MetaboLab - advanced NMR data processing and analysis for metabolomics

Background\ud Despite wide-spread use of Nuclear Magnetic Resonance (NMR) in metabolomics for the analysis of biological samples there is a lack of graphically driven, publicly available software to process large one and two-dimensional NMR data sets for statistical analysis.\ud \ud Results\ud Here we present MetaboLab, a MATLAB based software package that facilitates NMR data processing by providing automated algorithms for processing series of spectra in a reproducible fashion. A graphical user interface provides easy access to all steps of data processing via a script builder to generate MATLAB scripts, providing an option to alter code manually. The analysis of two-dimensional spectra (1H,13C-HSQC spectra) is facilitated by the use of a spectral library derived from publicly available databases which can be extended readily. The software allows to display specific metabolites in small regions of interest where signals can be picked. To facilitate the analysis of series of two-dimensional spectra, different spectra can be overlaid and assignments can be transferred between spectra. The software includes mechanisms to account for overlapping signals by highlighting neighboring and ambiguous assignments.\ud \ud Conclusions\ud The MetaboLab software is an integrated software package for NMR data processing and analysis, closely linked to the previously developed NMRLab software. It includes tools for batch processing and gives access to a wealth of algorithms available in the MATLAB framework. Algorithms within MetaboLab help to optimize the flow of metabolomics data preparation for statistical analysis. The combination of an intuitive graphical user interface along with advanced data processing algorithms facilitates the use of MetaboLab in a broader metabolomics context.\ud \u

A study of the English postposition ago in the speech of adult native speakers in advanced EFL recordings

Of the three aspects of intonation normally taught at EFL teacher/translator training colleges, namely the ‘chunking’ of speech into tone groups, the location of a main prominence or nucleus, and the behaviour of the pitch of the voice, or tone, it is the area of nucleus placement which has suffered from considerable neglect and insufficient training. The right contextual placement of the nucleus in English has proven to be quite a challenge for EFL teacher/translator trainees, a generally much more daunting task than when faced, for example, with having to make an appropriate tone choice. Consequently, when having to assign prominence to phrases containing elements such as ago, whose classification into lexical and non-lexical varies greatly in the literature, learners generally end up producing faulty accentual patterns which tend to deviate from native speaker norm. In the case of the elusive postposition ago, students almost invariably make it prominent in speech and in transcription, contrary to what is felt to be the case in native speaker English. This may be largely due to the misleading ‘adverbial’ nature assigned to it by most grammar books. The present research endeavours to shed light onto the prosodic behaviour of ago in a corpus of recordings from advanced EFL textbooks. The findings show a high percentage of occurrence of the intonational nucleus in the complement of the postposition ago, which seems to support the researcher’s view that phrases containing ago, if nuclear, will by default bear the intonational nucleus on the complement of the postposition rather than on the postposition itself –unless stronger psycholinguistic principles such as rhythmic alternation and rhythmic optimisation come into play, which may cause ago to become prominent. This prosodic behaviour also would support treatment of ago as a non-lexical item in the grammar of English. Further research with a larger and more varied corpus might provide a clearer picture of the prosodic behaviour of ago, a neglected deictic item which has long straddled between its adverbial and prepositional personalities in grammars and intonation manuals

A Pointing Solution for the Medium Size Telescopes for the Cherenkov Telescope Array

An important aspect of the calibration of the Cherenkov Telescope Array is the pointing, which enables an exact alignment of each telescope and therefore allows to transform a position in the sky to a point in the plane of the Cherenkov camera and vice versa. The favoured approach for the pointing calibration of the medium size telescopes (MST) is the installation of an optical CCD-camera in the dish of the telescope that captures the position of the Cherenkov camera and of the stars in the night sky simultaneously during data taking. The adaption of this approach is presented in this proceeding.Comment: 6 pages, 9 figures, Proceedings of the 6th International Symposium on High-Energy Gamma-Ray Astronomy (Gamma2016

Metabolomics of the Tumor Microenvironment in Pediatric Acute Lymphoblastic Leukemia

Stefano Tiziani, Yunyi Kang, Ricky Harjanto, Joshua Axelrod, Giovanni Paternostro, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of AmericaCarlo Piermarocchi, Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of AmericaWilliam Roberts, Rady Children’s Hospital, Department of Pediatrics, University of California San Diego, San Diego, California, United States of AmericaStefano Tiziani, Department of Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, Texas, United States of AmericaThe tumor microenvironment is emerging as an important therapeutic target. Most studies, however, are focused on the protein components, and relatively little is known of how the microenvironmental metabolome might influence tumor survival. In this study, we examined the metabolic profiles of paired bone marrow (BM) and peripheral blood (PB) samples from 10 children with acute lymphoblastic leukemia (ALL). BM and PB samples from the same patient were collected at the time of diagnosis and after 29 days of induction therapy, at which point all patients were in remission. We employed two analytical platforms, high-resolution magnetic resonance spectroscopy and gas chromatography-mass spectrometry, to identify and quantify 102 metabolites in the BM and PB. Standard ALL therapy, which includes l-asparaginase, completely removed circulating asparagine, but not glutamine. Statistical analyses of metabolite correlations and network reconstructions showed that the untreated BM microenvironment was characterized by a significant network-level signature: a cluster of highly correlated lipids and metabolites involved in lipid metabolism (p less than 0.006). In contrast, the strongest correlations in the BM upon remission were observed among amino acid metabolites and derivatives (p less than 9.2×10-10). This study provides evidence that metabolic characterization of the cancer niche could generate new hypotheses for the development of cancer therapies.This work was funded by the National Science Foundation (Grant No. 0829891). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Nutritional SciencesDell Pediatric Research InstituteEmail: [email protected] (GP), Email: [email protected] (ST

Fine-needle aspiration cytological features of Cherubism

Cherubism is a rare benign, non-neoplastic condition characterized by facial alteration due to symmetrically expansion of bilateral mandibles and maxillas. A fine-needle aspiration of a right cheek mass was performed in a 17-year-old teenager who was previously diagnosed Cherubism. The smears showed moderate cellularity with spindle cells mixed with multinucleated giant cells of osteoclast type. The cells appeared bland with normal nuclear/cytoplasm ratio. The nuclei were round or oval with smooth nuclear membranes and fine, evenly distributed chromatin. These cytologic features were considered consistent with but not diagnostic of Cherubism. Clinical correlations are needed in distinguishing Cherubism from other lesions containing giant cells. Diagn. Cytopathol. 2008;36:188–189. © 2008 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58043/1/20791_ftp.pd

Metabolomic profiling predicts outcome of rituximab therapy in rheumatoid arthritis.

ObjectiveTo determine whether characterisation of patients' metabolic profiles, utilising nuclear magnetic resonance (NMR) and mass spectrometry (MS), could predict response to rituximab therapy. 23 patients with active, seropositive rheumatoid arthritis (RA) on concomitant methotrexate were treated with rituximab. Patients were grouped into responders and non-responders according to the American College of Rheumatology improvement criteria, at a 20% level at 6 months. A Bruker Avance 700 MHz spectrometer and a Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap mass spectrometer were used to acquire (1)H-NMR and ultra high pressure liquid chromatography (UPLC)-MS/MS spectra, respectively, of serum samples before and after rituximab therapy. Data processing and statistical analysis were performed in MATLAB. 14 patients were characterised as responders, and 9 patients were considered non-responders. 7 polar metabolites (phenylalanine, 2-hydroxyvalerate, succinate, choline, glycine, acetoacetate and tyrosine) and 15 lipid species were different between responders and non-responders at baseline. Phosphatidylethanolamines, phosphatidyserines and phosphatidylglycerols were downregulated in responders. An opposite trend was observed in phosphatidylinositols. At 6 months, 5 polar metabolites (succinate, taurine, lactate, pyruvate and aspartate) and 37 lipids were different between groups. The relationship between serum metabolic profiles and clinical response to rituximab suggests that (1)H-NMR and UPLC-MS/MS may be promising tools for predicting response to rituximab

The Colonization of Space Physical Anthropology 225 -236

Abstract. The colonization of space implies an adaptation of both physical and cultural type. The human species is characterized by a great adaptive capacity that, in a basically Keyword. Space Anthropology, physical and cultural adaptation, colonization, interstellar travels, alien communication Even though this isn't well known, anthropologists have been studying problems and opportunities connected with space flights and colonization for several years. Conceiving the occupation of other planets in our solar system and later on of other planetary systems, does not exempt us from solving the problems on Earth, at least because we'd export the mentality that caused the same problems here. It means conceiving well organized, self-sufficient space colonies, socially harmonious, as the result of man's new attitude towards the environment. Which is to say, colonies which are evidence of the fact that the existing social conflicts and environmental dangers have been overcome. Is this science fiction? Many of the current scientific, technological and social achievements were considered as such, in the past. Anthropology deals with this particular field of research proposing some practical applications implying a new conception of what was the "space race" until a couple of decades ago, providing its knowledge about nutrition, evolution, environmental impact, human behaviour and conflict resolutio

Sensing, Design Optimization, and Motion Planning for Agile Pneumatic Artificial Muscle-Driven Robots

Mechanical compliance in robotic systems facilitates safe human-robot interaction and improves robot adaptation to environmental uncertainty. Several promising compliant actuator technologies have emerged from the field of soft robotics, in particular the pneumatic artificial muscle—a soft, lightweight actuator that contracts under pressure. The pneumatic muscle's passive compliance eliminates the need for precise high-bandwidth actuator control to simulate mechanical impedance. However, the pneumatic muscle is limited in practical robot applications—particularly, without sacrificing robot agility—due to several key challenges: development of compatible soft sensors, translation of conventional high-level control and planning techniques to pneumatic muscle-driven systems, and limitations in pneumatic muscle pressurization rate and force generation capabilities. This work seeks to address these challenges, via a threefold approach, to access the benefits of compliant robot actuation while maximizing the robot's dynamic capabilities. The first objective targets the development of a pneumatic muscle design with integrated sensing to enable kinematic and dynamic state estimation of muscle-actuated robots without hindering muscle compliance. The second objective focuses on the construction of a trajectory optimization framework for planning dynamic robot maneuvers using 'burst-inflation' muscle pressure control. Finally, the third objective explores a design optimization strategy utilizing biological joint mechanisms to compensate for pneumatic muscle limitations and maximize robot agility.Ph.D