Energy Flows in Low-Entropy Complex Systems

Nature's many complex systems--physical, biological, and cultural--are islands of low-entropy order within increasingly disordered seas of surrounding, high-entropy chaos. Energy is a principal facilitator of the rising complexity of all such systems in the expanding Universe, including galaxies, stars, planets, life, society, and machines. A large amount of empirical evidence--relating neither entropy nor information, rather energy--suggests that an underlying simplicity guides the emergence and growth of complexity among many known, highly varied systems in the 14-billion-year-old Universe, from big bang to humankind. Energy flows are as centrally important to life and society as they are to stars and galaxies. In particular, the quantity energy rate density--the rate of energy flow per unit mass--can be used to explicate in a consistent, uniform, and unifying way a huge collection of diverse complex systems observed throughout Nature. Operationally, those systems able to utilize optimal amounts of energy tend to survive and those that cannot are non-randomly eliminated.Comment: 12 pages, 2 figures, review paper for special issue on Recent Advances in Non-Equilibrium Statistical Mechanics and its Application. arXiv admin note: text overlap with arXiv:1406.273

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Factors Influencing Stem Density of Creekbank Spartina alterniflora in a New England Salt Marsh

Stem density patterns for smooth cordgrass, Spartina alterniflora, are highly variable both among years and within the growing season. These variations can have consequences for the overall primary productivity of the salt marsh system, as well as its ability to provide essential ecosystem functions. In this study, I explored factors that could be driving observed variations in four tidal creeks of the Plum Island Sound Estuary, Massachusetts. End of season stem densities were measured at two of the creeks over eight years. Seasonal stem densities were measured at all four of the creeks four times during a single growing season. My objectives were to assess the influence of temperature, precipitation, tide level, and solar radiation on stem density variations among years, and to determine whether seasonal loss of stems was due to self-thinning or tidal action. Years with higher precipitation were associated with higher densities (p = 0.001), which may be due to an alleviation of salt stress in those years. Patterns of seasonal stem loss were more consistent with patterns of self-thinning, which has not been previously considered for S. alterniflora, than tidal action, which has been the predominant assumption. However, self-thinning and tidal action may be working in conjunction to cause seasonal stem loss. These results increase our ability to estimate S. alterniflora productivity, and our understanding of the species’ ecology and its responses to current and future climatological events

On the analysis of tuberculosis studies with intermittent missing sputum data

In randomized studies evaluating treatments for tuberculosis (TB), individuals are scheduled to be routinely evaluated for the presence of TB using sputum cultures. One important endpoint in such studies is the time of culture conversion, the first visit at which a patient’s sputum culture is negative and remains negative. This article addresses how to draw inference about treatment effects when sputum cultures are intermittently missing on some patients. We discuss inference under a novel benchmark assumption and under a class of assumptions indexed by a treatment-specific sensitivity parameter that quantify departures from the benchmark assumption. We motivate and illustrate our approach using data from a randomized trial comparing the effectiveness of two treatments for adult TB patients in Brazil.Fil: Scharfstein, Daniel. University Johns Hopkins; Estados UnidosFil: Rotnitzky, Andrea Gloria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Torcuato Di Tella. Departamento de Economía; ArgentinaFil: Abraham, Maria. Statistics Collaborative; Estados UnidosFil: McDermott, Aidan. University Johns Hopkins; Estados UnidosFil: Chaisson, Richard. University Johns Hopkins; Estados UnidosFil: Geiter, Lawrence. Otsuka Novel Products; Estados Unido

Tuberculosis and Human Immunodeficiency Virus Infection

Progressive human immunodeficiency virus infection eventually leads to activation and dissemination of a wide variety of microorganisms normally held in check by the cellular immune system. Mycobacterium tuberculosis is one of these pathogens, and the disease caused by it has become a common presenting infection in the patient with AIDS. Dr. Richard E. Chaisson and Dr. Gary Slutkin have studied tuberculosis in the United States and worldwide, respectively. In this AIDS Commentary they address the unique nature of this infection, its diagnosis, and its treatment in the patient with AID

Reply to “At the crossroads between early or delayed antiretroviral therapy initiation during TB/HIV coinfection”

La digitalització dels textos, iniciada en la dècada dels setanta, ha originat sistemes i productes diversos que poden ser molt útils en la investigació literària. Un dels més coneguts, lâhipertext, és un bon exemple de les possibilitats de la lectura no seqüencial que caracteritza les obres de referència o determinades recerques en lâàmbit de la filologia, com ara lâedició de textos. La digitalització destaca les característiques tant hipertextuals com intertextuals de la literatura i ajuda a entendre, així, alguns dels seus trets constitutius. Dâaltra banda, la publicació en línia de textos de molt difícil abast proposada per comunitats científiques molt presents a Internet és una oferta plena de possibilitats i suggereix un camí a seguir per comunitats encara poc implantades, com ara la filologia catalana. | Digitisation of text, begun in the 1970s, has produced a diversity of systems and products that could be very useful for literary research. One of the better known examples, hypertext, demonstrates the potential for non-sequential reading that characterises the use made of reference works or specific searches performed in the field of philology, such as for text publishing. Digitisation highlights both | La digitalización de textos, iniciada en la década de los años setenta, ha dado lugar a sistemas y productos diversos que pueden ser muy útiles en la investigación literaria. Uno de los más conocidos, el hipertexto, constituye un buen ejemplo de las posibilidades de la lectura secuencial que caracteriza las obras de referencia o determinadas investigaciones en el ámbito de la Filología, como, por ejemplo, la edición de textos. La digitalización destaca las características tanto hipertextuales como intertextuales de la literatura facilitando, por tanto, su comprensión. Por otro lado, la publicación en línea de textos de muy difícil acceso, propuesta por comunidades científicas muy presentes en Internet, es una oferta llena de posibilidades y abre un camino a seguir por parte de comunidades poco implantadas todavía como es el caso de la Filología catalana

A Model of Habitability Within the Milky Way Galaxy

We present a model of the Galactic Habitable Zone (GHZ), described in terms of the spatial and temporal dimensions of the Galaxy that may favour the development of complex life. The Milky Way galaxy is modelled using a computational approach by populating stars and their planetary systems on an individual basis using Monte-Carlo methods. We begin with well-established properties of the disk of the Milky Way, such as the stellar number density distribution, the initial mass function, the star formation history, and the metallicity gradient as a function of radial position and time. We vary some of these properties, creating four models to test the sensitivity of our assumptions. To assess habitability on the Galactic scale, we model supernova rates, planet formation, and the time required for complex life to evolve. Our study improves on other literature on the GHZ by populating stars on an individual basis and by modelling SNII and SNIa sterilizations by selecting their progenitors from within this preexisting stellar population. Furthermore, we consider habitability on tidally locked and non-tidally locked planets separately, and study habitability as a function of height above and below the Galactic midplane. In the model that most accurately reproduces the properties of the Galaxy, the results indicate that an individual SNIa is ~5.6 \times more lethal than an individual SNII on average. In addition, we predict that ~1.2% of all stars host a planet that may have been capable of supporting complex life at some point in the history of the Galaxy. Of those stars with a habitable planet, ~75% of planets are predicted to be in a tidally locked configuration with their host star. The majority of these planets that may support complex life are found towards the inner Galaxy, distributed within, and significantly above and below, the Galactic midplane.Comment: Accepted for publication in Astrobiology. 40 pages, 12 figures, 3 table