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931.
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933.
The growing capacity to process and store animal tracks has spurred the development of new methods to segment animal trajectories into elementary units of movement. Key challenges for movement trajectory segmentation are to (i) minimize the need of supervision, (ii) reduce computational costs, (iii) minimize the need of prior assumptions (e.g. simple parametrizations), and (iv) capture biologically meaningful semantics, useful across a broad range of species. We introduce the Expectation-Maximization binary Clustering (EMbC), a general purpose, unsupervised approach to multivariate data clustering. The EMbC is a variant of the Expectation-Maximization Clustering (EMC), a clustering algorithm based on the maximum likelihood estimation of a Gaussian mixture model. This is an iterative algorithm with a closed form step solution and hence a reasonable computational cost. The method looks for a good compromise between statistical soundness and ease and generality of use (by minimizing prior assumptions and favouring the semantic interpretation of the final clustering). Here we focus on the suitability of the EMbC algorithm for behavioural annotation of movement data. We show and discuss the EMbC outputs in both simulated trajectories and empirical movement trajectories including different species and different tracking methodologies. We use synthetic trajectories to assess the performance of EMbC compared to classic EMC and Hidden Markov Models. Empirical trajectories allow us to explore the robustness of the EMbC to data loss and data inaccuracies, and assess the relationship between EMbC output and expert label assignments. Additionally, we suggest a smoothing procedure to account for temporal correlations among labels, and a proper visualization of the output for movement trajectories. Our algorithm is available as an R-package with a set of complementary functions to ease the analysis. 相似文献
934.
Aude Pflieger Pierre Waffo Teguo Yorgos Papastamoulis Stéphane Chaignepain Frederic Subra Soundasse Munir Olivier Delelis Paul Lesbats Christina Calmels Marie-Line Andreola Jean-Michel Merillon Corinne Auge-Gouillou Vincent Parissi 《PloS one》2013,8(11)
Polynucleotidyl transferases are enzymes involved in several DNA mobility mechanisms in prokaryotes and eukaryotes. Some of them such as retroviral integrases are crucial for pathogenous processes and are therefore good candidates for therapeutic approaches. To identify new therapeutic compounds and new tools for investigating the common functional features of these proteins, we addressed the inhibition properties of natural stilbenoids deriving from resveratrol on two models: the HIV-1 integrase and the eukaryote MOS-1 transposase. Two resveratrol dimers, leachianol F and G, were isolated for the first time in Vitis along with fourteen known stilbenoids: E-resveratrol, E-piceid, E-pterostilbene, E-piceatannol, (+)-E-ε-viniferin, E-ε-viniferinglucoside, E-scirpusin A, quadragularin A, ampelopsin A, pallidol, E-miyabenol C, E-vitisin B, hopeaphenol, and isohopeaphenol and were purified from stalks of Vitis vinifera (Vitaceae), and moracin M from stem bark of Milliciaexelsa (Moraceae). These compounds were tested in in vitro and in vivo assays reproducing the activity of both enzymes. Several molecules presented significant inhibition on both systems. Some of the molecules were found to be active against both proteins while others were specific for one of the two models. Comparison of the differential effects of the molecules suggested that the compounds could target specific intermediate nucleocomplexes of the reactions. Additionally E-pterostilbene was found active on the early lentiviral replication steps in lentiviruses transduced cells. Consequently, in addition to representing new original lead compounds for further modelling of new active agents against HIV-1 integrase, these molecules could be good tools for identifying such reaction intermediates in DNA mobility processes. 相似文献
935.
Paulo Pereira David Buzek J?rg Franke Wolfgang Senker Arkadiusz Kosmala Ulrich Hubbe Neil Manson Wout Rosenberg Roberto Assietti Frederic Martens Giovanni Barbanti Brodano Kai-Michael Scheufler 《PloS one》2015,10(3)
Minimally invasive lumbar interbody fusion (MILIF) offers potential for reduced operative morbidity and earlier recovery compared with open procedures for patients with degenerative lumbar disorders (DLD). Firm conclusions about advantages of MILIF over open procedures cannot be made because of limited number of large studies of MILIF in a real-world setting. Clinical effectiveness of MILIF in a large, unselected real-world patient population was assessed in this Prospective, monitored, international, multicenter, observational study. Objective: To observe and document short-term recovery after minimally invasive interbody fusion for DLD. Materials and Methods: In a predefined 4-week analysis from this study, experienced surgeons (≥30 MILIF surgeries pre-study) treated patients with DLD by one- or two-level MILIF. The primary study objective was to document patients’ short-term post-interventional recovery (primary objective) including back/leg pain (visual analog scale [VAS]), disability (Oswestry Disability Index [ODI]), health status (EQ-5D) and Patient satisfaction. Results: At 4 weeks, 249 of 252 patients were remaining in the study; the majority received one-level MILIF (83%) and TLIF was the preferred approach (94.8%). For one-level (and two-level) procedures, surgery duration was 128 (182) min, fluoroscopy time 115 (154) sec, and blood-loss 164 (233) mL. Time to first ambulation was 1.3 days and time to study-defined surgery recovery was 3.2 days. Patients reported significantly (P < 0.0001) reduced back pain (VAS: 2.9 vs 6.2), leg pain (VAS: 2.5 vs 5.9), and disability (ODI: 34.5% vs 45.5%), and a significantly (P < 0.0001) improved health status (EQ-5D index: 0.61 vs 0.34; EQ VAS: 65.4 vs 52.9) 4 weeks postoperatively. One adverse event was classified as related to the minimally invasive surgical approach. No deep site infections or deaths were reported. Conclusions: For experienced surgeons, MILIF for DLD demonstrated early benefits (short time to first ambulation, early recovery, high patient satisfaction and improved patient-reported outcomes) and low major perioperative morbidity at 4 weeks postoperatively. 相似文献
936.
Khyatiben V. Pathak Marissa I. McGilvrey Charles K. Hu Krystine Garcia-Mansfield Karen Lewandoski Zahra Eftekhari Yate-Ching Yuan Frederic Zenhausern Emmanuel Menashi Patrick Pirrotte 《Molecular & cellular proteomics : MCP》2020,19(10):1688-1705
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- •ETA present a diverse proteome and metabolome and can be employed for longitudinal studies of nosocomial infections affecting the lungs.
- •The proteome and metabolome of ETA and BAL share comparable features that may be leveraged for diagnostics.
- •ETA carries early signatures of host innate immunity against ventilator-associated pneumonia.
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938.
Serena Dollive Ying-Yu Chen Stephanie Grunberg Kyle Bittinger Christian Hoffmann Lee Vandivier Christopher Cuff James D. Lewis Gary D. Wu Frederic D. Bushman 《PloS one》2013,8(8)
Antibiotic use in humans has been associated with outgrowth of fungi. Here we used a murine model to investigate the gut microbiome over 76 days of treatment with vancomycin, ampicillin, neomycin, and metronidazole and subsequent recovery. Mouse stool was studied as a surrogate for the microbiota of the lower gastrointestinal tract. The abundance of fungi and bacteria was measured using quantitative PCR, and the proportional composition of the communities quantified using 454/Roche pyrosequencing of rRNA gene tags. Prior to treatment, bacteria outnumbered fungi by >3 orders of magnitude. Upon antibiotic treatment, bacteria dropped in abundance >3 orders of magnitude, so that the predominant 16S sequences detected became transients derived from food. Upon cessation of treatment, bacterial communities mostly returned to their previous numbers and types after 8 weeks, though communities remained detectably different from untreated controls. Fungal communities varied substantially over time, even in the untreated controls. Separate cages within the same treatment group showed radical differences, but mice within a cage generally behaved similarly. Fungi increased ∼40-fold in abundance upon antibiotic treatment but declined back to their original abundance after cessation of treatment. At the last time point, Candida remained more abundant than prior to treatment. These data show that 1) gut fungal populations change radically during normal mouse husbandry, 2) fungi grow out in the gut upon suppression of bacterial communities with antibiotics, and 3) perturbations due to antibiotics persist long term in both the fungal and bacterial microbiota. 相似文献
939.
On measures of dissimilarity between point patterns: Classification based on prototypes and multidimensional scaling
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Jorge Mateu Frederic P. Schoenberg David M. Diez Jonatan A. González Weipeng Lu 《Biometrical journal. Biometrische Zeitschrift》2015,57(2):340-358
This paper presents a collection of dissimilarity measures to describe and then classify spatial point patterns when multiple replicates of different types are available for analysis. In particular, we consider a range of distances including the spike‐time distance and its variants, as well as cluster‐based distances and dissimilarity measures based on classical statistical summaries of point patterns. We review and explore, in the form of a tutorial, their uses, and their pros and cons. These distances are then used to summarize and describe collections of repeated realizations of point patterns via prototypes and multidimensional scaling. We also show a simulation study to evaluate the performance of multidimensional scaling with two types of selected distances. Finally, a multivariate spatial point pattern of a natural plant community is analyzed through various of these measures of dissimilarity. 相似文献
940.