Developments in GRworkbench

The software tool GRworkbench is an ongoing project in visual, numerical General Relativity at The Australian National University. Recently, GRworkbench has been significantly extended to facilitate numerical experimentation in analytically-defined space-times. The numerical differential geometric engine has been rewritten using functional programming techniques, enabling objects which are normally defined as functions in the formalism of differential geometry and General Relativity to be directly represented as function variables in the C++ code of GRworkbench. The new functional differential geometric engine allows for more accurate and efficient visualisation of objects in space-times and makes new, efficient computational techniques available. Motivated by the desire to investigate a recent scientific claim using GRworkbench, new tools for numerical experimentation have been implemented, allowing for the simulation of complex physical situations.Comment: 14 pages. To appear A. Moylan, S.M. Scott and A.C. Searle, Developments in GRworkbench. Proceedings of the Tenth Marcel Grossmann Meeting on General Relativity, editors M. Novello, S. Perez-Bergliaffa and R. Ruffini. Singapore: World Scientific 200

Functional programming framework for GRworkbench

The software tool GRworkbench is an ongoing project in visual, numerical General Relativity at The Australian National University. Recently, the numerical differential geometric engine of GRworkbench has been rewritten using functional programming techniques. By allowing functions to be directly represented as program variables in C++ code, the functional framework enables the mathematical formalism of Differential Geometry to be more closely reflected in GRworkbench . The powerful technique of `automatic differentiation' has replaced numerical differentiation of the metric components, resulting in more accurate derivatives and an order-of-magnitude performance increase for operations relying on differentiation

Numerical wave optics and the lensing of gravitational waves by globular clusters

We consider the possible effects of gravitational lensing by globular clusters on gravitational waves from asymmetric neutron stars in our galaxy. In the lensing of gravitational waves, the long wavelength, compared with the usual case of optical lensing, can lead to the geometrical optics approximation being invalid, in which case a wave optical solution is necessary. In general, wave optical solutions can only be obtained numerically. We describe a computational method that is particularly well suited to numerical wave optics. This method enables us to compare the properties of several lens models for globular clusters without ever calling upon the geometrical optics approximation, though that approximation would sometimes have been valid. Finally, we estimate the probability that lensing by a globular cluster will significantly affect the detection, by ground-based laser interferometer detectors such as LIGO, of gravitational waves from an asymmetric neutron star in our galaxy, finding that the probability is insignificantly small.Comment: To appear in: Proceedings of the Eleventh Marcel Grossmann Meetin

Nine quick tips for efficient bioinformatics curriculum development and training.

Biomedical research is becoming increasingly data driven. New technologies that generate large-scale, complex data are continually emerging and evolving. As a result, there is a concurrent need for training researchers to use and understand new computational tools. Here we describe an efficient and effective approach to developing curriculum materials that can be deployed in a research environment to meet this need

Proteomic Analysis of Media from Lung Cancer Cells Reveals Role of 14-3-3 Proteins in Cachexia

Aims: At the time of diagnosis, 60% of lung cancer patients present with cachexia, a severe wasting syndrome that increases morbidity and mortality. Tumors secrete multiple factors that contribute to cachectic muscle wasting, and not all of these factors have been identified. We used Orbitrap electrospray ionization mass spectrometry to identify novel cachexia-inducing candidates in media conditioned with Lewis lung carcinoma cells (LCM). Results: One-hundred and 58 proteins were confirmed in three biological replicates. Thirty-three were identified as secreted proteins, including 14-3-3 proteins, which are highly conserved adaptor proteins known to have over 200 binding partners. We confirmed the presence of extracellular 14-3-3 proteins in LCM via western blot and discovered that LCM contained less 14-3-3 content than media conditioned with C2C12 myotubes. Using a neutralizing antibody, we depleted extracellular 14-3-3 proteins in myotube culture medium, which resulted in diminished myosin content. We identified the proposed receptor for 14-3-3 proteins, CD13, in differentiated C2C12 myotubes and found that inhibiting CD13 via Bestatin also resulted in diminished myosin content. Conclusions: Our novel findings show that extracellular 14-3-3 proteins may act as previously unidentified myokines and may signal via CD13 to help maintain muscle mass

The impact of maternal smoking during pregnancy on depressive and anxiety behaviors in children: the Norwegian Mother and Child Cohort Study.

BACKGROUND: Maternal smoking during pregnancy (MSDP) is associated with multiple adverse childhood outcomes including externalizing behaviors. However, the association between MSDP and internalizing (anxiety and depressive) behaviors in offspring has received less investigation. We aimed to assess the association between MSDP and childhood internalizing (anxiety and depressive) behaviors in a very large, well-characterized cohort study. METHODS: We assessed the association between MSDP and internalizing behaviors in offspring utilizing information drawn from 90,040 mother-child pairs enrolled in the Norwegian Mother and Child Cohort Study. Mothers reported smoking information, including status and frequency of smoking, twice during pregnancy. Mothers also reported their child\u27s internalizing behaviors at 18 months, 36 months, and 5 years. Associations between MSDP and childhood internalizing behaviors, including dose-response and timing of smoking in pregnancy, were assessed at each time point. RESULTS: MSDP was associated with increased internalizing behaviors when offspring were aged 18 months (B = 0.11, P <0.001) and 36 months (B = 0.06, P <0.01), adjusting for numerous potential confounders. Higher rates of smoking (e.g., >20 cigarettes per day) were associated with higher levels of internalizing behaviors. Maternal smoking during early pregnancy appeared to be the critical period for exposure. CONCLUSIONS: We found evidence supporting a potential role for MSDP in increasing internalizing (anxiety and depressive) behaviors in offspring. We also found evidence supportive of a possible causal relationship, including dose-dependency and support for a predominant role of early pregnancy exposure. Further investigation utilizing genetically informed designs are warranted to assess this association

Complementary medicine, exercise, meditation, diet, and lifestyle modification for anxiety disorders : a review of current evidence

Use of complementary medicines and therapies (CAM) and modification of lifestyle factors such as physical activity and exercise, and diet are being increasingly considered as potential therapeutic options for anxiety disorders. The objective of this metareview was to examine evidence across a broad range of CAM and lifestyle interventions in the treatment of anxiety disorders. In early 2012 we conducted a literature search of PubMed, Scopus, CINAHL, Web of Science, PsycInfo, and the Cochrane Library, for key studies, systematic reviews, and metaanalyses in the area. Our review found that in respect to treatment of generalized anxiety or specific anxiety disorders, CAM evidence revealed support for the herbal medicine Kava. One isolated study shows benefit for naturopathic medicine, whereas acupuncture, yoga, and Tai chi have tentative supportive evidence, which is hampered by overall poor methodology. The breadth of evidence does not support homeopathy for treating anxiety. Strong support exists for lifestyle modifications including adoption of moderate exercise and mindfulness meditation, whereas dietary improvement, avoidance of caffeine, alcohol, and nicotine offer encouraging preliminary data. In conclusion, certain lifestyle modifications and some CAMs may provide a beneficial role in the management of anxiety disorders

Complementary medicine, exercise, meditation, diet, and lifestyle modification for anxiety disorders : a review of current evidence

Use of complementary medicines and therapies (CAM) and modification of lifestyle factors such as physical activity and exercise, and diet are being increasingly considered as potential therapeutic options for anxiety disorders. The objective of this metareview was to examine evidence across a broad range of CAM and lifestyle interventions in the treatment of anxiety disorders. In early 2012 we conducted a literature search of PubMed, Scopus, CINAHL, Web of Science, PsycInfo, and the Cochrane Library, for key studies, systematic reviews, and metaanalyses in the area. Our review found that in respect to treatment of generalized anxiety or specific anxiety disorders, CAM evidence revealed support for the herbal medicine Kava. One isolated study shows benefit for naturopathic medicine, whereas acupuncture, yoga, and Tai chi have tentative supportive evidence, which is hampered by overall poor methodology. The breadth of evidence does not support homeopathy for treating anxiety. Strong support exists for lifestyle modifications including adoption of moderate exercise and mindfulness meditation, whereas dietary improvement, avoidance of caffeine, alcohol, and nicotine offer encouraging preliminary data. In conclusion, certain lifestyle modifications and some CAMs may provide a beneficial role in the management of anxiety disorders

Complementary Medicine, Exercise, Meditation, Diet, and Lifestyle Modification for Anxiety Disorders: A Review of Current Evidence

Use of complementary medicines and therapies (CAM) and modification of lifestyle factors such as physical activity, exercise, and diet are being increasingly considered as potential therapeutic options for anxiety disorders. The objective of this metareview was to examine evidence across a broad range of CAM and lifestyle interventions in the treatment of anxiety disorders. In early 2012 we conducted a literature search of PubMed, Scopus, CINAHL, Web of Science, PsycInfo, and the Cochrane Library, for key studies, systematic reviews, and metaanalyses in the area. Our paper found that in respect to treatment of generalized anxiety or specific disorders, CAM evidence revealed current support for the herbal medicine Kava. One isolated study shows benefit for naturopathic medicine, whereas acupuncture, yoga, and Tai chi have tentative supportive evidence, which is hampered by overall poor methodology. The breadth of evidence does not support homeopathy for treating anxiety. Strong support exists for lifestyle modifications including adoption of moderate exercise and mindfulness meditation, whereas dietary improvement, avoidance of caffeine, alcohol, and nicotine offer encouraging preliminary data. In conclusion, certain lifestyle modifications and some CAMs may provide a beneficial role in the treatment of anxiety disorders