Jason Xu, Samson Koelle, Peter Guttorp, Chuanfeng Wu, Cynthia Dunbar, Janis L. Abkowitz, Vladimir N. Minin.

Source: The Annals of Applied Statistics, Volume 13, Number 4, 2091--2119.

Abstract:
Single-cell lineage tracking strategies enabled by recent experimental technologies have produced significant insights into cell fate decisions, but lack the quantitative framework necessary for rigorous statistical analysis of mechanistic models describing cell division and differentiation. In this paper, we develop such a framework with corresponding moment-based parameter estimation techniques for continuous-time, multi-type branching processes. Such processes provide a probabilistic model of how cells divide and differentiate, and we apply our method to study hematopoiesis , the mechanism of blood cell production. We derive closed-form expressions for higher moments in a general class of such models. These analytical results allow us to efficiently estimate parameters of much richer statistical models of hematopoiesis than those used in previous statistical studies. To our knowledge, the method provides the first rate inference procedure for fitting such models to time series data generated from cellular barcoding experiments. After validating the methodology in simulation studies, we apply our estimator to hematopoietic lineage tracking data from rhesus macaques. Our analysis provides a more complete understanding of cell fate decisions during hematopoiesis in nonhuman primates, which may be more relevant to human biology and clinical strategies than previous findings from murine studies. For example, in addition to previously estimated hematopoietic stem cell self-renewal rate, we are able to estimate fate decision probabilities and to compare structurally distinct models of hematopoiesis using cross validation. These estimates of fate decision probabilities and our model selection results should help biologists compare competing hypotheses about how progenitor cells differentiate. The methodology is transferrable to a large class of stochastic compartmental and multi-type branching models, commonly used in studies of cancer progression, epidemiology and many other fields.

Yanjun Qian, Jianhua Z. Huang, Chiwoo Park, Yu Ding.

Source: The Annals of Applied Statistics, Volume 13, Number 3, 1537--1563.

Abstract:
In situ transmission electron microscope (TEM) adds a promising instrument to the exploration of the nanoscale world, allowing motion pictures to be taken while nano objects are initiating, crystalizing and morphing into different sizes and shapes. To enable in-process control of nanocrystal production, this technology innovation hinges upon a solution addressing a statistical problem, which is the capability of online tracking a dynamic, time-varying probability distribution reflecting the nanocrystal growth. Because no known parametric density functions can adequately describe the evolving distribution, a nonparametric approach is inevitable. Towards this objective, we propose to incorporate the dynamic evolution of the normalized particle size distribution into a state space model, in which the density function is represented by a linear combination of B-splines and the spline coefficients are treated as states. The closed-form algorithm runs online updates faster than the frame rate of the in situ TEM video, making it suitable for in-process control purpose. Imposing the constraints of curve smoothness and temporal continuity improves the accuracy and robustness while tracking the probability distribution. We test our method on three published TEM videos. For all of them, the proposed method is able to outperform several alternative approaches.

Fed up with their district’s unmet pledges to stop steering African American students into low-level classes, parents take action.

Children with specific language impairment are at risk for social difficulties. However, whether this occurs adaptively as a result of language impairment or occurs as a result of an underlying deficit in social cognition remains unclear.

We used eye tracking to explore how children with specific language impairment view social scenes. The overall gaze behavior resembled that of typically developing children. Significant attention to the speaker’s mouth may result in receiving less social-emotional information from the eyes. (Read the full article)

A team of social media analysts at an SA business school is tracking misinformation, disinformation, distortion and lies online.

As armed conflicts in Afghanistan, Iraq, Nigeria, South Sudan, Syria, Yemen, and elsewhere continued to inflict much suffering and instability around the world, the heads of the UN and International Committee of the Red Cross issued an unprecedented joint warning about the impact of today’s conflicts on civilians and called on states to redouble their efforts to find sustainable solutions to conflicts. Welcoming the call to action, Jean-Marie Guéhenno, President & CEO of the International Crisis Group, said: “It is imperative that the world do much more to respond to early warning signs and prevent wars breaking out in the first place”.

November saw further military escalation and setbacks in Syria, particularly after Turkey shot down a Russian warplane it claimed had violated its airspace. Meanwhile, several countries faced extremist attacks claimed by the Islamic State (IS), including in Lebanon, France and Bangladesh. Violence also rose in Turkey between the state and Kurdish insurgents. In Venezuela, political tensions and violence increased ahead of parliamentary elections scheduled for 6 December and could worsen, while both Nepal and Kosovo faced deepening political crises. In a positive step forward, Burkina Faso and Myanmar experienced peaceful and openly-contested elections last month.

The month saw an intensification of deadly violence in Burundi’s capital, Bujumbura, with over 80 people killed following clashes with security forces. The African Union Peace and Security Council (AU PSC) made a welcome statement of intent to deploy forces to halt the slide toward civil war and mass atrocities. In Afghanistan, fighting raged between government and Taliban forces, particularly in Helmand province, while in Djibouti, Ethiopia and Niger, political tensions heightened. In a positive step forward, a peace deal was signed in Libya but uncertainties remain over the viability of the agreement. As stressed by Jean-Marie Guéhenno, President and CEO of the International Crisis Group, in today’s Ten Conflicts to Watch in 2016, it “should be seen as a beginning, not an end, to the peace process”.

The month saw an intensification of Yemen’s war, amid heightened regional rivalries between Saudi Arabia and Iran complicating prospects for peace. Political tensions increased in Haiti, Guinea-Bissau and Moldova, where protests over endemic corruption and a lack of confidence in the government could escalate. In Africa, Boko Haram’s deadly attacks increased in northern Cameroon, and Burkina Faso was hit by an unprecedented terror attack. On the nuclear front, in East Asia, North Korea’s announcement that it had carried out a successful hydrogen bomb test was roundly condemned, while nuclear-related sanctions on Iran were rolled back in accordance with the July 2015 deal.

The month saw conflict continue to rage in Turkey’s south east between Ankara and the Kurdistan Workers’ Party (PKK), looking likely to further escalate in March. Afghanistan and Somalia both saw armed insurgencies capture new territories. In Africa, political tensions rose in Chad, Mozambique and Zimbabwe, while in Venezuela, deadlock between the opposition-held parliament and government has brought the country closer to political and economic implosion. In Asia, North Korea’s announcement of a satellite launch in violation of UN Security Council resolutions prompted international condemnation and calls for tough new sanctions. On a positive note, the coming month brings the possibility of a final agreement to end Colombia’s decades-old insurgency.

The month saw violent extremist movements, including the Islamic State (IS) and al-Qaeda-linked groups, carry out major deadly attacks in Turkey, Pakistan, Côte d’Ivoire, Tunisia and Belgium. In Libya, the arrival of Prime Minister Serraj in Tripoli despite warnings from multiple factions could lead to further destabilisation. Meanwhile in Central Africa, political violence rose in Burundi and could break out in Chad around the 10 April presidential election. Yemen, South Sudan and even Syria saw progress, of varying degrees, toward peace talks or implementation of agreements, and in Colombia the start of talks between the state and the National Liberation Army (ELN) could lead to the end of the 52-year-old conflict.

The month saw fighting escalate again in Syria and Afghanistan, and erupt in Nagorno-Karabakh between Armenian-backed separatists and Azerbaijani forces. In Bangladesh, election violence and killings by extremist groups showed how new heights of government-opposition rivalry and state repression have benefitted violent political party wings and extremist groups alike. Political tensions intensified in Iraq and Macedonia, and security forces severely supressed opposition protests in the Republic of Congo and Gambia. On a positive note, new governments were formed in the Central African Republic and South Sudan to consolidate peace gains, and talks to end Yemen’s one-year-old civil war got underway, albeit later than planned.

The month saw Venezuela’s political, economic and humanitarian crisis worsen amid heightened tensions between the government and opposition, a situation which could lead to state collapse and regional destabilisation. Another major setback in electing a new president in Haiti prompted fears of further civil unrest. In West Africa, deadly violence in central Mali and south-east Nigeria spiked, while a power struggle in Guinea-Bissau led to a dangerous standoff. In Libya, factions for and against the fledgling Government of National Accord (GNA) advanced on Sirte to expel the Islamic State (IS), risking clashes over oil facilities, while Turkey saw heightened political polarisation and an increase in violence in Kurdish areas. Ongoing peace talks, despite slow progress and ongoing violence, remain the best chance to end major combat in Yemen.

The month saw Venezuela’s political, economic and humanitarian crisis worsen amid heightened tensions between the government and opposition, a situation which could lead to state collapse and regional destabilisation. Another major setback in electing a new president in Haiti prompted fears of further civil unrest. In West Africa, deadly violence in central Mali and south-east Nigeria spiked, while a power struggle in Guinea-Bissau led to a dangerous standoff. In Libya, factions for and against the fledgling Government of National Accord (GNA) advanced on Sirte to expel the Islamic State (IS), risking clashes over oil facilities, while Turkey saw heightened political polarisation and an increase in violence in Kurdish areas. Ongoing peace talks, despite slow progress and ongoing violence, remain the best chance to end major combat in Yemen.

Expense tracking is one of the least enjoyable aspects of running a business. Thankfully, there are various cloud-based solutions that help small to midsize businesses (SMB) innovate and even automate expense reporting tasks. Here are nine of the most notable that we've tested for your business to consider.

Everyone's thinking about the Coronavirus Disease 2019 (COVID-19), and wondering if there are any cases near where they live. I recently used SAS Software to create a dashboard with a world map showing which countries had reported cases. And now that the virus has spread around the world, a world/country-level [...]

The post Tracking the Coronavirus Disease 2019 (COVID-19) in the United States appeared first on Graphically Speaking.

Now that COVID-19 is spreading in the US, I thought it might be helpful to view the data at a more granular level. Follow along as I plot the county data on a map and discuss how the color-binning can influence people's perception of the data. Maps like this can [...]

The post Tracking Coronavirus Disease 2019 (COVID-19) in the US at the state/county level appeared first on Graphically Speaking.

Agency: GSS Closing Date: 5/28/2020

Part of the explanation can be higher co-morbidity in certain cities and also a shortage of critical equipment like ventilators.

A state-wise comparison shows that the states with the highest cases like Delhi, Maharashtra and Gujarat still seem to be doubling every 10 days.

Uber doing away with the post-trip tracking feature that had drawn the ire of users is a sign of the torsion privacy concerns create when faced with the demands of a data-driven world.

This week LONGi announced that it would be supplying modules to what it says is the largest “bifacial+tracker” power generation project in the United States. The 224-MW project will be built in Mitchell County, Georgia and is expected to be complete this year.

As governments around the world consider how to monitor novel coronavirus outbreaks while reopening their societies, many are starting to bet on smartphone apps to help stem the pandemic.

ABSTRACT

Over the past decade, Candida auris has emerged as an urgent threat to public health. Initially reported from cases of ear infections in Japan and Korea, C. auris has since been detected around the world. While whole-genome sequencing has been extensively used to trace the genetic relationships of the global emergence and local outbreaks, a recent report in mBio describes a targeted genotyping method as a rapid and inexpensive method for classifying C. auris isolates (T. de Groot, Y. Puts, I. Berrio, A. Chowdhary, and J. F. Meis, mBio 11:e02971-19, https://doi.org/10.1128/mBio.02971-19, 2020).

Reactive oxygen and nitrogen species have been implicated in many biological processes and diseases, including immune responses, cardiovascular dysfunction, neurodegeneration, and cancer. These chemical species are short-lived in biological settings, and detecting them in these conditions and diseases requires the use of molecular probes that form stable, easily detectable, products. The chemical mechanisms and limitations of many of the currently used probes are not well-understood, hampering their effective applications. Boronates have emerged as a class of probes for the detection of nucleophilic two-electron oxidants. Here, we report the results of an oxygen-18–labeling MS study to identify the origin of oxygen atoms in the oxidation products of phenylboronate targeted to mitochondria. We demonstrate that boronate oxidation by hydrogen peroxide, peroxymonocarbonate, hypochlorite, or peroxynitrite involves the incorporation of oxygen atoms from these oxidants. We therefore conclude that boronates can be used as probes to track isotopically labeled oxidants. This suggests that the detection of specific products formed from these redox probes could enable precise identification of oxidants formed in biological systems. We discuss the implications of these results for understanding the mechanism of conversion of the boronate-based redox probes to oxidant-specific products.

Read our live coronavirus updates HERE Coronavirus: The symptoms

Companies are trying to figure out how to welcome back employees to their offices, and keep them safe once they return. The new normal might involve smartphone apps and badges to track employees.

Both companies said privacy and preventing governments from using the system to compile data on citizens was a primary goal.

A map of confirmed COVID-19 cases and deaths around the world. The respiratory disease has spread rapidly across six continents and has killed thousands of people.

Swansea City defender Joe Rodon is a name those outside of the Championship may not be too familiar with but the youngster is making an impact in Wales.

It is one of the most popular and important websites for cattle producers, rangers and carbon farmers in northern Australia, but its funding is about to run out.

"Whether it is in counterterrorism, counter-narcotics, money laundering, smuggling or combating international organized crime, Spain has long been and will continue to be a strong partner for the United States," said Attorney General Holder.

View our map and graphics to see where COVID-19 is hitting hardest in the U.S., which state outbreaks are growing the fastest and which are leveling off.

A map of confirmed COVID-19 cases and deaths around the world. The respiratory disease has spread rapidly across six continents and has killed thousands of people.