Computer-aided detection (CAD) for breast MRI: evaluation of efficacy at 3.0 T

OBJECTIVE: The purpose of the study was to evaluate the accuracy of 3.0-T breast MRI interpretation using manual and fully automated kinetic analyses. MATERIAL AND METHODS: Manual MRI interpretation was done on an Advantage Workstation. Retrospectively, all examinations were processed with a computer-aided detection (CAD) system. CAD data sets were interpreted by two experienced breast radiologists and two residents. For each lesion automated analysis of enhancement kinetics was evaluated at 50% and 100% thresholds. Forty-nine malignant and 22 benign lesions were evaluated. RESULTS: Using threshold enhancement alone, the sensitivity and specificity of CAD were 97.9% and 86.4%, respectively, for the 50% threshold, and 97.9% and 90%, respectively, for the 100% threshold. Manual interpretation by two breast radiologists showed a sensitivity of 84.6% and a specificity of 68.8%. For the same two radiologists the mean sensitivity and specificity for CAD-based interpretation was 90.4% (not significant) and 81.3% (significant at p < 0.05), respectively. With one-way ANOVA no significant differences were found between the two breast radiologists and the two residents together, or between any two readers separately. CONCLUSION: CAD-based analysis improved the specificity compared with manual analysis of enhancement. Automated analysis at 50% and 100% thresholds showed a high sensitivity and specificity for readers with varying levels of experience

Thinking Through our Processes: How the UCSC Community Psychology Research & Action Team Strives to Embody Ethical, Critically Reflexive Anti-racist Feminist Praxis

Co-written by eight people, this paper describes how the UCSC Community Psychology Research and Action Team (CPRAT) organizes itself in weekly group meetings and how this structure is an attempt to embody an ethical, critically reflexive anti-racist feminist praxis. First, we outline the community psychology core competency of an ethical, reflective practice (Dalton & Wolfe, 2012). We offer a friendly amendment to consider an ethical, critically reflexive anti-racist feminist praxis. Second, we discuss how we organize CPRAT meetings to uphold these ideas. We describe our current structure, which includes personal and project check-ins, rotating facilitation, and attention to broader professional development issues. Third, we provide two examples to illustrate our process: (a) why talking about poop matters in addressing imposter syndrome and (b) getting our team on the same page regarding a research site. We end the paper with a description of a “rough edge,” or an area for growth in our praxis

Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae

OBJECTIVES: The objective of this study was to determine the distribution and genetic basis of trimethoprim resistance in Actinobacillus pleuropneumoniae isolates from pigs in England. METHODS: Clinical isolates collected between 1998 and 2011 were tested for resistance to trimethoprim and sulphonamide. The genetic basis of trimethoprim resistance was determined by shotgun WGS analysis and the subsequent isolation and sequencing of plasmids. RESULTS: A total of 16 (out of 106) A. pleuropneumoniae isolates were resistant to both trimethoprim (MIC >32 mg/L) and sulfisoxazole (MIC ≥256 mg/L), and a further 32 were resistant only to sulfisoxazole (MIC ≥256 mg/L). Genome sequence data for the trimethoprim-resistant isolates revealed the presence of the dfrA14 dihydrofolate reductase gene. The distribution of plasmid sequences in multiple contigs suggested the presence of two distinct dfrA14-containing plasmids in different isolates, which was confirmed by plasmid isolation and sequencing. Both plasmids encoded mobilization genes, the sulphonamide resistance gene sul2, as well as dfrA14 inserted into strA, a streptomycin-resistance-associated gene, although the gene order differed between the two plasmids. One of the plasmids further encoded the strB streptomycin-resistance-associated gene. CONCLUSIONS: This is the first description of mobilizable plasmids conferring trimethoprim resistance in A. pleuropneumoniae and, to our knowledge, the first report of dfrA14 in any member of the Pasteurellaceae. The identification of dfrA14 conferring trimethoprim resistance in A. pleuropneumoniae isolates will facilitate PCR screens for resistance to this important antimicrobial

Disruption of Transforming Growth Factor β Signaling by a Novel Ligand-dependent Mechanism

Transforming growth factor (TGF)-β is the prototype in a family of secreted proteins that act in autocrine and paracrine pathways to regulate cell development and function. Normal cells typically coexpress TGF-β receptors and one or more isoforms of TGF-β, thus the synthesis and secretion of TGF-β as an inactive latent complex is considered an essential step in regula-ting the activity of this pathway. To determine whether intracellular activation of TGF-β results in TGF-β ligand–receptor interactions within the cell, we studied pristane-induced plasma cell tumors (PCTs). We now demonstrate that active TGF-β1 in the PCT binds to intracellular TGF-β type II receptor (TβRII). Disruption of the expression of TGF-β1 by antisense TGF-β1 mRNA restores localization of TβRII at the PCT cell surface, indicating a ligand-induced impediment in receptor trafficking. We also show that retroviral expression of a truncated, dominant-negative TβRII (dnTβRII) effectively competes for intracellular binding of active ligand in the PCT and restores cell surface expression of the endogenous TβRII. Analysis of TGF-β receptor–activated Smad2 suggests the intracellular ligand–receptor complex is not capable of signaling. These data are the first to demonstrate the formation of an intracellular TGF-β–receptor complex, and define a novel mechanism for modulating the TGF-β signaling pathway

Vertebrate ancient opsin photopigment spectra and the avian photoperiodic response

In mammals, photoreception is restricted to cones, rods and a subset of retinal ganglion cells. By contrast, non-mammalian vertebrates possess many extraocular photoreceptors but in many cases the role of these photoreceptors and their underlying photopigments is unknown. In birds, deep brain photoreceptors have been shown to sense photic changes in daylength (photoperiod) and mediate seasonal reproduction. Nonetheless, the specific identity of the opsin photopigment ‘sensor’ involved has remained elusive. Previously, we showed that vertebrate ancient (VA) opsin is expressed in avian hypothalamic neurons and forms a photosensitive molecule. However, a direct functional link between VA opsin and the regulation of seasonal biology was absent. Here, we report the in vivo and in vitro absorption spectra (λmax = ∼490 nm) for chicken VA photopigments. Furthermore, the spectral sensitivity of these photopigments match the peak absorbance of the avian photoperiodic response (λmax = 492 nm) and permits maximum photon capture within the restricted light environment of the hypothalamus. Such a correspondence argues strongly that VA opsin plays a key role in regulating seasonal reproduction in birds

WISE/NEOWISE observations of Active Bodies in the Main Belt

We report results based on mid-infrared photometry of 5 active main belt objects (AMBOs) detected by the Wide-field Infrared Survey Explorer (WISE) spacecraft. Four of these bodies, P/2010 R2 (La Sagra), 133P/Elst-Pizarro, (596) Scheila, and 176P/LINEAR, showed no signs of activity at the time of the observations, allowing the WISE detections to place firm constraints on their diameters and albedos. Geometric albedos were in the range of a few percent, and on the order of other measured comet nuclei. P/2010 A2 was observed on April 2-3, 2010, three months after its peak activity. Photometry of the coma at 12 and 22 {\mu}m combined with ground-based visible-wavelength measurements provides constraints on the dust particle mass distribution (PMD), dlogn/dlogm, yielding power-law slope values of {\alpha} = -0.5 +/- 0.1. This PMD is considerably more shallow than that found for other comets, in particular inbound particle fluence during the Stardust encounter of comet 81P/Wild 2. It is similar to the PMD seen for 9P/Tempel 1 in the immediate aftermath of the Deep Impact experiment. Upper limits for CO2 & CO production are also provided for each AMBO and compared with revised production numbers for WISE observations of 103P/Hartley 2.Comment: 32 Pages, including 5 Figure

AR2, a novel automatic muscle artifact reduction software method for ictal EEG interpretation: Validation and comparison of performance with commercially available software.

Objective: To develop a novel software method (AR2) for reducing muscle contamination of ictal scalp electroencephalogram (EEG), and validate this method on the basis of its performance in comparison to a commercially available software method (AR1) to accurately depict seizure-onset location. Methods: A blinded investigation used 23 EEG recordings of seizures from 8 patients. Each recording was uninterpretable with digital filtering because of muscle artifact and processed using AR1 and AR2 and reviewed by 26 EEG specialists. EEG readers assessed seizure-onset time, lateralization, and region, and specified confidence for each determination. The two methods were validated on the basis of the number of readers able to render assignments, confidence, the intra-class correlation (ICC), and agreement with other clinical findings. Results: Among the 23 seizures, two-thirds of the readers were able to delineate seizure-onset time in 10 of 23 using AR1, and 15 of 23 using AR2 (

Importance of Indigenous Peoples' lands for the conservation of Intact Forest Landscapes

Intact Forest Landscapes (IFLs) are critical strongholds for the environmental services that they provide, not least for their role in climate protection. On the basis of information about the distributions of IFLs and Indigenous Peoples’ lands, we examined the importance of these areas for conserving the world's remaining intact forests. We determined that at least 36% of IFLs are within Indigenous Peoples’ lands, making these areas crucial to the mitigation action needed to avoid catastrophic climate change. We also provide evidence that IFL loss rates have been considerably lower on Indigenous Peoples’ lands than on other lands, although these forests are still vulnerable to clearing and other threats. World governments must recognize Indigenous Peoples’ rights, including land tenure rights, to ensure that Indigenous Peoples play active roles in decision‐making processes that affect IFLs on their lands. Such recognition is critical given the urgent need to reduce deforestation rates in the face of escalating climate change and global biodiversity loss.Intact Forest Landscapes (IFLs) are critical strongholds for the environmental services that they provide, not least for their role in climate protection. On the basis of information about the distributions of IFLs and Indigenous Peoples' lands, we examined the importance of these areas for conserving the world's remaining intact forests. We determined that at least 36% of IFLs are within Indigenous Peoples' lands, making these areas crucial to the mitigation action needed to avoid catastrophic climate change. We also provide evidence that IFL loss rates have been considerably lower on Indigenous Peoples' lands than on other lands, although these forests are still vulnerable to clearing and other threats. World governments must recognize Indigenous Peoples' rights, including land tenure rights, to ensure that Indigenous Peoples play active roles in decision-making processes that affect IFLs on their lands. Such recognition is critical given the urgent need to reduce deforestation rates in the face of escalating climate change and global biodiversity loss.Peer reviewe

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behavior

<div><p>A calibrated computational model reflects behaviours that are expected or observed in a complex system, providing a baseline upon which sensitivity analysis techniques can be used to analyse pathways that may impact model responses. However, calibration of a model where a behaviour depends on an intervention introduced after a defined time point is difficult, as model responses may be dependent on the conditions at the time the intervention is applied. We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML). ASPASIA can generate and modify models using SBML solver output as an initial parameter set, allowing interventions to be applied once a steady state has been reached. Additionally, multiple SBML models can be generated where a subset of parameter values are perturbed using local and global sensitivity analysis techniques, revealing the model’s sensitivity to the intervention. To illustrate the capabilities of ASPASIA, we demonstrate how this tool has generated novel hypotheses regarding the mechanisms by which Th17-cell plasticity may be controlled <i>in vivo</i>. By using ASPASIA in conjunction with an SBML model of Th17-cell polarisation, we predict that promotion of the Th1-associated transcription factor T-bet, rather than inhibition of the Th17-associated transcription factor ROR<i>γ</i>t, is sufficient to drive switching of Th17 cells towards an IFN-<i>γ</i>-producing phenotype. Our approach can be applied to all SBML-encoded models to predict the effect that intervention strategies have on system behaviour. ASPASIA, released under the Artistic License (2.0), can be downloaded from <a href="http://www.york.ac.uk/ycil/software" target="_blank">http://www.york.ac.uk/ycil/software</a>.</p></div

SPON1 is associated with amyloid-β and APOE ϵ4-related cognitive decline in cognitively normal adults

Background: Genetic variation in Spondin-1, specifically rs11023139, has been associated with reduced rates of cognitive decline in individuals with Alzheimer\u27s disease. Objective: The aim of this study was to assess whether the association was present in cognitively normal older adults. Methods: Longitudinal cognitive decline was investigated using linear mixed modelling in a cohort of 590 cognitively normal older adults enrolled in the Australian Imaging, Biomarkers and Lifestyle Study. Results: No independent effect of Spondin-1 rs11023139 on cognitive decline was observed. However, significant associations were observed for the interaction between Apolipoprotein E (APOE) ϵ4 and rs11023139 in individuals with high amyloid-β burden. APOE ϵ4/rs11023139-A carriers declined significantly faster than APOE ϵ4/rs11023139-G-G carriers in measures of global cognition (p=0.011) and verbal episodic memory (p=0.020). Conclusion: These results suggest that carriage of the Spondin-1 rs11023139-A allele significantly contributes to a worsening of cognitive performance in APOE ϵ4 cognitively normal older adults with a high neocortical amyloid-β burden