate protection from IRI. Rag-1 knockout (KO) mice were protected in comparison to wild-type (WT) mice when subjected to IRI. ATL146e, a selective A(2A) agonist, did not confer additional protection. IFN-gamma is an important early signal in IRI and is thought to contribute to reperfusion injury. Because IFN-gamma is produced by kidney cells and T cells we performed IRI in BM chimeras in which the BM of WT mice was reconstituted with BM from IFN-gamma KO mice (IFN-gamma KO-->WT chimera). We observed marked reduction in IRI in comparison to WT-->WT chimeras providing additional indirect support for the role of T cells. To confirm the role of CD4+ A(2A)R in mediating protection from IRI, Rag-1 KO mice were subjected to ischemia-reperfusion. The protection observed in Rag-1 KO mice was reversed in Rag-1 KO mice that were adoptively transferred WT CD4+ cells (WT CD4+-->Rag-1 KO) or A(2A) KO CD4+ cells (A(2A) KO CD4+-->Rag-1 KO). ATL146e reduced injury in WT CD4+-->Rag-1 KO mice but not in A(2A) KO CD4+-->Rag-1 KO mice. Rag-1 KO mice reconstituted with CD4+ cells derived from IFN-gamma KO mice (IFN-gamma CD4+-->Rag-1 KO) were protected from IRI; ATL146e conferred no additional protection. These studies demonstrate that CD4+ IFN-gamma contributes to IRI and that A(2A) agonists mediate protection from IRI through action on CD4+ cells.
Trajectory Splitting: A Distributed Formulation for Collision Avoiding Trajectory Optimization (2021)

Efficient trajectory optimization is essential for avoiding collisions in unstructured environments, but it remains challenging to have both speed and quality in the solutions. One reason is that second-order optimality requires calculating Hessian matrices that can grow with O(N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) with the number of waypoints. Decreasing the waypoints can quadratically decrease computation time. Unfortunately, fewer waypoints result in lower quality trajectories that may not avoid the collision. To have both, dense waypoints and reduced computation time, we took inspiration from recent studies on consensus optimization and propose a distributed formulation of collocated trajectory optimization. It breaks a long trajectory into several segments, where each segment becomes a subproblem of a few waypoints. These subproblems are solved classically, but in parallel, and the solutions are fused into a single trajectory with a consensus constraint that enforces continuity of the segments through a consensus update. With this scheme, the quadratic complexity is distributed to each segment and enables solving for higher-quality trajectories with denser waypoints. Furthermore, the proposed formulation is amenable to using any existing trajectory optimizer for solving the subproblems. We compare the performance of our implementation of trajectory splitting against leading motion planning algorithms and demonstrate the improved computational efficiency of our method.
Functional feeding to alleviate gastrointestinal disorders associated with autism spectrum disorders: A systematic review (2022)

Background: gastrointestinal disorders (GIDs) are common comorbidities in patients with autism spectrum disorders (ASD); treatments with gluten- and casein-free (LGLC) diets or prebiotic/probiotic supplements may reduce the severity of GIDs. Objective: to integrate and discuss the evidence on the effectiveness of LGLC diet therapies and prebiotic/probiotic supplements on GIDs in patients with ASD. Methodology: the guidelines for the publication of systematic reviews and meta-analyses (PRISMA) were used. Participant characteristics, dietary interventions, prebiotic/prebiotic supplementation, effects of interventions on GIDs, risk of bias, and safety of treatments were analyzed. Results: fifteen investigations were analyzed; the prevalence of GIDs among patients with ASD was high (58 %; range, 27-83 %). In more than 20 % of the patients managed with LGLC diets or supplements GID severity decreased (mainly constipation, diarrhea, and abdominal pain). Increases in the counts of beneficial bacteria and a decrease in the proportion of pathogenic bacteria were reported after supplement use. However, all these investigations had significant methodological biases. Conclusions: although reductions in the frequency and severity of some GIDs have been found, the effectiveness of these treatments has not been proven yet. Given the methodological differences in the investigations, the design of rigorous studies to evaluate the therapeutic effects of these treatments on gastrointestinal health in patients with ASD is warranted.
Stress-Biased Rearrangements and Preyield Behavior in Glasses (2006)

On the basis of a physical picture of a glass as a mosaic of mesoscopic clusters differing in their yield characteristics, we propose a model for the preyield behavior in glassy materials; the model describes the stress-strain relationship at different strain rates in terms of one reduced variable. A test using experimental data for polycarbonate materials at different rates and temperatures appears favorable for the model. The model may be used to interpolate and extrapolate limited experimental data, and also provides a practical means to assess dynamic heterogeneities within polymeric glasses. When applied at different temperatures, the model gives insight into the dependence of the excitation energies on temperature (glassformer fragility) in the glassy state.
Performance driven design of fiber reinforced cementitious composites (1992)

In this experimental work the profits of using Normalplasticizer is investigated. Fourteen mixtures are made and tested. Acidic attack on specimens is observed. Problems seen during the mixing are noted. Test results have shown a considerable improvement in the workability and in uniform distribution, a considerable increase in the compressive, flexural strengths, improved resistance against acidic attack.
Enzymatic activity toward poly(L‐lactic acid) implants (1990)

Tissue reactions toward biodegradable poly(L-lactic acid) implants were monitored by studying the activity pattern of seven enzymes as a function of time: alkaline phosphatase, acid phosphatase, alpha-naphthylacetyl esterase, beta-glucuronidase, ATP-ase, NADH-reductase, and lactate dehydrogenase. Cell types were identified by their specific enzyme patterns, their morphology and location. Special attention was paid to the enzyme patterns of macrophages, fibroblasts and polymorphonuclear granulocytes (PMNs), being involved in foreign body reactions or inflammatory responses. One day after implantation, an influx of neutrophilic and eosinophilic granulocytes was observed, coinciding with activity of alkaline phosphatase (PMN's) and beta-glucuronidase (eosinophils). From day 3 on, macrophages containing ATP-ase, acid phosphatase and esterase could be observed. From day 7 on, lactate dehydrogenase, the enzyme normally involved in the conversion of lactic acid, and its coenzyme NADH-reductase were observed in macrophages and fibroblasts. These two enzymes demonstrated more activity than expected on basis of wound-healing reactions upon implantation of a nonbiodegradable, inert biomaterial (as, e.g., Teflon). It is concluded that the biodegradable poly (L-lactic acid) used in these implantation studies is tissue compatible, and evokes a foreign body reaction with minor macrophage and giant cell activity, as observed during this 3-week implantation period. Most enzyme patterns were simply due to a wound-healing reaction. The slightly increased levels of LDH and NADH suggest the release of lactic acid from the implant, and thus confirms the biodegradable nature of this polymer.
The Ghosting Technique Applied to Augmented Reality Visualization (2013)

Functional realism focuses on delivering to the user the best visual information from the target scene. The virtual scenes/objects do not need to behave or look like the real ones, but they need to help users in tasks execution. In this sense, this paper focuses on functional realism applied to Augmented Reality scenes. The technique presented here applies a visualization technique called Ghosting to generate an importance map from the real scene in order to blend in the virtual objects in a more adequate way. A careless augmentation can prejudice the user Augmented Reality based experience. The importance map is built from a saliency map, edge detection, super pixel representation and texture analysis. We present results in outdoor and indoor environments in order to prove the technique effectiveness.
ANALYSIS OF BACTERIAL CELL WALL PROTEINS AND HUMAN SERUM PROTEINS BOUND TO BACTERIAL CELL SURFACES (1981)

A method was developed for the characterization of proteins non-covalently bound to the cell wall of Gram-positive cocci. The method employs radioactive labelling of cell wall proteins followed by solubilisation and analysis on polyacrylamide gel electrophoresis in sodium dodecyl sulphate. Using this experimental procedure, protein patterns obtained from group A, C and G streptococcal strains showed marked similarities within each group. Protein peaks were also found to be shared between group C and G strains. Two major peaks with molecular weights of about 30 000 and 70 000 characterized group A strains, whereas group C and G strains showed one consistent peak of about 45 000, thus reflecting the closer relationship between these two groups as compared to group A streptococci. By incubating bacteria with human serum proteins before labelling, solubilisation and electrophoretic analysis, it was also possible to study external proteins specifically bound to the bacterial surface. A group G streptococcus, strain G 148, showed protein peaks corresponding to its known specific binding of human albumin and immunoglobulin G, but also additional protein peaks. When Staphylococcus aureus, strain Cowan I, was pre-incubated with human serum in excess, protein peaks corresponding to heavy and light chains of immunoglobulins were seen. Three more protein peaks of serum origin were also detected, indicating binding of proteins other than Ig to S. aureus. Experiments with protein A-coated Sepharose beads resulted in the same protein pattern, suggesting that binding of these different polypeptides is indeed mediated by protein A.
Characterization of a Monoclonal Antibody, D73H, that Maps to a Highly Conserved Region on Fibrinogen Bβ Chain (2000)

The primary structure of fibrinogen is highly conserved across species, yet often times monoclonal antibodies produced against the fibrinogen of one species will not crossreact with the fibrinogen of another. Herein, we describe the production and characterization of murine MAb, D73H, raised against human fibrinogen. D73H crossreacts with a highly conserved epitope on the Bbeta chain of fibrinogen from human, rat, bovine, guinea pig, and mouse. Western blotting revealed that D73H reacted with the Bbeta chain of plasmin fragment D, localizing its epitope to Bbeta134-461. A 7 kDa band was identified by D73H in Western blots of reduced fibrinogen CNBr-fragments. N-terminal sequencing mapped this fragment to Bbeta243-253, further localizing the epitope to Bbeta243-305. In silico analysis indicated that Bbeta243-305 is predominantly hydrophilic, and surface probability prediction indicated three potential antigenic determinants corresponding to Bbeta252-258, Bbeta262-269, and Bbeta279-286. Further in silico analysis of the crystal structure of fibrinogen fragment D-D indicated that Bbeta262-269 (FGRKWDPY) is predominantly alpha-helical and located on the surface of the molecule adjacent to a bend imposed in the beta chain at residue 260, which is near the junction between the rigid coiled-coil domain and the globular C-terminus. A synthetic peptide corresponding to Bbeta261-272 competitively inhibited the binding of D73H to the Bbeta chain of denatured intact fibrinogen and reduced and denatured Bbeta chain in Western blots, experimentally proving the validity of these predictive algorithms. Together these data indicate that, although plasmin resistant, Bbeta chain residues Bbeta261-272 comprising the D73H epitope are highly conserved across species, surface exposed, and immunogenic.