pinecone/core-2020-05-10-deduplication huggingface dataset:
COPD GWAS variant at 19q13.2 in relation with DNA methylation and gene expression

Chronic obstructive pulmonary disease (COPD) is among the major health burdens in adults. While cigarette smoking is the leading risk factor, a growing number of genetic variations have been discovered to influence disease susceptibility. Epigenetic modifications may mediate the response of the genome to smoking and regulate gene expression. Chromosome 19q13.2 region is associated with both smoking and COPD, yet its functional role is unclear. Our study aimed to determine whether rs7937 (RAB4B, EGLN2), a top genetic variant in 19q13.2 region identified in genome-wide association studies of COPD, is associated with differential DNA methylation in blood (N=1490) and gene expression in blood (N=721) and lungs (N=1087). We combined genetic and epigenetic data from the Rotterdam Study (RS) to perform the epigenome-wide association analysis of rs7937. Further, we used genetic and transcriptomic data from blood (RS) and from lung tissue (Lung expression quantitative trait loci mapping study), to perform the transcriptome-wide association study of rs7937. Rs7937 was significantly (FDR < 0.05) and consistently associated with differential DNA methylation in blood at 4 CpG sites in cis, independent of smoking. One methylation site (cg11298343-EGLN2) was also associated with COPD (P=0.001). Additionally, rs7937 was associated with gene expression levels in blood in cis (EGLN2), 42% mediated through cg11298343, and in lung tissue, in cis and trans (NUMBL, EGLN2, DNMT3A, LOC101929709 and PAK2). Our results suggest that changes of DNA methylation and gene expression may be intermediate steps between genetic variants and COPD, but further causal studies in lung tissue should confirm this hypothesis
Leisure activities and social factors influence the generation of cultural ecosystem service benefits

The relationship between cultural ecosystem services (CES) and the many diverse aspects of biodiversity is complex and multi-faceted. A large public survey in Wiltshire, UK, was used to assess associations between public benefits from certain species groups in the local countryside, and (i) social antecedents, (ii) engagement in different outdoor leisure activities (iii) indirect nature experience via media-related activities and (iv) species group charisma and abundance.\ud
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Practitioners of leisure activities with a nature-related theme, whether outdoor activities or indoor media-related activities, reported significantly higher levels of benefit from named species groups, as did respondents whose personal background demonstrated an elevated degree of nature-relatedness. Benefits were also related to the charisma of the species group: enhanced benefit through nature-related activities and social factors was significant for less charismatic species, but inconclusive for more charismatic species. Respondents who participated in outdoor leisure activities without a nature focus were unlikely to report enhanced benefits from species groups in the local landscape.\ud
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To maximise people’s CES benefits from broader aspects of biodiversity it may be necessary to encourage an active interest in biodiversity, leading people to participate or seek knowledge and understanding, and in turn develop a stronger sense of connectedness to nature
Examining the Links Between Perceived Impact of Pregnancy, Depressive Symptoms, and Quality of Life During Adolescent Pregnancy: The Buffering Role of Social Support

The aims of the current study were to examine the indirect effect of the perceived impact of pregnancy on quality of life (QoL) through the severity of depressive symptoms among a sample of pregnant adolescents, and to explore whether adolescents’ satisfaction with support from their mothers (SM) or partners (SP) was a buffer of this effect. Demographic and pregnancy-related data were collected for 395 pregnant adolescents age 12–19 and were controlled for testing the proposed indirect effect. SM and SP were tested as moderators of the links between perceived impact of pregnancy and depressive symptoms and between depressive symptoms and QoL. A computational tool for path analysis-based moderation and mediation analysis as well as their combination was used to test indirect and interaction effects (PROCESS). A significant indirect effect of the perceived impact of pregnancy on QoL through the severity of depressive symptoms was found (0.51, CI = 0.29/0.78). There was no significant direct effect of the perceived impact of pregnancy on QoL after controlling for the severity of depressive symptoms. SM and SP buffered the indirect effect by weakening the association between a negative perception of the impact of pregnancy and higher severity of depressive symptoms. Identifying adolescents with a negative perception of the impact of pregnancy, improving the quality of their relations with their mothers and partners, and promoting satisfactory support from these figures may be extremely important to prevent and treat depressive symptoms and, in so doing, improve adolescents’ QoL during pregnancy
Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls

Multiple sclerosis (MS) is an inflammatory CNS disease with a substantial genetic component, originally mapped to only the human leukocyte antigen (HLA) region. In the last 5 years, a total of seven genome-wide association studies and one meta-analysis successfully identified 57 non-HLA susceptibility loci. Here, we merged nominal statistical evidence of association and physical evidence of interaction to conduct a protein-interaction-network-based pathway analysis (PINBPA) on two large genetic MS studies comprising a total of 15,317 cases and 29,529 controls. The distribution of nominally significant loci at the gene level matched the patterns of extended linkage disequilibrium in regions of interest. We found that products of genome-wide significantly associated genes are more likely to interact physically and belong to the same or related pathways. We next searched for subnetworks (modules) of genes (and their encoded proteins) enriched with nominally associated loci within each study and identified those modules in common between the two studies. We demonstrate that these modules are more likely to contain genes with bona fide susceptibility variants and, in addition, identify several high-confidence candidates (including BCL10, CD48, REL, TRAF3, and TEC). PINBPA is a powerful approach to gaining further insights into the biology of associated genes and to prioritizing candidates for subsequent genetic studies of complex traits
Wounding of Arabidopsis halleri leaves enhances cadmium accumulation that acts as a defense against herbivory

Approximately 0.2 % of all angiosperms are classified as metal hyperaccumulators based on their extraordinarily high leaf metal contents, for example >1 % zinc, >0.1 % nickel or >0.01 % cadmium (Cd) in dry biomass. So far, metal hyperaccumulation has been considered to be a taxon-wide, constitutively expressed trait, the extent of which depends solely on available metal concentrations in the soil. Here we show that in the facultative metallophyte Arabidopsis halleri, both insect herbivory and mechanical wounding of leaves trigger an increase specifically in leaf Cd accumulation. Moreover, the Cd concentrations accumulated in leaves can serve as an elemental defense against herbivory by larvae of the Brassicaceae specialist small white (Pieris rapae), thus allowing the plant to take advantage of this non-essential trace element and toxin. Metal homeostasis genes are overrepresented in the systemic transcriptional response of roots to the wounding of leaves in A. halleri, supporting that leaf Cd accumulation is preceded by systemic signaling events. A similar, but quantitatively less pronounced transcriptional response was observed in A. thaliana, suggesting that the systemically regulated modulation of metal homeostasis in response to leaf wounding also occurs in non-hyperaccumulator plants. This is the first report of an environmental stimulus influencing metal hyperaccumulation
Climate impact on Italian fisheries (Mediterranean Sea)

Global warming is increasingly affecting marine ecosystems and ecological services they provide. One of the major consequences is a shift in species geographical distribution, which may affect resources availability to fisheries. We computed the mean temperature of the catch (MTC) for Italian catches from 1972 to 2012 to test if an increase of warmer-water species against colder-water ones was observed. We further analysed the relationship among MTC, landings, fishing effort and climatic factors through a Linear Mixed Models approach. Global MTC increased at a rate of 0.12 _C per decade. Though, by considering the influence of sea surface temperature (SST), a strongest increase (0.31 _C) was estimated in southernmost areas, while in the northernmost basin (Northern Adriatic Sea) a decrease of 0.14 _C was observed. SST resulted the most relevant driver, and the relationship between MTC and SST showed a high spatial variability both in terms of strength and sign, being positively stronger in southernmost areas while negative in the northernmost basin. The result is probably underestimated since several psychrophilous and thermophilous species were not included in the analysis. However, it seems that a change towards warmer-water species has already occurred in Italian marine ecosystems. Conversely, total landings temporal dynamics seem mostly driven by changes in fishing effort rather than by MTC and climatic factors. Consequently, fishery management strategies need to focalize primarily on fishing effort reduction, in order to reduce the pressure on the stocks while increasing their resilience to other stressors, among which global warmin
Taking aim at moving targets in computational cell migration

Cell migration is central to the development and maintenance of multicellular organisms. Fundamental understanding of cell migration can, for example, direct novel therapeutic strategies to control invasive tumor cells. However, the study of cell migration yields an overabundance of experimental data that require demanding processing and analysis for results extraction. Computational methods and tools have therefore become essential in the quantification and modeling of cell migration data. We review computational approaches for the key tasks in the quantification of in vitro cell migration: image pre-processing, motion estimation and feature extraction. Moreover, we summarize the current state-of-the-art for in silico modeling of cell migration. Finally, we provide a list of available software tools for cell migration to assist researchers in choosing the most appropriate solution for their needs
X-band 1H-DNP experiments and high power sub-THz wave irradiation effect on BDPA-doped toluene solution

To investigate the experimental technique and the high magnetic field effect in the dynamical
	nuclear polarization (DNP) experiments, the X-band 1H-DNP and the high power sub-THz wave
	irradiation experiments have been performed on bis-diphenylene-phenyl-allyl (BDPA)-doped
	toluene solution at room temperature. We have established the sample-shuttle X-band DNP
	experimental system, and investigated the external magnetic field, the microwave power and 1H-T_1
	^-1
	dependences of Overhauser enhancement factor (e). A maximal signal enhancement of
	approximately –19 has been observed. As for the sub-THz wave experiments, we have constructed
	the NMR and ESR measurement system for the experiments under the magnetic field of ~10.7 T,
	with a high power light source gyrotron CW-I (TE_<22,8> mode, f~299.23 GHz). When the high power
	sub-THz wave of a gyrotron was irradiated on the toluene solution in order to confirm the evidence
	of DNP, the sample has evaporated due to the electromagnetic (EM) wave heating
Optimal Inspection Policy for Three-state Systems Monitored by Variable Sample Size Control Charts

This paper presents the expected long-run cost per unit time for a system monitored by an adaptive control chart with variable sample sizes: if the control chart signals that the system is out of control, the sampling which follows will be conducted with a larger sample size. The system is supposed to have three states: in-control, out-of-control, and failed. Two levels of repair are applied to maintain the system. A minor repair will be conducted if an assignable cause is confirmed by an inspection, and a major repair will be performed if the system fails. Both the minor and major repairs are assumed to be perfect. We derive the expected long-run cost per unit time, which can be used to obtain the optimal inspection policy. Numerical examples are conducted to validate the derived cost
The Great Synchronization of International Trade Collapse

In this paper we examine the extent of international trade synchronization during periods of international trade collapses and US recessions. Using dynamic correlations based on monthly trade data for the G7 economies over the period 1961-2011, our results suggest rather idiosyncratic patterns of international trade synchronization during collapses of international trade and US recessions. During the great recession of 2007-2009, however, international trade experienced the most sudden, severe and globally synchronized collapse. (author's abstract
A Bayesian non-parametric hidden Markov random model for hemodynamic brain parcellation

Deriving a meaningful functional brain parcellation is a very challenging issue in task-related fMRI analysis. The joint parcellation detection estimation model addresses this issue by inferring the parcels from fMRI data. However, it requires a priori fixing the number of parcels through an initial mask for parcellation. Hence, this difficult task generally depends on the subject. The proposed automatic parcellation approach in this paper overcomes this limitation at the subject-level relying on a Dirichlet process mixture model combined with a hidden Markov random field to estimate the parcels and their number online. The proposed method adopts a variational expectation maximization strategy for inference. Compared to the model selection procedure in the joint parcellation detection estimation framework, our method appears more efficient in terms of computational time and does not require finely tuned initialization. Synthetic data experiments show that our method is able to estimate the right model order and an accurate parcellation. Real data results demonstrate the ability of our method to aggregate parcels with similar hemodynamic behaviour in the right motor and bilateral occipital cortices while its discriminating power is increased compared to its ancestors. Moreover, the obtained HRF estimates are close to the canonical HRF in both cortices
Blue mussel shell shape plasticity and natural environments: a quantitative approach

Shape variability represents an important direct response of organisms to selective environments. Here, we use a combination of geometric morphometrics and generalised additive mixed models (GAMMs) to identify spatial patterns of natural shell shape variation in the North Atlantic and Arctic blue mussels, Mytilus edulis and M. trossulus, with environmental gradients of temperature, salinity and food availability across 3980 km of coastlines. New statistical methods and multiple study systems at various geographical scales allowed the uncoupling of the developmental and genetic contributions to shell shape and made it possible to identify general relationships between blue mussel shape variation and environment that are independent of age and species influences. We find salinity had the strongest effect on the latitudinal patterns of Mytilus shape, producing shells that were more elongated, narrower and with more parallel dorsoventral margins at lower salinities. Temperature and food supply, however, were the main drivers of mussel shape heterogeneity. Our findings revealed similar shell shape responses in Mytilus to less favourable environmental conditions across the different geographical scales analysed. Our results show how shell shape plasticity represents a powerful indicator to understand the alterations of blue mussel communities in rapidly changing environments
Wave functions of composite hadron states and relationship to couplings
  of scattering amplitudes for general partial waves

In this paper we present the connection between scattering amplitudes in
momentum space and wave functions in coordinate space, generalizing previous
work done for s-waves to any partial wave. The relationship to the wave
function of the residues of the scattering amplitudes at the pole of bound
states or resonances is investigated in detail. A sum rule obtained for the
couplings provides a generalization to coupled channels, any partial wave and
bound or resonance states, of Weinberg's compositeness condition, which was
only valid for weakly bound states in one channel and s-wave. An example,
requiring only experimental data, is shown for the $\rho$ meson indicating that
it is not a composite particle of $\pi \pi$ but something else
Robertson-Walker fluid sources endowed with rotation characterised by
  quadratic terms in angular velocity parameter

Einstein's equations for a Robertson-Walker fluid source endowed with
rotation Einstein's equations for a Robertson-Walker fluid source endowed with
rotation are presented upto and including quadratic terms in angular velocity
parameter. A family of analytic solutions are obtained for the case in which
the source angular velocity is purely time-dependent. A subclass of solutions
is presented which merge smoothly to homogeneous rotating and non-rotating
central sources. The particular solution for dust endowed with rotation is
presented. In all cases explicit expressions, depending sinusoidally on polar
angle, are given for the density and internal supporting pressure of the
rotating source. In addition to the non-zero axial velocity of the fluid
particles it is shown that there is also a radial component of velocity which
vanishes only at the poles. The velocity four-vector has a zero component
between poles
uv asymptotically free QED as a broken YM theory in the unitary gauge

We compute the \beta-function of a YM theory, broken to U(1), by evaluating the coupling constant renormalization in the broken phase. We perform the calculation in the unitary gauge where only physical particles appear and the theory looks like a version of QED containing massive charged spin 1 particles. We consider an on-shell scattering process and after verifying that the non-renormalizable divergences which appear in the Green's functions cancel in the expression of the amplitude, we show that the coupling constant renormalization is entirely due to the photon self-energy as in QED. However we get the expected asymptotic freedom and the physical charge decreases logarithmically as a function of the symmetry breaking scale
Dynamical vertex mass generation and chiral symmetry breaking on the light-front

Naively, helicity flip amplitudes for fermions seem to vanish in the chiral limit of light-front QCD, which would make it nearly impossible to generate a small pion mass in this framework. Using a simple model, it is illustrated how a large helicity flip amplitude is generated dynamically by summing over an infinite number of Fock space components. While the kinetic mass is basically generated by a zero-mode induced counter-term, the vertex mass is generated dynamically by infinitesimally small, but nonzero, momenta. Implications for the renormalization of light-front Hamiltonians for fermions are discussed
Exponential energy growth due to slow parameter oscillations in quantum
  mechanical systems

It is shown that a periodic emergence and destruction of an additional
quantum number leads to an exponential growth of energy of a quantum mechanical
system subjected to a slow periodic variation of parameters. The main example
is given by systems (e.g., quantum billiards and quantum graphs) with
periodically divided configuration space. In special cases, the process can
also lead to a long period of cooling that precedes the acceleration, and to
the desertion of the states with a particular value of the quantum number
Production of exotic light and medium mass nuclei in 86,94,96Kr +48 Ca, 122,130,132Sn +12 C and 72,74,76Kr +40 Ca, 72,74,76Kr +40 Ar, 72,74,76Kr +32 S reactions at 4-10MeV/nucleon

International audienceThe mechanism of production of evaporation residues in low energy fusion reactions is investigated within the dinuclear system model. The model predictions for the production cross sections of exotic nuclei are compared with the available experimental data. The possibilities of production of doubly magic nucleus 100Sn via particle evaporation channels and 12C emission channel in the reactions 72;74;76Kr+40Ca, 72;74;76Kr+40Ar and 72;74;76Kr+32S are investigated at bombarding energies 4 6 MeV/nucleon
The Boarding Control System: Modelling and Control of a Surface Effect Ship for improved accessibility to Offshore Wind Turbines

The main contribution of this thesis is to introduce a control system that enables
access to offshore wind turbines for operation and maintenance (O&amp;M) in higher
sea states than what is possible today, while maintaining an acceptable level of
risk. The system is implemented on-board on a Surface Effect Ship (SES) which
introduces a new craft-concept to the turbine transfer vessels. Catamarans and
Small-water-area twin hulls (SWATHs) are currently dominating the market.
The control system is denoted the Boarding Control System (BCS) which is
a control algorithm that utilizes certain sensors and hardware to control air- ow
actuators on a SES. The controlled actuators regulates the air cushion pressure to
counteract, and compensate against, the vessel motions set up by sea wave propagations.
Hence, we perform motion damping in the vertical plane which ultimately
improves the accessibility to wind turbines.
The work presented in this thesis influenced the decision to build two vessels of
the Wave Craft class, build no. 21 and 22 by Umoe Mandal. The prototype, Umoe
Ventus, is currently operating at Borkum Riffgrund 1, a wind-farm in the German
sector of the North Sea.
The SES-dynamics related to the BCS is mathematically modelled and a controller
is designed. Stability investigations are performed and system performance
are given through simulation, model- and full-scale experimental testing.
The performance of the BCS proves that accessibility to offshore-structures is
possible in higher seas compared to the case where the system is inactive. Today
it is possible to access turbines in up to 1:5 - 1:75m signifcant wave height (Hs).
The SES with the BCS is tested in up to 2m Hs with no sign of reduced safety for
offshore personnel while boarding a turbine. The model-test results indicates that
access is possible in up to 2:5m Hs and at least 3:2m in long-crested seas (Section
2.5)