gebhart/patrepeval huggingface dataset:
Purification and enrichment of virus samples utilizing magnetic beads on a microfluidic system (2007)

This study reports a new microfluidic system with three integrated functional devices for pumping, mixing and separation of bio-samples by utilizing micro-electro-mechanical-systems technology. By using antibody-conjugated magnetic beads, the developed system can be used to purify and enrich virus samples such that the subsequent detection of viruses can be performed with a higher sensitivity. The target viruses were first captured by the antibody coated onto the magnetic beads by using a rotary micromixer which performed the incubation process. The viruses were then purified and enriched by a magnetic field generated by planar microcoils. The integrated microfluidic system can perform the whole purification and enrichment process automatically using a rotary micropump and appropriate microvalves. In addition, a numerical simulation was also employed to optimize the design of the microcoils and to investigate the magnetic field strength and distribution. The simulation results were consistent with experimental observations. Finally, the developed system was used to successfully perform the purification and enrichment of Dengue viruses. The detectable limit of Dengue viruses was found to be as low as 10(2) pfu ml(-1) by using this approach. Therefore, the integrated microsystem can perform incubation, transportation, mixing and purification of virus samples, possibly making it a promising platform for future biological and medical applications.
Aβ Immunotherapy: Intracerebral Sequestration of Aβ by an Anti-Aβ Monoclonal Antibody 266 with High Affinity to Soluble Aβ (2009)

Amyloid beta (Abeta) immunotherapy is emerging as a promising disease-modifying therapy for Alzheimer's disease, although the precise mechanisms whereby anti-Abeta antibodies act against amyloid deposition and cognitive deficits remain elusive. To test the "peripheral sink" theory, which postulates that the effects of anti-Abeta antibodies in the systemic circulation are to promote the Abeta efflux from brain to blood, we studied the clearance of (125)I-Abeta(1-40) microinjected into mouse brains after intraperitoneal administration of an anti-Abeta monoclonal antibody 266. (125)I-Abeta(1-40) was rapidly eliminated from brains with a half-life of approximately 30 min in control mice, whereas 266 significantly retarded the elimination of Abeta, presumably due to formation of Abeta-antibody complex in brains. Administration of 266 to APP transgenic mice increased the levels of monomer Abeta species in an antibody-bound form, without affecting that of total Abeta. We propose a novel mechanism of Abeta immunotherapy by the class of anti-Abeta antibodies that preferentially bind soluble Abeta, i.e., intracerebral, rather than peripheral, sequestration of soluble, monomer form of Abeta, thereby preventing the accumulation of multimeric toxic Abeta species in brains.
Mouse cloning with nucleus donor cells of different age and type (2001)

We have tested different cell types as sources for nucleus donors to determine differences in cloning efficiency. When donor nuclei were isolated from cumulus cells and injected into recipient oocytes from adult hybrid mice (B6D2F1 and B6C3F1), the success rate of cloning was 1.5-1.9%. When cumulus cell donor nuclei were isolated from adult inbred mice (C57BL/6, C3H/He, DBA/2, 129/SvJ, and 129/SvEvTac), reconstructed oocytes did not develop to full term or resulted in a very low success rate (0-0.3%) with the exception of 129 strains which yielded 0.7-1.4% live young. When fetal (13.5-15.5 dpc), ovarian, and testicular cells were used as nucleus donors, 2.2 and 1.0% of reconstructed oocytes developed into live offspring, respectively. When various types of adult somatic cells (fibroblasts, thymocytes, spleen cells, and macrophages) were used, oocytes receiving thymocyte nuclei never developed beyond implantation, whereas those receiving the nuclei of other cell types did. These results indicate that adult somatic cells are not necessarily inferior to younger cells (fetal and ES cells) in the context of mouse cloning. Although fetal cells are believed to have less genetic damage than adult somatic cells, the success rate of cloning using any cell types were very low. This may largely be due to technical problems and/or problems of genomic reprogramming by oocytes rather than the accumulation of mutational damage in adult somatic cells.
Isolation of CA dinucleotide repeats close to D6S105; linkage disequilibrium with haemochromatosis. (1994)

The gene for hereditary haemochromatosis (HC) is linked to HLA-A and D6S105 on chromosome 6p. Both markers have also been reported to display linkage disequilibrium with the disease. However, their physical localization relative to one another has not been established. We demonstrate by fluorescent in situ hybridisation that D6S105 lies at least 1-2 Mb telomeric of HLA-A. The haemochromatosis critical region extending from proximal of HLA-A to distal of D6S105 is therefore large. To improve the genetic resolution in this region more highly polymorphic markers are required. We have therefore isolated three novel CA dinucleotide repeats close to D6S105. A linkage disequilibrium study, with two of these microsatellites, in HC patients and controls lends support to the conclusion that D6S105 is a close marker to the haemochromatosis gene.
Design principles for superamphiphobic surfaces (2012)

To predict the properties of superamphiphobic layers we analyzed the wetting of a square and a hexagonal array of vertical pillars composed of spheres (radius R) partially sintered together. Apparent contact angles above 150° are obtained by pinning of a non-polar liquid surface at the underside of the top sphere resulting in a Fakir or Cassie state. Analytical equations are derived for the impalement pressure in the limiting case A0 ≫ R2, where A0 is the area of the regular unit cell containing a single pillar. The case of close pillars is investigated numerically. By balancing forces at the rim of a drop, we calculate the apparent receding contact angle. To describe drag reduction of a flowing liquid we calculate the apparent slip length. When considering pressure-induced flow through cylindrical capillaries of radius rc, significant drag reduction occurs only for thin capillaries. The mechanical stability with respect to normal forces and shear is analyzed. Nanoscopic silica glass pillars would be able to sustain the normal and shear stresses caused by capillary and drag forces. For a high impalement pressure and good mechanical stability A0 should be small and R (respectively the neck diameter) should be large, whereas a large A0 and a small R imply low contact angle hysteresis and high slip length.
Topical Instillation of Doxorubicin Hydrochloride in the Treatment of Recurring Superficial Transitional Cell Carcinoma of the Bladder (1977)

&lt;p&gt;The conventional definition of asphaltenes is based on their solubility in toluene and their insolubility in heptane. We have utilized this definition to study the influence of partial charge parametrization on the aggregation behavior of asphaltenes using classical atomistic molecular dynamics simulations performed on the microsecond time scale. Under consideration here are toluene- and heptane-based systems with different partial charges parametrized using the general AMBER force field (GAFF). Systems with standard GAFF partial charges calculated by the AM1-BCC and HF/6-31G*(RESP) methods were simulated alongside systems without partial charges. The partial charges implemented differ in terms of the resulting electrical negativity of the asphaltene polyaromatic core, with the AM1-BCC method giving the greatest magnitude of the total core charge. Based on our analysis of the molecular relaxation and orientation, and on the aggregation behavior of asphaltenes in toluene and heptane, we proposed to use the partial charges obtained by the AM1-BCC method for the study of asphaltene aggregates. A good agreement with available experimental data was observed on the sizes of the aggregates, their fractal dimensions, and the solvent entrainment for the model asphaltenes in toluene and heptane. From the results obtained, we conclude that for a better predictive ability, simulation parameters must be carefully chosen, with particular attention paid to the partial charges owing to their influence on the electrical negativity of the asphaltene core and on the asphaltenes aggregation.&lt;/p&gt;
Advanced Processing of GaN for Electronic Devices (2000)

This review focuses on understanding and optimization of several key aspects of GaN device processing. A novel rapid thermal processing up to 1500°C, in conjunction with AlN encapsulation, has been developed. The activation processes of implanted Si or Group VI donors, and common acceptors in GaN by using this ultrahigh-temperature annealing, along with its effects on surface degradation, dopant redistribution, and damage removal have been examined. 1400 degrees has proven to be the optimum temperature to achieve high activation efficiency and to repair the ion-induced lattice defects. Ion implantation was also employed to create high-resistivity GaN. Damage-related isolation with sheet resistances of 1012 Ω/square in n-GaN and 1010 Ω/square in p-GaN has been achieved by implant of O and transition metal elements. The effects of surface cleanliness on characteristics of GaN Schottky contacts have been investigated, and the reduction in barrier height was correlated with removing the native oxide that forms an insulating layer on the conventionally cleaned surface. W alloys have been deposited on Si-implanted samples and Mg-doped epilayers to achieve ohmic contacts with low resistance and better thermal stability than the existing non refractory contact schemes. Dry etching damage in GaN has been studied systematically using Schottky diode measurements. Wet chemical etching and thermal annealing processes have been developed to restore the ion-degraded material properties. Based on these technical improvements, attempts have been made to demonstrate GaN-based bipolar transistors. The devices operated in common base mode at current densities up to 3.6 kAcm−2and temperatures up to 300°C. The key issues that currently limit the device performance, such as high base resistance, poor impurity control, and defects resulting from the heteroepitaxial growth, have been addressed. A physically based simulation suggested that GaN bipolar devices may still suffer from small minority-carrier lifetime in the absence of aforementioned processing problems.
Retroviral-mediated transfer of the galactocerebrosidase gene in neural progenitor cells (1998)

Globoid cell leukodystrophy (GCL or Krabbe disease) is a recessive disease caused by mutations of the lysosomal enzyme galactocerebrosidase (GALC) and twitcher is the murine model of GCL. We have prepared retroviral packaging cell lines to transduce the GALC gene. Retroviral transduction restored GALC activity in GCL fibroblasts and increased such activity to very high levels in immortalized neural progenitor cells (ST14A cells). GALC activity was also normalized in twitcher fibroblasts co-cultured with ST14A cells over-expressing GALC, demonstrating that this enzyme is secreted and can be imported efficiently by GALC-deficient cells. These results give the necessary background to evaluate the therapeutic effect in twitcher of brain grafting of neural progenitor cells engineered to release high levels of GALC.
Hydrolysis of penicillins and related compounds by the cell-bound penicillin acylase of Escherichia coli (1969)

1. A method is given for the preparation of penicillin acylase by using Escherichia coli N.C.I.B. 8743 and a strain selected for higher yield. The enzyme is associated with the bacterial cells and removes the side chains of penicillins to give 6-amino-penicillanic acid and a carboxylic acid. 2. The rates of penicillin deacylation indicated that p-hydroxybenzylpenicillin was the best substrate, followed in diminishing order by benzyl-, dl-alpha-hydroxybenzyl-, 2-furylmethyl-, 2-thienylmethyl-, d-alpha-aminobenzyl-, n-propoxymethyl- and isobutoxymethyl-penicillin. Phenylpenicillin and dl-alpha-carboxybenzylpenicillin were not substrates and phenoxymethyl-penicillin was very poor. 3. Amides and esters of the above penicillins were also substrates for the deacylation reaction, as were cephalosporins with a thienylmethyl side chain. 4. For the deacylation of 2-furylmethylpenicillin at 21 degrees the optimum pH was 8.2. The optimum temperature was 60 degrees at pH7. 5. By using selection A of N.C.I.B. 8743 and determining reaction velocities by assaying yields of 6-amino-penicillanic acid in a 10min. reaction at 50 degrees and pH8.2, the K(m) for benzylpenicillin was found to be about 30mm and the K(m) for 2-furylmethylpenicillin, about 10mm. The V(max.) values were 0.6 and 0.24mumole/min./mg. of bacterial cells respectively.
Towards mobile ad-hoc WANs: terminodes (2002)

Terminodes are personal devices that provide functionality of both the terminals and the nodes of the network. A network of terminodes is an autonomous, fully self-organized, wireless network, independent of any infrastructure. It must be able to scale up to millions of units, without any fixed backbone or server. In this paper we present the main challenges and discuss the main technical directions.
Social Disorder as a Social Good (2010)

In complex systems, disorder and order are interrelated, so that disorder can be an inevitable consequence of ordering. Often this disorder can be disruptive, but sometimes it can be beneficial. Different social groups will argue over what they consider to be disordered, so that naming of something as ‘disorder’ is often a political action. However, although people may not agree on what disorder is, almost everyone agrees that it is bad. This primarily theoretical sketch explores the inevitability of disorder arising from ordering systems and argues that a representative democracy has to tolerate disorder so as to function.
Paraneoplastic brain stem encephalitis in a woman with anti-Ma2 antibody (2001)

A woman developed brain stem encephalopathy in association with serum anti-Ma2 antibodies and left upper lobe lung mass. T2 weighted MRI of the brain showed abnormalities involving the pons, left middle and superior cerebellar peduncles, and bilateral basal ganglia. Immunohistochemical analysis for serum antineuronal antibodies was confounded by the presence of a non-neuronal specific antinuclear antibody. Immunoblot studies showed the presence of anti-Ma2 antibodies. A premortem tissue diagnosis of the lung mass could not be established despite two CT guided needle biopsies, and the patient died as a result of rapid neurological deterioration. The necropsy showed that the lung lesion was an adenocarcinoma which expressed Ma2 immunoreactive protein. Neuropathological findings included prominent perivascular inflammatory infiltrates, glial nodules, and neuronophagia involving the brain stem, basal ganglia, hippocampus and the dentate nucleus of the cerebellum. Ma2 is an autoantigen previously identified in patients with germ cell tumours of the testis and paraneoplastic brain stem and limbic encephalitis. Our patient's clinical and immunopathological findings indicate that this disorder can affect women with lung adenocarcinoma, and that the encephalitic changes predominate in those regions of the brain known to express high concentrations of Ma proteins.
Recombinant IL-10 and IL-10/Fc treatment down-regulate egg antigen-specific delayed hypersensitivity reactions and egg granuloma formation in schistosomiasis (1996)

In infection with the helminth Schistosoma mansoni, parasite eggs elicit a Th cell-mediated hepatic granulomatous inflammation that leads to scarring, portal hypertension, hemorrhage, and death. On the other hand, the cytokine IL-10 has been shown to decrease egg Ag-specific Th cell responses by down-regulating MHC class II as well as B7 costimulatory molecule expression on accessory cells. We now test the effect of IL-10 in vivo on models of egg Ag-specific hypersensitivity as well as on the natural disease. Systemic administration of IL-10 significantly inhibited delayed-type hypersensitivity reactions to egg Ag as well as primary and secondary granuloma formation to eggs embolized in the lung. However, significant inhibition of hepatic granuloma formation associated with the natural infection required the use of an IL-10/Fc fusion protein with a prolonged in vivo half-life. Lymph node cells from IL-10/Fc-treated mice produced less IL-2 and IFN-gamma, and more IL-4 and IL-10 than control cells, suggesting that reduced egg granuloma formation resulted primarily from down-regulation of Th1 responses. These results indicate that suitable administration of exogenous IL-10 can be effective in ameliorating immunopathologic damage associated with schistosomiasis.
Physical and Functional Interaction of Murine and Xenopus Smad7 with Bone Morphogenetic Protein Receptors and Transforming Growth Factor-β Receptors (1998)

Members of the transforming growth factor-beta (TGF-beta) family transmit signals from membrane to nucleus via intracellular proteins known as Smads. A subclass of Smad proteins has recently been identified that antagonize, rather than transduce, TGF-beta family signals. Smad7, for example, binds to and inhibits signaling downstream of TGF-beta receptors. Here we report that the C-terminal MAD homology domain of murine Smad7 (mSmad7) is sufficient for both of these activities. In addition, we show that mSmad7 interacts with activated bone morphogenetic protein (BMP) type I receptors (BMPR-Is), inhibits BMPR-I-mediated Smad phosphorylation, and phenocopies the effect of known BMP antagonists when overexpressed in ventral cells of Xenopus embryos. Xenopus Smad7 (XSmad7, previously termed Smad8) and mSmad7 are nearly identical within their bioactive C-domain, but have quite distinct N-domains. We found that XSmad7, similar to mSmad7, interacted with BMP and TGF-beta type I receptors and inhibited receptor-mediated phosphorylation of downstream signal-transducing Smads. However, XSmad7 is a less efficient inhibitor of TbetaR-I-mediated responses in mammalian cells than is mSmad7. Furthermore, overexpression of XSmad7 in Xenopus embryos produces patterning defects that are not observed following overexpression of mSmad7, suggesting that mSmad7 and XSmad7 may preferentially target distinct signaling pathways. Our results are consistent with the possibility that the C-domain of antagonistic Smads is an effector domain whereas the N-domain may confer specificity for distinct signaling pathways.
The first sutureless, laser‐welded, end‐to‐end bowel anastomosis (1989)

The use of laser energy to weld together tissue offers great promise in the expanding field of laser surgery. The published results of laser welding intestinal tissue have, to date, been limited to the successful laser closures of small enterotomies. This is the first report of using laser energy alone to create an end-to-end small bowel anastomosis. A biocompatible, water-soluble, intraluminal stent was employed during the laser welding of this sutureless, stapleless ileal anastomosis in a rabbit model. Excellent recovery and healing were observed. The rapidity, ease, and potential for full precision automation of laser welding mandates further research.
Role of Nitric Oxide as Mediator of Nerve Injury in Inflammatory Neuropathies (2007)

Different lines of evidence suggest that nitric oxide (NO) plays a key role in the pathogenesis of inflammatory neuropathies; however, it is still unclear which structures in the peripheral nerve are the primary targets of NO-mediated nerve injury. To address this issue, we determined the expression of NO metabolites in sural nerve biopsies and in cerebrospinal fluid from patients with inflammatory neuropathies and studied the pathologic effects of NO in an in vitro model of myelinated Schwann cell-neuron cocultures. In cerebrospinal fluid samples, nitrite levels remained unaltered; however, nitrotyrosine, a marker for peroxynitrite formation, could be identified in nerve biopsies from patients with inflammatory neuropathies. In an in vitro model of Schwann cell neuron cocultures, high concentrations of NO induced robust demyelination, which was the result of NO-mediated axonal injury, whereas Schwann cell viability remained unaffected. These findings suggest that in contrast to Schwann cells, sensory neurons are the primary target of NO-mediated cytotoxicity and the loss of myelin is the result of selective damage to axons rather than a direct harmful effect to Schwann cells. Our findings imply that NO contributes to the pathologic changes seen in the inflamed peripheral nervous system, which is characterized by the features of axonal injury and subsequent myelin degradation, previously described as Wallerian-like degeneration.
The design of a QoS-controlled ATM-based communications system in Chorus (1995)

We describe the design of an application platform able to run distributed real-time and multimedia applications alongside conventional UNIX programs. The platform is embedded in a microkernel/PC environment and supported by an ATM-based, QoS-driven communications stack. In particular, we focus on resource-management aspects of the design and deal with CPU scheduling, network resource-management and memory-management issues. An architecture is presented that guarantees QoS levels of both communications and processing with varying degrees of commitment as specified by user-level QoS parameters. The architecture uses admission tests to determine whether or not new activities can be accepted and includes modules to translate user-level QoS parameters into representations usable by the scheduling, network, and memory-management subsystems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Two successive outbreaks of mumps in Nova Scotia among vaccinated adolescents and young adults (2006)

The predominance in these outbreaks of infected people of university age not only highlights an environment with potential for increased transmission but also raises questions about the efficacy of the MMR vaccine. The people affected may represent a "lost cohort" who do not have immunity from natural mumps infection and were not offered a 2-dose schedule. Given the current level of mumps activity around the world, clinicians should remain vigilant for symptoms of mumps.
Tau Protein and the Neurofibrillary Pathology of Alzheimer's Disease (1996)

Abundant neurofibrillary tangles, neuropil threads and senile plaque neurites constitute the neurofibrillary pathology of Alzheimer's disease. They form in the nerve cells that undergo degeneration in the disease, in which their regional distribution correlates with the degree of dementia. Each lesion contains the paired helical filament (PHF) as its major component. PHFs are composed of the microtubule-associated protein tau in a hyperphosphorylated state. PHF-tau is hyperphosphorylated on all six adult brain isoforms. As a consequence, tau is unable to bind to microtubules and is believed to self-assemble into the PHF. Several candidate protein kinases and protein phosphatases have been identified through in vitro experiments.