Robust Machine Learning Applied to Astronomical Datasets I: Star-Galaxy Classification of the SDSS DR3 Using Decision Trees

We provide classifications for all 143 million non-repeat photometric objects in the Third Data Release of the Sloan Digital Sky Survey (SDSS) using decision trees trained on 477,068 objects with SDSS spectroscopic data. We demonstrate that these star/galaxy classifications are expected to be reliable for approximately 22 million objects with r < ~20. The general machine learning environment Data-to-Knowledge and supercomputing resources enabled extensive investigation of the decision tree parameter space. This work presents the first public release of objects classified in this way for an entire SDSS data release. The objects are classified as either galaxy, star or nsng (neither star nor galaxy), with an associated probability for each class. To demonstrate how to effectively make use of these classifications, we perform several important tests. First, we detail selection criteria within the probability space defined by the three classes to extract samples of stars and galaxies to a given completeness and efficiency. Second, we investigate the efficacy of the classifications and the effect of extrapolating from the spectroscopic regime by performing blind tests on objects in the SDSS, 2dF Galaxy Redshift and 2dF QSO Redshift (2QZ) surveys. Given the photometric limits of our spectroscopic training data, we effectively begin to extrapolate past our star-galaxy training set at r ~ 18. By comparing the number counts of our training sample with the classified sources, however, we find that our efficiencies appear to remain robust to r ~ 20. As a result, we expect our classifications to be accurate for 900,000 galaxies and 6.7 million stars, and remain robust via extrapolation for a total of 8.0 million galaxies and 13.9 million stars. [Abridged]Comment: 27 pages, 12 figures, to be published in ApJ, uses emulateapj.cl

Secondary Science and Mathematics Teachers’ Environmental Issues Engagement through SocioScientific Reasoning

Among the many responsibilities of K-12 educators is to promote the development of environmental literacy among their students. Contentious environmental issues are often considered socioscientific issues (SSI; e.g., climate change) in that they are rooted in science, but a myriad of non-scientific (e.g., cultural, political, economic, etc.) factors must be addressed if those issues are to be successfully resolved. Teachers often report being ill-equipped to address these non-scientific factors, which may be due to struggles with employing socioscientific reasoning (SSR). SSR includes understanding the complexity of SSI, engaging in perspective-taking and ongoing inquiry about SSI, employing skepticism when dealing with potentially biased information concerning SSI, and recognizing the affordances of science and non-science considerations in resolving those issues. In this study, mathematics and science teachers who engaged in an SSI-oriented professional development demonstrated a range of sophistication across the dimensions of SSR, with science teachers tending to exhibit more sophistication in their SSR than mathematics teachers. Herein, we share and discuss the results of the study, including the prompts and scoring rubrics with exemplars, which can be used to prepare teachers to teach about contentious SSI and enable them to more effectively instruct and evaluate their students when doing so

Plant 4/1 protein: potential player in intracellular, cell-to-cell and long-distance signaling

Originally isolated as a result of its ability to interact with the movement protein of Tomato spotted wilt virus in a yeast two-hybrid system, the 4/1 protein is proving to be an excellent tool for studying intracellular protein trafficking and intercellular communication. Expression of 4/1 in vivo is tightly regulated, first appearing in the veins of the cotyledon and later in the vasculature of the leaf and stem in association with the xylem parenchyma and phloem parenchyma. Structural studies indicate that 4/1 proteins contain as many as five coiled–coil (CC) domains; indeed, the highest level of sequence identity among 4/1 proteins involves their C-terminal CC domains, suggesting that protein–protein interaction is important for biological function. Recent data predict that the tertiary structure of this C-terminal CC domain is strikingly similar to that of yeast protein She2p; furthermore, like She2p, 4/1 protein exhibits RNA-binding activity, and mutational analysis has shown that the C-terminal CC domain is responsible for RNA binding. The 4/1 protein contains a nuclear export signal. Additional microscopy studies involving leptomycin and computer prediction suggest the presence of a nuclear localization signal as well

The Varga Site: A Multicomponent, Stratified Campsite in the Canyonlands of Edwards County, Texas

Data recovery excavations at the Varga Site were conducted in two phases during 2002 by archeologists from the Cultural Resources Department of TRC Environmental Corporation’s (TRC’s) Austin office under contract to Texas Department of Transportation (TxDOT) Scientific Service Contract No. 572XXSA004. This mitigation program was necessitated by the proposed reconstruction of the crossing of a Ranch to Market Road over Hackberry Creek, immediately south of the site in northeastern Edwards County. These archeological investigations were conducted as part of the responsibilities of TxDOT under existing federal and state legislation for the protection of cultural resources. Geoarcheological trenching and hand-excavations within the existing 31 m wide road right-of-way of 7- m-wide paved Ranch to Market Road focused on the alluvial fines in the first terrace overlooking Hackberry Creek immediately adjacent to a spring. The southern edge of the terrace contains relatively fine-grained sediments ranging from 15 to 150 centimeter (cm) thick that overlie coarse stream gravels that extend to an unknown depth. The modern ground surface had been impacted by road construction and maintenance activities, as well as by light erosion. Block Excavations were conducted on both sides of the pavement and resulted in the hand-excavations of a total of 207.75 square meters (m2), including 83 m2 (66.2 m3) in Block A on the western side and a 124.75 m2 (38.26 m3) area in Block B on the eastern side. Archeological deposits in the investigated part of the site extend to the southern lip of the first terrace and extend about 50 m to the north. The excavations yielded evidence of a multiple component campsite with three distinct and a fourth less distinct prehistoric components. In Block A, the 100 to 150 cm thick fine-grained sediments yielded four intact cultural components. Block B only targeted the youngest, Toyah component. The fine-grained alluvial sediments that comprise the first terrace contain discrete occupations radiocarbon dated to the Late Prehistoric period Toyah phase (ca. 290 to 660 B.P.), the Late Archaic period (ca. 1,700 to 2,300 B.P.), and the Early Archaic period (ca. 5,200 to 6,300 B.P.). A Middle Archaic period (ca. 3,900 to 4,800 B.P.) component was also recognized, but was not as clearly defined as were the other three components. Krotovina disturbance was relatively extensive in parts of the investigated site area. Nevertheless, the archeological deposits exhibited a high degree of contextual integrity. The Toyah phase component contains a rich assemblage of cultural material (ca. 65,000 pieces), including lithic debitage (ca. 26,000), quantities of highly fragmented bones (ca. 18,700), small burned rocks (ca. 16,000), formal and informal stone tools (ca. 1,850), scattered ceramic sherds (ca. 100), and 11 burned rock features. This component was radiocarbon dated by 14 accepted dates to between 290 and 660 B.P. Preservation was generally good, but mixing and probable overprinting contributed to poor horizontal patterning and an inability to identify discrete activity areas. The Late Archaic period component consists primarily of a large, nearly 6 m diameter lens of burned rock that is interpreted as an incipient burned rock midden with an indistinct central pit oven. This feature was associated with a buried A horizon and exhibited a high degree of stratigraphic integrity. However, beyond the ill-defined boundaries of this burned rock feature, limited lithic debitage assemblage (ca. 1,800), a few mussel shell fragments, five isolated burned rock features, scattered burned rocks, and occasional chipped stone tools (ca. 30) totaling less than 6,000 pieces. Identified dart point styles associated with this midden include Frio, Marcos, Ensor, Castroville, and Edgewood. This component was radiocarbon dated by 11 accepted dates to a 600-year period between 1,700 and 2,310 B.P. The Middle Archaic component was not well-defined, but definitely present and dispersed below the Late Archaic component and above the Early Archaic component. These materials were vertically distributed over a 20 to 40 cm thick zone that lacked completely sterile levels or visible breaks in the stratigraphy between the other cultural events. Lithic debitage (ca. 4,400) dominates the recovered assemblage (ca. 6,000), with limited burned rocks (ca. 3,000), a few formal chipped stone tools (ca. 25), and moderate frequency of vertebrate remains (100 g) also present. Two poorly organized burned rock features were also identified and documented. Five Early Triangular projectile points and one Carrizo point fragment occurred within this component. Two wood charcoal assays and one radiocarbon date on a deer bone directly date this Middle Archaic component to ca. 900-radiocarbon year period between 3,910 and 4,820 B.P. These three absolute dates are stratigraphically in order compared to the radiocarbon dates from the cultural components above and below. The Early Archaic component was defined by quantities of dense cultural debris (ca. 135,000) within a roughly 30 cm thick zone directly on top and mixed into coarse river gravels and below the Middle Archaic component. The cultural material varied in depth from a shallow 50 cm below datum (bd) at the north end to a much deeper 120 cmbd in the southern end of Block A. The recovery of a robust assemblage of dart points (170 specimens) that consisted of Group 2—Early Corner-Notched, Bandy, Martindale, Gower, and Merrell dart points indicates that this zone represents many occupations that occurred over a relatively broad time frame. The dart points were associated with a diverse tool assemblage (ca. 1,300). Organic preservation was poor in this lower stratum, but occasional fragments of animal bone, plant seeds, and wood charcoal were recovered. Fifteen organic samples of diverse materials yielded radiocarbon dates that document a minimum use period of 1,080-radiocarbon years from 5,200 B.P. to 6,280 B.P. Greater insight and understanding of each of these four components represented was made possible through the employment of numerous technical analyses, including the radiocarbon dating of 66 samples, six optically stimulated luminescence dates, use-wear analysis and organic residue identifications on 156 stone specimens, petrographic analyses on 18 pottery and one local sediment samples, pollen and phytolith analyses on 25 paired samples, instrumental neutron activation analysis on 261 chert samples and 18 pottery sherds, fatty acid composition on eight pottery sherds and 94 burned rocks, stable carbon and nitrogen analyses on 112 samples, macrobotanical analyses on 44 float and 75 individual charcoal samples, and granulometric and compositional studies on 10 sediment samples. The combined results have contributed significantly to a greater understanding of the Varga Site as a whole and documented specific information concerning the behaviors of the people who occupied the site. These and other technical analyses are urged for other excavated sites in the future to continue to broaden our understanding of the human behaviors at specific sites and throughout the broader region. This will add to a growing database that will foster a better understanding of prehistoric lifeways across Texas

Dietary Choline Supplementation Attenuates High-Fat-Diet-Induced Hepatocellular Carcinoma in Mice

Background: Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death in the world. Choline deficiency has been well studied in the context of liver disease; however, less is known about the effects of choline supplementation in HCC. Objective: The objective of this study was to test whether choline supplementation could influence the progression of HCC in a high-fat-diet (HFD)-driven mouse model. Methods: Four-day-old male C57BL/6J mice were treated with the chemical carcinogen, 7,12-dimethylbenz[a]anthracene, and were randomly assigned at weaning to a cohort fed an HFD (60% kcal fat) or an HFD with supplemental choline (60% kcal fat, 1.2% choline; HFD+C) for 30 wk. Blood was isolated at 15 and 30 wk to measure immune cells by flow cytometry, and glucose-tolerance tests were performed 2 wk prior to killing. Overall tumor burden was quantified, hepatic lipids were measured enzymatically, and phosphatidylcholine species were measured by targeted MS methods. Gene expression and mitochondrial DNA were quantified by quantitative PCR. Results: HFD+C mice exhibited a 50-90% increase in both circulating choline and betaine concentrations in the fed state (P ≤ 0.05). Choline supplementation resulted in a 55% decrease in total tumor numbers, a 67% decrease in tumor surface area, and a 50% decrease in hepatic steatosis after 30 wk of diet (P ≤ 0.05). Choline supplementation increased the abundance of mitochondria and the relative expression of β-oxidation genes by 21% and ∼75-100%, respectively, in the liver. HFD+C attenuated circulating myeloid-derived suppressor cells at 15 wk of feeding (P ≤ 0.05). Conclusions: Choline supplementation attenuated HFD-induced HCC and hepatic steatosis in male C57BL/6J mice. These results suggest a therapeutic benefit of choline supplementation in blunting HCC progression

Association between monosodium glutamate intake and sleep-disordered breathing among Chinese adults with normal body weight

ObjectiveTo assess whether monosodium glutamate (MSG) intake is associated with sleep-disordered breathing (SDB).MethodsData from 1227 Chinese subjects who participated in the Jiangsu Nutrition Study were analyzed. All the participants were examined at two time points (baseline in 2002 and follow-up in 2007). The MSG intake was assessed quantitatively in 2002 and a sleep questionnaire was used to assess snoring and to construct an SDB probability score in 2007. Those within the fifth quintile of the score (highest) were defined as having a high probability of SDB.ResultsThe MSG intake was positively associated with snoring and a high probability of SDB in participants who had a normal body weight but in those who were overweight. A comparison of the extreme quartiles of MSG intake in subjects with a body mass index lower than 23 kg/m² showed an odds ratio of 2.02 (95% confidence interval 1.02-4.00) for snoring and an odds ratio of 3.11 (95% confidence interval 1.10-8.84) for a high probability of SDB. There was a joint effect between MSG and overweight in relation to SDB.ConclusionThe intake of MSG may increase the risk of SDB in Chinese adults with a normal body weight.Zumin Shi, Gary A. Wittert, Baojun Yuan, Yue Dai, Tiffany K. Gill, Gang Hu, Robert Adams, Hui Zuo, Anne W. Taylo

Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis

[EN] Viroids are small, single-stranded, non-protein coding and circular RNAs able to infect host plants in the absence of any helper virus. They may elicit symptoms in their hosts, but the underlying molecular pathways are only partially known. Here we address the role of post-transcriptional RNA silencing in plant-viroid-interplay, with major emphasis on the involvement of this sequence-specific RNA degradation mechanism in both plant antiviroid defence and viroid pathogenesis. This review is a tribute to the memory of Dr. Ricardo Flores, who largely contributed to elucidate this and other molecular mechanisms involved in plant-viroid interactions.The authors of this manuscript, former PhD students, post-doctoral fellows and colleagues of Dr. Ricardo Flores, would like to dedicate this review to his memory. Among many other achievement during his scientific career, Ricardo was responsible for major advances in efforts to dissect the molecular mechanisms underlying viroid pathogenesis. An exemplary and dedicated scientist, excellent mentor, and a treasured friend, Ricardo will be deeply missed.Di Serio, F.; Owens, RA.; Navarro, B.; Serra, P.; Martínez De Alba, AE.; Delgado Villar, SG.; Carbonell, A.... (2023). Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis. Virus Research. 323:1-6. https://doi.org/10.1016/j.virusres.2022.1989641632

ICTV Virus Taxonomy Profile: Pospiviroidae

[EN] Members of the family Pospiviroidae have single-stranded circular RNA genomes that adopt a rod-like or a quasi-rod-like conformation. These genomes contain a central conserved region that is involved in replication in the nucleus through an asymmetric RNA-RNA rolling-circle mechanism. Members of the family Pospiviroidae lack the hammerhead ribozymes that are typical of viroids classified in the family Avsunviroidae. The family Pospiviroidae includes the genera Apscaviroid, Cocadviroid, Coleviroid, Hostuviroid and Pospiviroid, with >25 species. This is a summary of the ICTV Report on the family Pospiviroidae, which is available at ictv.global/report/pospiviroidae.Production of this summary, the online chapter, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA).Di Serio, F.; Owens, RA.; Li, S.; Matousek, J.; Pallás Benet, V.; Randles, JW.; Sano, T.... (2021). ICTV Virus Taxonomy Profile: Pospiviroidae. Journal of General Virology. 102(2):1-2. https://doi.org/10.1099/jgv.0.00154312102