julilili42/papers huggingface dataset:
Object‐oriented finite element analysis of thermo‐hydro‐mechanical (THM) problems in porous media
2006-05-16

Abstract The design, implementation and application of a concept for object‐oriented in finite element analysis of multi‐field problems is presented in this paper. The basic idea of this concept is that the underlying governing equations of porous media mechanics can be classified into different types of partial differential equations (PDEs). In principle, similar types of PDEs for diverse physical problems differ only in material coefficients. Local element matrices and vectors arising from the finite element discretization of the PDEs are categorized into several types, regardless of which physical problem they belong to (i.e. fluid flow, mass and heat transport or deformation processes). Element (ELE) objects are introduced to carry out the local assembly of the algebraic equations. The object‐orientation includes a strict encapsulation of geometrical (GEO), topological (MSH), process‐related (FEM) data and methods of element objects. Geometric entities of an element such as nodes, edges, faces and neighbours are abstracted into corresponding geometric element objects (ELE–GEO). The relationships among these geometric entities form the topology of element meshes (ELE–MSH). Finite element objects (ELE–FEM) are presented for the local element calculations, in which each classification type of the matrices and vectors is computed by a unique function. These element functions are able to deal with different element types (lines, triangles, quadrilaterals, tetrahedra, prisms, hexahedra) by automatically choosing the related element interpolation functions. For each process of a multi‐field problem, only a single instance of the finite element object is required. The element objects provide a flexible coding environment for multi‐field problems with different element types. Here, the C++ implementations of the objects are given and described in detail. The efficiency of the new element objects is demonstrated by several test cases dealing with thermo‐hydro‐mechanical (THM) coupled problems for geotechnical applications. Copyright © 2006 John Wiley &amp; Sons, Ltd.
Structural characterization of nanocrystalline hydroxyapatite and adhesion of pre-osteoblast cells
2006-05-16

Nanocrystalline hydroxyapatite (Nano HA), a prototype of minerals of bones and teeth, attracts increasing interest in medicine and dentistry. Different parameters for synthesis and post-treatment were investigated to determine their effects on crystallinity of nano HA, and in vitro cell responses to nano HA were studied. XRD and TEM analyses indicate that the crystallinity of nano HA synthesized by a chemical method was within the range of 15–50 nm, which is adapted to natural minerals of hard tissues. Increasing the ageing temperature significantly increased the crystallinity of nano HA, while lengthening the ageing time or varying the post-ageing drying process did not have any influence on its crystallinity. Nano HA annealed between 300 and 900 °C showed a small increase in crystallinity with increasing annealing temperature due to the long-range ordering effect. Cell attachment and spreading on nano HA were lower than those on pure titanium, and decreased as the crystallinity of nano HA increased. However, cells on nano HA demonstrated well-developed filopodia and lamelliopodia, which facilitate migration of the cells on it. This may benefit osteogenesis at the interface between bone and nano HA in vivo.
Recombinant MOG from baculovirus inhibits anti-hMOG(30-50) antibodies detected by the synthetic antigen [Asn31(Glc)]hMOG(30-50)
2006-05-16

Elena Nardi, Silvia Mazzucco, Sabrina Mata, Mario Chelli, Benedetta Mazzanti, Elisabetta Traggiai, Mauro Ginanneschi, Francesco Pinto, Luca Massacesi, Marco Vergelli, Hubert Kalbacher, Francesco Lolli, and Anna M. Papini Dipartimento di Chimica Organica “Ugo Schiff” and C.N.R. CSCEA, Universita degli Studi di Firenze, I-50121 Firenze, Italy; Servizio di Neurofisiopatologia, Dipartimento di Scienze Neurologiche e Psichiatriche, and Dipartimento di Scienze Neurologiche e Psichiatriche, Universita degli Studi di Firenze, I-50134 Firenze, Italy; and Medizinisch und Naturwissenschaftliches Forschungszentrum, Universitat Tubingen, D-72074 Tubingen, Germany.
Amyloid fibril formation by partially unfolded islet amyloid polypeptide (IAPP)
2006-05-16

Aphrodite Kapurniotu, Jurgen Bernhagen, Rakez Kayed, Norma Greenfield, Herwig Brunner, and Wolfgang Voelter Physiological-chemical Institute, University of Tubingen, D-72076 Tubingen, Germany; Laboratory of Biochemistry, Chair for Interfacial Engineering, University of Stuttgart, Fraunhofer Institute FhIGB, D-70569 Stuttgart, Germany; and UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ 08854-5635, U.S.A.
Herding in the German Mutual Fund Industry
2006-05-17

Abstract This paper analyses the trading activity of German mutual funds in the 1998–2002 period to investigate whether German mutual fund managers are engaged in herding behaviour. Another objective of the study is to determine the impact of this herd‐like trading on stock prices. Our results provide evidence of herding and positive feedback trading by German mutual fund managers. We show that a significant portion of herding detected in the German market is associated with spurious herding as a consequence of changes in benchmark index composition. Investigating the impact of mutual fund herding on stock prices, we find that herding seems to neither destabilise nor stabilise stock prices.
Albomycin Uptake via a Ferric Hydroxamate Transport System ofStreptococcus pneumoniaeR6
2006-05-17

ABSTRACT The antibiotic albomycin is highly effective against Streptococcus pneumoniae , with an MIC of 10 ng/ml. The reason for the high efficacy was studied by measuring the uptake of albomycin into S. pneumoniae . Albomycin was transported via the system that transports the ferric hydroxamates ferrichrome and ferrioxamine B. These two ferric hydroxamates antagonized the growth inhibition by albomycin and salmycin. Cross-inhibition of the structurally different ferric hydroxamates to both antibiotics can be explained by the similar iron coordination centers of the four compounds. [ 55 Fe 3+ ]ferrichrome and [ 55 Fe 3+ ]ferrioxamine B were taken up by the same transport system into S. pneumoniae . Mutants in the adjacent fhuD , fhuB , and fhuG genes were transport inactive and resistant to the antibiotics. Albomycin, ferrichrome, ferrioxamine B, and salmycin bound to the isolated FhuD protein and prevented degradation by proteinase K. The fhu locus consisting of the fhuD , fhuB , fhuG , and fhuC genes determines a predicted ABC transporter composed of the FhuD binding lipoprotein, the FhuB and FhuG transport proteins, and the FhuC ATPase. It is concluded that active transport of albomycin mediates the high antibiotic efficacy in S. pneumoniae .
Prefrontal dopamine D4 receptors are involved in encoding fear extinction
2006-05-17

The medial prefrontal cortex is known to be crucially involved in the memory for fear extinction. It has been shown that the dopamine D4 receptor is abundantly localized in the medial prefrontal cortex of rodents and that this receptor subtype is involved in the mediation of fear-related behaviour. In the present study, we tested whether dopamine D4 receptors within the medial prefrontal cortex are involved in the learning and encoding of fear extinction. Infusions of the specific dopamine D4 receptor antagonist L-741,741 into the medial prefrontal cortex immediately before fear extinction did not affect fear extinction learning but attenuated the memory on fear extinction on the following day. These results suggest that medial prefrontal cortex dopamine D4 receptors are involved in the consolidation of fear extinction memory.
Regeneration following spinal cord injury, from experimental models to humans: where are we?
2006-05-17

Regeneration in the adult CNS following injury is extremely limited. Traumatic spinal cord injury causes a permanent neurological deficit followed by a very limited recovery due to failed regeneration attempts. In fact, it is now clear that the spinal cord intrinsically has the potential to regenerate, but cellular loss and the presence of an inhibitory environment strongly limit tissue regeneration and functional recovery. The molecular mechanisms responsible for failed regeneration are starting to be unveiled. This gain in knowledge led to the design of therapeutic strategies aimed to limit the tissue scar, to enhance the proregeneration versus the inhibitory environment, and to replace tissue loss, including the use of stem cells. They have been very successful in several animal models, although results are still controversial in humans. Nonetheless, novel experimental approaches hold great promise for use in humans.
Late Diagnosis of Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency
2006-05-17

Congenital adrenal hyperplasia results from 21-hydroxylase deficiency in more than ninety percent of cases. The classical form of 21-hydroxylase deficiency presents in the neonatal period with virilization or adrenal insufficiency, with or without concurrent salt wasting. We report on a rare case of classic 21-hydroxylase deficiency diagnosed in late adulthood. A 39-year-old male patient presented for workup of infertility. Urologic investigation revealed small testes, bilateral testicular masses, and asthenozoospermia. The patient's steroid metabolism showed markedly increased levels of adrenal androgens, in particular of 17-hydroxyprogesterone amd 21-deoxycortisol. The gas chromatographic-mass spectrometric (GC-MS) urinary steroid profile was dominated by metabolites of 17-hydroxyprogesterone, while the endogenous glucocorticoid production was subnormally low. ACTH levels in plasma were elevated. These hormonal findings were consistent with 21-hydroxylase deficiency. Therapy with dexamethasone was initiated. The CTP21A2 gene analysis revealed the mutation I172N (ATC --> AAC) in exon 4 of allele 1 and a large gene deletion in allele 2. Cases of 21-hydroxylase deficiency diagnosed in late adulthood are rare; however, clinicians should be alert of this possibility.
Colitogenic and non‐colitogenic commensal bacteria differentially trigger DC maturation and Th cell polarization: An important role for IL‐6
2006-05-18

Abstract We investigated whether commensal bacteria modulate activation and maturation of bone marrow‐derived DC and their ability to prime CD4 + T cells. We used Escherichia coli mpk, which induces colitis in gnotobiotic IL‐2‐deficient (IL‐2 –/– ) mice, and Bacteroides vulgatus mpk, which prevents E. coli ‐induced colitis. Stimulation of DC with E. coli induced TNF‐α, IL‐12 and IL‐6 secretion and expression of activation markers. Moreover, stimulation of DC with E. coli increased T cell activation and led to Th1 polarization. Stimulation with B. vulgatus led only to secretion of IL‐6, and DC were driven into a semi‐mature state with low expression of activation markers and did not promote Th1 responses. B. vulgatus ‐induced semi‐mature DC were non‐responsive to stimulation by E. coli in terms of maturation, T cell priming and TNF‐α but not IL‐6 production. The non‐responsiveness of B. vulgatus ‐stimulated DC was abrogated by addition of anti‐IL‐6 mAb or mimicked with rIL‐6. These data suggest that B. vulgatus ‐induced IL‐6 drives DC into a semi‐mature state in which they are non‐responsive to proinflammatory activation by E. coli . This in vitro mechanism might contribute to the prevention of E. coli ‐triggered colitis development by B. vulgatus in vivo ; high IL‐6 mRNA expression was consistently found in B. vulgatus ‐colonized or B. vulgatus/E. coli co‐colonized IL‐2 –/– mice and was associated with absence of colitis.
Late recovery from permanent traumatic vegetative state heralded by event-related potentials
2006-05-18

A post-traumatic vegetative state that holds for more than 12 months is defined as “permanent”, implying a very low probability of regaining consciousness. Here we report on a patient who emerged from a traumatic vegetative state after 20 months. Beginning from the 6th month, we observed an improvement in the event-related potentials (ERPs) of his brain to complex sensory and verbal stimulation, although the clinical examinations remained unchanged. The possible role of ERPs as predictors of regaining consciousness after a vegetative state is discussed. The vegetative state is a most severe neurological syndrome and includes the loss of all kinds of conscious behaviour despite preserved wakefulness.1 In patients with traumatic head injury, a vegetative state that holds for more than 1 year is considered to be “permanent”, which implies irreversibility. In fact, even minimal improvement after this period is extremely improbable. From time to time, however, cases of late emergence are reported,2,3 sometimes even 5 years after the incident.4 The statement “The available data are insufficient to provide a trustworthy estimate of the incidence of late improvement” (Childs and Merger,3 p 24) is still valid; figures varying as broadly as from 1.6% to 14% have been reported.1,3 Given the rarity of such cases, the slightest hint that such an unexpected improvement may occur would be useful. Here we describe a patient in whom cognitive components of cortical ERPs were consistently obtained for more than 1 year before clinical recovery. A 28-year-old man was admitted to an intensive care unit with a Glasgow Coma Scale score of 3 after a severe car accident. After 5 days, he regained vigilance but had diminished gaze fixation and could not follow even the simplest commands. Intensive stimulation resulted in generalised flexor responses. Three months ...
Magnetic moments of heavy baryons in the relativistic three-quark model
2006-05-19

The magnetic moments of ground state single, double and triple heavy baryons containing charm or bottom quarks are calculated in a relativistic three-quark model, which, in the heavy quark limit, is consistent with Heavy Quark Effective Theory and Heavy Hadron Chiral Perturbation Theory. The internal quark structure of baryons is modeled by baryonic three-quark currents with a spin-flavor structure patterned according to standard covariant baryonic wave functions and currents used in QCD sum rule calculations.
Sonography of Brachial Plexus Traction Injuries
2006-05-19

Sonography of the brachial plexus was technically feasible, although the entire brachial plexus could not be evaluated. Sonography appears to be a useful bedside imaging technique for assessing brachial plexus injury. The potential of sonography as a complementary diagnostic tool in the evaluation of these patients warrants further investigation.
Artemisinin in traditional tea preparations of Artemisia annua
2006-05-19

F.H. Jansen comments in a Letter to the Editor (Jansen 2006) on two recent studies by our group (Mueller et al., 2004; Räth et al., 2004) reporting on chemical, pharmacokinetic and clinical efficacy data on traditional tea preparations of the Chinese medicinal plant Artemisia annua, the source of the antimalarial compound artemisinin. Jansen is right in warning against an uncritical use of A. annua tea preparations, which may promote the development of resistance. However, I would like to respond to two points: The efficacy and safety of herbal medicines is a subject on which many people hold strong opinions, positive or negative. We should emphasize data rather than opinions. Artemisia annua preparations were (and are) used in traditional Chinese medicine. We tested the efficacy of such preparations. In the dose regimen used, a reduction of parasitaemia and a resolution of clinical symptoms were observed. However, the effect was inferior to that of modern antimalarials and resulted in unacceptably high recrudescence rates. This prevents a responsible use of this medication in therapeutic practice.
SLICK − Scoring and Energy Functions for Protein−Carbohydrate Interactions
2006-05-20

Protein-carbohydrate interactions are increasingly being recognized as essential for many important biomolecular recognition processes. From these, numerous biomedical applications arise in areas as diverse as drug design, immunology, or drug transport. We introduce SLICK, a package containing a scoring and an energy function, which were specifically designed to predict binding modes and free energies of sugars and sugarlike compounds to proteins. SLICK accounts for van der Waals interactions, solvation effects, electrostatics, hydrogen bonds, and CH...pi interactions, the latter being a particular feature of most protein-carbohydrate interactions. Parameters for the empirical energy function were calibrated on a set of high-resolution crystal structures of protein-sugar complexes with known experimental binding free energies. We show that SLICK predicts the binding free energies of predicted complexes (through molecular docking) with high accuracy. SLICK is available as part of our molecular modeling package BALL (www.ball-project.org).
Antioxidative properties of the gastrointestinal phytopharmaceutical remedy STW 5 (Iberogast®)
2006-05-20

Since inflammation is a common mechanism of many gastrointestinal diseases, reactive oxygen metabolites may play an important role in their pathophysiology. Therefore it is interesting to know, whether phytopharmaceuticals known to modulate gastrointestinal motor function reveal also antioxidative properties. We tested STW 5 (Iberogast), its constituent nine different plant extracts, and some isolated compounds which are present in STW 5 for characterizing their antioxidative and radical quenching activities. The test assays consisted in pure chemical and complex cellular systems in which different types of reactive species were produced. Quantification of the effects was based on chemiluminescence reactions. The results show that all extracts contribute to the effect of the complete remedy STW 5, in the chemical systems in a strongly additive manner, in the cellular systems in a supraadditive manner. The largest contributions resulted from the extracts from peppermint and melissa leaves. Comparison of effects from isolated phytochemical compounds from the extracts with that of the extracts itself shows that usually the extract is more effective than the monosubstance which indicates also the synergism within the whole plant extracts. This means that the plant extracts present in STW 5 provide strong radical quenching activities that could also be involved in the therapeutic gastrointestinal actions.
Microarray Biochips – Thousands of Reactions on a Small Chip (MOBA)
2006-05-22

Wolfgang Mönch, Johannes Donauer, Bernd M. Fischer, Rüdiger Frank, Günter Gauglitz, Carsten Glasenapp, Hanspeter Helm, Paul Hing, Matthias Hoffmann, Peter Uhd Jepsen, Thomas Kleine-Ostmann, Martin Koch, Holger Krause, Nicolae Leopold, Tina Mutschler, Frank Rutz, Titus Sparna, Hans Zappe
Characteristics of Optimization in Individual HPLC Modes: Sections 2.1.2 – 2.1.7
2006-05-22

This chapter contains sections titled: Column Selectivity in RP-Chromatography Introduction Main Section Hydrophobicity and Silanol Activity (Ion Exchange) Polar Interactions (Hydrogen Bonding) Reproducibility of the Selectivity References The Use of Principal Component Analysis for the Characterization of Reversed-Phase Liquid Chromatographic Stationary Phases Introduction Theory of Principal Component Analysis PCA of the Database of RP Silica Materials PCA of Polar Embedded, Enhanced Polar Selectivity, and AQ/Aqua Phases PCA of Perfluorinated Phases Use of PCA in the Identification of Column/Phase Equivalency Use of PCA in the Rational Selection of Stationary Phases for Method Development Proposed Solvent/Stationary Phase Optimization Strategy References Chemometrics – A Powerful Tool for Handling a Large Number of Data Introduction Chromatographic Tests and Their Importance in Column Selection Use of Principal Component Analysis (PCA) in the Evaluation and Selection of Test Compounds Physicochemical Properties of Test Compounds Chromatographic Properties of Test Compounds Use of PCA for the Evaluation of Chromatographic Supports Evaluation of Chromatographic Supports in Mobile Phases Composed of pH 7.0 Phosphate Buffer Evaluation of Chromatographic Supports in Mobile Phases Composed of pH 3.0 Phosphate Buffer How a Chromatographic Test can be Optimized by Chemometrics Test Compounds Mobile Phases Chromatographic Parameters and Batch (Column) Reproducibility Conclusion and Perspectives References Linear Free Energy Relationships (LFER) – Tools for Column Characterization and Method Optimization in HPLC? Characterization and Selection of Stationary Phases for HPLC What are LFERs and Why can they be Profitable in HPLC? How to Obtain Analyte Descriptors for the Multivariate Regression LFER Procedure Using the Solvation Equation Comparing Stationary Phases on the Basis of LFER Data The Influence of the Mobile Phase Expressed in LFER Parameters The Prediction of Chromatographic Selectivity from LFER Data An Empirical Approach to the Determination of LFER Solute Parameters (Descriptors) from HPLC Data How does this Strategy Differ from the Use of Predetermined Solute Descriptors The Experimental Plan Determination of the Five LFER Parameters – A Procedure in Eight Steps Variation of the Eluent Conditions Stationary Phase Characterization with Empirical LFER Parameters Concluding Remarks on LFER Applications in HPLC References Column Selectivity in Reversed-Phase Liquid Chromatography Introduction The "Subtraction" Model of Reversed-Phase Column Selectivity Applications Selecting "Equivalent" Columns Selecting Columns of Very Different Selectivity Conclusions References Understanding Selectivity by the Use of Suspended-State High-Resolution Magic-Angle Spinning NMR Spectroscopy Introduction Is the Comparison Between NMR and HPLC Valid? The Transferred Nuclear Overhauser Effect (trNOE) Suspended-State 1H HR/MAS T1 Relaxation Measurements Where do the Interactions Take Place? Hydrogen Bonding Some Practical Considerations Future Aspects References
Coupling Techniques
2006-05-22

This chapter contains sections titled: Immunochromatographic Techniques Introduction Binding Molecules Immunoassays Immunochromatographic Techniques Affinity Enrichment (Affinity SPE) "Weak Affinity Chromatography" (True Affinity Chromatography) Biochemical Detectors Examples Example 1: Affinity Extraction (Affinity SPE) Example 2: "Weak Affinity Chromatography" (WAC) Example 3: Biochemical Detection References Enhanced Characterization and Comprehensive Analyses by Two-Dimensional Chromatography Introduction How Can I Take Advantage? – Experimental Aspects 2D Data Presentation and Analysis The State-of-the-Art in 2D Chromatography Summary References LC/MS – Hints and Recommendations on Optimization and Troubleshooting Optimization of the Ionization Process Lost LC/MS Peaks Mobile Phase pH at the Edge of the Optimum Range Ion-Pairing Agents in the HPLC System Ion Suppression by the Sample Matrix or Sample Contaminants How Clean Should an LC/MS Ion Source Be? Ion Suppression References LC-NMR Coupling NMR Basics Sensitivity of the NMR Experiment NMR Spectroscopy in Flowing Systems NMR Probes for LC-NMR Practical Realization of Analytical HPLC-NMR and Capillary-HPLC-NMR Continuous-Flow Measurements Stopped-Flow Measurements Capillary Separations Outlook References