scispace - formally typeset
Search or ask a question

Showing papers by "San Diego State University published in 2011"


Journal ArticleDOI
TL;DR: PRINSEQ is presented for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets and can be used as a stand alone version or accessed online through a user-friendly web interface.
Abstract: Summary: Here, we present PRINSEQ for easy and rapid quality control and data preprocessing of genomic and metagenomic datasets. Summary statistics of FASTA (and QUAL) or FASTQ files are generated in tabular and graphical form and sequences can be filtered, reformatted and trimmed by a variety of options to improve downstream analysis. Availability and Implementation: This open-source application was implemented in Perl and can be used as a stand alone version or accessed online through a user-friendly web interface. The source code, user help and additional information are available at http://prinseq.sourceforge.net/. Contact:[email protected]; [email protected]

4,028 citations


Journal ArticleDOI
TL;DR: In this article, the Kepler mission released data for 156,453 stars observed from the beginning of the science observations on 2009 May 2 through September 16, and there are 1235 planetary candidates with transit-like signatures detected in this period.
Abstract: On 2011 February 1 the Kepler mission released data for 156,453 stars observed from the beginning of the science observations on 2009 May 2 through September 16. There are 1235 planetary candidates with transit-like signatures detected in this period. These are associated with 997 host stars. Distributions of the characteristics of the planetary candidates are separated into five class sizes: 68 candidates of approximately Earth-size (R_p < 1.25 R_⊕), 288 super-Earth-size (1.25 R_⊕ ≤ R_p < 2 R_⊕), 662 Neptune-size (2 R_⊕ ≤ R_p < 6 R_⊕), 165 Jupiter-size (6 R_⊕ ≤ R_p < 15 R_⊕), and 19 up to twice the size of Jupiter (15 R_⊕ ≤ R_p < 22 R_⊕). In the temperature range appropriate for the habitable zone, 54 candidates are found with sizes ranging from Earth-size to larger than that of Jupiter. Six are less than twice the size of the Earth. Over 74% of the planetary candidates are smaller than Neptune. The observed number versus size distribution of planetary candidates increases to a peak at two to three times the Earth-size and then declines inversely proportional to the area of the candidate. Our current best estimates of the intrinsic frequencies of planetary candidates, after correcting for geometric and sensitivity biases, are 5% for Earth-size candidates, 8% for super-Earth-size candidates, 18% for Neptune-size candidates, 2% for Jupiter-size candidates, and 0.1% for very large candidates; a total of 0.34 candidates per star. Multi-candidate, transiting systems are frequent; 17% of the host stars have multi-candidate systems, and 34% of all the candidates are part of multi-candidate systems.

1,241 citations


Journal ArticleDOI
TL;DR: SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments, is presented, and microbial surveys from neonatal intensive care units, offices and molecular biology laboratories are applied.
Abstract: Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.

1,131 citations


Journal ArticleDOI
TL;DR: In this paper, the authors use Brewer's optimal distinctiveness theory to develop a definition of employee inclusion in the work group as involving the satisfaction of the needs of both belongingness and uniqueness.

1,025 citations


Journal ArticleDOI
16 Sep 2011-Science
TL;DR: The detection of a planet whose orbit surrounds a pair of low-mass stars, comparable to Saturn in mass and size and on a nearly circular 229-day orbit around its two parent stars, suggests that the planet formed within a circumbinary disk.
Abstract: We report the detection of a planet whose orbit surrounds a pair of low-mass stars. Data from the Kepler spacecraft reveal transits of the planet across both stars, in addition to the mutual eclipses of the stars, giving precise constraints on the absolute dimensions of all three bodies. The planet is comparable to Saturn in mass and size and is on a nearly circular 229-day orbit around its two parent stars. The eclipsing stars are 20 and 69% as massive as the Sun and have an eccentric 41-day orbit. The motions of all three bodies are confined to within 0.5° of a single plane, suggesting that the planet formed within a circumbinary disk.

797 citations


Journal ArticleDOI
TL;DR: For both children and adolescents, the most consistent associations involved objectively measured environmental attributes and reported physical activity, and these findings support several recommendations for policy and environmental change from such groups as the IOM and National Physical Activity Plan.

787 citations


Journal ArticleDOI
03 Feb 2011-Nature
TL;DR: Kepler spacecraft observations of a single Sun-like star are reported that reveal six transiting planets, five with orbital periods between 10 and 47 days and a sixth planet with a longer period, among the smallest for which mass and size have both been measured.
Abstract: When an extrasolar planet passes in front of (transits) its star, its radius can be measured from the decrease in starlight and its orbital period from the time between transits. Multiple planets transiting the same star reveal much more: period ratios determine stability and dynamics, mutual gravitational interactions reflect planet masses and orbital shapes, and the fraction of transiting planets observed as multiples has implications for the planarity of planetary systems. But few stars have more than one known transiting planet, and none has more than three. Here we report Kepler spacecraft observations of a single Sun-like star, which we call Kepler-11, that reveal six transiting planets, five with orbital periods between 10 and 47 days and a sixth planet with a longer period. The five inner planets are among the smallest for which mass and size have both been measured, and these measurements imply substantial envelopes of light gases. The degree of coplanarity and proximity of the planetary orbits imply energy dissipation near the end of planet formation. NASA's Kepler mission, a space observatory designed to detect and study extrasolar planets that transit across the disk of their host star, has hit the jackpot with the discovery of a six-planet system orbiting a Sun-like star now named Kepler-11. Five of the planets have orbital periods of between 10 and 47 days, and these are among the smallest for which size and mass have both been measured. The sixth and outermost transiting planet has been less well characterized thus far. Only one other star has more than one confirmed transiting planet (Kepler-9, which has three). This newly discovered system resembles our own Solar System in being close to coplanar, but Kepler-11's planets orbit much closer to their star. Kepler is due to continue to return data on Kepler-11 and its planets for some time yet, and it should provide many valuable constraints on models of the formation and evolution of solar systems in general. When an extrasolar planet passes in front of its star (transits), its radius can be measured from the decrease in starlight and its orbital period from the time between transits. This study reports Kepler spacecraft observations of a single Sun-like star that reveal six transiting planets, five with orbital periods between 10 and 47 days plus a sixth one with a longer period. The five inner planets are among the smallest for which mass and size have both been measured, and these measurements imply substantial envelopes of light gases.

755 citations


Journal ArticleDOI
TL;DR: An ecologic model of sedentary behaviors is described, highlighting the behavior settings construct and the multiple levels of determinants of prolonged sitting time, which are likely to operate in distinct ways in these different contexts.

743 citations


Journal ArticleDOI
09 Mar 2011-PLOS ONE
TL;DR: DeconSeq is a robust framework for the rapid, automated identification and removal of sequence contamination in longer-read datasets (150 bp mean read length) and allows scientists to automatically detect and efficiently remove unwanted sequence contamination from their datasets while eliminating critical limitations of current methods.
Abstract: High-throughput sequencing technologies have strongly impacted microbiology, providing a rapid and cost-effective way of generating draft genomes and exploring microbial diversity. However, sequences obtained from impure nucleic acid preparations may contain DNA from sources other than the sample. Those sequence contaminations are a serious concern to the quality of the data used for downstream analysis, causing misassembly of sequence contigs and erroneous conclusions. Therefore, the removal of sequence contaminants is a necessary and required step for all sequencing projects. We developed DeconSeq, a robust framework for the rapid, automated identification and removal of sequence contamination in longer-read datasets (150 bp mean read length). DeconSeq is publicly available as standalone and web-based versions. The results can be exported for subsequent analysis, and the databases used for the web-based version are automatically updated on a regular basis. DeconSeq categorizes possible contamination sequences, eliminates redundant hits with higher similarity to non-contaminant genomes, and provides graphical visualizations of the alignment results and classifications. Using DeconSeq, we conducted an analysis of possible human DNA contamination in 202 previously published microbial and viral metagenomes and found possible contamination in 145 (72%) metagenomes with as high as 64% contaminating sequences. This new framework allows scientists to automatically detect and efficiently remove unwanted sequence contamination from their datasets while eliminating critical limitations of current methods. DeconSeq's web interface is simple and user-friendly. The standalone version allows offline analysis and integration into existing data processing pipelines. DeconSeq's results reveal whether the sequencing experiment has succeeded, whether the correct sample was sequenced, and whether the sample contains any sequence contamination from DNA preparation or host. In addition, the analysis of 202 metagenomes demonstrated significant contamination of the non-human associated metagenomes, suggesting that this method is appropriate for screening all metagenomes. DeconSeq is available at http://deconseq.sourceforge.net/.

670 citations


Journal ArticleDOI
TL;DR: A diagnostic goal is to recognize FAS as a disorder of brain rather than one of physical characteristics, highlighting the relationship between the two.
Abstract: When fetal alcohol syndrome (FAS) was initially described, diagnosis was based upon physical parameters including facial anomalies and growth retardation, with evidence of developmental delay or mental deficiency. Forty years of research has shown that FAS lies towards the extreme end of what are now termed fetal alcohol spectrum disorders (FASD). The most profound effects of prenatal alcohol exposure are on the developing brain and the cognitive and behavioral effects that ensue. Alcohol exposure affects brain development via numerous pathways at all stages from neurogenesis to myelination. For example, the same processes that give rise to the facial characteristics of FAS also cause abnormal brain development. Behaviors as diverse as executive functioning to motor control are affected. This special issue of Neuropsychology Review addresses these changes in brain and behavior highlighting the relationship between the two. A diagnostic goal is to recognize FAS as a disorder of brain rather than one of physical characteristics.

635 citations


Journal ArticleDOI
TL;DR: The first Earth-size exoplanet was discovered by NASA's Kepler mission as discussed by the authors, which used transit photometry to determine the frequency of Earthsize planets in or near the habitable zone of Sun-like stars.
Abstract: NASA's Kepler Mission uses transit photometry to determine the frequency of Earth-size planets in or near the habitable zone of Sun-like stars. The mission reached a milestone toward meeting that goal: the discovery of its first rocky planet, Kepler-10b. Two distinct sets of transit events were detected: (1) a 152 ± 4 ppm dimming lasting 1.811 ± 0.024 hr with ephemeris T [BJD] = 2454964.57375^(+0.00060)_(–0.00082) + N * 0.837495^(+0.000004)_(–0.000005) days and (2) a 376 ± 9 ppm dimming lasting 6.86 ± 0.07 hr with ephemeris T [BJD] = 2454971.6761^(+0.0020)_(–0.0023) + N * 45.29485^(+0.00065) _(–0.00076) days. Statistical tests on the photometric and pixel flux time series established the viability of the planet candidates triggering ground-based follow-up observations. Forty precision Doppler measurements were used to confirm that the short-period transit event is due to a planetary companion. The parent star is bright enough for asteroseismic analysis. Photometry was collected at 1 minute cadence for >4 months from which we detected 19 distinct pulsation frequencies. Modeling the frequencies resulted in precise knowledge of the fundamental stellar properties. Kepler-10 is a relatively old (11.9 ± 4.5 Gyr) but otherwise Sun-like main-sequence star with T_(eff) = 5627 ± 44 K, M_⋆ = 0.895 ± 0.060 M_⊙ , and R_⋆ = 1.056 ± 0.021 R_⊙. Physical models simultaneously fit to the transit light curves and the precision Doppler measurements yielded tight constraints on the properties of Kepler-10b that speak to its rocky composition: M_P = 4.56^9+1.17)_(–1.29) M_⊕, R_P = 1.416^(+0.033)_(–0.036) R_⊕, and ρ_P = 8.8^(+2.1)_(–2.9) g cm^(–3). Kepler-10b is the smallest transiting exoplanet discovered to date.

Journal ArticleDOI
Pelin Yilmaz1, Pelin Yilmaz2, Renzo Kottmann1, Dawn Field, Rob Knight3, Rob Knight4, James R. Cole5, Linda A. Amaral-Zettler6, Jack A. Gilbert7, Jack A. Gilbert8, Jack A. Gilbert9, Ilene Karsch-Mizrachi10, Anjanette Johnston10, Guy Cochrane, Robert Vaughan, Christopher I. Hunter, Joonhong Park11, Norman Morrison12, Philippe Rocca-Serra13, Peter Sterk, Manimozhiyan Arumugam, Mark J. Bailey, Laura K. Baumgartner4, Bruce W. Birren14, Martin J. Blaser15, Vivien Bonazzi10, Timothy F. Booth, Peer Bork, Frederic D. Bushman16, Pier Luigi Buttigieg1, Pier Luigi Buttigieg2, Patrick S. G. Chain5, Patrick S. G. Chain17, Patrick S. G. Chain18, Emily S. Charlson16, Elizabeth K. Costello4, Heather Huot-Creasy19, Peter Dawyndt20, Todd Z. DeSantis21, Noah Fierer4, Jed A. Fuhrman22, Rachel E. Gallery23, Dirk Gevers14, Richard A. Gibbs24, Inigo San Gil25, Antonio Gonzalez4, Jeffrey I. Gordon26, Robert P. Guralnick4, Wolfgang Hankeln2, Wolfgang Hankeln1, Sarah K. Highlander24, Philip Hugenholtz27, Janet K. Jansson21, Janet K. Jansson17, Andrew L. Kau26, Scott T. Kelley28, Jerry Kennedy4, Dan Knights4, Omry Koren29, Justin Kuczynski4, Nikos C. Kyrpides17, Robert Larsen4, Christian L. Lauber4, Teresa M. Legg4, Ruth E. Ley29, Catherine A. Lozupone4, Wolfgang Ludwig30, Donna Lyons4, Eamonn Maguire13, Barbara A. Methé31, Folker Meyer8, Brian D. Muegge26, Sara Nakielny4, Karen E. Nelson31, Diana R. Nemergut4, Josh D. Neufeld32, Lindsay K. Newbold, Anna Oliver, Norman R. Pace4, Giriprakash Palanisamy33, Jörg Peplies, Joseph F. Petrosino24, Lita M. Proctor10, Elmar Pruesse2, Elmar Pruesse1, Christian Quast1, Jeroen Raes34, Sujeevan Ratnasingham35, Jacques Ravel19, David A. Relman36, David A. Relman37, Susanna Assunta-Sansone13, Patrick D. Schloss, Lynn M. Schriml19, Rohini Sinha16, Michelle I. Smith26, Erica Sodergren26, Aymé Spor29, Jesse Stombaugh4, James M. Tiedje5, Doyle V. Ward14, George M. Weinstock26, Doug Wendel4, Owen White19, Andrew S. Whiteley, Andreas Wilke8, Jennifer R. Wortman19, Tanya Yatsunenko26, Frank Oliver Glöckner2, Frank Oliver Glöckner1 
TL;DR: To establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, the minimum information about any (x) sequence is presented (MIxS).
Abstract: Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Journal ArticleDOI
TL;DR: A review of research that has examined stress and its associated distress, and social and personal resources as pathways, highlights work on biomarkers and biological pathways related to SES that can serve as intermediate outcomes in future studies.
Abstract: Low socioeconomic status (SES) is a reliable correlate of poor physical health. Rather than treat SES as a covariate, health psychology has increasingly focused on the psychobiological pathways that inform understanding why SES is related to physical health. This review assesses the status of research that has examined stress and its associated distress, and social and personal resources as pathways. It highlights work on biomarkers and biological pathways related to SES that can serve as intermediate outcomes in future studies. Recent emphasis on the accumulation of psychobiological risks across the life course is summarized and represents an important direction for future research. Studies that test pathways from SES to candidate psychosocial pathways to health outcomes are few in number but promising. Future research should test integrated models rather than taking piecemeal approaches to evidence. Much work remains to be done, but the questions are of great health significance.

Journal ArticleDOI
TL;DR: This paper will provide a comprehensive review of the neuropsychological and behavioral effects of heavy prenatal alcohol exposure, including a discussion of the emerging neurobehavioral profile.
Abstract: Heavy prenatal alcohol exposure can cause alterations to the developing brain. The resulting neurobehavioral deficits seen following this exposure are wide-ranging and potentially devastating and, therefore, are of significant concern to individuals, families, communities, and society. These effects occur on a continuum, and qualitatively similar neuropsychological and behavioral features are seen across the spectrum of effect. The term fetal alcohol spectrum disorders (FASD) has been used to emphasize the continuous nature of the outcomes of prenatal alcohol exposure, with fetal alcohol syndrome (FAS) representing one point on the spectrum. This paper will provide a comprehensive review of the neuropsychological and behavioral effects of heavy prenatal alcohol exposure, including a discussion of the emerging neurobehavioral profile. Supporting studies of lower levels of exposure, brain-behavior associations, and animal model systems will be included when appropriate.

Journal ArticleDOI
TL;DR: In this article, the authors present a comprehensive catalog of eclipsing binary stars observed by Kepler in the first 44 days of operation, the data being publicly available through MAST as of 2010 June 15.
Abstract: The Kepler space mission is devoted to finding Earth-size planets orbiting other stars in their habitable zones. Its large, 105 deg2 field of view features over 156,000 stars that are observed continuously to detect and characterize planet transits. Yet, this high-precision instrument holds great promise for other types of objects as well. Here we present a comprehensive catalog of eclipsing binary stars observed by Kepler in the first 44 days of operation, the data being publicly available through MAST as of 2010 June 15. The catalog contains 1879 unique objects. For each object, we provide its Kepler ID (KID), ephemeris (BJD0, P 0), morphology type, physical parameters (T eff, log g, E(B – V)), the estimate of third light contamination (crowding), and principal parameters (T 2/T 1, q, fillout factor, and sin i for overcontacts, and T 2/T 1, (R 1 + R 2)/a, esin ω, ecos ω, and sin i for detached binaries). We present statistics based on the determined periods and measure the average occurrence rate of eclipsing binaries to be ~1.2% across the Kepler field. We further discuss the distribution of binaries as a function of galactic latitude and thoroughly explain the application of artificial intelligence to obtain principal parameters in a matter of seconds for the whole sample. The catalog was envisioned to serve as a bridge between the now public Kepler data and the scientific community interested in eclipsing binary stars.

Journal ArticleDOI
TL;DR: Assessing sitting time is an important new area for preventive medicine, in addition to assessing physical activity and sedentary behaviors, and population surveys that monitor lifestyle behaviors should add measures of sitting time to physical activity surveillance.

Journal ArticleDOI
TL;DR: Evaluating impacts of active travel policies is highly complex; however, many associations can be quantified, and identifying health-maximizing policies and conditions requires integrated HIAs.

Journal ArticleDOI
24 May 2011-PLOS ONE
TL;DR: It is suggested that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria that have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology.
Abstract: Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.

Journal ArticleDOI
TL;DR: In this paper, the authors presented a catalog of 1879 eclipsing binary systems identified within the 115-deg2 Kepler field of view (FOV), augmented with the second Kepler data release which increases the baseline nearly fourfold to 125 days.
Abstract: The Kepler Mission provides nearly continuous monitoring of ~156,000 objects with unprecedented photometric precision. Coincident with the first data release, we presented a catalog of 1879 eclipsing binary systems identified within the 115 deg2 Kepler field of view (FOV). Here, we provide an updated catalog augmented with the second Kepler data release which increases the baseline nearly fourfold to 125 days. Three hundred and eighty-six new systems have been added, ephemerides and principal parameters have been recomputed. We have removed 42 previously cataloged systems that are now clearly recognized as short-period pulsating variables and another 58 blended systems where we have determined that the Kepler target object is not itself the eclipsing binary. A number of interesting objects are identified. We present several exemplary cases: four eclipsing binaries that exhibit extra (tertiary) eclipse events; and eight systems that show clear eclipse timing variations indicative of the presence of additional bodies bound in the system. We have updated the period and galactic latitude distribution diagrams. With these changes, the total number of identified eclipsing binary systems in the Kepler FOV has increased to 2165, 1.4% of the Kepler target stars. An online version of this catalog is maintained at http://keplerEBs.villanova.edu.

Journal ArticleDOI
01 Sep 2011-Pain
TL;DR: It is suggested that ACT is an effective and acceptable adjunct intervention for patients with chronic pain and cognitive‐behavioral therapy may be more satisfactory.
Abstract: Individuals reporting chronic, nonmalignant pain for at least 6 months (N=114) were randomly assigned to 8 weekly group sessions of acceptance and commitment therapy (ACT) or cognitive-behavioral therapy (CBT) after a 4-6 week pretreatment period and were assessed after treatment and at 6-month follow-up. The protocols were designed for use in a primary care rather than specialty pain clinic setting. All participants remained stable on other pain and mood treatments over the course of the intervention. ACT participants improved on pain interference, depression, and pain-related anxiety; there were no significant differences in improvement between the treatment conditions on any outcome variables. Although there were no differences in attrition between the groups, ACT participants who completed treatment reported significantly higher levels of satisfaction than did CBT participants. These findings suggest that ACT is an effective and acceptable adjunct intervention for patients with chronic pain.

Journal ArticleDOI
TL;DR: The high prevalence and associated adverse health outcomes of late-life subthreshold depression indicate the major public health significance of this condition and suggest a need for further research on its neurobiology and treatment.

Journal ArticleDOI
TL;DR: In this article, the authors presented detailed optical photometry for 25 Type Ibc supernovae (SNe Ibc) within d 150 Mpc obtained with the robotic Palomar 60 inch telescope in 2004-2007.
Abstract: We present detailed optical photometry for 25 Type Ibc supernovae (SNe Ibc) within d 150 Mpc obtained with the robotic Palomar 60 inch telescope in 2004-2007. This study represents the first uniform, systematic, and statistical sample of multi-band SNe Ibc light curves available to date. We correct the light curves for host galaxy extinction using a new technique based on the photometric color evolution, namely, we show that the (V – R) color of extinction-corrected SNe Ibc at Δt 10 days after V-band maximum is tightly distributed, (V – R) V10 = 0.26 ± 0.06 mag. Using this technique, we find that SNe Ibc typically suffer from significant host galaxy extinction, E(B – V) 0.4 mag. A comparison of the extinction-corrected light curves for helium-rich (Type Ib) and helium-poor (Type Ic) SNe reveals that they are statistically indistinguishable, both in luminosity and decline rate. We report peak absolute magnitudes of MR = –17.9 ± 0.9 mag and MR = –18.3 ± 0.6 mag for SNe Ib and Ic, respectively. Focusing on the broad-lined (BL) SNe Ic, we find that they are more luminous than the normal SNe Ibc sample, MR = –19.0 ± 1.1 mag, with a probability of only 1.6% that they are drawn from the same population of explosions. By comparing the peak absolute magnitudes of SNe Ic-BL with those inferred for local engine-driven explosions (GRB-SN 1998bw, XRF-SN 2006aj, and SN 2009bb) we find a 25% probability that relativistic SNe are drawn from the overall SNe Ic-BL population. Finally, we fit analytic models to the light curves to derive typical 56Ni masses of M Ni 0.2 and 0.5 M ☉ for SNe Ibc and SNe Ic-BL, respectively. With reasonable assumptions for the photospheric velocities, we further extract kinetic energy and ejecta mass values of M ej 2 M ☉ and EK 1051 erg for SNe Ibc, while for SNe Ic-BL we find higher values, M ej 5 M ☉ and EK 1052 erg. We discuss the implications for the progenitors of SNe Ibc and their relation to those of engine-driven explosions.

Journal ArticleDOI
TL;DR: In this paper, the identity and characteristics of 305 released stars with planetary candidates are given, and five candidates are present in and near the habitable zone; two near super-Earth size, and three bracketing the size of Jupiter.
Abstract: In the spring of 2009, the Kepler Mission commenced high-precision photometry on nearly 156,000 stars to determine the frequency and characteristics of small exoplanets, conduct a guest observer program, and obtain asteroseismic data on a wide variety of stars. On 2010 June 15, the Kepler Mission released most of the data from the first quarter of observations. At the time of this data release, 705 stars from this first data set have exoplanet candidates with sizes from as small as that of Earth to larger than that of Jupiter. Here we give the identity and characteristics of 305 released stars with planetary candidates. Data for the remaining 400 stars with planetary candidates will be released in 2011 February. More than half the candidates on the released list have radii less than half that of Jupiter. Five candidates are present in and near the habitable zone; two near super-Earth size, and three bracketing the size of Jupiter. The released stars also include five possible multi-planet systems. One of these has two Neptune-size (2.3 and 2.5 Earth radius) candidates with near-resonant periods.

Journal ArticleDOI
TL;DR: Both GU and NGU findings reflect important aspects of network dysfunction associated with sociocommunicative, cognitive, and sensorimotor impairments in ASD, and suggest that underconnectivity findings may be contingent on specific methodological choices.
Abstract: Growing consensus suggests that autism spectrum disorders (ASD) are associated with atypical brain networks, thus shifting the focus to the study of connectivity. Many functional connectivity studies have reported underconnectivity in ASD, but results in others have been divergent. We conducted a survey of 32 functional connectivity magnetic resonance imaging studies of ASD for numerous methodological variables to distinguish studies supporting general underconnectivity (GU) from those not consistent with this hypothesis (NGU). Distinguishing patterns were apparent for several data analysis choices. The study types differed significantly with respect to low-pass filtering, task regression, and whole-brain field of view. GU studies were more likely to examine task-driven time series in regions of interest, without the use of low-pass filtering. Conversely, NGU studies mostly applied task regression (for removal of activation effects) and low-pass filtering, testing for correlations across the whole brain. Results thus suggest that underconnectivity findings may be contingent on specific methodological choices. Whereas underconnectivity reflects reduced efficiency of within-network communication in ASD, diffusely increased functional connectivity can be attributed to impaired experience-driven mechanisms (e.g., synaptic pruning). Both GU and NGU findings reflect important aspects of network dysfunction associated with sociocommunicative, cognitive, and sensorimotor impairments in ASD.

Journal ArticleDOI
TL;DR: From the analysis of the survey data, an important route of causality is found, as follows: IT personnel expertise, IT management capabilities, IT infrastructure flexibility, and process-oriented dynamic capabilities, and financial performance are found.
Abstract: Research Article Gimun Kim Konyang University gmkim@konyang.ac.kr Bongsik Shin San Diego State University bshin@mail.sdsu.edu Kyung Kyu Kim Yonsei University kyu.kim@yonsei.ac.kr Ho Geun Lee Yonsei University h.lee@yonsei.ac.kr More and more publications are highlighting the value of IT in affecting business processes. Recognizing firmlevel dynamic capabilities as key to improved firm performance, our work examines and empirically tests the influencing relationships among IT capabilities (IT personnel expertise, IT infrastructure flexibility, and IT management capabilities), process-oriented dynamic capabilities, and financial performance. Processoriented dynamic capabilities are defined as a firm’s ability to change (improve, adapt, or reconfigure) a business process better than the competition in terms of integrating activities, reducing cost, and capitalizing on business intelligence/learning. They encompass a broad category of changes in the firm’s processes, ranging from continual adjustments and improvements to radical one-time alterations. Although the majority of changes may be incremental, a firm’s capacity for timely changes also implies its readiness to execute radical alterations when the need arises. Grounded on the theoretical position, we propose a research model and gather a survey data set through a rigorous process that retains research validity. From the analysis of the survey data, we find an important route of causality, as follows: IT personnel expertise  IT management capabilities  IT infrastructure flexibility  process-oriented dynamic capabilities  financial performance. Based on this finding, we discuss the main contributions of our study in terms of the strategic role of IT in enhancing firm performance.

Journal ArticleDOI
TL;DR: The existing evidence on thirdhand smoke (THS) provides strong support for pursuing a programmatic research agenda to close gaps in current understanding of the chemistry, exposure, toxicology, and health effects of THS, as well as its behavioral, economic, and sociocultural considerations and consequences.
Abstract: Background: There is broad consensus regarding the health impact of tobacco use and secondhand smoke exposure, yet considerable ambiguity exists about the nature and consequences of thirdhand smoke (THS). Objectives: We introduce definitions of THS and THS exposure and review recent findings about constituents, indoor sorption–desorption dynamics, and transformations of THS; distribution and persistence of THS in residential settings; implications for pathways of exposure; potential clinical significance and health effects; and behavioral and policy issues that affect and are affected by THS. Discussion: Physical and chemical transformations of tobacco smoke pollutants take place over time scales ranging from seconds to months and include the creation of secondary pollutants that in some cases are more toxic (e.g., tobacco-specific nitrosamines). THS persists in real-world residential settings in the air, dust, and surfaces and is associated with elevated levels of nicotine on hands and cotinine in urine of nonsmokers residing in homes previously occupied by smokers. Much still needs to be learned about the chemistry, exposure, toxicology, health risks, and policy implications of THS. Conclusion: The existing evidence on THS provides strong support for pursuing a programmatic research agenda to close gaps in our current understanding of the chemistry, exposure, toxicology, and health effects of THS, as well as its behavioral, economic, and sociocultural considerations and consequences. Such a research agenda is necessary to illuminate the role of THS in existing and future tobacco control efforts to decrease smoking initiation and smoking levels, to increase cessation attempts and sustained cessation, and to reduce the cumulative effects of tobacco use on morbidity and mortality.

Journal ArticleDOI
TL;DR: Optimal doses of exercise by duration and intensity for the prevention or treatment of NASH have not been established; however, intensity may be more important than duration or total volume.

Journal ArticleDOI
TL;DR: In this article, the authors used an extensive collection of optical photometric and spectroscopic data taken from the literature to obtain a full dynamical model of the binary system, and found a black hole mass of 14.8 ± 1.0 M�, a companion mass of Mopt = 19.2 ± 2.9 M� and the angle of inclination of the orbital plane to our line of sight of i = 27.1 ± 0.8d eg.
Abstract: Cygnus X-1 is a binary star system that is comprised of a black hole and a massive giant companion star in a tight orbit. Building on our accurate distance measurement reported in the preceding paper, we first determine the radius of the companion star, thereby constraining the scale of the binary system. To obtain a full dynamical model of the binary, we use an extensive collection of optical photometric and spectroscopic data taken from the literature. By usingalloftheavailableobservationalconstraints,weshowthattheorbitisslightlyeccentric(boththeradialvelocity and photometric data independently confirm this result) and that the companion star rotates roughly 1.4 times its pseudosynchronous value. We find a black hole mass of M = 14.8 ± 1.0 M� , a companion mass of Mopt = 19.2 ± 1.9 M� , and the angle of inclination of the orbital plane to our line of sight of i = 27.1 ± 0. 8d eg.

Journal ArticleDOI
TL;DR: A survey-based study investigated whether this misperception is important and found that individuals who believe there is broad scientific disagreement tend to feel less certain that global warming is occurring and show less support for climate policy as mentioned in this paper.
Abstract: A significant proportion of the US public believe that climate scientists widely disagree about climate change Now a survey-based study investigates whether this misperception is important and finds that individuals who believe there is broad scientific disagreement tend to feel less certain that global warming is occurring and show less support for climate policy

Journal ArticleDOI
TL;DR: A growing body of evidence supports the development of public health recommendations to limit the time spent in screen-based behaviors and more research is needed to examine the prospective and experimental evidence of associations between overall sedentary time and health.