A global dataset on weather, lake physics, and phytoplankton dynamics

We compiled data from over 30 lakes across the globe to address how storms influence thermal structure and phytoplankton community dynamics mediated by lake conditions and functional traits. In addition to (generally) fortnightly phytoplankton samples (mean ± SD temporal coverage across all lakes = 20 ± 13 years), the dataset includes limnological variables from standard long-term monitoring programs (24 ± 15 years coverage), daily weather observations (16 ± 10 years coverage) and, when available, high-frequency lake water temperature and water chemistry profiles (12 ± 7 years coverage). All data have been standardized to similar formats and include complete metadata. We used the dataset to develop an R-package (“algaeClassify”), which assigns phytoplankton genus/species information to multiple functional trait groups, and here we provide a summary of ongoing research using the dataset to investigate: 1) the influence of storm events on seasonal phytoplankton succession, 2) the impact of storms on lake thermal structure, and 3) whether lake phytoplankton communities are shaped by long-term patterns in disturbance frequency and intensity. We give an overview on how to access these data, and we further highlight the opportunities the dataset provides for asking both basic and applied questions in limnology, ecology, climate change, and lake management

Deciphering exome sequencing data: Bringing mitochondrial DNA variants to light

The expanding use of exome sequencing (ES) in diagnosis generates a huge amount of data, including untargeted mitochondrial DNA (mtDNA) sequences. We developed a strategy to deeply study ES data, focusing on the mtDNA genome on a large unspecific cohort to increase diagnostic yield. A targeted bioinformatics pipeline assembled mitochondrial genome from ES data to detect pathogenic mtDNA variants in parallel with the "in-house" nuclear exome pipeline. mtDNA data coming from off-target sequences (indirect sequencing) were extracted from the BAM files in 928 individuals with developmental and/or neurological anomalies. The mtDNA variants were filtered out based on database information, cohort frequencies, haplogroups and protein consequences. Two homoplasmic pathogenic variants (m.9035T>C and m.11778G>A) were identified in 2 out of 928 unrelated individuals (0.2%): the m.9035T>C (MT-ATP6) variant in a female with ataxia and the m.11778G>A (MT-ND4) variant in a male with a complex mosaic disorder and a severe ophthalmological phenotype, uncovering undiagnosed Leber\u27s hereditary optic neuropathy (LHON). Seven secondary findings were also found, predisposing to deafness or LHON, in 7 out of 928 individuals (0.75%). This study demonstrates the usefulness of including a targeted strategy in ES pipeline to detect mtDNA variants, improving results in diagnosis and research, without resampling patients and performing targeted mtDNA strategies

The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice.

The gut microbiota-intestine-liver relationship is emerging as an important factor in multiple hepatic pathologies, but the hepatic sensors and effectors of microbial signals are not well defined. By comparing publicly available liver transcriptomics data from conventional vs. germ-free mice, we identified pregnane X receptor (PXR, NR1I2) transcriptional activity as strongly affected by the absence of gut microbes. Microbiota depletion using antibiotics in Pxr <sup>+/+</sup> vs Pxr <sup>-/-</sup> C57BL/6J littermate mice followed by hepatic transcriptomics revealed that most microbiota-sensitive genes were PXR-dependent in the liver in males, but not in females. Pathway enrichment analysis suggested that microbiota-PXR interaction controlled fatty acid and xenobiotic metabolism. We confirmed that antibiotic treatment reduced liver triglyceride content and hampered xenobiotic metabolism in the liver from Pxr <sup>+/+</sup> but not Pxr <sup>-/-</sup> male mice. These findings identify PXR as a hepatic effector of microbiota-derived signals that regulate the host's sexually dimorphic lipid and xenobiotic metabolisms in the liver. Thus, our results reveal a potential new mechanism for unexpected drug-drug or food-drug interactions. Video abstract

GPs' reasons for referral of patients with chest pain: a qualitative study

<p>Abstract</p> <p>Background</p> <p>Prompt diagnosis of an acute coronary syndrome is very important and urgent referral to a hospital is imperative because fast treatment can be life-saving and increase the patient's life expectancy and quality of life. The aim of our study was to identify GPs' reasons for referring or not referring patients presenting with chest pain.</p> <p>Methods</p> <p>In a semi-structured interview, 21 GPs were asked to describe why they do or do not refer a patient presenting with chest pain. Interviews were taped, transcribed and qualitatively analysed.</p> <p>Results</p> <p>Histories of 21 patients were studied. Six were not referred, seven were referred to a cardiologist and eight to the emergency department. GPs' reasons for referral were background knowledge about the patient, patient's age and cost-benefit estimation, the perception of a negative attitude from the medical rescue team, recent patient contact with a cardiologist without detection of a coronary disease and the actual presentation of signs and symptoms, gut feeling, clinical examination and ECG results.</p> <p>Conclusion</p> <p>This study suggests that GPs believe they do not exclusively use the 'classical' signs and symptoms in their decision-making process for patients presenting with chest pain. Background knowledge about the patient, GPs' personal ideas and gut feeling are also important.</p

Fermi-LAT Study of Gamma-ray Emission in the Direction of Supernova Remnant W49B

We present an analysis of the gamma-ray data obtained with the Large Area Telescope (LAT) onboard the Fermi Gamma-ray Space Telescope in the direction of SNR W49B (G43.3-0.2). A bright unresolved gamma-ray source detected at a significance of 38 sigma is found to coincide with SNR W49B. The energy spectrum in the 0.2-200 GeV range gradually steepens toward high energies. The luminosity is estimated to be 1.5x10^{36} (D/8 kpc)^2 erg s^-1 in this energy range. There is no indication that the gamma-ray emission comes from a pulsar. Assuming that the SNR shell is the site of gamma-ray production, the observed spectrum can be explained either by the decay of neutral pi mesons produced through the proton-proton collisions or by electron bremsstrahlung. The calculated energy density of relativistic particles responsible for the LAT flux is estimated to be remarkably large, U_{e,p}>10^4 eV cm^-3, for either gamma-ray production mechanism.Comment: 9 pages, 10 figure

The Spectral Energy Distribution of Fermi bright blazars

(Abridged) We have conducted a detailed investigation of the broad-band spectral properties of the \gamma-ray selected blazars of the Fermi LAT Bright AGN Sample (LBAS). By combining our accurately estimated Fermi gamma-ray spectra with Swift, radio, infra-red, optical and other hard X-ray/gamma-ray data, collected within three months of the LBAS data taking period, we were able to assemble high-quality and quasi-simultaneous Spectral Energy Distributions (SED) for 48 LBAS blazars.The SED of these gamma-ray sources is similar to that of blazars discovered at other wavelengths, clearly showing, in the usual Log $\nu$ - Log $\nu$ F$_\nu$ representation, the typical broad-band spectral signatures normally attributed to a combination of low-energy synchrotron radiation followed by inverse Compton emission of one or more components. We have used these SEDs to characterize the peak intensity of both the low and the high-energy components. The results have been used to derive empirical relationships that estimate the position of the two peaks from the broad-band colors (i.e. the radio to optical and optical to X-ray spectral slopes) and from the gamma-ray spectral index. Our data show that the synchrotron peak frequency $\nu_p^S$ is positioned between 10$^{12.5}$ and 10$^{14.5}$ Hz in broad-lined FSRQs and between $10^{13}$ and $10^{17}$ Hz in featureless BL Lacertae objects.We find that the gamma-ray spectral slope is strongly correlated with the synchrotron peak energy and with the X-ray spectral index, as expected at first order in synchrotron - inverse Compton scenarios. However, simple homogeneous, one-zone, Synchrotron Self Compton (SSC) models cannot explain most of our SEDs, especially in the case of FSRQs and low energy peaked (LBL) BL Lacs. (...)Comment: 85 pages, 38 figures, submitted to Ap

Fermi observations of TeV-selected AGN

We report on observations of TeV-selected AGN made during the first 5.5 months of observations with the Large Area Telescope (LAT) on-board the Fermi Gamma-ray Space Telescope (Fermi). In total, 96 AGN were selected for study, each being either (i) a source detected at TeV energies (28 sources) or (ii) an object that has been studied with TeV instruments and for which an upper-limit has been reported (68 objects). The Fermi observations show clear detections of 38 of these TeV-selected objects, of which 21 are joint GeV-TeV sources and 29 were not in the third EGRET catalog. For each of the 38 Fermi-detected sources, spectra and light curves are presented. Most can be described with a power law of spectral index harder than 2.0, with a spectral break generally required to accommodate the TeV measurements. Based on an extrapolation of the Fermi spectrum, we identify sources, not previously detected at TeV energies, which are promising targets for TeV instruments. Evidence for systematic evolution of the $\gamma$-ray spectrum with redshift is presented and discussed in the context of interaction with the EBL.Comment: 51 pages, 6 figures, accepted for The Astronomical Journa

Fermi Large Area Telescope Measurements of the Diffuse Gamma-Ray Emission at Intermediate Galactic Latitudes

The diffuse Galactic gamma-ray emission is produced by cosmic rays (CRs) interacting with the interstellar gas and radiation field. Measurements by the Energetic Gamma-Ray Experiment Telescope (EGRET) instrument on the Compton Gamma-Ray Observatory indicated excess gamma-ray emission > 1 GeV relative to diffuse Galactic gamma-ray emission models consistent with directly measured CR spectra (the so-called ``EGRET GeV excess''). The excess emission was observed in all directions on the sky, and a variety of explanations have been proposed, including beyond-the-Standard-Model scenarios like annihilating or decaying dark matter. The Large Area Telescope (LAT) instrument on the Fermi Gamma-ray Space Telescope has measured the diffuse gamma-ray emission with improved sensitivity and resolution compared to EGRET. We report on LAT measurements of the diffuse gamma-ray emission for energies 100 MeV to 10 GeV and Galactic latitudes 10 deg. <= |b| <= 20 deg. The LAT spectrum for this region of the sky is well reproduced by a diffuse Galactic gamma-ray emission model that is consistent with local CR spectra and inconsistent with the EGRET GeV excess.Comment: 2 figures, 1 table, accepted by Physical Review Letters, available online Dec. 18th, 200

Radio-Loud Narrow-Line Seyfert 1 as a New Class of Gamma-Ray AGN

We report the discovery with Fermi/LAT of gamma-ray emission from three radio-loud narrow-line Seyfert 1 galaxies: PKS 1502+036 (z=0.409), 1H 0323+342 (z=0.061) and PKS 2004-447 (z=0.24). In addition to PMN J0948+0022 (z=0.585), the first source of this type to be detected in gamma rays, they may form an emerging new class of gamma-ray active galactic nuclei (AGN). These findings can have strong implications on our knowledge about relativistic jets and the unified model of AGN.Comment: 16 pages, 1 figure. Accepted for publication on ApJ Letters. Corresponding author: Luigi Foschin

Fermi Large Area Telescope Observations of the Cosmic-Ray Induced gamma-ray Emission of the Earth's Atmosphere

We report on measurements of the cosmic-ray induced gamma-ray emission of Earth's atmosphere by the Large Area Telescope onboard the Fermi Gamma-ray Space Telescope. The LAT has observed the Earth during its commissioning phase and with a dedicated Earth-limb following observation in September 2008. These measurements yielded 6.4 x 10^6 photons with energies >100MeV and ~250hours total livetime for the highest quality data selection. This allows the study of the spatial and spectral distributions of these photons with unprecedented detail. The spectrum of the emission - often referred to as Earth albedo gamma-ray emission - has a power-law shape up to 500 GeV with spectral index Gamma = 2.79+-0.06.Comment: Accepted for publication in PR