On the number of signals in multivariate time series

We assume a second-order source separation model where the observed multivariate time series is a linear mixture of latent, temporally uncorrelated time series with some components pure white noise. To avoid the modelling of noise, we extract the non-noise latent components using some standard method, allowing the modelling of the extracted univariate time series individually. An important question is the determination of which of the latent components are of interest in modelling and which can be considered as noise. Bootstrap-based methods have recently been used in determining the latent dimension in various methods of unsupervised and supervised dimension reduction and we propose a set of similar estimation strategies for second-order stationary time series. Simulation studies and a sound wave example are used to show the method's effectiveness

Identification of transcriptional and metabolic programs related to mammalian cell size

SummaryBackgroundRegulation of cell size requires coordination of growth and proliferation. Conditional loss of cyclin-dependent kinase 1 in mice permits hepatocyte growth without cell division, allowing us to study cell size in vivo using transcriptomics and metabolomics.ResultsLarger cells displayed increased expression of cytoskeletal genes but unexpectedly repressed expression of many genes involved in mitochondrial functions. This effect appears to be cell autonomous because cultured Drosophila cells induced to increase cell size displayed a similar gene-expression pattern. Larger hepatocytes also displayed a reduction in the expression of lipogenic transcription factors, especially sterol-regulatory element binding proteins. Inhibition of mitochondrial functions and lipid biosynthesis, which is dependent on mitochondrial metabolism, increased the cell size with reciprocal effects on cell proliferation in several cell lines.ConclusionsWe uncover that large cell-size increase is accompanied by downregulation of mitochondrial gene expression, similar to that observed in diabetic individuals. Mitochondrial metabolism and lipid synthesis are used to couple cell size and cell proliferation. This regulatory mechanism may provide a possible mechanism for sensing metazoan cell size

Pareto optimality in multilayer network growth

We model the formation of multi-layer transportation networks as a multi-objective optimization process, where service providers compete for passengers, and the creation of routes is determined by a multi-objective cost function encoding a trade-off between efficiency and competition. The resulting model reproduces well real-world systems as diverse as airplane, train and bus networks, thus suggesting that such systems are indeed compatible with the proposed local optimization mechanisms. In the specific case of airline transportation systems, we show that the networks of routes operated by each company are placed very close to the theoretical Pareto front in the efficiency-competition plane, and that most of the largest carriers of a continent belong to the corresponding Pareto front. Our results shed light on the fundamental role played by multi-objective optimization principles in shaping the structure of large-scale multilayer transportation systems, and provide novel insights to service providers on the strategies for the smart selection of novel routes

Loss of the PTCH1 tumor suppressor defines a new subset of plexiform fibromyxoma.

BackgroundPlexiform fibromyxoma (PF) is a rare gastric tumor often confused with gastrointestinal stromal tumor. These so-called "benign" tumors often present with upper GI bleeding and gastric outlet obstruction. It was recently demonstrated that approximately one-third of PF have activation of the GLI1 oncogene, a transcription factor in the hedgehog (Hh) pathway, via a MALAT1-GLI1 fusion protein or GLI1 up-regulation. Despite this discovery, the biology of most PFs remains unknown.MethodsNext generation sequencing (NGS) was performed on formalin-fixed paraffin-embedded (FFPE) samples of PF specimens collected from three institutions (UCSD, NCI and OHSU). Fresh frozen tissue from one tumor was utilized for in vitro assays, including quantitative RT-PCR and cell viability assays following drug treatment.ResultsEight patients with PF were identified and 5 patients' tumors were analyzed by NGS. An index case had a mono-allelic PTCH1 deletion of exons 15-24 and a second case, identified in a validation cohort, also had a PTCH1 gene loss associated with a suspected long-range chromosome 9 deletion. Building on the role of Hh signaling in PF, PTCH1, a tumor suppressor protein, functions upstream of GLI1. Loss of PTCH1 induces GLI1 activation and downstream gene transcription. Utilizing fresh tissue from the index PF case, RT-qPCR analysis demonstrated expression of Hh pathway components, SMO and GLI1, as well as GLI1 transcriptional targets, CCND1 and HHIP. In turn, short-term in vitro treatment with a Hh pathway inhibitor, sonidegib, resulted in dose-dependent cell killing.ConclusionsFor the first time, we report a novel association between PTCH1 inactivation and the development of plexiform fibromyxoma. Hh pathway inhibition with SMO antagonists may represent a target to study for treating a subset of plexiform fibromyxomas

Optimal percolation in correlated multilayer networks with overlap

Multilayer networks have been found to be prone to abrupt cascading failures under random and targeted attacks, but most of the targeting algorithms proposed so far have been mainly tested on uncorrelated systems. Here we show that the size of the critical percolation set of a multilayer network is substantially affected by the presence of inter-layer degree correlations and edge overlap. We provide extensive numerical evidence which confirms that the state-of-the-art optimal percolation strategies consistently fail to identify minimal percolation sets in synthetic and real-world correlated multilayer networks, thus overestimating their robustness. We propose two new targeting algorithms, based on the local estimation of path disruptions away from a given node, and a family of Pareto-efficient strategies that take into account both intra-layer and inter-layer heuristics, and can be easily extended to multiplex networks with an arbitrary number of layers. We show that these strategies consistently outperform existing attacking algorithms, on both synthetic and real-world multiplex networks, and provide some interesting insights about the interplay of correlations and overlap in determining the hyperfragility of real-world multilayer networks. Overall, the results presented in the paper suggest that we are still far from having fully identified the salient ingredients determining the robustness of multiplex networks to targeted attacks.Comment: 14 pages, 9 figures, 1 tabl

Detection of H2D+ in a massive prestellar core in Orion B

Aims. The purpose of this study is to examine the prediction that the deuterated H3+ ion, H2D+, can be found exclusively in the coldest regions of molecular cloud cores. This is also a feasibility study for the detection of the ground-state line of ortho-H2D+ at 372 GHz with APEX. Methods. The 1(10)-1(11) transition of H2D+ at 372 GHz was searched towards selected positions in the massive star forming cloud OriB9, in the dark cloud L183, and in the low- to intermediate mass star-forming cloud R CrA. Results. The line was detected in cold, prestellar cores in the regions of OriB9 and L183, but only upper limits were obtained towards other locations which either have elevated temperatures or contain a newly born star. The H2D+ detection towards OriB9 is the first one in a massive star-forming region. The fractional ortho-H2D+ abundances (relative to H2) are estimated to be about 1.0E-10 in two cold cores in OriB9, and 3.0E-10 in the cold core of L183. Conclusions. The H2D+ detection in OriB9 shows that also massive star forming regions contain very cold prestellar cores which probably have reached matured chemical composition characterized, e.g., by a high degree of deuterium fractionation. Besides as a tracer of the interior parts of prestellar cores, H2D+ may therefore be used to put contraints on the timescales related to massive star formation

Non-Gaussian component analysis: testing the dimension of the signal subspace

Dimension reduction is a common strategy in multivariate data analysis which seeks a subspace which contains all interesting features needed for the subsequent analysis. Non-Gaussian component analysis attempts for this purpose to divide the data into a non-Gaussian part, the signal, and a Gaussian part, the noise. We will show that the simultaneous use of two scatter functionals can be used for this purpose and suggest a bootstrap test to test the dimension of the non-Gaussian subspace. Sequential application of the test can then for example be used to estimate the signal dimension

Nanoparticle formation by ozonolysis of inducible plant volatiles

International audienceWe present the first laboratory experiments of aerosol formation from oxidation of volatile organic species emitted by living plants, a process which for half a century has been known to take place in the atmosphere. We have treated white cabbage plants with methyl jasmonate in order to induce the production of monoterpenes and certain less-volatile sesqui- and homoterpenes. Ozone was introduced into the growth chamber in which the plants were placed, and the subsequent aerosol formation and growth of aerosols were monitored by measuring the particle size distributions continuously during the experiments. Our observations show similar particle formation rates as in the atmosphere but much higher growth rates. The results indicate that the concentrations of nonvolatile oxidation products of plant released precursors needed to induce the nucleation are roughly an order-of-magnitude higher than their concentrations during atmospheric nucleation events. Our results therefore suggest that if oxidized organics are involved in atmospheric nucleation events, their role is to participate in the growth of pre-existing molecular clusters rather than to form such clusters through homogeneous or ion-induced nucleation

Lactobacillus GG in inducing and maintaining remission of Crohn's disease

BACKGROUND: Experimental studies have shown that luminal antigens are involved in chronic intestinal inflammatory disorders such as Crohn's disease and ulcerative colitis. Alteration of the intestinal microflora by antibiotic or probiotic therapy may induce and maintain remission. The aim of this randomized, placebo-controlled trial was to determine the effect of oral Lactobacillus GG (L. GG) to induce or maintain medically induced remission. METHODS: Eleven patients with moderate to active Crohn's disease were enrolled in this trial to receive either L. GG (2 × 10(9 )CFU/day) or placebo for six months. All patients were started on a tapering steroid regime and received antibiotics for the week before the probiotic/placebo medication was initiated. The primary end point was sustained remission, defined as freedom from relapse at the 6 months follow-up visit. Relapse was defined as an increase in CDAI of >100 points. RESULTS: 5/11 patients finished the study, with 2 patients in each group in sustained remission. The median time to relapse was 16 ± 4 weeks in the L. GG group and 12 ± 4.3 weeks in the placebo group (p = 0.5). CONCLUSION: In this study we could not demonstrate a benefit of L. GG in inducing or maintaining medically induced remission in CD

A gastrointestinal stromal tumor with mesenteric and retroperitoneal invasion

<p>Abstract</p> <p>Background</p> <p>Gastrointestinal stromal tumors are rare visceral sarcomas arising in the gastrointestinal tract wall. In this report we present a case of gastrointestinal stromal tumors with mesenteric and retroperitoneal invasion, describe and discuss its computed tomography findings.</p> <p>Case presentation</p> <p>A 57-years-old male patient has been complaining of abdominal distention, weight lose, and hematuria. During physical examination, significant distention and multiple palpable tumor masses were identified on the abdomen. Abdominal computed tomography showed multiple, well-defined, soft tissue masses with homogenous and heterogeneous pattern, in the mesenteric and retroperitoneal areas. Unlike specific features of gastrointestinal stromal tumor, renal obstruction and atypical central calcification without chemotherapy that has not been yet described were seen in this case. Computed tomography did not reveal liver metastases and/or the lymph nodes with pathological size. Ultrasonography-guided true-cut^®biopsy was made, histopathologic and immunohistochemical analyses demonstrated stromal tumor which, C-KIT (+). The patient underwent left ureterectomy, left nephrectomy and total colectomy. Postoperative histopathological analyses revealed lower grade malignant GISTs. As of 17 months after the surgery, he is alive and free of recurrence.</p> <p>Conclusion</p> <p>When intraabdominal, multiple, large (>5 cm), well-circumscribed, homogenous or heterogeneous mass lesions without ascites, omental caking and lymph nodes metasteses were seen, gastrointestinal stromal tumors should be considered in the differential diagnosis.</p