Mapping Exoplanets

The varied surfaces and atmospheres of planets make them interesting places to live, explore, and study from afar. Unfortunately, the great distance to exoplanets makes it impossible to resolve their disk with current or near-term technology. It is still possible, however, to deduce spatial inhomogeneities in exoplanets provided that different regions are visible at different times---this can be due to rotation, orbital motion, and occultations by a star, planet, or moon. Astronomers have so far constructed maps of thermal emission and albedo for short period giant planets. These maps constrain atmospheric dynamics and cloud patterns in exotic atmospheres. In the future, exo-cartography could yield surface maps of terrestrial planets, hinting at the geophysical and geochemical processes that shape them.Comment: Updated chapter for Handbook of Exoplanets, eds. Deeg & Belmonte. 17 pages, including 6 figures and 4 pages of reference

Interacting Supernovae: Types IIn and Ibn

Supernovae (SNe) that show evidence of strong shock interaction between their ejecta and pre-existing, slower circumstellar material (CSM) constitute an interesting, diverse, and still poorly understood category of explosive transients. The chief reason that they are extremely interesting is because they tell us that in a subset of stellar deaths, the progenitor star may become wildly unstable in the years, decades, or centuries before explosion. This is something that has not been included in standard stellar evolution models, but may significantly change the end product and yield of that evolution, and complicates our attempts to map SNe to their progenitors. Another reason they are interesting is because CSM interaction is an efficient engine for making bright transients, allowing super-luminous transients to arise from normal SN explosion energies, and allowing transients of normal SN luminosities to arise from sub-energetic explosions or low radioactivity yield. CSM interaction shrouds the fast ejecta in bright shock emission, obscuring our normal view of the underlying explosion, and the radiation hydrodynamics of the interaction is challenging to model. The CSM interaction may also be highly non-spherical, perhaps linked to binary interaction in the progenitor system. In some cases, these complications make it difficult to definitively tell the difference between a core-collapse or thermonuclear explosion, or to discern between a non-terminal eruption, failed SN, or weak SN. Efforts to uncover the physical parameters of individual events and connections to possible progenitor stars make this a rapidly evolving topic that continues to challenge paradigms of stellar evolution.Comment: Final draft of a chapter in the "SN Handbook". Accepted. 25 pages, 3 fig

Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method

<p>Abstract</p> <p>Background</p> <p>Large biological data sets, such as expression profiles, benefit from reduction of random noise. Principal component (PC) analysis has been used for this purpose, but it tends to remove small features as well as random noise.</p> <p>Results</p> <p>We interpreted the PCs as a mere signal-rich coordinate system and sorted the squared PC-coordinates of each row in descending order. The sorted squared PC-coordinates were compared with the distribution of the ordered squared random noise, and PC-coordinates for insignificant contributions were treated as random noise and nullified. The processed data were transformed back to the initial coordinates as noise-reduced data. To increase the sensitivity of signal capture and reduce the effects of stochastic noise, this procedure was applied to multiple small subsets of rows randomly sampled from a large data set, and the results corresponding to each row of the data set from multiple subsets were averaged. We call this procedure Row-specific, Sorted PRincipal component-guided Noise Reduction (RSPR-NR). Robust performance of RSPR-NR, measured by noise reduction and retention of small features, was demonstrated using simulated data sets. Furthermore, when applied to an actual expression profile data set, RSPR-NR preferentially increased the correlations between genes that share the same Gene Ontology terms, strongly suggesting reduction of random noise in the data set.</p> <p>Conclusion</p> <p>RSPR-NR is a robust random noise reduction method that retains small features well. It should be useful in improving the quality of large biological data sets.</p

A Relativistic Type Ibc Supernova Without a Detected Gamma-ray Burst

Long duration gamma-ray bursts (GRBs) mark the explosive death of some massive stars and are a rare sub-class of Type Ibc supernovae (SNe Ibc). They are distinguished by the production of an energetic and collimated relativistic outflow powered by a central engine (an accreting black hole or neutron star). Observationally, this outflow is manifested in the pulse of gamma-rays and a long-lived radio afterglow. To date, central engine-driven SNe have been discovered exclusively through their gamma-ray emission, yet it is expected that a larger population goes undetected due to limited satellite sensitivity or beaming of the collimated emission away from our line-of-sight. In this framework, the recovery of undetected GRBs may be possible through radio searches for SNe Ibc with relativistic outflows. Here we report the discovery of luminous radio emission from the seemingly ordinary Type Ibc SN 2009bb, which requires a substantial relativistic outflow powered by a central engine. The lack of a coincident GRB makes SN 2009bb the first engine-driven SN discovered without a detected gamma-ray signal. A comparison with our extensive radio survey of SNe Ibc reveals that the fraction harboring central engines is low, ~1 percent, measured independently from, but consistent with, the inferred rate of nearby GRBs. Our study demonstrates that upcoming optical and radio surveys will soon rival gamma-ray satellites in pinpointing the nearest engine-driven SNe. A similar result for a different supernova is reported independently.Comment: To appear in Nature on Jan 28 2010. Embargoed for discussion in the press until 13:00 US Eastern Time on Jan 27 (Accepted version, 27 pages, Manuscript and Suppl. Info.

Day occupation is associated with psychopathology for adolescents and young adults with Down syndrome

Background: Young adults with Down syndrome experience increased rates of emotional and behavioural problems compared with the general population. Most adolescents with Down syndrome living in Western Australia participate in sheltered employment as their main day occupation. Relationship between day occupation and changes in behaviour has not been examined. Therefore, the aim of this research was to explore any relationship between post school day occupations and changes in the young person’s behaviour. Methods: The Down syndrome Needs Opinion Wishes database was used for case ascertainment of young adults aged 15 to 32 years with Down syndrome. Families of 118 young people in this population-based database completed questionnaires in 2004, 2009 and 2011. The questionnaires addressed both young person characteristics such as age, gender, presence of impairments, behaviour, functioning in activities of daily living, and family characteristics such as income and family functioning. Post-school day occupations in which the young people were participating included open and sheltered employment, training and day recreation programs. Change in behaviour of young adults who remained in the same post-school day occupation from 2009 to 2011 (n = 103) were examined in a linear regression model adjusting for confounding variables including age, gender, prior functioning and behaviour in 2004 and family income.Results: In comparison to those young adults attending open employment from 2009 to 2011, those attending day recreation programs were reported to experience worsening in behaviour both in the unadjusted (effect size -0.14, 95% CI -0.24, -0.05) and adjusted models (effect size -0.15, 95% CI -0.29, -0.01). Conclusions: We found that the behaviour of those participating in open employment improved compared to those attending other day occupations. Further examination of the direction of this association is required

Improved Somatic Mutagenesis in Zebrafish Using Transcription Activator-Like Effector Nucleases (TALENs)

Zinc Finger Nucleases (ZFNs) made by Context-Dependent Assembly (CoDA) and Transcription Activator-Like Effector Nucleases (TALENs) provide robust and user-friendly technologies for efficiently inactivating genes in zebrafish. These designer nucleases bind to and cleave DNA at particular target sites, inducing error-prone repair that can result in insertion or deletion mutations. Here, we assess the relative efficiencies of these technologies for inducing somatic DNA mutations in mosaic zebrafish. We find that TALENs exhibited a higher success rate for obtaining active nucleases capable of inducing mutations than compared with CoDA ZFNs. For example, all six TALENs tested induced DNA mutations at genomic target sites while only a subset of CoDA ZFNs exhibited detectable rates of mutagenesis. TALENs also exhibited higher mutation rates than CoDA ZFNs that had not been pre-screened using a bacterial two-hybrid assay, with DNA mutation rates ranging from 20%–76.8% compared to 1.1%–3.3%. Furthermore, the broader targeting range of TALENs enabled us to induce mutations at the methionine translation start site, sequences that were not targetable using the CoDA ZFN platform. TALENs exhibited similar toxicity to CoDA ZFNs, with >50% of injected animals surviving to 3 days of life. Taken together, our results suggest that TALEN technology provides a robust alternative to CoDA ZFNs for inducing targeted gene-inactivation in zebrafish, making it a preferred technology for creating targeted knockout mutants in zebrafish

Mini-open anterior spine surgery for anterior lumbar diseases

Minimally invasive surgeries including endoscopic surgery and mini-open surgery are current trend of spine surgery, and its main advantages are shorter recovery time and cosmetic benefits, etc. However, mini-open surgery is easier and less technique demanding than endoscopic surgery. Besides, anterior spinal fusion is better than posterior spinal fusion while considering the physiological loading, back muscle function, etc. Therefore, we aimed to introduce the modified “mini-open anterior spine surgery” (MOASS) and to evaluate the feasibility, effectiveness and safety in the treatment of various anterior lumbar diseases with this technique. A total of 61 consecutive patients (46 female, 15 male; mean age 58.2 years) from 1997 to 2004 were included in this study, with an average follow-up of 24–52 (mean 43) months. The disease entities included vertebral fracture (20), failed back surgery (13), segmental instability or spondylolisthesis (10), infection (8), herniated disc (5), undetermined lesion for biopsy (4), and hemivertebra (1). Lesions involved 13 cases at T12–L1, 18 at L1–L2, 18 at L2–L3, 22 at L3–L4 and 11 at L4–L5 levels. All patients received a single stage anterior-only procedure for their anterior lumbar disease. We used the subjective clinical results, Oswestry disability index, fusion rate, and complications to evaluate our clinical outcome. Most patients (91.8%) were subjectively satisfied with the surgery and had good-to-excellent outcomes. Mean operation time was 85 (62–124) minutes, and mean blood loss was 136 (minimal-250) ml in the past 6 years. Hospital stay ranged from 4–26 (mean 10.6) days. Nearly all cases had improved back pain (87%), physical function (90%) and life quality (85%). Most cases (95%) achieved solid or probable solid bony fusion. There were no major complications. Therefore, MOASS is feasible, effective and safe for patients with various anterior lumbar diseases

Mapping the categories of the Swedish primary health care version of ICD-10 to SNOMED CT concepts: Rule development and intercoder reliability in a mapping trial

<p>Abstract</p> <p>Background</p> <p>Terminologies and classifications are used for different purposes and have different structures and content. Linking or mapping terminologies and classifications has been pointed out as a possible way to achieve various aims as well as to attain additional advantages in describing and documenting health care data.</p> <p>The objectives of this study were:</p> <p>• to explore and develop rules to be used in a mapping process</p> <p>• to evaluate intercoder reliability and the assessed degree of concordance when the 'Swedish primary health care version of the International Classification of Diseases version 10' (ICD-10) is matched to the Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT)</p> <p>• to describe characteristics in the coding systems that are related to obstacles to high quality mapping.</p> <p>Methods</p> <p>Mapping (interpretation, matching, assessment and rule development) was done by two coders. The Swedish primary health care version of ICD-10 with 972 codes was randomly divided into an allotment of three sets of categories, used in three mapping sequences, A, B and C. Mapping was done independently by the coders and new rules were developed between the sequences. Intercoder reliability was measured by comparing the results after each set. The extent of matching was assessed as either 'partly' or 'completely concordant'</p> <p>Results</p> <p>General principles for mapping were outlined before the first sequence, A. New mapping rules had significant impact on the results between sequences A - B (p < 0.01) and A - C (p < 0.001). The intercoder reliability in our study reached 83%. Obstacles to high quality mapping were mainly a lack of agreement by the coders due to structural and content factors in SNOMED CT and in the current ICD-10 version. The predominant reasons for this were difficulties in interpreting the meaning of the categories in the current ICD-10 version, and the presence of many related concepts in SNOMED CT.</p> <p>Conclusion</p> <p>Mapping from ICD-10-categories to SNOMED CT needs clear and extensive rules. It is possible to reach high intercoder reliability in mapping from ICD-10-categories to SNOMED CT. However, several obstacles to high quality mapping remain due to structure and content characteristics in both coding systems.</p

Observational and Physical Classification of Supernovae

This chapter describes the current classification scheme of supernovae (SNe). This scheme has evolved over many decades and now includes numerous SN Types and sub-types. Many of these are universally recognized, while there are controversies regarding the definitions, membership and even the names of some sub-classes; we will try to review here the commonly-used nomenclature, noting the main variants when possible. SN Types are defined according to observational properties; mostly visible-light spectra near maximum light, as well as according to their photometric properties. However, a long-term goal of SN classification is to associate observationally-defined classes with specific physical explosive phenomena. We show here that this aspiration is now finally coming to fruition, and we establish the SN classification scheme upon direct observational evidence connecting SN groups with specific progenitor stars. Observationally, the broad class of Type II SNe contains objects showing strong spectroscopic signatures of hydrogen, while objects lacking such signatures are of Type I, which is further divided to numerous subclasses. Recently a class of super-luminous SNe (SLSNe, typically 10 times more luminous than standard events) has been identified, and it is discussed. We end this chapter by briefly describing a proposed alternative classification scheme that is inspired by the stellar classification system. This system presents our emerging physical understanding of SN explosions, while clearly separating robust observational properties from physical inferences that can be debated. This new system is quantitative, and naturally deals with events distributed along a continuum, rather than being strictly divided into discrete classes. Thus, it may be more suitable to the coming era where SN numbers will quickly expand from a few thousands to millions of events.Comment: Extended final draft of a chapter in the "SN Handbook". Comments most welcom