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PubMed Central
by Jain, Vishakha V.; Gupta, O. P.; Jajoo, Sumedh; Khiangate, Benjamin
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This article is from Journal of Family Medicine and Primary Care , volume 3 . Abstract Lymphangiomyomatosis (LAM) is a rare cystic interstitial lung disease that exclusively affects women of child bearing age and is associated with vascular proliferation of smooth muscle cells in the lung. We report a case of young female with pulmonary LAM presenting with recurrent pneumothorax.
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005212
340 p
Topics: gnas yig, gdan rabs/, rnam thar, ra lung dgon, Ralung Monastery Monastic chronicles
Free Music Archive
by BTB
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4 track electronica idm ep.
biorxiv
by Simon Joly; David J Bryant; Peter J Lockhart
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With the increasing use of massively parallel sequencing approaches in evolutionary biology, the need for fast and accurate methods suitable to investigate genetic structure and evolutionary history are more important than ever. We propose new distance measures for estimating genetic distances between individuals when allelic variation, gene dosage and recombination could compromise standard approaches. We present four distance measures based on single nucleotide polymorphisms (SNP) and...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/04/12/004184
biorxiv
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Various structures in the brain contain many important clues to the brains development and function. Among these, the organization of neuropil tissue at micron scales is of particular importance since such organization has a direct potential to affect the formation of synaptic connectivity between nearby axons and dendrites, thus, serving as an important factor contributing to the brains development and disorders. While the organization of the brain at large and intermediate scales had been...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/04/08/003863
biorxiv
by Gabriel Rosser; Ruth E. Baker; Judith P. Armitage; Alexander George Fletcher
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Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly-understood reorientation mechanism in the monoflagellate species Rhodobacter sphaeroides . The flagellum on this species rotates counterclockwise to propel the bacterium, periodically ceasing rotation to enable...
Topic: Microbiology
Source: http://biorxiv.org/content/early/2014/01/19/001917
biorxiv
by Sandeep Venkataram; Diamantis Sellis; Dmitri A Petrov
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Predicting the future evolutionary state of a population is a primary goal of evolutionary biology. One can differentiate between forward and backward predictability, where forward predictability is the probability of the same adaptive outcome occurring in independent evolutionary trials, and backward predictability is the likelihood of a particular adaptive path given the knowledge of the starting and final states. Most studies of evolutionary predictability assume that alleles along an...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/08/21/001016
biorxiv
by Adam Leache; Matthew Fujita; Vladimir Minin; Remco Bouckaert
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The multi-species coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/01/04/001172
biorxiv
by Niclas Thomas; Katharine Best; Mattia Cinelli; Shlomit Reich-Zeliger; Hila Gal; Eric Shifrut; Asaf Madi; Nir Friedman; John Shawe-Taylor; Benny Chain
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The clonal theory of adaptive immunity proposes that immunological responses are encoded by increases in the frequency of lymphocytes carrying antigen-specific receptors. In this study, we measure the frequency of different TcRs in CD4+ T cell populations of mice immunized with a complex antigen, killed Mycobacterium tuberculosis, using high throughput parallel sequencing of the TcR beta chain. In order to track the changes induced by immunization within this very heterogeneous repertoire, the...
Topic: Immunology
Source: http://biorxiv.org/content/early/2014/01/17/001883
biorxiv
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The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/05/09/005017
biorxiv
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Activity in the theta frequency band (4-8 Hz) over medial prefrontal regions has been consistently implicated in top-down cognitive control processes, including recognizing and resolving response conflict. It remains an unanswered question whether these theta-band dynamics are a neural mechanism of cognitive control, or instead are epiphenomenal to the neural computational machinery but are useful indices of brain function. Here we addressed this question by attempting to boost conflict...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/05/05/004747
Thanks to the reduced cost of RNA-Sequencing and other advanced methods for quantifying expression levels, accurate and expansive comparative expression data sets including data from multiple individuals per species are emerging. Comparative genomics has been greatly facilitated by the availability of statistical methods considering both between and within species variation for testing hypotheses regarding the evolution of DNA sequences. Similar methods are now needed to fully leverage...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/04/20/004374
biorxiv
by Christine Deffert; Michela G. Schäppi; Jean-Claude Pache; Julien Cachat; Dominique Vesin; Ruth Bisig; Xiaojuan Ma Mulone; Tiina Kelkka; Rikard Holmdahl; Irene Garcia; Maria L. Olleros; Karl-Heinz Krause
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Patients with chronic granulomatous disease(CGD) lack generation of reactive oxygen species (ROS) through the phagocyte NADPH oxidase NOX2. CGD is an immune deficiency that leads to frequent infections with certain pathogens; this is well documented for S. aureus and A. fumigatus, but less clear for mycobacteria. We therefore performed an extensive literature search which yielded 297 cases of CGD patients with mycobacterial infections; M.bovis BCG was most commonly recovered (74%). The...
Topic: Microbiology
Source: http://biorxiv.org/content/early/2014/06/03/005835
biorxiv
by Gurinder Singh Atwal
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The stochastic dynamics of multistable perception poses an enduring challenge to our understanding of neural signal processing in the brain. We show that the emergence of perception switching and stability can be understood using principles of probabilistic Bayesian inference where the prior temporal expectations are matched to a scale-free power spectrum, characteristic of fluctuations in the natural environment. The optimal percept dynamics are inferred by an exact mapping of the statistical...
Topic: Neuroscience
Source: http://biorxiv.org/content/early/2014/08/19/008177
biorxiv
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The effects of historical barriers in biogeographical patterns are expected to persist differently depending on dispersal abilities of organisms. We tested two hypotheses that plant groups with different dispersal abilities display different floristic patterns, and that historical barriers can explain floristic differentiation patterns in plants with low dispersal ability but not in plants with higher dispersal ability, in the seed plant flora of the Ryukyu Archipelago. This area is...
Topic: Ecology
Source: http://biorxiv.org/content/early/2014/08/07/007617
biorxiv
by Todd J. Treangen; Brian D. Ondov; Sergey Koren; Adam M. Phillippy
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Though many microbial species or clades now have hundreds of sequenced genomes, existing whole-genome alignment methods do not efficiently handle comparisons on this scale. Here we present the Harvest suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Combined they provide interactive core-genome alignments, variant calls,...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/07/22/007351
What does it mean when we say a cell?s biochemistry is regulated during changes to the phenotype? While there are a plethora of potential mechanisms and contributions to the final outcome, a more tractable approach is to examine the dynamics of mRNA. This way, we can assess the contributions of both known and unknown decay and aggregation processes for maintaining levels of gene product on a gene-by-gene basis. In this extended protocol, drug treatments that target specific cellular functions...
Topic: Cell Biology
Source: http://biorxiv.org/content/early/2014/06/20/006213
biorxiv
by Adrin Jalali; Nico Pfeifer
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Motivation: Molecular measurements from cancer patients such as gene expression and DNA methylation are usually very noisy. Furthermore, cancer types can be very heterogeneous. Therefore, one of the main assumptions for machine learning, that the underlying unknown distribution is the same for all samples, might not be completely fullfilled. We introduce a method, that can estimate this bias on a per-feature level and incorporate calculated feature confidences into a weighted combination of...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/09/15/008185
biorxiv
by Alexander Dilthey; Charles J Cox; Zamin Iqbal; Matthew R Nelson; Gil McVean
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In humans and many other species, while much is known about the extent and structure of genetic variation, such information is typically not used in assembling novel genomes. Rather, a single reference is used against which to map reads, which can lead to poor characterisation of regions of high sequence or structural diversity. Here, we introduce a population reference graph, which combines multiple reference sequences as well as catalogues of SNPs and short indels. The genomes of novel...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/07/08/006973
biorxiv
by Gargi Dayama; Sarah B Emery; Jeffrey M Kidd; Ryan E Mills
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The transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon. Many studies over the past decade have utilized reference genome sequences of numerous species to characterize the prevalence and contribution of nuclear mitochondrial insertions to human diseases. The recent advancement of high throughput sequencing technologies has enabled the interrogation of genomic variation at a much finer scale, and now allows for an exploration into...
Topic: Genomics
Source: http://biorxiv.org/content/early/2014/08/19/008144
biorxiv
by Jared A Grummer; Martha L. Calderón; Adrián Nieto Montes-de Oca; Eric N Smith; Fausto Mendez-de la Cruz; Adam Leache
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Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/09/02/008623
biorxiv
by Sune Pletscher-Frankild; Albert Pallejà; Kalliopi Tsafou; Janos X Binder; Lars Juhl Jensen
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Text mining is a flexible technology that can be applied to numerous different tasks in biology and medicine. We present a system for extracting disease–gene associations from biomedical abstracts. The system consists of a highly efficient dictionary-based tagger for named entity recognition of human genes and diseases, which we combine with a scoring scheme that takes into account co-occurrences both within and between sentences. We show that this approach is able to extract half of all...
Topic: Bioinformatics
Source: http://biorxiv.org/content/early/2014/08/25/008425
biorxiv
by Traver Hart; Kevin R Brown; Fabrice Sircoulomb; Robert Rottapel; Jason Moffat
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Technological advancement has opened the door to systematic genetics in mammalian cells. Genome-scale loss-of-function screens can assay fitness defects induced by partial gene knockdown, using RNA interference, or complete gene knockout, using new CRISPR techniques. These screens can reveal the basic blueprint required for cellular proliferation. Moreover, comparing healthy to cancerous tissue can uncover genes that are essential only in the tumor; these genes are targets for the development...
Topic: Systems Biology
Source: http://biorxiv.org/content/early/2014/03/17/003327
biorxiv
by Vincent Sonnay; Loïc Pellissier; Jean-Nicolas Pradervand; Luigi Maiorano; Anne Dubuis; Mary S. Wisz; Antoine Guisan
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Predicting spatial patterns of species diversity and composition using suitable environmental predictors is an essential element in conservation planning. Although species have distinct relationships to environmental conditions, some similarities may exist among species that share functional characteristics or traits. We investigated the relationship between species richness, composition and abiotic and biotic environment in different groups of butterflies that share ecological characteristics....
Topic: Ecology
Source: http://biorxiv.org/content/early/2014/01/27/002147
biorxiv
by Philip Gerlee; Alexander RA Anderson
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Many species engage in niche construction that ultimately leads to an increase in the carrying capacity of the population. We have investigated how the specificity of this behaviour affects evolutionary dynamics using a set of coupled logistic equations, where the carrying capacity of each genotype consists of two components: an intrinsic part and a contribution from all genotypes present in the population. The relative contribution of the two components is controlled by a specificity parameter...
Topic: Evolutionary Biology
Source: http://biorxiv.org/content/early/2014/02/05/002378
Eiichi Yamashita Interview I
by Densho Visual History Collection
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Interview location: Seattle, Washington Description of father Segment 3 of 19 [ Previous segment ] -- [ Next segment ] For more information, visit Densho
Topics: Japanese Americans, Oral history
George Oda Interview
by Manzanar National Historic Site Collection
movies

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Interview location: Wife's family background Segment 17 of 25 [ Previous segment ] -- [ Next segment ] For more information, visit Densho
Topics: Japanese Americans, Oral history
Emiko Namba Kikkawa Interview
by Oregon Nikkei Endowment Collection
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Interview location: Portland, Oregon Memories of the train ride to Minidoka Segment 10 of 15 [ Previous segment ] -- [ Next segment ] For more information, visit Densho
Topics: Japanese Americans, Oral history, Minidoka
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For Your Ears Only / On Air
by David Alpern
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Best of the Best II: Inside Watergate (2005); le Carre Beyond Cold War (1989); Nancy Reagan's Rebuttal (1989); Secret of Sinatra (1998); Faith and Shame, Art and Fame (2004); Archive - D-Day Real and Reel (2004) Lineup: I. BILLBOARD: BEST OF THE BEST II II. WATERGATE: INSIDE VIEWS - 6/6/05, 6/14/92, 10/22/89 Bob Woodward, "Washington Post" Assistant Managing Editor; Watergate Reporter - From Newsweek On Air 10/22/89 and Carl Bernstein, author; Watergate Reporter, from Newsweek On Air...
Topics: Watergate, Woodward, Bernstein, Graham, le Carre, Reagan, Sinatra, Sheed, Marcovicci, Abuse, Avedon
Source: http://gatewave.org/sites/all/files/fyeo/fyeo_140921_complete.mp3
PubMed Central
by Schnorr, Stephanie L.; Candela, Marco; Rampelli, Simone; Centanni, Manuela; Consolandi, Clarissa; Basaglia, Giulia; Turroni, Silvia; Biagi, Elena; Peano, Clelia; Severgnini, Marco; Fiori, Jessica; Gotti, Roberto; De Bellis, Gianluca; Luiselli, Donata; Brigidi, Patrizia; Mabulla, Audax; Marlowe, Frank; Henry, Amanda G.; Crittenden, Alyssa N.
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This article is from Nature Communications , volume 5 . Abstract Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher...
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996546
PubMed Central
by Meule, Adrian; Hermann, Tina; Kubler, Andrea
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This article is from Frontiers in Psychology , volume 5 . Abstract One of the most often used instruments for the assessment of food cravings is the Food Cravings Questionnaire (FCQ), which consists of a trait (FCQ-T; 39 items) and state (FCQ-S; 15 items) version. Scores on the FCQ-T have been found to be positively associated with eating pathology, body mass index (BMI), low dieting success and increases in state food craving during cognitive tasks involving appealing food stimuli. The current...
Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940888
Buddhist Digital Resource Center
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3, 4, 427 p
Topics: slob deb, bod skad/
287 p
Topics: gsung rtsom/, nag po skal bzang
4, 2, 127 p
Topics: gso rig, sman sbyor, Science of medicine Medicinal preparation
5, 9, 658 p
Topics: dgon pa/, khor yug, mtsho sngon zhing chen, si khron zhing chen/, kan su'u zhing chen, yun nan...
Buddhist Digital Resource Center
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, 2, 99 p
Topics: bca' khrims/, Bcaʼ khrims
Buddhist Digital Resource Center
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95 p
Topics: khor yug, slob gso, Environmental Slob sbyong
14, 3, 384 p
Topics: chos spyod, skad yig shan sbyar/