The mean and variance of phylogenetic diversity under rarefaction

Phylogenetic diversity (PD) depends on sampling intensity, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which means to take a random subset of a given size of the original sample. Exact analytical formulae for the mean and variance of species richness under rarefaction have existed for some time but no such solution exists for PD. We have derived exact formulae for the mean and variance of PD under rarefaction. We show that these formulae are correct by comparing exact solution mean and variance to that calculated by repeated random (Monte Carlo) subsampling of a dataset of stem counts of woody shrubs of Toohey Forest, Queensland, Australia. We also demonstrate the application of the method using two examples: identifying hotspots of mammalian diversity in Australasian ecoregions, and characterising the human vaginal microbiome. There is a very high degree of correspondence between the analytical and random subsampling methods for calculating mean and variance of PD under rarefaction, although the Monte Carlo method requires a large number of random draws to converge on the exact solution for the variance. Rarefaction of mammalian PD of ecoregions in Australasia to a common standard of 25 species reveals very different rank orderings of ecoregions, indicating quite different hotspots of diversity than those obtained for unrarefied PD. The application of these methods to the vaginal microbiome shows that a classical score used to quantify bacterial vaginosis is correlated with the shape of the rarefaction curve. The analytical formulae for the mean and variance of PD under rarefaction are both exact and more efficient than repeated subsampling. Rarefaction of PD allows for many applications where comparisons of samples of different depth is required.Comment: Final version to be published in Methods in Ecology and Evolutio

Diverter Decision Aiding for In-Flight Diversions

It was determined that artificial intelligence technology can provide pilots with the help they need in making the complex decisions concerning en route changes in a flight plan. A diverter system should have the capability to take all of the available information and produce a recommendation to the pilot. Phase three illustrated that using Joshua to develop rules for an expert system and a Statice database provided additional flexibility by permitting the development of dynamic weighting of diversion relevant parameters. This increases the fidelity of the AI functions cited as useful in aiding the pilot to perform situational assessment, navigation rerouting, flight planning/replanning, and maneuver execution. Additionally, a prototype pilot-vehicle interface (PVI) was designed providing for the integration of both text and graphical based information. Advanced technologies were applied to PVI design, resulting in a hierarchical menu based architecture to increase the efficiency of information transfer while reducing expected workload. Additional efficiency was gained by integrating spatial and text displays into an integrated user interface

Survival analysis of DNA mutation motifs with penalized proportional hazards

Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences encoding these antibodies to find variants with improved binding, though mutations are not distributed uniformly across sequence sites. Immunologists observe this nonuniformity to be consistent with "mutation motifs", which are short DNA subsequences that affect how likely a given site is to experience a mutation. Quantifying the effect of motifs on mutation rates is challenging: a large number of possible motifs makes this statistical problem high dimensional, while the unobserved history of the mutation process leads to a nontrivial missing data problem. We introduce an $\ell_1$-penalized proportional hazards model to infer mutation motifs and their effects. In order to estimate model parameters, our method uses a Monte Carlo EM algorithm to marginalize over the unknown ordering of mutations. We show that our method performs better on simulated data compared to current methods and leads to more parsimonious models. The application of proportional hazards to mutation processes is, to our knowledge, novel and formalizes the current methods in a statistical framework that can be easily extended to analyze the effect of other biological features on mutation rates

The Value of Integrating Evolutionary and Sociocultural Perspectives on Body Image

In our commentary, we lay out several lines of critique and commentary that we hope will challenge Davis and Arnocky to (1) consider how these points might be integrated into their model and (2) stimulate further research on these topics by scholars applying evolutionary and sociocultural lenses. For some of the critiques and questions we raise, we do not necessarily have clear answers, and we look forward to learning the Davis and Arnocky’ perspective

Kronecker Product Correlation Model and Limited Feedback Codebook Design in a 3D Channel Model

A 2D antenna array introduces a new level of control and additional degrees of freedom in multiple-input-multiple-output (MIMO) systems particularly for the so-called "massive MIMO" systems. To accurately assess the performance gains of these large arrays, existing azimuth-only channel models have been extended to handle 3D channels by modeling both the elevation and azimuth dimensions. In this paper, we study the channel correlation matrix of a generic ray-based 3D channel model, and our analysis and simulation results demonstrate that the 3D correlation matrix can be well approximated by a Kronecker production of azimuth and elevation correlations. This finding lays the theoretical support for the usage of a product codebook for reduced complexity feedback from the receiver to the transmitter. We also present the design of a product codebook based on Grassmannian line packing.Comment: 6 pages, 5 figures, to appear at IEEE ICC 201

Rural Competitiveness: Results of the 1996 Rural Manufacturing Survey

Establishments in metropolitan and nonmetropolitan locations are surprisingly similar in their adoption of new technologies, worker skill requirements, use of government programs and technical assistance, exports, and sources of financing, according to the results of a nationwide survey of 3,909 manufacturing businesses. The most widespread concern of both metro and nonmetro businesses appears to be with quality of labor. Survey respondents report rapidly increasing skill requirements, and many report problems finding qualified workers. Quality of local labor is the most frequently cited problem associated with nonmetro business locations. Access to credit, transportation, and telecommunications infrastructure is a problem of secondary importance for both metro and nonmetro respondents. Rural communities face a considerable challenge in supplying workers with needed skills. The fastest-growing skill requirements -- computer, interpersonal/teamwork, and problem-solving skills -- are not central to traditional academic instruction.rural manufacturing, sample survey, worker skills, manufacturing location, credit availability, technology adoption, Community/Rural/Urban Development,

Height and Body Mass on the Mating Market: Associations With Number of Sex Partners and Extra-Pair Sex Among Heterosexual Men and Women Aged 18–65

People with traits that are attractive on the mating market are better able to pursue their preferred mating strategy. Men who are relatively tall may be preferred by women because taller height is a cue to dominance, social status, access to resources, and heritable fitness, leading them to have more mating opportunities and sex partners. We examined height, education, age, ethnicity, and body mass index (BMI) as predictors of sexual history among heterosexual men and women (N = 60,058). The linear and curvilinear associations between self-reported height and sex partner number were small for men when controlling for education, BMI, and ethnicity (linear β = .05; curvilinear β = −.03). The mean and median number of sex partners for men of different heights were: very short (9.4; 5), short (11.0; 7), average (11.7; 7), tall (12.0; 7), very tall (12.1; 7), and extremely tall (12.3; 7). Men who were “overweight” reported a higher mean and median number of sex partners than men with other body masses. The results for men suggested limited variation in reported sex partner number across most of the height continuum, but that very short men report fewer partners than other men

α-Helical conformation in the C-terminal anchoring domains of E. coli penicillin-binding proteins 4, 5 and 6

AbstractThe E. coli low molecular mass penicillin-binding proteins (PBP's) are penicillin sensitive, enzymes involved in the terminal stages of peptidoglycan biosynthesesis. These PBP's are believed to anchor to the periplasmic face of the inner membrane via C-terminal amphiphilic α-helices but to date the only support for this hypothesis has been obtained from theoretical analysis. In this paper, the conformational behaviour of synthetic peptides corresponding to these C-terminal anchoring domains was studied as a function of solvent, pH, sodium dodecyl sulphate micelles and phospholipid (DOPC, DOPG) vesicles using circular dichroism (CD) spectroscopy. The CD data showed that in 2,2,2-trifluoroethanol or sodium dodecylsulphate, all three peptides have the capacity to form an α-helical conformation but in aqueous solution or in the presence of phospholipid vesicles only those peptides corresponding to the PBP5 and PBP6 C-termini were observed to do so. A pH dependent loss of α-helical conformation in the peptide corresponding to the PBP5 C-terminus was found to correlate with the susceptibility of PBP5 to membrane extraction. This correlation would agree with the hypothesis that an α-helical conformation is required for membrane interaction of the PBP5 C-terminal region

Midline Shift is Unrelated to Subjective Pupillary Reactivity Assessment on Admission in Moderate and Severe Traumatic Brain Injury.

BACKGROUND: This study aims to determine the relationship between pupillary reactivity, midline shift and basal cistern effacement on brain computed tomography (CT) in moderate-to-severe traumatic brain injury (TBI). All are important diagnostic and prognostic measures, but their relationship is unclear. METHODS: A total of 204 patients with moderate-to-severe TBI, documented pupillary reactivity, and archived neuroimaging were included. Extent of midline shift and basal cistern effacement were extracted from admission brain CT. Mean midline shift was calculated for each ordinal category of pupillary reactivity and basal cistern effacement. Sequential Chi-square analysis was used to calculate a threshold midline shift for pupillary abnormalities and basal cistern effacement. Univariable and multiple logistic regression analyses were performed. RESULTS: Pupils were bilaterally reactive in 163 patients, unilaterally reactive in 24, and bilaterally unreactive in 17, with mean midline shift (mm) of 1.96, 3.75, and 2.56, respectively (p = 0.14). Basal cisterns were normal in 118 patients, compressed in 45, and absent in 41, with mean midline shift (mm) of 0.64, 2.97, and 5.93, respectively (p < 0.001). Sequential Chi-square analysis identified a threshold for abnormal pupils at a midline shift of 7-7.25 mm (p = 0.032), compressed basal cisterns at 2 mm (p < 0.001), and completely effaced basal cisterns at 7.5 mm (p < 0.001). Logistic regression revealed no association between midline shift and pupillary reactivity. With effaced basal cisterns, the odds ratio for normal pupils was 0.22 (95% CI 0.08-0.56; p = 0.0016) and for at least one unreactive pupil was 0.061 (95% CI 0.012-0.24; p < 0.001). Basal cistern effacement strongly predicted midline shift (OR 1.27; 95% CI 1.17-1.40; p < 0.001). CONCLUSIONS: Basal cistern effacement alone is associated with pupillary reactivity and is closely associated with midline shift. It may represent a uniquely useful neuroimaging marker to guide intervention in traumatic brain injury