Minimizing off-target signals in RNA fluorescent in situ hybridization

Fluorescent in situ hybridization (FISH) techniques are becoming extremely sensitive, to the point where individual RNA or DNA molecules can be detected with small probes. At this level of sensitivity, the elimination of ‘off-target’ hybridization is of crucial importance, but typical probes used for RNA and DNA FISH contain sequences repeated elsewhere in the genome. We find that very short (e.g. 20 nt) perfect repeated sequences within much longer probes (e.g. 350–1500 nt) can produce significant off-target signals. The extent of noise is surprising given the long length of the probes and the short length of non-specific regions. When we removed the small regions of repeated sequence from either short or long probes, we find that the signal-to-noise ratio is increased by orders of magnitude, putting us in a regime where fluorescent signals can be considered to be a quantitative measure of target transcript numbers. As the majority of genes in complex organisms contain repeated k-mers, we provide genome-wide annotations of k-mer-uniqueness at http://cbio.mskcc.org/∼aarvey/repeatmap

Evaluating stratospheric ozone and water vapour changes in CMIP6 models from 1850 to 2100

Stratospheric ozone and water vapour are key components of the Earth system, and past and future changes to both have important impacts on global and regional climate. Here, we evaluate long-term changes in these species from the pre-industrial period (1850) to the end of the 21st century in Coupled Model Intercomparison Project phase 6 (CMIP6) models under a range of future emissions scenarios. There is good agreement between the CMIP multi-model mean and observations for total column ozone (TCO), although there is substantial variation between the individual CMIP6 models. For the CMIP6 multi-model mean, global mean TCO has increased from ∼300 DU in 1850 to ∼ 305 DU in 1960, before rapidly declining in the 1970s and 1980s following the use and emission of halogenated ozone-depleting substances (ODSs). TCO is projected to return to 1960s values by the middle of the 21st century under the SSP2-4.5, SSP3-7.0, SSP4-3.4, SSP4-6.0, and SSP5-8.5 scenarios, and under the SSP3-7.0 and SSP5-8.5 scenarios TCO values are projected to be ∼ 10 DU higher than the 1960s values by 2100. However, under the SSP1-1.9 and SSP1-1.6 scenarios, TCO is not projected to return to the 1960s values despite reductions in halogenated ODSs due to decreases in tropospheric ozone mixing ratios. This global pattern is similar to regional patterns, except in the tropics where TCO under most scenarios is not projected to return to 1960s values, either through reductions in tropospheric ozone under SSP1-1.9 and SSP1-2.6, or through reductions in lower stratospheric ozone resulting from an acceleration of the Brewer-Dobson circulation under other Shared Socioeconomic Pathways (SSPs). In contrast to TCO, there is poorer agreement between the CMIP6 multi-model mean and observed lower stratospheric water vapour mixing ratios, with the CMIP6 multi-model mean underestimating observed water vapour mixing ratios by ∼ 0.5 ppmv at 70 hPa. CMIP6 multi-model mean stratospheric water vapour mixing ratios in the tropical lower stratosphere have increased by ∼ 0.5 ppmv from the pre-industrial to the present-day period and are projected to increase further by the end of the 21st century. The largest increases (∼ 2 ppmv) are simulated under the future scenarios with the highest assumed forcing pathway (e.g. SSP5-8.5). Tropical lower stratospheric water vapour, and to a lesser extent TCO, shows large variations following explosive volcanic eruptions. © Author(s) 2021

Discovery of VHE gamma-rays from the high-frequency-peaked BL Lac object RGB J0152+017

Aims: The BL Lac object RGB J0152+017 (z=0.080) was predicted to be a very high-energy (VHE; > 100 GeV) gamma-ray source, due to its high X-ray and radio fluxes. Our aim is to understand the radiative processes by investigating the observed emission and its production mechanism using the High Energy Stereoscopic System (H.E.S.S.) experiment. Methods: We report recent observations of the BL Lac source RGB J0152+017 made in late October and November 2007 with the H.E.S.S. array consisting of four imaging atmospheric Cherenkov telescopes. Contemporaneous observations were made in X-rays by the Swift and RXTE satellites, in the optical band with the ATOM telescope, and in the radio band with the Nancay Radio Telescope. Results: A signal of 173 gamma-ray photons corresponding to a statistical significance of 6.6 sigma was found in the data. The energy spectrum of the source can be described by a powerlaw with a spectral index of 2.95+/-0.36stat+/-0.20syst. The integral flux above 300 GeV corresponds to ~2% of the flux of the Crab nebula. The source spectral energy distribution (SED) can be described using a two-component non-thermal synchrotron self-Compton (SSC) leptonic model, except in the optical band, which is dominated by a thermal host galaxy component. The parameters that are found are very close to those found in similar SSC studies in TeV blazars. Conclusions: RGB J0152+017 is discovered as a source of VHE gamma-rays by H.E.S.S. The location of its synchrotron peak, as derived from the SED in Swift data, allows clearly classification it as a high-frequency-peaked BL Lac (HBL).Comment: Accepted for publication in A&A Letters (5 pages, 4 figures

Assessing the Role of CD103 in Immunity to an Intestinal Helminth Parasite

In the intestine, the integrin CD103 is expressed on a subset of T regulatory (T(reg)) cells and a population of dendritic cells (DCs) that produce retinoic acid and promote immune homeostasis. However, the role of CD103 during intestinal helminth infection has not been tested.We demonstrate that CD103 is dispensable for the development of protective immunity to the helminth parasite Trichuris muris. While we observed an increase in the frequency of CD103(+) DCs in the lamina propria (LP) following acute high-dose infection with Trichuris, lack of CD103 had no effect on the frequency of CD11c(+) DCs in the LP or mesenteric lymph nodes (mLN). CD103-deficient (CD103(-/-)) mice develop a slightly increased and earlier T cell response but resolve infection with similar kinetics to control mice. Similarly, low-dose chronic infection of CD103(-/-) mice with Trichuris resulted in no significant difference in immunity or parasite burden. Absence of CD103 also had no effect on the frequency of CD4(+)CD25(+)Foxp3(+) T(reg) cells in the mLN or LP.These results suggest that CD103 is dispensable for intestinal immunity during helminth infection. Furthermore, lack of CD103 had no effect on DC or T(reg) recruitment or retention within the large intestine

Authenticating the writings of Julius Caesar

In this paper, we shed new light on the authenticity of the Corpus Caesarianum, a group of five commentaries describing the campaigns of Julius Caesar (100–44 BC), the founder of the Roman empire. While Caesar himself has authored at least part of these commentaries, the authorship of the rest of the texts remains a puzzle that has persisted for nineteen centuries. In particular, the role of Caesar’s general Aulus Hirtius, who has claimed a role in shaping the corpus, has remained in contention. Determining the authorship of documents is an increasingly important authentication problem in information and computer science, with valuable applications, ranging from the domain of art history to counter-terrorism research. We describe two state-of-the-art authorship verification systems and benchmark them on 6 present-day evaluation corpora, as well as a Latin benchmark dataset. Regarding Caesar’s writings, our analyses allow us to establish that Hirtius’s claims to part of the corpus must be considered legitimate. We thus demonstrate how computational methods constitute a valuable methodological complement to traditional, expert-based approaches to document authentication

Responses of Tectal Neurons to Contrasting Stimuli: An Electrophysiological Study in the Barn Owl

The saliency of visual objects is based on the center to background contrast. Particularly objects differing in one feature from the background may be perceived as more salient. It is not clear to what extent this so called “pop-out” effect observed in humans and primates governs saliency perception in non-primates as well. In this study we searched for neural-correlates of pop-out perception in neurons located in the optic tectum of the barn owl. We measured the responses of tectal neurons to stimuli appearing within the visual receptive field, embedded in a large array of additional stimuli (the background). Responses were compared between contrasting and uniform conditions. In a contrasting condition the center was different from the background while in the uniform condition it was identical to the background. Most tectal neurons responded better to stimuli in the contrsating condition compared to the uniform condition when the contrast between center and background was the direction of motion but not when it was the orientation of a bar. Tectal neurons also preferred contrasting over uniform stimuli when the center was looming and the background receding but not when the center was receding and the background looming. Therefore, our results do not support the hypothesis that tectal neurons are sensitive to pop-out per-se. The specific sensitivity to the motion contrasting stimulus is consistent with the idea that object motion and not large field motion (e.g., self-induced motion) is coded in the neural responses of tectal neurons

Evaluating stratospheric ozone and water vapour changes in CMIP6 models from 1850 to 2100

Stratospheric ozone and water vapour are key components of the Earth system, and past and future changes to both have important impacts on global and regional climate. Here, we evaluate long-term changes in these species from the pre-industrial period (1850) to the end of the 21st century in Coupled Model Intercomparison Project phase 6 (CMIP6) models under a range of future emissions scenarios. There is good agreement between the CMIP multi-model mean and observations for total column ozone (TCO), although there is substantial variation between the individual CMIP6 models. For the CMIP6 multi-model mean, global mean TCO has increased from ∼300 DU in 1850 to ∼ 305 DU in 1960, before rapidly declining in the 1970s and 1980s following the use and emission of halogenated ozone-depleting substances (ODSs). TCO is projected to return to 1960s values by the middle of the 21st century under the SSP2-4.5, SSP3-7.0, SSP4-3.4, SSP4-6.0, and SSP5-8.5 scenarios, and under the SSP3-7.0 and SSP5-8.5 scenarios TCO values are projected to be ∼ 10 DU higher than the 1960s values by 2100. However, under the SSP1-1.9 and SSP1-1.6 scenarios, TCO is not projected to return to the 1960s values despite reductions in halogenated ODSs due to decreases in tropospheric ozone mixing ratios. This global pattern is similar to regional patterns, except in the tropics where TCO under most scenarios is not projected to return to 1960s values, either through reductions in tropospheric ozone under SSP1-1.9 and SSP1-2.6, or through reductions in lower stratospheric ozone resulting from an acceleration of the Brewer-Dobson circulation under other Shared Socioeconomic Pathways (SSPs). In contrast to TCO, there is poorer agreement between the CMIP6 multi-model mean and observed lower stratospheric water vapour mixing ratios, with the CMIP6 multi-model mean underestimating observed water vapour mixing ratios by ∼ 0.5 ppmv at 70 hPa. CMIP6 multi-model mean stratospheric water vapour mixing ratios in the tropical lower stratosphere have increased by ∼ 0.5 ppmv from the pre-industrial to the present-day period and are projected to increase further by the end of the 21st century. The largest increases (∼ 2 ppmv) are simulated under the future scenarios with the highest assumed forcing pathway (e.g. SSP5-8.5). Tropical lower stratospheric water vapour, and to a lesser extent TCO, shows large variations following explosive volcanic eruptions

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta