julilili42/papers huggingface dataset:
MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked
2016-08-18

Abstract MASP-3 was discovered 15 years ago as the third mannan-binding lectin (MBL)-associated serine protease of the complement lectin pathway. Lacking any verified substrate its role remained ambiguous. MASP-3 was shown to compete with a key lectin pathway enzyme MASP-2 for MBL binding, and was therefore considered to be a negative complement regulator. Later, knock-out mice experiments suggested that MASP-1 and/or MASP-3 play important roles in complement pro-factor D (pro-FD) maturation. However, studies on a MASP-1/MASP-3-deficient human patient produced contradicting results. In normal resting blood unperturbed by ongoing coagulation or complement activation, factor D is present predominantly in its active form, suggesting that resting blood contains at least one pro-FD activating proteinase that is not a direct initiator of coagulation or complement activation. We have recently showed that all three MASPs can activate pro-FD in vitro . In resting blood, however, using our previously evolved MASP-1 and MASP-2 inhibitors we proved that neither MASP-1 nor MASP-2 activates pro-FD. Other plasma proteinases, particularly MASP-3, remained candidates for that function. For this study we evolved a specific MASP-3 inhibitor and unambiguously proved that activated MASP-3 is the exclusive pro-FD activator in resting blood, which demonstrates a fundamental link between the lectin and alternative pathways.
Can Sport Really Help to Meet the Millennium Development Goals? Evidence From Children in Peru
2016-08-18

In contrast to the popular policy claim that sport might serve as vehicle to meet the Millennium Development Goals, empirical evidence based on large-scale survey data is largely missing. We use panel data based on a cohort of children and employ propensity score matching to identify the effects of sports participation on child development in Peru. Our findings suggest that participation in a sports group has positive impacts on subjective health and a measure of social capital. However, and in contrast to developed countries, we find no statistically significant effects on well-being and human capital formation.
New limits on double electron capture of40Ca and180W
2016-08-18

We analyzed low-background data from the CRESST-II experiment with a total net exposure of 730 kg days to extract limits on double electron capture processes. We established new limits for Ca with y and y and for W with T y and y at 90% CL. Depending on the process, these values improve the currently best limits by a factor of 1.4-30.
The JEM-EUSO energy and $X_{max}$ reconstruction performances
2016-08-18

JEM‐EUSO is an international collaboration committed to the development of space‐based observatories for the study of cosmic rays at ultra‐high energies In this framework we are carrying out an extensive simulation study in order to evaluate the performances of the mission. In this contribution we focus on the energy and Xmax reconstruction performances. We therefore simulated several samples of cosmic ray events and we produced the detector response following a detailed simulation of the optics and of the detector. After the trigger recognized an excess, we analyze the received data to extract the basic shower parameters like direction, energy and Xmax . In this work we briefly describe the algorithms to reconstruct the energy and Xmax. We then present a study to assess the energy reconstruction performances in a set of fixed conditions and on the whole field of view. We also present preliminary results on the Xmax reconstruction in the center of the field of view.
Observation of neutrinos with JEM-EUSO: an updated view
2016-08-18

for the JEM-EUSO CollaborationSimilarly to extreme energy cosmic rays (EECRs), neutrinos at energies exceeding 5×10 19 eV are expected to interact in the Earth's atmosphere and create extensive air showers.The JEM-EUSO mission, developed to be hosted onboard the JEM module of the International Space Station, aims at detecting these extensive air showers from space by means of the fluorescent and diffusively reflected Cherenkov light they produce.In the present paper we investigate the capability of JEM-EUSO to trigger and detect neutrino induced events in the H-II Transfer Vehicle (HTV) configuration.We also discuss the status of their reconstruction feasibility considering JEM-EUSO's most recent design, which will be launched with Falcon 9 and delivered to the ISS by the SpaceX Dragon free-flying spacecraft.
The JEM-EUSO Program
2016-08-18

The JEM-EUSO mission, onboard the International Space Station (ISS), is currently being designed to unveil the nature and the origin of the ultra high energy (UHE) cosmic rays, at energies from a few E ∼ 10 19 eV up to the decade of E ∼ 10 20 eV.JEM-EUSO also addresses basic problems of fundamental physics at energies E ∼ 10 20 eV, unachievable by man-made accelerators.The instrument is designed to measure the arrival direction, the energy and, possibly, the nature of UHE particles.The mission basically consists of a wide field UV telescope that points along nadir from the ISS at night-time to detect the UV tracks associated to the propagation of the extended air showers induced by UHE primaries in the earth's atmosphere.The main goal is to identify the individual sources of the UHE cosmic rays and their association with known nearby astronomical objects.An infrared camera and a LIDAR improve the performance of the instrument.The program is proceeding in different steps.While the JEM-EUSO mission is being improved to allow the use of Space-X Dragon, the K-EUSO mission, an advanced version of the KLYPVE mission, already approved by ROSCOSMOS, modified with EUSO technology, and attached to the Russian module of the ISS, is in the stage of final definition.Two pathfinders have already been developed and operated: the first, the EUSO-Balloon flew on board a stratospheric balloon on August 2014; the second, EUSO-TA on ground, is in operation at the Telescope Array site.A third pathfinder, the Mini-EUSO mission, is approved by ASI and ROSCOSMOS, and will be installed inside the ISS.More short and long duration balloon flights are in addition envisaged.
Hot-electron-induced light amplification
2016-08-18

Electromagnetic coupling between resonant plasmonic oscillations of two closely spaced noble metal particles can lead to a strongly enhanced optical near field in the cavity formed by the gap between the metal particles. However, discoveries in quantum plasmonics show that an upper limit is imposed to the field enhancement by the intrinsic nonlocality of the dielectric response of the metal and the tunneling of the coherently oscillating conduction electrons through the gap. Here, we introduce and experimentally demonstrate optical amplification by radiative relaxation of hot electrons in a tunneling junction of a scanning tunneling microscope forming an extremely small point light source. When electrons tunnel from the sample to the tip, holes are left behind. These can be repopulated by hot electrons induced by the laser-driven plasmon oscillation on the metal surfaces enclosing the cavity and lead to a much higher electron to photon conversion efficiency. The dynamics of this system can be described by rate equations similar to laser equations. They show that the repopulation process can be efficiently stimulated by the gap mode’s near field. Our results demonstrate how optical enhancement inside the plasmonic cavity can be further increased by a stronger localization via tunneling through molecules.
Extensive studies of CaMoO4 crystals for dark matter experiments
2016-08-18

We present results of extensive studies of CaMoO4 crystals for dark matter experiments.Light emission kinetics and absolute light yield of the crystals were measured thoroughly at room temperature.The light emission kinetics of the crystal has a complicated multi-exponential behavior with the main component with 15-16 s decay time.The observed fast components with 12-46 ns decay time have small (1%) contribution to the total light yield.The latter was measured to be ~3000 photons per MeV at room temperature (22C).The temperature dependence of the crystals parameters were measured in the wide range of 1-300K.It is shown that CaMoO4 crystals are very interesting for dark matter experiments and for neutrinoless double-beta experiments too.
5 Constants of motion in the dynamics of a 2N-junction SQUID
2016-08-18

We show that a 2N junction SQUID (Superconducting QUantum Interference Device) made of 2N overdamped, shunted, identical junctions may be described as a system having only 6 degrees of freedom for any N ≥ 3.This is achieved by means of the reduction introduced by Watanabe and Strogatz (Physica D, 74, (1994) 197) for series biased arrays.In our case 6 rather than 3 degrees of freedom are necessary to describe the system, due to the requirement of phase quantization along the superconducting loop constituting the device.Generalization to multijunction parallel arrays is straightforward.
The photomorphogenic factors UV-B RECEPTOR 1, ELONGATED HYPOCOTYL 5, and HY5 HOMOLOGUE are part of the UV-B signalling pathway in grapevine and mediate flavonol accumulation in response to the environment
2016-08-19

Grapevine (Vitis vinifera L.) is a species well known for its adaptation to radiation. However, photomorphogenic factors related to UV-B responses have not been molecularly characterized. We cloned and studied the role of UV-B RECEPTOR (UVR1), ELONGATED HYPOCOTYL 5 (HY5), and HY5 HOMOLOGUE (HYH) from V. vinifera We performed gene functional characterizations, generated co-expression networks, and tested them in different environmental conditions. These genes complemented the Arabidopsis uvr8 and hy5 mutants in morphological and secondary metabolic responses to radiation. We combined microarray and RNA sequencing (RNA-seq) data with promoter inspections to identify HY5 and HYH putative target genes and their DNA binding preferences. Despite sharing a large set of common co-expressed genes, we found different hierarchies for HY5 and HYH depending on the organ and stress condition, reflecting both co-operative and partially redundant roles. New candidate UV-B gene markers were supported by the presence of HY5-binding sites. These included a set of flavonol-related genes that were up-regulated in a HY5 transient expression assay. We irradiated in vitro plantlets and fruits from old potted vines with high and low UV-B exposures and followed the accumulation of flavonols and changes in gene expression in comparison with non-irradiated conditions. UVR1, HY5, and HYH expression varied with organ, developmental stage, and type of radiation. Surprisingly, UVR1 expression was modulated by shading and temperature in berries, but not by UV-B radiation. We propose that the UV-B response machinery favours berry flavonol accumulation through the activation of HY5 and HYH at different developmental stages at both high and low UV-B exposures.
Effect of Noise-Optimized Monoenergetic Postprocessing on Diagnostic Accuracy for Detecting Incidental Pulmonary Embolism in Portal-Venous Phase Dual-Energy Computed Tomography
2016-08-19

Objectives The aim of this study was to evaluate the diagnostic accuracy of virtual monoenergetic images (MEI+) at low kiloelectronvolt levels for the detection of incidental pulmonary embolism (PE) in oncological follow-up portal-venous phase dual-energy (DE-CT pv ) staging. Materials and Methods Twenty-six patients with incidental PE in DE-CT pv staging, which was confirmed by computed tomography pulmonary angiography (CTPA), were included in this study. In addition, 26 matched control patients who were negative for PE in both DE-CT pv and CTPA were included. All examinations were performed on a third-generation DE-CT system in single-energy (CTPA) and dual-energy mode (DE-CT pv ). Subsequently, 2 series of MEI+ data sets were reconstructed at 40 and 55 keV from the DE-CT pv data and compared with CTPA and the linearly blended CT pv images. Diagnostic accuracy and diagnostic confidence were calculated and compared for MEI+ reconstructions and for CT pv images regarding the detection of PE with CTPA as standard of reference. Results In 3 patients, PE was only detectable in CTPA and in the 40-kV and 55-kV MEI+ reconstructions but not in CT pv images. Diagnostic accuracy increased significantly for both MEI+ series (40 keV; area under the curve [AUC], 0.928; 95% confidence interval [CI], 0.879–0.978; 55 keV; AUC, 0.960; 95% CI, 0.922–0.998) as compared with CT pv (AUC, 0.814; 95% CI, 0.741–0.887; P ≤ 0.004). Diagnostic confidence was rated highest in CTPA (median, 5; range, 3–5) followed by 55-keV MEI+ and 40-keV MEI+ (median, 5; range, 2–5 and median, 5; range, 2–5, respectively) and was lowest for CT pv (median, 4; range, 1–5), with significant differences to CTPA and MEI+ reconstructions ( P ≤ 0.001). Conclusions Monoenergetic image reconstructions from DE-CT data sets at low kiloelectronvolt levels improve diagnostic accuracy for the detection of incidental PE in oncological follow-up DE-CT pv staging, with the highest subjective diagnostic confidence in MEI+ at 55 keV.
Discrete wave-packet representation in nuclear matter calculations
2016-08-19

The Lippmann-Schwinger equation for the nucleon-nucleon -matrix as well as\\nthe corresponding Bethe-Goldstone equation to determine the Brueckner reaction\\nmatrix in nuclear matter are reformulated in terms of the resolvents for the\\ntotal two-nucleon Hamiltonians defined in free space and in medium\\ncorrespondingly. This allows to find solutions at many energies simultaneously\\nby using the respective Hamiltonian matrix diagonalization in the stationary\\nwave packet basis. Among other important advantages, this approach simplifies\\ngreatly the whole computation procedures both for coupled-channel -matrix\\nand the Brueckner reaction matrix. Therefore this principally novel scheme is\\nexpected to be especially useful for self-consistent nuclear matter\\ncalculations because it allows to accelerate in a high degree single-particle\\npotential iterations. Furthermore the method provides direct access to the\\nproperties of possible two-nucleon bound states in the nuclear medium. The\\ncomparison between reaction matrices found via the numerical solution of the\\nBethe-Goldstone integral equation and the straightforward Hamiltonian\\ndiagonalization shows a high accuracy of the method suggested. The proposed\\nfully discrete approach opens a new way to an accurate treatment of two- and\\nthree-particle correlations in nuclear matter on the basis of three-particle\\nBethe-Faddeev equation by an effective Hamiltonian diagonalization procedure.\\n
Functional Neuroimaging of Appetite and Gut–Brain Interactions
2016-08-19

This chapter discusses the main neuroimaging techniques that can be used to study food related brain processes and gut-brain interactions in humans and provides examples of relevant neuroimaging work in humans. Most commonly used neuroimaging techniques are positron emission tomography (PET), magnetic resonance imaging (MRI), electroencephalography (EEG), and magnetoencephalography (MEG). These techniques are explained with their strengths and weaknesses. There is a clear advantage with PET and functional MRI (fMRI), because both methods are suited to measure deeper brain structures with reasonable spatial and temporal resolution. MEG and EEG can be applied in particular to investigate higher cortical functions, such as cognitive control and their modulation by peripheral appetite signals. There is surprisingly little human work on the modulation of neuronal activity and food cue induced brain reactivity by nutrients and appetite hormones. The chapter reviews different types of human studies.
A recurrent mutation in KCNA2 as a novel cause of hereditary spastic paraplegia and ataxia
2016-08-20

The hereditary spastic paraplegias (HSPs) are heterogeneous neurodegenerative disorders with over 50 known causative genes. We identified a recurrent mutation in KCNA2 (c.881G&gt;A, p.R294H), encoding the voltage‐gated K + ‐channel, K V 1.2, in two unrelated families with HSP, intellectual disability (ID), and ataxia. Follow‐up analysis of &gt; 2,000 patients with various neurological phenotypes identified a de novo p.R294H mutation in a proband with ataxia and ID. Two‐electrode voltage‐clamp recordings of Xenopus laevis oocytes expressing mutant K V 1.2 channels showed loss of function with a dominant‐negative effect. Our findings highlight the phenotypic spectrum of a recurrent KCNA2 mutation, implicating ion channel dysfunction as a novel HSP disease mechanism. Ann Neurol 2016
Phenol-soluble modulins alpha induce G2/M phase transition delay and impair immune response of eukaryotic cells
2016-08-21

Staphylococcus aureus is responsible for a wide range of infections in human and animals. We found that S aureus slowed down host cell proliferation and induced a cytopathic effect. We demonstrated that S aureus induced a G2/M phase transition delay in host cells, which was associated with accumulation of the cyclin-dependent kinase Cdk1/cdc2 and unphosphorylated histone H3. We found that a G2 phase delay was preferential for bacterial internalization and intracellular proliferation. Using size exclusion chromatography and mass spectroscopy analysis, we identified phenol-soluble modulin alpha (PSMα) peptides as the candidates for this effect. The implication of PSMα in cell cycle alteration was confirmed by testing of synthetic PSMα and by comparison of LACwt with the isogenic mutant LAC∆psm, which lacks the operon encoding PSMα. The delay was associated with a decrease of defensins expression in a G2 phase, suggesting that PSMα-induced G2/M phase transition delay deteriorates antibacterial state of the epithelial surface. Investigation of the response to Escherichia coli and S. aureus showed a higher expression of key cytokines IL-6, IL-8, as well as IL-32 (which is involved in dendritic cell maturation) in E. coli-infected host cells. Comparison of cytokines expression in response to LACwt with isogenic mutants, which lack the operon encoding PSMs, show that PSMs inhibit interleukins production, thus impair the innate and adaptive immune response during S. aureus infection. Therefore we show, that PSMs alter the host cell cycle, resulting in a reduction of defense response of host’ cells, that reveal a newly-identified mechanism for promoting infection.
Telomere shortening leads to an acceleration of synucleinopathy and impaired microglia response in a genetic mouse model
2016-08-22

Parkinson's disease is one of the most common neurodegenerative disorders of the elderly and ageing hence described to be a major risk factor. Telomere shortening as a result of the inability to fully replicate the ends of linear chromosomes is one of the hallmarks of ageing. The role of telomere dysfunction in neurological diseases and the ageing brain is not clarified and there is an ongoing discussion whether telomere shortening is linked to Parkinson's disease. Here we studied a mouse model of Parkinson's disease (Thy-1 [A30P] α-synuclein transgenic mouse model) in the background of telomere shortening (Terc knockout mouse model). α-synuclein transgenic mice with short telomeres (αSYN(tg/tg) G3Terc(-/-)) developed an accelerated disease with significantly decreased survival. This accelerated phenotype of mice with short telomeres was characterized by a declined motor performance and an increased formation of α-synuclein aggregates. Immunohistochemical analysis and mRNA expression studies revealed that the disease end-stage brain stem microglia showed an impaired response in αSYN(tg/tg) G3Terc(-/-) microglia animals. These results provide the first experimental data that telomere shortening accelerates α-synuclein pathology that is linked to limited microglia function in the brainstem.
Improving ancient DNA genome assembly
2016-08-22

Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer. We used this two-layer assembly to generate assemblies for an ancient sample and compared the results to current de novo assembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
A new motor synergy that serves the needs of oculomotor and eye lid systems while keeping the downtime of vision minimal
2016-08-22

The purpose of blinks is to keep the eyes hydrated and to protect them. Blinks are rarely noticed by the subject as blink-induced alterations of visual input are blanked out without jeopardizing the perception of visual continuity, features blinks share with saccades. Although not perceived, the blink-induced disconnection from the visual environment leads to a loss of information. Therefore there is critical need to minimize it. Here we demonstrate evidence for a new type of eye movement serving a distinct oculomotor demand, namely the resetting of eye torsion, likewise inevitably causing a loss of visual information. By integrating this eye movement into blinks, the inevitable down times of vision associated with each of the two behaviors are synchronized and the overall downtime minimized.
Bioinformatics support for the Tubiom community gut microbiome project
2016-08-22

The Tübiom project is a community-based project aimed at constructing a large, representative reference database of human gut microbiome profiles. The goal is to collect 10 000 profiles, along with detailed metadata on each participants health and lifestyle. All samples will be processed using identical sequencing and analysis protocols to ensure comparability. The project has four technical components: sequencing, sequence analysis, data storage and visualisation. The project website http://www.tuebiom.de allows interested people to learn about the project, order a sampling kit and fill-in the metadata questionnaire. Once a sample as been submitted and processed, a participant can explore the taxonomic profile of their gut microbiome and compare it to the typical profile of different comparison groups.This community-based project also hopes to engage participants in science-propagation, spread knowledge about the gut microbiome and the importance of this area of research. Here we provide a brief introduction to the Tübiom project and describe the bioinformatics framework that we have developed for it.