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https://www.readbyqxmd.com/read/29451947/a-wild-bootstrap-approach-for-the-aalen-johansen-estimator
#1
Tobias Bluhmki, Claudia Schmoor, Dennis Dobler, Markus Pauly, Juergen Finke, Martin Schumacher, Jan Beyersmann
We suggest a wild bootstrap resampling technique for nonparametric inference on transition probabilities in a general time-inhomogeneous Markov multistate model. We first approximate the limiting distribution of the Nelson-Aalen estimator by repeatedly generating standard normal wild bootstrap variates, while the data is kept fixed. Next, a transformation using a functional delta method argument is applied. The approach is conceptually easier than direct resampling for the transition probabilities. It is used to investigate a non-standard time-to-event outcome, currently being alive without immunosuppressive treatment, with data from a recent study of prophylactic treatment in allogeneic transplanted leukemia patients...
February 16, 2018: Biometrics
https://www.readbyqxmd.com/read/29449836/changes-in-microbial-energy-metabolism-measured-by-nanocalorimetry-during-growth-phase-transitions
#2
Alberto Robador, Douglas E LaRowe, Steven E Finkel, Jan P Amend, Kenneth H Nealson
Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29445794/high-pressure-dissociation-of-selenium-and-tellurium
#3
Xin Li, Xiaoli Huang, Xin Wang, Mingkun Liu, Gang Wu, Yanping Huang, Xin He, Fangfei Li, Qiang Zhou, Bingbing Liu, Tian Cui
Pressure-induced molecular dissociation provides significant insights into chemical bonding, governing the physical properties of molecular solids. Here the typical molecular solids, selenium and tellurium, have been explored experimentally to unearth the process of pressure-induced molecular dissociation. Before molecular dissociation, both commensurately and incommensurately modulated structures have been observed in these two elements. Upon compression, the successive commensurate-incommensurate phase transitions are proved by the soft amplitude (AMP) mode...
February 15, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29416021/visualizing-heavy-fermion-confinement-and-pauli-limited-superconductivity-in-layered-cecoin5
#4
András Gyenis, Benjamin E Feldman, Mallika T Randeria, Gabriel A Peterson, Eric D Bauer, Pegor Aynajian, Ali Yazdani
Layered material structures play a key role in enhancing electron-electron interactions to create correlated metallic phases that can transform into unconventional superconducting states. The quasi-two-dimensional electronic properties of such compounds are often inferred indirectly through examination of bulk properties. Here we use scanning tunneling microscopy to directly probe in cross-section the quasi-two-dimensional electronic states of the heavy fermion superconductor CeCoIn5. Our measurements reveal the strong confined nature of quasiparticles, anisotropy of tunneling characteristics, and layer-by-layer modulated behavior of the precursor pseudogap gap phase...
February 7, 2018: Nature Communications
https://www.readbyqxmd.com/read/29415263/scepath-energy-landscape-based-inference-of-transition-probabilities-and-cellular-trajectories-from-single-cell-transcriptomic-data
#5
Suoqin Jin, Adam L MacLean, Tao Peng, Qing Nie
Motivation: Single-cell RNA-sequencing (scRNA-seq) offers unprecedented resolution for studying cellular decision-making processes. Robust inference of cell state transition paths and probabilities is an important yet challenging step in the analysis of these data. Results: Here we present scEpath, an algorithm that calculates energy landscapes and probabilistic directed graphs in order to reconstruct developmental trajectories. We quantify the energy landscape using "single-cell energy" and distance-based measures, and find that the combination of these enables robust inference of the transition probabilities and lineage relationships between cell states...
February 5, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29393058/emergence-of-a-new-valence-ordered-structure-and-collapse-of-the-magnetic-order-under-high-pressure-in-euptp
#6
Akihiro Mitsuda, Shigeki Manabe, Masafumi Umeda, Hirofumi Wada, Kazuyuki Matsubayashi, Yoshiya Uwatoko, Masaichiro Mizumaki, Naomi Kawamura, Kiyofumi Nitta, Naohisa HIrao, Yasuo Ohishi, Naoki Ishimatsu
The layered hexagonal EuPtP is a rare substance that exhibits two successive valence transitions occurring simultaneously with valence ordering transitions and an antiferromagnetic order. Anticipating that the application of pressure to this sample would induce a new valence-ordered structure and/or a new phenomenon associated with valence fluctuation, we examined the electrical resistivity ρ, the Eu L<sub>3</sub>-edge X-ray absorption spectroscopy, and the powder X-ray diffraction under high pressure...
February 2, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29391171/approximate-bayesian-computation-reveals-the-importance-of-repeated-measurements-for-parameterising-cell-based-models-of-growing-tissues
#7
Jochen Kursawe, Ruth E Baker, Alexander G Fletcher
The growth and dynamics of epithelial tissues govern many morphogenetic processes in embryonic development. A recent quantitative transition in data acquisition, facilitated by advances in genetic and live-imaging techniques, is paving the way for new insights to these processes. Computational models can help us understand and interpret observations, and then make predictions for future experiments that can distinguish between hypothesised mechanisms. Increasingly, cell-based modelling approaches such as vertex models are being used to help understand the mechanics underlying epithelial morphogenesis...
January 29, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29360744/melanins-in-fossil-animals-is-it-possible-to-infer-life-history-traits-from-the-coloration-of-extinct-species
#8
REVIEW
Juan J Negro, Clive Finlayson, Ismael Galván
Paleo-colour scientists have recently made the transition from describing melanin-based colouration in fossil specimens to inferring life-history traits of the species involved. Two such cases correspond to counter-shaded dinosaurs: dark-coloured due to melanins dorsally, and light-coloured ventrally. We believe that colour reconstruction of fossils based on the shape of preserved microstructures-the majority of paleo-colour studies involve melanin granules-is not without risks. In addition, animals with contrasting dorso-ventral colouration may be under different selection pressures beyond the need for camouflage, including, for instance, visual communication or ultraviolet (UV) protection...
January 23, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29358391/evolutionary-history-of-carbon-monoxide-dehydrogenase-acetyl-coa-synthase-one-of-the-oldest-enzymatic-complexes
#9
Panagiotis S Adam, Guillaume Borrel, Simonetta Gribaldo
Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of uncultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes...
January 22, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29348571/high-resolution-time-series-reveals-cohesive-but-short-lived-communities-in-coastal-plankton
#10
Antonio M Martin-Platero, Brian Cleary, Kathryn Kauffman, Sarah P Preheim, Dennis J McGillicuddy, Eric J Alm, Martin F Polz
Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29347631/phase-transitions-in-restricted-boltzmann-machines-with-generic-priors
#11
Adriano Barra, Giuseppe Genovese, Peter Sollich, Daniele Tantari
We study generalized restricted Boltzmann machines with generic priors for units and weights, interpolating between Boolean and Gaussian variables. We present a complete analysis of the replica symmetric phase diagram of these systems, which can be regarded as generalized Hopfield models. We underline the role of the retrieval phase for both inference and learning processes and we show that retrieval is robust for a large class of weight and unit priors, beyond the standard Hopfield scenario. Furthermore, we show how the paramagnetic phase boundary is directly related to the optimal size of the training set necessary for good generalization in a teacher-student scenario of unsupervised learning...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347521/inverse-problem-for-multispecies-ferromagneticlike-mean-field-models-in-phase-space-with-many-states
#12
Micaela Fedele, Cecilia Vernia
In this paper we solve the inverse problem for the Curie-Weiss model and its multispecies version when multiple thermodynamic states are present as in the low temperature phase where the phase space is clustered. The inverse problem consists of reconstructing the model parameters starting from configuration data generated according to the distribution of the model. We demonstrate that, without taking into account the presence of many states, the application of the inversion procedure produces very poor inference results...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29338005/inferring-cell-state-by-quantitative-motility-analysis-reveals-a-dynamic-state-system-and-broken-detailed-balance
#13
Jacob C Kimmel, Amy Y Chang, Andrew S Brack, Wallace F Marshall
Cell populations display heterogeneous and dynamic phenotypic states at multiple scales. Similar to molecular features commonly used to explore cell heterogeneity, cell behavior is a rich phenotypic space that may allow for identification of relevant cell states. Inference of cell state from cell behavior across a time course may enable the investigation of dynamics of transitions between heterogeneous cell states, a task difficult to perform with destructive molecular observations. Cell motility is one such easily observed cell behavior with known biomedical relevance...
January 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29318635/plant-evolution-landmarks-on-the-path-to-terrestrial-life
#14
REVIEW
Jan de Vries, John M Archibald
Contents I. II. III. IV. ORCID References SUMMARY: Photosynthetic eukaryotes thrive anywhere there is sunlight and water. But while such organisms are exceptionally diverse in form and function, only one phototrophic lineage succeeded in rising above its substrate: the land plants (embryophytes). Molecular phylogenetic data show that land plants evolved from streptophyte algae most closely related to extant Zygnematophyceae, and one of the principal aims of plant evolutionary biology is to uncover the key features of such algae that enabled this important transition...
January 10, 2018: New Phytologist
https://www.readbyqxmd.com/read/29317508/spatiotemporally-heterogeneous-population-dynamics-of-gut-bacteria-inferred-from-fecal-time-series-data
#15
Hidetoshi Inamine, Stephen P Ellner, Peter D Newell, Yuan Luo, Nicolas Buchon, Angela E Douglas
A priority in gut microbiome research is to develop methods to investigate ecological processes shaping microbial populations in the host from readily accessible data, such as fecal samples. Here, we demonstrate that these processes can be inferred from the proportion of ingested microorganisms that is egested and their egestion time distribution, by using general mathematical models that link within-host processes to statistics from fecal time series. We apply this framework to Drosophila melanogaster and its gut bacterium Acetobacter tropicalis Specifically, we investigate changes in their interactions following ingestion of a food bolus containing bacteria in a set of treatments varying the following key parameters: the density of exogenous bacteria ingested by the flies (low/high) and the association status of the host (axenic or monoassociated with A...
January 9, 2018: MBio
https://www.readbyqxmd.com/read/29317377/multiparametric-mri-for-the-detection-of-local-recurrence-of-prostate-cancer-in-the-setting-of-biochemical-recurrence-after-low-dose-rate-brachytherapy
#16
Luca F Valle, Matthew D Greer, Joanna H Shih, Tristan Barrett, Yan Mee Law, Andrew B Rosenkrantz, Haytham Shebel, Akhil Muthigi, Daniel Su, Maria J Merino, Bradford J Wood, Peter A Pinto, Andra V Krauze, Aradhana Kaushal, Peter L Choyke, Barış Türkbey, Deborah E Citrin
PURPOSE: Prostate multiparametric magnetic resonance imaging (mpMRI) has utility in detecting post-radiotherapy local recurrence. We conducted a multireader study to evaluate the diagnostic performance of mpMRI for local recurrence after low dose rate (LDR) brachytherapy. METHODS: A total of 19 patients with biochemical recurrence after LDR brachytherapy underwent 3T endorectal coil mpMRI with T2-weighted imaging, dynamic contrast-enhanced imaging (DCE) and diffusion-weighted imaging (DWI) with pathologic confirmation...
January 2018: Diagnostic and Interventional Radiology: Official Journal of the Turkish Society of Radiology
https://www.readbyqxmd.com/read/29304275/intrinsic-disorder-in-a-well-folded-globular-protein
#17
Nahren Manuel Mascarenhas, Vishram L Terse, Shachi Gosavi
The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins of the topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5 and chain B: β1-α1-β2). Further, like naturally occurring single-chain proteins of a similar size, monellin folds cooperatively with no detectable intermediates. However, the two monellin chains, A and B, are marginally structured in isolation and fold only upon binding to each other. Thus, monellin presents a unique opportunity to understand the design of intrinsically disordered proteins that fold upon binding...
January 5, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29288234/recovery-from-n-deprivation-is-a-transcriptionally-and-functionally-distinct-state-in-chlamydomonas
#18
Chia-Hong Tsai, Sahra Uygun, Rebecca Roston, Shin-Han Shiu, Christoph Benning
Facing adverse conditions such as nitrogen (N) deprivation, microalgae enter cellular quiescence, a reversible cell cycle arrest with drastic changes in metabolism allowing cells to remain viable. Recovering from N deprivation and quiescence is an active and orderly process as we are showing here for Chlamydomonas reinhardtii. We conducted comparative transcriptomics on this alga to discern processes relevant to quiescence in the context of N deprivation and recovery following refeeding. A mutant with slow recovery from N deprivation, compromised hydrolysis of triacylglycerols 7 (cht7), was included to better define the regulatory processes governing the respective transitions...
December 29, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29286778/negative-spin-exchange-in-a-multielectron-quantum-dot
#19
Frederico Martins, Filip K Malinowski, Peter D Nissen, Saeed Fallahi, Geoffrey C Gardner, Michael J Manfra, Charles M Marcus, Ferdinand Kuemmeth
We use a one-electron quantum dot as a spectroscopic probe to study the spin properties of a gate-controlled multielectron GaAs quantum dot at the transition between odd and even occupation numbers. We observe that the multielectron ground-state transitions from spin-1/2-like to singletlike to tripletlike as we increase the detuning towards the next higher charge state. The sign reversal in the inferred exchange energy persists at zero magnetic field, and the exchange strength is tunable by gate voltages and in-plane magnetic fields...
December 1, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29282103/within-host-evolution-of-enterococcus-faecium-during-longitudinal-carriage-and-transition-to-bloodstream-infection-in-immunocompromised-patients
#20
Danesh Moradigaravand, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Catherine Ludden, Charles Crawley, Nicholas M Brown, M Estée Török, Julian Parkhill, Sharon J Peacock
BACKGROUND: Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease. METHODS: We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment...
December 27, 2017: Genome Medicine
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