Susheela P. Singh, Ana-Maria Staicu, Robert R. Dunn, Noah Fierer, Brian J. Reich.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2341--2362.

Abstract:
The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes. However, to harness the power of microbial communities we must understand not only how they affect us, but also how they can be influenced to improve outcomes. This area has been dominated by methods that reduce community composition to summary metrics, which can fail to fully exploit the complexity of community data. Recently, methods have been developed to model the abundance of taxa in a community, but they can be computationally intensive and do not account for spatial effects underlying microbial settlement. These spatial effects are particularly relevant in the microbiome setting because we expect communities that are close together to be more similar than those that are far apart. In this paper, we propose a flexible Bayesian spike-and-slab variable selection model for presence-absence indicators that accounts for spatial dependence and cross-dependence between taxa while reducing dimensionality in both directions. We show by simulation that in the presence of spatial dependence, popular distance-based hypothesis testing methods fail to preserve their advertised size, and the proposed method improves variable selection. Finally, we present an application of our method to an indoor fungal community found within homes across the contiguous United States.

Ian L. Dryden, Kwang-Rae Kim, Charles A. Laughton, Huiling Le.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2213--2234.

Abstract:
Molecular dynamics simulations produce huge datasets of temporal sequences of molecules. It is of interest to summarize the shape evolution of the molecules in a succinct, low-dimensional representation. However, Euclidean techniques such as principal components analysis (PCA) can be problematic as the data may lie far from in a flat manifold. Principal nested spheres gives a fundamentally different decomposition of data from the usual Euclidean subspace based PCA [ Biometrika 99 (2012) 551–568]. Subspaces of successively lower dimension are fitted to the data in a backwards manner with the aim of retaining signal and dispensing with noise at each stage. We adapt the methodology to 3D subshape spaces and provide some practical fitting algorithms. The methodology is applied to cluster analysis of peptides, where different states of the molecules can be identified. Also, the temporal transitions between cluster states are explored.

Stephen E. Fienberg

Source: Ann. Appl. Stat., Volume 4, Number 2, 533--534.

Cook, William, 1815-1897

Luis Gutiérrez, Eduardo Gutiérrez-Peña, Ramsés H. Mena.

Source: Bayesian Analysis, Volume 14, Number 2, 427--447.

Abstract:
This work presents a Bayesian predictive approach to statistical shape analysis. A modeling strategy that starts with a Gaussian distribution on the configuration space, and then removes the effects of location, rotation and scale, is studied. This boils down to an application of the projected normal distribution to model the configurations in the shape space, which together with certain identifiability constraints, facilitates parameter interpretation. Having better control over the parameters allows us to generalize the model to a regression setting where the effect of predictors on shapes can be considered. The methodology is illustrated and tested using both simulated scenarios and a real data set concerning eight anatomical landmarks on a sagittal plane of the corpus callosum in patients with autism and in a group of controls.

Gregorio Quintana-Ortí, Amelia Simó.

Source: Statistical Science, Volume 34, Number 2, 236--252.

Abstract:
This paper is focused on kernel regression when the response variable is the shape of a 3D object represented by a configuration matrix of landmarks. Regression methods on this shape space are not trivial because this space has a complex finite-dimensional Riemannian manifold structure (non-Euclidean). Papers about it are scarce in the literature, the majority of them are restricted to the case of a single explanatory variable, and many of them are based on the approximated tangent space. In this paper, there are several methodological innovations. The first one is the adaptation of the general method for kernel regression analysis in manifold-valued data to the three-dimensional case of Kendall’s shape space. The second one is its generalization to the multivariate case and the addressing of the curse-of-dimensionality problem. Finally, we propose bootstrap confidence intervals for prediction. A simulation study is carried out to check the goodness of the procedure, and a comparison with a current approach is performed. Then, it is applied to a 3D database obtained from an anthropometric survey of the Spanish child population with a potential application to online sales of children’s wear.

The terraced hills of the Andes, the rice paddies of southern China, the oasis systems of the Maghreb: agriculture molds landscapes and places. Agriculture also shapes livelihoods, lifestyles, food traditions and cultures. What kind of plants grow or can’t grow, how they are harvested and what people eat define people’s lives.  Because our natural resources are under great strain, we need [...]

Here's what you need to know to preserve your copy of history

No SARS-CoV-2 infections have yet been detected in our closest living relatives. But there is precedent for viruses jumping from people to other great apes

Universities, libraries and museums are among the organizations seeking personal stories about the pandemic's effects on daily life

Dreamscape is an escape from the relentless pace of cityscapes. A matrix caught between reality and a dream. A moment frozen amongst the chaos there is calm.

Open for visitors, these houses model upcycling at its finest

Press release about the Basel Committee publishing consultation paper on revisions to the credit valuation adjustment risk framework, 28 November 2019.

Businesses in Cape Breton are helping customers get creative with DIY take-home kits to make everything from mermaid-themed terrariums to bubble tea.

There are better sports documentaries than The Last Dance, but the entertaining series on the Michael Jordan-led Bulls dynasty might be a better fit for this particular time.

Last month, the National Arts Centre launched #CanadaPerforms, an initiative that pays musicians and writers to perform from their living rooms. Poet Zoey Roy gave an intimate performance from her living room in Kingston. 

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If the president had listened to the World Health Organization, American lives would have been saved.

Zanu PF's limited commitment to the Global Political Agreement (GPA) and the resultant institutionalisation of the Government of National Unity (GNU) is why the party began to push for elections as from 2010, a strategy seen as steering the total collapse of the agreement.

IT is a truth universally acknowledged – at least by its advocates – that all things inexorably advance the cause of independence.

On the potholed drive home from the pub the other night, a creature ran into the beam of our lights. Long, low and lean, for a moment it looked like an otter. One has occasionally been sighted in our village, though like Loch Ness’s fabled monster this is a source of some dispute. But in another second it was clear that this beast was not from the riverbank but the woods.

DRAKE - DARK LANE DEMO TAPES

Three Ga. high school seniors have been charged with aggravated sexual battery and consumption of alcohol by a minor stemming from an alleged sexual assault during a post-prom party.

Three high school basketball players in Tennessee were charged with aggravated rape and aggravated assault in late December after allegedly sending one of their 15-year-old teammates to the hospital.

The business of buying things for schools is a key part of making sure that hard-fought K-12 funding actually turns into a quality education at the school and classroom level.

IT’S all too easy to lose track of many of the quirky, moving, interesting films that have been shot in Scotland over the years. Some of the sparkling gems on these pages attracted decent reviews upon release before fading from view; others slipped under most people’s radar. The 10 films here are funny, or dark, or insightful. All have something to say; all are worth tracking down, and watching, whether it’s for the first time, or the first time since they were released.

Tax-credit scholarship programs in 17 states collected $1.1 billion in contributions in 2017, a new analysis from the GAO finds.

Lorraine Wilson

Internet use has rapidly become a commonplace activity, especially among adolescents. Poor mental health and several somatic health problems are associated with heavy Internet use by adolescents.

Results of this study provide evidence of a U-shaped relationship between intensity of Internet use and poorer mental health of adolescents. Heavy Internet users were also confirmed to be at increased risk for somatic health problems in this nationally representative sample of adolescents. (Read the full article)

Preterm infants from 33 gestational weeks can detect specific shape features (prism and cylinder) by touch (without visual control), and remember them; however, nothing is known about such abilities earlier in development.

The preterm infant, even when very immature (from 28 gestational weeks), is endowed with tactile sensory abilities: the exploration and memorization of an object by touch, the discrimination of a novel object, and the recognition of a familiar object after interference. (Read the full article)

Although studies have examined family socioeconomic status as income and educational and employment status, emerging research suggests indicators of material hardship, such as diaper need, are increasingly important to child health. Diaper need has not been examined in the scientific literature.

This study quantifies diaper need, proposes a method to measure diaper need, and explores psychosocial and demographic variables associated with diaper need in a large sample of low-income families. (Read the full article)

In parts of sub-Saharan Africa, sexual assault incidence among adolescents is as high as 24%, resulting in serious physical and mental health problems. In the United States, empowerment and self-defense training have been shown to decrease incidence of sexual assault.

This study evaluated an empowerment and self-defense training intervention for adolescent girls in the African context. This intervention proved highly effective at preventing sexual assault and should be replicable in other countries in sub-Saharan Africa and around the world. (Read the full article)

Hypothermia treatment of neonatal encephalopathy reduces death and disability from 66% to 50%; additional neuroprotective therapies are needed. We previously found in animal models that adding 50% xenon to the breathing gas during cooling doubled neuroprotection.

This clinical feasibility study used 50% xenon for 3 to 18 hours in 14 cooled infants with cardiovascular, respiratory, and amplitude-integrated EEG monitoring. This depressed seizures, with no blood pressure reduction. Xenon is ready for randomized clinical trials in newborns. (Read the full article)

Tapentadol is used in the treatment of chronic pain, specifically diabetic neuropathy. It has known action on the μ-opioid receptor leading to drowsiness and apneas. There is no published information on the effects of tapentadol in small children.

After an accidental overdose in a child, tapentadol may be expected to cause μ-opioid clinical effects similar to other opioids. While the opioid effects predominate sympathomimetic effects are also seen. The risk of respiratory depression and dyspnea should be acknowledged. (Read the full article)

"We can do better," Germany coach Silvia Neid concluded after her side joined France and Sweden in making it to the quarter-finals of the Olympic tournament in unspectacular fashion.