AN IMPROVED ESTIMATOR FOR ASSESSING THE MEASURE OF AGREEMENT WITH A GOLD STANDARD

St. Laurent (1998, Biometrics 54, 537-545) developed a measure of agreement for method comparison studies in which an approximate method of measurement is compared to a gold standard method of measurement. The measure of agreement proposed was shown to be related to a population intraclass correlation coefficient. This paper develops a family of estimators for the measure of agreement based on pivotal quantities. A blend of two particular members of the family is suggested as an estimator itself. In general, this estimator outperforms the maximum likelihood estimator in terms of bias and mean-squared error

Biases in Thorpe-scale estimates of turbulence dissipation. Part I : Assessments from large-scale overturns in oceanographic data

Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2497–2521, doi:10.1175/JPO-D-14-0128.1.Oceanic density overturns are commonly used to parameterize the dissipation rate of turbulent kinetic energy. This method assumes a linear scaling between the Thorpe length scale LT and the Ozmidov length scale LO. Historic evidence supporting LT ~ LO has been shown for relatively weak shear-driven turbulence of the thermocline; however, little support for the method exists in regions of turbulence driven by the convective collapse of topographically influenced overturns that are large by open-ocean standards. This study presents a direct comparison of LT and LO, using vertical profiles of temperature and microstructure shear collected in the Luzon Strait—a site characterized by topographically influenced overturns up to O(100) m in scale. The comparison is also done for open-ocean sites in the Brazil basin and North Atlantic where overturns are generally smaller and due to different processes. A key result is that LT/LO increases with overturn size in a fashion similar to that observed in numerical studies of Kelvin–Helmholtz (K–H) instabilities for all sites but is most clear in data from the Luzon Strait. Resultant bias in parameterized dissipation is mitigated by ensemble averaging; however, a positive bias appears when instantaneous observations are depth and time integrated. For a series of profiles taken during a spring tidal period in the Luzon Strait, the integrated value is nearly an order of magnitude larger than that based on the microstructure observations. Physical arguments supporting LT ~ LO are revisited, and conceptual regimes explaining the relationship between LT/LO and a nondimensional overturn size are proposed. In a companion paper, Scotti obtains similar conclusions from energetics arguments and simulations.B.D.M. and S.K.V. gratefully acknowledge the support of the Office of Naval Research under Grants N00014-12-1-0279, N00014-12-1-0282, and N00014-12-1-0938 (Program Manager: Dr. Terri Paluszkiewicz). S.K.V. also acknowledges support of the National Science Foundation under Grant OCE-1151838. L.S.L. acknowledges support for BBTRE by the National Science Foundation by Contract OCE94-15589 and NATRE and IWISE by the Office of Naval Research by Contracts N00014-92-1323 and N00014-10-10315. J.N.M. was supported through Grant 1256620 from the National Science Foundation and the Office of Naval Research (IWISE Project).2016-04-0

Conservation status of caribou in the western mountains of Canada: Protections under the species at risk act, 2002-2014

In April 2014, the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) reviewed the status of caribou in the western mountains of Canada, in keeping with the ten-year reassessment mandate under the Species at Risk Act. Assessed as two ‘nationally significant’ populations in 2002, COSEWIC revised the conservation units for all caribou in Canada, recognising eleven extant Designatable Units (DUs), three of which -- Northern Mountain, Central Mountain, and Southern Mountain -- are found only in western Canada. The 2014 assessment concluded that the condition of many subpopulations in all three DUs had deteriorated. As a result of small and declining population sizes, the Central Mountain and Southern Mountain DUs are now recognised as endangered. Recent declines in a number of Northern Mountain DU subpopulations did not meet thresholds for endangered or threatened, and were assessed as of special concern. Since the passage of the federal Species at Risk Act in 2002, considerable areas of habitat were managed or conserved for caribou, although disturbance from cumulative human development activities has increased during the same period. Government agencies and local First Nations are attempting to arrest the steep decline of some subpopulations by using predator control, maternal penning, population augmentation, and captive breeding. Based on declines, future developments and current recovery effects, we offer the following recommendations: 1) where recovery actions are necessary, commit to simultaneously reducing human intrusion into caribou ranges, restoring habitat over the long term, and conducting short-term predator control, 2) carefully consider COSEWIC’s new DU structure for management and recovery actions, especially regarding translocations, 3) carry out regular surveys to monitor the condition of Northern Mountain caribou subpopulations and immediately implement preventative measures where necessary, and 4) undertake a proactive, planned approach coordinated across jurisdictions to conserve landscape processes important to caribou conservation

Even Between-Lap Pacing Despite High Within-Lap Variation During Mountain Biking

Purpose: Given the paucity of research on pacing strategies during competitive events, this study examined changes in dynamic high-resolution performance parameters to analyze pacing profiles during a multiple-lap mountain-bike race over variable terrain. Methods: A global-positioning-system (GPS) unit (Garmin, Edge 305, USA) recorded velocity (m/s), distance (m), elevation (m), and heart rate at 1 Hz from 6 mountain-bike riders (mean ± SD age = 27.2 ± 5.0 y, stature = 176.8 ± 8.1 cm, mass = 76.3 ± 11.7 kg, VO2max = 55.1 ± 6.0 mL · kg–1 . min–1) competing in a multilap race. Lap-by-lap (interlap) pacing was analyzed using a 1-way ANOVA for mean time and mean velocity. Velocity data were averaged every 100 m and plotted against race distance and elevation to observe the presence of intralap variation. Results: There was no significant difference in lap times (P = .99) or lap velocity (P = .65) across the 5 laps. Within each lap, a high degree of oscillation in velocity was observed, which broadly reflected changes in terrain, but high-resolution data demonstrated additional nonmonotonic variation not related to terrain. Conclusion: Participants adopted an even pace strategy across the 5 laps despite rapid adjustments in velocity during each lap. While topographical and technical variations of the course accounted for some of the variability in velocity, the additional rapid adjustments in velocity may be associated with dynamic regulation of self-paced exercise

Impacts of Atmospheric Nitrogen Deposition on Surface Waters of the Western North Atlantic Mitigated by Multiple Feedbacks

The impacts of atmospheric nitrogen deposition (AND) on the chlorophyll and nitrogen dynamics of surface waters in the western North Atlantic (25 degrees N-45 degrees N, 65 degrees W-80 degrees W) are examined with a biogeochemical ocean model forced with a regional atmospheric chemistry model (Community Multiscale Air Quality, CMAQ). CMAQ simulations with year-specific emissions reveal the existence of a hot spot of AND over the Gulf Stream. The impact of the hot spot on the oceanic biogeochemistry is mitigated in three ways by physical and biogeochemical processes. First, AND significantly contributes to surface oceanic nitrogen concentrations only during the summer period, when the stratification is maximal and the background nitrogen inventories are minimal. Second, the increase in summer surface nitrate concentrations is accompanied by a reduction in upward nitrate diffusion at the base of the surface layer. This negative feedback partly cancels the nitrogen enrichment from AND. Third, gains in biomass near the surface force a shoaling of the euphotic layer and a reduction of about 5% in deep primary production and biomass on the continental shelf. Despite these mitigating processes, the impacts of AND remain substantial. AND increases surface nitrate concentrations in the Gulf Stream region by 14% during the summer (2% on average over the year). New primary production increases by 22% in this region during summer (8% on average). Although these changes may be difficult to distinguish from natural variability in observations, the results support the view that AND significantly enhances local carbon export

Epoxide-Mediated CifR Repression of cif Gene Expression Utilizes Two Binding Sites in Pseudomonas aeruginosa

Pseudomonas aeruginosa secretes an epoxide hydrolase virulence factor that reduces the apical membrane expression of ABC transporters such as the cystic fibrosis transmembrane conductance regulator (CFTR). This virulence factor, named CFTR inhibitory factor (Cif), is regulated by a TetR-family, epoxide-responsive repressor known as CifR via direct binding and repression. We identified two sites of CifR binding in the intergenic space between cifR and morB, the first gene in the operon containing the cif gene. We have mapped these binding sites and found they are 27 bp in length, and they overlap the -10 and +1 sites of both the cifR and morB regulatory region and the start of transcription, respectively. In addition, we found that CifR binds to each repression site with differing affinity. Mutagenesis of these binding sites resulted in a loss of DNA binding in vitro, and mutation of one of these sites in vivo resulted in an increase in transcription of both the cif and cifR genes. We characterized cif and cifR gene expression in sputum and found that, whereas cif gene expression varied relative to an in vitro coculture control, cifR gene expression was consistently higher. Analysis of a longitudinal sample of CF isolates from nine patients revealed that Cif protein was expressed over time, although variably, and these changes could not be linked to mutations in the cifR gene or the promoters of these genes. Finally, we tested CifR responsiveness to other epoxides and showed that CifR can respond to multiple epoxides to various degrees

A deeper look at the association between childhood maltreatment and reflective functioning

Childhood maltreatment is theorized as impeding the development of reflective functioning (RF; ability to perceive and interpret oneself and others in terms of mental states). However, previous research typically failed to support this association or yielded small sized and mixed associations. This study aims to provide a deeper look at the association between childhood maltreatment and RF by characterizing two non-mentalizing categories. One-hundred-and-sixteen pregnant women (mean age = 27.62, SD = 4.52) from the community (48.3% with a university degree, 96.5% in a relationship with the other parent) retrospectively reported on childhood abuse and neglect using the Childhood Trauma Questionnaire. They also participated in the Adult Attachment Interview subsequently coded using the Reflective Functioning Scale. Participants with poor to low RF were allocated to one of two groups (disavowal-distancing or distorted-inconsistent) using indicators provided in the RF Scale. No association was found between childhood maltreatment and overall RF when controlling for education level. A multinomial logistic regression revealed that childhood maltreatment was strongly predictive of a disrupted, over-analytical and inconsistent reflection about mental states but not of a tendency to discourse little about mental states. This tendency was rather only predicted by education level. Findings suggest that childhood maltreatment would lead to specific impairments in RF and that not considering how individuals fail to mentalize about attachment relationships may mask strong associations between RF and its determinants and correlates, including childhood maltreatment

Hypothermic retrograde venous perfusion with adenosine cools the spinal cord and reduces the risk of paraplegia after thoracic aortic clamping

AbstractObjective: We evaluated the utility of retrograde venous perfusion to cool the spinal cord and protect neurologic function during aortic clamping. We hypothesized that hypothermic adenosine would preserve the spinal cord during ischemia. Methods: Six swine (group I) underwent thoracic aortic occlusion for 30 minutes at normothermia. Group II animals underwent spinal cooling by retrograde perfusion of the paravertebral veins with hypothermic (4°C) saline solution during aortic occlusion. The spinal cords of group III animals were cooled with a hypothermic adenosine solution in a similar fashion. Intrathecal temperature was monitored and somatosensory evoked potentials assessed the functional status of spinal pathways. Results: Spinal cooling without systemic hypothermia significantly improved neurologic Tarlov scores in group III (4.8 ± 0.2) and group II (3.8 ± 0.4) when compared with group I scores (1.3 ± 0.6) (P < .001). Furthermore, 5 of the 6 animals in group III displayed completely normal neurologic function, whereas only one animal in group II and no animals in group I did (P = .005). Somatosensory evoked potentials were lost 10.6 ± 1.4 minutes after ischemia in group I. In contrast, spinal cooling caused rapid cessation of neural transmission with loss of somatosensory evoked potentials at 6.9 ± 1.2 minutes in group II and 7.0 ± 0.8 minutes in group III (P = .06). Somatosensory evoked potential amplitudes returned to 85% of baseline in group III and 90% of baseline in group II compared with only 10% of baseline in group I (P = .01). Conclusions: We conclude that retrograde cooling of the spinal cord is possible and protects against ischemic injury and that adenosine enhances this effect. The efficacy of this method may be at least partly attributed to a more rapid reduction in metabolic and electrical activity of the spinal cord during ischemia. (J Thorac Cardiovasc Surg 2000;119:588-95