InBios International, Inc. announces the U.S. Food and Drug Administration (FDA) issued an emergency use authorization (EUA) for its diagnostic test that can be used immediately by CLIA...

(PRWeb April 08, 2020)

Read the full story at https://www.prweb.com/releases/inbios_receives_emergency_use_authorization_for_its_smart_detect_sars_cov_2_rrt_pcr_kit_for_detection_of_the_virus_causing_covid_19/prweb17036897.htm

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.

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.

Gabriela V. Cohen Freue, David Kepplinger, Matías Salibián-Barrera, Ezequiel Smucler.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2065--2090.

Abstract:
In large-scale quantitative proteomic studies, scientists measure the abundance of thousands of proteins from the human proteome in search of novel biomarkers for a given disease. Penalized regression estimators can be used to identify potential biomarkers among a large set of molecular features measured. Yet, the performance and statistical properties of these estimators depend on the loss and penalty functions used to define them. Motivated by a real plasma proteomic biomarkers study, we propose a new class of penalized robust estimators based on the elastic net penalty, which can be tuned to keep groups of correlated variables together in the selected model and maintain robustness against possible outliers. We also propose an efficient algorithm to compute our robust penalized estimators and derive a data-driven method to select the penalty term. Our robust penalized estimators have very good robustness properties and are also consistent under certain regularity conditions. Numerical results show that our robust estimators compare favorably to other robust penalized estimators. Using our proposed methodology for the analysis of the proteomics data, we identify new potentially relevant biomarkers of cardiac allograft vasculopathy that are not found with nonrobust alternatives. The selected model is validated in a new set of 52 test samples and achieves an area under the receiver operating characteristic (AUC) of 0.85.

Ye Zhang, Zhigang Yao, Patrik Forssén, Torgny Fornstedt.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2011--2042.

Abstract:
The means to obtain the rate constants of a chemical reaction is a fundamental open problem in both science and the industry. Traditional techniques for finding rate constants require either chemical modifications of the reactants or indirect measurements. The rate constant map method is a modern technique to study binding equilibrium and kinetics in chemical reactions. Finding a rate constant map from biosensor data is an ill-posed inverse problem that is usually solved by regularization. In this work, rather than finding a deterministic regularized rate constant map that does not provide uncertainty quantification of the solution, we develop an adaptive variational Bayesian approach to estimate the distribution of the rate constant map, from which some intrinsic properties of a chemical reaction can be explored, including information about rate constants. Our new approach is more realistic than the existing approaches used for biosensors and allows us to estimate the dynamics of the interactions, which are usually hidden in a deterministic approximate solution. We verify the performance of the new proposed method by numerical simulations, and compare it with the Markov chain Monte Carlo algorithm. The results illustrate that the variational method can reliably capture the posterior distribution in a computationally efficient way. Finally, the developed method is also tested on the real biosensor data (parathyroid hormone), where we provide two novel analysis tools—the thresholding contour map and the high order moment map—to estimate the number of interactions as well as their rate constants.

Kurtis Shuler, Marilou Sison-Mangus, Juhee Lee.

Source: Bayesian Analysis, Volume 15, Number 2, 559--578.

Abstract:
We propose a Bayesian sparse multivariate regression method to model the relationship between microbe abundance and environmental factors for microbiome data. We model abundance counts of operational taxonomic units (OTUs) with a negative binomial distribution and relate covariates to the counts through regression. Extending conventional nonlocal priors, we construct asymmetric nonlocal priors for regression coefficients to efficiently identify relevant covariates and their effect directions. We build a hierarchical model to facilitate pooling of information across OTUs that produces parsimonious results with improved accuracy. We present simulation studies that compare variable selection performance under the proposed model to those under Bayesian sparse regression models with asymmetric and symmetric local priors and two frequentist models. The simulations show the proposed model identifies important covariates and yields coefficient estimates with favorable accuracy compared with the alternatives. The proposed model is applied to analyze an ocean microbiome dataset collected over time to study the association of harmful algal bloom conditions with microbial communities.

Subhash Kulkarni
Oct 31, 2018; 38:9346-9354
Symposium and Mini-Symposium

Fabrizio Benedetti
Nov 9, 2005; 25:10390-10402
Symposia and Mini-Symposia

KM Harris
Aug 1, 1989; 9:2982-2997
Articles

Biodiversity may sound complicated, but it’s a fairly simple concept: the existence of many different types of plants and animals makes the world a healthier and more productive place. A mix of genetics, species and habitats allows Earth’s ecosystems to keep up with challenges like population growth and climate change. Biodiversity is important to us because it plays a crucial [...]

Buy fresh and seasonal produce at the Farmers’ Market on
Wednesday 26 February from 12.00 – 16.00 hours, and be sure to visit the [...]

The bright blue pigment that adorns the Bust of Nefertiti’s crown can now be used to study molecular biology

A rare bloom of microscopic organisms capable of making their own blue light has transformed several of the state’s beaches

New Brunswickers needn't worry about all the buzz around 'murder hornets' because they wouldn't survive the cold winters, says biologist.

British product designer Lucy Hughes has invented a biodegradable plastic made from fish offcuts

Contribution by Mr Fabio Panetta, Member of the Executive Board of the European Central Bank, published by Politico on 21 April 2020.

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

One major goal of integrative and comparative biology is to understand and explain the interaction between the performance and behavior of animals in their natural environment. The Caviomorph, Octodon degu, is a native rodent species from Chile, and represents a unique model to study physiological and behavioral traits, including cognitive and sensory abilities. Degus live in colonies and have a well-structured social organization, with a mostly diurnal–crepuscular circadian activity pattern. More notable is the fact that in captivity, they reproduce and live between 5 and 7 yr and show hallmarks of neurodegenerative diseases (including Alzheimer's disease), diabetes, and cancer.

CNA Staff, May 4, 2020 / 11:45 am (CNA).- Modern society is formulating an “anti-Christian creed” and punishing those who resist it with “social excommunication,” Benedict XVI has said in a new biography, published in Germany May 4.

In a wide-ranging interview at the end of the 1,184-page book, written by German author Peter Seewald, the pope emeritus said the greatest threat facing the Church was a “worldwide dictatorship of seemingly humanistic ideologies.”

Benedict XVI, who resigned as pope in 2013, made the comment in response to a question about what he had meant at his 2005 inauguration, when he urged Catholics to pray for him “that I may not flee for fear of the wolves.”

He told Seewald that he was not referring to internal Church matters, such as the "Vatileaks" scandal, which led to the conviction of his personal butler, Paolo Gabriele, for stealing confidential Vatican documents. 

In an advanced copy of “Benedikt XVI - Ein Leben” (A Life), seen by CNA, the pope emeritus said: “Of course, issues such as ‘Vatileaks’ are exasperating and, above all, incomprehensible and highly disturbing to people in the world at large.”

“But the real threat to the Church and thus to the ministry of St. Peter consists not in these things, but in the worldwide dictatorship of seemingly humanistic ideologies, and to contradict them constitutes exclusion from the basic social consensus.”

He continued: “A hundred years ago, everyone would have thought it absurd to speak of homosexual marriage. Today whoever opposes it is socially excommunicated. The same applies to abortion and the production of human beings in the laboratory.”

“Modern society is in the process of formulating an ‘anti-Christian creed,’ and resisting it is punishable by social excommunication. The fear of this spiritual power of the Antichrist is therefore only too natural, and it truly takes the prayers of a whole diocese and the universal Church to resist it.”

The biography, issued by Munich-based publisher Droemer Knaur, is available only in German. An English translation, “Benedict XVI, The Biography: Volume One,” will be published in the U.S. on Nov. 17.

In the interview, the 93-year-old former pope confirmed that he had written a spiritual testament, which could be published after his death, as did Pope St. John Paul II.

Benedict said that he had fast-tracked the cause of John Paul II because of “the obvious desire of the faithful” as well as the example of the Polish pope, with whom he had worked closely for more than two decades in Rome.

He insisted that his resignation had “absolutely nothing” to do with the episode involving Paolo Gabriele, and explained that his 2010 visit to the tomb of Celestine V, the last pope to resign before Benedict XVI, was “rather coincidental.” He also defended the title “emeritus” for a retired pope.

Benedict XVI lamented the reaction to his various public comments since his resignation, citing criticism of his tribute read at the funeral of Cardinal Joachim Meisner in 2017, in which he said that God would prevent the ship of the Church from capsizing. He explained that his words were “taken almost literally from the sermons of St. Gregory the Great.”

Seewald asked the pope emeritus to comment on the “dubia” submitted by four cardinals, including Cardinal Meisner, to Pope Francis in 2016 regarding the interpretation of his apostolic exhortation Amoris laetitia.

Benedict said that he did not want to comment directly, but referred to his last general audience, on Feb. 27, 2013.

Summing up his message that day, he  said: “In the Church, amid all the toils of humanity and the confusing power of the evil spirit, one will always be able to discern the subtle power of God's goodness.”

“But the darkness of successive historical periods will never allow the unadulterated joy of being a Christian ... There are always moments in the Church and in the life of the individual Christian in which one feels profoundly that the Lord loves us, and this love is joy, is ‘happiness’.”

Benedict said that he treasured the memory of his first meeting with the newly elected Pope Francis at Castel Gandolfo and that his personal friendship with his successor has continued to grow.

Author Peter Seewald has conducted four book-length interviews with Benedict XVI. The first, “Salt of the Earth,” was published in 1997, when the future pope was prefect of the Vatican Congregation for the Doctrine of the Faith. It was followed by “God and the World” in 2002, and “Light of the World” in 2010.

In 2016, Seewald published “Last Testament,” in which Benedict XVI reflected on his decision to step down as pope.

Publisher Droemer Knaur said that Seewald had spent many hours talking to Benedict for the new book, as well as speaking to his brother, Msgr. Georg Ratzinger and his personal secretary, Archbishop Georg Gänswein.

In an interview with Die Tagespost April 30, Seewald said that he had shown the Pope Emeritus a few chapters of the book before publication. Benedict XVI, he added, had praised the chapter on Pope Pius XI’s 1937 encyclical Mit brennender Sorge.
 

 

OBJECTIVES:

To determine if a multicomponent intervention was associated with increased use of first-line antibiotics (cephalexin or sulfamethoxazole and trimethoprim) among children with uncomplicated urinary tract infections (UTIs) in outpatient settings.

A Ukrainian pastor responds to nearly 100 per cent unemployment in his village by starting biofuel and cash crop business enterprises.

OMEGA Diagnostics shares jumped 77 per cent after it announced it is part of the UK rapid test consortium working to jointly develop and manufacture an antibody test.

A BIOTECH veteran has hailed a Glasgow firm that claims to have discovered two separate potential treatments for Covid-19 patients for use before they are put on ventilators.

Source: Ámbito - A dos meses de la cumbre mundial que este año tendrá lugar en Bonn, el cambio climático volvió a irrumpir con toda su fuerza y la temperatura amenaza con convertir a 2017 en el año más caluroso desde que se tiene registro. En nuestro país, la fatídica serie de inundaciones sobre la cuenca del río Salado dejó miles de hectáreas bajo las aguas en La Pampa, el sur de Córdoba y el oeste de Buenos Aires. "El cambio climático está afectando y afectará el desarrollo de los países y Argentina es una de las economías emergentes más vulnerables", alertaron especialistas del Banco Mundial.

Source: El tiempo - Una subida de 2°C altera la metilación del ADN y la expresión de genes claves para la supervivencia y el desarrollo. Este estudio ofrece una nueva visión sobre las consecuencias del cambio climático en los peces a través de modificaciones epigenéticas en todo el genoma

Source: Infobae - El cambio climático es probablemente el mayor desafío ambiental y social que enfrenta la humanidad, y que fue generado por el ser humano. Es un problema global que se resuelve en forma global, en donde existen muchos matices que hacen difícil el consenso entre los países respecto a las decisiones que deben tomarse. Sin embargo, todos reconocen el siguiente principio como marco de discusión: principio de responsabilidades comunes pero diferenciadas. Este principio reconoce que todos los países tienen responsabilidad común de solucionar el problema, aunque no todos en el mismo nivel y grado, ya que históricamente los países desarrollados han contaminado más a efecto de construir sus economías que aquellos que están en vías de desarrollo. Y no todos los países tienen la misma capacidad y recursos para enfrentar la problemática.

The standard initial management for infants and children with acute pyelonephritis is intravenous antibiotic treatment.

Our results support the use of an oral cefixime treatment of initial episodes of acute pyelonephritis involving a gram-negative bacteria strain in children aged 1 month to 3 years who are without urological abnormalities and without clinical hemodynamic impairment. (Read the full article)

Some but not all randomized trials have shown effects of probiotics on incidence and duration of diarrhea and respiratory tract infections among children in developing countries. Calcium improves resistance to intestinal infections in adults, but efficacy in children is unknown.

Lactobacillus reuteri DSM17938 may prevent diarrhea, especially in children with lower nutritional status. Regular calcium milk, alone or with Lactobacillus casei CRL431, did not reduce diarrhea. None of the interventions affected respiratory tract infections in these Indonesian children. (Read the full article)

Overall antibiotic prescribing rates for children declined throughout the 1990s and early 2000s. These declines were concurrent with changes in practice related to acute otitis media, the most common reason for antibiotic treatment in young children.

The downward trend in antibiotic-dispensing rates to young children in 16 Massachusetts communities ended by 2004–2005 and remained stable thereafter. This trend was driven by a declining otitis media diagnosis rate. Antibiotic treatment of diagnosed otitis media remained constant. (Read the full article)

Ideal empirical antibiotic choices are based on local susceptibility data. These choices are important for ensuring positive patient outcomes, but pediatric-specific data may not be available.

Antibiotic susceptibilities differ by age group within a tertiary-care hospital. Knowing these differences, pediatricians chose empirical antibiotic therapy more likely to be successful. Children with infectious diseases would benefit from reporting of pediatric-specific susceptibility results. (Read the full article)

Inflammatory bowel disease pathogenesis is incompletely understood. Previous pediatric studies suggested associations between antibiotic use and inflammatory bowel disease development but were limited by recall bias, lack of controls, incomplete antibiotic capture, or included exposures between symptom onset and diagnosis.

Our population-based cohort study suggests that certain childhood antibiotic exposures are associated with an increased risk of developing inflammatory bowel disease. Our findings have implications for understanding the condition’s pathogenesis and provide additional stimulus for reducing unnecessary childhood antibiotic use. (Read the full article)

Understanding human disease genomics requires large population-based studies. There is lack of standardization, as well as social and ethical concerns surrounding the consent process for pediatric participation in a biorepository.

The study identifies specific barriers to pediatric participation in biorepositories relative to adults, and proposes strategies to improve ethical and responsible participation of pediatric-aged patients in large-scale genomics and biorepository-driven research without significantly increasing research burden for affected families. (Read the full article)

Several meta-analyses evaluating probiotics in preterm infants suggest a beneficial effect for the prevention of necrotizing enterocolitis and death, but less for nosocomial infection. Lactobacillus reuteri may reduce these outcomes because of its immunomodulation and bactericidal properties.

Although L reuteri did not appear to decrease the rate of death or nosocomial infection, the trends suggest a protective role consistent with the literature. Feeding intolerance and duration of hospitalization were significantly decreased in premature infants ≤1500 g. (Read the full article)

It has been suggested that maternal immune activation during pregnancy is associated with cardinal behaviors of autism in the offspring. Epidemiologic studies have yielded conflicting results concerning the association between any infection during pregnancy and the development of autism.

This population-based cohort study investigated the association between specific common infectious diseases, febrile episodes, or use of antibiotics during pregnancy by using maternal population-based self-reported data. (Read the full article)

Although the metabolic syndrome is associated with obesity, not all obese children have insulin resistance and metabolic syndrome, and nonobese children may develop these abnormalities. Associated factors have not been well described.

There was a 6.6% prevalence of nonobese children who were insulin-resistant, associated with a family history of hypertension. There was a 21.3% prevalence of obese who were not insulin-resistant, associated with a low waist circumference. (Read the full article)