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The procedure, which has only been conducted a few times in history, could be a groundbreaking new treatment for patients suffering from lung cancer.

The post In a Revolutionary Medical Treatment, Man’s Lung Was Removed, Cleaned, and Replaced—No Transplant Necessary appeared first on Good News Network.

We live and cooperate in networks. However, links in networks only allow for pairwise interactions, thus making the framework suitable for dyadic games, but not for games that are played in groups of more than two players. To remedy this, we introduce higher-order interactions, where a link can connect more than two individuals, and study their evolutionary dynamics. We first consider a public goods game on a uniform hypergraph, showing that it corresponds to the replicator dynamics in the well-mixed limit, and providing an exact theoretical foundation to study cooperation in networked groups. We also extend the analysis to heterogeneous hypergraphs that describe interactions of groups of different sizes and characterize the evolution of cooperation in such cases. Finally, we apply our new formulation to study the nature of group dynamics in real systems, showing how to extract the actual dependence of the synergy factor on the size of a group from real-world collaboration data in science and technology. Our work is a first step towards the implementation of new actions to boost cooperation in social groups.

Most optimization-based community detection approaches formulate the problem in a single or bi-objective framework. In this paper, we propose two variants of a three-objective formulation using a customized non-dominated sorting genetic algorithm III (NSGA-III) to find community structures in a network. In the first variant, named NSGA-III-KRM, we considered Kernel k means, Ratio cut, and Modularity, as the three objectives, whereas the second variant, named NSGA-III-CCM, considers Community score, Community fitness and Modularity, as three objective functions. Experiments are conducted on four benchmark network datasets. Comparison with state-of-the-art approaches along with decomposition-based multi-objective evolutionary algorithm variants (MOEA/D-KRM and MOEA/D-CCM) indicates that the proposed variants yield comparable or better results. This is particularly significant because the addition of the third objective does not worsen the results of the other two objectives. We also propose a simple method to rank the Pareto solutions so obtained by proposing a new measure, namely the ratio of the hyper-volume and inverted generational distance (IGD). The higher the ratio, the better is the Pareto set. This strategy is particularly useful in the absence of empirical attainment function in the multi-objective framework, where the number of objectives is more than two.

Bernie Sanders' voting record is not progressive. It has been reported on Facebook that Bernie has voted 98% of the time in agreement with Senate Democrats and 93% of the time in agreement with Hillary Clinton. And here is Bernie Sanders' illustrious "progressive" voting record...LOL. Show this to all his crazed cult followers who claim he is a progressive and has done so much for us...LOL. Continue reading →

These memes will make you us want to quit Stalin and overthrow capitalism right Mao.

Ernesto Cardenal, the poet and cleric who became a symbol of revolutionary verse throughout Latin America, died Sunday at a Managua hospital at 95.

Boris Macek
Feb 1, 2008; 7:299-307
Research

Consider these scenarios. Scandal A: A prominent politician gets caught sleeping with a campaign aide and plunges himself into an ugly paternity dispute -- all while his cancer-stricken wife is fighting for her life.

How does your genetic inheritance, culture and history influence your health? Biological anthropologist Lara Durgavich discusses the field of evolutionary medicine as a gateway to understanding the quirks of human biology -- including why a genetic mutation can sometimes have beneficial effects -- and emphasizes how unraveling your own evolutionary past could glean insights into your current and future health.

Mental illness -- Genetic aspects.

Mohamad Elmasri, Maxwell J. Farrell, T. Jonathan Davies, David A. Stephens.

Source: The Annals of Applied Statistics, Volume 14, Number 1, 221--240.

Abstract:
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data; however, large species interaction databases are typically sparse and covariates are limited to only a fraction of species. On the other hand, evolutionary relationships, encoded as phylogenetic trees, can act as proxies for underlying traits and historical patterns of parasite sharing among hosts. We show that, using a network-based conditional model, phylogenetic information provides strong predictive power in a recently published global database of host-parasite interactions. By scaling the phylogeny using an evolutionary model, our method allows for biological interpretation often missing from latent variable models. To further improve on the phylogeny-only model, we combine a hierarchical Bayesian latent score framework for bipartite graphs that accounts for the number of interactions per species with host dependence informed by phylogeny. Combining the two information sources yields significant improvement in predictive accuracy over each of the submodels alone. As many interaction networks are constructed from presence-only data, we extend the model by integrating a correction mechanism for missing interactions which proves valuable in reducing uncertainty in unobserved interactions.

Khanh N. Dinh, Roman Jaksik, Marek Kimmel, Amaury Lambert, Simon Tavaré.

Source: Statistical Science, Volume 35, Number 1, 129--144.

Abstract:
Recent years have seen considerable work on inference about cancer evolution from mutations identified in cancer samples. Much of the modeling work has been based on classical models of population genetics, generalized to accommodate time-varying cell population size. Reverse-time, genealogical views of such models, commonly known as coalescents, have been used to infer aspects of the past of growing populations. Another approach is to use branching processes, the simplest scenario being the classical linear birth-death process. Inference from evolutionary models of DNA often exploits summary statistics of the sequence data, a common one being the so-called Site Frequency Spectrum (SFS). In a bulk tumor sequencing experiment, we can estimate for each site at which a novel somatic point mutation has arisen, the proportion of cells that carry that mutation. These numbers are then grouped into collections of sites which have similar mutant fractions. We examine how the SFS based on birth-death processes differs from those based on the coalescent model. This may stem from the different sampling mechanisms in the two approaches. However, we also show that despite this, they are quantitatively comparable for the range of parameters typical for tumor cell populations. We also present a model of tumor evolution with selective sweeps, and demonstrate how it may help in understanding the history of a tumor as well as the influence of data pre-processing. We illustrate the theory with applications to several examples from The Cancer Genome Atlas tumors.

To commemorate the 250th anniversary of the publication of his “Letters From a Pennsylvania Farmer” and the role John Dickinson played in setting the stage for the American Revolution, the Delaware Department of State has launched a new website, de.gov/johndickinson, and a slate of special programming to take place over the coming months.

The celebration of the life and works of Delaware statesman and “Penman of the Revolution” John Dickinson continues into the New Year with programs slated to explore his legacy and honor his contributions to the history of the state and the nation.

The celebration of the life and works of Delaware statesman John Dickinson comes to a close with a special program featuring Gov. John Carney and an annual wreath-laying at the graveside of the “Penman of the Revolution.”

Hallowed grounds believed to be the final resting place of some two dozen American soldiers who perished in the only major battle of the Revolutionary War fought in Delaware will soon become property of the state’s historic preservation agency, according to an agreement announced today.

Finding out how flight evolved or animals moved onto land is all about a collision of palaeontology and genetics, argue two new books

ABSTRACT

Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris.

IMPORTANCE In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology.

Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here, we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies (GWAS). We find that most common summary statistics have distributions that differ substantially from those seen in well-mixed populations, especially when Wright’s neighborhood size is < 100 and sampling is spatially clustered. "Stepping-stone" models reproduce some of these effects, but discretizing the landscape introduces artifacts that in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations revealed surprisingly little systematic bias. We also show that the combination of spatially autocorrelated environments and limited dispersal causes GWAS to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms.

The question of the relative evolutionary roles of adaptive and nonadaptive processes has been a central debate in population genetics for nearly a century. While advances have been made in the theoretical development of the underlying models, and statistical methods for estimating their parameters from large-scale genomic data, a framework for an appropriate null model remains elusive. A model incorporating evolutionary processes known to be in constant operation, genetic drift (as modulated by the demographic history of the population) and purifying selection, is lacking. Without such a null model, the role of adaptive processes in shaping within- and between-population variation may not be accurately assessed. Here, we investigate how population size changes and the strength of purifying selection affect patterns of variation at "neutral" sites near functional genomic components. We propose a novel statistical framework for jointly inferring the contribution of the relevant selective and demographic parameters. By means of extensive performance analyses, we quantify the utility of the approach, identify the most important statistics for parameter estimation, and compare the results with existing methods. Finally, we reanalyze genome-wide population-level data from a Zambian population of Drosophila melanogaster, and find that it has experienced a much slower rate of population growth than was inferred when the effects of purifying selection were neglected. Our approach represents an appropriate null model, against which the effects of positive selection can be assessed.

Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term and to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses.

Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence, and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein-coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1434 protein-coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein-coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cell pathways, including BMP and Wnt signaling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome-wide scale over macroevolutionary time is feasible. Although the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.

Manoella Gemaque Cavalcante, Cleusa Yoshiko Nagamachi, Julio Cesar Pieczarka, and Renata Coelho Rodrigues Noronha

Eukaryotic genomes exhibit substantial accumulation of repetitive DNA sequences. These sequences can participate in chromosomal reorganization events and undergo molecular cooption to interfere with the function and evolution of genomes. In turtles, repetitive DNA sequences appear to be accumulated at probable break points and may participate in events such as non-homologous recombination and chromosomal rearrangements. In this study, repeated sequences of 5S rDNA, U2 snRNA and Tc1/Mariner transposons were amplified from the genomes of the turtles, Podocnemis expansa and Podocnemis unifilis, and mapped by fluorescence in situ hybridization. Our data confirm the 2n=28 chromosomes for these species (the second lowest 2n in the order Testudines). We observe high conservation of the co-located 5S rDNA and U2 snRNA genes on a small chromosome pair (pair 13), and surmise that this represents the ancestral condition. Our analysis reveals a wide distribution of the Tc1/Mariner transposons and we discuss how the mobility of these transposons can act on karyotypic reorganization events (contributing to the 2n decrease of those species). Our data add new information for the order Testudines and provide important insights into the dynamics and organization of these sequences in the chelonian genomes.

Pangolins lack two genes that function to sound the alarm when a virus enters the body, triggering an immune response in most other mammals. The findings from the Medical University of Vienna, Austria, are significant because, while the exotic animals can be carriers of coronavirus, they appear able to tolerate it through some other unknown mechanism. Understanding how pangolins are able to survive coronavirus may point to possible treatment options for humans.

Largely overlooked in the incessant coronavirus news coverage in the United States was the death from COVID-19 of Mahmoud Jibril, one of Libya’s 2011 revolutionary leaders, in a Cairo hospital on April 5. Of all the Libyans who appealed to world leaders to go beyond lip service in support of the 2011 uprising, Jibril was…

A fail-safe filter that delivers water easily with a sip or a squeeze could save lives in places where water-borne illnesses thrive, but look for it first as a trendy gym accessory.

Even when made using hydro-electricity, aluminum production had a big carbon footprint.

Sumita Panjwani, a lady scientist in Chhattisgarh, has found a revolutionary way to use paddy stubble instead of burning it. She has managed to put it

250-million-year-old evolutionary remnants were found in muscles of human embryos. Strikingly, some of the atavistic limb muscles muscles, such as the

The study, published in Evolution, Medicine, and Public Health, examines why some people are more susceptible to a particular stress fracture known as

DR DAVID UNWIN: Thanks to low carb, my GP practice in Southport, Merseyside, has changed, with nearly 50 per cent of my patients having put their type 2 into remission.

London, May 8: The anteater-like mammals, pangolins, possess an evolutionary advantage against coronavirus, according to researchers, who say that understanding the animal's immune system may help develop new treatment options for COVID-19. According to the scientists from the Medical

Cham, Switzerland : Springer, c2019.

Dewey Library - HB97.3.H6336 2019

Online Resource

Schecter, Stephen (Professor of mathematics), author

Online Resource

Online Resource

Hayden Library - QH324.2.C433 2018

Barker Library - NC975.5.V45 A2 2019

Hayden Library - PQ7378.K86 2016

Dewey Library - HQ1413.E A77 2020

Hayden Library - B2799.M55 A23 2019

Little is known about long-lived David Grim (1737-1826) outside of the brief personal account of his life held by the New-York Historical Society Library. What can be said is that his memory was sound. A tavern keeper, merchant, and owner of Hessian’s Coffee House from 1767 to 1789, Grim sought to leave behind more than an...

The post “A Correct and Perfect Recollection”: David Grim’s Map of Prerevolutionary Manhattan appeared first on New-York Historical Society.