Search

Contains fulltext : 294827.pdf (Publisher’s version ) (Open Access)

The importance of the chromosphere in the mass and energy transport within the solar atmosphere is now widely recognised. This review discusses the physics of magnetohydrodynamic (MHD) waves and instabilities in large-scale chromospheric structures as well as in magnetic flux tubes. We highlight a number of key observational aspects that have helped our understanding of the role of the solar chromosphere in various dynamic processes and wave phenomena, and the heating scenario of the solar chromosphere is also discussed. The review focuses on the physics of waves and invokes the basics of plasma instabilities in the context of this important layer of the solar atmosphere. Potential implications, future trends and outstanding questions are also delineated., Comment: This is an invited review article in the special issue "Solar and Heliospheric Plasma Structures: Waves, Turbulence, and Dissipation" of JGR - Space Physics (57 pages, 9 figures, Paper #2020JA029097R) with Editors: Leon Ofman and Shreekrishna Tripathi

This paper investigates the changes in spatial properties when magnetohydrodynamic (MHD) waves undergo resonant damping in the Alfv\'en continuum. The analysis is carried out for a 1D cylindrical pressure-less plasma with a straight magnetic field. The effect of the damping on the spatial wave variables is determined by using complex frequencies that arise as a result of the resonant damping. Compression and vorticity are used to characterise the spatial evolution of the MHD wave. The most striking result is the huge spatial variation in the vorticity component parallel to the magnetic field. Parallel vorticity vanishes in the uniform part of the equilibrium. However, when the MHD wave moves into the non-uniform part, parallel vorticity explodes to values that are orders of magnitude higher than those attained by the transverse components in planes normal to the straight magnetic field. In the non-uniform part of the equilibrium plasma, the MHD wave is controlled by parallel vorticity and resembles an Alfv\'en wave, with the unfamiliar property that it has pressure variations even in the linear regime.

It is widely accepted in the MHD turbulence community that the nonlinear cascade of wave energy requires counter-propagating Alfv\'enic wave-packets, along some mean magnetic field. This fact is an obvious outcome of the MHD equations under the assumptions of incompressibility and homogeneity. Despite attempts to relax these assumptions in the context of MHD turbulence, the central idea of turbulence generation persists. However, once the assumptions of incompressiblity and homogeneity break down, the generally accepted picture of turbulent cascade generation is not universal. In this paper, we show that perpendicular inhomogeneities (across the mean magnetic field) lead to propagating wave solutions which are necessarily described by co-propagating Els\"asser fields, already in the incompressible case. One simple example of these wave solutions is the surface Alfv\'en wave on a planar discontinuity across the magnetic field. We show through numerical simulations how the nonlinear self-deformation of these unidirectionally propagating waves leads to a cascade of wave energy across the magnetic field. The existence of this type of unidirectional cascade might have an additional strong effect on the turbulent dissipation rate of dominantly outward propagating Alfv\'enic waves in structured plasma, as in the solar corona and solar wind., Comment: ApJ manuscript, accepted 24th of July 2019

The Els\"{a}sser variables are often used in studies of plasma turbulence, in helping differentiate between MHD waves propagating parallel or anti-parallel to the main magnetic field. While for pure Alfv\'en waves in a homogeneous plasma the method is strictly valid, we show that compressible, magnetoacoustic waves are in general described by both Els\"{a}sser variables. Furthermore, in a compressible and inhomogeneous plasma, the pure MHD waves (Alfv\'en, fast and slow) are no longer normal modes, but waves become linearly coupled or display mixed properties of Alfv\'en and magnetoacoustic nature. These waves are necessarily described by both Els\"{a}sser variables and therefore the Els\"{a}sser formalism cannot be used to strictly separate parallel and anti-parallel propagating waves. Nevertheless, even in an inhomogeneous plasma, for a highly Alfv\'enic wave the Els\"{a}sser variable corresponding to the propagation direction appears still dominating. We suggest that for Alfv\'enic waves, the relative amplitude of Els\"{a}sser variables depends on the local degree of inhomogeneity and other plasma and wave properties. This finding has implications for turbulence studies in inhomogeneous and compressible plasmas, such as the solar corona and solar wind.

The Els\"{a}sser variables are often used in studies of plasma turbulence, in helping differentiate between MHD waves propagating parallel or anti-parallel to the main magnetic field. While for pure Alfv\'en waves in a homogeneous plasma the method is strictly valid, we show that compressible, magnetoacoustic waves are in general described by both Els\"{a}sser variables. Furthermore, in a compressible and inhomogeneous plasma, the pure MHD waves (Alfv\'en, fast and slow) are no longer normal modes, but waves become linearly coupled or display mixed properties of Alfv\'en and magnetoacoustic nature. These waves are necessarily described by both Els\"{a}sser variables and therefore the Els\"{a}sser formalism cannot be used to strictly separate parallel and anti-parallel propagating waves. Nevertheless, even in an inhomogeneous plasma, for a highly Alfv\'enic wave the Els\"{a}sser variable corresponding to the propagation direction appears still dominating. We suggest that for Alfv\'enic waves, the relative amplitude of Els\"{a}sser variables depends on the local degree of inhomogeneity and other plasma and wave properties. This finding has implications for turbulence studies in inhomogeneous and compressible plasmas, such as the solar corona and solar wind.

It is widely accepted in the MHD turbulence community that the nonlinear cascade of wave energy requires counter-propagating Alfv\'enic wave-packets, along some mean magnetic field. This fact is an obvious outcome of the MHD equations under the assumptions of incompressibility and homogeneity. Despite attempts to relax these assumptions in the context of MHD turbulence, the central idea of turbulence generation persists. However, once the assumptions of incompressiblity and homogeneity break down, the generally accepted picture of turbulent cascade generation is not universal. In this paper, we show that perpendicular inhomogeneities (across the mean magnetic field) lead to propagating wave solutions which are necessarily described by co-propagating Els\"asser fields, already in the incompressible case. One simple example of these wave solutions is the surface Alfv\'en wave on a planar discontinuity across the magnetic field. We show through numerical simulations how the nonlinear self-deformation of these unidirectionally propagating waves leads to a cascade of wave energy across the magnetic field. The existence of this type of unidirectional cascade might have an additional strong effect on the turbulent dissipation rate of dominantly outward propagating Alfv\'enic waves in structured plasma, as in the solar corona and solar wind., Comment: ApJ manuscript, accepted 24th of July 2019

We present the results of combined INTEGRAL and XMM-Newton observations of the supergiant fast X-ray transient (SFXT) IGR J17354$-$3255. Three XMM-Newton observations of lengths 33.4 ks, 32.5 ks and 21.9 ks were undertaken, the first an initial pointing to identify the correct source in the field of view and the latter two performed around periastron. Simultaneous INTEGRAL observations across $\sim66\%$ of the orbital cycle were analysed but the source was neither detected by IBIS/ISGRI nor by JEM-X. The XMM-Newton light curves display a range of moderately bright X-ray activity but there are no particularly strong flares or outbursts in any of the three observations. We show that the spectral shape measured by XMM-Newton can be fitted by a consistent model throughout the observation, suggesting that the observed flux variations are driven by obscuration from a wind of varying density rather than changes in accretion mode. The simultaneous INTEGRAL data rule out simple extrapolation of the simple powerlaw model beyond the XMM-Newton energy range., Comment: 13 pages, 9 figures, This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society Published by Oxford University Press

We present the results of combined INTEGRAL and XMM-Newton observations of the supergiant fast X-ray transient (SFXT) IGR J17354$-$3255. Three XMM-Newton observations of lengths 33.4 ks, 32.5 ks and 21.9 ks were undertaken, the first an initial pointing to identify the correct source in the field of view and the latter two performed around periastron. Simultaneous INTEGRAL observations across $\sim66\%$ of the orbital cycle were analysed but the source was neither detected by IBIS/ISGRI nor by JEM-X. The XMM-Newton light curves display a range of moderately bright X-ray activity but there are no particularly strong flares or outbursts in any of the three observations. We show that the spectral shape measured by XMM-Newton can be fitted by a consistent model throughout the observation, suggesting that the observed flux variations are driven by obscuration from a wind of varying density rather than changes in accretion mode. The simultaneous INTEGRAL data rule out simple extrapolation of the simple powerlaw model beyond the XMM-Newton energy range., Comment: 13 pages, 9 figures, This article has been accepted for publication in Monthly Notices of the Royal Astronomical Society Published by Oxford University Press

Background Painful diabetic neuropathy (PDN) is known to negatively affect psychosocial functioning as expressed by enhanced levels of anxiety and depression. The aim of this study was to specify diabetes and pain-related fears. MethodsThis questionnaire-based cross-sectional study included 154 patients with PDN (mean age 65.76.6years). Correlation analyses corrected for age, gender, pain intensity, pain duration and insulin treatment were performed to assess the associations of fear of hypoglycaemia (Hypoglycaemia Fear Survey, HFS), kinesiophobia (Tampa Scale of Kinesiophobia, TSK), fear of pain (Pain Anxiety Symptom Scale, PASS-20), fear of falling (Falls Efficacy Scale-I, FES-I), fear of fatigue (Tampa Scale of Fatigue, TSF) and fear of negative evaluation (Brief Fear of Negative Evaluation Scale, BFNE), with quality of life (QoL) (Norfolk Quality of Life Questionnaire, Diabetic Neuropathy Version, QOL-DN) and disability (Pain Disability Index, PDI), respectively. ResultsIn univariate analyses, all fears were independently associated with QOL-DN and PDI (p

Background Painful diabetic neuropathy (PDN) is known to negatively affect psychosocial functioning as expressed by enhanced levels of anxiety and depression. The aim of this study was to specify diabetes and pain-related fears. MethodsThis questionnaire-based cross-sectional study included 154 patients with PDN (mean age 65.76.6years). Correlation analyses corrected for age, gender, pain intensity, pain duration and insulin treatment were performed to assess the associations of fear of hypoglycaemia (Hypoglycaemia Fear Survey, HFS), kinesiophobia (Tampa Scale of Kinesiophobia, TSK), fear of pain (Pain Anxiety Symptom Scale, PASS-20), fear of falling (Falls Efficacy Scale-I, FES-I), fear of fatigue (Tampa Scale of Fatigue, TSF) and fear of negative evaluation (Brief Fear of Negative Evaluation Scale, BFNE), with quality of life (QoL) (Norfolk Quality of Life Questionnaire, Diabetic Neuropathy Version, QOL-DN) and disability (Pain Disability Index, PDI), respectively. ResultsIn univariate analyses, all fears were independently associated with QOL-DN and PDI (p

Item does not contain fulltext, Complex regional pain syndrome type I (CRPS-I) highly affects patients' ability to perform daily life activities. Pain-related fear might be a key target to reduce disability in chronic pain. Current treatments aiming at reducing pain show little improvements on pain and disability, whereas novel exposure-based treatments targeting pain-related fears have shown to be promising. We conducted a randomized controlled trial (N = 46) comparing exposure in vivo (EXP) with pain-contingent treatment as usual (TAU), for CRPS-I patients with at least moderate levels of pain-related fear. Primary outcome is self-reported disability, for upper and lower extremity, respectively. Secondary outcomes are self-reported pain-intensity, pain-catastrophizing, perceived harmfulness of physical activity, and health-related quality of life. Pretreatment to posttreatment and pretreatment to 6-month follow-up change scores were tested using randomization-based inference. EXP was superior to TAU in reducing upper extremity disability from pretreatment to posttreatment (between-group difference, 1.082; 95% confidence interval [CI], 0.563-1.601; P < 0.001) and from pretreatment to 6-month follow-up (1.303; 95% CI, 0.917-1.690; P < 0.001). EXP was superior in reducing lower extremity disability from pretreatment to 6-month follow-up (3.624; 95% CI, 0.467-6.781; P = 0.02), but not from pretreatment to posttreatment (3.055; 95% CI, -0.018 to 6.128; P = 0.054). All secondary outcomes significantly favored EXP pretreatment to posttreatment, as well as pretreatment to 6-month follow-up. Exposure to daily activities shows to be more effective than a protective pain-contingent TAU in reducing self-reported disability in daily life of CRPS-I patients with at least moderate levels of pain-related fear.

Item does not contain fulltext, OBJECTIVE: Assessment of the effectiveness of the Assessment of Burden of COPD (ABC) tool on disease-specific quality of life in patients with Chronic Obstructive Pulmonary Disease (COPD). DESIGN: Cluster-randomised controlled trial. METHOD: This concerned a trial in 39 Dutch primary care practices and 17 hospitals, involving 357 patients with COPD (postbronchodilator FEV1/FVC ratio < 0.7) aged >/= 40 years. Healthcare providers were randomized to an intervention or control group. Patients in the intervention group were treated with the ABC tool. This innovative tool consists of a short validated questionnaire and a number of objective parameters, which collectively give a visual overview of the combined integral health; the tool subsequently produces an individualized treatment plan by means of a treatment algorithm. Patients in the control group received usual care. The primary outcome measure was the proportion of patients with a clinically relevant improvement in disease-specific quality of life measured, as measured by means of the St. George's Respiratory Questionnaire (SGRQ) score, between baseline and 18 months follow-up. Secondary outcomes included the SGRQ total score and the Patient Assessment of Chronic Illness Care (PACIC) score. RESULTS: At 18-month follow-up, a significant and clinically relevant improvement in the SGRQ score was seen in 34% of the patients (N=49) in the intervention group, and in the control group this figure was 22% (N=33). This difference between the two groups was significant (OR 1.85, 95% CI 1.08 to 3.16). Patients in the intervention group experienced a higher quality of care than patients in the control group (0.32 points difference in PACIC, 95% CI 0.14 to 0.50). CONCLUSION: Use of the ABC tool increases the disease-specific quality of life and the quality of care for COPD patients; it may therefore offer a valuable contribution to improvements in the daily care of COPD. Replication of this study in other (non-Dutch) health-ca

We present the results of a 30ks XMM-Newton observation of the supergiant fast X-ray transient (SFXT) SAX J1818.6-1703 - the first in-depth soft X-ray study of this source around periastron. INTEGRAL observations shortly before and after the XMM-Newton observation show the source to be in an atypically active state. Over the course of the XMM-Newton observation, the source shows a dynamic range of ~100 with a luminosity greater than 1$\times$10$^{35}$ erg s$^{-1}$ for the majority of the observation. After an ~6 ks period of low luminosity (~10$^{34}$ erg s$^{-1}$) emission, SAX J1818.6-1703 enters a phase of fast flaring activity, with flares 250 s long, separated by ~2ks. The source then enters a larger flare event of higher luminosity and ~8 ks duration. Spectral analysis revealed evidence for a significant change in spectral shape during the observation with a photon index varying from {\Gamma} ~ 2.5 during the initial low luminosity emission phase, to {\Gamma} ~ 1.9 through the fast flaring activity, and a significant change to {\Gamma} ~ 0.3 during the main flare. The intrinsic absorbing column density throughout the observation (n$_H$ ~ 5$\times$10$^{23}$ cm$^{-2}$) is among the highest measured from an SFXT, and together with the XMM-Newton and INTEGRAL luminosities, consistent with the neutron star encountering an unusually dense wind environment around periastron. Although other mechanisms cannot be ruled out, we note that the onset of the brighter flares occurs at 3$\times$10$^{35}$ erg s$^{-1}$, a luminosity consistent with the threshold for the switch from a radiative-dominated to Compton cooling regime in the quasi-spherical settling accretion model., Comment: 11 pages, 8 figures, Accepted for publication in MNRAS

Respiratory infections are a major cause of pulmonary decline in children with cystic fibrosis (CF). We compared the prevalence of infection in early life at geographically distant CF treatment centres participating in the same surveillance programme in Australia. Lower airway microbiology, inflammation and structural lung disease at annual review were evaluated for 260 children 0-8 years old with CF at 1032 visits to CF treatment centres in Melbourne or Perth. Melbourne patients were more likely to be culture-positive for common respiratory pathogens at all age groups (odds ratio (OR) 1.85, 95% CI 1.33-2.58). Subjects <2 years old in Melbourne were also more likely to have neutrophil elastase present (OR 3.11, 95% CI 1.62-5.95). Bronchiectasis (OR 2.02, 95% CI 1.21-3.38) and air trapping (OR 2.53, 95% CI 1.42-4.51) in subjects 2-5 years old was more common in Melbourne subjects. The severity of structural lung disease was also worse in Melbourne patients >5 years old. Patients at both centres had a similar rate of hospitalisations and prescribed antibiotics. No procedural differences were identified that could explain the disparity between pathogen prevalence. Geographical differences in early acquisition of infection may contribute to variability in outcomes between CF centres.

Item does not contain fulltext, Complex regional pain syndrome type I (CRPS-I) highly affects patients' ability to perform daily life activities. Pain-related fear might be a key target to reduce disability in chronic pain. Current treatments aiming at reducing pain show little improvements on pain and disability, whereas novel exposure-based treatments targeting pain-related fears have shown to be promising. We conducted a randomized controlled trial (N = 46) comparing exposure in vivo (EXP) with pain-contingent treatment as usual (TAU), for CRPS-I patients with at least moderate levels of pain-related fear. Primary outcome is self-reported disability, for upper and lower extremity, respectively. Secondary outcomes are self-reported pain-intensity, pain-catastrophizing, perceived harmfulness of physical activity, and health-related quality of life. Pretreatment to posttreatment and pretreatment to 6-month follow-up change scores were tested using randomization-based inference. EXP was superior to TAU in reducing upper extremity disability from pretreatment to posttreatment (between-group difference, 1.082; 95% confidence interval [CI], 0.563-1.601; P < 0.001) and from pretreatment to 6-month follow-up (1.303; 95% CI, 0.917-1.690; P < 0.001). EXP was superior in reducing lower extremity disability from pretreatment to 6-month follow-up (3.624; 95% CI, 0.467-6.781; P = 0.02), but not from pretreatment to posttreatment (3.055; 95% CI, -0.018 to 6.128; P = 0.054). All secondary outcomes significantly favored EXP pretreatment to posttreatment, as well as pretreatment to 6-month follow-up. Exposure to daily activities shows to be more effective than a protective pain-contingent TAU in reducing self-reported disability in daily life of CRPS-I patients with at least moderate levels of pain-related fear.

Item does not contain fulltext, OBJECTIVE: Assessment of the effectiveness of the Assessment of Burden of COPD (ABC) tool on disease-specific quality of life in patients with Chronic Obstructive Pulmonary Disease (COPD). DESIGN: Cluster-randomised controlled trial. METHOD: This concerned a trial in 39 Dutch primary care practices and 17 hospitals, involving 357 patients with COPD (postbronchodilator FEV1/FVC ratio < 0.7) aged >/= 40 years. Healthcare providers were randomized to an intervention or control group. Patients in the intervention group were treated with the ABC tool. This innovative tool consists of a short validated questionnaire and a number of objective parameters, which collectively give a visual overview of the combined integral health; the tool subsequently produces an individualized treatment plan by means of a treatment algorithm. Patients in the control group received usual care. The primary outcome measure was the proportion of patients with a clinically relevant improvement in disease-specific quality of life measured, as measured by means of the St. George's Respiratory Questionnaire (SGRQ) score, between baseline and 18 months follow-up. Secondary outcomes included the SGRQ total score and the Patient Assessment of Chronic Illness Care (PACIC) score. RESULTS: At 18-month follow-up, a significant and clinically relevant improvement in the SGRQ score was seen in 34% of the patients (N=49) in the intervention group, and in the control group this figure was 22% (N=33). This difference between the two groups was significant (OR 1.85, 95% CI 1.08 to 3.16). Patients in the intervention group experienced a higher quality of care than patients in the control group (0.32 points difference in PACIC, 95% CI 0.14 to 0.50). CONCLUSION: Use of the ABC tool increases the disease-specific quality of life and the quality of care for COPD patients; it may therefore offer a valuable contribution to improvements in the daily care of COPD. Replication of this study in other (non-Dutch) health-ca

Item does not contain fulltext, OBJECTIVE: Assessment of the effectiveness of the Assessment of Burden of COPD (ABC) tool on disease-specific quality of life in patients with Chronic Obstructive Pulmonary Disease (COPD). DESIGN: Cluster-randomised controlled trial. METHOD: This concerned a trial in 39 Dutch primary care practices and 17 hospitals, involving 357 patients with COPD (postbronchodilator FEV1/FVC ratio < 0.7) aged >/= 40 years. Healthcare providers were randomized to an intervention or control group. Patients in the intervention group were treated with the ABC tool. This innovative tool consists of a short validated questionnaire and a number of objective parameters, which collectively give a visual overview of the combined integral health; the tool subsequently produces an individualized treatment plan by means of a treatment algorithm. Patients in the control group received usual care. The primary outcome measure was the proportion of patients with a clinically relevant improvement in disease-specific quality of life measured, as measured by means of the St. George's Respiratory Questionnaire (SGRQ) score, between baseline and 18 months follow-up. Secondary outcomes included the SGRQ total score and the Patient Assessment of Chronic Illness Care (PACIC) score. RESULTS: At 18-month follow-up, a significant and clinically relevant improvement in the SGRQ score was seen in 34% of the patients (N=49) in the intervention group, and in the control group this figure was 22% (N=33). This difference between the two groups was significant (OR 1.85, 95% CI 1.08 to 3.16). Patients in the intervention group experienced a higher quality of care than patients in the control group (0.32 points difference in PACIC, 95% CI 0.14 to 0.50). CONCLUSION: Use of the ABC tool increases the disease-specific quality of life and the quality of care for COPD patients; it may therefore offer a valuable contribution to improvements in the daily care of COPD. Replication of this study in other (non-Dutch) health-ca

This report focuses on developing concepts and design principles for blue and green infrastructure that not only support climate resilience but also contribute to a healthy and liveable urban environment. We will first assess the effectiveness of blue and green infrastructure on the basis of available literature and experience from the city of Utrecht. Secondly, we will formulate principles for the design of blue and green infrastructure in the urban landscape.

We present the results of a 30ks XMM-Newton observation of the supergiant fast X-ray transient (SFXT) SAX J1818.6-1703 - the first in-depth soft X-ray study of this source around periastron. INTEGRAL observations shortly before and after the XMM-Newton observation show the source to be in an atypically active state. Over the course of the XMM-Newton observation, the source shows a dynamic range of ~100 with a luminosity greater than 1$\times$10$^{35}$ erg s$^{-1}$ for the majority of the observation. After an ~6 ks period of low luminosity (~10$^{34}$ erg s$^{-1}$) emission, SAX J1818.6-1703 enters a phase of fast flaring activity, with flares 250 s long, separated by ~2ks. The source then enters a larger flare event of higher luminosity and ~8 ks duration. Spectral analysis revealed evidence for a significant change in spectral shape during the observation with a photon index varying from {\Gamma} ~ 2.5 during the initial low luminosity emission phase, to {\Gamma} ~ 1.9 through the fast flaring activity, and a significant change to {\Gamma} ~ 0.3 during the main flare. The intrinsic absorbing column density throughout the observation (n$_H$ ~ 5$\times$10$^{23}$ cm$^{-2}$) is among the highest measured from an SFXT, and together with the XMM-Newton and INTEGRAL luminosities, consistent with the neutron star encountering an unusually dense wind environment around periastron. Although other mechanisms cannot be ruled out, we note that the onset of the brighter flares occurs at 3$\times$10$^{35}$ erg s$^{-1}$, a luminosity consistent with the threshold for the switch from a radiative-dominated to Compton cooling regime in the quasi-spherical settling accretion model., Comment: 11 pages, 8 figures, Accepted for publication in MNRAS

Contains fulltext : 155092.PDF (publisher's version ) (Open Access), PURPOSE: To determine the frequency and prognostic value of elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) in metastatic colorectal cancer (mCRC) patients in relation to microsatellite instability (MSI) status and MSH3 protein expression. MATERIAL AND METHODS: The frequency of EMAST was evaluated in mCRC patients with MSI tumors and microsatellite stable (MSS) tumors. A literature overview was performed to compare the frequency of EMAST in our study with existing data. Immunohistochemistry for MSH3 was compared with EMAST status. Outcome was studied in terms of overall survival (OS) of mCRC patients with MSI and MSS tumors. RESULTS: EMAST was evaluated in 89 patients with MSI tumors (including 39 patients with Lynch syndrome) and 94 patients with MSS tumors. EMAST was observed in 45.9% (84 out of 183) of patients, with an increased frequency in MSI tumors (79.8% versus 13.8%, p < 0.001). We found no correlation between EMAST and MSH3 protein expression. There was no effect of EMAST on prognosis in patients with MSS tumors, but patients with MSI / non-EMAST tumors had a significantly better prognosis than patients with MSI / EMAST tumors (OS: HR 3.22, 95% CI 1.25-8.30). CONCLUSION: Frequency of EMAST was increased in mCRC patients with MSI tumors, compared to MSS tumors. Our data suggest that the presence of EMAST correlates with worse OS in these patients. There was no effect of EMAST on the prognosis of patients with MSS tumors. A limitation of our study is the small number of patients in our subgroup analysis.

In this paper we show that the phase mixing of continuum Alfv\'{e}n waves and/or continuum slow waves in magnetic structures of the solar atmosphere as, e.g., coronal arcades, can create the illusion of wave propagation across the magnetic field. This phenomenon could be erroneously interpreted as fast magnetosonic waves. The cross-field propagation due to phase mixing of continuum waves is apparent because there is no real propagation of energy across the magnetic surfaces. We investigate the continuous Alfv\'{e}n and slow spectra in 2D Cartesian equilibrium models with a purely poloidal magnetic field. We show that apparent superslow propagation across the magnetic surfaces in solar coronal structures is a consequence of the existence of continuum Alfv\'{e}n waves and continuum slow waves that naturally live on those structures and phase mix as time evolves. The apparent cross-field phase velocity is related to the spatial variation of the local Alfv\'{e}n/slow frequency across the magnetic surfaces and is slower than the Alfv\'{e}n/sound velocities for typical coronal conditions. Understanding the nature of the apparent cross-field propagation is important for the correct analysis of numerical simulations and the correct interpretation of observations., Comment: 41 pages, 7 figures, accepted for publication in ApJ

We report and analyze the observational evidence of global kink oscillations in a solar filament as observed in H alpha by National Solar Observatory (NSO)/Global Oscillation Network Group (GONG) instrument. An M1.1-class flare in active region 11692 on 2013 March 15 induced a global kink mode in the filament lying in the south-west of AR11692.We find periods of about 61 - 67 minutes and damping times of 92 - 117 minutes at three vertical slice positions chosen in and around the filament apex. We find that the waves are damped. From the observed global kink mode period and damping time scale using the theory of resonant absorption we perform prominence seismology. We estimate a lower cut-off value for the inhomogeneity length-scale to be around 0.34 - 0.44 times the radius of the filament cross-section., Comment: 3 figures, Accepted for publication in RAA

The ratio of the period of the fundamental mode to that of the first overtone of kink oscillations, from here on the "period ratio", is a seismology tool that can be used to infer information about the spatial variation of density along solar magnetic flux tubes. The period ratio is 2 in longitudinally homogeneous thin tubes, but it differs from 2 due to longitudinal inhomogeneity. In this paper we investigate the period ratio in longitudinally inhomogeneous prominence threads and explore its implications for prominence seismology. We numerically solve the two-dimensional eigenvalue problem of kink oscillations in a model of a prominence thread. We take into account three nonuniform density profiles along the thread. In agreement with previous works that used simple piecewise constant density profiles, we find that the period ratio is larger than 2 in prominence threads. When the ratio of the central density to that at the footpoints is fixed, the period ratio depends strongly on the form of the density profile along the thread. The more concentrated the dense prominence plasma near the center of the tube, the larger the period ratio. However, the period ratio is found to be independent of the specific density profile when the spatially averaged density in the thread is the same for all the profiles. An empirical fit of the dependence of the period ratio on the average density is given and its use for prominence seismology is discussed., Comment: Accepted for publication in A&A

Contains fulltext : 155092.PDF (publisher's version ) (Open Access), PURPOSE: To determine the frequency and prognostic value of elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) in metastatic colorectal cancer (mCRC) patients in relation to microsatellite instability (MSI) status and MSH3 protein expression. MATERIAL AND METHODS: The frequency of EMAST was evaluated in mCRC patients with MSI tumors and microsatellite stable (MSS) tumors. A literature overview was performed to compare the frequency of EMAST in our study with existing data. Immunohistochemistry for MSH3 was compared with EMAST status. Outcome was studied in terms of overall survival (OS) of mCRC patients with MSI and MSS tumors. RESULTS: EMAST was evaluated in 89 patients with MSI tumors (including 39 patients with Lynch syndrome) and 94 patients with MSS tumors. EMAST was observed in 45.9% (84 out of 183) of patients, with an increased frequency in MSI tumors (79.8% versus 13.8%, p < 0.001). We found no correlation between EMAST and MSH3 protein expression. There was no effect of EMAST on prognosis in patients with MSS tumors, but patients with MSI / non-EMAST tumors had a significantly better prognosis than patients with MSI / EMAST tumors (OS: HR 3.22, 95% CI 1.25-8.30). CONCLUSION: Frequency of EMAST was increased in mCRC patients with MSI tumors, compared to MSS tumors. Our data suggest that the presence of EMAST correlates with worse OS in these patients. There was no effect of EMAST on the prognosis of patients with MSS tumors. A limitation of our study is the small number of patients in our subgroup analysis.

In this paper we show that the phase mixing of continuum Alfv\'{e}n waves and/or continuum slow waves in magnetic structures of the solar atmosphere as, e.g., coronal arcades, can create the illusion of wave propagation across the magnetic field. This phenomenon could be erroneously interpreted as fast magnetosonic waves. The cross-field propagation due to phase mixing of continuum waves is apparent because there is no real propagation of energy across the magnetic surfaces. We investigate the continuous Alfv\'{e}n and slow spectra in 2D Cartesian equilibrium models with a purely poloidal magnetic field. We show that apparent superslow propagation across the magnetic surfaces in solar coronal structures is a consequence of the existence of continuum Alfv\'{e}n waves and continuum slow waves that naturally live on those structures and phase mix as time evolves. The apparent cross-field phase velocity is related to the spatial variation of the local Alfv\'{e}n/slow frequency across the magnetic surfaces and is slower than the Alfv\'{e}n/sound velocities for typical coronal conditions. Understanding the nature of the apparent cross-field propagation is important for the correct analysis of numerical simulations and the correct interpretation of observations., Comment: 41 pages, 7 figures, accepted for publication in ApJ

We report and analyze the observational evidence of global kink oscillations in a solar filament as observed in H alpha by National Solar Observatory (NSO)/Global Oscillation Network Group (GONG) instrument. An M1.1-class flare in active region 11692 on 2013 March 15 induced a global kink mode in the filament lying in the south-west of AR11692.We find periods of about 61 - 67 minutes and damping times of 92 - 117 minutes at three vertical slice positions chosen in and around the filament apex. We find that the waves are damped. From the observed global kink mode period and damping time scale using the theory of resonant absorption we perform prominence seismology. We estimate a lower cut-off value for the inhomogeneity length-scale to be around 0.34 - 0.44 times the radius of the filament cross-section., Comment: 3 figures, Accepted for publication in RAA

The ratio of the period of the fundamental mode to that of the first overtone of kink oscillations, from here on the "period ratio", is a seismology tool that can be used to infer information about the spatial variation of density along solar magnetic flux tubes. The period ratio is 2 in longitudinally homogeneous thin tubes, but it differs from 2 due to longitudinal inhomogeneity. In this paper we investigate the period ratio in longitudinally inhomogeneous prominence threads and explore its implications for prominence seismology. We numerically solve the two-dimensional eigenvalue problem of kink oscillations in a model of a prominence thread. We take into account three nonuniform density profiles along the thread. In agreement with previous works that used simple piecewise constant density profiles, we find that the period ratio is larger than 2 in prominence threads. When the ratio of the central density to that at the footpoints is fixed, the period ratio depends strongly on the form of the density profile along the thread. The more concentrated the dense prominence plasma near the center of the tube, the larger the period ratio. However, the period ratio is found to be independent of the specific density profile when the spatially averaged density in the thread is the same for all the profiles. An empirical fit of the dependence of the period ratio on the average density is given and its use for prominence seismology is discussed., Comment: Accepted for publication in A&A

Contains fulltext : 136846pub.pdf (publisher's version ) (Closed access), Lynch syndrome is caused by germline mutations in the mismatch repair (MMR) genes. Tumors are characterized by microsatellite instability (MSI). However, a considerable number of MSI-positive tumors have no known molecular mechanism of development. By using Sanger and ion semiconductor sequencing, 25 MSI-positive tumors were screened for somatic mutations and loss of heterozygosity in mutL homolog 1 (MLH1) and mutS homolog 2 (MSH2). In 13 of 25 tumors (8 MLH1-deficient and 5 MSH2-deficient tumors), we identified 2 somatic mutations in these genes. We conclude that 2 acquired events explain the MMR-deficiency in more than 50% of the MMR-deficient tumors without causal germline mutations or promoter methylation.

XMM-Newton observations of the supergiant fast X-ray transient IGR$~$J17544$-$2619 are reported and placed in the context of an analysis of archival INTEGRAL/IBIS data that provides a refined estimate of the orbital period at 4.9272$\pm$0.0004 days. A complete outburst history across the INTEGRAL mission is reported. Although the new XMM-Newton observations (each lasting $\sim$15 ks) targeted the peak flux in the phase-folded hard X-ray light curve of IGR$~$J17544$-$2619, no bright outbursts were observed, the source spending the majority of the exposure at intermediate luminosities of the order of several 10$^{33}\,$erg$\,$s$^{-1}$ (0.5$\,-\,$10$\,$keV) and displaying only low level flickering activity. For the final portion of the exposure, the luminosity of IGR$~$J17544$-$2619 dropped to $\sim$4$\times$10$^{32}\,$erg$\,$s$^{-1}$ (0.5 - 10 keV), comparable with the lowest luminosities ever detected from this source, despite the observations being taken near to periastron. We consider the possible orbital geometry of IGR$~$J17544$-$2619 and the implications for the nature of the mass transfer and accretion mechanisms for both IGR$~$J17544$-$2619 and the SFXT population. We conclude that accretion under the `quasi-spherical accretion' model provides a good description of the behaviour of IGR$~$J17544$-$2619, and suggest an additional mechanism for generating outbursts based upon the mass accumulation rate in the hot shell (atmosphere) that forms around the NS under the quasi-spherical formulation. Hence we hope to aid in explaining the varied outburst behaviours observed across the SFXT population with a consistent underlying physical model., Comment: 12 pages, 5 figures, accepted for publication in MNRAS

Contains fulltext : 138103.pdf (Publisher’s version ) (Closed access), Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 x 10(-11) for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.

Contains fulltext : 136846pub.pdf (publisher's version ) (Closed access), Lynch syndrome is caused by germline mutations in the mismatch repair (MMR) genes. Tumors are characterized by microsatellite instability (MSI). However, a considerable number of MSI-positive tumors have no known molecular mechanism of development. By using Sanger and ion semiconductor sequencing, 25 MSI-positive tumors were screened for somatic mutations and loss of heterozygosity in mutL homolog 1 (MLH1) and mutS homolog 2 (MSH2). In 13 of 25 tumors (8 MLH1-deficient and 5 MSH2-deficient tumors), we identified 2 somatic mutations in these genes. We conclude that 2 acquired events explain the MMR-deficiency in more than 50% of the MMR-deficient tumors without causal germline mutations or promoter methylation.

Contains fulltext : 138103.pdf (Publisher’s version ) (Closed access), Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 x 10(-11) for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.

Contains fulltext : 138103.pdf (Publisher’s version ) (Closed access), Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 x 10(-11) for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.

Contains fulltext : 136846pub.pdf (publisher's version ) (Closed access), Lynch syndrome is caused by germline mutations in the mismatch repair (MMR) genes. Tumors are characterized by microsatellite instability (MSI). However, a considerable number of MSI-positive tumors have no known molecular mechanism of development. By using Sanger and ion semiconductor sequencing, 25 MSI-positive tumors were screened for somatic mutations and loss of heterozygosity in mutL homolog 1 (MLH1) and mutS homolog 2 (MSH2). In 13 of 25 tumors (8 MLH1-deficient and 5 MSH2-deficient tumors), we identified 2 somatic mutations in these genes. We conclude that 2 acquired events explain the MMR-deficiency in more than 50% of the MMR-deficient tumors without causal germline mutations or promoter methylation.

XMM-Newton observations of the supergiant fast X-ray transient IGR$~$J17544$-$2619 are reported and placed in the context of an analysis of archival INTEGRAL/IBIS data that provides a refined estimate of the orbital period at 4.9272$\pm$0.0004 days. A complete outburst history across the INTEGRAL mission is reported. Although the new XMM-Newton observations (each lasting $\sim$15 ks) targeted the peak flux in the phase-folded hard X-ray light curve of IGR$~$J17544$-$2619, no bright outbursts were observed, the source spending the majority of the exposure at intermediate luminosities of the order of several 10$^{33}\,$erg$\,$s$^{-1}$ (0.5$\,-\,$10$\,$keV) and displaying only low level flickering activity. For the final portion of the exposure, the luminosity of IGR$~$J17544$-$2619 dropped to $\sim$4$\times$10$^{32}\,$erg$\,$s$^{-1}$ (0.5 - 10 keV), comparable with the lowest luminosities ever detected from this source, despite the observations being taken near to periastron. We consider the possible orbital geometry of IGR$~$J17544$-$2619 and the implications for the nature of the mass transfer and accretion mechanisms for both IGR$~$J17544$-$2619 and the SFXT population. We conclude that accretion under the `quasi-spherical accretion' model provides a good description of the behaviour of IGR$~$J17544$-$2619, and suggest an additional mechanism for generating outbursts based upon the mass accumulation rate in the hot shell (atmosphere) that forms around the NS under the quasi-spherical formulation. Hence we hope to aid in explaining the varied outburst behaviours observed across the SFXT population with a consistent underlying physical model., Comment: 12 pages, 5 figures, accepted for publication in MNRAS

We report on combined INTEGRAL and XMM-Newton observations of the supergiant fast X-ray transient IGR J16418-4532. The observations targeted the X-ray eclipse region of IGR J16418-4532s orbit with continuous INTEGRAL observations across ~25% of orbital phase and two quasi-simultaneous XMM-Newton observations of length 20ks and 14ks, occurring during and just after the eclipse respectively. An enhanced INTEGRAL emission history is provided with 19 previously unreported outbursts identified in the archival 18-60 keV data set. The XMM-Newton eclipse observation showed prominent Fe-emission and a flux of 2.8*10^-13 erg cm^-2 s^-1 (0.5 - 10 keV). Through the comparison of the detected eclipse and post eclipse flux, the supergiant mass loss rate through the stellar wind was determined as \dot{M}_{w} = 2.3-3.8*10^-7 M_{\odot} yr^-1. The post eclipse XMM-Newton observation showed a dynamic flux evolution with signatures of the X-ray pulsation, a period of flaring activity, structured nH variations and the first ever detection of an X-ray intensity dip, or 'off-state', in a pulsating supergiant fast X-ray transient. Consideration is given to the origin of the X-ray dip and we conclude that the most applicable of the current theories of X-ray dip generation is that of a transition between Compton cooling dominated and radiative cooling dominated subsonic accretion regimes within the 'quasi-spherical' model of wind accretion. Under this interpretation, which requires additional confirmation, the neutron star in IGR J16418-4532 possesses a magnetic field of ~10^14 G, providing tentative observational evidence of a highly magnetised neutron star in a supergiant fast X-ray transient for the first time. The implications of these results on the nature of IGR J16418-4532 itself and the wider SFXT class are discussed., Comment: 17 pages, 10 figures, accepted for publication in MNRAS

Temporal analysis of INTEGRAL/IBIS data has revealed a 5.7195\pm0.0007 day periodicity in the supergiant fast X-ray transient (SFXT) source AX J1845.0-0433, which we interpret as the orbital period of the system. The new-found knowledge of the orbital period is utilised to investigate the geometry of the system by means of estimating an upper limit for the size of the supergiant (<27 R_{\sun}) as well as the eccentricity of the orbit (\epsilon<0.37)., Comment: 6 pages, 6 figures, accepted for publication in MNRAS

We present rare observational evidence of vertical kink oscillations in a laminar and diffused large-scale plasma curtain as observed by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO). The X6.9 class flare in the Active Region 11263 on 09 August 2011, induces a global large-scale disturbance that propagates in a narrow lane above the plasma curtain and creates a low density region that appears as a dimming in the observational image data. This large-scale propagating disturbance acts as a non-periodic driver that interacts asymmetrically and obliquely with the top of the plasma curtain, and triggers the observed oscillations. In the deeper layers of the curtain, we find evidence of vertical kink oscillations with two periods (795 s and 530 s). On the magnetic surface of the curtain where the density is inhomogeneous due to the coronal dimming, non-decaying vertical oscillations are also observed (period $\approx$ 763-896 s). We infer that the global large-scale disturbance triggers vertical kink oscillations in the deeper layers as well as on the surface of the large-scale plasma curtain. The properties of the excited waves strongly depend on the local plasma and magnetic field conditions., Comment: ApJ, 29 Pages, 5 Figures

Observations show that waves are ubiquitous in the solar atmosphere and may play an important role for plasma heating. The study of waves in the solar corona is usually based on linear ideal magnetohydrodynamics (MHD) for a fully ionized plasma. However, the plasma in the photosphere and the chromosphere is only partially ionized. Here we investigate theoretically the impact of partial ionization on MHD wave propagation in cylindrical flux tubes in the two-fluid model. We derive the general dispersion relation that takes into account the effects of neutral-ion collisions and the neutral gas pressure. We take the neutral-ion collision frequency as an arbitrary parameter. Particular results for transverse kink modes and slow magnetoacoustic modes are shown. We find that the wave frequencies only depend on the properties of the ionized fluid when the neutral-ion collision frequency is much lower that the wave frequency. For high collision frequencies realistic of the solar atmosphere ions and neutrals behave as a single fluid with an effective density corresponding to the sum of densities of both fluids and an effective sound velocity computed as the average of the sound velocities of ions and neutrals. The MHD wave frequencies are modified accordingly. The neutral gas pressure can be neglected when studying transverse kink waves but it has to be taken into account for a consistent description of slow magnetoacoustic waves. The MHD waves are damped due to neutral-ion collisions. The damping is most efficient when the wave frequency and the collision frequency are of the same order of magnitude. For high collision frequencies slow magnetoacoustic waves are more efficiently damped than transverse kink waves. In addition, we find the presence of cut-offs for certain combinations of parameters that cause the waves to become non-propagating., Comment: Accepted for publication in A&A

We present rare observational evidence of vertical kink oscillations in a laminar and diffused large-scale plasma curtain as observed by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO). The X6.9 class flare in the Active Region 11263 on 09 August 2011, induces a global large-scale disturbance that propagates in a narrow lane above the plasma curtain and creates a low density region that appears as a dimming in the observational image data. This large-scale propagating disturbance acts as a non-periodic driver that interacts asymmetrically and obliquely with the top of the plasma curtain, and triggers the observed oscillations. In the deeper layers of the curtain, we find evidence of vertical kink oscillations with two periods (795 s and 530 s). On the magnetic surface of the curtain where the density is inhomogeneous due to the coronal dimming, non-decaying vertical oscillations are also observed (period $\approx$ 763-896 s). We infer that the global large-scale disturbance triggers vertical kink oscillations in the deeper layers as well as on the surface of the large-scale plasma curtain. The properties of the excited waves strongly depend on the local plasma and magnetic field conditions., Comment: ApJ, 29 Pages, 5 Figures

Temporal analysis of INTEGRAL/IBIS data has revealed a 5.7195\pm0.0007 day periodicity in the supergiant fast X-ray transient (SFXT) source AX J1845.0-0433, which we interpret as the orbital period of the system. The new-found knowledge of the orbital period is utilised to investigate the geometry of the system by means of estimating an upper limit for the size of the supergiant (<27 R_{\sun}) as well as the eccentricity of the orbit (\epsilon<0.37)., Comment: 6 pages, 6 figures, accepted for publication in MNRAS