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https://www.readbyqxmd.com/read/28097055/comprehensive-transcriptome-analysis-provides-new-insights-into-nutritional-strategies-and-phylogenetic-relationships-of-chrysophytes
#1
Daniela Beisser, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk
BACKGROUND: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms...
2017: PeerJ
https://www.readbyqxmd.com/read/28094438/environmental-niche-conservatism-explains-the-accumulation-of-species-richness-in-mediterranean-hotspot-plant-genera
#2
Alexander Skeels, Marcel Cardillo
The causes of exceptionally high plant diversity in Mediterranean-climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus...
January 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28087598/bayesian-network-inference-modeling-identifies-trib1-as-a-novel-regulator-of-cell-cycle-progression-and-survival-in-cancer-cells
#3
Rina Gendelman, Heming Xing, Olga K Mirzoeva, Preeti Sarde, Christina Curtis, Heidi Feiler, Paul McDonagh, Joe W Gray, Iya Khalil, W Michael Korn
Molecular networks governing cellular responses to targeted therapies are complex dynamic systems with non-intuitive behaviors. Here we applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell cycle arrest caused by inhibition of MEK1/2. Through simulation of reverse-engineered Bayesian network modeling, we generated predictions of G1-S transition...
January 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28068340/phylogeography-of-rift-valley-fever-virus-in-africa-and-the-arabian-peninsula
#4
Abdallah M Samy, A Townsend Peterson, Matthew Hall
Rift Valley Fever is an acute zoonotic viral disease caused by Rift Valley Fever virus (RVFV) that affects ruminants and humans in Sub-Saharan Africa and the Arabian Peninsula. We used phylogenetic analyses to understand the demographic history of RVFV populations, using sequence data from the three minigenomic segments of the virus. We used phylogeographic approaches to infer RVFV historical movement patterns across its geographic range, and to reconstruct transitions among host species. Results revealed broad circulation of the virus in East Africa, with many lineages originating in Kenya...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28066502/a-correlated-binary-model-for-ignorable-missing-data-application-to-rheumatoid-arthritis-clinical-data
#5
Francis Erebholo, Victor Apprey, Paul Bezandry, John Kwagyan
Incomplete data are common phenomenon in research that adopts the longitudinal design approach. If incomplete observations are present in the longitudinal data structure, ignoring it could lead to bias in statistical inference and interpretation. We adopt the disposition model and extend it to the analysis of longitudinal binary outcomes in the presence of monotone incomplete data. The response variable is modeled using a conditional logistic regression model. The nonresponse mechanism is assumed ignorable and developed as a combination of Markov's transition and logistic regression model...
April 2016: Journal of Data Science: JDS
https://www.readbyqxmd.com/read/28065983/herschel-hifi-observations-of-the-circumstellar-ammonia-lines-in-irc-10216
#6
M R Schmidt, J H He, R Szczerba, V Bujarrabal, J Alcolea, J Cernicharo, L Decin, K Justtanont, D Teyssier, K M Menten, D A Neufeld, H Olofsson, P Planesas, A P Marston, A M Sobolev, A de Koter, F L Schöier
CONTEXT: A discrepancy exists between the abundance of ammonia (NH3) derived previously for the circumstellar envelope (CSE) of IRC+10216 from far-IR submillimeter rotational lines and that inferred from radio inversion or mid-infrared (MIR) absorption transitions. AIMS: To address the discrepancy described above, new high-resolution far-infrared (FIR) observations of both ortho- and para-NH3 transitions toward IRC+10216 were obtained with Herschel, with the goal of determining the ammonia abundance and constraining the distribution of NH3 in the envelope of IRC+10216...
August 2016: Astronomy and Astrophysics
https://www.readbyqxmd.com/read/28058975/the-spatial-coefficient-of-variation-in-arterial-spin-labeling-cerebral-blood-flow-images
#7
Henri Jmm Mutsaerts, Jan Petr, Lena Václavů, Jan W van Dalen, Andrew D Robertson, Matthan W Caan, Mario Masellis, Aart J Nederveen, Edo Richard, Bradley J MacIntosh
Macro-vascular artifacts are a common arterial spin labeling (ASL) finding in populations with prolonged arterial transit time (ATT) and result in vascular regions with spuriously increased cerebral blood flow (CBF) and tissue regions with spuriously decreased CBF. This study investigates whether there is an association between the spatial signal distribution of a single post-label delay ASL CBF image and ATT. In 186 elderly with hypertension (46% male, 77.4 ± 2.5 years), we evaluated associations between the spatial coefficient of variation (CoV) of a CBF image and ATT...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28057833/cognitive-skills-and-the-evolution-of-social-systems
#8
REVIEW
Russell D Fernald
How do animal social skills influence evolution? Complex animal social behaviors require many cognitive skills including individual recognition and observational learning. For social systems to evolve, these abilities need to be transmitted genetically or culturally and supported by the evolution of underlying neural systems. Because animal skill sets are so varied, it seems best to describe animal cognitive behaviors as being a social calculus that can change with experience, which has evolved to match and facilitate the complexity of the social system where it arose...
January 1, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28057728/the-effects-of-increasing-the-number-of-taxa-on-inferences-of-molecular-convergence
#9
Gregg W C Thomas, Matthew W Hahn, Yoonsoo Hahn
Convergent evolution provides insight into the link between phenotype and genotype. Recently, large-scale comparative studies of convergent evolution have become possible, but researchers are still trying to determine the best way to design these types of analyses. One aspect of molecular convergence studies that has not yet been investigated is how taxonomic sample size affects inferences of molecular convergence. Here we show that increased sample size decreases the amount of inferred molecular convergence associated with the three convergent transitions to a marine environment in mammals...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28057005/intragenerational-social-mobility-and-functional-somatic-symptoms-in-a-northern-swedish-context-analyses-of-diagonal-reference-models
#10
Frida Jonsson, Miguel San Sebastian, Anne Hammarström, Per E Gustafsson
BACKGROUND: Research indicate that social class mobility could be potentially important for health, but whether this is due to the movement itself or a result of people having been integrated in different class contexts is, to date, difficult to infer. In addition, although several theories suggest that transitions between classes in the social hierarchy can be stressful experiences, few studies have empirically examined whether such movements may have health effects, over and above the implications of "being" in these classes...
January 3, 2017: International Journal for Equity in Health
https://www.readbyqxmd.com/read/28055211/multidimensional-large-amplitude-dynamics-in-the-pyridine-water-complex
#11
Rebecca B Mackenzie, Christopher T Dewberry, Ryan D Cornelius, C J Smith, Kenneth R Leopold
Aqueous pyridine plays an important role in a variety of catalytic processes aimed at harnessing solar energy. In this work, the pyridine-water interaction is studied by microwave spectroscopy and density functional theory calculations. Water forms a hydrogen bond to the nitrogen with the oxygen tilted slightly toward either of the ortho-hydrogens of the pyridine, and a tunneling motion involving in-plane rocking of the water interconverts the resulting equivalent structures. A pair of tunneling states with severely perturbed rotational spectra is identified and their energy separation, ΔE, is inferred from the perturbations and confirmed by direct measurement...
January 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28042857/estimation-of-ground-reaction-forces-and-moments-during-gait-using-only-inertial-motion-capture
#12
Angelos Karatsidis, Giovanni Bellusci, H Martin Schepers, Mark de Zee, Michael S Andersen, Peter H Veltink
Ground reaction forces and moments (GRF&M) are important measures used as input in biomechanical analysis to estimate joint kinetics, which often are used to infer information for many musculoskeletal diseases. Their assessment is conventionally achieved using laboratory-based equipment that cannot be applied in daily life monitoring. In this study, we propose a method to predict GRF&M during walking, using exclusively kinematic information from fully-ambulatory inertial motion capture (IMC). From the equations of motion, we derive the total external forces and moments...
December 31, 2016: Sensors
https://www.readbyqxmd.com/read/28030543/human-inferences-about-sequences-a-minimal-transition-probability-model
#13
Florent Meyniel, Maxime Maheu, Stanislas Dehaene
The brain constantly infers the causes of the inputs it receives and uses these inferences to generate statistical expectations about future observations. Experimental evidence for these expectations and their violations include explicit reports, sequential effects on reaction times, and mismatch or surprise signals recorded in electrophysiology and functional MRI. Here, we explore the hypothesis that the brain acts as a near-optimal inference device that constantly attempts to infer the time-varying matrix of transition probabilities between the stimuli it receives, even when those stimuli are in fact fully unpredictable...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/28028238/major-transitions-in-dinoflagellate-evolution-unveiled-by-phylotranscriptomics
#14
Jan Janouškovec, Gregory S Gavelis, Fabien Burki, Donna Dinh, Tsvetan R Bachvaroff, Sebastian G Gornik, Kelley J Bright, Behzad Imanian, Suzanne L Strom, Charles F Delwiche, Ross F Waller, Robert A Fensome, Brian S Leander, Forest L Rohwer, Juan F Saldarriaga
Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28018015/bayesian-nonparametric-estimation-for-dynamic-treatment-regimes-with-sequential-transition-times
#15
Yanxun Xu, Peter Müller, Abdus S Wahed, Peter F Thall
We analyze a dataset arising from a clinical trial involving multi-stage chemotherapy regimes for acute leukemia. The trial design was a 2 × 2 factorial for frontline therapies only. Motivated by the idea that subsequent salvage treatments affect survival time, we model therapy as a dynamic treatment regime (DTR), that is, an alternating sequence of adaptive treatments or other actions and transition times between disease states. These sequences may vary substantially between patients, depending on how the regime plays out...
2016: Journal of the American Statistical Association
https://www.readbyqxmd.com/read/28011454/predicting-neurosurgical-outcomes-in-focal-epilepsy-patients-using-computational-modelling
#16
Nishant Sinha, Justin Dauwels, Marcus Kaiser, Sydney S Cash, M Brandon Westover, Yujiang Wang, Peter N Taylor
Surgery can be a last resort for patients with intractable, medically refractory epilepsy. For many of these patients, however, there is substantial risk that the surgery will be ineffective. The prediction of who is likely to benefit from a surgical approach is crucial for being able to inform patients better, conduct principled prospective clinical trials, and ultimately tailor therapeutic approaches to these patients more effectively. Dynamical computational models, informed with patient data, can be used to make predictions and give mechanistic insight...
December 23, 2016: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28009838/modeling-driver-behavior-near-intersections-in-hidden-markov-model
#17
Juan Li, Qinglian He, Hang Zhou, Yunlin Guan, Wei Dai
Intersections are one of the major locations where safety is a big concern to drivers. Inappropriate driver behaviors in response to frequent changes when approaching intersections often lead to intersection-related crashes or collisions. Thus to better understand driver behaviors at intersections, especially in the dilemma zone, a Hidden Markov Model (HMM) is utilized in this study. With the discrete data processing, the observed dynamic data of vehicles are used for the inference of the Hidden Markov Model...
December 21, 2016: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28009262/cell-lineage-trees-bear-fruit
#18
Jordi Garcia-Ojalvo
Two inference approaches harness the information present in cell lineage trees to better understand the dynamic transitions between cell states.
December 21, 2016: Cell Systems
https://www.readbyqxmd.com/read/28005952/microrna-and-transcription-factor-gene-regulatory-network-analysis-reveals-key-regulatory-elements-associated-with-prostate-cancer-progression
#19
Mehdi Sadeghi, Bijan Ranjbar, Mohamad Reza Ganjalikhany, Faiz M Khan, Ulf Schmitz, Olaf Wolkenhauer, Shailendra K Gupta
Technological and methodological advances in multi-omics data generation and integration approaches help elucidate genetic features of complex biological traits and diseases such as prostate cancer. Due to its heterogeneity, the identification of key functional components involved in the regulation and progression of prostate cancer is a methodological challenge. In this study, we identified key regulatory interactions responsible for primary to metastasis transitions in prostate cancer using network inference approaches by integrating patient derived transcriptomic and miRomics data into gene/miRNA/transcription factor regulatory networks...
2016: PloS One
https://www.readbyqxmd.com/read/28000700/different-kinds-of-genetic-markers-permit-inference-of-paleolithic-and-neolithic-expansions-in-humans
#20
Carla Aimé, Frédéric Austerlitz
Recent population genetic studies have provided valuable insights on the demographic history of our species. However, some issues such as the dating of the first demographic expansions in human populations remain puzzling. Indeed, although a few genetic studies argued that the first human expansions were concomitant with the Neolithic transition, many others found signals of expansion events starting during the Palaeolithic. Here we performed a simulation study to show that these contradictory findings may result from the differences in the genetic markers used, especially if two successive expansion events occurred...
December 21, 2016: European Journal of Human Genetics: EJHG
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