julilili42/papers huggingface dataset:
Superconducting quantum interference devices with submicron Nb/HfTi/Nb junctions for investigation of small magnetic particles
2011-07-18

We investigated, at temperature 4.2 K, electric transport, flux noise, and resulting spin sensitivity of miniaturized Nb direct current superconducting quantum interference devices (SQUIDs) based on submicron Josephson junctions with HfTi barriers. The SQUIDs are either of the magnetometer-type or gradiometric in layout. In the white noise regime, for the best magnetometer we obtain a flux noise SΦ1/2=250nΦ0/Hz1/2, corresponding to a spin sensitivity Sμ1/2≥29μB/Hz1/2. For the gradiometer we find SΦ1/2=300nΦ0/Hz1/2 and Sμ1/2≥44μB/Hz1/2. The devices can still be optimized with respect to flux noise and coupling between a magnetic particle and the SQUID, leaving room for further improvement towards single spin resolution.
Patterns of divergence in the olive sunbird Cyanomitra olivacea (Aves: Nectariniidae) across the African rainforest-savanna ecotone
2011-07-18

In the debate over modes of vertebrate diversification in tropical rainforests, two competing hypotheses of speciation predominate: those that emphasize the role of geographical isolation during glacial periods and those that stress the role of ecology and diversifying selection across ecotones or environmental gradients. To investigate the relative roles of selection versus isolation in refugia, we contrasted genetic and morphologic divergence of the olive sunbird (Cyanomitra olivacea) at 18 sites (approximately 200 individuals) across the forest–savanna ecotone of Central Africa in a region considered to have harboured three hypothesized refugia during glacial periods. Habitats were characterized using bioclimatic and satellite remote-sensing data. We found relatively high levels of gene flow between ecotone and forest populations and between refugia. Consistent with a pattern of divergence-with-gene-flow, we found morphological characters to be significantly divergent across the gradient [forest versus ecotone (mean ± SD): wing length 60.47 ± 1.81 mm versus 62.18 ± 1.35 mm; tarsus length 15.51 ± 0.82 mm versus 16.00 ± 0.57 mm; upper mandible length 21.77 ± 1.09 mm versus 23.19 ± 0.98 mm, respectively]. Within-habitat comparisons across forest and ecotone sites showed no significant differences in morphology. The results show that divergence in morphological traits is tied to environmental variables across the gradient and is occurring despite gene flow. The pattern of divergence-with-gene-flow found is similar to that described for other rainforest species across the gradient. These results suggest that neither refugia, nor isolation-by-distance have played a major role in divergence in the olive sunbird, although ecological differences along the forest and savanna ecotone may impose significant selection pressures on the phenotype and potentially be important in diversification.
Biogenic Fe(III) Minerals Lower the Efficiency of Iron-Mineral-Based Commercial Filter Systems for Arsenic Removal
2011-07-18

Millions of people worldwide are affected by As (arsenic) contaminated groundwater. Fe(III) (oxy)hydroxides sorb As efficiently and are therefore used in water purification filters. Commercial filters containing abiogenic Fe(III) (oxy)hydroxides (GEH) showed varying As removal, and it was unclear whether Fe(II)-oxidizing bacteria influenced filter efficiency. We found up to 10(7) Fe(II)-oxidizing bacteria/g dry-weight in GEH-filters and determined the performance of filter material in the presence and absence of Fe(II)-oxidizing bacteria. GEH-material sorbed 1.7 mmol As(V)/g Fe and was ~8 times more efficient than biogenic Fe(III) minerals that sorbed only 208.3 μmol As(V)/g Fe. This was also ~5 times more efficient than a 10:1-mixture of GEH-material and biogenic Fe(III) minerals that bound 322.6 μmol As(V)/g Fe. Coprecipitation of As(V) with biogenic Fe(III) minerals removed 343.0 μmol As(V)/g Fe, while As removal by coprecipitation with biogenic minerals in the presence of GEH-material was slightly less efficient as GEH-material only and yielded 1.5 mmol As(V)/g Fe. The present study thus suggests that the formation of biogenic Fe(III) minerals lowers rather than increases As removal efficiency of the filters probably due to the repulsion of the negatively charged arsenate by the negatively charged biogenic minerals. For this reason we recommend excluding microorganisms from filters (e.g., by activated carbon filters) to maintain their high As removal capacity.
Extramammary Paget's Disease: Extended Subclinical Growth Detected Using Three-Dimensional Histology in Routine Paraffin Procedure and Course of the Disease
2011-07-18

Subclinical spread of EMPD demonstrated using 3D histology with paraffin sectioning can be large. Three-dimensional histology allows individually defined safety margins to be locally adjusted to subclinical growth and gives low recurrence rates. The authors have indicated no significant interest with commercial supporters.
Compensation of RF field and receiver coil induced inhomogeneity effects in abdominal MR images by a priori knowledge on the human adipose tissue distribution
2011-07-18

Abstract Purpose: To reliably compensate bias field effects in abdominal areas to accurately quantify visceral adipose tissue using standard T1‐weighted sequences on MR scanners with up to 3 Tesla (T) field strength. Materials and Methods: Compensation is achieved in two steps: The bias field is first estimated by picking and fitting sampling points from the subcutaneous adipose tissue, using active contours and a thin plate fitting spline. Then, additional sampling points from visceral adipose tissue compartments are detected by thresholding and the bias field estimation is refined. It was compared with an established method using a simulated abdominal image and real 3T data. Results: At low bias field amplitudes (40–50%), the simulation study showed a good reduction of the mean coefficients of variance (CV) for both approaches (&gt;80%). At higher amplitudes, the CV reduction was significantly higher for our approach (83.6%), compared with LEMS (54.3%). In the real data study, our approach showed reliable reduction of the inhomogeneities, while the LEMS algorithm sometimes even amplified the inhomogeneities. Conclusion: The proposed method enables accurate and reliable segmentation of abdominal adipose tissue using simple thresholding techniques, even in severely corrupted images slices, obtained when using high field strengths and/or phased‐array coils. J. Magn. Reson. Imaging 2011;. © 2011 Wiley‐Liss, Inc.
Interactions with human blood in vitro and pharmacokinetic properties in mice of liposomal N4-octadecyl-1-beta-D-arabinofuranosylcytosine, a new anticancer drug
2011-07-18

The interactions of N4-octadecyl-1-beta-D-arabinofuranosylcytosine (NOAC), a lipophilic derivative of 1-beta-D-arabinofuranosylcytosine (ara-C), were studied in vitro with human blood components. Binding of NOAC incorporated into liposomes to erythrocytes (Ec) was saturated at 63 nmol/10(9) Ec and binding analysis resulted in a weak affinity of 3 x 10(3) liters/mol and 4 x 10(7) binding sites per Ec. The Ec partition coefficient D(Ec) was approximately 4, which demonstrates the high accumulation of NOAC in Ec membranes. The calculated fraction f(b) of drug bound to plasma proteins was 30%. Analysis of serum protein binding of NOAC was done by density gradient ultracentrifugation and agarose gel electrophoresis. Liposomal NOAC was distributed to low-density lipoproteins (LDL) at 36%, to high-density lipoproteins at 21%, to albumin and other proteins at 12% and to very-low-density lipoproteins at 5%. Comparable results were obtained for the analog N4-hexadecyl-1-beta-D-arabinofuranosylcytosine and when the drugs were dissolved in dimethyl sulfoxide. The biodistribution of liposomal NOAC in ICR mice after intravenous application revealed a biphasic blood concentration versus time curve with a distribution half-life t1/2alpha of 23 min and an elimination half-life t1/2beta of 7 h. The drug was distributed mainly into the liver with an organ load of 69% and with an elimination half-life of 8 h. The strong affinity of NOAC to LDL might be exploited for the enhanced uptake of the drug in tumor cells expressing high numbers of LDL receptor molecules.
Modulation of cortical inhibition by rTMS – findings obtained from animal models
2011-07-19

Abstract Transcranial magnetic stimulation (TMS) has become a popular method to non‐invasively stimulate the human brain. The opportunity to modify cortical excitability with repetitive stimulation (rTMS) has especially gained interest for its therapeutic potential. However, details of the cellular mechanisms of the effects of rTMS are scarce. Currently favoured are long‐term changes in the efficiency of excitatory synaptic transmission, with low‐frequency rTMS depressing it, but high‐frequency rTMS augmenting. Only recently has modulation of cortical inhibition been considered as an alternative way to explain lasting changes in cortical excitability induced by rTMS. Adequate animal models help to highlight stimulation‐induced changes in cellular processes which are not assessable in human rTMS studies. In this review article, we summarize findings obtained with our rat models which indicate that distinct inhibitory cell classes, like the fast‐spiking cells characterized by parvalbumin expression, are most sensitive to certain stimulation protocols, e.g. intermittent theta burst stimulation. We discuss how our findings can support the recently suggested models of gating and homeostatic plasticity as possible mechanisms of rTMS‐induced changes in cortical excitability.
Range of outward migration and influence of the disc’s mass on the migration of giant planet cores
2011-07-19

\\n Context. The migration of planets plays an important role in the early\\n planet-formation process. An important problem has been that standard migration theories\\n predict very rapid inward migration, which poses problems for population synthesis models.\\n However, it has been shown recently that low-mass planets\\n (20–30 MEarth) that are still embedded in the protoplanetary\\n disc can migrate outwards under certain conditions. Simulations have been performed mostly\\n for planets at given radii for a particular disc model. \\n Aims. Here, we plan to extend previous work and consider different\\n masses of the disc to quantify the influence of the physical disc conditions on planetary\\n migration. The migration behaviour of the planets will be analysed for a variety of\\n positions in the disc. \\n Methods. We perform three-dimensional (3D) radiation hydrodynamical\\n simulations of embedded planets in protoplanetary discs. We use the explicit-implicit 3D\\n hydrodynamical code NIRVANA that includes full tensor viscosity, and implicit radiation\\n transport. For planets on circular orbits at various locations we measure the radial\\n dependence of the torques for three different planetary masses. \\n Results. For all considered planet masses (20–30\\n MEarth) in this study we find outward migration within a\\n limited radial range of the disc, typically from about 0.5 up to 1.5–2.5\\n aJup. Inside and outside this interval, migration is inward\\n and given by the Lindblad value for large radii. Interestingly, the fastest outward\\n migration occurs at a radius of about aJup for different disc\\n and planet masses. Because outward migration stops at a certain location in the disc,\\n there exists a zero-torque distance for planetary embryos, where they can continue to grow\\n without moving too fast. For higher disc masses\\n (Mdisc &gt; 0.02 M⊙)\\n convection ensues, which changes the structure of the disc and therefore the torque on the\\n planet as well.\\n Conclusions. Outward migration stops at different points in the disc for\\n different planetary masses, resulting in a quite extended region where the formation of\\n larger cores might be easier. In higher mass discs, convection changes the disc’s\\n structure resulting in fluctuations in the surface density, which influence the torque\\n acting on the planet, and therefore its migration rate. Because convection is a 3D effect,\\n 2D simulations of massive discs with embedded planets should be handled with care. \\n
Tracking the evolutionary history of Cortinarius species in section Calochroi, with transoceanic disjunct distributions
2011-07-19

Our results indicate that each of the Calochroi species has undergone a relatively independent evolutionary history, hypothesised as follows: 1) a widely distributed ancestral population of C. arcuatorum diverged into distinctive sympatric populations in the New World; 2) two divergent lineages in C. elegantior gave rise to the New World and Old World haplotypes, respectively; and 3) the low levels of genetic divergence within C. aureofulvus and C. napus may be the result of more recent demographic population expansions. The scenario of migration via the Bering Land Bridge provides the most probable explanation for contemporaneous disjunct geographic distributions of these species, but it does not offer an explanation for the low degree of genetic divergence between populations of C. aureofulvus and C. napus. Our findings are mostly consistent with the designation of New World allopatric populations as separate species from the European counterpart species C. arcuatorum and C. elegantior. We propose the synonymy of C. albobrunnoides, C. albobrunnoides var. violaceovelatus and C. subpurpureophyllus var. sulphureovelatus with C. napus. The results also reinforce previous observations that linked C. arcuatorum and C. aureofulvus displaying distributions in parts of North America and Europe. Interpretations of the population structure of these fungi suggest that host tree history has heavily influenced their modern distributions; however, the complex issues related to co-migration of these fungi with their tree hosts remain unclear at this time.
Fermion energies in the background of a cosmic string
2011-07-19

We provide a thorough exposition, including technical and numerical details,\\nof previously published results on the quantum stabilization of cosmic strings.\\nStabilization occurs through the coupling to a heavy fermion doublet in a\\nreduced version of the standard model. We combine the vacuum polarization\\nenergy of fermion zero-point fluctuations and the binding energy of occupied\\nenergy levels, which are of the same order in a semi-classical expansion.\\nPopulating these bound states assigns a charge to the string. We show that\\nstrings carrying fermion charge become stable if the electro-weak bosons are\\ncoupled to a fermion that is less than twice as heavy as the top quark. The\\nvacuum remains stable in our model, because neutral strings are not\\nenergetically favored. These findings suggests that extraordinarily large\\nfermion masses or unrealistic couplings are not required to bind a cosmic\\nstring in the standard model.\\n
GaggleBridge: collaborative data analysis
2011-07-19

Abstract Motivation: Tools aiding in collaborative data analysis are becoming ever more important as researchers work together over long distances. We present an extension to the Gaggle framework, which has been widely adopted as a tool to enable data exchange between different analysis programs on one computer. Results: Our program, GaggleBridge, transparently extends this functionality to allow data exchange between Gaggle users at different geographic locations using network communication. GaggleBridge can automatically set up SSH tunnels to traverse firewalls while adding some security features to the Gaggle communication. Availability: GaggleBridge is available as open-source software implemented in the Java language at http://it.inf.uni-tuebingen.de/gb. Contact: florian.battke@uni-tuebingen.de Supplementary Information: Supplementary data are available at Bioinformatics online.
An Unusual Location of Deep Venous Thrombosis Associated with Ischemic Stroke and Persistent Foramen Ovale
2011-07-19

Up to 40% of ischemic strokes have no known cause (cryptogenic). The prevalence of persistent foramen ovale (PFO) amongst patients with cryptogenic stroke (CS) is twice as high as that of the normal population, therefore suggesting a causal relationship between the two entities. However, PFO by itself is not sufficient to cause stroke, as an embolic source is needed. This source is often unknown, making the causal relationship between CS and PFO hard to demonstrate. The most frequent, although still seldom, identifiable cause of embolism in an otherwise cryptogenic stroke associated with PFO is a deep venous thrombosis (DVT) of the lower extremities. Here, we present a unique case of brachiocephalic venous DVT associated with PFO and ischemic stroke in a young patient. As the search for DVT in patients with PFO and stroke is often limited to the lower extremities, this case may suggest that an unspecified number of DVTs are overlooked. Our report lends support to paradoxical embolism as a mechanism of stroke in patients with PFO and does, at least in selected cases, suggest a more detailed search for DVT beyond the lower extremities.
Identification of RNF213 as a Susceptibility Gene for Moyamoya Disease and Its Possible Role in Vascular Development
2011-07-20

&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;p&gt;Moyamoya disease is an idiopathic vascular disorder of intracranial arteries. Its susceptibility locus has been mapped to 17q25.3 in Japanese families, but the susceptibility gene is unknown.&lt;/p&gt; &lt;h3&gt;Methodology/Principal Findings&lt;/h3&gt;&lt;p&gt;Genome-wide linkage analysis in eight three-generation families with moyamoya disease revealed linkage to 17q25.3 (&lt;em&gt;P&lt;/em&gt;&lt;10&lt;sup&gt;-4&lt;/sup&gt;). Fine mapping demonstrated a 1.5-Mb disease locus bounded by D17S1806 and rs2280147. We conducted exome analysis of the eight index cases in these families, with results filtered through Ng criteria. There was a variant of p.N321S in &lt;em&gt;PCMTD1&lt;/em&gt; and p.R4810K in &lt;em&gt;RNF213&lt;/em&gt; in the 1.5-Mb locus of the eight index cases. The p.N321S variant in &lt;em&gt;PCMTD1&lt;/em&gt; could not be confirmed by the Sanger method. Sequencing &lt;em&gt;RNF213&lt;/em&gt; in 42 index cases confirmed p.R4810K and revealed it to be the only unregistered variant. Genotyping 39 SNPs around &lt;em&gt;RNF213&lt;/em&gt; revealed a founder haplotype transmitted in 42 families. Sequencing the 260-kb region covering the founder haplotype in one index case did not show any coding variants except p.R4810K. A case-control study demonstrated strong association of p.R4810K with moyamoya disease in East Asian populations (251 cases and 707 controls) with an odds ratio of 111.8 (&lt;em&gt;P&lt;/em&gt; = 10&lt;sup&gt;−119&lt;/sup&gt;). Sequencing of &lt;em&gt;RNF213&lt;/em&gt; in East Asian cases revealed additional novel variants: p.D4863N, p.E4950D, p.A5021V, p.D5160E, and p.E5176G. Among Caucasian cases, variants p.N3962D, p.D4013N, p.R4062Q and p.P4608S were identified. &lt;em&gt;RNF213&lt;/em&gt; encodes a 591-kDa cytosolic protein that possesses two functional domains: a Walker motif and a RING finger domain. These exhibit ATPase and ubiquitin ligase activities. Although the mutant alleles (p.R4810K or p.D4013N in the RING domain) did not affect transcription levels or ubiquitination activity, knockdown of &lt;em&gt;RNF213&lt;/em&gt; in zebrafish caused irregular wall formation in trunk arteries and abnormal sprouting vessels.&lt;/p&gt; &lt;h3&gt;Conclusions/Significance&lt;/h3&gt;&lt;p&gt;We provide evidence suggesting, for the first time, the involvement of &lt;em&gt;RNF213&lt;/em&gt; in genetic susceptibility to moyamoya disease.&lt;/p&gt; &lt;/div&gt;
Biological Motion Processing as a Hallmark of Social Cognition
2011-07-20

Visual processing of biological motion (BM) produced by living organisms is of immense value for successful daily-life activities and, in particular, for adaptive social behavior and nonverbal communication. Investigation of BM perception in neurodevelopmental disorders related to autism, preterm birth, and genetic conditions substantially contributes to our understanding of the neural mechanisms underpinning the extraordinary tuning to BM. The most prominent research outcome is that patients with daily-life deficits in social cognition are also compromised on visual body motion processing. This raises the question of whether performance on body motion perception tasks may serve a hallmark of social cognition. Overall, the findings highlight the role of structural and functional brain connectivity for proper functioning of the neural circuitry involved in BM processing and visual social cognition that share topographically and dynamically overlapping neural networks.
Raman Spectroscopy: A Noninvasive Analysis Tool for the Discrimination of Human Skin Cells
2011-07-20

Noninvasive monitoring of tissue-engineered (TE) constructs during their in vitro maturation or postimplantation in vivo is highly relevant for graft evaluation. However, traditional methods for studying cell and matrix components in engineered tissues such as histology, immunohistochemistry, or biochemistry require invasive tissue processing, resulting in the need to sacrifice of TE constructs. Raman spectroscopy offers the unique possibility to analyze living cells label-free in situ and in vivo solely based on their phenotype-specific biochemical fingerprint. In this study, we aimed to determine the applicability of Raman spectroscopy for the noninvasive identification and spectral separation of primary human skin fibroblasts, keratinocytes, and melanocytes, as well as immortalized keratinocytes (HaCaT cells). Multivariate analysis of cell-type-specific Raman spectra enabled the discrimination between living primary and immortalized keratinocytes. We further noninvasively distinguished between fibroblasts, keratinocytes, and melanocytes. Our findings are especially relevant for the engineering of in vitro skin models and for the production of artificial skin, where both the biopsy and the transplant consist of several cell types. To realize a reproducible quality of TE skin, the determination of the purity of the cell populations as well as the detection of potential molecular changes are important. We conclude therefore that Raman spectroscopy is a suitable tool for the noninvasive in situ quality control of cells used in skin tissue engineering applications.
Chromatin Immunoprecipitation from Dorsal Root Ganglia Tissue following Axonal Injury
2011-07-20

Axons in the central nervous system (CNS) do not regenerate while those in the peripheral nervous system (PNS) do regenerate to a limited extent after injury (Teng et al., 2006). It is recognized that transcriptional programs essential for neurite and axonal outgrowth are reactivated upon injury in the PNS (Makwana et al., 2005). However the tools available to analyze neuronal gene regulation in vivo are limited and often challenging. The dorsal root ganglia (DRG) offer an excellent injury model system because both the CNS and PNS are innervated by a bifurcated axon originating from the same soma. The ganglia represent a discrete collection of cell bodies where all transcriptional events occur, and thus provide a clearly defined region of transcriptional activity that can be easily and reproducibly removed from the animal. Injury of nerve fibers in the PNS (e.g. sciatic nerve), where axonal regeneration does occur, should reveal a set of transcriptional programs that are distinct from those responding to a similar injury in the CNS, where regeneration does not take place (e.g. spinal cord). Sites for transcription factor binding, histone and DNA modification resulting from injury to either PNS or CNS can be characterized using chromatin immunoprecipitation (ChIP). Here, we describe a ChIP protocol using fixed mouse DRG tissue following axonal injury. This powerful combination provides a means for characterizing the pro-regeneration chromatin environment necessary for promoting axonal regeneration.