Magneto-frictional Modeling Of Coronal Nonlinear Force-free Fields. I. Testing With Analytic Solutions

We report our implementation of the magneto-frictional method in the Message Passing Interface Adaptive Mesh Refinement Versatile Advection Code (MPI-AMRVAC). The method aims at applications where local adaptive mesh refinement (AMR) is essential to make follow-up dynamical modeling affordable. We quantify its performance in both domain-decomposed uniform grids and block-adaptive AMR computations, using all frequently employed force-free, divergence-free, and other vector comparison metrics. As test cases, we revisit the semi-analytic solution of Low and Lou in both Cartesian and spherical geometries, along with the topologically challenging Titov-Démoulin model. We compare different combinations of spatial and temporal discretizations, and find that the fourth-order central difference with a local Lax-Friedrichs dissipation term in a single-step marching scheme is an optimal combination. The initial condition is provided by the potential field, which is the potential field source surface model in spherical geometry. Various boundary conditions are adopted, ranging from fully prescribed cases where all boundaries are assigned with the semi-analytic models, to solar-like cases where only the magnetic field at the bottom is known. Our results demonstrate that all the metrics compare favorably to previous works in both Cartesian and spherical coordinates. Cases with several AMR levels perform in accordance with their effective resolutions. The magneto-frictional method in MPI-AMRVAC allows us to model a region of interest with high spatial resolution and large field of view simultaneously, as required by observation-constrained extrapolations using vector data provided with modern instruments. The applications of the magneto-frictional method to observations are shown in an accompanying paper

Flux cancellation and the evolution of the eruptive filament of 2011 June 7

We investigate whether flux cancellation is responsible for the formation of a very massive filament resulting in the spectacular 2011 June 7 eruption. We analyse and quantify the amount of flux cancellation that occurs in NOAA AR 11226 and its two neighbouring ARs (11227 & 11233) using line-of-sight magnetograms from the Heliospheric Magnetic Imager. During a 3.6-day period building up to the filament eruption, 1.7 x 10^21 Mx, 21% of AR 11226's maximum magnetic flux, was cancelled along the polarity inversion line (PIL) where the filament formed. If the flux cancellation continued at the same rate up until the eruption then up to 2.8 x 10^21 Mx (34% of the AR flux) may have been built into the magnetic configuration that contains the filament plasma. The large flux cancellation rate is due to an unusual motion of the positive polarity sunspot, which splits, with the largest section moving rapidly towards the PIL. This motion compresses the negative polarity and leads to the formation of an orphan penumbra where one end of the filament is rooted. Dense plasma threads above the orphan penumbra build into the filament, extending its length, and presumably injecting material into it. We conclude that the exceptionally strong flux cancellation in AR 11226 played a significant role in the formation of its unusually massive filament. In addition, the presence and coherent evolution of bald patches in the vector magnetic field along the PIL suggests that the magnetic field configuration supporting the filament material is that of a flux rope.Comment: 18 pages, 7 figures. Submitted to ApJ in December 2015, accepted in June 201

Causes of Post-Colonoscopy Colorectal Cancers Based on World Endoscopy Organization System of Analysis

Background & Aims Postcolonoscopy colorectal cancer (PCCRC) is CRC diagnosed after a colonoscopy in which no cancer was found. A consensus article from the World Endoscopy Organization (WEO) proposed an approach for investigating and categorizing PCCRCs detected within 4 years of a colonoscopy. We aimed to identify cases of PCCRC and the factors that cause them, test the WEO system of categorization, quantify the proportion of avoidable PCCRCs, and propose a target rate for PCCRCs detected within 3 years of a colonoscopy that did not detect CRC. Methods We performed a retrospective analysis of 107 PCCRCs identified at a single medical center in England from January 1, 2010, through December 31, 2017 using coding and endoscopy data. For each case, we reviewed clinical, pathology, radiology, and endoscopy findings. Using the WEO recommendations, we performed a root-cause analysis of each case, categorizing lesions as follows: possible missed lesion, prior examination adequate; possible missed lesion, prior examination inadequate; detected lesion, not resected; or likely incomplete resection of previously identified lesion. We determined whether PCCRCs could be attributed to the colonoscopist for technical or decision-making reasons, and whether the PCCRC was avoidable or unavoidable, based on the WEO categorization and size of tumor. The endoscopy reporting system provided performance data for individual endoscopists. Results Of the PCCRCs identified, 43% were in high-risk patients (those with inflammatory bowel disease, previous CRC, previous multiple large polyps, or hereditary cancer syndromes) and 66% were located distal to the hepatic flexure. There was no correlation between postcolonoscopy colorectal tumor size and time to diagnosis after index colonoscopy. Bowel preparation was poor in 19% of index colonoscopies, and only 36% of complete colonoscopies had adequate photodocumentation of completion. Development of 73% of PCCRCs was determined to be affected by technical endoscopic factors, 17% of PCCRCs by administrative factors (follow-up procedures delayed/not booked by administrative staff), and 27% of PCCRCs by decision-making factors. Twenty-seven percent of PCCRCs were categorized as possible missed lesion, prior examination adequate; 58% as possible missed lesion, prior examination inadequate; 8% as detected lesion, not resected; and 7% as incomplete resection of previously observed lesion; 89% were deemed to be avoidable. Conclusions In a retrospective analysis of PCCRCs, using the WEO system of categorization, we found 43% to occur in high-risk patients; this might be reduced with more vigilant surveillance. Measures are needed to reduce technical, decision-making, and administrative factors. We found that 89% of PCCRCs may be avoidable. If half of avoidable PCCRCs could be prevented, the target rate of 2% for the PCCRC-3y (cancer diagnosed between 6 and 36 months after index colonoscopy) benchmark would be achievable

Measuring the magnetic field of a trans-equatorial loop system using coronal seismology

Context. EIT waves are freely-propagating global pulses in the low corona which are strongly associated with the initial evolution of coronal mass ejections (CMEs). They are thought to be large-Amplitude, fast-mode magnetohydrodynamic waves initially driven by the rapid expansion of a CME in the low corona. Aims. An EIT wave was observed on 6 July 2012 to impact an adjacent trans-equatorial loop system which then exhibited a decaying oscillation as it returned to rest. Observations of the loop oscillations were used to estimate the magnetic field strength of the loop system by studying the decaying oscillation of the loop, measuring the propagation of ubiquitous transverse waves in the loop and extrapolating the magnetic field from observed magnetograms. Methods. Observations from the Atmospheric Imaging Assembly onboard the Solar Dynamics Observatory (SDO/AIA) and the Coronal Multi-channel Polarimeter (CoMP) were used to study the event. An Empirical Mode Decomposition analysis was used to characterise the oscillation of the loop system in CoMP Doppler velocity and line width and in AIA intensity. Results. The loop system was shown to oscillate in the 2nd harmonic mode rather than at the fundamental frequency, with the seismological analysis returning an estimated magnetic field strength of 5.5 ± 1.5 G. This compares to the magnetic field strength estimates of 1-9 G and 3-9 G found using the measurements of transverse wave propagation and magnetic field extrapolation respectively.Fil: Long, David M.. Colegio Universitario de Londres; Reino UnidoFil: Valori, G.. Colegio Universitario de Londres; Reino UnidoFil: Pérez-Suárez, D.. Colegio Universitario de Londres; Reino UnidoFil: Morton, R. J.. University Of Northumbria; Reino UnidoFil: Vasquez, Alberto Marcos. Consejo Nacional de Investigaciónes Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomía y Física del Espacio; Argentin

Coronal magnetic reconnection driven by CME expansion -- the 2011 June 7 event

Coronal mass ejections (CMEs) erupt and expand in a magnetically structured solar corona. Various indirect observational pieces of evidence have shown that the magnetic field of CMEs reconnects with surrounding magnetic fields, forming, e.g., dimming regions distant from the CME source regions. Analyzing Solar Dynamics Observatory (SDO) observations of the eruption from AR 11226 on 2011 June 7, we present the first direct evidence of coronal magnetic reconnection between the fields of two adjacent ARs during a CME. The observations are presented jointly with a data-constrained numerical simulation, demonstrating the formation/intensification of current sheets along a hyperbolic flux tube (HFT) at the interface between the CME and the neighbouring AR 11227. Reconnection resulted in the formation of new magnetic connections between the erupting magnetic structure from AR 11226 and the neighboring active region AR 11227 about 200 Mm from the eruption site. The onset of reconnection first becomes apparent in the SDO/AIA images when filament plasma, originally contained within the erupting flux rope, is re-directed towards remote areas in AR 11227, tracing the change of large-scale magnetic connectivity. The location of the coronal reconnection region becomes bright and directly observable at SDO/AIA wavelengths, owing to the presence of down-flowing cool, dense (10^{10} cm^{-3}) filament plasma in its vicinity. The high-density plasma around the reconnection region is heated to coronal temperatures, presumably by slow-mode shocks and Coulomb collisions. These results provide the first direct observational evidence that CMEs reconnect with surrounding magnetic structures, leading to a large-scale re-configuration of the coronal magnetic field.Comment: 12 pages, 12 figure

Variation in post-colonoscopy colorectal cancer across colonoscopy providers in English National Health Service: population based cohort study

Objectives: To quantify post-colonoscopy colorectal cancer (PCCRC) rates in England by using recent World Endoscopy Organisation guidelines, compare incidence among colonoscopy providers, and explore associated factors that could benefit from quality improvement initiatives. Design: Population based cohort study. Setting: National Health Service in England between 2005 and 2013. Population: All people undergoing colonoscopy and subsequently diagnosed as having colorectal cancer up to three years after their investigation (PCCRC-3yr). Main outcome measures: National trends in incidence of PCCRC (within 6-36 months of colonoscopy), univariable and multivariable analyses to explore factors associated with occurrence, and funnel plots to measure variation among providers. Results: The overall unadjusted PCCRC-3yr rate was 7.4% (9317/126 152), which decreased from 9.0% in 2005 to 6.5% in 2013 (P<0.01). Rates were lower for colonoscopies performed under the NHS bowel cancer screening programme (593/16 640, 3.6%), while they were higher for those conducted by non-NHS providers (187/2009, 9.3%). Rates were higher in women, in older age groups, and in people with inflammatory bowel disease or diverticular disease, in those with higher comorbidity scores, and in people with previous cancers. Substantial variation in rates among colonoscopy providers remained after adjustment for case mix. Conclusions: Wide variation exists in PCCRC-3yr rates across NHS colonoscopy providers in England. The lowest incidence was seen in colonoscopies performed under the NHS bowel cancer screening programme. Quality improvement initiatives are needed to address this variation in rates and prevent colorectal cancer by enabling earlier diagnosis, removing premalignant polyps, and therefore improving outcomes

Post-colonoscopy colorectal cancer (PCCRC) rates vary considerably depending on the method used to calculate them: a retrospective observational population-based study of PCCRC in the English National Health Service

OBJECTIVE: Post-colonoscopy colorectal cancer (PCCRC) is a key quality indicator of colonoscopy. This study compares methods for defining PCCRC rates, proposes a new method of calculating them and quantifies them across the English National Health Service (NHS). DESIGN: This retrospective observational population-based study involved all individuals with a first primary diagnosis of colorectal cancer made between 2001 and 2010 and treated in the English NHS. Previously published methods for deriving PCCRC rates were applied to the linked routine health data for this population to investigate the effect on the rate. A new method, based on the year of the colonoscopy rather than colorectal cancer diagnosis, was then used to calculate PCCRC rates. RESULTS: Of 297 956 individuals diagnosed with colorectal cancer, a total of 94 648 underwent a colonoscopy in the 3 years prior to their diagnosis. The application of the published methods and exclusion criteria to the dataset produced significantly different PCCRC rates from 2.5% to 7.7%. The new method demonstrates that PCCRC rates within 3 years of colonoscopy (without exclusions) decreased in the English NHS over 8 years, falling from 10.6% to 7.3% for colonoscopies performed in 2001 and 2007 respectively. CONCLUSIONS: The method used to determine PCCRC rates significantly affects findings with potential to substantially underestimate rates. To enable international benchmarking there needs to be a standardised method for defining PCCRC. This study proposes a new methodology using colonoscopy as a denominator and between 2001 and 2007 this method indicated an 8.6% PCCRC rate across the English NHS. It also demonstrated PCCRC rates have fallen over time

Primary familial brain calcification linked to deletion of 5' noncoding region of SLC20A2

OBJECTIVES: Primary familial brain calcification (PFBC) is a rare neurological disease often inherited as a dominant trait. Mutations in four genes (SLC20A2, PDGFB, PDGFRB, and XPR1) have been reported in patients with PFBC. Of these, point mutations or small deletions in SLC20A2 are most common. Thus far, only one large deletion covering entire SLC20A2 and several smaller, exonic deletions of SLC20A2 have been reported. The aim of this study was to identify the causative gene defect in a Finnish PFBC family with three affected patients. MATERIALS AND METHODS: A Finnish family with three PFBC patients and five unaffected subjects was studied. Sanger sequencing was used to exclude mutations in the coding and splice site regions of SLC20A2, PDGFRB, and PDGFB. Whole-exome (WES) and whole-genome sequencing (WGS) were performed to identify the causative mutation. A SNP array was used in segregation analysis. RESULTS: Copy number analysis of the WGS data revealed a heterozygous deletion of ~578 kb on chromosome 8. The deletion removes the 5' UTR region, the noncoding exon 1 and the putative promoter region of SLC20A2 as well as the coding regions of six other genes. CONCLUSIONS: Our results support haploinsufficiency of SLC20A2 as a pathogenetic mechanism in PFBC. Analysis of copy number variations (CNVs) is emerging as a crucial step in the molecular genetic diagnostics of PFBC, and it should not be limited to coding regions, as causative variants may reside in the noncoding parts of known disease-associated genes

Experience of 170 cases of ductal carcinoma in ' (DCIS)

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Hsa-miR-210-3p expression in breast cancer and its putative association with worse outcome in patients treated with Docetaxel

MicroRNA-210-3p is the most prominent hypoxia regulated microRNA, and it has been found significantly overexpressed in different human cancers. We performed the expression analysis of miR-210-3p in a retrospective cohort of breast cancer patients with a median follow-up of 76 months (n = 283). An association between higher levels of miR-210-3p and risk of disease progression (HR: 2.13, 95%CI: 1.33-3.39, P = 0.002) was found in the subgroup of patients treated with Epirubicin and Cyclophosphamide followed by Docetaxel. Moreover, a cut off value of 20.966 established by ROC curve analyses allowed to discriminate patients who developed distant metastases with an accuracy of 85% at 3- (AUC: 0.870, 95%CI: 0.690-1.000) and 83% at 5-years follow up (AUC: 0.832, 95%CI: 0.656-1.000). Whereas the accuracy in discriminating patients who died for the disease was of 79.6% at both 5- (AUC: 0.804, 95%CI: 0.517-1.000) and 10-years (AUC: 0.804. 95%CI: 0.517-1.000) follow-up. In silico analysis of miR-210-3p and Docetaxel targets provided evidence for a putative molecular cross-talk involving microtubule regulation, drug efflux metabolism and oxidative stress response. Overall, our data point to the miR-210-3p involvement in the response to therapeutic regimens including Docetaxel in sequential therapy with anthracyclines, suggesting it may represent a predictive biomarker in breast cancer patients