Multiplexed Illumina sequencing libraries from picogram quantities of DNA

Background: High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. Results: We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Conclusions: Application of this method allows whole genome studies from samples where material or yields are limiting

CitDet: A Benchmark Dataset for Citrus Fruit Detection

In this letter, we present a new dataset to advance the state of the art in detecting citrus fruit and accurately estimate yield on trees affected by the Huanglongbing (HLB) disease in orchard environments via imaging. Despite the fact that significant progress has been made in solving the fruit detection problem, the lack of publicly available datasets has complicated direct comparison of results. For instance, citrus detection has long been of interest in the agricultural research community, yet there is an absence of work, particularly involving public datasets of citrus affected by HLB. To address this issue, we enhance state-of-the-art object detection methods for use in typical orchard settings. Concretely, we provide high-resolution images of citrus trees located in an area known to be highly affected by HLB, along with high-quality bounding box annotations of citrus fruit. Fruit on both the trees and the ground are labeled to allow for identification of fruit location, which contributes to advancements in yield estimation and potential measure of HLB impact via fruit drop. The dataset consists of over 32,000 bounding box annotations for fruit instances contained in 579 high-resolution images. In summary, our contributions are the following: (i) we introduce a novel dataset along with baseline performance benchmarks on multiple contemporary object detection algorithms, (ii) we show the ability to accurately capture fruit location on tree or on ground, and finally (ii) we present a correlation of our results with yield estimations.Comment: Submitted to IEEE Robotics and Automation Letters (RA-L

What Next-Generation 21 cm Power Spectrum Measurements Can Teach Us About the Epoch of Reionization

A number of experiments are currently working towards a measurement of the 21 cm signal from the Epoch of Reionization. Whether or not these experiments deliver a detection of cosmological emission, their limited sensitivity will prevent them from providing detailed information about the astrophysics of reionization. In this work, we consider what types of measurements will be enabled by a next-generation of larger 21 cm EoR telescopes. To calculate the type of constraints that will be possible with such arrays, we use simple models for the instrument, foreground emission, and the reionization history. We focus primarily on an instrument modeled after the $\sim 0.1~\rm{km}^2$ collecting area Hydrogen Epoch of Reionization Array (HERA) concept design, and parameterize the uncertainties with regard to foreground emission by considering different limits to the recently described "wedge" footprint in k-space. Uncertainties in the reionization history are accounted for using a series of simulations which vary the ionizing efficiency and minimum virial temperature of the galaxies responsible for reionization, as well as the mean free path of ionizing photons through the IGM. Given various combinations of models, we consider the significance of the possible power spectrum detections, the ability to trace the power spectrum evolution versus redshift, the detectability of salient power spectrum features, and the achievable level of quantitative constraints on astrophysical parameters. Ultimately, we find that $0.1~\rm{km}^2$ of collecting area is enough to ensure a very high significance ($\gtrsim30\sigma$) detection of the reionization power spectrum in even the most pessimistic scenarios. This sensitivity should allow for meaningful constraints on the reionization history and astrophysical parameters, especially if foreground subtraction techniques can be improved and successfully implemented.Comment: 27 pages, 18 figures, updated SKA numbers in appendi

Saccadic Eye Movement Characteristics in Adult Niemann-Pick Type C Disease: Relationships with Disease Severity and Brain Structural Measures

Niemann-Pick Type C disease (NPC) is a rare genetic disorder of lipid metabolism. A parameter related to horizontal saccadic peak velocity was one of the primary outcome measures in the clinical trial assessing miglustat as a treatment for NPC. Neuropathology is widespread in NPC, however, and could be expected to affect other saccadic parameters. We compared horizontal saccadic velocity, latency, gain, antisaccade error percentage and self-paced saccade generation in 9 adult NPC patients to data from 10 age-matched controls. These saccadic measures were correlated with appropriate MRI-derived brain structural measures (e.g., dorsolateral prefrontal cortex, frontal eye fields, supplemental eye fields, parietal eye fields, pons, midbrain and cerebellar vermis) and with measures of disease severity and duration. The best discriminators between groups were reflexive saccade gain and the two volitional saccade measures. Gain was also the strongest correlate with disease severity and duration. Most of the saccadic measures showed strongly significant correlations with neurophysiologically appropriate brain regions. While our patient sample is small, the apparent specificity of these relationships suggests that as new diagnostic methods and treatments become available for NPC, a broader range of saccadic measures may be useful tools for the assessment of disease progression and treatment efficacy.No external funding was received for this study. JCLL self-funded computational, travel and accommodation costs to conduct his component of this research in Melbourne

High-resolution Xist binding maps reveal 2-step spreading during X-inactivation

The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes1-3. During XCI, Xist coats the future inactive X (Xi)4 and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic)5. How Xist spreads silencing on a 150 Mb scale is unclear. Here we generate high-resolution maps of Xist binding on the X chromosome across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism, initially targeting gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but may concentrate near escapee boundaries. Xist binding is linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped off Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time-scale of hours instead of days, suggesting a previously primed Xi chromatin state. We conclude that Xist spreading takes distinct stage-specific forms: During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and -poor regions

Low-Frequency Radio Recombination Lines Away From the Inner Galactic Plane

Diffuse radio recombination lines (RRLs) in the Galaxy are possible foregrounds for redshifted 21~cm experiments. We use EDGES drift scans centered at $-26.7^o$~declination to characterize diffuse RRLs across the southern sky. We find RRLs averaged over the large antenna beam ($72^o \times 110^o$) reach minimum amplitudes between right ascensions~2-6~h. In this region, the C$\alpha$ absorption amplitude is $33\pm11$~mK (1$\sigma$) averaged over 50-87~MHz ($27\gtrsim z \gtrsim15$ for the 21~cm line) and increases strongly as frequency decreases. C$\beta$ and H$\alpha$ lines are consistent with no detection with amplitudes of $13\pm14$ and $12\pm10$~mK (1$\sigma$), respectively. At 108-124.5~MHz ($z\approx11$) in the same region, we find no evidence for carbon or hydrogen lines at the noise level of 3.4~mK (1$\sigma$). Conservatively assuming observed lines come broadly from the diffuse interstellar medium, as opposed to a few compact regions, these amplitudes provide upper limits on the intrinsic diffuse lines. The observations support expectations that Galactic RRLs can be neglected as significant foregrounds for a large region of sky until redshifted 21~cm experiments, particularly those targeting Cosmic Dawn, move beyond the detection phase. We fit models of the spectral dependence of the lines averaged over the large beam of EDGES, which may contain multiple line sources with possible line blending, and find that including degrees of freedom for expected smooth, frequency-dependent deviations from local thermodynamic equilibrium (LTE) is preferred over simple LTE assumptions for C$\alpha$ and H$\alpha$ lines. For C$\alpha$ we estimate departure coefficients $0.79<b_n\beta_n<4.5$ along the inner Galactic Plane and $0<b_n\beta_n<2.3$ away from the inner Galactic Plane.Comment: 25 pages, 14 figures, 3 tables, submitted to AA

Microsecond Carrier Lifetimes, Controlled p-Doping, and Enhanced Air Stability in Low-Bandgap Metal Halide Perovskites.

Mixed lead-tin halide perovskites have sufficiently low bandgaps (∼1.2 eV) to be promising absorbers for perovskite-perovskite tandem solar cells. Previous reports on lead-tin perovskites have typically shown poor optoelectronic properties compared to neat lead counterparts: short photoluminescence lifetimes (<100 ns) and low photoluminescence quantum efficiencies (<1%). Here, we obtain films with carrier lifetimes exceeding 1 μs and, through addition of small quantities of zinc iodide to the precursor solutions, photoluminescence quantum efficiencies under solar illumination intensities of 2.5%. The zinc additives also substantially enhance the film stability in air, and we use cross-sectional chemical mapping to show that this enhanced stability is because of a reduction in tin-rich clusters. By fabricating field-effect transistors, we observe that the introduction of zinc results in controlled p-doping. Finally, we show that zinc additives also enhance power conversion efficiencies and the stability of solar cells. Our results demonstrate substantially improved low-bandgap perovskites for solar cells and versatile electronic applications.EPSRC (EP/M005143/1 and DTP funding) Royal Society ER

Representations of the family in postwar British amateur film: family histories in the Lane and Scrutton collection at the East Anglian Film Archive

This article examines the construction of the postwar British family in amateur film with reference to the Sidney Lane and Cecil Scrutton collection held at the East Anglian Film Archive (EAFA), particularly the films covering 1948 – 1961. Heather Norris Nicholson argues that home movies contribute to 'an understanding of leisure and visual-related practices of consumption as well as the social processes by which people came to give themselves, and others, identities' in the mid-twentieth century (Nicholson, 2004, p. 323). By considering the social and historical contexts in which these home movies were produced, and using accompanying notes by one of the filmmaker’s sons, the leisure time films of Lane and Scrutton can be analysed in order to understand how the amateur cine hobby ideologically constructed family, community and national identity in postwar Britain. The images of Christmas parties, daytrips and holidays in these films reveal much about this particular family, and are therefore very illuminating to the social historian and film scholar of today

Annual cycle observations of aerosols capable of ice formation in central Arctic clouds

The Arctic is warming faster than anywhere else on Earth, prompting glacial melt, permafrost thaw, and sea ice decline. These severe consequences induce feedbacks that contribute to amplified warming, affecting weather and climate globally. Aerosols and clouds play a critical role in regulating radiation reaching the Arctic surface. However, the magnitude of their effects is not adequately quantified, especially in the central Arctic where they impact the energy balance over the sea ice. Specifically, aerosols called ice nucleating particles (INPs) remain understudied yet are necessary for cloud ice production and subsequent changes in cloud lifetime, radiative effects, and precipitation. Here, we report observations of INPs in the central Arctic over a full year, spanning the entire sea ice growth and decline cycle. Further, these observations are size-resolved, affording valuable information on INP sources. Our results reveal a strong seasonality of INPs, with lower concentrations in the winter and spring controlled by transport from lower latitudes, to enhanced concentrations of INPs during the summer melt, likely from marine biological production in local open waters. This comprehensive characterization of INPs will ultimately help inform cloud parameterizations in models of all scales