Placing Confidence Limits on Polarization Measurements

The determination of the true source polarization given a set of measurements is complicated by the requirement that the polarization always be positive. This positive bias also hinders construction of upper limits, uncertainties, and confidence regions, especially at low signal-to-noise levels. We generate the likelihood function for linear polarization measurements and use it to create confidence regions and upper limits. This is accomplished by integrating the likelihood function over the true polarization (parameter space), rather than the measured polarization (data space). These regions are valid for both low and high signal-to-noise measurements.Comment: 8 pages, 3 figures, 1 table, submitted to PAS

Magnetic Field Structure around Low-Mass Class 0 Protostars: B335, L1527 and IC348-SMM2

We report new 350 micron polarization observations of the thermal dust emission from the cores surrounding the low-mass, Class 0 YSOs L1527, IC348-SMM2 and B335. We have inferred magnetic field directions from these observations, and have used them together with results in the literature to determine whether magnetically regulated core-collapse and star-formation models are consistent with the observations. These models predict a pseudo-disk with its symmetry axis aligned with the core magnetic field. The models also predict a magnetic field pinch structure on a scale less than or comparable to the infall radii for these sources. In addition, if the core magnetic field aligns (or nearly aligns) the core rotation axis with the magnetic field before core collapse, then the models predict the alignment (or near alignment) of the overall pinch field structure with the bipolar outflows in these sources. We show that if one includes the distorting effects of bipolar outflows on magnetic fields, then in general the observational results for L1527 and IC348-SMM2 are consistent with these magnetically regulated models. We can say the same for B335 only if we assume the distorting effects of the bipolar outflow on the magnetic fields within the B335 core are much greater than for L1527 and IC348-SMM2. We show that the energy densities of the outflows in all three sources are large enough to distort the magnetic fields predicted by magnetically regulated models.Comment: Accepted for publication in The Astrophysical Journa

A \u3cem\u3eColletotrichum graminicola\u3c/em\u3e Mutant Deficient in the Establishment of Biotrophy Reveals Early Transcriptional Events in the Maize Anthracnose Disease Interaction

Background: Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A “Mixed Effects” Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C. graminicola gene expression during infection and colonization. Additionally, the in planta transcriptome of the wild-type was compared with that of a mutant strain impaired in the establishment of biotrophy, allowing detailed dissection of events occurring specifically during penetration, and during early versus late biotrophy. Results: More than 2000 fungal genes were differentially transcribed during appressorial maturation, penetration, and colonization. Secreted proteins, secondary metabolism genes, and membrane receptors were over-represented among the differentially expressed genes, suggesting that the fungus engages in an intimate and dynamic conversation with the host, beginning prior to penetration. This communication process probably involves reception of plant signals triggering subsequent developmental progress in the fungus, as well as production of signals that induce responses in the host. Later phases of biotrophy were more similar to necrotrophy, with increased production of secreted proteases, inducers of plant cell death, hydrolases, and membrane bound transporters for the uptake and egress of potential toxins, signals, and nutrients. Conclusions: This approach revealed, in unprecedented detail, fungal genes specifically expressed during critical phases of host penetration and biotrophic establishment. Many encoded secreted proteins, secondary metabolism enzymes, and receptors that may play roles in host-pathogen communication necessary to promote susceptibility, and thus may provide targets for chemical or biological controls to manage this important disease. The differentially expressed genes could be used as ‘landmarks’ to more accurately identify developmental progress in compatible versus incompatible interactions involving genetic variants of both host and pathogen

A Comparative Genomic Analysis of Putative Pathogenicity Genes in the Host-Specific Sibling Species \u3cem\u3eColletotrichum graminicola\u3c/em\u3e and \u3cem\u3eColletotrichum sublineola\u3c/em\u3e

Background: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains. Results: Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another. Conclusions: Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases

A comparative study on approximate entropy measure and poincaré plot indexes of minimum foot clearance variability in the elderly during walking

Background: Trip-related falls which is a major problem in the elderly population, might be linked to declines in the balance control function due to ageing. Minimum foot clearance (MFC) which provides a more sensitive measure of the motor function of the locomotor system, has been identified as a potential gait parameter associated with trip-related falls in older population. This paper proposes nonlinear indexes (approximate entropy (ApEn) and Poincaré plot indexes) of MFC variability and investigates the relationship of MFC with derived indexes of elderly gait patterns. The main aim is to find MFC variability indexes that well correlate with balance impairments. Methods: MFC data during treadmill walking for 14 healthy elderly and 10 elderly participants with balance problems and a history of falls (falls risk) were analysed using a PEAK-2D motion analysis system. ApEn and Poincaré plot indexes of all MFC data sets were calculated and compared. Results: Significant relationships of mean MFC with Poincaré plot indexes (SD1, SD2) and ApEn (r = 0.70, p < 0.05; r = 0.86, p < 0.01; r = 0.74, p < 0.05) were found in the falls-risk elderly group. On the other hand, such relationships were absent in the healthy elderly group. In contrast, the ApEn values of MFC data series were significantly (p < 0.05) correlated with Poincaré plot indexes of MFC in the healthy elderly group, whereas correlations were absent in the falls-risk group. The ApEn values in the falls-risk group (mean ApEn = 0.18 ± 0.03) was significantly (p < 0.05) higher than that in the healthy group (mean ApEn = 0.13 ± 0.13). The higher ApEn values in the falls-risk group might indicate increased irregularities and randomness in their gait patterns and an indication of loss of gait control mechanism. ApEn values of randomly shuffled MFC data of falls risk subjects did not show any significant relationship with mean MFC. Conclusion: Results have implication for quantifying gait dynamics in normal and pathological conditions, thus could be useful for the early diagnosis of at-risk gait. Further research should provide important information on whether falls prevention intervention can improve the gait performance of falls risk elderly by monitoring the change in MFC variability indexes

A comparative study on approximate entropy measure and poincaré plot indexes of minimum foot clearance variability in the elderly during walking

Background: Trip-related falls which is a major problem in the elderly population, might be linked to declines in the balance control function due to ageing. Minimum foot clearance (MFC) which provides a more sensitive measure of the motor function of the locomotor system, has been identified as a potential gait parameter associated with trip-related falls in older population. This paper proposes nonlinear indexes (approximate entropy (ApEn) and Poincaré plot indexes) of MFC variability and investigates the relationship of MFC with derived indexes of elderly gait patterns. The main aim is to find MFC variability indexes that well correlate with balance impairments. Methods: MFC data during treadmill walking for 14 healthy elderly and 10 elderly participants with balance problems and a history of falls (falls risk) were analysed using a PEAK-2D motion analysis system. ApEn and Poincaré plot indexes of all MFC data sets were calculated and compared. Results: Significant relationships of mean MFC with Poincaré plot indexes (SD1, SD2) and ApEn (r = 0.70, p < 0.05; r = 0.86, p < 0.01; r = 0.74, p < 0.05) were found in the falls-risk elderly group. On the other hand, such relationships were absent in the healthy elderly group. In contrast, the ApEn values of MFC data series were significantly (p < 0.05) correlated with Poincaré plot indexes of MFC in the healthy elderly group, whereas correlations were absent in the falls-risk group. The ApEn values in the falls-risk group (mean ApEn = 0.18 ± 0.03) was significantly (p < 0.05) higher than that in the healthy group (mean ApEn = 0.13 ± 0.13). The higher ApEn values in the falls-risk group might indicate increased irregularities and randomness in their gait patterns and an indication of loss of gait control mechanism. ApEn values of randomly shuffled MFC data of falls risk subjects did not show any significant relationship with mean MFC. Conclusion: Results have implication for quantifying gait dynamics in normal and pathological conditions, thus could be useful for the early diagnosis of at-risk gait. Further research should provide important information on whether falls prevention intervention can improve the gait performance of falls risk elderly by monitoring the change in MFC variability indexes

Joint 3D modelling of the polarized Galactic synchrotron and thermal dust foreground diffuse emission

We present for the first time a coherent model of the polarized Galactic synchrotron and thermal dust emissions which are the main diffuse foreground for the measurement of the polarized power spectra of the CMB fluctuations with the Planck satellite mission. We produce 3D models of the Galactic magnetic field including regular and turbulent components, and of the distribution of matter in the Galaxy, relativistic electrons and dust grains. By integrating along the line of sight we construct maps of the polarized Galactic synchrotron and thermal dust emission for each of these models and compare them to currently available data. We consider the 408 MHz all-sky continuum survey, the 23 GHz band of the Wilkinson Microwave Anisotropy Probe and the 353 GHz Archeops data.}{The best-fit parameters obtained are consistent with previous estimates in the literature based only on synchrotron emission and pulsar rotation measurements. They allows us to reproduce the large scale structures observed on the data. Poorly understood local Galactic structures and turbulence make difficult an accurate reconstruction of the observations in the Galactic plane. Finally, using the best-fit model we are able to estimate the expected polarized foreground contamination at the Planck frequency bands. For the CMB bands, 70, 100, 143 and 217 GHz, at high Galactic latitudes although the CMB signal dominates in general, a significant foreground contribution is expected at large angular scales. In particular, this contribution will dominate the CMB signal for the B modes expected from realistic models of a background of primordial gravitational waves

Polarisation Observations of VY Canis Majoris Water Vapour 5{32}-4{41} 620.701 GHz Maser Emission with HIFI

CONTEXT: Water vapour maser emission from evolved oxygen-rich stars remains poorly understood. Additional observations, including polarisation studies and simultaneous observation of different maser transitions may ultimately lead to greater insight. AIMS: We have aimed to elucidate the nature and structure of the VY CMa water vapour masers in part by observationally testing a theoretical prediction of the relative strengths of the 620.701 GHz and the 22.235 GHz maser components of ortho water vapour. METHODS: In its high-resolution mode (HRS) the Herschel Heterodyne Instrument for the Infrared (HIFI) offers a frequency resolution of 0.125 MHz, corresponding to a line-of-sight velocity of 0.06 km/s, which we employed to obtain the strength and linear polarisation of maser spikes in the spectrum of VY CMa at 620.701 GHz. Simultaneous ground based observations of the 22.235 GHz maser with the Max-Planck-Institut f\"ur Radioastronomie 100-meter telescope at Effelsberg, provided a ratio of 620.701 GHz to 22.235 GHz emission. RESULTS:We report the first astronomical detection to date of water vapour maser emission at 620.701 GHz. In VY CMa both the 620.701 and the 22.235 GHz polarisation are weak. At 620.701 GHz the maser peaks are superposed on what appears to be a broad emission component, jointly ejected asymmetrically from the star. We observed the 620.701 GHz emission at two epochs 21 days apart, both to measure the potential direction of linearly polarised maser components and to obtain a measure of the longevity of these components. Although we do not detect significant polarisation levels in the core of the line, they rise up to approximately 6% in its wings

Parkinson's disease biomarkers: perspective from the NINDS Parkinson's Disease Biomarkers Program

Biomarkers for Parkinson's disease (PD) diagnosis, prognostication and clinical trial cohort selection are an urgent need. While many promising markers have been discovered through the National Institute of Neurological Disorders and Stroke Parkinson's Disease Biomarker Program (PDBP) and other mechanisms, no single PD marker or set of markers are ready for clinical use. Here we discuss the current state of biomarker discovery for platforms relevant to PDBP. We discuss the role of the PDBP in PD biomarker identification and present guidelines to facilitate their development. These guidelines include: harmonizing procedures for biofluid acquisition and clinical assessments, replication of the most promising biomarkers, support and encouragement of publications that report negative findings, longitudinal follow-up of current cohorts including the PDBP, testing of wearable technologies to capture readouts between study visits and development of recently diagnosed (de novo) cohorts to foster identification of the earliest markers of disease onset