recount3: summaries and queries for large-scale RNA-seq expression and splicing

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio

Time-resolved measurements of fast electron recirculation for relativistically intense femtosecond scale laser-plasma interactions

A key issue in realising the development of a number of applications of high-intensity lasers is the dynamics of the fast electrons produced and how to diagnose them. We report on measurements of fast electron transport in aluminium targets in the ultra-intense, short-pulse (<50 fs) regime using a high resolution temporally and spatially resolved optical probe. The measurements show a rapidly (≈0.5c) expanding region of Ohmic heating at the rear of the target, driven by lateral transport of the fast electron population inside the target. Simulations demonstrate that a broad angular distribution of fast electrons on the order of 60° is required, in conjunction with extensive recirculation of the electron population, in order to drive such lateral transport. These results provide fundamental new insight into fast electron dynamics driven by ultra-short laser pulses, which is an important regime for the development of laser-based radiation and particle sources

Sensitivity of the Himalayan orography representation in simulation of winter precipitation using Regional Climate Model (RegCM) nested in a GCM

This document is the Accepted Manuscript version of the following article: Tiwari, P.R., Kar, S.C., Mohanty, U.C., Climate Dynamics (2017). The final publication is available at Springer via https://link.springer.com/article/10.1007%2Fs00382-017-3567-3. The Accepted Manuscript is under embargo. Embargo end date: 24 February 2018.The role of the Himalayan orography representationin a Regional Climate Model (RegCM4) nested inNCMRWF global spectral model is examined in simulatingthe winter circulation and associated precipitation over theNorthwest India (NWI; 23°–37.5°N and 69°–85°E) region.For this purpose, nine different set of orography representationsfor nine distinct precipitation years (three years eachfor wet, normal and dry) have been considered by increasing(decreasing) 5, 10, 15, and 20% from the mean height(CNTRL) of the Himalaya in RegCM4 model. Validationwith various observations revealed a good improvementin reproducing the precipitation intensity and distributionwith increased model height compared to the resultsobtained from CNTRL and reduced orography experiments.Further it has been found that, increase in heightby 10% (P10) increases seasonal precipitation about 20%,while decrease in height by 10% (M10) results around 28%reduction in seasonal precipitation as compared to CNTRLexperiment over NWI region. This improvement in precipitationsimulation comes due to better representation ofvertical pressure velocity and moisture transport as thesefactors play an important role in wintertime precipitationprocesses over NWI region. Furthermore, a comparison of model-simulated precipitation with observed precipitationat 17 station locations has been also carried out. Overall,the results suggest that when the orographic increment of10% (P10) is applied on RegCM4 model, it has better skillin simulating the precipitation over the NWI region andthis model is a useful tool for further regional downscalingstudies.Peer reviewe

Micron-scale mapping of megagauss magnetic fields using optical polarimetry to probe hot electron transport in petawatt-class laser-solid interactions

The transport of hot, relativistic electrons produced by the interaction of an intense petawatt laser pulse with a solid has garnered interest due to its potential application in the development of innovative x-ray sources and ion-acceleration schemes. We report on spatially and temporally resolved measurements of megagauss magnetic fields at the rear of a 50-μm thick plastic target, irradiated by a multi-picosecond petawatt laser pulse at an incident intensity of ~1020 W/cm2. The pump-probe polarimetric measurements with micron-scale spatial resolution reveal the dynamics of the magnetic fields generated by the hot electron distribution at the target rear. An annular magnetic field profile was observed ~5 ps after the interaction, indicating a relatively smooth hot electron distribution at the rear-side of the plastic target. This is contrary to previous time-integrated measurements, which infer that such targets will produce highly structured hot electron transport. We measured large-scale filamentation of the hot electron distribution at the target rear only at later time-scales of ~10 ps, resulting in a commensurate large-scale filamentation of the magnetic field profile. Three-dimensional hybrid simulations corroborate our experimental observations and demonstrate a beam-like hot electron transport at initial time-scales that may be attributed to the local resistivity profile at the target rear

The Stem Species of Our Species: A Place for the Archaic Human Cranium from Ceprano, Italy

One of the present challenges in the study of human evolution is to recognize the hominin taxon that was ancestral to Homo sapiens. Some researchers regard H. heidelbergensis as the stem species involved in the evolutionary divergence leading to the emergence of H. sapiens in Africa, and to the evolution of the Neandertals in Europe. Nevertheless, the diagnosis and hypodigm of H. heidelbergensis still remain to be clarified. Here we evaluate the morphology of the incomplete cranium (calvarium) known as Ceprano whose age has been recently revised to the mid of the Middle Pleistocene, so as to test whether this specimen may be included in H. heidelbergensis. The analyses were performed according to a phenetic routine including geometric morphometrics and the evaluation of diagnostic discrete traits. The results strongly support the uniqueness of H. heidelbergensis on a wide geographical horizon, including both Eurasia and Africa. In this framework, the Ceprano calvarium – with its peculiar combination of archaic and derived traits – may represent, better than other penecontemporaneous specimens, an appropriate ancestral stock of this species, preceding the appearance of regional autapomorphic features

Prevalence, and associated risk factors, of self-reported diabetes mellitus in a sample of adult urban population in Greece: MEDICAL Exit Poll Research in Salamis (MEDICAL EXPRESS 2002)

BACKGROUND: The continuous monitoring and future prediction of the growing epidemic of diabetes mellitus worldwide presuppose consistent information about the extent of the problem. The aim of this study was to determine the prevalence of diagnosed diabetes and to identify associated risk factors in a sample of adult urban Greek population. METHODS: A cross-sectional population-based survey was conducted in municipality of Salamis, Greece, during an election day (2002). The study sample consisted of 2805 participants, aged 20–94 years. Data were collected using a standardized short questionnaire that was completed by a face-to-face interview. Multiple regression analyses were performed to evaluate the association of diabetes with potential risk factors. RESULTS: The overall prevalence of diagnosed diabetes was 8.7% (95% CI 7.7–9.8%). After age adjustment for the current adult population (2001 census) of Greece, the projection prevalence was calculated to 8.2%. Multivariate logistic regression analysis identified as independent risk factors: increasing age (odds ratio, OR = 1.07, 95% CI 1.06–1.08), male sex (OR = 1.43, 95% CI 1.04–1.95), overweight and obesity (OR = 1.97, 95% CI 1.29–3.01 and OR = 3.76, 95% CI 2.41–5.86, respectively), family history of diabetes (OR = 6.91, 95% CI 5.11–9.34), hypertension (OR = 2.19, 95% CI 1.60–2.99) and, among women, lower educational level (OR = 2.62, 95% CI 1.22–5.63). The prevalence of overweight and obesity, based on self-reported BMI, were 44.2% and 18.4%, respectively. Moreover, the odds for diabetes in obese subjects with family history were 25-fold higher than those with normal weight and without family history of diabetes, while the odds in overweight subjects with family history of diabetes were 15-fold higher. CONCLUSIONS: Our findings indicated that the prevalence of diabetes is high in Greek population. It is suggested that the main modifiable contributing factor is obesity, whose effect is extremely increased upon positive heredity presence

Guiding of relativistic electron beams in dense matter by laser-driven magnetostatic fields

Intense lasers interacting with dense targets accelerate relativistic electron beams, whichtransport part of the laser energy into the target depth. However, the overall laser-to-targetenergy coupling efficiency is impaired by the large divergence of the electron beam, intrinsicto the laser-plasma interaction. Here we demonstrate that an efficient guiding ofMeV electrons with about 30MA current in solid matter is obtained by imposing a laserdrivenlongitudinal magnetostatic field of 600 T. In the magnetized conditions the transportedenergy density and the peak background electron temperature at the 60-μm-thicktarget's rear surface rise by about a factor of five, as unfolded from benchmarked simulations.Such an improvement of energy-density flux through dense matter paves the ground foradvances in laser-driven intense sources of energetic particles and radiation, driving matter toextreme temperatures, reaching states relevant for planetary or stellar science as yet inaccessibleat the laboratory scale and achieving high-gain laser-driven thermonuclear fusion

Heme Degrading Protein HemS Is Involved in Oxidative Stress Response of Bartonella henselae

Bartonellae are hemotropic bacteria, agents of emerging zoonoses. These bacteria are heme auxotroph Alphaproteobacteria which must import heme for supporting their growth, as they cannot synthesize it. Therefore, Bartonella genome encodes for a complete heme uptake system allowing the transportation of this compound across the outer membrane, the periplasm and the inner membranes. Heme has been proposed to be used as an iron source for Bartonella since these bacteria do not synthesize a complete system required for iron Fe3+uptake. Similarly to other bacteria which use heme as an iron source, Bartonellae must transport this compound into the cytoplasm and degrade it to allow the release of iron from the tetrapyrrole ring. For Bartonella, the gene cluster devoted to the synthesis of the complete heme uptake system also contains a gene encoding for a polypeptide that shares homologies with heme trafficking or degrading enzymes. Using complementation of an E. coli mutant strain impaired in heme degradation, we demonstrated that HemS from Bartonella henselae expressed in E. coli allows the release of iron from heme. Purified HemS from B. henselae binds heme and can degrade it in the presence of a suitable electron donor, ascorbate or NADPH-cytochrome P450 reductase. Knocking down the expression of HemS in B. henselae reduces its ability to face H2O2 induced oxidative stress

Wind speed variability over the Canary Islands, 1948-2014: focusing on trend differences at the land-ocean interface and below-above the trade-wind inversion layer

This study simultaneously examines wind speed trends at the land?ocean interface, and below?above the trade-wind inversion layer in the Canary Islands and the surrounding Eastern North Atlantic Ocean: a key region for quantifying the variability of trade-winds and its response to large-scale atmospheric circulation changes. Two homogenized data sources are used: (1) observed wind speed from nine land-based stations (1981?2014), including one mountain weather station (Izaña) located above the trade-wind inversion layer; and (2) simulated wind speed from two atmospheric hindcasts over ocean (i.e., SeaWind I at 30 km for 1948?2014; and SeaWind II at 15 km for 1989?2014). The results revealed a widespread significant negative trend of trade-winds over ocean for 1948?2014, whereas no significant trends were detected for 1989?2014. For this recent period wind speed over land and ocean displayed the same multi-decadal variability and a distinct seasonal trend pattern with a strengthening (late spring and summer; significant in May and August) and weakening (winter?spring?autumn; significant in April and September) of trade-winds. Above the inversion layer at Izaña, we found a predominance of significant positive trends, indicating a decoupled variability and opposite wind speed trends when compared to those reported in boundary layer. The analysis of the Trade Wind Index (TWI), the North Atlantic Oscillation Index (NAOI) and the Eastern Atlantic Index (EAI) demonstrated significant correlations with the wind speed variability, revealing that the correlation patterns of the three indices showed a spatio-temporal complementarity in shaping wind speed trends across the Eastern North Atlantic.C. A. -M. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 703733 (STILLING project). This research was also supported by the Research Projects: Swedish BECC, MERGE, VR (2014–5320), PCIN-2015-220, CGL2014-52135-C03-01 and Red de variabilidad y cambio climático RECLIM (CGL2014-517221-REDT). M.M is indebted to the Spanish Government for funding through the “Ramón y Cajal” program and supported by Grant PORTIO (BIA2015-70644-R