Spatially resolved transcriptomics (SRT) is a growing field that links gene expression to anatomical context. SRT approaches that use next-generation sequencing (NGS) combine RNA sequencing with histological or fluorescent imaging to generate spatial maps of gene expression in intact tissue sections. These technologies directly couple gene expression measurements with high-resolution histological or immunofluorescent images that contain rich morphological information about the tissue under study. While broad access to NGS-based spatial transcriptomic technology is now commercially available through the Visium platform from the vendor 10× Genomics, computational tools for extracting image-derived metrics for integration with gene expression data remain limited. We developed VistoSeg as a MATLAB pipeline to process, analyze and interactively visualize the high-resolution images generated in the Visium platform. VistoSeg outputs can be easily integrated with accompanying transcriptomic data to facilitate downstream analyses in common programing languages including R and Python. VistoSeg provides user-friendly tools for integrating image-derived metrics from histological and immunofluorescent images with spatially resolved gene expression data. Integration of this data enhances the ability to understand the transcriptional landscape within tissue architecture. VistoSeg is freely available at http://research.libd.org/VistoSeg/.

The interaction of relativistically intense lasers with opaque targets represents a highly non-linear, multi-dimensional parameter space. This limits the utility of sequential 1D scanning of experimental parameters for the optimization of secondary radiation, although to-date this has been the accepted methodology due to low data acquisition rates. High repetition-rate (HRR) lasers augmented by machine learning present a valuable opportunity for efficient source optimization. Here, an automated, HRR-compatible system produced high-fidelity parameter scans, revealing the influence of laser intensity on target pre-heating and proton generation. A closed-loop Bayesian optimization of maximum proton energy, through control of the laser wavefront and target position, produced proton beams with equivalent maximum energy to manually optimized laser pulses but using only 60% of the laser energy. This demonstration of automated optimization of laser-driven proton beams is a crucial step towards deeper physical insight and the construction of future radiation sources.

We present the development and characterization of a high-stability, multi-material, multi-thickness tape-drive target for laser-driven acceleration at repetition rates of up to 100 Hz. The tape surface position was measured to be stable on the sub-micrometre scale, compatible with the high-numerical aperture focusing geometries required to achieve relativistic intensity interactions with the pulse energy available in current multi-Hz and near-future higher repetition-rate lasers ($>$kHz). Long-term drift was characterized at 100 Hz demonstrating suitability for operation over extended periods. The target was continuously operated at up to 5 Hz in a recent experiment for 70,000 shots without intervention by the experimental team, with the exception of tape replacement, producing the largest data-set of relativistically intense laser–solid foil measurements to date. This tape drive provides robust targetry for the generation and study of high-repetition-rate ion beams using next-generation high-power laser systems, also enabling wider applications of laser-driven proton sources.

This paper provides an overview and appraisal of the International Design Engineering Annual (IDEA) challenge - a virtually hosted design hackathon run with the aim of generating a design research dataset that can provide insights into design activities at virtually hosted hackathons. The resulting dataset consists of 200+ prototypes with over 1300 connections providing insights into the products, processes and people involved in the design process. The paper also provides recommendations for future deployments of virtual hackathons for design research.

Crop rotation is a non-chemical strategy adopted by farmers to manage weeds. However, not all crops in a rotation are equally profitable. Thus, there is potentially a trade-off between the costs and benefits of this strategy. The objective of the current study is to quantify this trade-off for the rotational control of an important weed (Alopecurus myosuroides). Data from 745 farms were used to parameterize a farm-level mixed-integer goal-programming model of the economics of spring cropping for weed control in UK agriculture. On average, the short-term loss of profit from spring cropping is greater than the benefits in terms of reduced herbicide usage and yield increases. These costs are greater when weed densities are low, so that spring cropping is an expensive strategy in the early stages of an infestation. However, there is a great deal of farm-to-farm variation: factors such as soil type and farm size are important and the current study highlights that economic modelling at the farm level is important in enabling farmers to make informed decisions. In general, however, if spring cropping is to be a successful strategy then the benefits to farmers will be in terms of long-term reductions in weed densities, but this will be at the expense of short-term profitability.

Stroke is a leading cause of morbidity and mortality in the US, with secondary damage following the initial insult contributing significantly to overall poor outcome. Prior investigations have shown that the metabolism of certain polyamines such as spermine, spermidine, and putrescine are elevated in ischemic parenchyma, resulting in an increase in their metabolite concentration. Polyamine metabolites tend to be cytotoxic, leading to neuronal injury in the penumbra following stroke and expansion of the area of infarcted tissue. Although the precise mechanism is unclear, the presence of reactive aldehydes produced through polyamine metabolism, such as 3-aminopropanal and acrolein, have been shown to correlate with the incidence of cerebral vasospasm, disruption of oxidative metabolism and mitochondrial functioning, and disturbance of cellular calcium ion channels. Regulation of the polyamine metabolic pathway, therefore, may have the potential to limit injury following cerebral ischemia. To this end, we review this pathway in detail with an emphasis on clinical applicability.

The energy transfer by stimulated Brillouin backscatter from a long pump pulse (15 ps) to a short seed pulse (1 ps) has been investigated in a proof-of-principle demonstration experiment. The two pulses were both amplified in different beamlines of a Nd:glass laser system, had a central wavelength of 1054 nm and a spectral bandwidth of 2 nm, and crossed each other in an underdense plasma in a counter-propagating geometry, off-set by $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}10^\circ $. It is shown that the energy transfer and the wavelength of the generated Brillouin peak depend on the plasma density, the intensity of the laser pulses, and the competition between two-plasmon decay and stimulated Raman scatter instabilities. The highest obtained energy transfer from pump to probe pulse is 2.5%, at a plasma density of $0.17 n_{cr}$, and this energy transfer increases significantly with plasma density. Therefore, our results suggest that much higher efficiencies can be obtained when higher densities (above $0.25 n_{cr}$) are used.

We surveyed 399 US acute care hospitals regarding availability of on-site Legionella testing; 300 (75.2%) did not offer Legionella testing on site. Availability varied according to hospital size and geographic location. On-site access to testing may improve detection of Legionnaires disease and inform patient management and prevention efforts.

Infect Control Hosp Epidemiol 2014;35(7):898–900

Serotype 1 Streptococcus pneumoniae is a cause of invasive pneumococcal disease (IPD) worldwide and has been associated with IPD outbreaks, while carriage is rarely detected in healthy adults or children. This study details an Australian multi-state and territory outbreak of serotype 1 S. pneumoniae IPD between 2010 and 2012. Molecular characterization demonstrated the outbreak was largely due to the clonal expansion of sequence type 306, MLVA type 261 S. pneumoniae serotype 1.

The European Fire Ant, Myrmica rubra (Linnaeus) (Hymenoptera: Formicidae), is an invasive stinging ant that has only recently been recorded in Newfoundland, Canada. The goal of the present study was to investigate the origins of M. rubra ants in Newfoundland. We analysed mtDNA sequences from the cytochrome b and cytochrome c oxidase I genes of ants from six localities in Newfoundland, and neighbouring regions of eastern Canada and the United States of America, and compared them with mtDNA data from a recent wide-scale phylogeographical study of the ant throughout Europe. There is evidence for at least four distinct sources of ants on the island. The putative routes of colonisation of the ant to Newfoundland are discussed, as are the possible reasons why it went undiscovered for many decades.

The Dawn spacecraft orbited Asteroid (4) Vesta for a year, and returned disk-resolved images and spectra covering visible and near-infrared wavelengths at scales as high as 20 m/pix. The visible geometric albedo of Vesta is ~ 0.36. The disk-integrated phase function of Vesta in the visible wavelengths derived from Dawn approach data, previous ground-based observations, and Rosetta OSIRIS observations is consistent with an IAU H-G phase law with H=3.2 mag and G=0.28. Hapke's modeling yields a disk-averaged single-scattering albedo of 0.50, an asymmetry factor of -0.25, and a roughness parameter of ~20 deg at 700 nm wavelength. Vesta's surface displays the largest albedo variations observed so far on asteroids, ranging from ~0.10 to ~0.76 in geometric albedo in the visible wavelengths. The phase function of Vesta displays obvious systematic variations with respect to wavelength, with steeper slopes within the 1- and 2-micron pyroxene bands, consistent with previous ground-based observations and laboratory measurement of HED meteorites showing deeper bands at higher phase angles. The relatively high albedo of Vesta suggests significant contribution of multiple scattering. The non-linear effect of multiple scattering and the possible systematic variations of phase function with albedo across the surface of Vesta may invalidate the traditional algorithm of applying photometric correction on airless planetary surfaces.

Our adaptive optics observations of nearby AGN at spatial resolutions as small as 0.″085 show strong evidence for recent, but no longer active, nuclear star formation. We begin by describing observations that highlight two contrasting methods by which gas can flow into the central tens of parsecs. Gas accumulation in this region will inevitably lead to a starburst, and we discuss the evidence for such events. We then turn to the impact of stellar evolution on the further inflow of gas by combining a phenomenological approach with analytical modelling and hydrodynamic simulations. These complementary perspectives paint a picture in which all the processes are ultimately regulated by the mass accretion rate into the central hundred parsecs, and the ensuing starburst that occurs there. The resulting supernovae delay accretion by generating a starburst wind, which leaves behind a clumpy interstellar medium. This provides an ideal environment for slower stellar outflows to accrete inwards and form a dense turbulent disk on scales of a few parsecs. Such a scenario may resolve the discrepancy between the larger scale structure seen with adaptive optics and the small-scale structure seen with VLTI.

NASA's Deep Space 1 (DSl) spacecraft successfully encountered comet 19P/Borrelly near perihelion and the Miniature Integrated Camera and Spectrometer (MICAS) imaging system onboard DS1 returned the first high-resolution images of a Jupiter-family comet nucleus and surrounding environment. The images span solar phase angles from 88° to 52°, providing stereoscopic coverage of the dust coma and nucleus. Numerous surface features are revealed on the 8-km long nucleus in the highest resolution images (47-58 m/pixel). A smooth, broad basin containing brighter regions and mesa-like structures is present in the central part of the nucleus that seems to be the source of jet-like dust features seen in the coma. High ridges seen along the jagged terminator lead to rugged terrain on both ends of the nucleus containing dark patches and smaller series of parallel grooves. No evidence of impact craters with diameters larger than about 200-m are present, indicating a young and active surface. The nucleus is very dark with albedo variations from 0.007 to 0.035. Short-wavelength, infrared spectra from 1.3 to 2.6 μm revealed a hot, dry surface consistent with less than about 10% actively sublimating. Two types of dust features are seen: broad fans and highly collimated “jets” in the sunward hemisphere that can be traced to the surface. The source region of the main jet feature, which resolved into at least three smaller “jets” near the surface, is consistent with an area around the rotation pole that is constantly illuminated by the sun during the encounter. Within a few nuclear radii, entrained dust is rapidly accelerated and fragmented and geometrical effects caused from extended source regions are present, as evidenced in radial intensity profiles centered on the jet features that show an increase in source strength with increasing cometocentric distance. Asymmetries in the dust from dayside to nightside are pronounced and may show evidence of lateral flow transporting dust to structures observed in the nightside coma. A summary of the initial results of the Deep Space 1 Mission is provided, highlighting the new knowledge that has been gained thus far.