julilili42/papers huggingface dataset:
Increased Circulating Progenitor Cells in Alzheimer's Disease Patients with Moderate to Severe Dementia: Evidence for Vascular Repair and Tissue Regeneration?
2010-01-07

Cerebrovascular dysfunction is a common finding in patients with Alzheimer's disease (AD) and may contribute to cognitive decline. Abundant evidence suggests that vascular and neuronal repair mechanisms are mediated by circulating progenitor cells in vivo. Whether CD34+ and, specifically, CD34+/CD133+ progenitor cells are involved in the pathophysiology of AD is poorly understood so far. In the present study, peripheral blood concentrations of circulating CD34+/CD133+ and CD34+ progenitor cells were measured in 45 AD patients and in 30 healthy elderly controls by flow cytometry. The severity of dementia was assessed by Mini-Mental Status Examination and Clinical Dementia Rating scale. AD patients were stratified into two groups showing mild (n=17) and moderate to severe (n= 28) dementia. In the present study, AD patients with moderate to severe dementia, but not those with mild dementia, showed significantly increased circulating CD34+/CD133+ and CD34+ progenitor cells compared to healthy elderly controls independent of cardiovascular risk factors and medication. In addition, the number of circulating CD34+/CD133+ progenitor cells in AD patients was significantly inversely correlated with cognitive function, age, and plasma levels of SDF-1, the most potent chemokine for progenitor cells. Our findings suggest a stage-dependent upregulation of circulating CD34+/CD133+ and CD34+ progenitor cells in AD patients, which could take part in tissue healing processes of the brain in AD.
ChemInform Abstract: Biosynthetic Capacities of Actinomycetes. Part. 50. Piceamycin and Its N‐Acetylcysteine Adduct Is Produced by Streptomyces sp. GB 4—2.
2010-01-07

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Tailoring gold nanostructures for near-field optical applications
2010-01-08

A method of combined thin-film deposition, electron beam lithography, and ion milling is presented for the fabrication of gold and silver nanostructures. The flexibility of lithographical processes for the variation of geometric parameters is combined with three-dimensional control over the surface evolution. Depending on the etching angle, different shapes ranging from cones over rods to cups can be achieved. These size- and shape-tunable structures present a toolbox for nano-optical investigations. As an example, optical properties of systematically varying structures are examined in a parabolic mirror confocal microscope.
Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families
2010-01-08

An important aspect of the functional annotation of enzymes is not only the type of reaction catalysed by an enzyme, but also the substrate specificity, which can vary widely within the same family. In many cases, prediction of family membership and even substrate specificity is possible from enzyme sequence alone, using a nearest neighbour classification rule. However, the combination of structural information and sequence information can improve the interpretability and accuracy of predictive models. The method presented here, Active Site Classification (ASC), automatically extracts the residues lining the active site from one representative three-dimensional structure and the corresponding residues from sequences of other members of the family. From a set of representatives with known substrate specificity, a Support Vector Machine (SVM) can then learn a model of substrate specificity. Applied to a sequence of unknown specificity, the SVM can then predict the most likely substrate. The models can also be analysed to reveal the underlying structural reasons determining substrate specificities and thus yield valuable insights into mechanisms of enzyme specificity. We illustrate the high prediction accuracy achieved on two benchmark data sets and the structural insights gained from ASC by a detailed analysis of the family of decarboxylating dehydrogenases. The ASC web service is available at http://asc.informatik.uni-tuebingen.de/.
Effect of Phytic Acid on Suicidal Erythrocyte Death
2010-01-08

Phytic acid, an anticarcinogenic food component, stimulates apoptosis of tumor cells. Similar to apoptosis, human erythrocytes may undergo suicidal death or eryptosis, characterized by cell membrane scrambling and cell shrinkage. Triggers of eryptosis include energy depletion. Phytate intake could cause anemia, an effect attributed to iron complexation. The present experiments explored whether phytic acid influences eryptosis. Supernatant hemoglobin concentration was determined to reveal hemolysis, annexin V-binding in FACS analysis was utilized to identify erythrocytes with scrambled cell membrane, forward scatter in FACS analysis was taken as a measure of cell volume, and a luciferin-luciferase assay was employed to determine erythrocyte ATP content. As a result, phytic acid (>or=1 mM) did not lead to significant hemolysis, but significantly increased the percentage of annexin V-binding erythrocytes, significantly decreased forward scatter, and significantly decreased cellular ATP content. In conclusion, phytic acid stimulates suicidal human erythrocyte death, an effect paralleling its proapoptotic effect on nucleated cells.
Schistosoma japonicum infection and rectal carcinoid tumour: underreported coincidence or neglected association?
2010-01-08

SUMMARY Schistosoma japonicum infection associated with a rectal carcinoid in an asymptomatic 44-year-old female from the Philippines is described. A systematic review of the literature could not identify similar reports, suggesting a rare coincidence. However, epidemiological data on the frequency of both conditions as well as published results of a colorectal screening programme from China indicate that underreporting of this concurrence is likely. Moreover, several studies suggest a causal link between schistosomiasis caused by S . japonicum and more common gastrointestinal malignancies such as colorectal carcinoma. Hence the presented case and the apparent neglect of this observation in the current literature allow speculation on a role of S. japonicum in the pathogenesis of rare gastrointestinal neoplasms such as carcinoid tumours as well. Future reports on similar observations could help to determine the need for systematic investigations and are strongly encouraged.
Facilitating an importance index
2010-01-11

Summary 1. An unresolved question in plant ecology is how the balance between positive and negative interactions changes with environmental conditions. Recently, the debate has been expanded by Brooker &amp; Kikvidze (2008) , reintroducing the importance, rather than the intensity, of interactions as the appropriate concept for empirical studies. Importance is the difference in performance with interactions relative to all affecting factors. 2. Positive interactions among plants (facilitation) are common in nature. However, the advocated importance indices fail to address facilitation and can thus not be applied to studying shifts in the balance between positive and negative interactions. The deficiencies of the current importance indices are both conceptual as well as mathematical. In particular, their maximum performance estimator is based on the assumption that it can only be attained in the absence of neighbours. 3. We suggest two major improvements. First, we use the target’s overall maximum performance as a surrogate for the plant optimum, i.e. we allow the possibility of higher performance with neighbours (i.e. facilitation). Second, we propose an alternative approach to treat the factors affecting measured performance. The new index is limited in its range [−1, 1], is symmetrical for competition and facilitation, and it preserves the intuitive nature of the original index by Brooker &amp; Kikvidze (2008) . 4. Synthesis . The concept of interaction importance is useful for studying interactions along environmental gradients. In contrast to previous indices, our index accommodates facilitative interactions and thus offers a significant conceptual and methodological advancement. We advocate its use in future empirical studies.
Origin of spatial genetic structure in an expanding oak population
2010-01-11

Spatial genetic structure (SGS) results from the interplay of several demographical processes that are difficult to tease apart. In this study, we explore the specific effects of seed and pollen dispersal and of early postdispersal mortality on the SGS of a seedling cohort (N = 786) recruiting within and around an expanding pedunculate oak (Quercus robur) stand. Using data on dispersal (derived from parentage analysis) and mortality (monitored in the field through two growing seasons), we decompose the overall SGS of the cohort into its components by contrasting the SGS of dispersed (i.e. growing away from their mother tree) vs. nondispersed (i.e. growing beneath their mother tree) and initial vs. surviving seedlings. Patterns differ strongly between nondispersed and dispersed seedlings. Nondispersed seedlings are largely responsible for the positive kinship values observed at short distances in the studied population, whereas dispersed seedlings determine the overall SGS at distances beyond c. 30 m. The paternal alleles of nondispersed seedlings show weak yet significantly positive kinships up to c. 15 m, indicating some limitations in pollen flow that should further promote pedigree structures at short distances. Seedling mortality does not alter SGS, except for a slight increase in the nondispersed group. Field data reveal that mortality in this group is negatively density-dependent, probably because of small-scale variation in light conditions. Finally, we observe a remarkable similarity between the SGS of the dispersed seedlings and that of the adults, which probably reflects dispersal processes during the initial expansion of the population. Overall, this study demonstrates that incorporating individual-level complementary information into analyses can greatly improve the detail and confidence of ecological inferences drawn from SGS.
Three-Dimensional Orientation of Single Molecules in a Tunable Optical λ/2 Microresonator
2010-01-11

A tightly focused radially polarized laser beam forms an unusual bimodal field distribution in an optical lambda/2-microresonator. We use a single-molecule dipole to probe the vector properties of this field distribution by tuning the resonator length with nanometer precision. Comparing calculated and experimental excitation patterns provides the three-dimensional orientation of the single-molecule dipole in the microresonator.
The role of successional stage and small‐scale disturbance for establishment of pioneer grass Corynephorus canescens
2010-01-11

Abstract Question: Which mechanisms promote the maintenance of the protected pioneer grass Corynephorus canescens in a mosaic landscape? Which are the interactive effects of small‐scale disturbances, successional stage and year‐to‐year variation on early establishment probabilities of C. canescens ? Location: Brandenburg, NE Germany. Methods: We measured emergence and survival rates over 3 yr in a sowing‐experiment conducted in three successional stages ( C. canescens ‐dominated site, ruderal forb site and pioneer forest) under two different regimes of mechanical ground disturbance (disturbed versus undisturbed control). Results: Overall, disturbance led to higher emergence in a humid year and to lower emergence in a very dry year. Apparently, when soil moisture was sufficient, the main factor limiting C. canescens' establishment was competition, while in the dry year, water became the limiting factor. Survival rates were not affected by disturbance. In humid years, C. canescen s emerged in higher numbers in open successional stages while in the dry year, emergence rates were higher in late stages, suggesting an important role of late successional stages for the persistence of C. canescens . Conclusions: Our results suggest that small‐scale disturbances can promote germination of C. canescens . However, disturbances should be carefully planned. The optimal strategy for promoting C. canescens is to apply disturbances just before seed dispersal and not during dry years. At the landscape scale, a mosaic of different vegetation types is beneficial for the protected pioneer grass as facilitation by late‐successional species may be an important mechanism for the persistence of C. canescens , especially in dry years.
Effect of TMS on Oculomotor Behavior but not Perceptual Stability during Smooth Pursuit Eye Movements
2010-01-11

During smooth pursuit eye movements, we do not mistake the shift of the retinal image induced by the visual background for motion of the world around us but instead perceive a stable world. The goal of this study was to search for the neuronal substrates providing perceptual stability. To this end, pursuit eye movements across a background stimulus and perceptual stability were measured in the absence and presence, respectively, of transcranial magnetic stimulation (TMS) applied to 6 different brain regions, that is, primary visual cortex (V1), area MT+/V5, left and right temporoparietal junctions (TPJs), medial parieto-occipital cortex (POC), and the lateral cerebellum (LC). Stimulation of MT+/V5 and the cerebellum induced significant decreases in pursuit gain independent of background presentation, whereas stimulation of TPJ impaired the suppression of the optokinetic reflex induced by background stimulation. In contrast to changes in pursuit, only nonsignificant modifications in perceptual stability were observed. We conclude that MT+/V5, TPJ, and the LC contribute to pursuit eye movements and that TPJ supports the suppression of optokinesis. The lack of significant influences of TMS on perception suggests that motion perception invariance is not based on a localized but rather a highly distributed network featuring parallel processing.
Interpolation of Steady‐State Concentration Data by Inverse Modeling
2010-01-11

In most groundwater applications, measurements of concentration are limited in number and sparsely distributed within the domain of interest. Therefore, interpolation techniques are needed to obtain most likely values of concentration at locations where no measurements are available. For further processing, for example, in environmental risk analysis, interpolated values should be given with uncertainty bounds, so that a geostatistical framework is preferable. Linear interpolation of steady‐state concentration measurements is problematic because the dependence of concentration on the primary uncertain material property, the hydraulic conductivity field, is highly nonlinear, suggesting that the statistical interrelationship between concentration values at different points is also nonlinear. We suggest interpolating steady‐state concentration measurements by conditioning an ensemble of the underlying log‐conductivity field on the available hydrological data in a conditional Monte Carlo approach. Flow and transport simulations for each conditional conductivity field must meet the measurements within their given uncertainty. The ensemble of transport simulations based on the conditional log‐conductivity fields yields conditional statistical distributions of concentration at points between observation points. This method implicitly meets physical bounds of concentration values and non‐Gaussianity of their statistical distributions and obeys the nonlinearity of the underlying processes. We validate our method by artificial test cases and compare the results to kriging estimates assuming different conditional statistical distributions of concentration. Assuming a beta distribution in kriging leads to estimates of concentration with zero probability of concentrations below zero or above the maximal possible value; however, the concentrations are not forced to meet the advection‐dispersion equation.
First appraisal of brain pathology owing to A30P mutant alpha‐synuclein
2010-01-12

Abstract Familial Parkinson disease (PD) due to the A30P mutation in the SNCA gene encoding alpha‐synuclein is clinically associated with PD symptoms. In this first pathoanatomical study of the brain of an A30P mutation carrier, we observed neuronal loss in the substantia nigra, locus coeruleus, and dorsal motor vagal nucleus, as well as widespread occurrence of alpha‐synuclein immunopositive Lewy bodies, Lewy neurites, and glial aggregates. Alpha‐synuclein aggregates ultrastructurally resembled Lewy bodies, and biochemical analyses disclosed a significant load of insoluble alpha‐synuclein, indicating neuropathological similarities between A30P disease patients and idiopathic PD, with a more severe neuropathology in A30P carriers. ANN NEUROL 2010;67:684–689
Modulation of mitochondrial function and morphology by interaction of Omi/HtrA2 with the mitochondrial fusion factor OPA1
2010-01-12

Loss of Omi/HtrA2 function leads to nerve cell loss in mouse models and has been linked to neurodegeneration in Parkinson's and Huntington's disease. Omi/HtrA2 is a serine protease released as a pro-apoptotic factor from the mitochondrial intermembrane space into the cytosol. Under physiological conditions, Omi/HtrA2 is thought to be involved in protection against cellular stress, but the cytological and molecular mechanisms are not clear. Omi/HtrA2 deficiency caused an accumulation of reactive oxygen species and reduced mitochondrial membrane potential. In Omi/HtrA2 knockout mouse embryonic fibroblasts, as well as in Omi/HtrA2 silenced human HeLa cells and Drosophila S2R+ cells, we found elongated mitochondria by live cell imaging. Electron microscopy confirmed the mitochondrial morphology alterations and showed abnormal cristae structure. Examining the levels of proteins involved in mitochondrial fusion, we found a selective up-regulation of more soluble OPA1 protein. Complementation of knockout cells with wild-type Omi/HtrA2 but not with the protease mutant [S306A]Omi/HtrA2 reversed the mitochondrial elongation phenotype and OPA1 alterations. Finally, co-immunoprecipitation showed direct interaction of Omi/HtrA2 with endogenous OPA1. Thus, we show for the first time a direct effect of loss of Omi/HtrA2 on mitochondrial morphology and demonstrate a novel role of this mitochondrial serine protease in the modulation of OPA1. Our results underscore a critical role of impaired mitochondrial dynamics in neurodegenerative disorders.
The Sklené garnet peridotite: petrology, geochemistry, and structure of a mantle-derived boudin in Moldanubian granulite
2010-01-12

The Moldanubian Sklené garnet peridotite, which preserves mineralogical, geochemical, and structural evidence for a protracted mantle evolution, is a small boudin (~1 m) enclosed by granulite of the Gföhl Assemblage.The peridotite has a porphyroclastic texture, in which large garnet and smaller olivine and pyroxene porphyroclasts (Stage 1) reside in a fine-grained, recrystallized matrix of olivine, pyroxene, and pargasitic amphibole (Stage 2).Garnet is surrounded by kelyphite, consisting of an outer zone of pargasite and an inner zone of spinel and pyroxene (Stage 3).Lattice-preferred orientations (LPO) for olivine, orthopyroxene, and clinopyroxene were measured by electron backscatter diffraction.The LPO of olivine (mostly Stage 2) has an [010] maximum parallel to the Z fabric direction and [100] and [001] girdles in the X-Y fabric plane.Both orthopyroxene and clinopyroxene have [010] maxima parallel to Z and [001] girdles in the X-Y plane.The Sklené peridotite is slightly depleted in incompatible major and minor elements relative to primitive mantle.Whole-rock REE contents are 0.3 to 0.8 times that of primitive mantle, with a convex upward pattern, and Rb, Th, U, Pb, and Sr show positive anomalies in an extended element plot.Among the highly siderophile elements, Os, Ir, Ru, and Pt are unfractionated, but Pd and Re are significantly depleted.A Sm-Nd garnet-whole rock-clinopyroxene isochron yields a cooling age of 338 ± 13 Ma, and ε Nd and ( 87 Sr/ 86 Sr) i values for clinopyroxene (at 335 Ma) are +4.5 and 0.7035, respectively.By comparison with other Moldanubian garnet peridotites in the Czech Republic, the Sklené peridotite likely represents a fragment of subcontinental lithospheric mantle.It experienced early partial fusion and depletion of incompatible elements at moderate pressure in the spinel stability field, followed by transport to high-pressure conditions at 1230 oC and 50 kbar, where the Stage 1 garnet-bearing assemblage was stabilized.Subsequently, the depleted peridotite was metasomatized by transient, primitive basaltic melts, with the addition of Rb, Th, U, Pb, and Sr. Dynamic recrystallization, possibly with a progressive transition to grain size sensitive creep, occurred during Stage 2 at ~915 oC and 24 kbar in a flattening-dominated, transpressive deformation regime.This event occurred prior to incorporation of the peridotite in granulite and may reflect the early stages of convergence between Brunia and Moldanubia.The static recrystallization and local growth of spinel within kelyphite at 900 oC and 17-21 kbar (Stage 3) probably took place after entrainment in granulite and was likely isofacial with granulite peak metamorphism.
Swift monitoring of the new accreting millisecond X-ray pulsar IGR J17511-3057 in outburst
2010-01-12

\\n Context. A new accreting millisecond X-ray pulsar, IGR J17511-3057, was discovered in outburst on 2009 September 12 during \\n the <sans-serif>INTEGRAL</sans-serif> Galactic bulge monitoring programme.\\n Aims. To study the evolution of the source X-ray flux and spectral properties during the outburst, we requested a Swift monitoring of IGR J17511-3057.\\n Methods. In this paper we report on the results of the first two weeks of monitoring the source.\\n Results. The persistent emission of IGR J17511-3057 during the outburst is modelled well with an absorbed blackbody ( keV) and a power-law component (Γ –2), similar to what has been observed from other previously known millisecond pulsars. Swift also detected three type-I Xray bursts from this source. By assuming that the peak luminosity of these bursts is equal to the Eddington value for a pure helium \\ntype-I X-ray burst, we derived an upper limit to the source distance of ~10 kpc. The theoretically expected recurrence time of the bursts according to the helium burst hypothesis is 0.2–0.9 days, in agreement with the observations.\\n