Out-of-Model Effects and Overdispersion in Gate Set Tomography.
Abstract not provided.
Ostrove, Corey↗
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Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks
Abstract Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss .
59 BASIC BIOLOGICAL SCIENCES↗
Induction of chromatin damage and distribution of isochromatid breaks in human fibroblast cells exposed to heavy ions
The frequency of chromatid breaks and the distribution of isochromatid breaks were measured in G2-phase normal human fibroblasts prematurely condensed a short time after exposure to low- or high-LET radiations. The average number of isochromatid breaks from a single particle traversal increased with increasing LET values, while the average number of chromatid-type breaks appeared to reach a plateau. The distribution of isochromatid breaks after high-LET iron particles exposure was overdispersed compared to gamma-rays, indicating that a single iron particle traversal through a cell nucleus can produce multiple isochromatid breaks.
NASA Center JSC↗
Complex Spatial Structure in a Population of Didymopanax pittieri, A Tree of Wind-Exposed Lower Montane Rain Forest
Didymopanax pittieri is a common shade-intolerant tree colonizing treefall gaps in the elfin forests on windswept ridgecrests in the lower montane rain forests of the Cordillera de Tilarain, Costa Rica. All D. pittieri taller than > 0.5 m in a 5.2-ha elfin forested portion of a gridded study watershed in the Monteverde Cloud Forest Preserve were located, mapped, and measured. This local population of D. pittieri is spatially inhomogeneous, in that density increases with increasing wind exposure; D. pittieri are more abundant near ridge crests than lower on windward slopes. The important and ubiquitous phenomenon of spatial inhomogeneity in population density is addressed and corrected for in spatial analyses by the application of the inhomogeneous version of Ripley's K. The spatial patterns of four size classes of D. pittieri (<5 cm dbh, 5-10 cm dbh, 10-20 cm dbh, and> 20 cm dbh) were investigated. Within the large-scale trend in density driven by wind exposure, D. pittieri saplings are clumped at the scale of treefall gaps and at the scale of patches of aggregated gaps. D. pittieri 5-10 cm dbh are randomly distributed, apparently due to competitive thinning of sapling clumps during the early stages of gap-phase regeneration. D. pittieri larger than 10 cm dbh are overdispersed at a scale larger than that of patches of gaps. Natural disturbance can influence the distribution of shade intolerant tree populations at several different spatial scales, and can have discordant effects at different life history stages.
Lawton, Robert M.↗
Changes in Alertness and Performance Over Time During Long-Haul Flying Across Multiple Time Zones
BACKGROUND: Long-haul pilots experience high levels of fatigue and circadian disruptions due to long work hours and flying over multiple time zones. The aim of this study was to describe changes in alertness and performance among flight crews during long-haul flights crossing multiple time zones. METHODS: All pilots flying long-haul operations from a single airline were eligible to participate. All participants collected data for ~2 weeks of their normal work schedule within airline operations, with at least two long-haul rotations, including rest days and layovers. Participants wore an Actiwach throughout the entire study period and completed a sleep diary (at bedtime, upon waking up and after each nap). Each participant completed a 5-min Psychomotor Vigilance Task (PVT) and a Karolinska Sleepiness Scale (KSS) pre-flight, on top-of-descent (TOD; inflight) and at the end of each flight (post-flight). Response speed (1/RT x 1000), lapses (RT > 500 ms), and alertness were assessed over time pre-flight, TOD, post-flight, using mixed-effects models with participant as a random factor. Linear models were assumed for response speed and alertness, while a negative binomial distribution was specified for lapses due to overdispersion. RESULTS: Forty-four long-haul pilots participated in the study (5 female; mean age 44.25 ± 10.06 yrs; mean flight hours 9834.3; ± 5334.1 hrs). Lapses increased post-flight relative to pre-flight (F(2, 665) = 3.67, p < 0.05). There was a main effect of response speed (F(2, 665) = 21.45, p < 0.001) with slower speed inflight and postflight compared to preflight (p < 0.001). The KSS increased over time from M = 4.02 (± 1.35) preflight to M = 5.15 (± 1.58) inflight, to M = 6.7 (± 1.51) postflight (F(2, 701) = 182.63, p < 0.001). DISCUSSION: Our preliminary analyses showed that both performance and subjective alertness worsened from the beginning to the end of a flight. Additional analyses will be conducted to investigate the changes in alertness and performance by direction of travel, sleep history, and flight timing and duration.
long-haul↗
Zero-Truncated Poisson Tensor Decomposition for Sparse Count Data
We propose a novel statistical inference paradigm for zero-inflated multiway count data that dispenses with the need to distinguish between true and false zero counts. Our approach ignores all zero entries and applies zero-truncated Poisson regression on the positive counts. Inference is accomplished via tensor completion that imposes low-rank structure on the Poisson parameter space. Our main result shows that an $\textit{N}$-way rank-R parametric tensor 𝓜 ϵ (0, ∞) $I$Χ∙∙∙Χ$I$ generating Poisson observations can be accurately estimated from approximately $IR^2 \text{log}^2_2(I)$ non-zero counts for a nonnegative canonical polyadic decomposition. Several numerical experiments are presented demonstrating that our zero-truncated paradigm is comparable to the ideal scenario where the locations of false zero counts are known $\textit{a priori}$.
97 MATHEMATICS AND COMPUTING↗