Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA.

High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how these individual events are combined into complete RNA transcript isoforms. Because of this shortfall, long-distance information is required to complement short-read sequencing to analyze transcriptomes on the level of full-length RNA transcript isoforms. While long-read sequencing technology can provide this long-distance information, there are issues with both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long-read sequencing technologies that prevent their widespread adoption. Briefly, PacBio sequencers produce low numbers of reads with high accuracy, while ONT sequencers produce higher numbers of reads with lower accuracy. Here, we introduce and validate a long-read ONT-based sequencing method. At the same cost, our Rolling Circle Amplification to Concatemeric Consensus (R2C2) method generates more accurate reads of full-length RNA transcript isoforms than any other available long-read sequencing method. These reads can then be used to generate isoform-level transcriptomes for both genome annotation and differential expression analysis in bulk or single-cell samples

Higher-Order Angular Galaxy Correlations in the SDSS: Redshift and Color Dependence of non-Linear Bias

We present estimates of the N-point galaxy, area-averaged, angular correlation functions $\bar{\omega}_{N}$($\theta$) for $N$ = 2,...,7 for galaxies from the fifth data release of the Sloan Digital Sky Survey. Our parent sample is selected from galaxies with $18 \leq r < 21$, and is the largest ever used to study higher-order correlations. We subdivide this parent sample into two volume limited samples using photometric redshifts, and these two samples are further subdivided by magnitude, redshift, and color (producing early- and late-type galaxy samples) to determine the dependence of $\bar{\omega}_{N}$($\theta$) on luminosity, redshift, and galaxy-type. We measure $\bar{\omega}_{N}$($\theta$) using oversampling techniques and use them to calculate the projected, $s_{N}$. Using models derived from theoretical power-spectra and perturbation theory, we measure the bias parameters $b_1$ and $c_2$, finding that the large differences in both bias parameters ($b_1$ and $c_2$) between early- and late-type galaxies are robust against changes in redshift, luminosity, and $\sigma_8$, and that both terms are consistently smaller for late-type galaxies. By directly comparing their higher-order correlation measurements, we find large differences in the clustering of late-type galaxies at redshifts lower than 0.3 and those at redshifts higher than 0.3, both at large scales ($c_2$ is larger by $\sim0.5$ at $z > 0.3$) and small scales (large amplitudes are measured at small scales only for $z > 0.3$, suggesting much more merger driven star formation at $z > 0.3$). Finally, our measurements of $c_2$ suggest both that $\sigma_8 < 0.8$ and $c_2$ is negative.Comment: 46 pages, 19 figures, Accepted to Ap

Calcium and magnesium absorption and retention by growing goats offered diets with different calcium sources

Calcium addition is necessary in order to balance the high phosphorus concentrations that are characteristic of high-concentrate ruminant diets. However, calcium sources differ in their bioavailability. Our objective was to determine apparent calcium and magnesium absorption and retention in goats offered diets containing different sources of calcium. Spanish-Boer goats (n = 18; 19.6 ± 1.88 kg) were stratified by body weight (BW) and sex and randomized to dietary treatments consisting of Purina Antlermax 16 containing either calcium carbonate (CC), Calmin (CM) or Milk Cal (MC). Goats were adapted to a control, corn-based high-concentrate diet on pasture and then moved to individual 1.0 × 1.5-m pens with plastic coated expanded metal floors, and adjusted to their respective diets along with removal of hay from the diet over a 7-d period. Goats were then offered their respective diets at a total of 2% of BW in equal feedings at 8:30 AM and 5:00 PM for an additional 14-d adaption period to diet and facilities followed by a 7-d collection of total urine and feces. Data were analyzed using PROC MIXED of SAS. Calcium and magnesium intake were not different (P ≥ 0.12) among diets. Calcium and magnesium apparent absorption and retention (g/d and % of intake) were greatest (P \u3c 0.05) in goats offered CC and did not differ (P ≥ 0.20) between goats offered the CM and MC diets. Therefore, calcium and magnesium were more available for goats from the diet containing calcium carbonate compared with diets containing Calmin and Milk Cal

Discussion of Bar Applicants Taking Noncommunist Oath

With responses from two Bar members

Electrochemical Solutions for Advanced Life Support

The Oxygen Generating Assembly (OGA) on-board the International Space Station (ISS) employs a polymer electrolyte membrane (PEM) water electrolysis cell stack to electrochemically dissociate water into its two components oxygen and hydrogen. Oxygen is provided to the cabin atmosphere for crew respiration while the hydrogen is delivered to a carbon dioxide reduction system to recover oxygen as water. The design of the OGA evolved over a number of years to arrive at the system solution that is currently operational on ISS. Future manned missions to space will require advanced technologies that eliminate the need for resupply from earth and feature in-situ resource utilization to sustain crew life and to provide useful materials to the crew. The architects planning such missions should consider all potential solutions at their disposal to arrive at an optimal vehicle solution that minimizes crew maintenance time, launch weight, installed volume and energy consumption demands. Skyre is developing new technologies through funding from NASA, the Department of Energy, and internal investment based on PEM technology that could become an integral part of these new vehicle solutions. At varying stages of Technology Readiness Level (TRL) are: an oxygen concentrator and compressor that can separate oxygen from an air stream and provide an enriched oxygen resource for crew medical use and space suit recharge without any moving parts in the pure oxygen stream; a regenerative carbon dioxide removal system featuring a PEM-based sorbent regenerator; a carbon dioxide reduction system that electrochemically produces organic compounds that could serve as fuels or as a useful intermediary to more beneficial compounds; and an electrochemical hydrogen separator and compressor for hydrogen recycle. The technical maturity of these projects is presented along with pertinent performance test data that could be beneficial in future study efforts

Analytical Chemistry of Plastic Debris: Sampling, Methods, and Instrumentation

Approaches for the collection and analysis of plastic debris in environmental matrices are rapidly evolving. Such plastics span a continuum of sizes, encompassing large (macro-), medium (micro-, typically defined as particles between 1 μm and 5 mm), and smaller (nano-) plastics. All are of environmental relevance. Particle sizes are dynamic. Large plastics may fragment over time, while smaller particles may agglomerate in the field. The diverse morphologies (fragment, fiber, sphere) and chemical compositions of microplastics further complicate their characterization. Fibers are of growing interest and present particular analytical challenges due to their narrow profiles. Compositional classes of emerging concern include tire wear, paint chips, semisynthetics (e.g., rayon), and bioplastics. Plastics commonly contain chemical additives and fillers, which may alter their toxicological potency, behavior (e.g., buoyancy), or detector response (e.g., yield fluorescence) during analysis. Field sampling methods often focus on \u3e20 μm and even \u3e300 μm sized particles and will thus not capture smaller microplastics (which may be most abundant and bioavailable). Analysis of a limited subgroup (selected polymer types, particle sizes, or shapes) of microplastics, while often operationally necessary, can result in an underestimation of actual sample content. These shortcomings complicate calls for toxicological studies of microplastics to be based on “environmentally relevant concentrations.” Sample matrices of interest include water (including wastewater, ice, snow), sediment (soil, dust, wastewater sludge), air, and biota. Properties of the environment, and of the particles themselves, may concentrate plastic debris in select zones (e.g., gyres, shorelines, polar ice, wastewater sludge). Sampling designs should consider such patchy distributions. Episodic releases due to weather and anthropogenic discharges should also be considered. While water grab samples and sieving are commonplace, novel techniques for microplastic isolation, such as continuous flow centrifugation, show promise. The abundance of nonplastic particulates (e.g., clay, detritus, biological material) in samples interferes with microplastic detection and characterization. Their removal is typically accomplished using a combination of gravity separation and oxidative digestion (including strong bases, peroxide, enzymes); unfortunately, aggressive treatments may damage more labile plastics. Microscope-based infrared or Raman detection is often applied to provide polymer chemistry and morphological data for individual microplastic particles. However, the sheer number of particles in many samples presents logistical hurdles. In response, instruments have been developed that employ detector arrays and rapid scanning lasers. The addition of dyes to stain particulates may facilitate spectroscopic detection of some polymer types. Most researchers provide microplastic data in the form of the abundances of polymer types within particle size, polymer, and morphology classes. Polymer mass data in samples remain rare but are essential to elucidating fate. Rather than characterizing individual particles in samples, solvent extraction (following initial sample prep, such as sediment size class sorting), combined with techniques such as thermoanalysis (e.g., pyrolysis), has been used to generate microplastic mass data. However, this may obviate the acquisition of individual particle morphology and compositional information. Alternatively, some techniques (e.g., electron and atomic force microscopy and matrix-assisted laser desorption mass spectrometry) are adept at providing highly detailed data on the size, morphology, composition, and surface chemistry of select particles. Ultimately, the analyst must select the approach best suited for their study goals. Robust quality control elements are also critical to evaluate the accuracy and precision of the sampling and analysis techniques. Further, improved efforts are required to assess and control possible sample contamination due to the ubiquitous distribution of microplastics, especially in indoor environments where samples are processed.https://scholarworks.wm.edu/vimsbooks/1198/thumbnail.jp

HST Images Flash Ionization of Old Ejecta by the 2011 Eruption of Recurrent Nova T Pyxidis

T Pyxidis is the only recurrent nova surrounded by knots of material ejected in previous outbursts. Following the eruption that began on 2011 April 14.29, we obtained seven epochs (from 4 to 383 days after eruption) of Hubble Space Telescope narrowband Ha images of T Pyx . The flash of radiation from the nova event had no effect on the ejecta until at least 55 days after the eruption began. Photoionization of hydrogen located north and south of the central star was seen 132 days after the beginning of the eruption. That hydrogen recombined in the following 51 days, allowing us to determine a hydrogen atom density of at least 7e5 cm^-3 - at least an order of magnitude denser than the previously detected, unresolved [NII] knots surrounding T Pyx. Material to the northwest and southeast was photoionized between 132 and 183 days after the eruption began. 99 days later that hydrogen had recombined. Both then (282 days after outburst) and 101 days later, we detected almost no trace of hydrogen emission around T Pyx. There is a large reservoir of previously unseen, cold diffuse hydrogen overlapping the previously detected, [NII] - emitting knots of T Pyx ejecta. The mass of this newly detected hydrogen is probably an order of magnitude larger than that of the [NII] knots. We also determine that there is no significant reservoir of undetected ejecta from the outer boundaries of the previously detected ejecta out to about twice that distance, near the plane of the sky. The lack of distant ejecta is consistent with the Schaefer et al (2010) scenario for T Pyx, in which the star underwent its first eruption within five years of 1866 after many millennia of quiescence, followed by the six observed recurrent nova eruptions since 1890. This lack of distant ejecta is not consistent with scenarios in which T Pyx has been erupting continuously as a recurrent nova for many centuries or millennia.Comment: 27 pages, 10 figures, submitted to the Astrophysical Journa

Validation of Annual Growth-Zone Formation in Gray Triggerfish Balistes capriscus Dorsal Spines, Fin Rays, and Vertebrae

The goal of this study was to validate annual growth-zone formation in the gray triggerfish Balistes capriscus dorsal spines, fin rays, and vertebrae. Adult gray triggerfish (n = 4) were chemically marked by injecting with 50 mg of oxytetracycline (OTC) per kilogram body mass and reared in a 2,300-liter aquaculture tank. Fish were exposed to ambient light and water temperature mimicked bottom temperatures observed at an approximately 30-m depth in the northern Gulf of Mexico. Fish died after 262 d and their first dorsal spines, pectoral fin rays, and vertebrae were extracted and sectioned. One translucent zone formed distal to the OTC mark in all hardpart types during the study period. Additional fin rays and vertebrae with corresponding dorsal spines were sampled from fish (n = 27 and 59, respectively) during fishery-independent surveys to compare translucent zone counts between hardparts. There was a significant difference between translucent zone counts between fin ray and dorsal spine sections (tdf = 1,25 = 23.15, P = 0.004). Fin ray counts on average were one zone greater than dorsal spine counts. Translucent zone counts in vertebrae were similar to those counted in dorsal spines with no significant difference between structures (tdf = 1,57 = 1.90, P = 0.062). The percentage of dorsal spines with translucent margins increased in winter months, peaking in February, and dropped to the lowest values in summer. The combined results of this study validate annual translucent zone formation in gray triggerfish hardparts, with dorsal spines being the preferred ageing structure for production ageing

Impact of the SPOP Mutant Subtype on the Interpretation of Clinical Parameters in Prostate Cancer.

Purpose: Molecular characterization of prostate cancer, including The Cancer Genome Atlas, has revealed distinct subtypes with underlying genomic alterations. One of these core subtypes, SPOP (speckle-type POZ protein) mutant prostate cancer, has previously only been identifiable via DNA sequencing, which has made the impact on prognosis and routinely used risk stratification parameters unclear. Methods: We have developed a novel gene expression signature, classifier (Subclass Predictor Based on Transcriptional Data), and decision tree to predict the SPOP mutant subclass from RNA gene expression data and classify common prostate cancer molecular subtypes. We then validated and further interrogated the association of prostate cancer molecular subtypes with pathologic and clinical outcomes in retrospective and prospective cohorts of 8,158 patients. Results: The subclass predictor based on transcriptional data model showed high sensitivity and specificity in multiple cohorts across both RNA sequencing and microarray gene expression platforms. We predicted approximately 8% to 9% of cases to be SPOP mutant from both retrospective and prospective cohorts. We found that the SPOP mutant subclass was associated with lower frequency of positive margins, extraprostatic extension, and seminal vesicle invasion at prostatectomy; however, SPOP mutant cancers were associated with higher pretreatment serum prostate-specific antigen (PSA). The association between SPOP mutant status and higher PSA level was validated in three independent cohorts. Despite high pretreatment PSA, the SPOP mutant subtype was associated with a favorable prognosis with improved metastasis-free survival, particularly in patients with high-risk preoperative PSA levels. Conclusion: Using a novel gene expression model and a decision tree algorithm to define prostate cancer molecular subclasses, we found that the SPOP mutant subclass is associated with higher preoperative PSA, less adverse pathologic features, and favorable prognosis. These findings suggest a paradigm in which the interpretation of common risk stratification parameters, particularly PSA, may be influenced by the underlying molecular subtype of prostate cancer