Corn Monoculture: No Friend of Biodiversity

Federal mandates for corn ethanol, which encourage farmers to plant more corn, may threaten the biodiversity of grasslands

Effects of Training Set Size on Supervised Machine-Learning Land-Cover Classification of Large-Area High-Resolution Remotely Sensed Data

The size of the training data set is a major determinant of classification accuracy. Neverthe- less, the collection of a large training data set for supervised classifiers can be a challenge, especially for studies covering a large area, which may be typical of many real-world applied projects. This work investigates how variations in training set size, ranging from a large sample size (n = 10,000) to a very small sample size (n = 40), affect the performance of six supervised machine-learning algo- rithms applied to classify large-area high-spatial-resolution (HR) (1–5 m) remotely sensed data within the context of a geographic object-based image analysis (GEOBIA) approach. GEOBIA, in which adjacent similar pixels are grouped into image-objects that form the unit of the classification, offers the potential benefit of allowing multiple additional variables, such as measures of object geometry and texture, thus increasing the dimensionality of the classification input data. The six supervised machine-learning algorithms are support vector machines (SVM), random forests (RF), k-nearest neighbors (k-NN), single-layer perceptron neural networks (NEU), learning vector quantization (LVQ), and gradient-boosted trees (GBM). RF, the algorithm with the highest overall accuracy, was notable for its negligible decrease in overall accuracy, 1.0%, when training sample size decreased from 10,000 to 315 samples. GBM provided similar overall accuracy to RF; however, the algorithm was very expensive in terms of training time and computational resources, especially with large training sets. In contrast to RF and GBM, NEU, and SVM were particularly sensitive to decreasing sample size, with NEU classifications generally producing overall accuracies that were on average slightly higher than SVM classifications for larger sample sizes, but lower than SVM for the smallest sample sizes. NEU however required a longer processing time. The k-NN classifier saw less of a drop in overall accuracy than NEU and SVM as training set size decreased; however, the overall accuracies of k-NN were typically less than RF, NEU, and SVM classifiers. LVQ generally had the lowest overall accuracy of all six methods, but was relatively insensitive to sample size, down to the smallest sample sizes. Overall, due to its relatively high accuracy with small training sample sets, and minimal variations in overall accuracy between very large and small sample sets, as well as relatively short processing time, RF was a good classifier for large-area land-cover classifications of HR remotely sensed data, especially when training data are scarce. However, as performance of different supervised classifiers varies in response to training set size, investigating multiple classification algorithms is recommended to achieve optimal accuracy for a project

Model studies on the role of moist convection as a mechanism for interaction between the mesoscales

A three year research effort is described which had as its goal the development of techniques to improve the numerical prediction of cumulus convection on the meso-beta and meso-gamma scales. Two MESO models are used, the MASS (mesoscale) and TASS (cloud scale) models. The primary meteorological situation studied is the 28-29 Jun. 1986 Cooperative Huntsville Meteorological Experiment (COHMEX) study area on a day with relatively weak large scale forcing. The problem of determining where and when convection should be initiated is considered to be a major problem of current approaches. Assimilation of moisture data from satellite, radar, and surface data is shown to significantly improve mesoscale simulations. The TASS model is shown to reproduce some observed mesoscale features when initialized with 3-D observational data. Convection evolution studies center on comparison of the Kuo and Fritsch-Chappell cumulus parameterization schemes to each other, and to cloud model results. The Fritsch-Chappell scheme is found to be superior at about 30 km resolution, while the Kuo scheme does surprisingly well in simulating convection down to 10 km in cases where convergence features are well-resolved by the model grid. Results from MASS-TASS interaction experiments are presented and discussed. A discussion of the future of convective simulation is given, with the conclusion that significant progress is possible on several fronts in the next few years

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Internal and external cooling methods and their effect on body temperature, thermal perception and dexterity

© 2018 The Authors. Published by PLOS. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1371/journal.pone.0191416© 2018 Maley et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Objective The present study aimed to compare a range of cooling methods possibly utilised by occupational workers, focusing on their effect on body temperature, perception and manual dexterity. Methods Ten male participants completed eight trials involving 30 min of seated rest followed by 30 min of cooling or control of no cooling (CON) (34C, 58% relative humidity). The cooling methods utilised were: ice cooling vest (CV0), phase change cooling vest melting at 14C (CV14), evaporative cooling vest (CVEV), arm immersion in 10C water (AI), portable water-perfused suit (WPS), heliox inhalation (HE) and ice slushy ingestion (SL). Immediately before and after cooling, participants were assessed for fine (Purdue pegboard task) and gross (grip and pinch strength) manual dexterity. Rectal and skin temperature, as well as thermal sensation and comfort, were monitored throughout. Results Compared with CON, SL was the only method to reduce rectal temperature (P = 0.012). All externally applied cooling methods reduced skin temperature (P0.05). Conclusion The present study observed that ice ingestion or ice applied to the skin produced the greatest effect on rectal and skin temperature, respectively. AI should not be utilised if workers require subsequent fine manual dexterity. These results will help inform future studies investigating appropriate pre-cooling methods for the occupational worker.This project is financially supported by the US Government through the Technical Support Working Group within the Combating Terrorism Technical Support Office.Published versio

The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel.

BACKGROUND: Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. A lack of clinically germane research has led to equivocal, and occasionally conflicting, healthcare respiratory protection recommendations from public health organizations, professional societies, and experts. METHODS: The Respiratory Protection Effectiveness Clinical Trial (ResPECT) is a prospective comparison of respiratory protective equipment to be conducted at multiple U.S. study sites. Healthcare personnel who work in outpatient settings will be cluster-randomized to wear N95 respirators or medical masks for protection against infections during respiratory virus season. Outcome measures will include laboratory-confirmed viral respiratory infections, acute respiratory illness, and influenza-like illness. Participant exposures to patients, coworkers, and others with symptoms and signs of respiratory infection, both within and beyond the workplace, will be recorded in daily diaries. Adherence to study protocols will be monitored by the study team. DISCUSSION: ResPECT is designed to better understand the extent to which N95s and MMs reduce clinical illness among healthcare personnel. A fully successful study would produce clinically relevant results that help clinician-leaders make reasoned decisions about protection of healthcare personnel against occupationally acquired respiratory infections and prevention of spread within healthcare systems. TRIAL REGISTRATION: The trial is registered at clinicaltrials.gov, number NCT01249625 (11/29/2010)

Collisions with Black Holes and Deconfined Plasmas

We use AdS/CFT to investigate i) high energy collisions with balls of deconfined plasma surrounded by a confining phase and ii) the rapid localized heating of a deconfined plasma. Both of these processes are dual to collisions with black holes, where they result in the nucleation of a new "arm" of the horizon reaching out in the direction of the incident object. We study the resulting non-equilibrium dynamics in a universal limit of the gravitational physics which may indicate universal behavior of deconfined plasmas at large N_c. Process (i) produces "virtual" arms of the plasma ball, while process (ii) can nucleate surprisingly large bubbles of a higher temperature phase.Comment: 25 pages, 9 figure

Self-adaptive differential evolution algorithm applied to water distribution system optimization

Differential evolution (DE) is a relatively new technique that has recently been used to optimize the design for water distribution systems (WDSs). Several parameters need to be determined in the use of DE, including population size, N; mutation weighting factor, F; crossover rate, CR, and a particular mutation strategy. It has been demonstrated that the search behavior of DE is especially sensitive to the F and CR values. These parameters need to be fine-tuned for different optimization problems because they are generally problem-dependent. A self-adaptive differential evolution (SADE) algorithm is proposed to optimize the design of WDSs. Three new contributions are included in the proposed SADE algorithm: (1) instead of pre-specification, the control parameters of F and CR are encoded into the chromosome of the SADE algorithm, and hence are adapted by means of evolution; (2) F and CR values of the SADE algorithm apply at the individual level rather than the generational level normally used by the traditional DE algorithm; and (3) a new convergence criterion is proposed for the SADE algorithm as the termination condition, thereby avoiding pre-specifying a fixed number of generations or computational budget to terminate the evolution. Four WDS case studies have been used to demonstrate the effectiveness of the proposed SADE algorithm. The results show that the proposed algorithm exhibits good performance in terms of solution quality and efficiency. The advantage of the proposed SADE algorithm is that it reduces the effort required to fine-tune algorithm parameter values.Feifei Zheng, Aaron C. Zecchin and Angus R. Simpso

Mapping Copy Number Variation by Population Scale Genome Sequencing

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.Organismic and Evolutionary Biolog