julilili42/papers huggingface dataset:
A FEAST FOR CROWS: BIRD PREDATION ON IRREGULAR ECHINOIDS FROM BRITTANY, FRANCE
2014-06-12

Selective feeding behavior of birds on burrowing irregular spatangoid sea urchins, normally out of reach for such predators, is described. Behavioral observations were made on Carrion Crows (Corvus corone) feeding on spatangoid sea urchins (Echinocardium cordatum) during low tide on two different beaches in Brittany, France. The on-site searching behavior of individuals and flocks of crows on the surf line was observed together with characteristic feeding traces on the sediment. Wound morphologies on collected tests were documented with respect to possible preservation potential and recognition in the fossil record. Documented traces on feeding sites allow for clear identification of predator species and can be linked to observed bird behavior. The two sites differ in sea urchin size and the resulting predation traces on the echinoid tests. Predation on smaller specimens fragments the test, whereas predation on larger specimens leaves a characteristic wound morphology that is mainly restricted to the aboral side of the test. The wound morphology resulting from test puncturing involves both extensive inter- and intraplate fragmentation but does not completely destroy the tests. These predation traces are compared to other observed records of bird predation on echinoids. The potential for recognition and preservation in the rock record is then discussed.
Leaf pubescence as a possibility to increase water use efficiency by promoting condensation
2014-06-13

Abstract There is various evidence that the presence of condensed water, e.g. dew, improves plant water relations. Because particularly plants in drier environments are expected to benefit from atmospheric water, it may be assumed that special adaptations promoting exploitation of dew water evolved in these habitats. Surface characteristics affect dewfall and retention of dew water. Leaf surface characteristics such as hairs (trichomes), which are often present in plants of arid environments, may therefore play a substantial role in dew harvesting. In this study, it is analysed to what extent (1) the presence of hygrophilic aerosoles promotes dewfall by reducing vapour saturation pressure (‘early condensation’), (2) dew water can be stored within a dense trichome layer, (3) the presence of dew water increases humidity directly above the leaf surface, thereby reducing water loss from the leaf interior by decreasing the water potential gradient between leaf interior and exterior, and (4) dew evaporation reduces transpiration further by evaporative cooling. A physical framework is provided in this contribution that shows that these processes are in fact possible under natural conditions. Copyright © 2014 John Wiley &amp; Sons, Ltd.
Biochemical and Cellular Analysis of Human Variants of the DYT1 Dystonia Protein, TorsinA/TOR1A
2014-06-13

Early-onset dystonia is associated with the deletion of one of a pair of glutamic acid residues (c.904_906delGAG/c.907_909delGAG; p.Glu302del/Glu303del; ΔE 302/303) near the carboxyl-terminus of torsinA, a member of the AAA(+) protein family that localizes to the endoplasmic reticulum lumen and nuclear envelope. This deletion commonly underlies early-onset DYT1 dystonia. While the role of the disease-causing mutation, torsinAΔE, has been established through genetic association studies, it is much less clear whether other rare human variants of torsinA are pathogenic. Two missense variations have been described in single patients: R288Q (c.863G>A; p.Arg288Gln; R288Q) identified in a patient with onset of severe generalized dystonia and myoclonus since infancy and F205I (c.613T>A, p.Phe205Ile; F205I) in a psychiatric patient with late-onset focal dystonia. In this study, we have undertaken a series of analyses comparing the biochemical and cellular effects of these rare variants to torsinAΔE and wild-type (wt) torsinA to reveal whether there are common dysfunctional features. The results revealed that the variants, R288Q and F205I, are more similar in their properties to torsinAΔE protein than to torsinAwt. These findings provide functional evidence for the potential pathogenic nature of these rare sequence variants in the TOR1A gene, thus implicating these pathologies in the development of dystonia.
Alterations in the Cerebellar (Phospho)Proteome of a Cyclic Guanosine Monophosphate (cGMP)-dependent Protein Kinase Knockout Mouse
2014-06-13

The cyclic nucleotide cyclic guanosine monophosphate (cGMP) plays an important role in learning and memory, but its signaling mechanisms in the mammalian brain are not fully understood. Using mass-spectrometry-based proteomics, we evaluated how the cerebellum adapts its (phospho)proteome in a knockout mouse model of cGMP-dependent protein kinase type I (cGKI). Our data reveal that a small subset of proteins in the cerebellum (∼3% of the quantified proteins) became substantially differentially expressed in the absence of cGKI. More changes were observed at the phosphoproteome level, with hundreds of sites being differentially phosphorylated between wild-type and knockout cerebellum. Most of these phosphorylated sites do not represent known cGKI substrates. An integrative computational network analysis of the data indicated that the differentially expressed proteins and proteins harboring differentially phosphorylated sites largely belong to a tight network in the Purkinje cells of the cerebellum involving important cGMP/cAMP signaling nodes (e.g. PDE5 and PKARIIβ) and Ca(2+) signaling (e.g. SERCA3). In this way, removal of cGKI could be linked to impaired cerebellar long-term depression at Purkinje cell synapses. In addition, we were able to identify a set of novel putative (phospho)proteins to be considered in this network. Overall, our data improve our understanding of cerebellar cGKI signaling and suggest novel players in cGKI-regulated synaptic plasticity.
Multi-frequency study of DEM L299 in the Large Magellanic Cloud
2014-06-13

\\n Aims. We have studied the H <sc>ii </sc>region <ext-link ext-link-type="aoi">DEM L299</ext-link> in the Large Magellanic Cloud (LMC) to understand its physical characteristics and morphology in different wavelengths.\\n Methods. We performed a spectral analysis of archived XMM-Newton EPIC data and studied the morphology of <ext-link ext-link-type="aoi">DEM L299</ext-link> in X-ray, optical, and radio wavelengths. We used Hα, [S <sc>ii</sc>], and [O <sc>iii</sc>] data from the Magellanic Cloud Emission Line Survey (MCELS) and radio 21 cm line data from the Australia Telescope Compact Array (ATCA) and the Parkes Telescope as well as radio continuum data (3 cm, 6 cm, 20 cm, 36 cm) from ATCA and from the Molonglo Synthesis Telescope (MOST).\\n Results. Our morphological studies imply that, in addition to the supernova remnant SNR B0543-68.9 reported in previous studies, a superbubble also overlaps the SNR in projection. The position of the SNR is clearly defined through the [S <sc>ii</sc>]/Hα flux ratio image. Moreover, the optical images show a shell-like structure that is located farther to the north and is filled with diffuse X-ray emission, which again indicates the superbubble. Radio 21 cm line data show a shell around both objects. Radio continuum data show diffuse emission at the position of <ext-link ext-link-type="aoi">DEM L299</ext-link>, which appears clearly distinguished from the H <sc>ii</sc> region LHA 120-N 164 that lies south-west of it. We determined the spectral index of SNR B0543-68.9 to be α = −0.34, which indicates the dominance of thermal emission and therefore a rather mature remnant. We determined the basic properties of the diffuse X-ray emission for the SNR, the superbubble, and a possible blowout region of the bubble, as suggested by the optical and X-ray data. We obtained an age of (8.9+9.2-5.4) kyr for the SNR and a temperature of (0.64+0.73-0.20) keV for the hot gas inside the SNR, as well as a thermal energy content and temperature of the hot gas inside the superbubble of (4.3+8.1-2.6) × 1050 φ0.5 erg and (0.74+0.36-0.30) keV, with φ being the gas-filling factor. \\n Conclusions. We conclude that <ext-link ext-link-type="aoi">DEM L299</ext-link> consists of a superposition of SNR B0543-68.9 and a superbubble, which we identified based on optical data. \\n
Novel chemistry of invasive plants: exotic species have more unique metabolomic profiles than native congeners
2014-06-14

Abstract It is often assumed that exotic plants can become invasive when they possess novel secondary chemistry compared with native plants in the introduced range. Using untargeted metabolomic fingerprinting, we compared a broad range of metabolites of six successful exotic plant species and their native congeners of the family Asteraceae. Our results showed that plant chemistry is highly species‐specific and diverse among both exotic and native species. Nonetheless, the exotic species had on average a higher total number of metabolites and more species‐unique metabolites compared with their native congeners. Herbivory led to an overall increase in metabolites in all plant species. Generalist herbivore performance was lower on most of the exotic species compared with the native species. We conclude that high chemical diversity and large phytochemical uniqueness of the exotic species could be indicative of biological invasion potential.
16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy
2014-06-16

Rolandic epilepsy (RE) is the most common idiopathic focal childhood epilepsy. Its molecular basis is largely unknown and a complex genetic etiology is assumed in the majority of affected individuals. The present study tested whether six large recurrent copy number variants at 1q21, 15q11.2, 15q13.3, 16p11.2, 16p13.11 and 22q11.2 previously associated with neurodevelopmental disorders also increase risk of RE. Our association analyses revealed a significant excess of the 600 kb genomic duplication at the 16p11.2 locus (chr16: 29.5-30.1 Mb) in 393 unrelated patients with typical (n = 339) and atypical (ARE; n = 54) RE compared with the prevalence in 65,046 European population controls (5/393 cases versus 32/65,046 controls; Fisher's exact test P = 2.83 × 10(-6), odds ratio = 26.2, 95% confidence interval: 7.9-68.2). In contrast, the 16p11.2 duplication was not detected in 1738 European epilepsy patients with either temporal lobe epilepsy (n = 330) and genetic generalized epilepsies (n = 1408), suggesting a selective enrichment of the 16p11.2 duplication in idiopathic focal childhood epilepsies (Fisher's exact test P = 2.1 × 10(-4)). In a subsequent screen among children carrying the 16p11.2 600 kb rearrangement we identified three patients with RE-spectrum epilepsies in 117 duplication carriers (2.6%) but none in 202 carriers of the reciprocal deletion. Our results suggest that the 16p11.2 duplication represents a significant genetic risk factor for typical and atypical RE.
Raman spectroscopy as an analytical tool for melanoma research
2014-06-16

Raman spectroscopy is a powerful noninvasive tool to distinguish between melanocytes and melanoma cells, to analyze the specific type of cell death in melanoma cells, and to predict the susceptibility of melanoma cells to anticancer drugs.
Vertical and lateral flux on the continental slope off Pakistan: correlation of sediment core and trap results
2014-06-16

Abstract. Due to the lack of bioturbation, the varve-laminated muds from the oxygen minimum zone (OMZ) off Pakistan provide a unique opportunity to precisely determine the vertical and lateral sediment fluxes in the nearshore part of the northeastern Arabian Sea. West of Karachi (Hab area), the results of two sediment trap stations (EPT and WPT) were correlated with 16 short sediment cores on a depth transect crossing the OMZ. The top of a distinct, either reddish- or light-gray silt layer, 210Pb-dated as AD 1905 ± 10, was used as an isochronous stratigraphic marker bed to calculate sediment accumulation rates. In one core, the red and gray layer were separated by a few (5–10) thin laminae. According to our varve model, this contributes &lt; 10 years to the dating uncertainty, assuming that the different layers are almost synchronous. We directly compared the accumulation rates with the flux rates from the sediment traps that collected the settling material within the water column above. All traps on the steep Makran continental slope show exceptionally high, pulsed winter fluxes of up to 5000 mg m−2 d−1. Based on core results, the flux at the seafloor amounts to 4000 mg m−2 d−1 and agrees remarkably well with the bulk winter flux of material, as well as with the flux of the individual bulk components of organic carbon, calcium carbonate and opal. However, due to the extreme mass of remobilized matter, the high winter flux events exceeded the capacity of the shallow traps. Based on our comparisons, we argue that high-flux events must occur regularly during winter within the upper OMZ off Pakistan to explain the high accumulations rates. These show distribution patterns that are a negative function of water depth and distance from the shelf. Some of the sediment fractions show marked shifts in accumulation rates near the lower boundary of the OMZ. For instance, the flux of benthic foraminifera is lowered but stable below ~1200–1300 m. However, flux and sedimentation in the upper eastern Makran area are dominated by the large amount of laterally advected fine-grained material and by the pulsed nature of the resuspension events at the upper margin during winter.
Estimation of Mass Balance of the Grosser Aletschgletscher, Swiss Alps, from ICESat Laser Altimetry Data and Digital Elevation Models
2014-06-17

Traditional glaciological mass balance measurements of mountain glaciers are a demanding and cost intensive task. In this study, we combine data from the Ice Cloud and Elevation Satellite (ICESat) acquired between 2003 and 2009 with air and space borne Digital Elevation Models (DEMs) in order to derive surface elevation changes of the Grosser Aletschgletscher in the Swiss Alps. Three different areas of the glacier are covered by one nominal ICESat track, allowing us to investigate the performance of the approach under different conditions in terms of ICESat data coverage, and surface characteristics. In order to test the sensitivity of the derived trend in surface lowering, several variables were tested. Employing correction for perennial snow accumulation, footprint selection and adequate reference DEM, we estimated a mean mass balance of −0.92 ± 0.18 m w.e. a−1. for the whole glacier in the studied time period. The resulting mass balance was validated by a comparison with another geodetic approach based on the subtraction of two DEMs for the years 1999 and 2009. It appears that the processing parameters need to be selected depending on the amount of available ICESat measurements, quality of the elevation reference and character of the glacier surface.
A quantitative study of Cooperative Awareness Messages in production VANETs
2014-06-17

In Vehicular Ad-hoc Networks (VANETs), vehicles gather Cooperative Awareness Messages (CAMs) sent from other vehicles via wireless broadcast. Each received message has to be processed by an in-vehicle system. In series implementations, such an in-vehicle system needs to cope with limited resources whose capacity is not yet defined. Therefore, information about the received CAM rate is a crucial input for the development of series VANET products. CAMs from distant vehicles are less likely to be received than those of nearby vehicles. Designers of applications leveraging CAM information are interested in the frequency of received CAMs originating from vehicles depending on their distance. In this paper, we study future CAM rates depending on various parameters. We set up a road traffic simulation for selected highway scenarios. We estimate the rates of generated CAMs and introduce the notion of relative channel load. We present a new approximative channel model to determine a vehicle's message reception probability. That model is used to simulate the rates of received CAMs for each vehicle. Moreover, we investigate the origin of received CAMs and times between consecutive CAMs received from the same sender (inter-reception times) depending on distance. Most results depend on the penetration rate of VANET technology that will increase in the near future. We derive approximative formulae and use them to validate our simulation results. They are quite accurate, and so they may also serve for simple forecasts. The results from our analysis show that the rates of generated and received CAMs lead to several challenges for the design of an efficient and robust VANET implementation.
Key network approach reveals new insight into Alzheimer's disease
2014-06-17

Alzheimer's disease (AD) is a severe neurodegenerative disorder without curative treatment. Extensive data on pathological molecular processes have been accumulated over the last years. These data combined allows a systems biology approach to identify key regulatory elements of AD and to establish a model descriptive of the disease process which can be used for the development of therapeutic agents. In this study, the authors propose a closed network that uses a set of nodes (amyloid beta, tau, beta‐secretase, glutamate, cyclin‐dependent kinase 5, phosphoinositide 3‐kinase and hypoxia‐induced factor 1 alpha) as key elements of importance to the pathogenesis of AD. The proposed network, in total 39 nodes, is able to become a novel tool capable of providing new insights into AD, such as feedback loops. Further, it highlights interconnections between pathways and identifies their combination for therapy of AD.
Live-Surgery at Neurosurgical Training Courses: Essential Infrastructure, Technical Setup and Educational Considerations
2014-06-17

Objective: To report about the infrastructure and technical setup for live-surgeries at neurosurgical training courses. Methods: From 2007 to 2013, 13 neurosurgical training courses with live surgeries have been organized at the department of neurosurgery. Here, we share our experience and report the essential setup. Results: Our department organized seven skull base, five cervical-spine, and one spinal-cord-stimulation hands-on dissection course with live surgeries. The course structure includes lectures, cadaver dissections, and live surgeries. The technical setup includes video transmission via an IP-based network with fiber glass backbone between OR and lecture room. Up to four video signals may be transmitted contemporaneously (microscope, endoscope, X-ray, overview). Two bidirectional audio streams allow a continuous interaction. In the anatomy, master-piece dissections and personal tutorials for a group of four participants are essential to achieve an adequate educational level. During surgery bidirectional discussions offer the participant to interfere and ask on the point. Important issues are careful selection of live operated patients with a well presentable pathology, plan always with a buffer of at least one patient, and chose didactic cases to show the technique. The live-surgery should include intraoperative setup, positioning, anesthesiological procedures, and handling of intraoperative situations. Matching the awareness for ecological protection and educational demands in medicine the courses can be transmitted as a web stream to faculties worldwide to offer participation without traveling, which is a rewarding option for neurosurgeons in developing countries. Conclusion: A professionally prepared step-by-step education including surgical anatomy, cadaver dissection with masterpiece, and live surgeries with online discussion offers a high level training with enrichment of both participants and tutors.
Depiction of the Petrosal Vein Complex with 3D-MR-Venography
2014-06-17

Objective: Petrosal vein occlusion may be well tolerated, but sometimes it causes deleterious consequences. It would be crucial identifying the subgroup of patients who does not tolerate the occlusion. Design: Aim of this study was to depict the petrosal vein, main branches and anastomoses with a high-resolution, contrast-medium enhanced 3D-GRE-MR-venography (CE-3D-MRV). Patients/Methods: Total 20 patients (40 sides) were examined with a 3D-GRE-sequence at the 3 T MRT (Skyra, Siemens) with the following parameters: repetition time 7.96 ms, echo time 2.53 ms, flip angel 25 degrees, band 130Hz/pixel, FOV 254×280 mm2, matrix 640×640, slice thickness 0.625 mm, voxel 0.5×0.5×0.625 mm3, acquisition time 2.04 min. Two radiologists identified and measured independently the veins, their diameters, and anastomoses (PACS, General Electrics). Results: In all patients we identified a vena petrosa (1VP/case = 50%, 2VP/case = 42%, 3VP/case = 8%) and assigned the contributaries (63% vena cerebelli superior, 63% vena fissura cerebellopontina, 56% vena pontina transversa, 10% vena mesencephalica lateralis). In 85% of the cases we identified relevant anastomoses between the respective petrosal veins or to the supratentorial territory. The mean diameter of the petrosal veins was 2.3±?1.0 mm (range, 0.5-5.1 mm). Conclusion: The CE-3D-MRV gives an excellent image of the petrosal vein system and thus seems to offer the possibility to identify preoperatively patients with lack of sufficient anastomoses.
Analysis of Molecular Networks Uncovers Potential Targets in Vestibular Schwannoma
2014-06-17

Objective: Understanding molecular pathway mechanisms of the formation of vestibular schwannoma may lead to potential therapeutic targets. Study Design: We performed gene expression profiling of 49 schwannomas (36 sporadic and 13 NF2-associated cases) and 7 normal control vestibular nerves. Results: We identified over 4,000 differentially expressed genes between control and schwannoma with network analysis uncovering proliferation and antiapoptotic pathways previously not implicated in vestibular schwannomas. Using several distinct clustering technologies, we could not reproducibly identify subtypes of schwannomas suggesting that our schwannoma cohort was molecularly distinct from normal tissue yet highly similar among themselves. At the molecular level the PI3K/AKT/mTOR signaling network was overexpressed in our schwannoma cohort and evaluated for therapeutic targeting. Testing compounds BEZ235 and PKI-587 both novel dual inhibitors of PI3K and mTOR attenuated tumor growth in a preclinical cell line model of schwannoma (HEI-293). In vitro findings demonstrated that ablation of the PI3K/AKT/mTOR pathway with next generation inhibitors lead to decreased cell viability and increased cell death. Conclusion: The discovery of novel molecular targets in vestibular schwannoma by transcriptional profiling as compared with appropriate controls may lead to effective therapeutic strategies and shed insight into the molecular ontogeny of this tumor.