Xi Chen, Jason D. Lee, Xin T. Tong, Yichen Zhang.

Source: The Annals of Statistics, Volume 48, Number 1, 251--273.

Abstract:
The stochastic gradient descent (SGD) algorithm has been widely used in statistical estimation for large-scale data due to its computational and memory efficiency. While most existing works focus on the convergence of the objective function or the error of the obtained solution, we investigate the problem of statistical inference of true model parameters based on SGD when the population loss function is strongly convex and satisfies certain smoothness conditions. Our main contributions are twofold. First, in the fixed dimension setup, we propose two consistent estimators of the asymptotic covariance of the average iterate from SGD: (1) a plug-in estimator, and (2) a batch-means estimator, which is computationally more efficient and only uses the iterates from SGD. Both proposed estimators allow us to construct asymptotically exact confidence intervals and hypothesis tests. Second, for high-dimensional linear regression, using a variant of the SGD algorithm, we construct a debiased estimator of each regression coefficient that is asymptotically normal. This gives a one-pass algorithm for computing both the sparse regression coefficients and confidence intervals, which is computationally attractive and applicable to online data.

Michael E. Sobel, Martin A. Lindquist.

Source: The Annals of Applied Statistics, Volume 14, Number 1, 452--472.

Abstract:
Neuroscientists often use functional magnetic resonance imaging (fMRI) to infer effects of treatments on neural activity in brain regions. In a typical fMRI experiment, each subject is observed at several hundred time points. At each point, the blood oxygenation level dependent (BOLD) response is measured at 100,000 or more locations (voxels). Typically, these responses are modeled treating each voxel separately, and no rationale for interpreting associations as effects is given. Building on Sobel and Lindquist ( J. Amer. Statist. Assoc. 109 (2014) 967–976), who used potential outcomes to define unit and average effects at each voxel and time point, we define and estimate both “point” and “cumulated” effects for brain regions. Second, we construct a multisubject, multivoxel, multirun whole brain causal model with explicit parameters for regions. We justify estimation using BOLD responses averaged over voxels within regions, making feasible estimation for all regions simultaneously, thereby also facilitating inferences about association between effects in different regions. We apply the model to a study of pain, finding effects in standard pain regions. We also observe more cerebellar activity than observed in previous studies using prevailing methods.

Zhonghua Liu, Ian Barnett, Xihong Lin.

Source: The Annals of Applied Statistics, Volume 14, Number 1, 433--451.

Abstract:
Principal component analysis (PCA) is a popular method for dimension reduction in unsupervised multivariate analysis. However, existing ad hoc uses of PCA in both multivariate regression (multiple outcomes) and multiple regression (multiple predictors) lack theoretical justification. The differences in the statistical properties of PCAs in these two regression settings are not well understood. In this paper we provide theoretical results on the power of PCA in genetic association testings in both multiple phenotype and SNP-set settings. The multiple phenotype setting refers to the case when one is interested in studying the association between a single SNP and multiple phenotypes as outcomes. The SNP-set setting refers to the case when one is interested in studying the association between multiple SNPs in a SNP set and a single phenotype as the outcome. We demonstrate analytically that the properties of the PC-based analysis in these two regression settings are substantially different. We show that the lower order PCs, that is, PCs with large eigenvalues, are generally preferred and lead to a higher power in the SNP-set setting, while the higher-order PCs, that is, PCs with small eigenvalues, are generally preferred in the multiple phenotype setting. We also investigate the power of three other popular statistical methods, the Wald test, the variance component test and the minimum $p$-value test, in both multiple phenotype and SNP-set settings. We use theoretical power, simulation studies, and two real data analyses to validate our findings.

Armin Schwartzman, Andrew J. Schork, Rong Zablocki, Wesley K. Thompson.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2509--2538.

Abstract:
Analysis of genome-wide association studies (GWAS) is characterized by a large number of univariate regressions where a quantitative trait is regressed on hundreds of thousands to millions of single-nucleotide polymorphism (SNP) allele counts, one at a time. This article proposes an estimator of the SNP heritability of the trait, defined here as the fraction of the variance of the trait explained by the SNPs in the study. The proposed GWAS heritability (GWASH) estimator is easy to compute, highly interpretable and is consistent as the number of SNPs and the sample size increase. More importantly, it can be computed from summary statistics typically reported in GWAS, not requiring access to the original data. The estimator takes full account of the linkage disequilibrium (LD) or correlation between the SNPs in the study through moments of the LD matrix, estimable from auxiliary datasets. Unlike other proposed estimators in the literature, we establish the theoretical properties of the GWASH estimator and obtain analytical estimates of the precision, allowing for power and sample size calculations for SNP heritability estimates and forming a firm foundation for future methodological development.

Johann Gagnon-Bartsch, Yotam Shem-Tov.

Source: The Annals of Applied Statistics, Volume 13, Number 3, 1464--1483.

Abstract:
The gold standard for identifying causal relationships is a randomized controlled experiment. In many applications in the social sciences and medicine, the researcher does not control the assignment mechanism and instead may rely upon natural experiments or matching methods as a substitute to experimental randomization. The standard testable implication of random assignment is covariate balance between the treated and control units. Covariate balance is commonly used to validate the claim of as good as random assignment. We propose a new nonparametric test of covariate balance. Our Classification Permutation Test (CPT) is based on a combination of classification methods (e.g., random forests) with Fisherian permutation inference. We revisit four real data examples and present Monte Carlo power simulations to demonstrate the applicability of the CPT relative to other nonparametric tests of equality of multivariate distributions.

Three children have now died in New York state from a possible complication from the coronavirus involving swollen blood vessels and heart problems, Gov. Andrew Cuomo said Saturday. At least 73 children in New York have been diagnosed with symptoms similar to Kawasaki disease — a rare inflammatory condition in children — and toxic shock syndrome.

The infections and deaths are spread across roughly two farms and 189 meat and processed food factories.

Nicolas Garcia Trillos, Daniel Sanz-Alonso.

Source: Bayesian Analysis, Volume 15, Number 1, 29--56.

Abstract:
The Bayesian update can be viewed as a variational problem by characterizing the posterior as the minimizer of a functional. The variational viewpoint is far from new and is at the heart of popular methods for posterior approximation. However, some of its consequences seem largely unexplored. We focus on the following one: defining the posterior as the minimizer of a functional gives a natural path towards the posterior by moving in the direction of steepest descent of the functional. This idea is made precise through the theory of gradient flows, allowing to bring new tools to the study of Bayesian models and algorithms. Since the posterior may be characterized as the minimizer of different functionals, several variational formulations may be considered. We study three of them and their three associated gradient flows. We show that, in all cases, the rate of convergence of the flows to the posterior can be bounded by the geodesic convexity of the functional to be minimized. Each gradient flow naturally suggests a nonlinear diffusion with the posterior as invariant distribution. These diffusions may be discretized to build proposals for Markov chain Monte Carlo (MCMC) algorithms. By construction, the diffusions are guaranteed to satisfy a certain optimality condition, and rates of convergence are given by the convexity of the functionals. We use this observation to propose a criterion for the choice of metric in Riemannian MCMC methods.

Jon Cockayne, Chris J. Oates, Ilse C.F. Ipsen, Mark Girolami.

Source: Bayesian Analysis, Volume 14, Number 3, 937--1012.

Abstract:
A fundamental task in numerical computation is the solution of large linear systems. The conjugate gradient method is an iterative method which offers rapid convergence to the solution, particularly when an effective preconditioner is employed. However, for more challenging systems a substantial error can be present even after many iterations have been performed. The estimates obtained in this case are of little value unless further information can be provided about, for example, the magnitude of the error. In this paper we propose a novel statistical model for this error, set in a Bayesian framework. Our approach is a strict generalisation of the conjugate gradient method, which is recovered as the posterior mean for a particular choice of prior. The estimates obtained are analysed with Krylov subspace methods and a contraction result for the posterior is presented. The method is then analysed in a simulation study as well as being applied to a challenging problem in medical imaging.

Masaki Yamamoto
May 22, 2019; 39:4179-4192
Neurobiology of Disease

A prominent theory claims that the right temporoparietal junction (rTPJ) is especially associated with embodied processes relevant to perspective-taking. In the present study, we use high-definition transcranial direct current stimulation to provide evidence that the rTPJ is causally associated with the embodied processes underpinning perspective-taking. Eighty-eight young human adults were stratified to receive either rTPJ or dorsomedial PFC anodal high-definition transcranial direct current stimulation in a sham-controlled, double-blind, repeated-measures design. Perspective-tracking (line-of-sight) and perspective-taking (embodied rotation) were assessed using a visuo-spatial perspective-taking task that required understanding what another person could see or how they see it, respectively. Embodied processing was manipulated by positioning the participant in a manner congruent or incongruent with the orientation of an avatar on the screen. As perspective-taking, but not perspective-tracking, is influenced by bodily position, this allows the investigation of the specific causal role for the rTPJ in embodied processing. Crucially, anodal stimulation to the rTPJ increased the effect of bodily position during perspective-taking, whereas no such effects were identified during perspective-tracking, thereby providing evidence for a causal role for the rTPJ in the embodied component of perspective-taking. Stimulation to the dorsomedial PFC had no effect on perspective-tracking or taking. Therefore, the present study provides support for theories postulating that the rTPJ is causally involved in embodied cognitive processing relevant to social functioning.

SIGNIFICANCE STATEMENT The ability to understand another's perspective is a fundamental component of social functioning. Adopting another perspective is thought to involve both embodied and nonembodied processes. The present study used high-definition transcranial direct current stimulation (HD-tDCS) and provided causal evidence that the right temporoparietal junction is involved specifically in the embodied component of perspective-taking. Specifically, HD-tDCS to the right temporoparietal junction, but not another hub of the social brain (dorsomedial PFC), increased the effect of body position during perspective-taking, but not tracking. This is the first causal evidence that HD-tDCS can modulate social embodied processing in a site-specific and task-specific manner.

As an important cognitive bias, the framing effect shows that our decision preferences are sensitive to the verbal description (i.e., frame) of options. This study focuses on the neural underpinnings of the social framing effect, which is based on decision-making regarding other people. A novel paradigm was used in which participants made a trade-off between economic benefits and the feelings of others. This decision was described as either a "harm" to, or "not helping," other persons in two conditions (Harm frame vs Help frame). Both human males and females were recruited. Participants behaved more prosocially for Harm frame compared with Help frame, resulting in a significant social framing effect. Using functional magnetic resonance imaging, Experiment 1 showed that the social framing effect was associated with stronger activation in the temporoparietal junction (TPJ), especially its right part. The functional connectivity between the right TPJ (rTPJ) and medial prefrontal cortex predicted the social framing effect on the group level. In Experiment 2, we used transcranial direct current stimulation to modulate the activity of the rTPJ and found that the social framing effect became more prominent under anodal (excitatory) stimulation, while the nonsocial framing effect elicited by the economic gain/loss gambling frame remained unaffected. The rTPJ results might be associated with moral conflicts modulated by the social consequences of an action or different levels of mentalizing with others under different frame conditions, but alternative interpretations are also worth noting. These findings could help elucidate the psychological mechanisms of the social framing effect.

SIGNIFICANCE STATEMENT Previous studies have suggested that the framing effect is generated from an interaction between the amygdala and anterior cingulate cortex. This opinion, however, is based on findings from nonsocial framing tasks. Recent research has highlighted the importance of distinguishing between the social and nonsocial framing effects. The current study focuses on the social framing effect and finds out that the temporoparietal junction and its functional connectivity with the medial prefrontal cortex play a significant role. Additionally, modulating the activity of this region leads to changes in social (but not nonsocial) framing effect. Broadly speaking, these findings help understand the difference in neural mechanisms between social and nonsocial decision-making. Meanwhile, they might be illuminating to promote helping behavior in society.

June 18 was the world’s first Sustainable Gastronomy Day. This begs the questions: 1) What in the world is sustainable gastronomy? 2) Why is it important enough to have a “day” dedicated to it? and 3) Even so, why should I care? What is Sustainable Gastronomy?  Gastronomy is sometimes called the art of food. It can also refer to a style of [...]

A new theory suggests the hot, harsh planet’s interior could have contained volatiles like water

The pint-sized, mustachioed Gaul immortalized in the French cartoon has spawned films, a theme park and many other spin-offs

Architects and designers restored royal ruins across Europe to their former glory

Over his five-decade-plus career, the "Strega Nona" author contributed to more than 270 books

Female dolphins, it seems, aren’t immune to the allure of a harmonizing boy band

Traces of lead pollution frozen in a glacier confirm that British lead production waned just before the death of Thomas Becket

The purplish-blue pigment, derived from a Portuguese fruit, fell out of use by the 19th century

In the days before his death, the New York man spoke often of his lost twin and the lessons humanity seemed not to have learned

Expelled by animals as a waste product, the gas appears to play a crucial role in keeping these bizarre, burrowing rodents safe

The medieval English longbow first came to prominence during the Hundred Years War. In 1346, English forces used it to devastating effect to cut down a superior French army.

A contemporary weapons expert is about to test a medieval war hammer on a steel breastplate from that era. The aim is to find out how much damage this fearsome instrument of death could deal.

A 17-year-old boy from Riverview, N.B., has died after the small motorbike he was riding collided with a minivan in Lower Coverdale, a settlement southeast of Moncton. 

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Independent MHA Eddie Joyce is suing four people, including the premier, for defamation over the handling of a harassment complaint that saw him turfed from the Liberal cabinet and caucus in 2018.

The province is still on track to move to a lower alert level Monday, which would ease some of the public health measures in place aimed at curbing COVID-19.

Eine Bibel-App bietet Tausenden von Kurden Zugang zu Gottes Wort.

Buenos Aires, Argentina: la tripulación del Logos Hope junto a Juventud con una Misión comparten el amor de Dios por los ancianos.

Durante un viaje misionero de un mes, Eduardo aprendió a escuchar y reconocer la voz de Dios, tanto personalmente como ministrando a otros.

This rapid and efficient method to prepare highly purified recombinant adeno-associated viruses (rAAVs) is based on binding of negatively charged rAAV capsids to an anion-exchange resin that is pH dependent.

This is a simple method for rapid preparation of recombinant adeno-associated virus (rAAV) stocks, which can be used for in vivo gene delivery. The purity of these vectors is considerably lower than that obtained by either CsCl gradient centrifugation or by combination of iodixanol gradient ultracentrifugation followed by column chromatography.

Colloidal gold–antibody conjugates are easy to prepare and are an excellent choice for microscopic applications. Colloidal gold is an aqueous suspension of nanometer-sized particles of gold. Typically, chloroauric acid, HAuCl₄, is reduced with dilute solutions of sodium citrate, as described here. This will cause the gold to form small aggregates that will associate with proteins. Gold particles of specific sizes can be isolated and differentiated microscopically, allowing these particles to be used for multiple-label experiments. Colloidal gold-labeled antibodies are widely used in electron microscopy (EM), and can be used for light microscopy but require additional steps (silver enhancement).

There are many uses for antibodies labeled with metal ions. Most of these methods involve first attaching a metal chelator to the antibody molecule. This is achieved using standard cross-linking chemistry and then adding the desired metal at appropriate concentration and pH. The method described here outlines a basic procedure for creating a lanthanide conjugate. Lanthanide conjugates are used for proximity assays, as MRI contrast agents, or for mass cytometry experiments. Different metals and chelators can be substituted, but the basic procedures are similar.

The last time Charlene Chiddenton saw her father in person was on March 7 — visitor restrictions at long-term care homes during the pandemic had kept them apart — and less than two months later, she was saying goodbye to her father by video call.

A woman who lost her sister to COVID-19 at the start of the month is thanking the staff at Northwood who took "excellent" care of her in her final days. Jean Harrigan, 90, is being remembered for her caring and lively nature.

Matt Keough, the former Oakland Athletics pitcher and special assistant, has died. He was 64. He was an American League all-star as a rookie in 1978 and two years later comeback player of the year.

Making Tierra Mía, says the director of the Smithsonian Latino Center, proved transformative in giving voice to the people

The union that represents thousands of Manitoba workers is asking what safety protocols were in place when a construction worker was killed after a trench wall collapsed on him earlier this week.

1. Bharat Biotech to lead human monoclonal antibodies project  The Hindu
2. Bharat Biotech leads CSIR project to develop antibodies against Covid-19  Times of India
3. Bharat Biotech To Lead CSIR’s Project To Develop Human Monoclonal Antibodies For Covid-19 Therapy  Swarajya
4. Bharat Biotech to develop human antibodies for COVID-19 therapy  Telangana Today
5. Bharat Biotech vows human monoclonal antibodies to neutralise COVID-19 in 6 months  Mumbai Mirror
6. View Full coverage on Google News

Former Hamilton Tiger-Cats running back and three time Grey Cup champion Dave Fleming has died. He was 76. The Tiger-Cats made the announcement on Thursday. A cause of death was not provided.

Ralph Goodale says building water diversion conduits in Lake Diefenbaker could help grow Saskatchewan's economy and environment but it comes with a $3 billion price tag.

Don Shula, who won the most games of any NFL coach and led the Miami Dolphins to the only perfect season in league history, died Monday at his home, the team said. He was 90.