Shedding Light on Photosynthesis: The Impacts of Atmospheric Conditions and Plant Canopy Structure on Ecosystem Carbon Uptake.

The Earth’s climate is influenced by complex interactions of physical, chemical, and biological processes that link terrestrial ecosystems and the atmosphere. One of these interactions involves the use of light in photosynthesis, which allows plants to remove CO2 from the atmosphere and slow the unprecedented rate of climate change the Earth is experiencing. However, modeling future climate remains challenging, in part because of limited knowledge of mechanisms controlling the effects of light on gross ecosystem CO2 uptake (conceptually, photosynthetic activity integrated across all leaves in a plant canopy). Unlike previous studies, this dissertation uses data from atmospheric science, ecosystem ecology, and plant physiology to provide evidence for mechanistic links between physical, biophysical, and ecological controls on the effects of light on processes tied to gross ecosystem CO2 uptake—specifically, ecosystem gross primary production (GPP) and leaf photosynthesis. First, this dissertation empirically demonstrates that the dominant effect of clouds is to reduce total light above canopies. However, optically thin clouds increase scattered, diffuse light, which canopies use more efficiently than they use direct light. This offsets reductions in total light and results in no net change in GPP under thin clouds, while GPP decreases under optically thick clouds because both diffuse and direct light decrease. Second, ground-based measurements indicate that the rate of increase in GPP with diffuse light changes throughout the day. The magnitude of increase depends on how canopies interact with the angle of incoming light to biophysically alter the distribution of light within canopies and thus, the proportions of leaves contributing to GPP. Third, the distribution of species and light within one forest canopy leads to differences in some of the rate-limiting biochemical reactions in leaf photosynthesis. These field-based data indicate which assumptions representing canopies in Earth system models may not have support in situ, and could be contributing to errors in model estimates of future climate. Overall, this dissertation identifies mechanisms through which clouds and plant canopy structure alter land-atmosphere CO2 fluxes and subsequently, Earth’s climate. It also provides an important interdisciplinary framework for testing assumptions about the feedbacks that living organisms form with their environment.PhDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133446/1/chengs_1.pd

Cleaved end-face quality of microstructured polymer optical fibres

The cutting of a microstructured polymer optical fibre to form an optical end-face is studied. The effect of the temperature and speed of the cutting blade on the end-face is qualitatively assessed and it is found that for fibres at temperatures in the range 70–90 C, a blade at a similar temperature moving at a speed of less than 0.5 mm/s produces a good quality end-face. The nature of the damage caused by the cutting process was examined and found to vary with fibre temperature, blade quality and cut depth. Thermo-mechanical analysis showed that the drawn material was significantly more visco-elastic than the annealed raw material in the 70-90 C temperature range. The behaviour of the surface damage with cut depth was found to be consistent with the behaviour of a visco-elastic material

Mutational Analysis in Pediatric Thyroid Cancer and Correlations with Age, Ethnicity, and Clinical Presentation.

BackgroundWell-differentiated thyroid cancer (WDTC) incidence in pediatrics is rising, most being papillary thyroid carcinoma (PTC). The objective of the study was to assess the prevalence of different mutations in pediatric WDTC and correlate the genotype with the clinical phenotype.MethodsThis is a single-center retrospective study. Thyroid tissue blocks from 42 consecutive pediatric WDTC patients who underwent thyroidectomy between 2001 and 2013 were analyzed at Quest Diagnostics for BRAF(V600E), RAS mutations (N,K,H), and RET/PTC and PAX8/PPARγ rearrangements, using validated molecular methods. Thyroid carcinomas included PTC, follicular thyroid carcinoma (FTC), and follicular variant of PTC (FVPTC).ResultsThirty-nine samples (29 females) were genotyped. The mean age at diagnosis was 14.7 years (range 7.9-18.4 years), and most were Hispanic (56.4%) or Caucasian (35.9%). The mean follow-up period was 2.9 years. Mutations were noted in 21/39 (53.8%), with both BRAF(V600E) (n = 9), and RET/PTC (n = 6) detected only in PTC. Mutations were detected in 2/5 FTC (PAX8/PPARγ and NRAS) and 3/6 FVPTC cases (PAX8/PPARγ). Of 28 PTC patients, 57.1% had mutations: 32.1% with BRAF(V600E), 21.4% with RET/PTC, and 3.6% with NRAS. Of patients with BRAF(V600E), 77.8% were Hispanic and 88.9% were >15 years, while all RET/PTC-positive patients were ≤15 years (p = 0.003). Tumor size, lymph node involvement, and distant metastasis at diagnosis (or soon after (131)I ablation) did not vary significantly based on the mutation.ConclusionsBRAF(V600E) was the most common mutation, especially in older and Hispanic adolescents. A larger, ethnically diverse pediatric cohort followed long term will enable the genotypic variability, clinical presentation, and response to therapy to be better assessed

Processes of Care Associated With Risk of Mortality and Recurrent Stroke Among Patients With Transient Ischemic Attack and Nonsevere Ischemic Stroke

Importance: Early evaluation and management of patients with transient ischemic attack (TIA) and nonsevere ischemic stroke improves outcomes. Objective: To identify processes of care associated with reduced risk of death or recurrent stroke among patients with TIA or nonsevere ischemic stroke. Design, Setting, and Participants: This cohort study included all patients with TIA or nonsevere ischemic stroke at Department of Veterans Affairs emergency department or inpatient settings from October 2010 to September 2011. Multivariable logistic regression was used to model associations of processes of care and without-fail care, defined as receiving all guideline-concordant processes of care for which patients are eligible, with risk of death and recurrent stroke. Data were analyzed from March 2018 to April 2019. Main Outcomes and Measures: Risk of all-cause mortality and recurrent ischemic stroke at 90 days and 1 year was calculated. Overall, 28 processes of care were examined. Without-fail care was assessed for 6 processes: brain imaging, carotid artery imaging, hypertension medication intensification, high- or moderate-potency statin therapy, antithrombotics, and anticoagulation for atrial fibrillation. Results: Among 8076 patients, the mean (SD) age was 67.8 (11.6) years, 7752 patients (96.0%) were men, 5929 (73.4%) were white, 474 (6.1%) had a recurrent ischemic stroke within 90 days, 793 (10.7%) had a recurrent ischemic stroke within 1 year, 320 (4.0%) died within 90 days, and 814 (10.1%) died within 1 year. Overall, 9 processes were independently associated with lower odds of both 90-day and 1-year mortality after adjustment for multiple comparisons: carotid artery imaging (90-day adjusted odds ratio [aOR], 0.49; 95% CI, 0.38-0.63; 1-year aOR, 0.61; 95% CI, 0.52-0.72), antihypertensive medication class (90-day aOR, 0.58; 95% CI, 0.45-0.74; 1-year aOR, 0.70; 95% CI, 0.60-0.83), lipid measurement (90-day aOR, 0.68; 95% CI, 0.51-0.90; 1-year aOR, 0.64; 95% CI, 0.53-0.78), lipid management (90-day aOR, 0.46; 95% CI, 0.33-0.65; 1-year aOR, 0.67; 95% CI, 0.53-0.85), discharged receiving statin medication (90-day aOR, 0.51; 95% CI, 0.36-0.73; 1-year aOR, 0.70; 95% CI, 0.55-0.88), cholesterol-lowering medication intensification (90-day aOR, 0.47; 95% CI, 0.26-0.83; 1-year aOR, 0.56; 95% CI, 0.41-0.77), antithrombotics by day 2 (90-day aOR, 0.56; 95% CI, 0.40-0.79; 1-year aOR, 0.69; 95% CI, 0.55-0.87) or at discharge (90-day aOR, 0.59; 95% CI, 0.41-0.86; 1-year aOR, 0.69; 95% CI, 0.54-0.88), and neurology consultation (90-day aOR, 0.67; 95% CI, 0.52-0.87; 1-year aOR, 0.74; 95% CI, 0.63-0.87). Anticoagulation for atrial fibrillation was associated with lower odds of 1-year mortality only (aOR, 0.59; 95% CI, 0.40-0.85). No processes were associated with reduced risk of recurrent stroke after adjustment for multiple comparisons. The rate of without-fail care was 15.3%; 1216 patients received all guideline-concordant processes of care for which they were eligible. Without-fail care was associated with a 31.2% lower odds of 1-year mortality (aOR, 0.69; 95% CI, 0.55-0.87) but was not independently associated with stroke risk. Conclusions and Relevance: Patients who received 6 readily available processes of care had lower adjusted mortality 1 year after TIA or nonsevere ischemic stroke. Clinicians caring for patients with TIA and nonsevere ischemic stroke should seek to ensure that patients receive all guideline-concordant processes of care for which they are eligible

A Single Visualization Technique for Displaying Multiple Metabolite-Phenotype Associations.

To assist with management and interpretation of human metabolomics data, which are rapidly increasing in quantity and complexity, we need better visualization tools. Using a dataset of several hundred metabolite measures profiled in a cohort of ~1500 individuals sampled from a population-based community study, we performed association analyses with eight demographic and clinical traits and outcomes. We compared frequently used existing graphical approaches with a novel 'rain plot' approach to display the results of these analyses. The 'rain plot' combines features of a raindrop plot and a conventional heatmap to convey results of multiple association analyses. A rain plot can simultaneously indicate effect size, directionality, and statistical significance of associations between metabolites and several traits. This approach enables visual comparison features of all metabolites examined with a given trait. The rain plot extends prior approaches and offers complementary information for data interpretation. Additional work is needed in data visualizations for metabolomics to assist investigators in the process of understanding and convey large-scale analysis results effectively, feasibly, and practically