Boyu Ren, Sergio Bacallado, Stefano Favaro, Tommi Vatanen, Curtis Huttenhower, Lorenzo Trippa.

Source: The Annals of Applied Statistics, Volume 14, Number 1, 494--517.

Abstract:
Detecting associations between microbial compositions and sample characteristics is one of the most important tasks in microbiome studies. Most of the existing methods apply univariate models to single microbial species separately, with adjustments for multiple hypothesis testing. We propose a Bayesian analysis for a generalized mixed effects linear model tailored to this application. The marginal prior on each microbial composition is a Dirichlet process, and dependence across compositions is induced through a linear combination of individual covariates, such as disease biomarkers or the subject’s age, and latent factors. The latent factors capture residual variability and their dimensionality is learned from the data in a fully Bayesian procedure. The proposed model is tested in data analyses and simulation studies with zero-inflated compositions. In these settings and within each sample, a large proportion of counts per microbial species are equal to zero. In our Bayesian model a priori the probability of compositions with absent microbial species is strictly positive. We propose an efficient algorithm to sample from the posterior and visualizations of model parameters which reveal associations between covariates and microbial compositions. We evaluate the proposed method in simulation studies, and then analyze a microbiome dataset for infants with type 1 diabetes which contains a large proportion of zeros in the sample-specific microbial compositions.

Bryan D. Martin, Daniela Witten, Amy D. Willis.

Source: The Annals of Applied Statistics, Volume 14, Number 1, 94--115.

Abstract:
Using a sample from a population to estimate the proportion of the population with a certain category label is a broadly important problem. In the context of microbiome studies, this problem arises when researchers wish to use a sample from a population of microbes to estimate the population proportion of a particular taxon, known as the taxon’s relative abundance . In this paper, we propose a beta-binomial model for this task. Like existing models, our model allows for a taxon’s relative abundance to be associated with covariates of interest. However, unlike existing models, our proposal also allows for the overdispersion in the taxon’s counts to be associated with covariates of interest. We exploit this model in order to propose tests not only for differential relative abundance, but also for differential variability. The latter is particularly valuable in light of speculation that dysbiosis , the perturbation from a normal microbiome that can occur in certain disease conditions, may manifest as a loss of stability, or increase in variability, of the counts associated with each taxon. We demonstrate the performance of our proposed model using a simulation study and an application to soil microbial data.

John R. Tipton, Mevin B. Hooten, Connor Nolan, Robert K. Booth, Jason McLachlan.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2363--2388.

Abstract:
Multivariate compositional count data arise in many applications including ecology, microbiology, genetics and paleoclimate. A frequent question in the analysis of multivariate compositional count data is what underlying values of a covariate(s) give rise to the observed composition. Learning the relationship between covariates and the compositional count allows for inverse prediction of unobserved covariates given compositional count observations. Gaussian processes provide a flexible framework for modeling functional responses with respect to a covariate without assuming a functional form. Many scientific disciplines use Gaussian process approximations to improve prediction and make inference on latent processes and parameters. When prediction is desired on unobserved covariates given realizations of the response variable, this is called inverse prediction. Because inverse prediction is often mathematically and computationally challenging, predicting unobserved covariates often requires fitting models that are different from the hypothesized generative model. We present a novel computational framework that allows for efficient inverse prediction using a Gaussian process approximation to generative models. Our framework enables scientific learning about how the latent processes co-vary with respect to covariates while simultaneously providing predictions of missing covariates. The proposed framework is capable of efficiently exploring the high dimensional, multi-modal latent spaces that arise in the inverse problem. To demonstrate flexibility, we apply our method in a generalized linear model framework to predict latent climate states given multivariate count data. Based on cross-validation, our model has predictive skill competitive with current methods while simultaneously providing formal, statistical inference on the underlying community dynamics of the biological system previously not available.

Carolyn M. Rutter, Jonathan Ozik, Maria DeYoreo, Nicholson Collier.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2189--2212.

Abstract:
Microsimulation models (MSMs) are used to inform policy by predicting population-level outcomes under different scenarios. MSMs simulate individual-level event histories that mark the disease process (such as the development of cancer) and the effect of policy actions (such as screening) on these events. MSMs often have many unknown parameters; calibration is the process of searching the parameter space to select parameters that result in accurate MSM prediction of a wide range of targets. We develop Incremental Mixture Approximate Bayesian Computation (IMABC) for MSM calibration which results in a simulated sample from the posterior distribution of model parameters given calibration targets. IMABC begins with a rejection-based ABC step, drawing a sample of points from the prior distribution of model parameters and accepting points that result in simulated targets that are near observed targets. Next, the sample is iteratively updated by drawing additional points from a mixture of multivariate normal distributions and accepting points that result in accurate predictions. Posterior estimates are obtained by weighting the final set of accepted points to account for the adaptive sampling scheme. We demonstrate IMABC by calibrating CRC-SPIN 2.0, an updated version of a MSM for colorectal cancer (CRC) that has been used to inform national CRC screening guidelines.

Piotr Kokoszka, Neda Mohammadi Jouzdani.

Source: Bernoulli, Volume 26, Number 3, 2383--2399.

Abstract:
This paper is concerned with frequency domain theory for functional time series, which are temporally dependent sequences of functions in a Hilbert space. We consider a variance decomposition, which is more suitable for such a data structure than the variance decomposition based on the Karhunen–Loéve expansion. The decomposition we study uses eigenvalues of spectral density operators, which are functional analogs of the spectral density of a stationary scalar time series. We propose estimators of the variance components and derive convergence rates for their mean square error as well as their asymptotic normality. The latter is derived from a frequency domain invariance principle for the estimators of the spectral density operators. This principle is established for a broad class of linear time series models. It is a main contribution of the paper.

Akio Fujiwara, Koichi Yamagata.

Source: Bernoulli, Volume 26, Number 3, 2105--2142.

Abstract:
We herein develop a theory of contiguity in the quantum domain based upon a novel quantum analogue of the Lebesgue decomposition. The theory thus formulated is pertinent to the weak quantum local asymptotic normality introduced in the previous paper [Yamagata, Fujiwara, and Gill, Ann. Statist. 41 (2013) 2197–2217], yielding substantial enlargement of the scope of quantum statistics.

Saint Paul schools are in the market for a vendor to provide background checks, while the Education Technology Joint Powers Authority is seeking media repositories. A Texas district wants quotes on technology for new campuses.

The post Calif. Ed-Tech Consortium Seeks Media Repository Solutions; Saint Paul District Needs Background Check Services appeared first on Market Brief.

The staffer of Vice President Mike Pence who tested positive for coronavirus is apparently his press secretary and the wife of White House senior adviser Stephen Miller.Reports emerged on Friday that a member of Pence's staff had tested positive for COVID-19, creating a delay in his flight to Iowa amid concern over who may have been exposed. Later in the day, Trump said the staffer is a "press person" named Katie.Politico reported he was referring to Katie Miller, Pence's press secretary and the wife of Stephen Miller. This report noted this raises the risk that "a large swath of the West Wing's senior aides may also have been exposed." She confirmed her positive diagnosis to NBC News, saying she does not have symptoms.Trump spilled the beans to reporters, saying Katie Miller "hasn't come into contact with me" but has "spent some time with the vice president." This news comes one day after a personal valet to Trump tested positive for COVID-19, which reportedly made the president "lava level mad." Pence and Trump are being tested for COVID-19 every day.Asked Friday if he's concerned about the potential spread of coronavirus in the White House, Trump said "I'm not worried, no," adding that "we've taken very strong precautions."More stories from theweek.com Outed CIA agent Valerie Plame is running for Congress, and her launch video looks like a spy movie trailer 7 scathing cartoons about America's rush to reopen Trump says he couldn't have exposed WWII vets to COVID-19 because the wind was blowing the wrong way

The news comes shortly after a valet who served meals to President Trump also tested positive for the virus.

Steven Poser
Jun 1, 2003; 23:4420-4427
Cellular

Jennifer L. Zamanian
May 2, 2012; 32:6391-6410
Neurobiology of Disease

Irune Diaz-Aparicio
Feb 12, 2020; 40:1453-1482
Development Plasticity Repair

Michele Bellesi
May 24, 2017; 37:5263-5273
Cellular

Fiona Doetsch
Jul 1, 1997; 17:5046-5061
Articles

Italian translation of the BIS press release about the BIS Quarterly Review, September 2017

French translation of the press release about the Basel Committee publishing a discussion paper on "The regulatory treatment of sovereign exposures" (7 December 2017)

French translation of "Pillar 3 disclosure requirements - updated framework", December 2018

To view more press releases, please visit http://www.snl.com/irweblinkx/news.aspx?iid=1024452.

To view more press releases, please visit http://www.snl.com/irweblinkx/news.aspx?iid=1024452.

Microglial cells are considered as sensors of brain pathology by detecting any sign of brain lesions, infections, or dysfunction and can influence the onset and progression of neurological diseases. They are capable of sensing their neuronal environment via many different signaling molecules, such as neurotransmitters, neurohormones and neuropeptides. The neuropeptide VGF has been associated with many metabolic and neurological disorders. TLQP21 is a VGF-derived peptide and has been shown to signal via C3aR1 and C1qBP receptors. The effect of TLQP21 on microglial functions in health or disease is not known. Studying microglial cells in acute brain slices, we found that TLQP21 impaired metabotropic purinergic signaling. Specifically, it attenuated the ATP-induced activation of a K⁺ conductance, the UDP-stimulated phagocytic activity, and the ATP-dependent laser lesion-induced process outgrowth. These impairments were reversed by blocking C1qBP, but not C3aR1 receptors. While microglia in brain slices from male mice lack C3aR1 receptors, both receptors are expressed in primary cultured microglia. In addition to the negative impact on purinergic signaling, we found stimulating effects of TLQP21 in cultured microglia, which were mediated by C3aR1 receptors: it directly evoked membrane currents, stimulated basal phagocytic activity, evoked intracellular Ca²⁺ transient elevations, and served as a chemotactic signal. We conclude that TLQP21 has differential effects on microglia depending on C3aR1 activation or C1qBP-dependent attenuation of purinergic signaling. Thus, TLQP21 can modulate the functional phenotype of microglia, which may have an impact on their function in health and disease.

SIGNIFICANCE STATEMENT The neuropeptide VGF and its peptides have been associated with many metabolic and neurological disorders. TLQP21 is a VGF-derived peptide that activates C1qBP receptors, which are expressed by microglia. We show here, for the first time, that TLQP21 impairs P2Y-mediated purinergic signaling and related functions. These include modulation of phagocytic activity and responses to injury. As purinergic signaling is central for microglial actions in the brain, this TLQP21-mediated mechanism might regulate microglial activity in health and disease. We furthermore show that, in addition to C1qBP, functional C3aR1 responses contribute to TLQP21 action on microglia. However, C3aR1 responses were only present in primary cultures but not in situ, suggesting that the expression of these receptors might vary between different microglial activation states.

"We thought it was a good idea to get a comprehensive record of the site while we could in case the water levels rise," says one official

Nadia, a four-year-old Malayan tiger, is the first known animal to test positive for coronavirus in the United States

Closing arguments were presented at the trial of Phillip Lionel Levac on Friday at Regina Court of Queen's Bench.

Tensions are rising on Manitoulin Island because a First Nation is stopping travellers on provincial highways that go through the community. But opinions on M'Chigeeng's attempt to protect its people from COVID-19 are not divided along racial lines. 

Three residents at a long-term care facility in Sault Ste. Marie have tested positive for COVID-19, prompting officials to declare an outbreak at Extendicare Maple View.

The Porcupine Health Unit is declaring a COVID-19 outbreak at a long-term care home in Iroquois Falls.

Provincial surveillance testing has returned a positive case of COVID-19 in a resident of Wikwemikong Nursing Home on Manitoulin Island. Ogimaa Duke Peltier says every staff member and resident underwent tests Tuesday and Wednesday of this week and the results are starting to come in.

Holland America and Princess cruise lines issued notices this week cancelling the remainder of the season in Atlantic Canada, citing global health concerns, and that's taking a huge bite out of the Port of Sydney's budget.

Solar Opposites (date: 5/9/2020 - Rank: 4)

Figure skater Michael Marinaro gets emotional as he talks about his grandmother who passed away from COVID-19. Marinaro and his partner Kirsten Moore-Towers joined fellow Canadian Kaitlyn Weaver who was hosting a livestream with figure skating legends to raise money for the UN Foundation's COVID-19 Solidarity Response Fund.

On Patriots' Day, we celebrate musician, publisher, and patriot Josiah Flagg (1737-1794), a friend of Paul Revere and major figure in Early American music.

1. Some White House staff to wear masks after valet tests positive: Trump  Times of India
2. U.S. President Trump says will be tested for coronavirus daily  The Hindu
3. US VP Mike Pence’s staffer, married to a Trump aide, tests positive for Covid-19  Livemint
4. Trump's U-turn on the coronavirus task force wasn't really a U-turn at all  The Independent
5. Aide to Vice President Pence tests positive for coronavirus  Times of India
6. View Full coverage on Google News

The German soccer league reported 10 positive tests for the coronavirus among 36 clubs in the Bundesliga and second division on Monday.

Doug Flutie can feel CFL commissioner Randy Ambrosie's pain as Ambrosie continues to discuss potential contingency plans for the 2020 CFL season in response to the COVID-19 pandemic.

Saskatchewan's unemployment rate soared in April due to the COVID-19 economic shutdown but an economist says it's not likely to get much worse.

UFC 249 will proceed as planned Saturday night despite Ronaldo "Jacare" Souza being ruled out Friday following a positive test for the coronavirus. He was scheduled to oppose Uriah Hall in Jacksonville, Fla.

The mullahs are cold calculators.

Region of Waterloo Public Health says there are 44 positive cases of COVID-19 at the Breslau meat processing facility Conestoga Meats.

The White House says it is conducting contact tracing after the U.S. vice-president's press secretary, Katie Miller, tested positive for coronavirus.

The NHL is hoping to convince teams the league should move the 2020 draft to early June and hold it virtually, according to a report.

Former Montreal Canadiens enforcer Georges Laraque's biggest challenge is trying to breathe clearly as he fights COVID-19 at a Montreal hospital. "The nights are the worst. I have fevers a couple times a night. I have to get up and take pills."

By Dr. Grazie Pozo Christie

When Archbishop Jose Gomez was elected to head the U.S. Conference of Catholic Bishops (USCCB) earlier this month, he tweeted that it was an honor - and not only for him, but for “every Latino Catholic in the country.” He’s right about that. We Latino Catholics feel it a great honor and a point of pride that a fellow Hispanic should take the lead. Not just because he is Latino, but because he’s a man with a sterling character and gentle manner, a man well known both for his sympathetic attitude toward the plight of immigrants and his traditional approach to social issues. This is a powerful and attractive combination to our growing Hispanic Catholic Church.

Gomez, a native of Monterrey, Mexico and a naturalized U.S. citizen, presides over the Los Angeles diocese, the largest and one of the most diverse dioceses in the country. Its parishes encompass more than thirty ethnicities, celebrating masses in languages from Igbo to Hungarian to Tagalog. The catholicity, that is, the universality--of the Catholic Church is a palpable thing in L.A., not simply a doctrinal concept. It’s the result of a constant and varied immigration. 

As leader of the USCCB, Archbishop Gomez will head an American Catholic Church that is about 58% non-Hispanic white and 34% Latino - a church in which most members under 30 are Hispanic. A significant number of the 2.7 million Hispanics that attend mass in Spanish are undocumented, and an even greater number probably know or love someone whose presence here is precarious. Gomez brings a history of heartfelt public support for the undocumented workers that America relies on to farm our crops, tidy our lawns, man our factories, and look after our children. He has been an especially vocal advocate of “dreamers.” “In a special way, I pray for #Dreamers, the day before #Scotus hears oral arguments on the legality of DACA,” he tweeted just after his election.

Archbishop Gomez is the author of the excellent “Immigration and the Next America.” The 2013 book neatly lays out his assessment of our current situation and his vision for a better future. He chronicles the historical background of a nation founded by Puritans searching for freedom but also (and even earlier) colonized by Spanish missionary migrants in a successful quest to evangelize the native population. He assesses a present-day America that lacks moral consensus and is crazed with consumerism, a nation confused about everything from the meaning of sexuality to the value (if any) of human life. He sees a country in which the ties of traditional American values and civic virtues that once bound us to one another are frayed, a country whose uneasy citizenry worries about what the “Next America” will look like. 

Gomez does not downplay the importance of legal norms and the very real toll that the chaos and lawlessness of illegal immigration takes, especially along our southern border. He argues, however, that fear and uncertainty may tempt us to “abandon our commitment to liberty and justice for all, in favor of an insular, racial definition of who can be a true American.” American Catholics, members of an immigrant Church in a country with a long history of anti-Catholic bias have a special responsibility in today’s debates over immigration reform. We bring to the table not only the memory of our ancestor’s experience of discrimination and the Church’s energetic response to the material and spiritual needs of successive waves of migrants, but also its rich tradition of teaching on human dignity and social justice. Catholics are especially suited to envision the face of the “Next America” in a way faithful to the Christian obligation of benevolence to strangers. 

U.S. Hispanics have a lot to be happy about in Archbishop Gomez’s election. He is a man with a tender heart for the vulnerable people in our midst who can also articulate a way forward on immigration that is attractive and optimistic - one based on the highest ideals that are our shared inheritance in this diverse country. He is also a man who bridges the liberal/conservative divide by quietly affirming the traditional mores and values that Hispanics are bent on preserving. But then, I venture to say that his election gives all American Catholics reason to be happy too. 

Idiopathic acute eosinophilic pneumonia is a rare and potentially life-threatening condition that is defined by bilateral pulmonary infiltrates and fever in the presence of pulmonary eosinophilia. It often presents acutely in previously healthy individuals and can be difficult to distinguish from infectious pneumonia. Although the exact etiology of idiopathic acute eosinophilic pneumonia remains unknown, an acute hypersensitivity reaction to an inhaled antigen is suggested, which is further supported by recent public health risks of vaping (electronic cigarette) use and the development of lung disease. In this case, a patient with a year-long history of vaping in conjunction with tetrahydrocannabinol cartridge use who was diagnosed with idiopathic acute eosinophilic pneumonia with associated bilateral hilar lymphadenopathy is described.

Polycystic ovary syndrome (PCOS) is a common female reproductive disorder that often manifests during adolescence and is associated with disruptions in health-related quality of life. Prompt evaluation and clinical support after diagnosis may prevent associated complications and optimize overall health management. This article incorporates the most recent evidence and consensus guidelines to provide an updated review of the pathogenesis, clinical presentation, diagnostic evaluation, and management strategies for adolescents with this complex condition. We will review the recent international guidelines on PCOS; because the diagnosis of PCOS remains controversial, management of this condition is inconsistent. In 2019, PCOS remains a common, yet neglected, condition, in part, because of the lack of agreement around both diagnosis and management.

THAT potato paratha then, being freshly made as I stand by idly at the counter, spring rain pouring from those raised shutters above and streaming onto open decking right behind. It would be miserable waiting for it out here were it not for the following.

I TOOK a bottle of Cot home the other day to share with a friend and his reaction got me thinking about the subject matter for this week's column, so here’s to wines and blends you may not have come across.