Flux calibration of medium-resolution spectra from 300 nm to 2500 nm: Model reference spectra and telluric correction

While the near-infrared wavelength regime is becoming more and more important for astrophysics there is a marked lack of spectrophotometric standard star data that would allow the flux calibration of such data. Furthermore, flux calibrating medium- to high-resolution \'echelle spectroscopy data is challenging even in the optical wavelength range, because the available flux standard data are often too coarsely sampled. We will provide standard star reference data that allow users to derive response curves from 300nm to 2500nm for spectroscopic data of medium to high resolution, including those taken with \'echelle spectrographs. In addition we describe a method to correct for moderate telluric absorption without the need of observing telluric standard stars. As reference data for the flux standard stars we use theoretical spectra derived from stellar model atmospheres. We verify that they provide an appropriate description of the observed standard star spectra by checking for residuals in line cores and line overlap regions in the ratios of observed (X-shooter) spectra to model spectra. The finally selected model spectra are then corrected for remaining mismatches and photometrically calibrated using independent observations. The correction of telluric absorption is performed with the help of telluric model spectra.We provide new, finely sampled reference spectra without telluric absorption for six southern flux standard stars that allow the users to flux calibrate their data from 300 nm to 2500 nm, and a method to correct for telluric absorption using atmospheric models.Comment: Reference spectra available at CDS. Published in A&A 568, A9, 201

Nitrogen uptake and internal recycling in Zostera marina exposed to oyster farming: eelgrass potential as a natural biofilter

Oyster farming in estuaries and coastal lagoons frequently overlaps with the distribution of seagrass meadows, yet there are few studies on how this aquaculture practice affects seagrass physiology. We compared in situ nitrogen uptake and the productivity of Zostera marina shoots growing near off-bottom longlines and at a site not affected by oyster farming in San Quintin Bay, a coastal lagoon in Baja California, Mexico. We used benthic chambers to measure leaf NH4 (+) uptake capacities by pulse labeling with (NH4)-N-15 (+) and plant photosynthesis and respiration. The internal N-15 resorption/recycling was measured in shoots 2 weeks after incubations. The natural isotopic composition of eelgrass tissues and vegetative descriptors were also examined. Plants growing at the oyster farming site showed a higher leaf NH4 (+) uptake rate (33.1 mmol NH4 (+) m(-2) day(-1)) relative to those not exposed to oyster cultures (25.6 mmol NH4 (+) m(-2) day(-1)). We calculated that an eelgrass meadow of 15-16 ha (which represents only about 3-4 % of the subtidal eelgrass meadow cover in the western arm of the lagoon) can potentially incorporate the total amount of NH4 (+) excreted by oysters (similar to 5.2 x 10(6) mmol NH4 (+) day(-1)). This highlights the potential of eelgrass to act as a natural biofilter for the NH4 (+) produced by oyster farming. Shoots exposed to oysters were more efficient in re-utilizing the internal N-15 into the growth of new leaf tissues or to translocate it to belowground tissues. Photosynthetic rates were greater in shoots exposed to oysters, which is consistent with higher NH4 (+) uptake and less negative delta C-13 values. Vegetative production (shoot size, leaf growth) was also higher in these shoots. Aboveground/belowground biomass ratio was lower in eelgrass beds not directly influenced by oyster farms, likely related to the higher investment in belowground biomass to incorporate sedimentary nutrients

Five thousand years of fire history in the high North Atlantic region: Natural variability and ancient human forcing

Biomass burning influences global atmospheric chemistry by releasing greenhouse gases and climate-forcing aerosols. There is controversy about the magnitude and timing of Holocene changes in biomass burning emissions from millennial to centennial timescales and, in particular, about the possible impact of ancient civilizations. Here we present a 5gkyr record of fire activity proxies levoglucosan, black carbon, and ammonium measured in the RECAP (Renland ice cap) ice core, drilled in coastal eastern Greenland, and therefore affected by processes occurring in the high North Atlantic region. Levoglucosan and ammonium fluxes are high from 5 to 4.5gkyrgBP (thousand years before 2000gCE) followed by an abrupt decline, possibly due to monotonic decline in Northern Hemisphere summer insolation. Levoglucosan and black carbon show an abrupt decline at 1.1gkyrgBP, suggesting a decline in the wildfire regime in Iceland due to the extensive land clearing caused by Viking colonizers. All fire proxies reach a minimum during the second half of the last century, after which levoglucosan and ammonium fluxes increase again, in particular over the last 200 years. We find that the fire regime reconstructed from RECAP fluxes seems mainly related to climatic changes; however over the last millennium human activities might have influenced wildfire frequency/occurrence substantially

Greenland ice core evidence of the 79 AD Vesuvius eruption

Volcanic tephra are independent age horizons and can synchronize strata of various paleoclimate records in- cluding ice and sediment cores. The Holocene section of the Greenland Ice Core Project (GRIP) ice core is dated by multi-parameter annual layer counting, and contains peaks in acidity, SO 2− and microparticle concentrations at a depth of 4 429.1 to 429.3 m, which have not previously been definitively ascribed to a volcanic eruption. Here, we identify tephra par- ticles and determine that volcanic shards extracted from a depth of 429.3 m in the GRIP ice core are likely due to the 79 AD Vesuvius eruption. The chemical composition of the tephra particles is consistent with the K-phonolitic compo- sition of the Vesuvius juvenile ejecta and differs from the chemical composition of other major eruptions (≥VEI 4) between 50–100 AD

The 3' region of Human Papillomavirus type 16 early mRNAs decrease expression

BACKGROUND: High risk human papillomavirus (HR-HPV) infects mucosal surfaces and HR-HPV infection is required for development of cervical cancer. Accordingly, enforced expression of the early HR-HPV proteins can induce immortalisation of human cells. In most cervical cancers and cervical cancer cell lines the HR-HPV double stranded DNA genome has been integrated into the host cell genome. METHODS: We have used a retroviral GUS reporter system to generate pools of stably transfected HaCaT and SiHa cells. The HPV-16 early sequences that are deleted upon integration of the HPV-16 genome was inserted into the 3' UTR of the reporter mRNA. Pools containing thousands of independent integrations were tested for the steady state levels of the reporter mRNA by Real Time PCR and reporter protein by a GUS enzymatic activity assays. In addition, we tested the cellular distribution and half lives of the reporter mRNAs. The integrity of the reporter mRNAs were tested by northern blotting. RESULTS: We show that the 3' region of the HPV-16 early mRNAs (HPV-16 nucleotide (nt.) 2582–4214) act in cis to decrease both mRNA and protein levels. This region seems to affect transcription from the exogenous minimal CMV promoter or processing of the reporter mRNA. The observed repression was most pronounced at the protein level, suggesting that this sequence may also affect translation. For the HPV types: 2, 6, 11, 13, 18, 30, 31, and 35 we have investigated the regulatory effect of the regions corresponding to the HPV-16 nt. 3358–4214. For all types, except HPV-18, the region was found to repress expression by posttranscriptional mechanisms. CONCLUSION: We find that the 3' region of HPV-16 early mRNAs interfere with gene expression. It is therefore possible that the deletion of the 3' part of early HPV-16 mRNAs occurring during cervical oncogenesis could contribute to transformation of cells through deregulation of the viral oncogene synthesis. Moreover, we find that the corresponding region from several other HPV types also repress expression, suggesting that the repression by this region may be a general feature of the HPV life cycle

Deconvolution of Serum Cortisol Levels by Using Compressed Sensing

The pulsatile release of cortisol from the adrenal glands is controlled by a hierarchical system that involves corticotropin releasing hormone (CRH) from the hypothalamus, adrenocorticotropin hormone (ACTH) from the pituitary, and cortisol from the adrenal glands. Determining the number, timing, and amplitude of the cortisol secretory events and recovering the infusion and clearance rates from serial measurements of serum cortisol levels is a challenging problem. Despite many years of work on this problem, a complete satisfactory solution has been elusive. We formulate this question as a non-convex optimization problem, and solve it using a coordinate descent algorithm that has a principled combination of (i) compressed sensing for recovering the amplitude and timing of the secretory events, and (ii) generalized cross validation for choosing the regularization parameter. Using only the observed serum cortisol levels, we model cortisol secretion from the adrenal glands using a second-order linear differential equation with pulsatile inputs that represent cortisol pulses released in response to pulses of ACTH. Using our algorithm and the assumption that the number of pulses is between 15 to 22 pulses over 24 hours, we successfully deconvolve both simulated datasets and actual 24-hr serum cortisol datasets sampled every 10 minutes from 10 healthy women. Assuming a one-minute resolution for the secretory events, we obtain physiologically plausible timings and amplitudes of each cortisol secretory event with R[superscript 2] above 0.92. Identification of the amplitude and timing of pulsatile hormone release allows (i) quantifying of normal and abnormal secretion patterns towards the goal of understanding pathological neuroendocrine states, and (ii) potentially designing optimal approaches for treating hormonal disorders.National Science Foundation (U.S.). Graduate Research Fellowship ProgramNational Institutes of Health (U.S.) (NIH DP1 OD003646)National Science Foundation (U.S.) (0836720)National Science Foundation (U.S.). Office of Emerging Frontiers in Research and Innovation (EFRI-0735956

Low-frequency components in harbor porpoise (Phocoena phocoena) clicks : communication signal, by-products, or artifacts?

Author Posting. © Acoustical Society of America, 2008. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 124 (2008): 4059-4068, doi:10.1121/1.2945154.Underwater sound signals for biosonar and communication normally have different source properties to serve the purposes of generating efficient acoustic backscatter from small objects or conveying information to conspecifics. Harbor porpoises (Phocoena phocoena) are nonwhistling toothed whales that produce directional, narrowband, high-frequency (HF) echolocation clicks. This study tests the hypothesis that their 130 kHz HF clicks also contain a low-frequency (LF) component more suited for communication. Clicks from three captive porpoises were analyzed to quantify the LF and HF source properties. The LF component is 59 (S.E.M=1.45 dB) dB lower than the HF component recorded on axis, and even at extreme off-axis angles of up to 135°, the HF component is 9 dB higher than the LF component. Consequently, the active space of the HF component will always be larger than that of the LF component. It is concluded that the LF component is a by-product of the sound generator rather than a dedicated pulse produced to serve communication purposes. It is demonstrated that distortion and clipping in analog tape recorders can explain some of the prominent LF components reported in earlier studies, emphasizing the risk of erroneous classification of sound types based on recording artifacts.This work was supported by the Carlsberg Foundation and Oticon, and via a Steno Scholarship from the Danish Natural Science Research Council to PTM

MicroRNAs are deeply linked to the emergence of the complex octopus brain

Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the (Octopus vulgaris). We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains