Conceptualization and Application of Deep Learning and Applied Statistics for Flight Plan Recommendation

The Air Forces Pilot Training Next (PTN) program seeks a more efficient pilot training environment emphasizing the use of virtual reality flight simulators alongside periodic real aircraft experience. The PTN program wants to accelerate the training pace and progress in undergraduate pilot training compared to traditional undergraduate pilot training. Currently, instructor pilots spend excessive time planning and scheduling flights. This research focuses on methods to auto-generate the planning of in-flight events using hybrid filtering and deep learning techniques. The resulting approach captures temporal trends of user-specific and program-wide student performance to recommend a feasible set of graded flight events for evaluation in a student’s next training exercise to improve their progress toward fully qualified status

Remote sensing of transpiration and heat fluxes using multi-angle observations

Surface energy balance is a major determinant of land surface temperature and the Earth's climate. To date, there is no approach that can produce effective, physically consistent, global and multi-decadal energy–water flux data over land. Net radiation (R[subscript n]) can be quantified regionally using satellite retrievals of surface reflectance and thermal emittance with errors b10%. However, consistent, useful retrieval of latent heat flux (λE) from remote sensing is not yet possible. In theory, λE could be inferred as a residual of R[subscript n], ground heat (G) and sensible heat (H) fluxes (R[subscript n]–H–G). However, large uncertainties in remote sensing of both H and G result in low accuracies for λE. Where vegetation is the dominant surface cover, λE is largely driven by transpiration of intercellular water through leaf stomata during the photosynthetic uptake of carbon. In these areas, satellite retrievals of photosynthesis (GPP) could be used to quantify transpiration rates through stomatal conductance. Here, we demonstrate how remote sensing of GPP could be applied to obtain λE from passive optical measurements of vegetation leaf reflectance related to the photosynthetic rate independent of knowledge of H, R[subscript n] and G. We validate the algorithm using five structurally and physiologically diverse eddy flux sites in western and central Canada. Results show that transpiration and H were accurately predicted from optical data and highly significant relationships were found between the energy budget obtained from eddy flux measurements and remote sensing (0.64 ≤ r² ≤ 0.85). We conclude that spaceborne estimates of GPP could significantly improve not only estimates of the carbon balance but also the energy balance over land.This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.elsevier.com/Keywords: Multi-angle remote sensing AMSPEC, Ball–Berry relationship, Transpiration, GPP, Stomatal conductanc

An expert-based system to predict population survival rate from health data

This work was supported by the Office of Naval Research Marine Mammal Biology Program [grant number N00014-17-1-2868].Timely detection and understanding of causes for population decline are essential for effective wildlife management and conservation. Assessing trends in population size has been the standard approach but we propose that monitoring population health could prove more effective. We collated data from seven bottlenose dolphin (Tursiops truncatus) populations in southeastern U.S. to develop the Veterinary Expert System for Outcome Prediction (VESOP), which estimates survival probability using a suite of health measures identified by experts as indices for inflammatory, metabolic, pulmonary, and neuroendocrine systems. VESOP was implemented using logistic regression within a Bayesian analysis framework, and parameters were fit using records from five of the sites that had a robust stranding network and frequent photographic identification (photo-ID) surveys to document definitive survival outcomes. We also conducted capture-mark-recapture (CMR) analyses of photo-ID data to obtain separate estimates of population survival rates for comparison with VESOP survival estimates. VESOP analyses found multiple measures of health, particularly markers of inflammation, were predictive of 1- and 2-year individual survival. The highest mortality risk one year following health assessment related to low alkaline phosphatase, with an odds ratio of 10.2 (95% CI 3.41-26.8), while 2-year mortality was most influenced by elevated globulin (9.60; 95% CI 3.88-22.4); both are markers of inflammation. The VESOP model predicted population-level survival rates that correlated with estimated survival rates from CMR analyses for the same populations (1-year Pearson's r = 0.99; p = 1.52e-05, 2-year r = 0.94; p = 0.001). While our proposed approach will not detect acute mortality threats that are largely independent of animal health, such as harmful algal blooms, it is applicable for detecting chronic health conditions that increase mortality risk. Random sampling of the population is important and advancement in remote sampling methods could facilitate more random selection of subjects, obtainment of larger sample sizes, and extension of the approach to other wildlife species.Publisher PDFPeer reviewe

Lower limb ischemic preconditioning combined with dietary nitrate supplementation does not influence time-trial performance in well-trained cyclists

OBJECTIVES: Dietary nitrate (NO3-) supplementation and ischaemic preconditioning (IPC) can independently improve exercise performance. The purpose of this study was to explore whether NO3- supplementation, ingested prior to an IPC protocol, could synergistically enhance parameters of exercise.DESIGN: Double-blind randomized crossover trial.METHODS: Ten competitive male cyclists (age 34±6years, body mass 78.9±4.9kg, V⋅O2peak 55±4 mLkgmin-1) completed an incremental exercise test followed by three cycling trials comprising a square-wave submaximal component and a 16.1km time-trial. Oxygen uptake (V⋅O2) and muscle oxygenation kinetics were measured throughout. The baseline (BASE) trial was conducted without any dietary intervention or IPC. In the remaining two trials, participants received 3×5min bouts of lower limb bilateral IPC prior to exercise. Participants ingested NO3--rich gel (NIT+IPC) 90min prior to testing in one trial and a low NO3- placebo in the other (PLA+IPC). Plasma NO3- and nitrite (NO2-) were measured immediately before and after application of IPC.RESULTS: Plasma [NO3-] and [NO2-] were higher before and after IPC in NIT+IPC compared to BASE (P0.4). Performance in the time-trial was similar between trials (BASE 1343±72s, PLA+IPC 1350±75s, NIT+IPC 1346±83s, P=0.98).CONCLUSIONS: Pre-exercise IPC did not improve sub-maximal exercise or performance measures, either alone or in combination with dietary NO3- supplementation

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

Functional Copy-Number Alterations in Cancer

Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples. Computational analysis is needed (1) to deduce from raw array data actual amplification or deletion events for chromosomal fragments and (2) to distinguish causal chromosomal alterations from functionally neutral ones. We present a comprehensive computational approach, RAE, designed to robustly map chromosomal alterations in tumor samples and assess their functional importance in cancer. To demonstrate the methodology, we experimentally profile copy number changes in a clinically aggressive subtype of soft-tissue sarcoma, pleomorphic liposarcoma, and computationally derive a portrait of candidate oncogenic alterations and their target genes. Many affected genes are known to be involved in sarcomagenesis; others are novel, including mediators of adipocyte differentiation, and may include valuable therapeutic targets. Taken together, we present a statistically robust methodology applicable to high-resolution genomic data to assess the extent and function of copy-number alterations in cancer

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled duplications contain protein-coding genes that are mostly involved in reproductive function