Greater data science at baccalaureate institutions

Donoho's JCGS (in press) paper is a spirited call to action for statisticians, who he points out are losing ground in the field of data science by refusing to accept that data science is its own domain. (Or, at least, a domain that is becoming distinctly defined.) He calls on writings by John Tukey, Bill Cleveland, and Leo Breiman, among others, to remind us that statisticians have been dealing with data science for years, and encourages acceptance of the direction of the field while also ensuring that statistics is tightly integrated. As faculty at baccalaureate institutions (where the growth of undergraduate statistics programs has been dramatic), we are keen to ensure statistics has a place in data science and data science education. In his paper, Donoho is primarily focused on graduate education. At our undergraduate institutions, we are considering many of the same questions.Comment: in press response to Donoho paper in Journal of Computational Graphics and Statistic

Microbial carbon mineralization in tropical lowland and montane forest soils of Peru

Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., "positive priming effects" that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding (13)C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils.This study was financed by the UK Natural Environment Research Council (NERC) grant NE/G018278/1 and is a product of the Andes Biodiversity and Ecosystem Research Group consortium (www.andesconservation.org); Patrick Meir was also supported by ARC FT110100457

The role of area-level deprivation and gender in participation in population-based faecal immunochemical test (FIT) colorectal cancer screening

This study aimed to investigate the effects of sex and deprivation on participation in a population-based faecal immunochemical test (FIT) colorectal cancer screening programme. The study population included 9785 individuals invited to participate in two rounds of a population-based biennial FIT-based screening programme, in a relatively deprived area of Dublin, Ireland. Explanatory variables included in the analysis were sex, deprivation category of area of residence and age (at end of screening). The primary outcome variable modelled was participation status in both rounds combined (with “participation” defined as having taken part in either or both rounds of screening). Poisson regression with a log link and robust error variance was used to estimate relative risks (RR) for participation. As a sensitivity analysis, data were stratified by screening round. In both the univariable and multivariable models deprivation was strongly associated with participation. Increasing affluence was associated with higher participation; participation was 26% higher in people resident in the most affluent compared to the most deprived areas (multivariable RR = 1.26: 95% CI 1.21–1.30). Participation was significantly lower in males (multivariable RR = 0.96: 95%CI 0.95–0.97) and generally increased with increasing age (trend per age group, multivariable RR = 1.02: 95%CI, 1.01–1.02). No significant interactions between the explanatory variables were found. The effects of deprivation and sex were similar by screening round. Deprivation and male gender are independently associated with lower uptake of population-based FIT colorectal cancer screening, even in a relatively deprived setting. Development of evidence-based interventions to increase uptake in these disadvantaged groups is urgently required

An Environmental Science and Engineering Framework for Combating Antimicrobial Resistance

On June 20, 2017, members of the environmental engineering and science (EES) community convened at the Association of Environmental Engineering and Science Professors (AEESP) Biennial Conference for a workshop on antimicrobial resistance. With over 80 registered participants, discussion groups focused on the following topics: risk assessment, monitoring, wastewater treatment, agricultural systems, and synergies. In this study, we summarize the consensus among the workshop participants regarding the role of the EES community in understanding and mitigating the spread of antibiotic resistance via environmental pathways. Environmental scientists and engineers offer a unique and interdisciplinary perspective and expertise needed for engaging with other disciplines such as medicine, agriculture, and public health to effectively address important knowledge gaps with respect to the linkages between human activities, impacts to the environment, and human health risks. Recommendations that propose priorities for research within the EES community, as well as areas where interdisciplinary perspectives are needed, are highlighted. In particular, risk modeling and assessment, monitoring, and mass balance modeling can aid in the identification of “hot spots” for antibiotic resistance evolution and dissemination, and can help identify effective targets for mitigation. Such information will be essential for the development of an informed and effective policy aimed at preserving and protecting the efficacy of antibiotics for future generations

An infrared survey of brightest cluster galaxies: Paper I

We report on an imaging survey with the Spitzer Space Telescope of 62 brightest cluster galaxies with optical line emission. These galaxies are located in the cores of X-ray luminous clusters selected from the ROSAT All-Sky Survey. We find that about half of these sources have a sign of excess infrared emission; 22 objects out of 62 are detected at 70 microns, 18 have 8 to 5.8 micron flux ratios above 1.0 and 28 have 24 to 8 micron flux ratios above 1.0. Altogether 35 of 62 objects in our survey exhibit at least one of these signs of infrared excess. Four galaxies with infrared excesses have a 4.5/3.6 micron flux ratio indicating the presence of hot dust, and/or an unresolved nucleus at 8 microns. Three of these have high measured [OIII](5007A)/Hbeta flux ratios suggesting that these four, Abell 1068, Abell 2146, and Zwicky 2089, and R0821+07, host dusty active galactic nuclei (AGNs). 9 objects (including the four hosting dusty AGNs) have infrared luminosities greater than 10^11 L_sol and so can be classified as luminous infrared galaxies (LIRGs). Excluding the four systems hosting dusty AGNs, the excess mid-infrared emission in the remaining brightest cluster galaxies is likely related to star formation.Comment: accepted for publication in ApJ

Microbial carbon mineralization in tropical lowland and montane forest soils of Peru

Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g. ‘positive priming effects’ that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding 13C labelled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesised that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils

A Manhattan information needs snapshot

Master of ScienceDepartment of Journalism and Mass CommunicationsSam MwangiThe author conducted the following information ecosystem snapshot in the City of Manhattan, Kansas over a nearly 14-month period starting in Spring 2021 and concluding in Summer 2022. The aim was to get a preliminary understanding of how well local news and information meets residents of African, Asian and Hispanic/Latin descent where they are; find out how well our community participants believed local storytellers and information sources served their interests; whether they believed their communities were understood and reflected in the stories and images of Manhattan as presented by local communicators; and in what ways they believed local news and information flows could be improved in order to better serve Manhattan in its entirety. This qualitative, exploratory study is informed by an understanding of storytelling as central to health and thriving communities. Community stories help people cultivate identity and a sense of place or community (Anderson, 1991), with access to information and networks of discourse serving to empower individuals and communities to take collective action in their own interest as well as uplift one another in times of need. The study employs Communication Infrastructure Theory as its guiding lens (Ball-Rokeach, Kim & Matei, 2001), positing that communities are built around systems of communication that are made up of varying levels of storytelling networks within a unique local infrastructure that directly impacts access to and interplay between networks. This interplays well with the Listening Post Collective’s concept of an information ecosystem, and the study further made use of the LPC Playbook of strategies (Listening Post Collective) for community assessment to help inform its methods of engagement and outreach for this snapshot report. While Manhattan has fared better than many communities in the nation, with more than a fourth of U.S. newspapers going defunct since 2005 (Abernathy et al., 2022), findings from the 2020 Riley County Community Needs Assessment (Gregory et al., 2020) indicating a need for better access to community information and news as well as changing racial and ethnic demographics over the last 10 years locally (U.S. Census Bureau, 2021a) warrants inquiry into how well Manhattan’s storytellers are prepared to serve its proportionally increasing historical minority populations. To begin to get an answer to that question, the study sought a purposive sample of residents of African, Asian, and Hispanic/Latin descent to share their perspective on how well they’ve done thus far. The author spoke with 9 participants through 8 separate interviews – each coming from different backgrounds, working, or leading in different fields, and representing different segments of their respective communities. Participant responses were then analyzed for emergent themes in addition to recommendations for improvement. Some highlights: Residents of African, Asian, and Hispanic/Latin descent face barriers in Manhattan’s storytelling networks. Conversations raised a trio of different barrier subthemes. Participants of Chinese and Hispanic/Latin descent noted that there can be varied access to translated information among local government and community service organizations in Manhattan, effectively closing a door to those residents who only speak languages other than English or speak those languages far better than they do English. Social or interpersonal division was also noted across demographic groups. African American as well as Hispanic/Latin participants told the author about a lack of connective tissue in their communities outside of Kansas State University. Regional and class differences also proved potential sources of interpersonal conflict, which a participant of Chinese descent says impacted her engagement and information sharing in local storytelling networks. Reputation matters. The stories told by local journalistic organizations as well as the accuracy of those stories are remembered by people in the community. When an error is made, it can be hard to move past. Additionally, local media at times has cultivated a reputation for sensation and a focus on issues and voices that often does not include Manhattan’s historical minority communities. Low investment and a lack of understanding is how participants described Manhattan storytellers’ performance in communicating with the city’s minority populaces. Lack of coverage as well as episodic, parachute or shallow reporting was how local news was described to the author across demographics. The same was said for government and community organization outreach, which to varying degrees were described as missing the mark

The ASTRO-H X-ray Observatory

The joint JAXA/NASA ASTRO-H mission is the sixth in a series of highly successful X-ray missions initiated by the Institute of Space and Astronautical Science (ISAS). ASTRO-H will investigate the physics of the high-energy universe via a suite of four instruments, covering a very wide energy range, from 0.3 keV to 600 keV. These instruments include a high-resolution, high-throughput spectrometer sensitive over 0.3-2 keV with high spectral resolution of Delta E < 7 eV, enabled by a micro-calorimeter array located in the focal plane of thin-foil X-ray optics; hard X-ray imaging spectrometers covering 5-80 keV, located in the focal plane of multilayer-coated, focusing hard X-ray mirrors; a wide-field imaging spectrometer sensitive over 0.4-12 keV, with an X-ray CCD camera in the focal plane of a soft X-ray telescope; and a non-focusing Compton-camera type soft gamma-ray detector, sensitive in the 40-600 keV band. The simultaneous broad bandpass, coupled with high spectral resolution, will enable the pursuit of a wide variety of important science themes.Comment: 22 pages, 17 figures, Proceedings of the SPIE Astronomical Instrumentation "Space Telescopes and Instrumentation 2012: Ultraviolet to Gamma Ray

Legumes increase grassland productivity with no effect on nitrous oxide emissions

Aims: Grasslands are important agricultural production systems, where ecosystem functioning is affected by land management practices. Grass-legume mixtures are commonly cultivated to increase grassland productivity while reducing the need for nitrogen (N) fertiliser. However, little is known about the effect of this increase in productivity on greenhouse gas (GHG) emissions in grass-legume mixtures. The aim of this study was to investigate interactions between the proportion of legumes in grass-legume mixtures and N-fertiliser addition on productivity and GHG emissions. We tested the hypotheses that an increase in the relative proportion of legumes would increase plant productivity and decrease GHG emissions, and the magnitude of these effects would be reduced by N-fertiliser addition. Methods: This was tested in a controlled environment mesocosm experiment with one grass and one legume species grown in mixtures in different proportions, with or without N-fertiliser. The effects on N cycling processes were assessed by measurement of above- and below-ground biomass, shoot N uptake, soil physico-chemical properties and GHG emissions. Results: Above-ground productivity and shoot N uptake were greater in legume-grass mixtures compared to grass or legume monocultures, in fertilised and unfertilised soils. However, we found no effect of legume proportion on N2O emissions, total soil N or mineral-N in fertilised or unfertilised soils. Conclusions: This study shows that the inclusion of legumes in grass-legume mixtures positively affected productivity, however N cycle were in the short-term unaffected and mainly affected by nitrogen fertilisation. Legumes can be used in grassland management strategies to mitigate climate change by reducing crop demand for N-fertilisers

Vascular endothelial growth factor-A165b prevents diabetic neuropathic pain and sensory neuronal degeneration

Diabetic peripheral neuropathy affects up to half of diabetic patients. This neuronal damage leads to sensory disturbances, including allodynia and hyperalgesia. Many growth factors have been suggested as useful treatments for prevention of neurodegeneration, including the vascular endothelial growth factor (VEGF) family. VEGF-A is generated as two alternative splice variant families. The most widely studied isoform, VEGF-A165a is both pro-angiogenic and neuroprotective, but pro-nociceptive and increases vascular permeability in animal models. Streptozotocin (STZ)-induced diabetic rats develop both hyperglycaemia and many of the resulting diabetic complications seen in patients, including peripheral neuropathy. In the present study, we show that the anti-angiogenic VEGF-A splice variant, VEGF-A165b, is also a potential therapeutic for diabetic neuropathy. Seven weeks of VEGF-A165b treatment in diabetic rats reversed enhanced pain behaviour in multiple behavioural paradigms and was neuroprotective, reducing hyperglycaemia-induced activated caspase 3 (AC3) levels in sensory neuronal subsets, epidermal sensory nerve fibre loss and aberrant sciatic nerve morphology. Furthermore, VEGF-A165b inhibited a STZ-induced increase in Evans Blue extravasation in dorsal root ganglia (DRG), saphenous nerve and plantar skin of the hind paw. Increased transient receptor potential ankyrin 1 (TRPA1) channel activity is associated with the onset of diabetic neuropathy. VEGF-A165b also prevented hyperglycaemia-enhanced TRPA1 activity in an in vitro sensory neuronal cell line indicating a novel direct neuronal mechanism that could underlie the anti-nociceptive effect observed in vivo. These results demonstrate that in a model of Type I diabetes VEGF-A165b attenuates altered pain behaviour and prevents neuronal stress, possibly through an effect on TRPA1 activity