Experimental Biological Protocols with Formal Semantics

Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from data. However, integration between automated tasks in the process of biological discovery is still lacking, largely due to incompatible or missing formal representations. While theories are expressed formally as computational models, existing languages for encoding and automating experimental protocols often lack formal semantics. This makes it challenging to extract novel understanding by identifying when theory and experimental evidence disagree due to errors in the models or the protocols used to validate them. To address this, we formalize the syntax of a core protocol language, which provides a unified description for the models of biochemical systems being experimented on, together with the discrete events representing the liquid-handling steps of biological protocols. We present both a deterministic and a stochastic semantics to this language, both defined in terms of hybrid processes. In particular, the stochastic semantics captures uncertainties in equipment tolerances, making it a suitable tool for both experimental and computational biologists. We illustrate how the proposed protocol language can be used for automated verification and synthesis of laboratory experiments on case studies from the fields of chemistry and molecular programming

Angka Kematian Dan Faktor Risiko Stroke Sebagai Penyebab Dasar Kematian Di Kabupaten Padang Pariaman Provinsi Sumatera Barat

Mortality data are one of important indicators for the publich health The aim of this study is to know about the death rate, characteristics and risk factors of stroke as underlying cause of death in Padang Pariaman district. The mortality data in 2010 was analyzed using SPSS 16. The results showed that the entire death data was amount of 2642 and crude death rate was 6.71. Proportion of stroke in the district was 19.3% and stroke mortality rate was 1.29 per 1000 population in the year 2010, The risk factors of stroke as underlying cause of death after adjusted with education, employment and place of death were age and gender. The age of 40 – 64 years had the risk with OR of 6.45 (95% CI 2.77 – 14.28, p < 0.0001) and age of > 65 years had the risk of 10.29 (95% CI 4.47 – 23.69, p < 0.0001) compared to 20 – 39 year old. Women had greater risk than that of men with OR of 1.43 (95% CI 1.16 – 1.76, p < 0.001). The mortality rate of stroke as an underlying cause of death is high, so it is necessary to prevent the disease by appropriate intervention program

The ALHAMBRA survey: Accurate merger fractions by PDF analysis of photometric close pairs

Our goal is to develop and test a novel methodology to compute accurate close pair fractions with photometric redshifts. We improve the current methodologies to estimate the merger fraction f_m from photometric redshifts by (i) using the full probability distribution functions (PDFs) of the sources in redshift space, (ii) including the variation in the luminosity of the sources with z in both the selection of the samples and in the luminosity ratio constrain, and (iii) splitting individual PDFs into red and blue spectral templates to deal robustly with colour selections. We test the performance of our new methodology with the PDFs provided by the ALHAMBRA photometric survey. The merger fractions and rates from the ALHAMBRA survey are in excellent agreement with those from spectroscopic work, both for the general population and for red and blue galaxies. With the merger rate of bright (M_B <= -20 - 1.1z) galaxies evolving as (1+z)^n, the power-law index n is larger for blue galaxies (n = 2.7 +- 0.5) than for red galaxies (n = 1.3 +- 0.4), confirming previous results. Integrating the merger rate over cosmic time, we find that the average number of mergers per galaxy since z = 1 is N_m = 0.57 +- 0.05 for red galaxies and N_m = 0.26 +- 0.02 for blue galaxies. Our new methodology exploits statistically all the available information provided by photometric redshift codes and provides accurate measurements of the merger fraction by close pairs only using photometric redshifts. Current and future photometric surveys will benefit of this new methodology.Comment: Submitted to A&A, 15 pages, 15 figures, 6 tables. Comments are welcome. Close pair systems available at https://cloud.iaa.csic.es/alhambra/catalogues/ClosePairs

The ALHAMBRA Survey: Bayesian Photometric Redshifts with 23 bands for 3 squared degrees

The ALHAMBRA (Advance Large Homogeneous Area Medium Band Redshift Astronomical) survey has observed 8 different regions of the sky, including sections of the COSMOS, DEEP2, ELAIS, GOODS-N, SDSS and Groth fields using a new photometric system with 20 contiguous ~ $300\AA$ filters covering the optical range, combining them with deep $JHKs$ imaging. The observations, carried out with the Calar Alto 3.5m telescope using the wide field (0.25 sq. deg FOV) optical camera LAICA and the NIR instrument Omega-2000, correspond to ~700hrs on-target science images. The photometric system was designed to maximize the effective depth of the survey in terms of accurate spectral-type and photo-zs estimation along with the capability of identification of relatively faint emission lines. Here we present multicolor photometry and photo-zs for ~438k galaxies, detected in synthetic F814W images, complete down to I~24.5 AB, taking into account realistic noise estimates, and correcting by PSF and aperture effects with the ColorPro software. The photometric ZP have been calibrated using stellar transformation equations and refined internally, using a new technique based on the highly robust photometric redshifts measured for emission line galaxies. We calculate photometric redshifts with the BPZ2 code, which includes new empirically calibrated templates and priors. Our photo-zs have a precision of $dz/(1+z_s)=1$ for I<22.5 and 1.4% for 22.5<I<24.5. Precisions of less than 0.5% are reached for the brighter spectroscopic sample, showing the potential of medium-band photometric surveys. The global $P(z)$ shows a mean redshift =0.56 for I=0.86 for I<24.5 AB. The data presented here covers an effective area of 2.79 sq. deg, split into 14 strips of 58.5'x15.5' and represents ~32 hrs of on-target.Comment: The catalog data and a full resolution version of this paper is available at https://cloud.iaa.csic.es/alhambra

J-PLUS: analysis of the intracluster light in the Coma cluster

The intracluster light (ICL) is a luminous component of galaxy clusters composed of stars that are gravitationally bound to the cluster potential but do not belong to the individual galaxies. Previous studies of the ICL have shown that its formation and evolution are intimately linked to the evolutionary stage of the cluster. Thus, the analysis of the ICL in the Coma cluster will give insights into the main processes driving the dynamics in this highly complex system. Using a recently developed technique, we measure the ICL fraction in Coma at several wavelengths, using the J-PLUS unique filter system. The combination of narrow- and broadband filters provides valuable information on the dynamical state of the cluster, the ICL stellar types, and the morphology of the diffuse light. We use the Chebyshev-Fourier Intracluster Light Estimator (CICLE) to disentangle the ICL from the light of the galaxies, and to robustly measure the ICL fraction in seven J-PLUS filters. We obtain the ICL fraction distribution of the Coma cluster at different optical wavelengths, which varies from $\sim 7\%-21\%$, showing the highest values in the narrowband filters J0395, J0410, and J0430. This ICL fraction excess is distinctive pattern recently observed in dynamically active clusters (mergers), indicating a higher amount of bluer stars in the ICL compared to the cluster galaxies. Both the high ICL fractions and the excess in the bluer filters are indicative of a merging state. The presence of younger/lower-metallicity stars the ICL suggests that the main mechanism of ICL formation for the Coma cluster is the stripping of the stars in the outskirts of infalling galaxies and, possibly, the disruption of dwarf galaxies during past/ongoing mergers.Comment: 10 pages, 3 figures, 1 table. Accepted for publication in A&

Evidence for Ubiquitous, High-EW Nebular Emission in z~7 Galaxies: Towards a Clean Measurement of the Specific Star Formation Rate using a Sample of Bright, Magnified Galaxies

Growing observational evidence now indicates that nebular line emission has a significant impact on the rest-frame optical fluxes of z~5-7 galaxies observed with Spitzer. This line emission makes z~5-7 galaxies appear more massive, with lower specific star formation rates. However, corrections for this line emission have been very difficult to perform reliably due to huge uncertainties on the overall strength of such emission at z>~5.5. Here, we present the most direct observational evidence yet for ubiquitous high-EW [OIII]+Hbeta line emission in Lyman-break galaxies at z~7, while also presenting a strategy for an improved measurement of the sSFR at z~7. We accomplish this through the selection of bright galaxies in the narrow redshift window z~6.6-7.0 where the IRAC 4.5 micron flux provides a clean measurement of the stellar continuum light. Observed 4.5 micron fluxes in this window contrast with the 3.6 micron fluxes which are contaminated by the prominent [OIII]+Hbeta lines. To ensure a high S/N for our IRAC flux measurements, we consider only the brightest (H_{160}<26 mag) magnified galaxies we have identified in CLASH and other programs targeting galaxy clusters. Remarkably, the mean rest-frame optical color for our bright seven-source sample is very blue, [3.6]-[4.5]=-0.9+/-0.3. Such blue colors cannot be explained by the stellar continuum light and require that the rest-frame EW of [OIII]+Hbeta be greater than 637 Angstroms for the average source. The bluest four sources from our seven-source sample require an even more extreme EW of 1582 Angstroms. Our derived lower limit for the mean [OIII]+Hbeta EW could underestimate the true EW by ~2x based on a simple modeling of the redshift distribution of our sources. We can also set a robust lower limit of >~4 Gyr^-1 on the specific star formation rates based on the mean SED for our seven-source sample. (abridged)Comment: 9 pages, 6 figures, 1 table, submitted to the Astrophysical Journa

Stable nondegenerate optical parametric oscillation at degenerate frequencies in Na:KTP

We report the realization of a light source specifically designed for the generation of bright continuous-variable entangled beams and for Heisenberg-limited inteferometry. The source is a nondegenerate, single-mode, continuous-wave optical parametric oscillator in Na:KTP, operated at frequency degeneracy and just above threshold, which is also of interest for the study of critical fluctuations at the transition point. The residual frequency-difference jitter is $\pm$ 150 kHz for a 3 MHz cold cavity half-width at half maximum. We observe 4 dB of photon-number-difference squeezing at 200 kHz. The Na:KTP crystal is noncritically phase-matched for a 532 nm pump and polarization crosstalk is therefore practically nonexistent

CLASH: z ~ 6 young galaxy candidate quintuply lensed by the frontier field cluster RXC J2248.7-4431

We present a quintuply lensed z ~ 6 candidate discovered in the field of the galaxy cluster RXC J2248.7-4431 (z ~ 0.348) targeted within the Cluster Lensing and Supernova survey with Hubble (CLASH) and selected in the deep HST Frontier Fields survey. Thanks to the CLASH 16-band HST imaging, we identify the quintuply lensed z ~ 6 candidate as an optical dropout in the inner region of the cluster, the brightest image having magAB=24.81+-0.02 in the f105w filter. We perform a detailed photometric analysis to verify its high-z and lensed nature. We get as photometric redshift z_phot ~ 5.9, and given the extended nature and NIR colours of the lensed images, we rule out low-z early type and galactic star contaminants. We perform a strong lensing analysis of the cluster, using 13 families of multiple lensed images identified in the HST images. Our final best model predicts the high-z quintuply lensed system with a position accuracy of 0.8''. The magnifications of the five images are between 2.2 and 8.3, which leads to a delensed UV luminosity of L_1600 ~ 0.5L*_1600 at z=6. We also estimate the UV slope from the observed NIR colours, finding a steep beta=-2.89+-0.38. We use singular and composite stellar population SEDs to fit the photometry of the hiz candidate, and we conclude that it is a young (age <300 Myr) galaxy with mass of M ~ 10^8Msol, subsolar metallicity (Z<0.2Zsol) and low dust content (AV ~ 0.2-0.4).Comment: 21 pages, 13 figures, 6 tables, submitted to MNRAS on 11 Aug 2013, accepted on 23 Nov 201

A Census of Star-Forming Galaxies in the z~9-10 Universe based on HST+Spitzer Observations Over 19 CLASH clusters: Three Candidate z~9-10 Galaxies and Improved Constraints on the Star Formation Rate Density at z~9

We utilise a two-color Lyman-Break selection criterion to search for z~9-10 galaxies over the first 19 clusters in the CLASH program. A systematic search yields three z~9-10 candidates. While we have already reported the most robust of these candidates, MACS1149-JD, two additional z~9 candidates are also found and have H_{160}-band magnitudes of ~26.2-26.9. A careful assessment of various sources of contamination suggests <~1 contaminants for our z~9-10 selection. To determine the implications of these search results for the LF and SFR density at z~9, we introduce a new differential approach to deriving these quantities in lensing fields. Our procedure is to derive the evolution by comparing the number of z~9-10 galaxy candidates found in CLASH with the number of galaxies in a slightly lower redshift sample (after correcting for the differences in selection volumes), here taken to be z~8. This procedure takes advantage of the fact that the relative volumes available for the z~8 and z~9-10 selections behind lensing clusters are not greatly dependent on the details of the lensing models. We find that the normalization of the UV LF at z~9 is just 0.28_{-0.20}^{+0.39}\times that at z~8, ~1.4_{-0.8}^{+3.0}x lower than extrapolating z~4-8 LF results. While consistent with the evolution in the UV LF seen at z~4-8, these results marginally favor a more rapid evolution at z>8. Compared to similar evolutionary findings from the HUDF, our result is less insensitive to large-scale structure uncertainties, given our many independent sightlines on the high-redshift universe.Comment: 22 pages, 11 figures, 5 tables, accepted for publication in the Astrophysical Journal, updated to include the much deeper Spitzer/IRAC observations over our three z~9-10 candidate