The effect of topology on the structure and free energy landscape of DNA kissing complexes

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0 or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction

Sage Grouse Groceries: Forb Response to Piñon-Juniper Treatments

AbstractJuniper and piñon coniferous woodlands have increased 2- to 10-fold in nine ecoregions spanning the Intermountain Region of the western United States. Control of piñon-juniper woodlands by mechanical treatments and prescribed fire are commonly applied to recover sagebrush steppe rangelands. Recently, the Sage Grouse Initiative has made conifer removal a major part of its program to reestablish sagebrush habitat for sage grouse (Centrocercus urophasianus) and other species. We analyzed data sets from previous and ongoing studies across the Great Basin characterizing cover response of perennial and annual forbs that are consumed by sage grouse to mechanical, prescribed fire, and low-disturbance fuel reduction treatments. There were 11 sites in western juniper (Juniperus occidentalis Hook.) woodlands, 3 sites in singleleaf piñon (Pinus monophylla Torr. & Frém.) and Utah juniper (Juniperus osteosperma [Torr.] Little), 2 sites in Utah juniper, and 2 sites in Utah juniper and Colorado piñon (Pinus edulis Engelm). Western juniper sites were located in mountain big sagebrush (A. tridentata ssp. vaseyana) steppe associations, and the other woodlands were located in Wyoming big sagebrush (A. tridentata ssp. wyomingensis) associations. Site potential appears to be a major determinant for increasing perennial forbs consumed by sage grouse following conifer control. The cover response of perennial forbs, whether increasing (1.5- to 6-fold) or exhibiting no change, was similar regardless of conifer treatment. Annual forbs favored by sage grouse benefitted most from prescribed fire treatments with smaller increases following mechanical and fuel reduction treatments. Though forb abundance may not consistently be enhanced, mechanical and fuel reduction conifer treatments remain good preventative measures, especially in phase 1 and 2 woodlands, which, at minimum, maintain forbs on the landscape. In addition, these two conifer control measures, in the short term, are superior to prescribed fire for maintaining the essential habitat characteristics of sagebrush steppe for sage grouse

Re-assessing global water storage trends from GRACE time series

Monitoring changes in freshwater availability is critical for human society and sustainable economic development. To identify regions experiencing secular change in their water resources, many studies compute linear trends in the total water storage (TWS) anomaly derived from the Gravity Recovery and Climate Experiment (GRACE) mission data. Such analyses suggest that several major water systems are under stress (Rodell et al 2009 Nature 460 999–1002; Long et al 2013 Geophys. Res. Lett. 40 3395–401; Richey et al 2015 Water Resour. Res. 51 5217–38; Voss et al 2013 Water Resour. Res. 49 904–14; Famiglietti 2014 Nat. Clim. Change. 4 945–8; Rodell et al 2018 Nature 557 651–9). TWS varies in space and time due to low frequency natural variability, anthropogenic intervention, and climate-change (Hamlington et al 2017 Sci. Rep. 7 995; Nerem et al 2018 Proc. Natl Acad. Sci.). Therefore, linear trends from a short time series can only be interpreted in a meaningful way after accounting for natural spatiotemporal variability in TWS (Paolo et al 2015 Science 348 327–31; Edward 2012 Geophys. Res. Lett. 39 L01702). In this study, we first show that GRACE TWS trends from a short time series cannot determine conclusively if an observed change is unprecedented or severe. To address this limitation, we develop a novel metric, trend to variability ratio (TVR), that assesses the severity of TWS trends observed by GRACE from 2003 to 2015 relative to the multi-decadal climate-driven variability. We demonstrate that the TVR combined with the trend provides a more informative and complete assessment of water storage change. We show that similar trends imply markedly different severity of TWS change, depending on location. Currently more than 3.2 billion people are living in regions facing severe water storage depletion w.r.t. past decades. Furthermore, nearly 36% of hydrological catchments losing water in the last decade have suffered from unprecedented loss. Inferences from this study can better inform water resource management

Numerical Nonlinear Algebra

Numerical nonlinear algebra is a computational paradigm that uses numerical analysis to study polynomial equations. Its origins were methods to solve systems of polynomial equations based on the classical theorem of B\'ezout. This was decisively linked to modern developments in algebraic geometry by the polyhedral homotopy algorithm of Huber and Sturmfels, which exploits the combinatorial structure of the equations and led to efficient software for solving polynomial equations. Subsequent growth of numerical nonlinear algebra continues to be informed by algebraic geometry and its applications. These include new approaches to solving, algorithms for studying positive-dimensional varieties, certification, and a range of applications both within mathematics and from other disciplines. With new implementations, numerical nonlinear algebra is now a fundamental computational tool for algebraic geometry and its applications. We survey some of these innovations and some recent applications.Comment: 40 pages, many figure

Western Juniper Field Guide: Asking the Right Questions to Select Appropriate Management Actions

Strong evidence indicates that western juniper has significantly expanded its range since the late 1800s by encroaching into landscapes once dominated by shrubs and herbaceous vegetation (fig. 1). Woodland expansion affects soil resources, plant community structure and composition, water, nutrient and fire cycles, forage production, wildlife habitat, and biodiversity. Goals of juniper management include an attempt to restore ecosystem function and a more balanced plant community that includes shrubs, grasses, and forbs, and to increase ecosystem resilience to disturbances. Developing a management strategy can be a difficult task due to uncertainty about how vegetation, soils, hydrologic function, and wildlife will respond to treatments. When developing a management strategy, the first and possibly most important step towards success is asking the right questions. Identifying the attributes of the area to be treated and selecting the right treatments to be applied are of utmost importance. One must ask questions addressing the kind of site (that is, potential natural vegetation, soils, etc.), the current state of the site (that is, successional, hydrologic, etc.), what components need to be restored, how the management unit fits in with the overall landscape mosaic, and the long-term goals and objectives for the area or region. Keep in mind sagebrush-steppe vegetation is dynamic and management strategies must take into account multi-decade time frames. This guide provides a set of tools that will help field biologists, land managers, and private landowners conduct rapid qualitative field assessments that address the kind of site and its current state. These tools include a list of questions to be addressed and a series of photographs, keys, tables, and figures to help evaluate a site. Conducting this assessment will help prioritize sites to be treated, select the best treatment, and predict outcomes. Success of a juniper management program may be greatly enhanced if an interdisciplinary team of local managers and resource specialists, who are experienced with vegetation, fuels, soils, hydrology, wildlife, and economic and sociological aspects of the local resource, use this guide to aid their decision-making

A service evaluation of passive remote monitoring technology for patients in a high-secure forensic psychiatric hospital:a qualitative study

Background: Technology has the potential to remotely monitor patient safety in real-time that helps staff and without disturbing the patient. However, staff and patients’ perspectives on using passive remote monitoring within an inpatient setting is lacking. The study aim was to explore stakeholders’ perspectives about using Oxehealth passive monitoring technology within a high-secure forensic psychiatric hospital in the UK as part of a wider mixed-methods service evaluation.Methods: Semi-structured interviews were conducted with staff and patients with experience of using Oxehealth technology face-to-face within a private room in Broadmoor Hospital. We applied thematic analysis to the data of each participant group separately. Themes and sub-themes were integrated, finalised, and presented in a thematic map. Design, management, and analysis was meaningfully informed by both staff and patients.Results: Twenty-four participants were interviewed (n = 12 staff, n = 12 patients). There were seven main themes: detecting deterioration and improving health and safety, “big brother syndrome”, privacy and dignity, knowledge and understanding, acceptance, barriers to use and practice issues and future changes needed. Oxehealth technology was considered acceptable to both staff and patients if the technology was used to detect deterioration and improve patient’s safety providing patient’s privacy was not invaded. However, overall acceptance was lower when knowledge and understanding of the technology and its camera was limited. Most patients could not understand why both physical checks through bedroom windows, and Oxehealth was needed to monitor patients, whilst staff felt Oxehealth should not replace physical checks of patients as reassures staff on patient safety.Conclusions: Oxehealth technology is considered viable and acceptable by most staff and patients but there is still some concern about its possible intrusive nature. However, more support and education for new patients and staff to better understand how Oxehealth works in the short- and long-term could be introduced to further improve acceptability. A feasibility study or pilot trial to compare the impact of Oxehealth with and without physical checks may be needed

Vegetation Response to Western Juniper Slash Treatments

The expansion of pion-juniper woodlands the past 100 years in the western United States has resulted in large scale efforts to kill trees and recover sagebrush steppe rangelands. It is important to evaluate vegetation recovery following woodland control to develop best management practices. In this study, we compared two fuel reduction treatments and a cut-and-leave (CUT) treatment used to control western juniper (Juniperus occidentalis spp. occidentalis Hook.) of the northwestern United States. Treatments were; CUT, cut-and-broadcast burn (BURN), and cut-pile-and-burn the pile (PILE). A randomized complete block design was used with five replicates of each treatment located in a curl leaf mahogany (Cercocarpus ledifolius Nutt. ex Torr. & A. Gray)/mountain big sagebrush (Artemisia tridentata Nutt. spp. vaseyana (Rydb.) Beetle)/Idaho fescue (Festuca idahoensis Elmer) association. In 2010, 4 years after tree control the cover of perennial grasses (PG) [Sandberg's bluegrass (Poa secunda J. Pres) and large bunchgrasses] were about 4 and 5 % less, respectively, in the BURN (7.1 ± A 0.6 %) than the PILE (11.4 ± A 2.3 %) and CUT (12.4 ± A 1.7 %) treatments (P < 0.0015). In 2010, cover of invasive cheatgrass (Bromus tectorum L.) was greater in the BURN (6.3 ± A 1.0 %) and was 50 and 100 % greater than PILE and CUT treatments, respectively. However, the increase in perennial bunchgrass density and cover, despite cheatgrass in the BURN treatment, mean it unlikely that cheatgrass will persist as a major understory component. In the CUT treatment mahogany cover increased 12.5 % and density increased in from 172 ± A 25 to 404 ± A 123 trees/ha. Burning, killed most or all of the adult mahogany, and mahogany recovery consisted of 100 and 67 % seedlings in the PILE and BURN treatments, respectively. After treatment, juniper presence from untreated small trees (< 1 m tall; PILE and CUT treatments) and seedling emergence (all treatments) represented 25-33 % of pre-treatment tree density. To maintain recovery of herbaceous, shrub, and mahogany species additional control of reestablished juniper will be necessary.This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springer.com/Keywords: Pinon–juniper, Fire, Cercocarpus, Bunchgrass, Fuel reductionKeywords: Pinon–juniper, Fire, Cercocarpus, Bunchgrass, Fuel reductio

Restoration of Mountain Big Sagebrush Steppe Following Prescribed Burning to Control Western Juniper

Western juniper (Juniperus occidentalis ssp. occidentalis Hook) encroachment into mountain big sagebrush (Artemisia tridentata spp. vaseyana (Rydb.) Beetle) steppe has reduced livestock forage production, increased erosion risk, and degraded sagebrush-associated wildlife habitat. Western juniper has been successfully controlled with partial cutting followed by prescribed burning the next fall, but the herbaceous understory and sagebrush may be slow to recover. We evaluated the effectiveness of seeding perennial herbaceous vegetation and sagebrush at five sites where juniper was controlled by partially cutting and prescribed burning. Treatments tested at each site included an unseeded control, herbaceous seed mix (aerially seeded), and the herbaceous seed mix plus sagebrush seed. In the third year post-treatment, perennial grass cover and density were twice as high in plots receiving the herbaceous seed mix compared to the control plots. Sagebrush cover and density in the sagebrush seeded plots were between 74- and 290-fold and 62- and 155-fold greater than the other treatments. By the third year after treatment, sagebrush cover was as high as 12% in the sagebrush seeded plots and between 0% and 0.4% where it was not seeded. These results indicate that aerial seeding perennial herbaceous vegetation can accelerate the recovery of perennial grasses which likely stabilize the site. Our results also suggest that seeding mountain big sagebrush after prescribed burning encroaching juniper can rapidly recover sagebrush cover and density. In areas where sagebrush habitat is limited, seeding sagebrush after juniper control may increase sagebrush habitat and decrease the risks to sagebrush-associated species.Keywords: Fire, Sage-grouse, Recovery, Aerial seeding, Habitat, Artemisia tridentataKeywords: Fire, Sage-grouse, Recovery, Aerial seeding, Habitat, Artemisia tridentat

Numerical Algebraic Geometry: A New Perspective on String and Gauge Theories

The interplay rich between algebraic geometry and string and gauge theories has recently been immensely aided by advances in computational algebra. However, these symbolic (Gr\"{o}bner) methods are severely limited by algorithmic issues such as exponential space complexity and being highly sequential. In this paper, we introduce a novel paradigm of numerical algebraic geometry which in a plethora of situations overcomes these short-comings. Its so-called 'embarrassing parallelizability' allows us to solve many problems and extract physical information which elude the symbolic methods. We describe the method and then use it to solve various problems arising from physics which could not be otherwise solved.Comment: 36 page