julilili42/papers huggingface dataset:
Ontogenetic shifts in interactions among annual plants
2006-01-30

1 Interactions among plants strongly influence the structure and dynamics of plant populations and communities. However, most empirical studies of plant–plant interactions failed to make repeated measures of responses to neighbouring individuals and thereby neglected possible changes in interactions throughout the life history of the plants. 2 We tested the hypothesis that competition between annual species intensifies from early to late life-history stages, by sequentially measuring interactions in neighbour-removal experiments at three study sites located along a rainfall gradient in Israel. 3 Two annual species, Biscutella didyma and Hymenocarpos circinnatus, grew with and without neighbours in their natural habitats. Five response variables representing consecutive life-history stages (seedling survival, juvenile biomass, adult survival, number of seeds and final biomass) were recorded throughout the whole growing season. 4 The direction and intensity of interactions varied considerably between environments and life stages. On average, growth-related response variables indicated higher competition intensity at the productive end of the climatic gradient, while survival indicated either facilitation at the dry end or no trend along the gradient. 5 Temporal changes occurred, with moderate facilitation soon after germination shifting to strong competition at the end of the growing season. 6 Our results demonstrate that the outcome of experimental studies on plant–plant interactions may depend not only on the environmental productivity but more so on the life stage at which the target plant is studied.
Different Transport Mechanisms in Plant and Human AMT/Rh-type Ammonium Transporters
2006-01-30

The conserved family of AMT/Rh proteins facilitates ammonium transport across animal, plant, and microbial membranes. A bacterial homologue, AmtB, forms a channel-like structure and appears to function as an NH3 gas channel. To evaluate the function of eukaryotic homologues, the human RhCG glycoprotein and the tomato plant ammonium transporter LeAMT1;2 were expressed and compared in Xenopus oocytes and yeast. RhCG mediated the electroneutral transport of methylammonium (MeA), which saturated with Km = 3.8 mM at pHo 7.5. Uptake was strongly favored by increasing the pHo and was inhibited by ammonium. Ammonium induced rapid cytosolic alkalinization in RhCG-expressing oocytes. Additionally, RhCG expression was associated with an alkali-cation conductance, which was not significantly permeable to NH4+ and was apparently uncoupled from the ammonium transport. In contrast, expression of the homologous LeAMT1;2 induced pHo-independent MeA+ uptake and specific NH4+ and MeA+ currents that were distinct from endogenous currents. The different mechanisms of transport, including the RhCG-associated alkali-cation conductance, were verified by heterologous expression in appropriate yeast strains. Thus, homologous AMT/Rh-type proteins function in a distinct manner; while LeAMT1;2 carries specifically NH4+, or cotransports NH3/H+, RhCG mediates electroneutral NH3 transport.
Laser Microscopy of Tunneling Magnetoresistance in Manganite Grain-Boundary Junctions
2006-01-30

Using low-temperature scanning laser microscopy we directly image electric transport in a magnetoresistive element, a manganite thin film intersected by a grain boundary (GB). Imaging at variable temperature allows reconstruction and comparison of the local resistance versus temperature for both the manganite film and the GB. Imaging at low temperature also shows that the GB switches between different resistive states due to the formation and growth of magnetic domains along the GB. We observe different types of domain wall growth; in most cases a domain wall nucleates at one edge of the bridge and then proceeds towards the other edge.
A CD14 Domain with Lipopolysaccharide‐Binding and ‐Neutralizing Activity
2006-01-30

Abstract The interaction of lipopolysaccharide with CD14 plays a key role in signaling that activates an early defense against pathogens but also contributes to the development of sepsis and septic shock. Here we have mapped the entire 356‐amino‐acid protein with synthetic 20‐amino‐acid peptides and have identified a new lipopolysaccharide‐binding domain with a strong LPS‐neutralizing activity. Moreover, analysis of the structure–activity relationship of this peptide, which corresponds to amino acids 81–100 of human CD14, revealed that leucines 87, 91, and 94 are essential for these activities. The functional relevance of these residues was confirmed by cellular expression of mutant CD14 proteins that are no longer able to bind LPS. Furthermore, the peptide provided a basis for the generation of highly soluble analogues with stronger lipopolysaccharide‐neutralizing activity.
Prediction of experimentally unknownredistances of organic molecules from Dunning basis set extrapolations forab initiopost‐HF calculations
2006-01-30

Abstract An approach to estimate equilibrium r e bond lengths of organic molecules which contain standard bonding situations for CC, CH, CO and CN distances from only one equation is presented. For this, optimizations of molecular geometries using correlated post‐Hartree–Fock and density functional methods have been performed. A selection scheme was developed to determine the most reliable methodology for prediction of equilibrium r e distances of covalent bonds from a set of investigated theoretical methods. Consequently, distances computed in the CCSD(T) procedure via exponential extrapolation from a consecutive set of Dunning cc‐pVXZ basis sets by use of Eqn (2) are accurate up to ± 0.0005 Å in comparison to experimentally available r e distances. Applications for predictions of the experimentally unknown r e distances of methanol, methylamine and methylenimine are presented. Additionally the estimation of r e distances of larger, chemically more interesting molecules is possible by lower order calculations (e.g. DFT B3LYP/cc‐pVDZ) via linear correlation statistics using the results from our r e reference model system via Eqn (3). Copyright © 2006 John Wiley &amp; Sons, Ltd.
Crystal Structure of μ‐Oxo‐bis[9,22‐(bisbutyloxy)hemiporphyrazinato]iron(III)
2006-01-30

Abstract The crystal structure of the title compound, C 68 H 60 N 16 O 5 Fe 2 , shows a dinuclear complex of two crystallographically independent, distorted hemiporphrazinato iron complexes with five‐coordinate iron and oxygen as bridging ligand. The Fe1‐O1‐Fe2 angle is 151.16°, the Fe‐O bond lengths are Fe1‐O1 [1.771(2) Å] and Fe2‐O1 [1.773(2) Å]. The dinuclear complexes have a staggered conformation with a dihedral angle of 26.2°, but coaxially to form tetrameric units is not observed. The molecule is characterized by short Fe‐N (isoindole) bonds [1.998(3) Å] and long Fe‐N (pyridine) bonds, values range from [2.175(3) Å] to [2.245(3) Å].
Reliability and validity of the International Cooperative Ataxia Rating Scale: A study in 156 spinocerebellar ataxia patients
2006-01-31

Abstract To evaluate the efficacy of treatments in spinocerebellar ataxias (SCAs), appropriate clinical scales are required. This study evaluated metric properties of the International Cooperative Ataxia Rating Scale (ICARS) in 156 SCA patients and 8 controls. ICARS was found to be a reliable scale satisfying accepted criteria for interrater reliability, test–retest reliability, and internal consistency. Although validity testing was limited, we found evidence of validity of ICARS when ataxia disease stages and Barthel index were used as external criteria. On the other hand, our study revealed two major problems associated with the use of ICARS. First, the redundant and overlapping nature of several items gave rise to a considerable number of contradictory ratings. Second, a factorial analysis showed that the rating results were determined by four different factors that did not coincide with the ICARS subscales, thus questioning the justification of ICARS subscore analysis in clinical trials. © 2006 Movement Disorder Society
Echoplanar diffusion tensor imaging of the lower leg musculature using eddy current nulled stimulated echo preparation
2006-01-31

Abstract A sequence for echoplanar diffusion tensor imaging of musculature was developed using a stimulated echo preparation. The strategy was optimized in order to obtain reliable diffusion tensor data in a short measuring time. Image distortion problems due to eddy currents arising from long‐lasting diffusion sensitizing gradients could be overcome by insertion of additional gradient pulses in the TM interval of the stimulated echo preparation. In contrast to former approaches with similar intention, the proposed strategy does not influence the stimulated echo signal itself and does not lead to prolonged echo time as in the case of spin echo methods. Phantom measurements were performed to compare eddy current induced distortion effects in diffusion weighted images. The diffusion tensor in the musculature of the lower leg was investigated in four healthy subjects and maps of the trace and the three eigenvalues of the diffusion tensor, fractional anisotropy maps, and angle maps were calculated. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Pumping fluid by magnetic surface stress
2006-01-31

A magnetic field rotating on the free surface of a ferrofluid layer is shown to induce considerable fluid motion towards the direction the field is rolling. The measured flow velocity (i) increases with the square of the magnetic field amplitude, (ii) is proportional to the thickness of the fluid layer and (iii) has a maximum at a fluid specific frequency. The pumping speed can be estimated with a two-dimensional flow model. We compare the pumping performance of a magnetic fluid based on magnetite with the performance of a novel fluid based on cobalt.
Opto-numerical procedures supporting dynamic lower limbs monitoring and their medical diagnosis
2006-01-31

New optical full-field shape measurement systems allow transient shape capture at rates between 15 and 30 Hz. These frequency rates are enough to monitor controlled movements used e.g. for medical examination purposes. In this paper we present a set of algorithms which may be applied for processing of data gathered by fringe projection method implemented for lower limbs shape measurement. The purpose of presented algorithms is to locate anatomical structures based on the limb shape and its deformation in time. The algorithms are based on local surface curvature calculation and analysis of curvature maps changes during the measurement sequence. One of anatomical structure of high medical interest that is possible to scan and analyze, is patella. Tracking of patella position and orientation under dynamic conditions may lead to detect pathological patella movements and help in knee joint disease diagnosis. Therefore the usefulness of the algorithms developed was proven at examples of patella localization and monitoring.
MPI‐DING reference glasses for in situ microanalysis: New reference values for element concentrations and isotope ratios
2006-02-01

We present new analytical data of major and trace elements for the geological MPI‐DING glasses KL2‐G, ML3B‐G, StHs6/80‐G, GOR128‐G, GOR132‐G, BM90/21‐G, T1‐G, and ATHO‐G. Different analytical methods were used to obtain a large spectrum of major and trace element data, in particular, EPMA, SIMS, LA‐ICPMS, and isotope dilution by TIMS and ICPMS. Altogether, more than 60 qualified geochemical laboratories worldwide contributed to the analyses, allowing us to present new reference and information values and their uncertainties (at 95% confidence level) for up to 74 elements. We complied with the recommendations for the certification of geological reference materials by the International Association of Geoanalysts (IAG). The reference values were derived from the results of 16 independent techniques, including definitive (isotope dilution) and comparative bulk (e.g., INAA, ICPMS, SSMS) and microanalytical (e.g., LA‐ICPMS, SIMS, EPMA) methods. Agreement between two or more independent methods and the use of definitive methods provided traceability to the fullest extent possible. We also present new and recently published data for the isotopic compositions of H, B, Li, O, Ca, Sr, Nd, Hf, and Pb. The results were mainly obtained by high‐precision bulk techniques, such as TIMS and MC‐ICPMS. In addition, LA‐ICPMS and SIMS isotope data of B, Li, and Pb are presented.
Changing Paradigms—An Update on the Multidisciplinary Management of Malignant Glioma
2006-02-01

Learning Objectives After completing this course, the reader will be able to: List the different major subtypes of glioma and identify the appropriate treatment strategies for patients with high-grade and low-grade gliomas.Discuss the available evidence for the treatment of newly diagnosed glioblastoma, anaplastic astrocytoma, and anaplastic oligodendroglioma.Identify approved agents and other active or investigational agents used to treat patients with newly diagnosed and recurrent glioma. CME Access and take the CME test online and receive 1 AMA PRA category 1 credit at CME.TheOncologist.com
The Elemental Abundances in Bare Planetary Nebula Central Stars and the Shell Burning in AGB Stars
2006-02-01

We review the observed properties of extremely hot hydrogen-deficient post-AGB stars of spectral type [WC] and PG1159. Their H-deficiency is probably caused by a (very) late helium-shell flash or a AGB final thermal pulse, laying bare interior stellar regions which are usually kept hidden below the hydrogen envelope. Thus, the photospheric element abundances of these stars allow to draw conclusions about details of nuclear burning and mixing processes in the precursor AGB stars. We summarize the state-of-the-art of stellar evolution models which simulate AGB evolution and the occurrence of a late He-shell flash. We compare predicted element abundances to those determined by quantitative spectral analyses performed with advanced non-LTE model atmospheres. A good qualitative and quantitative agreement is found. Future work can contribute to an even more complete picture of the nuclear processes in AGB stars.
Role of Iron in Neurodegenerative Disorders
2006-02-01

Although the pathophysiology underlying a number of neurodegenerative diseases is complex and, in many aspects, only partly understood, increased iron levels in pathologically relevant brain areas and iron-mediated oxidative stress seem to play a central role in many of them. Much has been learned from monogenetically caused disturbances of brain iron metabolism including pantothenate kinase-associated neurodegeneration type 2, hereditary ferritinopathies affecting the basal ganglia, and aceruloplasminemia that may well be applied to the most common neurodegenerative disorders associated with brain iron accumulation including Parkinson disease and Alzheimer disease. Iron-mediated oxidative stress in neurodegenerative diseases caused by other genetic pathways like Huntington disease and Friedreich ataxia underscore the complex interaction of this trace metal and genetic variations. Therapeutical strategies derived from application of iron chelators in monogenetically caused disturbances of brain iron metabolism and new iron and oxidative stress diminishing substances in animal models of Parkinson disease are promising and warrant further investigational effort.
Alpha Phase Reset Contributes to the Generation of ERPs
2006-02-01

An unresolved question in electroencephalogram (EEG) research is whether event-related potentials (ERPs) are generated by phase-reset or evoked response. We analyzed data of a visual feature detection task and will show 1) phase concentration in the alpha frequency range, 2) ongoing alpha activity prior to stimulus onset, 3) evoked alpha oscillation in the ERP, 4) lack of power increase during phase concentration, 5) decrease in amplitude variance during early evoked components preceding a decrease in power, and 6) the same cortical sources for induced prestimulus power and evoked poststimulus power. Because none of these data provide unequivocal evidence for phase reset, we additionally tested the basic assumption of the evoked model, which is the additivity of the evoked response on the basis of a simulation approach. Our findings suggest that nonadditive processes-typical for a phase reset-are involved in the generation of the ERP. Thus, together with the other findings this study provides unequivocal evidence for phase resetting in the human EEG.
SGK1 Kinase Upregulates GLUT1 Activity and Plasma Membrane Expression
2006-02-01

Phosphatidylinositol 3-kinase (PI3 kinase) inhibition disrupts the ability of insulin to stimulate GLUT1 and GLUT4 translocation into the cell membrane and thus glucose transport. The effect on GLUT4 but not on GLUT1 is mediated by activation of protein kinase B (PKB). The serum- and glucocorticoid-inducible kinase SGK1, a further kinase downstream of PI3 kinase, regulates several transporters by enhancing their plasma membrane abundance. GLUT1 contains a consensus site (95Ser) for phosphorylation by SGK1. Thus, the present study investigated whether GLUT1 is regulated by the kinase. Tracer-flux studies in Xenopus oocytes and HEK-293 cells demonstrated that GLUT1 transport is enhanced by constitutively active S422DSGK1. The effect requires the kinase catalytical activity since the inactive mutant K127NSGK1 failed to modulate GLUT1. GLUT1 stimulation by S422DSGK1 is not due to de novo protein synthesis but rather to an increase of the transporter’s abundance in the plasma membrane. Kinetic analysis revealed that SGK1 enhances maximal transport rate without altering GLUT1 substrate affinity. These observations suggest that SGK1 regulates GLUT1 and may contribute to or account for the PI3 kinase–dependent but PKB-independent stimulation of GLUT1 by insulin.
Iris pigment epithelial translocation in the treatment of exudative macular degeneration: a 3-year follow-up.
2006-02-01

Transplanted autologous iris pigment epithelial cells were well tolerated for 3 years and stabilization of visual acuity was achieved in most patients. These results suggest that iris pigment epithelial cells may serve as a substitute for retinal pigment epithelial cells after choroidal neovascularization removal in patients with exudative macular degeneration; however, whether these cells will be of any value for the restoration of vision and possible protection against choroidal neovascularization recurrence awaits further clinical observation and additional research.
A New Variant in the Human Kv1.3 Gene Is Associated with Low Insulin Sensitivity and Impaired Glucose Tolerance
2006-02-01

We show that a variant in the promoter of the Kv1.3 gene is associated with impaired glucose tolerance and lower insulin sensitivity. Therefore, the Kv1.3 channel represents a candidate gene for type 2 diabetes.
The Genome of the Novel Phage Rtp, with a Rosette-Like Tail Tip, IsHomologous to the Genome of Phage T1
2006-02-01

ABSTRACT Anew Escherichia coli phage, named Rtp, was isolated and shown to be closely related to phage T1. Electron microscopy revealed that phage Rtp has a morphologically unique tail tip consisting of four leaf-like structures arranged in a rosette, whereas phage T1 has thinner, flexible leaves that thicken toward the ends. In contrast to T1, Rtp did not require FhuA and TonB for infection. The 46.2-kb genome of phage Rtp encodes 75 open reading frames, 47 of which are homologous to phage T1 genes. Like phage T1, phage Rtp encodes a large number of small genes at the genome termini that exhibit no sequence similarity to known genes. Six predicted genes larger than 300 nucleotides in the highly homologous region of Rtp are not found in T1. Two predicted HNH endonucleases are encoded at positions different from those in phage T1. The sequence similarity of rtp37 , - 38 , - 39 , - 41 , - 42 , and - 43 to equally arranged genes of lambdoid phages suggests a common tail assembly initiation complex. Protein Rtp43 is homologous to the λ J protein, which determines λ host specificity. Since the two proteins differ most in the C-proximal area, where the binding site to the LamB receptor resides in the J protein, we propose that Rtp43 contributes to Rtp host specificity. Lipoproteins similar to the predicted lipoprotein Rtp45 are found in a number of phages (encoded by cor genes) in which they prevent superinfection by inactivating the receptors. We propose that, similar to the proposed function of the phage T5 lipoprotein, Rtp45 prevents inactivation of Rtp by adsorption to its receptor during cells lysis. Rtp52 is a putative transcriptional regulator, for which 10 conserved inverted repeats were identified upstream of genes in the Rtp genome. In contrast, the much larger E. coli genome has only one such repeat sequence.
Fornix Lesions Decouple the Induction of Hippocampal Arc Transcription from Behavior But Not Plasticity
2006-02-01

The immediate-early gene (IEG) Arc is transcribed after behavioral and physiological treatments that induce synaptic plasticity and is implicated in memory consolidation. The relative contributions of neuronal activity and learning-related plasticity to the behavioral induction of Arc remain to be defined. To differentiate the contributions of each, we assessed the induction of Arc transcription in rats with fornix lesions that impair hippocampal learning yet leave cortical connectivity and neuronal firing essentially intact. Arc expression was assessed after exploration of novel environments and performance of a novel water maze task during which normal rats learned the spatial location of an escape platform. During the same task, rats with fornix lesions learned to approach a visible platform but did not learn its spatial location. Rats with fornix lesions had normal baseline levels of hippocampal Arc mRNA, but unlike normal rats, expression was not increased in response to water maze training. The integrity of signaling pathways controlling Arc expression was demonstrated by stimulation of the medial perforant path, which induced normal synaptic potentiation and Arc in rats with fornix lesions. Together, the results demonstrate that Arc induction can be decoupled from behavior and is more likely to indicate the engagement of synaptic plasticity mechanisms than synaptic or neuronal activity per se. The results further imply that fornix lesions may impair memory in part by decoupling neuronal activity from signaling pathways required for long-lasting hippocampal synaptic plasticity.
On sampling distributions for coalescent processes with simultaneous multiple collisions
2006-02-01

Recursions for a class of sampling distributions of allele configurations are derived for the situation where the genealogy of the underlying population is modelled by a coalescent process with simultaneous multiple collisions of ancestral lineages. These recursions describe a new family of partition structures in terms of the composition probability function, parametrized by the infinitesimal rates of the coalescent process. For the Kingman coalescent process with only binary mergers of ancestral lines, the recursion reduces to that known for the classical Ewens sampling distribution. We solve the recursion for the star-shaped coalescent. The asymptotic behaviour of the number K&lt;sub&gt;n&lt;/sub&gt; of alleles (types) for large sample size n is studied, in particular for the star-shaped coalescent and the Bolthausen-Sznitman coalescent.