gebhart/patrepeval huggingface dataset:
Hydrophobic Enhancement of Dopa-Mediated Adhesion in a Mussel Foot Protein (2012)

Dopa (3,4-dihydroxyphenylalanine) is recognized as a key chemical signature of mussel adhesion and has been adopted into diverse synthetic polymer systems. Dopa's notorious susceptibility to oxidation, however, poses significant challenges to the practical translation of mussel adhesion. Using a surface forces apparatus to investigate the adhesion of mussel foot protein 3 (Mfp3) "slow", a hydrophobic protein variant of the Mfp3 family in the plaque, we have discovered a subtle molecular strategy correlated with hydrophobicity that appears to compensate for Dopa instability. At pH 3, where Dopa is stable, Mfp3 slow, like Mfp3 "fast" adhesion to mica, is directly proportional to the mol % of Dopa present in the protein. At pH of 5.5 and 7.5, however, loss of adhesion in Mfp3 slow was less than half that occurring in Mfp3 fast, purportedly because Dopa in Mfp3 slow is less prone to oxidation. Indeed, cyclic voltammetry showed that the oxidation potential of Dopa in Mfp3 slow is significantly higher than in Mfp3 fast at pH of 7.5. A much greater difference between the two variants was revealed in the interaction energy of two symmetric Mfp3 slow films (E(ad) = -3 mJ/m(2)). This energy corresponds to the energy of protein cohesion which is notable for its reversibility and pH independence. Exploitation of aromatic hydrophobic sequences to protect Dopa against oxidation as well as to mediate hydrophobic and H-bonding interactions between proteins provides new insights for developing effective artificial underwater adhesives.
Assembly of Aβ Amyloid Protofibrils:  An in Vitro Model for a Possible Early Event in Alzheimer's Disease (1999)

Amyloid fibrils comprising primarily the peptides A beta 40 and A beta 42 are a defining feature of the Alzheimer's disease (AD) brain, and convergent evidence suggests that the process of their formation plays a central role in the AD pathogenic pathway. Elucidation of fibril assembly is critical for the discovery of potential AD diagnostics and therapeutics, since the pathogenic entity is not necessarily the product fibril, but could be a precursor species whose formation is linked to fibrillogenesis in vivo. Atomic force microscopy allowed the identification of an unanticipated intermediate in in vitro fibril formation, the A beta amyloid protofibril. This manuscript describes studies of the structure of the A beta 40 protofibril and its in vitro assembly and disassembly using atomic force microscopy (AFM). The A beta 40 protofibril has a height of ca. 4.3 +/- 0.5 nm and a periodicity of ca. 20 +/- 4.7 nm. The rate of its elongation depends on the total concentration of A beta 40, the temperature, and ionic strength of the medium. A beta 42 and A beta 40 protofibrils elongate at a comparable rate. Statistical analysis of AFM data reveals a decrease in the number of protofibrils with time, indicating that coalescence of smaller protofibrils contributes to protofibril elongation. Similar analysis reveals that protofibrils shorten while the number of protofibrils also decrease following dilution, indicating that protofibril disassembly does not proceed by a reverse of the assembly process. These investigations provide systematic data defining factors affecting A beta fibrillization and, thus, should be valuable in the design of high-throughput assays to identify agents which alter A beta protofibril assembly.
Moving towards a Fully Automatic Knowledge Assessment Tool (2007)

Information about a studentâ??s level or state of knowledge is a key aspect for efficient, personalized learning activities. E-learning systems gain such information in two ways: directly by examining usersâ?? self-assessment and administering predefined tests and indirectly by making inferences on observed user behaviors. However, most of the current solution approaches either demand excessive manpower or lack required reliability. To overcome these problems, we have developed the e-Examiner, an assessment tool that supports the assessment process by creating automatically test items, assessing studentsâ?? answers and providing feedback. In this paper, we firstly give an overview about a variety of computer-assisted and computer-based assessment systems and methods that support formative assessment activities. Secondly, we introduce the overall concept and architecture of the e-Examiner. Thirdly, we outline implementation details and evaluation results of our prototype implementation. Our solution approach is based on the set of statistical similarity measures defined by the ROUGE toolset for automatic summary evaluation.
Investigation of Antibacterial Activity and Related Mechanism of a Series of Nano-Mg(OH)<sub>2</sub> (2013)

Here we reported the antibacterial effect and related mechanism of three nano-Mg(OH)(2) slurries using Escherichia coli as model bacteria. X-ray diffraction (XRD), scanning electron microscopy (SEM) and laser particle size analysis revealed that the as-synthesized Mg(OH)(2)_(MgCl2), Mg(OH)(2)_(MgSO4) and Mg(OH)(2)_(MgO) are all composed by nanoflakes with different sizes, and their aggregates in water are 5.5, 4.5, and 1.2 μm, respectively. Bactericidal tests showed that the antibacterial efficiency is conversely correlated with the size of Mg(OH)(2) aggregates. Transmission electron microscopy (TEM) observation have not provided evidence of cellular internalization, however, the antibacterial effect is positive correlation to the loss of integrity of cell walls. SEM and zeta potential analysis revealed that the adhering ability of Mg(OH)(2) on the bacterial surface is Mg(OH)(2)_(MgCl2) > Mg(OH)(2)_(MgSO4) > Mg(OH)(2)_(MgO), indicating the toxicity of Mg(OH)(2) may be caused by the electrostatic interaction-induced external adsorption. Confocal laser scanning microscopy (CLSM) further revealed that the adhering of Mg(OH)(2) on the bacterial surface could increase the permeability of cell membranes. Taken together, the antibacterial mechanism of nano-Mg(OH)(2) could be as follows: nano-Mg(OH)(2) adsorbed on the bacterial surface by charge attraction first, and then destroyed the integrity of cell walls, which resulting in the final death of bacteria.
Behaviour of implantable coronary stents during magnetic resonance imaging (1999)

BACKGROUND: Magnetic resonance imaging (MRI) becomes more and more a routine diagnostic tool in clinical cardiology. In patients undergoing MRI, metallic implants may be harmful by motion or heating under certain circumstances. Many cardiac patients have implanted intracoronary stents. However, the safety of these metallic implants and especially their temperature behaviour during MRI has not been sufficiently tested. METHODS: This study investigated motion and temperature changes of 14 different stents for intracoronary application in two clinical scanners at field strengths of 1.0 and 1.5 T. At 1.5 T these studies were repeated after implantation of the stents into the coronary arteries of excised porcine hearts. Furthermore, the clinical status of 33 patients was assessed after a cardiac MR study and compared with a group of 33 patients matched for age, sex and risk factors for restenosis. RESULTS: No visible motion of the stents was observed. Furthermore, using a highly sensitive infrared camera any significant heating of the stents during MRI could be excluded. The rate of clinical events was not different in patients after MRI as compared with the control group. CONCLUSION: It is concluded that MRI is safe in patients with the currently available intracoronary stents.
Optimal pump wavelength in the /sup 4/I/sub 15/2/-/sup 4/I/sub 13/2/ absorption band for efficient Er/sup 3+/-doped fiber amplifiers (1989)

The authors report the measured gain of a highly efficient erbium-doped fiber amplifier pumped at wavelengths between 1.46 and 1.51 mu m. The optimal pump wavelength, lambda /sub opt/, was determined to be 1.475 mu m. At this wavelength, the maximum gain coefficients for signals at 1.531 and 1.544 mu m were 2.3 and 2.6 dB/mW, respectively. At lambda /sub opt/, high gains ranging from 32 dB at pump power P/sub p/=20 mW up to 40 dB at P/sub p/=80 mW were obtained. These modest pump powers are within the capabilities of currently available 1.48- mu m diode lasers. The width about lambda /sub opt/ for 3-dB gain variation exceeded 27 nm for P/sub p/=10 mW and 40 nm for P/sub p/>20 mW. With this weak dependence on pump wavelength, single-longitudinal-mode lasers do not have a significant advantage over practical Fabry-Perot multimode pump lasers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Endoscopic endonasal skull base surgery: analysis of complications in the authors' initial 800 patients (2010)

Endoscopic endonasal skull base surgery provides a viable median corridor based on anatomical landmarks and is customized according to the specific pathological process. This corridor should be considered as the sole access or may be combined with traditional approaches. With the incremental acquisition of skills and experience, endoscopic endonasal approaches have an acceptable safety profile in select patients presenting with various skull base pathologies.
Collagen fibril bundles: a branching assembly unit in tendon morphogenesis (1989)

The assembly, deposition and organization of collagen fibril bundles and their composite fibrils were studied during morphogenesis of the chick embryo tendon using electron microscopy, serial sections and computer-assisted three-dimensional reconstruction techniques. The 14-day chick embryo is a stage when tendon architecture is being established and rapid changes in the mechanical properties occur between days 14 and 17 of development. Tendon matrix structure develops from discrete subunits, bundles of collagen fibrils. The bundles branch; undergo a gradual rotation over several micrometers; are intimately associated with the cellular elements of the developing tendon; and form arborizing networks within and among fascicles. The organization of discrete fibril segments into bundles, during the establishment of tendon architecture and function, where the segmental fibrillar components could interact with the interfibrillar matrix as well as with adjacent fibrils would contribute to the stabilization of this structure. The observed gradual rotation of the bundles would serve to stabilize the immature bundle through the physical twining of the composite fibrils while the extensive branching of the bundles observed at 14-days of development and their intimate association with the cellular elements would provide a higher order of structure stabilization.
A Shrink Wrapping Approach to Remeshing Polygonal Surfaces (1999)

Due to their simplicity and flexibility, polygonal meshes are about to become the standard representation for surface geometry in computer graphics applications. Some algorithms in the context of multiresolution representation and modeling can be performed much more efficiently and robustly if the underlying surface tesselations have the special subdivision connectivity. In this paper, we propose a new algorithm for converting a given unstructured triangle mesh into one having subdivision connectivity. The basic idea is to simulate the shrink wrapping process by adapting the deformable surface technique known from image processing. The resulting algorithm generates subdivision connectivity meshes whose base meshes only have a very small number of triangles. The iterative optimization process that distributes the mesh vertices over the given surface geometry guarantees low local distortion of the triangular faces. We show several examples and applications including the progressive transmission of subdivision surfaces.
Medical treatment of inflammatory bowel disease: new therapies, new drugs. (1987)

Ulcerative colitis, ulcerative proctitis and Crohn's disease are chronic inflammatory conditions that affect the gastrointestinal tract. Conventional treatment has stressed the role of anti-inflammatory agents to suppress the inflammatory response. New compounds that can deliver 5-aminosalicylic acid to the colon have recently been released in Canada. Metronidazole and azathioprine may also be of benefit in Crohn's disease. Therapy with cyclosporine and clonidine should be based on the results of further clinical trials. The use of nutritional support as primary therapy in Crohn's disease appears promising. At present, both pharmacologic and nutritional therapies should be considered in the treatment of inflammatory bowel disease.
Bone Turnover across the Menopause Transition: Correlations with Inhibins and Follicle-Stimulating Hormone (2006)

Decreases in inhibin levels across the menopause transition are associated with increasing bone turnover, regardless of changes in sex steroids or FSH.
Multiple Incremental Decremental Learning of Support Vector Machines (2009)

We propose a multiple incremental decremental algorithm of Support Vector Machine (SVM). Conventional single incremental decremental SVM can update the trained model efficiently when single data point is added to or removed from the training set. When we add and/or remove multiple data points, this algorithm is time-consuming because we need to repeatedly apply it to each data point. The proposed algorithm is computationally more efficient when multiple data points are added and/or removed simultaneously. The single incremental decremental algorithm is built on an optimization technique called parametric programming. We extend the idea and introduce multi-parametric programming for developing the proposed algorithm. Experimental results on synthetic and real data sets indicate that the proposed algorithm can significantly reduce the computational cost of multiple incremental decremental operation. Our approach is especially useful for online SVM learning in which we need to remove old data points and add new data points in a short amount of time. 1
Efficacy of (<i>S</i>)‐1‐(3‐hydroxy‐2‐phosphonylmethoxypropyl)cytosine and 9‐(1,3‐dihydroxy‐2‐propoxymethyl)guanine for the treatment of murine cytomegalovirus infection in severe combined immunodeficiency mice (1992)

Mice with severe combined immunodeficiency (SCID) inoculated intraperitoneally with murine cytomegalovirus (MCMV) develop a wasting syndrome at 3-4 days and die at 6-9 days after the infection. 9-(1,3-Dihydroxy-2-propoxymethyl)guanine (DHPG, ganciclovir) and (S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine (HPMPC) were compared for their efficacy against MCMV-induced disease and mortality in SCID mice. Under all treatment conditions, i.e., administration of the test compounds for 5 consecutive days starting on the day of infection (day 0), for 5 consecutive days starting on day 4 after the infection, 2 periods of 3 consecutive days starting on day 0 and day 9 after infection, or as a single dose on day 3 before infection, HPMPC proved far superior to ganciclovir in delaying the onset of the disease and increasing the lifespan of the MCMV-infected mice.
Detection of bacteriophage VSH-1<i>svp38</i>gene in<i>Brachyspira</i>spirochetes (2003)

VSH-1 is a mitomycin C-inducible, non-lytic, phage-like agent that packages random 7.5-kb fragments of the Brachyspira hyodysenteriae genome. VSH-1 is the first recognized mechanism for gene transfer between B. hyodysenteriae cells. To analyze the distribution of VSH-1 among spirochetes, a 344-bp probe for gene svp38, encoding the VSH-1 major head protein, was amplified by polymerase chain reaction and used in Southern blot hybridizations with genomic DNA from various spirochete genera. The svp38 probe hybridized to a 40-kb SalI-SmaI fragment of the B. hyodysenteriae B78(T) chromosome, indicating VSH-1 DNA insertion into the chromosome at a unique site. Restriction endonuclease digested DNAs of 27 spirochete strains representing six Brachyspira species (B. hyodysenteriae, B. innocens, B. pilosicoli, B. murdochii, B. intermedia, B. alvinipulli) contained a single fragment hybridizing with the svp38 probe. DNAs from spirochete species of the genera Treponema, Spirochaeta, Borrelia, and Leptospira did not hybridize with the probe. VSH-1-like agents appear to be widely distributed among Brachyspira species and, as has been demonstrated for B. hyodysenteriae, may serve as useful gene transfer agents for those other species.
Characterization of temperature-dependent biophysical properties during laser mediated cartilage reshaping (1999)

Laser radiation can be used to reshape cartilage tissue into new morphologic configurations. When a critical temperature is attained, mechanically deformed cartilage becomes malleable and may be reshaped into new geometric configurations that harden as the tissue cools. This temperature dependent process results in mechanical stress relaxation and is characteristic of a phase transformation. The principal advantages of using laser radiation for the generation of thermal energy in tissue are precise control of both the space-time temperature distribution and time-dependent thermal denaturation kinetics. We illustrate the utility of laser mediated cartilage reshaping in ex vivo porcine model of reconstructive nasal and laryngeal surgery, and attempt to determine the temperature range in which accelerated stress relaxation occurs during laser mediated cartilage reshaping. Optimization of the reshaping process requires identification of the temperature dependence of this phase transformation and its relationship to observed changes in cartilage optical (diffuse scattering), mechanical (internal stress), and thermodynamic properties (heat capacity). Light scattering, infrared radiometry, and modulated differential scanning calorimetry were used to measure temperature-dependent changes in the biophysical properties of cartilage tissue during fast (laser mediated) and slow heating (conventional calorimetric beating). Our studies using MDSC and laser probe techniques have identified changes in tissue thermodynamic and optical properties suggestive of a phase transformation occurring near 60/spl deg/C. Clinically, reshaped cartilage tissue can be used to recreate the underlying cartilaginous framework of structures in the head and neck such as the ear, larynx, trachea, and nose.
Synthesis and reactions of 2,2′-biphenylylenebisdiethylphosphine. Formation of cyclic diquaternary dibromides with alkylene dibromides, and the nature and probable mechanism of their thermal decomposition (1967)

The synthesis of the above diphosphine is described. It forms cyclic diquaternary dibromides by union with the alkylene dibromides, Br·[CH2]n·Br, where n= 1–4, and a similar salt with o-xylylene dibromide. These salts, and the dimethiodide of the diphosphine, when heated, undergo a novel degradation to give 9-alkyl-9-phosphafluorenes. These reactions are compared with those shown by the analogous cyclic tetramethyl diarsonium dibromides, in which the dibromides formed from Br·[CH2]n·Br where n= 2–4 undergo a similar degradation to give the 9-alkyl-9-arsafluorenes, but the other members lose alkyl bromide with retention of the heterocyclic ring as a ditertiary arsine. The strictly analogous tetraethyl diarsonium dibromides undergo thermal decomposition with degradation of the heterocyclic ring. It is suggested that the ring contraction reactions shown by all these series of salts when heated are examples of a general internal nucleophilic displacement mechanism; other examples of this are discussed.Alkaline hydrolysis of certain of the above heterocyclic phosphonium salts occurs with ring-opening to give phosphine oxides.
CD4+ T Cells Mediate Abscess Formation in Intra-abdominal Sepsis by an IL-17-Dependent Mechanism (2003)

Abscess formation associated with intra-abdominal sepsis causes severe morbidity and can be fatal. Previous studies have implicated T cells in the pathogenesis of abscess formation, and we have recently shown that CD4(+) T cells activated in vitro by zwitterionic capsular polysaccharides from abscess-inducing bacteria such as Staphylococcus aureus and Bacteroides fragilis initiate this host response when transferred to naive rats. In this study, we show that mice deficient in alphabetaTCR-bearing T cells or CD4(+) T cells fail to develop abscesses following challenge with B. fragilis or abscess-inducing zwitterionic polysaccharides, compared with CD8(-/-) or wild-type animals. Transfer of CD4(+) T cells from wild-type mice to alphabetaTCR(-/-) animals reconstituted this ability. The induction of abscesses required T cell costimulation via the CD28-B7 pathway, and T cell transfer experiments with STAT4(-/-) and STAT6(-/-) mice demonstrated that this host response is dependent on STAT4 signaling. Significantly higher levels of IL-17, a proinflammatory cytokine produced almost exclusively by activated CD4(+) T cells, were associated with abscess formation in Th2-impaired (STAT6(-/-)) mice, while STAT4(-/-) mice had significantly lower levels of this cytokine than control animals. The formation of abscesses was preceded by an increase in the number of activated CD4(+) T cells in the peritoneal cavity 24 h following bacterial challenge. Confocal laser-scanning microscopy analysis revealed that CD4(+) T cells comprise the abscess wall in these animals and produce IL-17 at this site. Administration of a neutralizing Ab specific for IL-17 prevented abscess formation following bacterial challenge in mice. These data delineate the specific T cell response necessary for the development of intra-abdominal abscesses and underscore the role of IL-17 in this disease process.
Tumour Hypoxia Affects the Responsiveness of Cancer Cells to Chemotherapy and Promotes Cancer Progression (2008)

A solid tumour forms an organ-like structure that is comprised of cancer cells as well as stroma cells (fibroblasts, inflammatory cells) that are embedded in an extracellular matrix and are nourished by vascular network. However, tumoral microenvironment is heterogeneous due to the abnormal vasculature network and high proliferation rate of cancer cells. Because of these features, some regions are starved from oxygen, a phenomenon called hypoxia. Transient hypoxia is associated with inadequate blood flow while chronic hypoxia is the consequence of the increased oxygen diffusion distance due to tumour expansion. Both types of hypoxia are correlated with poor outcome for patients. Moreover, hypoxia also enhances chemoresistance of cancer cells. Firstly, the delivery of drugs in hypoxic area and cellular uptake of it are affected by hypoxia or associated acidity. Secondly, some chemotherapeutic drugs require oxygen to generate free radicals that contribute to cytotoxicity. Last, hypoxia induces cellular adaptations that compromise the effectiveness of chemotherapy. In response to nutrient deprivation due to hypoxia, the rate of proliferation of cancer cells decreases but chemotherapeutic drugs are more effective against proliferating cells. On the other hand, hypoxia induces adaptation by post-translational and transcriptional changes that promote cell survival and resistance to chemotherapy. Through these changes, hypoxia promotes angiogenesis, shift to glycolytic metabolism, expression of ABC transporters, cell survival by inducing the expression of genes encoding growth factors and the modulation of apoptotic process. The aim of this review is to provide a description of known hypoxia-induced mechanisms of chemoresistance at a cellular level.