Detecting Soil Macrofauna Using Ground-Penetrating Radar

Fossorial amphibians spend up to ten months belowground, but research into this critical habitat has been impeded by a lack of noninvasive detection methods. Ground-penetrating radar (GPR), however, offers a promising tool because amphibians have theoretically strong electromagnetic (EM) contrasts relative to the soil matrix, and thus potentially high detectability. The objectives of this study were to (1) evaluate GPR by (2) experimentally-inducing three soil thermal regimes that promote stratification in the burrowing depths of 15 Eastern American Toads (Anaxyrus americanus americanus) during the winter of 2011–2012 in Madison, WI, USA. We calculated reflectability and established the unique electronic signature of the toads in GPR datasets through measuring the water contents of the soil and toads as a proxy for the relative dielectric constant, an EM metric in GPR assessment. As toads emerged in the spring of 2012, we verified the GPR imagery with their emergence locations. The contrast in relative dielectric constants between the toads and the soil provided reflectance ratings that were 12–24 times greater than the detectable limit and confirmed that the toads were distinguishable from other soil features. The winter mortality of the toads, however, was 73%, which limited the replication with which GPR could be evaluated. We attribute the depth and rate of frost penetration from the treatments and weather of 2012 as the probable cause of mortality. Future research and conservation efforts may be facilitated with GPR by tracking temperate species belowground and linking behavior to environmental stressors

Hedgehog signaling is required at multiple stages of zebrafish tooth development

Background. The accessibility of the developing zebrafish pharyngeal dentition makes it an advantageous system in which to study many aspects of tooth development from early initiation to late morphogenesis. In mammals, hedgehog signaling is known to be essential for multiple stages of odontogenesis; however, potential roles for the pathway during initiation of tooth development or in later morphogenesis are incompletely understood. Results. We have identified mRNA expression of the hedgehog ligands shha and the receptors ptc1 and ptc2 during zebrafish pharyngeal tooth development. We looked for, but did not detect, tooth germ expression of the other known zebrafish hedgehog ligands shhb, dhh, ihha, or ihhb, suggesting that as in mammals, only Shh participates in zebrafish tooth development. Supporting this idea, we found that morphological and gene expression evidence of tooth initiation is eliminated in shha mutant embryos, and that morpholino antisense oligonucleotide knockdown of shha, but not shhb, function prevents mature tooth formation. Hedgehog pathway inhibition with the antagonist compound cyclopamine affected tooth formation at each stage in which we applied it: arresting development at early stages and disrupting mature tooth morphology when applied later. These results suggest that hedgehog signaling is required continuously during odontogenesis. In contrast, over-expression of shha had no effect on the developing dentition, possibly because shha is normally extensively expressed in the zebrafish pharyngeal region. Conclusion. We have identified previously unknown requirements for hedgehog signaling for early tooth initiation and later morphogenesis. The similarity of our results with data from mouse and other vertebrates suggests that despite gene duplication and changes in the location of where teeth form, the roles of hedgehog signaling in tooth development have been largely conserved during evolution. © 2010 Jackman et al; licensee BioMed Central Ltd

Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding

SummaryThe LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 Å resolution. The structure establishes a 10-stranded β fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design

On infimum Dickey–Fuller unit root tests allowing for a trend break under the null

Trend breaks appear to be prevalent in macroeconomic time series. Consequently, to avoid the catastrophic impact that unmodelled trend breaks have on power, it is standard empirical practice to employ unit root tests which allow for such effects. A popularly applied approach is the infimum ADF-type test. Its appeal has endured with practitioners despite results which show that the infimum ADF statistic diverges to −∞−∞ as the sample size diverges, with the consequence that the test has an asymptotic size of unity when a break in trend is present under the unit root null hypothesis. The result for additive outlier-type breaks in trend (but not intercept) is refined and shows that divergence to −∞−∞ occurs only when the true break fraction is smaller than 2/32/3. An alternative testing strategy based on the maximum of the original infimum statistic and the corresponding statistic constructed using the time-reversed sample data is considered

Prevalence of, and Resident and Facility Characteristics Associated With Antipsychotic Use in Assisted Living vs. Long-Term Care Facilities: A Cross-Sectional Analysis from Alberta, Canada

BACKGROUND: Potentially inappropriate antipsychotic use in long-term care (LTC) facilities has been the focus of significant policy and clinical attention over the past 20 years. However, most initiatives aimed at reducing the use of these medications have overlooked assisted living (AL) settings. OBJECTIVE: We sought to compare the prevalence of antipsychotic use (including potentially inappropriate use) among older AL and LTC residents and to explore the resident and facility-level factors associated with use in these two populations. METHODS: We performed cross-sectional analyses of 1089 residents (mean age 85 years; 77% female) from 59 AL facilities and 1000 residents (mean age 85 years; 66% female) from 54 LTC facilities, in Alberta, Canada. Research nurses completed comprehensive resident assessments at baseline (2006-2007). Facility-level factors were assessed using standardized administrator interviews. Generalized linear models were used to estimate odds ratios for associations, accounting for clustering by facility. RESULTS: Over a quarter of residents in AL (26.4%) and LTC (31.8%) were using antipsychotics (p = 0.006). Prevalence of potentially inappropriate use was similar in AL and LTC (23.4 vs. 26.8%, p = 0.09). However, among users, the proportion of antipsychotic use deemed potentially inappropriate was significantly higher in AL than LTC (AL: 231/287 = 80.5%; LTC: 224/318 = 70.4%; p = 0.004). In both settings, comparable findings regarding associations between resident characteristics (including dementia, psychiatric disorders, frailty, behavioral symptoms, and antidepressant use) and antipsychotic use were observed. Few facility characteristics were associated with overall antipsychotic use, but having a pharmacist on staff (AL), or an affiliated physician (LTC) was associated with a lower likelihood of potentially inappropriate antipsychotic use. CONCLUSION: Our findings illustrate the importance of including AL settings in clinical and policy initiatives aimed at reducing inappropriate antipsychotic use among older vulnerable residents

University vs. Research Institute? The Dual Pillars of German Science Production, 1950–2010

The world’s third largest producer of scientific research, Germany, is the origin of the research university and the independent, extra-university research institute. Its dual-pillar research policy differentiates these organizational forms functionally: universities specialize in advanced research-based teaching; institutes specialize intensely on research. Over the past decades this policy affected each sector differently: while universities suffered a lingering “legitimation crisis,” institutes enjoyed deepening “favored sponsorship”—financial and reputational advantages. Universities led the nation’s reestablishment of scientific prominence among the highly competitive European and global science systems after WWII. But sectoral analysis of contributions to science, technology, engineering, mathematics, and medical and health journal publications (1950–2010) finds that Germany’s small to medium-sized independent research institutes have made significant, growing contributions, particularly in publishing in higher impact journals proportionally more than their size. Simultaneously—despite dual-pillar policy implications—the university sector continues to be absolutely and relatively successful; not eclipsed by the institutes. Universities have consistently produced two-thirds of the nation’s publications in the highest quality journals since at least 1980 and have increased publications at a logarithmic rate; higher than the international mean. Indeed, they led Germany into the global mega-science style of production. Contrary to assumed benefits of functional differentiation, our results indicate that relative to their size, each sector has produced approximately similar publication records. While institutes have succeeded, the larger university sector, despite much less funding growth, has remained fundamental to German science production. Considering these findings, we discuss the future utility of the dual-pillar policy

Single-Atom Control of Arsenic Incorporation in Silicon for High-Yield Artificial Lattice Fabrication

Artificial lattices constructed from individual dopant atoms within a semiconductor crystal hold promise to provide novel materials with tailored electronic, magnetic, and optical properties. These custom engineered lattices are anticipated to enable new, fundamental discoveries in condensed matter physics and lead to the creation of new semiconductor technologies including analog quantum simulators and universal solid-state quantum computers. In this work, we report precise and repeatable, substitutional incorporation of single arsenic atoms into a silicon lattice. We employ a combination of scanning tunnelling microscopy hydrogen resist lithography and a detailed statistical exploration of the chemistry of arsine on the hydrogen terminated silicon (001) surface, to show that single arsenic dopants can be deterministically placed within four silicon lattice sites and incorporated with 97$\pm$2% yield. These findings bring us closer to the ultimate frontier in semiconductor technology: the deterministic assembly of atomically precise dopant and qubit arrays at arbitrarily large scales

Factors contributing to disparities in mortality among patients with non-small-cell lung cancer

Historically, non-small-cell lung cancer (NSCLC) patients who are non-white, have low incomes, low educational attainment, and non-private insurance have worse survival. We assessed whether differences in survival were attributable to sociodemographic factors, clinical characteristics at diagnosis, or treatments received. We surveyed a multiregional cohort of patients diagnosed with NSCLC from 2003 to 2005 and followed through 2012. We used Cox proportional hazard analyses to estimate the risk of death associated with race/ethnicity, annual income, educational attainment, and insurance status, unadjusted and sequentially adjusting for sociodemographic factors, clinical characteristics, and receipt of surgery, chemotherapy, and radiotherapy. Of 3250 patients, 64% were white, 16% black, 7% Hispanic, and 7% Asian; 36% of patients had income

Factors contributing to disparities in mortality among patients with non–small‐cell lung cancer

Historically, non–small‐cell lung cancer (NSCLC) patients who are non‐white, have low incomes, low educational attainment, and non‐private insurance have worse survival. We assessed whether differences in survival were attributable to sociodemographic factors, clinical characteristics at diagnosis, or treatments received. We surveyed a multiregional cohort of patients diagnosed with NSCLC from 2003 to 2005 and followed through 2012. We used Cox proportional hazard analyses to estimate the risk of death associated with race/ethnicity, annual income, educational attainment, and insurance status, unadjusted and sequentially adjusting for sociodemographic factors, clinical characteristics, and receipt of surgery, chemotherapy, and radiotherapy. Of 3250 patients, 64% were white, 16% black, 7% Hispanic, and 7% Asian; 36% of patients had incomes <$20 000/y; 23$60 000/y, not attending college, and not having private insurance were all associated with an increased risk of mortality. Black‐white differences were not statistically significant after adjustment for sociodemographic factors, although patients with patients without a high school diploma and patients with incomes <$40 000/y continued to have an increased risk of mortality. Differences by educational attainment were not statistically significant after adjustment for clinical characteristics. Differences by income were not statistically significant after adjustment for clinical characteristics and treatments. Clinical characteristics and treatments received primarily contributed to mortality disparities by race/ethnicity and socioeconomic status in patients with NSCLC. Additional efforts are needed to assure timely diagnosis and use of effective treatment to lessen these disparities.Using data from the Cancer Care Outcomes Research and Surveillance (CanCORS) consortium, a large, multi‐regional observational study of newly diagnosed cancer patients, we documented higher unadjusted mortality for NSCLC among patients who were black, have lower income, less well‐educated, and with non‐private insurance. We used a series of Cox proportional hazards model to estimate the increased risk of death associated with sociodemographic factors, clinical characteristics, and treatments received to determine what accounted for the disparities. We found that patients’ clinical characteristics and treatments received primarily contributed to the mortality disparities that we observed in patients with NSCLC.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146607/1/cam41796.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146607/2/cam41796_am.pd

Genetic and ecological consequences of recent habitat fragmentation in a narrow endemic plant species within an urban context

Understanding the timescales that shape spatial genetic structure is pivotal to ascertain the impact of habitat fragmentation on the genetic diversity and reproductive viability of long-lived plant populations. Combining genetic and ecological information with current and past fragmentation conditions allows the identification of the main drivers important in shaping population structure and declines in reproduction, which is crucial for informing conservation strategies. Using historic aerial photographs, we defined the past fragmentation conditions for the shrub Conospermum undulatum, a species now completely embedded in an urban area. We explored the impact of current and past conditions on its genetic layout and assessed the effects of genetic and environmental factors on its reproduction. The historically high structural connectivity was evident in the genetics of the species. Despite the current intense fragmentation, we found similar levels of genetic diversity across populations and a weak spatial genetic structure. Historical connectivity was negatively associated with genetic differentiation among populations and positively related to within-population genetic diversity. Variation partitioning of reproductive performance explained ~ 66% of the variance, showing significant influences for genetic (9%), environmental (15%), and combined (42%) fractions. Our study highlights the importance of considering the historical habitat dynamics when investigating fragmentation consequences in long-lived plants. A detailed characterization of fragmentation from 1953 has shown how low levels of genetic fixation are due to extensive gene flow through the non-fragmented landscape. Moreover, knowledge of the relationships between genetic and environmental variation and reproduction can help to implement effective conservation strategies, particularly in highly dynamic landscapes