bluuebunny/crossref_metadata_2025 huggingface dataset:
Poly(ADP-ribose) polymerase 1 regulates nuclear reprogramming and promotes iPSC generation without c-Myc
Authors: Chiou Shih-Hwa , Jiang Bo-Hwa , Yu Yung-Luen , Chou Shih-Jie , Tsai Ping-Hsing , Chang Wei-Chao , Chen Liang-Kung , Chen Li-Hsin , Chien Yueh , Chiou Guang-Yuh
Published: January 2013

Poly(ADP-ribose) polymerase 1 (Parp1) catalyzes poly(ADP-ribosylation) (PARylation) and induces replication networks involved in multiple nuclear events. Using mass spectrometry and Western blotting, Parp1 and PARylation activity were intensively detected in induced pluripotent stem cells (iPSCs) and embryonic stem cells, but they were lower in mouse embryonic fibroblasts (MEFs) and differentiated cells. We show that knockdown of Parp1 and pharmacological inhibition of PARylation both reduced the efficiency of iPSC generation induced by Oct4/Sox2/Klf4/c-Myc. Furthermore, Parp1 is able to replace Klf4 or c-Myc to enhance the efficiency of iPSC generation. In addition, mouse iPSCs generated from Oct4/Sox2/Parp1-overexpressing MEFs formed chimeric offspring. Notably, the endogenous Parp1 and PARylation activity was enhanced by overexpression of c-Myc and repressed by c-Myc knockdown. A chromatin immunoprecipitation assay revealed a direct interaction of c-Myc with the Parp1 promoter. PAR-resin pulldown, followed by proteomic analysis, demonstrated high levels of PARylated Chd1L, DNA ligase III, SSrp1, Xrcc-6/Ku70, and Parp2 in pluripotent cells, which decreased during the differentiation process. These data show that the activation of Parp1, partly regulated by endogenous c-Myc, effectively promotes iPSC production and helps to maintain a pluripotent state by posttranslationally modulating protein PARylation.
Mode-coupling theory and beyond: A diagrammatic approach
Authors: Szamel Grzegorz
Published: January 2013

For almost thirty years, mode-coupling theory has been the most widely discussed and used but also the most controversial theory of the glass transition. In this paper we briefly review the reasons for both its popularity and its controversy. We emphasize the need for the development of approaches that would be able to evaluate corrections to and extensions of the existing (standard) mode-coupling theory. Next, we review our diagrammatic formulation of the dynamics of interacting Brownian particles.We show that within this approach the standardmode-coupling theory can be derived in a very simple way. Finally, we use our diagrammatic approach to calculate two corrections to the mode-coupling theory's expression for the so-called irreducible memory function. These corrections involve re-summations of well-defined classes of non-mode-coupling diagrams.
ACUTE UNILATERAL TOXOPLASMA RETINOCHOROIDITIS ASSOCIATED WITH ADALIMUMAB, A TUMOR NECROSIS FACTOR-α ANTAGONIST
Authors: Radwan Alaa , Baheti Ujwala , Arcinue Cheryl A. , Hinkle David M.
Published: January 2013

Purpose:

The purpose of this study was to report a case of a patient with unilateral toxoplasma retinochoroiditis while on treatment with adalimumab, an anti–tumor necrosis factor α agent for ulcerative colitis.

Methods:

This is a descriptive case report.

Results and Discussion:

In addition to the patient with toxoplasma retinochoroiditis, there is one published report of two patients who developed toxoplasma chorioretinitis while on anti–tumor necrosis factor α therapy for rheumatoid arthritis: one was on adalimumab and methotrexate and the other one was on etanercept and methotrexate.

Conclusion:

The authors need to be aware of this potentially vision threatening risk with anti–tumor necrosis factor α therapy.
SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY CHARACTERISTICS OF RETAINED SUBRETINAL PERFLUORO-n-OCTANE
Authors: Sigler Eric J. , Randolph John C. , Rafieetary Mohammad R. , Charles Steve , Calzada Jorge I.
Published: January 2013

Purpose:

To describe the spectral domain optical coherence tomography characteristics of retained subretinal perfluoro-n-octane (SR-PFO) after vitreoretinal surgery.

Methods:

Consecutive patients referred for retained SR-PFO after pars plana vitrectomy for retinal detachment were prospectively evaluated with spectral domain optical coherence tomography. The clinical findings, fundus autofluorescence, spectral domain optical coherence tomography images, and anatomical outcomes, were reviewed.

Results:

Three consecutive patients presented to the vitreoretinal service with history of retinal detachment and pervious vitrectomy with intraoperative PFO. Subretinal PFO bubbles were observed on clinical examination and imaging studies, including spectral domain optical coherence tomography. Case 1 had subfoveal PFO removal and developed a postoperative choroidal neovascular membrane. Case 2 had multiple foci of SR-PFO after giant retinal tear repair. Case 3 had superotemporal SR-PFO that remained stable for several years without migration or other associated pathology.

Conclusion:

Subretinal PFO appears as a low-reflectance spherical mass, often with a pinpoint focus of hyperreflectance at the apex of the bubble. Optical coherence tomography details beneath subretinal PFO appear relatively hyperreflectant compared to adjacent tissue. Long-term observation revealed preferential absence of the outer retinal layers with no nerve fiber layer erosion, subretinal inflammatory precipitates, or proliferative vitreoretinopathy. Some evidence of retinal pigment epithelial disruption was observed but seemed to remain stable or improve with observation. The authors suggest management involving follow-up with close observation in SR-PFO unless present in the subfoveal region. Choroidal neovascular membrane can occur after SR-PFO removal and may be successfully managed with intravitreal bevacizumab.
Prevalence of Rupture in Poly Implant Prothèse Silicone Breast Implants, Recalled from the European Market in 2010
Authors: Maijers Maria C. , Niessen Francisus B.
Published: January 2013

Background:

Known complications of silicone breast implants are rupture and silicone leakage, complications that are related not only to generation and implant age but also to the manufacturer. Implants from the French manufacturer Poly Implant Prothèse showed more rupture than expected and were banned from the European market in 2010. Clinics in Europe recalled their patients, but prevalence of rupture in these implants has not been previously reported.

Methods:

All women who underwent breast augmentation in 2000 and 2001 in the Jan van Goyen Clinic, Amsterdam, The Netherlands, were informed about concerns regarding the quality of their implants. Medical records were used to trace manufacturer and implantation specifics. One hundred twelve women with proven Poly Implant Prothèse implants were enrolled in this study. All women underwent physical examination and magnetic resonance imaging and were interviewed for complaints to determine the prevalence of symptomatic and asymptomatic rupture.

Results:

Two hundred twenty-four Poly Implant Prothèse implants were evaluated with a mean implant age of 122 months. Of these 224 implants, 54 had ruptured. Magnetic resonance imaging showed that 33 percent of women had at least one ruptured implant. There was no significant difference in rupture rate of implants manufactured in 2000 and 2001.

Conclusions:

One third of the women who had undergone breast augmentation with Poly Implant Prothèse implants were shown to have at least one ruptured implant after 10 years; 45.9 percent had bilateral rupture and 13.5 percent had extracapsular leakage. These were mostly asymptomatic ruptures. The rupture prevalence rate for Poly Implant Prothèse implants after 10 years is 24 percent.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
A Standardized Operative Team for Major Head and Neck Cancer Ablation and Reconstruction
Authors: Doherty Christopher , Nakoneshny Steven C. , Harrop Allan R. , Matthews T. Wayne , Schrag Christiaan , McKenzie David C. , De Haas William , Davis Roger B. , Dort Joseph C.
Published: January 2013

Background:

Prolonged procedure time in head and neck cancer ablation and free flap reconstruction cases has been shown to significantly increase perioperative complications. The authors' objective was to evaluate the effectiveness of a standardized surgical nursing team for head and neck cancer ablation and free flap reconstruction operations for reducing procedure time.

Methods:

A retrospective cohort analysis of consecutive patients presenting for head and neck cancer ablation and free flap reconstruction between January 1, 2007, and September 1, 2010, was performed. A standardized head and neck surgical nursing team was introduced on May 1, 2009, at our center. Procedure time and case time were measured before and after the introduction of the team. Univariable analyses were performed to evaluate the difference in procedure and case time between the two cohorts. A multivariable linear regression model was developed to control for confounding variables.

Results:

There were 52 cases before the team was introduced and 49 cases after. Mean procedure time was reduced by 47.1 minutes (p = 0.04) and mean case time was reduced by 68.9 minutes (p = 0.01) after team introduction. The multivariable linear regression analysis demonstrated a significant reduction in operative time after team introduction, controlling for confounding variables.

Conclusions:

The introduction of a standardized surgical nursing team led to a significant reduction in procedure and case time. A standardized team approach improves operating room efficiency in complex cases such as free flap reconstruction following tumor ablation.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Silicone Nanoparticles Do Not Induce Immune Responses by Naïve Human Peripheral Blood Mononuclear Cells
Authors: Nair Narayanan , Pilakka-Kanthikeel Sudheesh , Saiyed Zainulabedin , Yndart Adriana , Nair Madhavan
Published: January 2013

Background:

Several studies have reported adverse immunological effects of silicone due to their ability to induce proinflammatory molecules, such as tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). In recent years, use of nanoparticles has been under fast development for therapeutic drug targeting, diagnostic imaging, and immune response in various fields of nanomedicine. The authors hypothesize that immune responses induced by in vivo use of silicone materials can be reduced or eliminated by the use of nanosilicone.

Methods:

Peripheral blood mononuclear cells obtained from naïve normal subjects were cultured with different concentrations of silicone nanoparticles and microparticles for 24 hours. The culture supernatants were quantitated for TNF-α, IL-6, and interferon-γ (IFN-γ) secretion by enzyme-linked immunosorbent assay. The pellets were used for specific IL-6, TNF-α, and IFN-γ gene expression by real-time polymerase chain reaction, respectively. Cytotoxicity was evaluated by XTT viability assay. Results were compared between silicone nanoparticles and microparticles and untreated controls.

Results:

Silicone nanoparticles up to 100 μg/ml did not induce any detectable levels of specific TNF-α, IFN-γ, and IL-6 gene expression and protein production and the results were comparable to those for untreated controls. Silicone microparticles at 100 μg/ml, however, significantly induced the production and gene expression of TNF-α, IL-6, and IFN-γ by peripheral blood mononuclear cells. XTT viability assay showed that silicone nanoparticles or microparticles, even at the highest concentration used, were not cytotoxic to cells.

Conclusions:

The results suggest that silicone nanoparticles can be engineered to avoid immune recognition and subsequent silicone microparticle–related adverse effects and thus may be of therapeutic significance in the cosmetic industry, plastic surgery, and aesthetic medicine.
Evaluation of Plastic Surgery Training Programs
Authors: Roostaeian Jason , Fan Kenneth L. , Sorice Sarah , Tabit Christina J. , Liao Eileen , Rahgozar Paymon , Tanna Neil , Bradley James P.
Published: January 2013

Background:

The authors aimed to differentiate between combined/integrated and independent (traditional) methods of plastic surgery training with regard to quality of trainees, caliber of graduates, and practice or career outcomes once graduated.

Methods:

To compare combined/integrated with independent residency program training, the authors conducted a Web-based survey of the American Society of Plastic Surgeons members looking at their experience and practice outcomes (n = 1056) and interviews of plastic surgery faculty looking at the quality of trainees (n = 72). The member survey evaluated background information, research credentials, pathway satisfaction, postgraduation activities, current practice, and academic affiliation. Faculty teacher interviews focused on knowledge base, diagnostic and treatment judgment, technical abilities, research capabilities, and prediction of future career success.

Results:

The member survey showed no difference (p > 0.05) between combined/integrated and independent trainees in practice type (cosmetic/reconstructive), practice volume, or academic achievements. Combined/integrated trained surgeons are three times more likely to recommend their training pathway and two times more likely to enter fellowship after residency. Alpha Omega Alpha Honor Medical Society membership correlated with a greater likelihood of having an academic practice at 5 and 10 years or more and higher professorship titles. Faculty evaluations showed that combined/integrated residents were superior in knowledge (49 percent versus 32 percent) but that independent residents were superior in technical ability (51 percent versus 20 percent) and research (57 percent versus 19 percent). Most faculty were unable to choose a pathway producing superior residents.

Conclusions:

Regarding future practice outcomes, there was not a superior training pathway. Regarding quality of trainees, there were differences in faculty evaluations, but there was no consensus on a better pathway.
Evidence-Based Practices for Thromboembolism Prevention
Authors: Murphy Robert X. , Alderman Amy , Gutowski Karol , Kerrigan Carolyn , Rosolowski Karie , Schechter Loren , Schmitz DeLaine , Wilkins Edwin
Published: January 2013

In July of 2011, the American Society of Plastic Surgeons Executive Committee approved the Venous Thromboembolism Task Force Report. The report includes a summary of the scientific literature relevant to venous thromboembolism and plastic surgery along with five evidence-based recommendations. The recommendations are divided into two sections: risk stratification and prevention. The risk stratification recommendations are based on the 2005 Caprini Risk Assessment Module, which has been validated in the scientific literature as an effective tool for risk-stratifying plastic and reconstructive surgery patients based on individual risk factors for 60-day venous thromboembolism. The three prophylaxis recommendations are dependent on an individual patient's 2005 Caprini Risk Assessment Module score.
Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in
Rhodobacter sphaeroides
chemotaxis
Authors: Hamadeh Abdullah , Ingalls Brian , Sontag Eduardo
Published: January 2013

The chemotaxis pathway of the bacterium
Rhodobacter sphaeroides
shares many similarities with that of
Escherichia coli
. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent theoretical results have correctly predicted that the
E. coli
output behaviour is unchanged under scaling of its ligand input signal; this property is known as fold-change detection (FCD). In the light of recent experimental results suggesting that
R. sphaeroides
may also show FCD, we present theoretical assumptions on the
R. sphaeroides
chemosensory dynamics that can be shown to yield FCD behaviour. Furthermore, it is shown that these assumptions make FCD a property of this system that is robust to structural and parametric variations in the chemotaxis pathway, in agreement with experimental results. We construct and examine models of the full chemotaxis pathway that satisfy these assumptions and reproduce experimental time-series data from earlier studies. We then propose experiments in which models satisfying our theoretical assumptions predict robust FCD behaviour where earlier models do not. In this way, we illustrate how
transient dynamic phenotypes
such as FCD can be used for the purposes of discriminating between models that reproduce the same experimental time-series data.
Independent component analysis: recent advances
Authors: Hyvärinen Aapo
Published: January 2013

Independent component analysis is a probabilistic method for learning a linear transform of a random vector. The goal is to find components that are maximally independent and non-Gaussian (non-normal). Its fundamental difference to classical multi-variate statistical methods is in the assumption of non-Gaussianity, which enables the identification of original, underlying components, in contrast to classical methods. The basic theory of independent component analysis was mainly developed in the 1990s and summarized, for example, in our monograph in 2001. Here, we provide an overview of some recent developments in the theory since the year 2000. The main topics are: analysis of causal relations, testing independent components, analysing multiple datasets (three-way data), modelling dependencies between the components and improved methods for estimating the basic model.
Gravitational wave astronomy: needle in a haystack
Authors: Cornish Neil J
Published: January 2013

A worldwide array of highly sensitive ground-based interferometers stands poised to usher in a new era in astronomy with the first direct detection of gravitational waves. The data from these instruments will provide a unique perspective on extreme astrophysical objects, such as neutron stars and black holes, and will allow us to test Einstein’s theory of gravity in the strong field, dynamical regime. To fully realize these goals, we need to solve some challenging problems in signal processing and inference, such as finding rare and weak signals that are buried in non-stationary and non-Gaussian instrument noise, dealing with high-dimensional model spaces, and locating what are often extremely tight concentrations of posterior mass within the prior volume. Gravitational wave detection using space-based detectors and pulsar timing arrays bring with them the additional challenge of having to isolate individual signals that overlap one another in both time and frequency. Promising solutions to these problems will be discussed, along with some of the challenges that remain.
Markov chain Monte Carlo inference for Markov jump processes via the linear noise approximation
Authors: Stathopoulos Vassilios , Girolami Mark A.
Published: January 2013

Bayesian analysis for Markov jump processes (MJPs) is a non-trivial and challenging problem. Although exact inference is theoretically possible, it is computationally demanding, thus its applicability is limited to a small class of problems. In this paper, we describe the application of Riemann manifold Markov chain Monte Carlo (MCMC) methods using an approximation to the likelihood of the MJP that is valid when the system modelled is near its thermodynamic limit. The proposed approach is both statistically and computationally efficient whereas the convergence rate and mixing of the chains allow for fast MCMC inference. The methodology is evaluated using numerical simulations on two problems from chemical kinetics and one from systems biology.
A study of infrasonic anisotropy and multipathing in the atmosphere using seismic networks
Authors: Hedlin Michael A. H. , Walker Kristoffer T.
Published: January 2013

We discuss the use of reverse time migration (RTM) with dense seismic networks for the detection and location of sources of atmospheric infrasound. Seismometers measure the response of the Earth's surface to infrasound through acoustic-to-seismic coupling. RTM has recently been applied to data from the USArray network to create a catalogue of infrasonic sources in the western US. Specifically, several hundred sources were detected in 2007–2008, many of which were not observed by regional infrasonic arrays. The influence of the east–west stratospheric zonal winds is clearly seen in the seismic data with most detections made downwind of the source. We study this large-scale anisotropy of infrasonic propagation, using a winter and summer source in Idaho. The bandpass-filtered (1–5 Hz) seismic waveforms reveal in detail the two-dimensional spread of the infrasonic wavefield across the Earth's surface within approximately 800 km of the source. Using three-dimensional ray tracing, we find that the stratospheric winds above 30 km altitude in the ground-to-space (G2S) atmospheric model explain well the observed anisotropy pattern. We also analyse infrasound from well-constrained explosions in northern Utah with a denser IRIS PASSCAL seismic network. The standard G2S model correctly predicts the anisotropy of the stratospheric duct, but it incorrectly predicts the dimensions of the shadow zones in the downwind direction. We show that the inclusion of finer-scale structure owing to internal gravity waves infills the shadow zones and predicts the observed time durations of the signals. From the success of this method in predicting the observations, we propose that multipathing owing to fine scale, layer-cake structure is the primary mechanism governing propagation for frequencies above approximately 1 Hz and infer that stochastic approaches incorporating internal gravity waves are a useful improvement to the standard G2S model for infrasonic propagation modelling.
Abductive learning of quantized stochastic processes with probabilistic finite automata
Authors: Chattopadhyay Ishanu , Lipson Hod
Published: January 2013

We present an unsupervised learning algorithm (GenESeSS) to infer the causal structure of quantized stochastic processes, defined as stochastic dynamical systems evolving over discrete time, and producing quantized observations. Assuming ergodicity and stationarity,GenESeSSinfers probabilistic finite state automata models from a sufficiently long observed trace. Our approach is abductive; attempting to infer a simple hypothesis, consistent with observations and modelling framework that essentially fixes the hypothesis class. The probabilistic automata we infer have no initial and terminal states, have no structural restrictions and are shown to be probably approximately correct-learnable. Additionally, we establish rigorous performance guarantees and data requirements, and show thatGenESeSScorrectly infers long-range dependencies. Modelling and prediction examples on simulated and real data establish relevance to automated inference of causal stochastic structures underlying complex physical phenomena.
Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability
Authors: Raue Andreas , Kreutz Clemens , Theis Fabian Joachim , Timmer Jens
Published: January 2013

Increasingly complex applications involve large datasets in combination with nonlinear and high-dimensional mathematical models. In this context, statistical inference is a challenging issue that calls for pragmatic approaches that take advantage of both Bayesian and frequentist methods. The elegance of Bayesian methodology is founded in the propagation of information content provided by experimental data and prior assumptions to the posterior probability distribution of model predictions. However, for complex applications, experimental data and prior assumptions potentially constrain the posterior probability distribution insufficiently. In these situations, Bayesian Markov chain Monte Carlo sampling can be infeasible. From a frequentist point of view, insufficient experimental data and prior assumptions can be interpreted as non-identifiability. The profile-likelihood approach offers to detect and to resolve non-identifiability by experimental design iteratively. Therefore, it allows one to better constrain the posterior probability distribution until Markov chain Monte Carlo sampling can be used securely. Using an application from cell biology, we compare both methods and show that a successive application of the two methods facilitates a realistic assessment of uncertainty in model predictions.
Signal processing for molecular and cellular biological physics: an emerging field
Authors: Little Max A. , Jones Nick S.
Published: January 2013

Recent advances in our ability to watch the molecular and cellular processes of life in action—such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer—raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.
Transdimensional inference in the geosciences
Authors: Sambridge M. , Bodin T. , Gallagher K. , Tkalčić H.
Published: January 2013

Seismologists construct images of the Earth's interior structure using observations, derived from seismograms, collected at the surface. A common approach to such inverse problems is to build a single ‘best’ Earth model, in some sense. This is despite the fact that the observations by themselves often do not require, or even allow, a single best-fit Earth model to exist. Interpretation of optimal models can be fraught with difficulties, particularly when formal uncertainty estimates become heavily dependent on the regularization imposed. Similar issues occur across the physical sciences with model construction in ill-posed problems. An alternative approach is to embrace the non-uniqueness directly and employ an inference process based on parameter space sampling. Instead of seeking a best model within an optimization framework, one seeks an ensemble of solutions and derives properties of that ensemble for inspection. While this idea has itself been employed for more than 30 years, it is now receiving increasing attention in the geosciences. Recently, it has been shown that transdimensional and hierarchical sampling methods have some considerable benefits for problems involving multiple parameter types, uncertain data errors and/or uncertain model parametrizations, as are common in seismology. Rather than being forced to make decisions on parametrization, the level of data noise and the weights between data types in advance, as is often the case in an optimization framework, the choice can be informed by the data themselves. Despite the relatively high computational burden involved, the number of areas where sampling methods are now feasible is growing rapidly. The intention of this article is to introduce concepts of transdimensional inference to a general readership and illustrate with particular seismological examples. A growing body of references provide necessary detail.
Using topology to tame the complex biochemistry of genetic networks
Authors: Thattai Mukund
Published: January 2013

Living cells are controlled by networks of interacting genes, proteins and biochemicals. Cells use the emergent collective dynamics of these networks to probe their surroundings, perform computations and generate appropriate responses. Here, we consider genetic networks, interacting sets of genes that regulate one another’s expression. It is possible to infer the interaction topology of genetic networks from high-throughput experimental measurements. However, such experiments rarely provide information on the detailed nature of each interaction. We show that topological approaches provide powerful means of dealing with the missing biochemical data. We first discuss the biochemical basis of gene regulation, and describe how genes can be connected into networks. We then show that, given weak constraints on the underlying biochemistry, topology alone determines the emergent properties of certain simple networks. Finally, we apply these approaches to the realistic example of quorum-sensing networks: chemical communication systems that coordinate the responses of bacterial populations.
Random time series in astronomy
Authors: Vaughan Simon
Published: January 2013

Progress in astronomy comes from interpreting the signals encoded in the light received from distant objects: the distribution of light over the sky (images), over photon wavelength (spectrum), over polarization angle and over time (usually called light curves by astronomers). In the time domain, we see transient events such as supernovae, gamma-ray bursts and other powerful explosions; we see periodic phenomena such as the orbits of planets around nearby stars, radio pulsars and pulsations of stars in nearby galaxies; and we see persistent aperiodic variations (‘noise’) from powerful systems such as accreting black holes. I review just a few of the recent and future challenges in the burgeoning area of time domain astrophysics, with particular attention to persistently variable sources, the recovery of reliable noise power spectra from sparsely sampled time series, higher order properties of accreting black holes, and time delays and correlations in multi-variate time series.
Gaussian processes for time-series modelling
Authors: Roberts S. , Osborne M. , Ebden M. , Reece S. , Gibson N. , Aigrain S.
Published: January 2013

In this paper, we offer a gentle introduction to Gaussian processes for time-series data analysis. The conceptual framework of Bayesian modelling for time-series data is discussed and the foundations of Bayesian non-parametric modelling presented for
Gaussian processes
. We discuss how domain knowledge influences design of the Gaussian process models and provide case examples to highlight the approaches.
Modulated oscillations in many dimensions
Authors: Olhede S. C.
Published: January 2013

Modulated oscillations are described via their time-varying amplitude and frequency. For multivariate signals, there is structure in the signal beyond this local amplitude and frequency defined for each signal component, in turn describing the commonality of the components. The multivariate structure encodes how the common oscillation is present in each component signal. This structure will also be evolving. I review the special case of the representation of both bivariate and trivariate oscillations. Additionally, existing results on the general multivariate oscillation are covered. I discuss the difference between a model of a multivariate oscillation compared with other common signal models of phenomena observed in several channels, and how their properties are different. I show how for the multivariate signal the global dimensionality of the signal is built up from local one-dimensional contributions, and introduce the purely unidirectional signal, to quantify how any given signal is different from the closest such signal. I illustrate the properties of the derived representation of the multivariate signal with synthetic examples, and discuss the representation of data from observations in physical oceanography.
Bayesian non-parametrics and the probabilistic approach to modelling
Authors: Ghahramani Zoubin
Published: January 2013

Modelling is fundamental to many fields of science and engineering. A model can be thought of as a representation of possible data one could predict from a system. The probabilistic approach to modelling uses probability theory to express all aspects of uncertainty in the model. The probabilistic approach is synonymous with Bayesian modelling, which simply uses the rules of probability theory in order to make predictions, compare alternative models, and learn model parameters and structure from data. This simple and elegant framework is most powerful when coupled with flexible probabilistic models. Flexibility is achieved through the use of Bayesian non-parametrics. This article provides an overview of probabilistic modelling and an accessible survey of some of the main tools in Bayesian non-parametrics. The survey covers the use of Bayesian non-parametrics for modelling unknown functions, density estimation, clustering, time-series modelling, and representing sparsity, hierarchies, and covariance structure. More specifically, it gives brief non-technical overviews of Gaussian processes, Dirichlet processes, infinite hidden Markov models, Indian buffet processes, Kingman’s coalescent, Dirichlet diffusion trees and Wishart processes.
Rotary components, random ellipses and polarization: a statistical perspective
Authors: Walden A. T.
Published: January 2013

Rotary analysis decomposes vector motions on the plane into counter-rotating components, which have proved particularly useful in the study of geophysical flows influenced by the rotation of the Earth. For stationary random signals, the motion at any frequency takes the form of a random ellipse. Although there are numerous applications of rotary analysis, relatively little attention has been paid to the statistical properties of the random ellipses or to the estimated rotary coefficient, which measures the tendency to rotate counterclockwise or clockwise. The precise statistical structure of the ellipses is reviewed, including the random behaviour of the ellipse orientation, aspect ratio and intensity. Special attention is then paid to spectral matrix estimation from physical data and to hypothesis testing and confidence intervals computed using the estimated matrices.
Similarity and denoising
Authors: Vitányi Paul M. B.
Published: January 2013

We can discover the effective similarity among pairs of finite objects and denoise a finite object using the Kolmogorov complexity of these objects. The drawback is that the Kolmogorov complexity is not computable. If we approximate it, using a good real-world compressor, then it turns out that on natural data the processes give adequate results in practice. The methodology is parameter-free, alignment-free and works on individual data. We illustrate both methods with examples.
Model-based machine learning
Authors: Bishop Christopher M.
Published: January 2013

Several decades of research in the field of machine learning have resulted in a multitude of different algorithms for solving a broad range of problems. To tackle a new application, a researcher typically tries to map their problem onto one of these existing methods, often influenced by their familiarity with specific algorithms and by the availability of corresponding software implementations. In this study, we describe an alternative methodology for applying machine learning, in which a bespoke solution is formulated for each new application. The solution is expressed through a compact modelling language, and the corresponding custom machine learning code is then generated automatically. Thismodel-basedapproach offers several major advantages, including the opportunity to create highly tailored models for specific scenarios, as well as rapid prototyping and comparison of a range of alternative models. Furthermore, newcomers to the field of machine learning do not have to learn about the huge range of traditional methods, but instead can focus their attention on understanding a single modelling environment. In this study, we show how probabilistic graphical models, coupled with efficient inference algorithms, provide a very flexible foundation for model-based machine learning, and we outline a large-scale commercial application of this framework involving tens of millions of users. We also describe the concept ofprobabilistic programmingas a powerful software environment for model-based machine learning, and we discuss a specific probabilistic programming language calledInfer.NET, which has been widely used in practical applications.
Inference for the physical sciences
Authors: Jones Nick S. , Maccarone Thomas J.
Published: January 2013

There is a disconnect between developments in modern data analysis and some parts of the physical sciences in which they could find ready use. This introduction, and this issue, provides resources to help experimental researchers access modern data analysis tools and exposure for analysts to extant challenges in physical science. We include a table of resources connecting statistical and physical disciplines and point to appropriate books, journals, videos and articles. We conclude by highlighting the relevance of each of the articles in the associated issue.
Parvibacter caecicola gen. nov., sp. nov., a bacterium of the family

Coriobacteriaceae

isolated from the caecum of a mouse
Authors: Clavel Thomas , Charrier Cédric , Wenning Mareike , Haller Dirk
Published: January 2013

A single strain, NR06T, was isolated from the intestine of a TNFdeltaARE mouse. Based on phylogenetic analysis of partial 16S rRNA gene sequences, strain NR06T belongs in the family

Coriobacteriaceae

within the

Actinobacteria

. The most closely related species with validly published names are members of the genera

Adlercreutzia

,

Asaccharobacter

and

Enterorhabdus

(<96 % sequence similarity). Strain NR06T was characterized by a high prevalence of monomethylmenaquinone-6 (MMK-6; 76 %) and the presence of meso-diaminopimelic acid in the cell wall. One of the major cellular fatty acids of strain NR06T was C15 : 0 ISO. Glucose was detected as a whole cell sugar. Strain NR06T was resistant to the antibiotic colistin and was positive for arginine and leucine arylamidase activity. Based on these characteristics, strain NR06T differed from related described bacteria. Therefore, the name Parvibacter caecicola gen. nov., sp. nov. is proposed to accommodate the novel bacterium. The type strain of the type species is NR06T ( = DSM 22242T = CCUG 57646T).
Streptomyces

chilikensis sp. nov., a halophilic streptomycete isolated from brackish water sediment
Authors: Ray Lopamudra , Suar Mrutyunjay , Pattnaik Ajit Kumar , Raina Vishakha
Published: January 2013

A novel actinobacterial strain, designated RC 1830T, was isolated from the sediment of estuarine coastal brackish water lagoon of Chilika Lake, in Khurdha district of Odisha, India, and characterized using a polyphasic approach. Strain RC 1830T was halophilic and alkali-tolerant and found to hydrolyse chitin, starch, tributyrin, lecithin, Tween 80, cellulose, gelatin and casein. The diagnostic presence of ll-diaminopimelic acid, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C16 : 0, iso-C17 : 0, anteiso-C17 : 0 as major cellular fatty acids and MK-9(H4 and H6) as major menaquinones noticeably associated the strain to the genus

Streptomyces

. After comparison and analysis of the near complete 16S rRNA gene sequence with representative strains of other streptomycetes, it was evident that strain RC 1830T belonged to the genus

Streptomyces

, and exhibited the highest sequence similarities of 99.53 %, 99.25 %, 99.11 %, 99.10 % and 99. 06 % to

Streptomyces fragilis

DSM 40044T,

Streptomyces coelicoflavus

NBRC 15399T,

Streptomyces flaveolus

NBRC 3715T,

Streptomyces

lavenduligrisesus NBRC 13405T and

Streptomyces eurythermus

ATCC 14975T, respectively. Reconstruction of a phylogenetic tree for the genus

Streptomyces

revealed that strain RC 1830T formed a distinct phyletic line and clustered with its most closely related neighbour

S. fragilis

DSM 40044T. The DNA–DNA relatedness values between strain RC 1830T and the most closely related type strain

S. fragilis

DSM 40044T were determined to be 17.7±4.55 %. Additionally, morphological, biochemical and physiological tests were able to distinguish the strain from the most closely related type strain

S. fragilis

DSM 40044T and other closely related neighbours,

S. coelicoflavus

DSM 41471T and

Streptomyces flaveolus

DSM 40061T. Based on a range of phenotypic and genotypic properties, strain RC 1830T is suggested to represent a novel species of the genus

Streptomyces

for which the name

Streptomyces

chilikensis sp. nov. is proposed. The type strain is RC 1830T ( = JCM 18411T = DSM 42072T).
Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream
Authors: Ramana V. Venkata , Raj P. Shalem , Tushar L. , Sasikala Ch. , Ramana Ch. V.
Published: January 2013

Two strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus

Rhodomicrobium

and clustered with

Rhodomicrobium vannielii

DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with

R. vannielii

DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus

Rhodomicrobium

, for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).
Muricauda

taeanensis sp. nov., isolated from a marine tidal flat
Authors: Kim Jeong Myeong , Jin Hyun Mi , Jeon Che Ok
Published: January 2013

A novel Gram-stain-negative, heterotrophic, moderate halophilic and strictly aerobic bacterium, strain 105T, was isolated from a tidal flat of Taean in Korea. Cells were catalase- and oxidase-positive long rods that showed gliding motility. Optimum temperature, pH and salinity for the growth of strain 105T were observed at 30–37 °C, at pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl, respectively. The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. Phosphatidylethanolamine and five unidentified lipids were identified as the major polar lipids. The genomic DNA G+C content of strain 105T was 42.4 mol% and MK-6 was detected as the predominant isoprenoid quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 105T formed a phyletic lineage with members of the genus

Muricauda

. Strain 105T was most closely related to

Muricauda aquimarina

SW-63T (97.6 %),

Muricauda beolgyonensis

BB-My12T (97.5 %),

Muricauda lutimaris

SMK-108T (97.5 %),

Muricauda ruestringensis

B1T (97.3 %),

Muricauda flavescens

CL-SS4T (97.2 %) and

Muricauda olearia

(96.2 %). The DNA–DNA relatedness values of strain 105T with

M. aquimarina

JCM 11811T,

M. beolgyonensis

KCTC 23501T,

M. lutimaris

KCTC 22173T,

M. ruestringensis

DSM 13258T and

M. flavescens

JCM 11812T were 17.2±6.0, 8.7±2.2, 3.7±0.5, 11.0±1.9 and 7.1±1.3 %, respectively. On the basis of phenotypic and molecular features, strain 105T represents a novel species of the genus

Muricauda

, for which the name

Muricauda

taeanensis sp. nov. is proposed. The type strain is 105T ( = KACC 16195T = JCM 17757T).
Methylobacterium

trifolii sp. nov. and

Methylobacterium

thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces
Authors: Wellner S. , Lodders N. , Glaeser S. P. , Kämpfer P.
Published: January 2013

Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus

Methylobacterium

. The closest relatives of strains C34T and T5 were

Methylobacterium gnaphalii

23eT (98.0 and 98.5 % sequence similarity, respectively) and

Methylobacterium organophilum

JCM 2833T (97.0 and 97.2 %, respectively). Strain TA73T showed the highest sequence similarities to

Methylobacterium marchantiae

JT1T and

Methylobacterium bullatum

F3.2T (both 97.9 %), followed by

Methylobacterium phyllosphaerae

CBMB27T and

Methylobacterium brachiatum

DSM 19569T (both 97.8 %),

Methylobacterium cerastii

C15T and

Methylobacterium radiotolerans

JCM 2831T (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73T and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34T and T5. Physiological and biochemical analysis, including DNA–DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA–DNA hybridization studies also showed high similarities between strains C34T and T5 (59.6–100 %). Therefore, the isolates represent two novel species within the genus

Methylobacterium

, for which the names

Methylobacterium

trifolii sp. nov. (type strain TA73T = LMG 25778T = CCM 7786T) and

Methylobacterium

thuringiense sp. nov. (type strain C34T = LMG 25777T = CCM 7787T) are proposed.
Taxonomy, morphology and molecular systematics of three oligotrich ciliates, including a description of Apostrombidium parakielum spec. nov. (Ciliophora, Oligotrichia)
Authors: Song Wen , Li Jiamei , Liu Weiwei , Jiang Jiamei , Rasheid Khaled A. S. Al- , Hu Xiaozhong
Published: January 2013

Three oligotrich ciliates, Apostrombidium parakielum spec. nov., Novistrombidium apsheronicum (Alekperov & Asadullayeva, 1997) Agatha, 2003 and Novistrombidium testaceum (Anigstein, 1914) Song & Bradbury, 1998 were collected from the coastal waters of China and their morphology and small-subunit rRNA (SSU rRNA) gene sequences were studied. The novel species can be recognized by the combination of its obconical body shape, 14–16 anterior and 6–8 ventral membranelles, somatic kinety in three parts and conspicuously long dorsal cilia. Based on the data obtained for this novel species, an improved diagnosis of the genus Apostrombidium is supplied. Descriptions of the population of N. apsheronicum and N. testaceum collected in this study are also provided and compared with the existing descriptions. In addition, the phylogenetic positions of these three species are inferred from their SSU rRNA gene sequence data. The results indicate that the genus Apostrombidium, the systematics of which has not previously been discussed using molecular information, clusters with Varistrombidium kielum and Omegastrombidium elegans, whereas N. testaceum and N. apsheronicum form a single clade.
In Vivo Imaging of Zebrafish Retina
Authors: Williams Philip R. , Morgan Joshua L. , Kerschensteiner Daniel , Wong Rachel O.L.
Published: January 2013

Neuronal circuits of the vertebrate retina are organized into stereotyped laminae. This orderly arrangement makes the retina an ideal model system for imaging studies aimed at understanding how circuits assemble during development. In particular, live-cell imaging techniques are readily applied to the developing retina to monitor dynamic changes over time in cell structure and connectivity. Such imaging studies have collectively revealed novel strategies by which retinal neurons contact their presynaptic and postsynaptic partners to establish synaptic connections. We describe here the procedures developed in our laboratory for confocal and multiphoton live-cell imaging of the developing retina using in vivo preparations. Zebrafish larvae are an ideal specimen for in vivo imaging experiments as they can be made to remain transparent throughout development. Isolated retinal cells can be readily labeled by DNA injection into the one-cell staged embryo, or via transplantation of fluorescently labeled cells from stable transgenics.