gebhart/patrepeval huggingface dataset:
Optimal routing in multihop packet radio networks (2002)

An optimal routing algorithm for slotted Aloha PRNs (packet radio networks) which minimizes the average packet delay is developed. The network topology and traffic are arbitrary but fixed. The packet radio nodes serve as sources (and sinks) of traffic as well as repeaters which forward packets to other nodes. The optimal routing algorithm captures the important PRN features discussed and avoids routes that result in high levels of interference and delay. Numerical results which show that optimal routing can result in dramatic performance improvements are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Changes in aortic lysyl oxidase activity in diet-induced atherosclerosis in the rabbit. (1981)

This study assessed the responses of lysyl oxidase, the enzyme that initiates covalent crosslinking in elastic and collagen, by studying the aortic tissue of rabbits after arteriosclerosis had been induced by diet. Rabbits in the experimental group were fed an atherogenic diet of rabbit chow supplemented with 8% peanut oil and 2% cholesterol for varying periods of time, while the control group was fed only rabbit chow. Lysyl oxidase activity was found to be distributed throughout the length of the thoracic and abdominal aortas of the normal rabbits, However, rabbits fed the atherogenic diet showed marked increases in enzyme in the aortic arch, a change that was initially evident after 30 days and became greatest (2.5 times that of the controls) after 90 days. Enzyme activity in the study rabbits increased only minimally in the abdominal aortic wall. Aortic prolyl hydroxylase activity measured after 60 days of feeding changed in degree and manner similar to lysyl oxidase activity. These region-specific changes in enzyme activities correlated with the distribution and severity of aortic lesions in this model of the disease. Lysyl oxidase activity increased dramatically in this model of atherosclerosis, suggesting that this extracellular enzyme activity may prove to be a vulnerable and accessible point of control of the fibrotic response in atherosclerosis.
Comparison of a Multiplex Reverse Transcriptase–Polymerase Chain Reaction for BCR-ABL to Fluorescence In Situ Hybridization, Southern Blotting, and Conventional Cytogenetics in the Monitoring of Patients With Ph1-Positive Leukemias (2000)

A multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) assay for both major forms of BCR-ABL was compared with fluorescence in situ hybridization (FISH), karyotyping, and Southern blotting for disease monitoring in 37 follow-up bone marrow samples from 32 patients with Ph1-positive leukemia. Of these 37 samples, 33 were from patients with chronic myeloid leukemia (CML) (26 post allogeneic bone marrow transplantation [AlloBMT] and seven during interferon-alpha therapy) and 4 from Ph1-positive acute lymphoblastic leukemia (ALL) patients (1 post AlloBMT and 3 post high dose chemotherapy). For the 27 samples studied after AlloBMT (26 CML and 1 Ph1-positive ALL) the time after transplantation ranged from 1 to 107 months (median 47.5 months). In 8 (22%) of the 37 samples there were discrepant results among methods. The discrepancy rates relative to other techniques were: karyotyping 17% (5 of 29), Southern blotting 18% (6 of 33), multiplex RT-PCR 8% (3 of 37), and FISH 8% (3 of 37). Therefore, the relative accuracy of each method for disease monitoring in Ph1-positive leukemia was: 83% (24 of 29) for karyotyping, 82% (27 of 33) for Southern blotting, 92% (34 of 37) for FISH, and 92% (34 of 37) for multiplex RT-PCR. This multiplex RT-PCR assay appears equivalent to FISH in terms of accuracy, simplicity, and turnaround time and both are superior to Southern blot and conventional cytogenetics in the laboratory monitoring of Ph1-positive leukemias.
Formation of Solid-Supported Lipid Bilayers:  An Integrated View (2006)

Supported lipid bilayers (SLBs) are popular models of cell membranes with potential bio-technological applications. A qualitative understanding of the process of SLB formation after exposure of small lipid vesicles to a hydrophilic support is now emerging. Recent studies have revealed a stunning variety of effects that can take place during this self-organization process. The ensemble of results in our group has revealed unprecedented insight into intermediates of the SLB-formation process and has helped to identify a number of parameters that are determinant for the lipid deposition on solid supports. The pathway of lipid deposition can be tuned by electrostatic interactions and by the presence of calcium. We emphasize the importance of the solid support in the SLB-formation process. Our results suggest that the molecular-level interaction between lipids and the solid support needs to be considered explicitly, to understand the rupture of vesicles and the formation of SLBs as well as to predict the properties of the resulting SLB. The impact of the SLB-formation process on the quality and the physical properties of the resulting SLB as well as implications for other types of surface-confined lipid bilayers are discussed.
Structure determination of extracellular fragments of amyloid proteins involved in Alzheimer's disease and Dutch‐type hereditary cerebral haemorrhage with amyloidosis (1994)

Amyloid deposition is a biochemical and histopathologic hallmark of various clinical forms of amyloidoses including Alzheimer's disease and the Dutch-type hereditary cerebral haemorrhage with amyloidosis. The self-aggregating peptides responsible for these irreversible deposits have been sequenced but the mechanisms involved in the aggregation processes are not well understood. In order to gain an understanding of the possible structures prior to self-association, the extracellular fragment of the Alzheimer amyloid protein (beta A4) responsible for the deposits (the 'native' fragment) and a mutant of this with a single residue substitution (which is responsible for deposits in the Dutch-type amyloidosis) were examined by 1H-NMR spectroscopy. Interproton distance constraints were derived from NMR experimental data and incorporated into tertiary structure calculations using a simulated annealing protocol. Solution conformations of the fragment peptides associated with the two forms of amyloidoses are presented and compared. Although in both peptides the existence of a mixture of conformations in equilibrium is likely, one such population of structures possesses a flexible N-terminus and a well defined C-terminal region. The latter region includes a helical segment and a terminal turn-like structure. These structural features may be important for the basis of amyloid formation. Comparison of the calculated structures of the two peptides revealed a conformationally different region arising from the conservative substitution of Gln22 for Glu22. This region may be responsible for altered binding in the mutant peptide, giving rise to the clinically different form of amyloidosis.
Fluid−Liquid Transitions of Poly(ethylene-co-octene-1) in Supercritical Ethylene Solutions (2000)

Fluid−liquid pressures are measured and correlated with two SAFT equations of state for poly(ethylene-co-octene-1) solutions in supercritical ethylene at temperatures up to 180 °C. These cloud-point pressures are found to depend strongly on the molecular weight of the polymer and the branch density but weakly on the polymer concentration in the range from 0.05 to 0.15 polymer weight fraction. EO solutions in ethylene are found to exhibit U-LCST behavior.
Structural modifications of LixV2O5 in a composite cathode (0≤x < 2) investigated by Raman microspectrometry (2011)

Abstract The structural behaviour of the Li x V 2 O 5 active material in a composite electrode is determined upon lithium insertion/extraction in the 4–2.15 V potential range (0≤ x &lt; 2) using Raman microspectrometry. For the first time, a detailed description of phase transitions occurring in the V 2 O 5 composite electrode is provided by Raman spectroscopy, on the basis of a complete assignment of the spectra. This approach has been successful because of the knowledge of the Raman fingerprints of the chemically lithiated compounds, combined with a rigorous and systematic deconvolution of the Raman spectra obtained for the electrochemically lithiated materials. The successive emergence of α, ε, δ and γ phases is clearly established, as well as the α/ε, ε/δ and δ/γ biphasic regions corresponding to the 3.4, 3.2 and 2.3 V potential plateaus, respectively. This study shows that Raman spectroscopy constitutes a sensitive and relevant tool to explore the emergence of the various phases governing the electrochemical properties of cathode materials for lithium batteries. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Serological responses of cats to feline immunodeficiency virus (1990)

The proteins of feline immunodeficiency virus (FIV) were identified by sodium dodecylsulphate poly-acrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. Purified [35S]methionine/cysteine-labelled virus contained proteins of Mr 120, 24, 17, and 10kD, of which the most prominent were p24 and p17, and minor components of 62, 54, 52, 41 and 32kD. Sera from FIV-infected cats precipitated two glycoproteins (gp) of Mr 120kD (gp120) and 41kD (gp41) from lysates of [14C]glucosamine-labelled infected cells. Purified virus contained very little or no detectable glycoproteins. The serological response to individual viral proteins was followed in experimentally infected cats by immunoblotting. Since purified virus was a poor source of gp120, a method using FIV-infected cell lysates was developed. Cats produced antibodies to gp120, p55, p24 and p17. (The p55 was presumed to be a precursor of p24 and p17.) Following infection, antibodies developed first to p24 and subsequently to p17, p55 and gp120. Sera from cats infected with three separate isolates of FIV, two from the UK and one from the USA, had cross-reacting antibodies to all of these viral proteins. The criteria for identification of seropositive cats were defined. The minimum requirement for a positive immunoblot was antibody to gp120 or to at least three core proteins (p55, p24 and p17). Comparison of two commercial enzyme-linked immunosorbent assay (ELISA) kits and immunoblotting indicated that false-positive results occurred as a result of non-specific reactions in the ELISA systems.
Mice Lacking Endogenous IL-10–Producing Regulatory B Cells Develop Exacerbated Disease and Present with an Increased Frequency of Th1/Th17 but a Decrease in Regulatory T Cells (2011)

IL-10-producing B cells, also known as regulatory B cells (Bregs), play a key role in controlling autoimmunity. In this study, we report that chimeric mice specifically lacking IL-10-producing B cells (IL-10(-/-)B cell) developed an exacerbated arthritis compared with chimeric wild-type (WT) B cell mice. A significant decrease in the absolute numbers of Foxp3 regulatory T cells (Tregs), in their expression level of Foxp3, and a marked increase in inflammatory Th1 and Th17 cells were detected in IL-10(-/-) B cell mice compared with WT B cell mice. Reconstitution of arthritic B cell deficient (μMT) mice with different B cell subsets revealed that the ability to modulate Treg frequencies in vivo is exclusively restricted to transitional 2 marginal zone precursor Bregs. Moreover, transfer of WT transitional 2 marginal zone precursor Bregs to arthritic IL-10(-/-) mice increased Foxp3(+) Tregs and reduced Th1 and Th17 cell frequencies to levels measured in arthritic WT mice and inhibited inflammation. In vitro, IL-10(+/+) B cells established longer contact times with arthritogenic CD4(+)CD25(-) T cells compared with IL-10(-/-) B cells in response to Ag stimulation, and using the same culture conditions, we observed upregulation of Foxp3 on CD4(+) T cells. Thus, IL-10-producing B cells restrain inflammation by promoting differentiation of immunoregulatory over proinflammatory T cells.
Inhibiting HIV Fusion with a β-Peptide Foldamer (2005)

Linear peptides derived from the HIV gp41 C-terminus (C-peptides), such as the 36-residue Fuzeon, are potent HIV fusion inhibitors. These molecules bind to the N-peptide region of gp41 and inhibit an intramolecular protein-protein interaction that powers fusion of the viral and host cell membranes. The N-peptide region contains a surface pocket that is occupied in the post-fusion state by three alpha-helical residues found near the gp41 C-terminus: Trp628, Trp631, and Ile635-the WWI epitope. Here, we describe a set of beta3-decapeptides (betaWWI-1-4) in which the WWI epitope is presented on one face of a short 14-helix stabilized by macrodipole neutralization and side chain-side chain salt bridges. betaWWI-1-4 bind in vitro to IZN17, a validated gp41 model, and inhibit syncytia formation in cell culture. Molecules lacking a complete WWI functional epitope neither bind IZN17 nor inhibit syncytia formation. These results provide evidence that short beta-peptide 14-helices can inhibit an intramolecular protein-protein interaction in vivo. Molecules related to betaWWI-1-4 could represent starting points for the development of highly potent inhibitors or antigens effective against HIV or other viruses, including SARS, Ebola, HRSV, and influenza, that employ common fusion mechanisms.
The combination of tumor necrosis factor ? blockade with interleukin-1 and interleukin-17 blockade is more effective for controlling synovial inflammation and bone resorption in an ex vivo model (2001)

The inhibitory effect of sTNFR on IL-6 production and collagen degradation in RA synovium and bone was increased in combination with sIL-17R and sIL-1RII. These results support the concept of combination therapy, which may increase the percentage of responding patients as well as the degree of individual patient response.
Gecko-Inspired Carbon Nanotube-Based Self-Cleaning Adhesives (2008)

The design of reversible adhesives requires both stickiness and the ability to remain clean from dust and other contaminants. Inspired by gecko feet, we demonstrate the self-cleaning ability of carbon nanotube-based flexible gecko tapes.
IKKγ Serves as a Docking Subunit of the IκB Kinase (IKK) and Mediates Interaction of IKK with the Human T-cell Leukemia Virus Tax Protein (1999)

The tax gene product of human T-cell leukemia virus type I induces activation of transcription factor NF-kappaB, which contributes to deregulated expression of various cellular genes. Tax expression triggers persistent phosphorylation and degradation of the NF-kappaB inhibitory proteins IkappaBalpha and IkappaBbeta, resulting in constitutive nuclear expression of NF-kappaB. Recent studies demonstrate that Tax activates the IkappaB kinase (IKK), although the underlying mechanism remains unclear. In this report, we show that Tax physically interacts with a regulatory component of the IKK complex, the NF-kappaB essential modulator or IKKgamma (NEMO/IKKgamma). This molecular interaction appears to be important for recruiting Tax to the IKK catalytic subunits, IKKalpha and IKKbeta. Expression of NEMO/IKKgamma greatly promotes binding of Tax to IKKalpha and IKKbeta and stimulates Tax-mediated IKK activation. Interestingly, a mutant form of Tax defective in IKK activation exhibited a markedly diminished level of NEMO/IKKgamma association. These findings suggest that the physical interaction of Tax with NEMO/IKKgamma may play an important role in Tax-mediated IKK activation.
Demonstration of photoluminescence in nonanodized silicon (1992)

The formation of photoluminescent porous Si in an etchant solution made from the HF-HNO3-CH3COOH system is reported. The porous Si is characterized on the basis of its photoluminescence (PL) spectra and the degradation of the PL during exposure to laser irradiation. The surface topography as characterized by atomic force microscopy (AFM) reveals features on the order of 400–600 Å. The effect of annealing the porous Si in vacuum on the PL intensity is described and correlated to the breakdown of Si—H bonds on the porous Si surface.
Release of Growth Factors, Cytokines and Therapeutic Molecules by Hyaluronan-based Hydrogels (2012)

Hyaluronan (HA) is a highly biocompatible biopolymer that is widely used for a variety of therapeutic purposes including surgical preparations, adhesion prevention, viscosupplementation and drug and cytokine delivery. Delivery can be accomplished effectively when HA-based carriers are synthesized in the form of hydrogels, though doing so normally requires chemical modification of the native HA structure. Solute delivery from HA-based gels can be either "simple", that is from a gel not including separate components intended to control release, or "regulated" when specific components are included for that purpose. A variety of modified forms of HA have been developed and used for delivery of desired molecules in therapeutic, clinical, veterinary and laboratory research environments, and the number of such applications is likely to grow in future years.
Structure of a receptor-binding fragment from human luteinizing hormone beta-subunit determined by [1H]- and [15N]nuclear magnetic resonance spectroscopy. (1992)

The structure of the glycoprotein hormones (LH, CG, FSH, and TSH) and their mechanism of receptor recognition are problems of long-standing interest and speculation. Here we describe the two-dimensional [1H]nuclear magnetic resonance ([1H]NMR) analysis of a linear peptide model for the intercysteine sequence (38-57) from the beta-subunit of human (h) LH. This sequence contains functional determinants for receptor binding and postreceptor activation and is predicted by computer-based modeling to fold as a compact minidomain containing a central amphipathic helix. To test this prediction, an Arg-extended disulfide-free (38-57) analog of enhanced solubility was prepared for complementary circular-dichroic and two-dimensional NMR studies. The linear peptide retains ovarian membrane receptor-binding activity. Although the peptide is not highly structured in aqueous solution, circular-dichroic analysis shows partial alpha-helix formation in a lipophilic medium (50% trifluoroethanol). Complete sequential assignment is obtained in 50% trifluoroethanol based on homonuclear and [15N]edited heteronuclear NMR methods. alpha-Helix-related (i,i + 3) connectivities are observed by nuclear-Overhauser effect spectroscopy that define an amphipathic alpha-helical segment (residues 41-48). Additional long range nuclear-Overhauser effects are observed in the C-terminal region that are consistent with beta-turns involving one or more proline residues; these may serve to reverse the direction of the peptide chain. A nuclear-Overhauser effect contact is identified between residues 38 and 55 at opposite ends of the linear sequence, suggesting that a loop configuration is significantly populated in this solvent system. These results, taken together, characterize elements of ordered structure in the 38-57 peptide, which appear to be distinguishing features of hLH (and the homologous region of hCG). We propose that the structure of this peptide provides a model for the structure of the corresponding region of native hLH in the hormone-receptor complex.
Annealing effects on structural and transport properties of rf-sputtered CoFeB∕MgO∕CoFeB magnetic tunnel junctions (2006)

Annealing effects on the structural and transport properties of sputtered CoFeB∕MgO∕CoFeB magnetic tunnel junctions deposited on SiO2∕Si were investigated. At the as-deposited state, the CoFeB was amorphous at the CoFeB∕MgO interface. High-resolution transmission electron microscope image clearly shows that after annealing at 270°C for 1h, crystallization of amorphous CoFeB (three to four monolayers) with lattice matching to MgO (100) occurred locally at the interface between MgO and CoFeB, producing a magnetoresistance (MR) around 35%–40%. After annealing at 360°C for 40min, the MR increased to 102%. The increase in the MR with annealing is attributed to the complete formation of (100) crystalline structure of CoFeB well lattice matched with the (100)-oriented MgO barrier. The bias voltage dependence of the MR shows a consistent correlation with each CoFeB∕MgO interface.
Enhancing the Global Ocean Observing System to meet evidence based needs for the ecosystem‐based management of coastal ecosystem services (2014)

Abstract Ecosystem‐based approaches ( EBAs ) to managing anthropogenic pressures on ecosystems, adapting to changes in ecosystem states (indicators of ecosystem health), and mitigating the impacts of state changes on ecosystem services are needed for sustainable development. EBAs are informed by integrated ecosystem assessments ( IEAs ) that must be compiled and updated frequently for EBAs to be effective. Frequently updated IEAs depend on the sustained provision of data and information on pressures, state changes, and impacts of state changes on services. Nowhere is this truer than in the coastal zone, where people and ecosystem services are concentrated and where anthropogenic pressures converge. This study identifies the essential indicator variables required for the sustained provision of frequently updated IEAs , and offers an approach to establishing a global network of coastal observations within the framework of the G lobal O cean O bserving S ystem. The need for and challenges of capacity‐building are highlighted, and examples are given of current programmes that could contribute to the implementation of a coastal ocean observing system of systems on a global scale. This illustrates the need for new approaches to ocean governance that can achieve coordinated integration of existing programmes and technologies as a first step towards this goal.
Neurodegeneration with Tau Accumulation in a Transgenic Mouse Expressing V337M Human Tau (2002)

Formation of neurofibrillary tangles (NFTs) is a common neuropathological feature found in several neurodegenerative diseases, including Alzheimer's disease. We have developed a transgenic (Tg) mouse expressing mutant human tau (V337M), derived from frontotemporal dementia parkinsonism-17. V337M Tg mice revealed tau aggregations in the hippocampus, which fulfills the histological criteria for NFTs in human neurodegenerative diseases. Concurrent with the accumulation of RNA and phosphorylated tau, neurons exhibited morphological characteristics of degenerating neurons, which include a loss of microtubules, accumulation of ribosomes, plasma and nuclear membrane ruffling, and swelling of the Golgi network. Thus, mutant tau induces neuronal degeneration associated with the accumulation of RNA and phosphorylated tau. The functional consequences of this neuronal degeneration was evidenced by the reduction of hippocampal neural activity and behavioral abnormality in Tg mice.