In-Vitro Validated Methods for Encoding Digital Data in Deoxyribonucleic Acid (DNA)

Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both increased the capacity and decreased the cost of storing information in de novo synthesized DNA pools. In this survey, we review methods for translating digital data to and/or from DNA molecules. An emphasis is placed on methods which have been validated by storing and retrieving real-world data via in-vitro experiments

Janus II: a new generation application-driven computer for spin-system simulations

This paper describes the architecture, the development and the implementation of Janus II, a new generation application-driven number cruncher optimized for Monte Carlo simulations of spin systems (mainly spin glasses). This domain of computational physics is a recognized grand challenge of high-performance computing: the resources necessary to study in detail theoretical models that can make contact with experimental data are by far beyond those available using commodity computer systems. On the other hand, several specific features of the associated algorithms suggest that unconventional computer architectures, which can be implemented with available electronics technologies, may lead to order of magnitude increases in performance, reducing to acceptable values on human scales the time needed to carry out simulation campaigns that would take centuries on commercially available machines. Janus II is one such machine, recently developed and commissioned, that builds upon and improves on the successful JANUS machine, which has been used for physics since 2008 and is still in operation today. This paper describes in detail the motivations behind the project, the computational requirements, the architecture and the implementation of this new machine and compares its expected performances with those of currently available commercial systems.Comment: 28 pages, 6 figure

Bsx, a novel hypothalamic factor linking feeding with locomotor activity, is regulated by energy availability

Es un estudio en modelos de rata acerca del papel de BSX, la actividad y la alimentación.We recently reported that the hypothalamic homeobox domain transcription factor Bsx plays an essential role in the central nervous system control of spontaneous physical activity and the generation of hyperphagic responses. Moreover, we found Bsx to be a master regulator for the hypothalamic expression of key orexigenic neuropeptide Y and agouti gene-related protein. We now hypothesized that Bsx, which is expressed in the dorsomedial and arcuate nucleus (ARC) of the hypothalamus, is regulated by afferent signals in response to peripheral energy balance. Bsx expression was analyzed using in situ hybridization in fed vs. fasted (24 h) and ghrelin vs. leptin-treated rats, as well as in mice deficient for leptin or the ghrelin signaling. Ghrelin administration increased, whereas ghrelin receptor antagonist decreased ARC Bsx expression. Leptin injection attenuated the fasting-induced increase in ARC Bsx levels but had no effect in fed rats. Dorsomedial hypothalamic nucleus Bsx expression was unaffected by pharmacological modifications of leptin or ghrelin signaling. Obese leptin-deficient (ob/ob) mice, but not obese melanocortin 4 receptor-knockout mice, showed higher expression of Bsx, consistent with dependency from afferent leptin rather than increased adiposity per se. Interestingly, exposure to a high-fat diet triggered Bsx expression, consistent with the concept that decreased leptin signaling due to a highfat diet induced leptin resistance. Our data indicate that ARC Bsx expression is specifically regulated by afferent energy balance signals, including input from leptin and ghrelin. Future studies will be necessary to test if Bsx may be involved in the pathogenesis of leptin resistance

Temporal sampling, resetting, and adaptation orchestrate gradient sensing in sperm

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Cell Biology 198 (2012): 1075-1091, doi:10.1083/jcb.201204024.Sperm, navigating in a chemical gradient, are exposed to a periodic stream of chemoattractant molecules. The periodic stimulation entrains Ca2+ oscillations that control looping steering responses. It is not known how sperm sample chemoattractant molecules during periodic stimulation and adjust their sensitivity. We report that sea urchin sperm sampled molecules for 0.2–0.6 s before a Ca2+ response was produced. Additional molecules delivered during a Ca2+ response reset the cell by causing a pronounced Ca2+ drop that terminated the response; this reset was followed by a new Ca2+ rise. After stimulation, sperm adapted their sensitivity following the Weber–Fechner law. Taking into account the single-molecule sensitivity, we estimate that sperm can register a minimal gradient of 0.8 fM/µm and be attracted from as far away as 4.7 mm. Many microorganisms sense stimulus gradients along periodic paths to translate a spatial distribution of the stimulus into a temporal pattern of the cell response. Orchestration of temporal sampling, resetting, and adaptation might control gradient sensing in such organisms as well.This work was supported by the German Research Foundation and the Fonds der Chemischen Industrie.2013-03-1

Violent Deaths of Iraqi Civilians, 2003–2008: Analysis by Perpetrator, Weapon, Time, and Location

Madelyn Hsiao-Rei Hicks and colleagues provide a detailed analysis of Iraqi civilian violent deaths during 2003-2008 of the Iraq war and show that of 92,614 deaths, unknown perpetrators caused 74% of deaths, Coalition forces 12%, and Anti-Coalition forces 11%

Hot, rocky and warm, puffy super-Earths orbiting TOI-402 (HD 15337)

Context: The Transiting Exoplanet Survey Satellite (TESS) is revolutionising the search for planets orbiting bright and nearby stars. In sectors 3 and 4, TESS observed TOI-402 (TIC-120896927), a bright V = 9.1 K1 dwarf also known as HD 15337, and found two transiting signals with periods of 4.76 and 17.18 days and radii of 1.90 and 2.21 R⊕, respectively. This star was observed prior to the TESS detection as part of the radial-velocity (RV) search for planets using the HARPS spectrometer, and 85 precise RV measurements were obtained before the launch of TESS over a period of 14 yr. Aims: In this paper, we analyse the HARPS RV measurements in hand to confirm the planetary nature of these two signals. Methods: HD 15337 happens to present a stellar activity level similar to the Sun, with a magnetic cycle of similar amplitude and RV measurements that are affected by stellar activity. By modelling this stellar activity in the HARPS radial velocities using a linear dependence with the calcium activity index log(RHK′), we are able, with a periodogram approach, to confirm the periods and the planetary nature of TOI-402.01 and TOI-402.02. We then derive robust estimates from the HARPS RVs for the orbital parameters of these two planets by modelling stellar activity with a Gaussian process and using the marginalised posterior probability density functions obtained from our analysis of TESS photometry for the orbital period and time of transit. Results: By modelling TESS photometry and the stellar host characteristics, we find that TOI-402.01 and TOI-402.02 have periods of 4.75642 ± 0.00021 and 17.1784 ± 0.0016 days and radii of 1.70 ± 0.06 and 2.52 ± 0.11 R⊕ (precision 3.6 and 4.2%), respectively. By analysing the HARPS RV measurements, we find that those planets are both super-Earths with masses of 7.20 ± 0.81 and 8.79 ± 1.68 M⊕ (precision 11.3 and 19.1%), and small eccentricities compatible with zero at 2σ. Conclusions: Although having rather similar masses, the radii of these two planets are very different, putting them on different sides of the radius gap. By studying the temporal evolution under X-ray and UV (XUV) driven atmospheric escape of the TOI-402 planetary system, we confirm, under the given assumptions, that photo-evaporation is a plausible explanation for this radius difference. Those two planets, being in the same system and therefore being in the same irradiation environment are therefore extremely useful for comparative exoplanetology across the evaporation valley and thus bring constraints on the mechanisms responsible for the radius gap

Spitzer Reveals Evidence of Molecular Absorption in the Atmosphere of the Hot Neptune LTT 9779b

Non-rocky sub-Jovian exoplanets in high-irradiation environments are rare. LTT 9779b, also known as Transiting Exoplanet Survey Satellite (TESS) object of interest (TOI) 193.01, is one of the few such planets discovered to date, and the first example of an ultrahot Neptune. The planet's bulk density indicates that it has a substantial atmosphere, so to investigate its atmospheric composition and shed further light on its origin, we obtained Spitzer InfraRed Array Camera secondary eclipse observations of LTT 9779b at 3.6 and 4.5 μm. We combined the Spitzer observations with a measurement of the secondary eclipse in the TESS bandpass. The resulting secondary eclipse spectrum strongly prefers a model that includes CO absorption over a blackbody spectrum, incidentally making LTT 9779b the first TESS exoplanet (and the first ultrahot Neptune) with evidence of a spectral feature in its atmosphere. We did not find evidence of a thermal inversion, at odds with expectations based on the atmospheres of similarly irradiated hot Jupiters. We also report a nominal dayside brightness temperature of 2305 ± 141 K (based on the 3.6 μm secondary eclipse measurement), and we constrained the planet's orbital eccentricity to e < 0.01 at the 99.7% confidence level. Together with our analysis of LTT 9779b's thermal phase curves reported in a companion paper, our results set the stage for similar investigations of a larger sample of exoplanets discovered in the hot-Neptune desert, investigations that are key to uncovering the origin of this population