Assessing Water Policy Implications of the Changing Agriculture in New Mexico

Agriculture is the dominant water sector in New Mexico, responsible for more than 80% of water withdrawals in 2015 (USGS 2018). Water policy needs to be extremely adaptive and informed to meet the needs of not only farmers, but cities, industry and riparian uses. Since 1840, the U.S. Department of Agriculture (USDA) has conducted census surveys assessing all levels of agriculture. These data are physically published at the county, state, and national level on a 5-year cycle, detailing various material counts such as acreage, yields, and water usage, as well as socioeconomic estimates of farm costs, revenues, and hired workers. Digitally, these data can be found on the USDA’s Quick Stats online webpage, however is limited to the 1997 census - current. Haines et al., (2018) has used a computer digitizer to sort through all published reports from 1840 to current, and house them in R data frames (.rda) freely available for download on the Inter-University Consortium for Political and Social Research (ICPSR) website. For this project, we have developed a program in R-Studio which uses a New Mexico subset of this data set for the years 1978 – 2012. The code outputs tabular and graphical figures with minimal user inputs and minimal data entry. We believe this is a valuable tool for students, professors, and researchers to quickly examine data for shifts and trends in agriculture and examine how they relate to water in New Mexico. As water managers are made aware of shifts and trends in agriculture, the coming water policy can be ‘right sized’ to fit the needs of the state as it moves forward

Immediate chest X-ray for patients at risk of lung cancer presenting in primary care: randomised controlled feasibility trial

Background: Achieving earlier stage diagnosis is one option for improving lung cancer outcomes in the United Kingdom. Patients with lung cancer typically present with symptoms to general practitioners several times before referral or investigation. Methods: We undertook a mixed methods feasibility individually randomised controlled trial (the ELCID trial) to assess the feasibility and inform the design of a definitive, fully powered, UK-wide, Phase III trial of lowering the threshold for urgent investigation of suspected lung cancer. Patients over 60, with a smoking history, presenting with new chest symptoms to primary care, were eligible to be randomised to intervention (urgent chest X-ray) or usual care. Results: The trial design and materials were acceptable to GPs and patients. We randomised 255 patients from 22 practices, although the proportion of eligible patients who participated was lower than expected. Survey responses (89%), and the fidelity of the intervention (82% patients X-rayed within 3 weeks) were good. There was slightly higher anxiety and depression in the control arm in participants aged >75. Three patients (1.2%) were diagnosed with lung cancer. Conclusions: We have demonstrated the feasibility of individually randomising patients at higher risk of lung cancer, to a trial offering urgent investigation or usual care

Psychosocial impact of undergoing prostate cancer screening for men with BRCA1 or BRCA2 mutations.

OBJECTIVES: To report the baseline results of a longitudinal psychosocial study that forms part of the IMPACT study, a multi-national investigation of targeted prostate cancer (PCa) screening among men with a known pathogenic germline mutation in the BRCA1 or BRCA2 genes. PARTICPANTS AND METHODS: Men enrolled in the IMPACT study were invited to complete a questionnaire at collaborating sites prior to each annual screening visit. The questionnaire included sociodemographic characteristics and the following measures: the Hospital Anxiety and Depression Scale (HADS), Impact of Event Scale (IES), 36-item short-form health survey (SF-36), Memorial Anxiety Scale for Prostate Cancer, Cancer Worry Scale-Revised, risk perception and knowledge. The results of the baseline questionnaire are presented. RESULTS: A total of 432 men completed questionnaires: 98 and 160 had mutations in BRCA1 and BRCA2 genes, respectively, and 174 were controls (familial mutation negative). Participants' perception of PCa risk was influenced by genetic status. Knowledge levels were high and unrelated to genetic status. Mean scores for the HADS and SF-36 were within reported general population norms and mean IES scores were within normal range. IES mean intrusion and avoidance scores were significantly higher in BRCA1/BRCA2 carriers than in controls and were higher in men with increased PCa risk perception. At the multivariate level, risk perception contributed more significantly to variance in IES scores than genetic status. CONCLUSION: This is the first study to report the psychosocial profile of men with BRCA1/BRCA2 mutations undergoing PCa screening. No clinically concerning levels of general or cancer-specific distress or poor quality of life were detected in the cohort as a whole. A small subset of participants reported higher levels of distress, suggesting the need for healthcare professionals offering PCa screening to identify these risk factors and offer additional information and support to men seeking PCa screening

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Data from: Re-growing a tropical dry forest: functional plant trait composition and community assembly during succession

A longstanding goal of ecology and conservation biology is to understand the environmental and biological controls of forest succession. However, the patterns and mechanisms that guide successional trajectories, especially within tropical forests, remain unclear. We collected leaf functional trait and abiotic data across a 110-year chronosequence within a tropical dry forest in Costa Rica. Focusing on six key leaf functional traits related to resource acquisition and competition, along with measures of forest stand structure, we propose a mechanistic framework to link species composition, community trait distributions, and forest structure. We quantified the community-weighted trait distributions for specific leaf area, leaf dry matter concentration, leaf phosphorus concentration, leaf carbon to nitrogen ratio, and leaf stable isotopic carbon and nitrogen. We assessed several prominent hypotheses for how these functional measures shift in response to changing environmental variables (soil water content, bulk density and pH) across the chronosequence. Increasingly, older forests differed significantly from younger forests in species composition, above ground biomass and shifted trait distributions. Early stages of succession were uniformly characterized by lower values of community-weighted mean specific leaf area, leaf stable nitrogen isotope, and leaf phosphorus concentration. Leaf dry matter concentration and leaf carbon to nitrogen ratio were lower during earlier stages of succession, and each trait reached an optimum during intermediate stages of succession. The leaf carbon isotope ratio was the only trait to decrease linearly with increasing stand age indicating reduced water use efficiency in older forests. However, in contrast to expectations, community-weighted trait variances did not generally change through succession, and when compared to null expectations were lower than expected. The observed directional shift in community-weighted mean trait values is consistent with the ‘productivity filtering’ hypothesis where a directional shift in water and light availability shifts physiological strategies from ‘slow’ to ‘fast’. In contrast to expectations arising from niche based ecology, none of the community trait distributions were over-dispersed. Instead, patterns of trait dispersion are consistent with the abiotic filtering and/or competitive hierarchy hypotheses

FEBuzzardCWVCalculation.R

R-script for calculating the community weighted variance (CWV) for each plot

FEBuzzardCWMCalculations.R

R-script for calculating the community weighted mean (CWM) trait values by plot

FEBuzzardSpTraits

Species mean trait data for six traits: SLA (cm2 g-1 ), LDMC, LPC (mg g-1 ), d13C, d15N and CN within each plot across the chronosequence

Data Paper. Data Paper

<h2>File List</h2><div> <p><a href="Individuals.csv">Individuals.csv</a> (MD5: ): Height, condition, location of individual saguaros at plot X</p> <p><a href="NurseInfo.csv">NurseInfo.csv</a> (MD5: ): Nurse plant information at plot X</p> <p><a href="Species.csv">Species.csv</a> (MD5: ): Summary of plant codes and nomenclature of species detected</p> <p><a href="Boundaries.shp">Boundaries.shp</a> (MD5: ): Layer depicting plot boundaries</p> <p>PlotX1908.shp: Layer depicting saguaros surveyed in 1908 that are within plot X (see ShpFiles.zip)</p> <p>All *.shp files are provided as the .zip file <a href="ShpFiles.zip">ShpFiles.zip</a> (MD5: ); all *.csv files can be downloaded at once using <a href="CsvFiles.zip">CsvFiles.zip</a> (MD5: ).</p> </div><h2>Description</h2><div> <p>The saguaro cactus (<i>Carnegiea gigantea</i>) is one of the most iconic perennials in the Sonoran Desert. The ecological importance of this species has motivated studies that explored its physiological adaptations to deserts, factors controlling its recruitment and distribution, and changes in its population density and extent over time. The population of saguaros on Tumamoc Hill (Tucson, Arizona) is one of the best studied. Saguaros on and nearby Tumamoc Hill were mapped in 1908, and in 1964 R. M. Turner and J. R. Hastings established four 250-m wide plots within the original census area. Plots were established on the north, south, east, and west-facing slopes of Tumamoc Hill, and each plot extends from the top to the base of the hill. Plots were resurveyed in 1970, 1987, 1993, and between 2010 and 2012. In this data paper, we present all information associated with this monitoring program, which includes digital versions of Spalding’s original 1908 saguaro map as well as information regarding individual saguaros located in each of the four plots. Collected data include plant height, number of branches, and plant condition, as well as plant location. Starting in 1993, we also noted the identity and condition of plant species growing in close proximity to each saguaro. The archived data set described here contains information pertaining to >5800 saguaros.<br> Past analyses of these data include reconstructions of regeneration patterns from observed age structures and the determination of the average height-specific growth rates for plants on each slope. The findings from these studies have broadened our understanding of the relationship between saguaro regeneration patterns and climate. These data have also provided pivotal information regarding regional trends of saguaro populations throughout the Sonoran Desert. As a group, the Tumamoc Hill censuses constitute one of the longest spatially explicit monitoring efforts for a single species in the world.  They provide an observational baseline for future comparisons relating individual growth and population demographics to rising CO2 levels, climate change, vegetation change, or changes in other biotic or abiotic factors.   </p> <p> <i>Key words</i>: Carnegiea gigantea;<i> long-term monitoring; permanent plots; population dynamics; saguaro cactus; Sonoran Desert; spatially explicit data</i>. </p> </div