A Generalized Theory of DNA Looping and Cyclization

We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise boundary conditions on DNA, which necessitates a treatment beyond the Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be treated as a heteropolymer with sequence-dependent intrinsic curvature and stiffness. In this framework, we independently compute enthlapic and entropic contributions to the $J$ factor and show that even at small length scales $(\sim \ell_{p})$ entropic effects are significant. We propose a simple analytic formula to describe our numerical results for a homogenous DNA in planar loops, which can be used to predict experimental cyclization and loop formation rates as a function of loop size and binding geometry. We also introduce an effective torsional persistence length that describes the coupling between twist and bending of DNA when looped.Comment: 6 pages, 4 figures, submitted to EP

THE ADOPTION AND DIFFUSION OF LEVEL FIELDS AND BASINS

Strategic investments in agriculture often are lumpy and irreversible, with significant impacts on operating and fixed costs. Leveling cotton fields to zero slope in central Arizona is a strategic decision made by relatively younger farmers who are farming fine-textured soils in irrigation districts with higher expected water costs. The diffusion of the technology across the region between 1968-89 appears to be both a function of institutional changes (e.g., the Groundwater Management Act of 1980, the Central Arizona Project) and the long-run expected price changes induced by these new policies.Crop Production/Industries,

Reconstruction of Cluster Masses using Particle Based Lensing I: Application to Weak Lensing

We present Particle-Based Lensing (PBL), a new technique for gravitational lensing mass reconstructions of galaxy clusters. Traditionally, most methods have employed either a finite inversion or gridding to turn observational lensed galaxy ellipticities into an estimate of the surface mass density of a galaxy cluster. We approach the problem from a different perspective, motivated by the success of multi-scale analysis in smoothed particle hydrodynamics. In PBL, we treat each of the lensed galaxies as a particle and then reconstruct the potential by smoothing over a local kernel with variable smoothing scale. In this way, we can tune a reconstruction to produce constant signal-noise throughout, and maximally exploit regions of high information density. PBL is designed to include all lensing observables, including multiple image positions and fluxes from strong lensing, as well as weak lensing signals including shear and flexion. In this paper, however, we describe a shear-only reconstruction, and apply the method to several test cases, including simulated lensing clusters, as well as the well-studied ``Bullet Cluster'' (1E0657-56). In the former cases, we show that PBL is better able to identify cusps and substructures than are grid-based reconstructions, and in the latter case, we show that PBL is able to identify substructure in the Bullet Cluster without even exploiting strong lensing measurements. We also make our codes publicly available.Comment: Accepted for publication in ApJ; Codes available at http://www.physics.drexel.edu/~deb/PBL.htm ; 12 pages,9 figures, section 3 shortene

A hybrid CA-PDE Model of chlamydia trachomatis infection in the female genital tract

Chlamydia trachomatis is amongst the most common sexually transmitted diseases in the world and when left untreated, may lead to serious sequelae particularly in women such as pelvic inflammatory disease, ectopic pregnancy and infertility. Currently, most mathematical modelling in the literature regarding Chlamydia is based on time dependent differential equations. The serious pathology associated with C. trachomatis occurs when the chlamydial infection ascends to the upper genital tract. But no modelling study has investigated the important spatial aspects of the disease. In this work, we include spatiotemporal considerations of the progression of chlamydial infection in the genital tract. This novel direction is achieved using cellular automata modelling with probabilistic decision processes. In this presentation, the modelling strategy will be described, as well as its relationship with existing models and the advances in understanding that are achieved with such a model. Such an approach provides valuable insights into disease progression and will lead to experimentally testable predictions and a basis for further investigation in this area

Relapse to opioid use in opioid-dependent individuals released from compulsory drug detention centres compared with those from voluntary methadone treatment centres in Malaysia: a two-arm, prospective observational study

Background Detention of people who use drugs into compulsory drug detention centres (CDDCs) is common throughout East and Southeast Asia. Evidence-based pharmacological therapies for treating substance use disorders, such as opioid agonist treatments with methadone, are generally unavailable in these settings. We used a unique opportunity where CDDCs coexisted with voluntary drug treatment centres (VTCs) providing methadone in Malaysia to compare the timing and occurrence of opioid relapse (measured using urine drug testing) in individuals transitioning from CDDCs versus methadone maintenance in VTCs. Methods We did a parallel, two-arm, prospective observational study of opioid-dependent individuals aged 18 years and older who were treated in Malaysia in the Klang Valley in two settings: CDDCs and VTCs. We used sequential sampling to recruit individuals. Assessed individuals in CDDCs were required to participate in services such as counselling sessions and manual labour. Assessed individuals in VTCs could voluntarily access many of the components available in CDDCs, in addition to methadone therapy. We undertook urinary drug tests and behavioural interviews to assess individuals at baseline and at 1, 3, 6, 9, and 12 months post-release. The primary outcome was time to opioid relapse post-release in the community confi rmed by urinary drug testing in individuals who had undergone baseline interviewing and at least one urine drug test (our analytic sample). Relapse rates between the groups were compared using time-to-event methods. This study is registered at ClinicalTrials.gov (NCT02698098). Findings Between July 17, 2012, and August 21, 2014, we screened 168 CDDC attendees and 113 VTC inpatients; of these, 89 from CDDCs and 95 from VTCs were included in our analytic sample. The baseline characteristics of the two groups were similar. In unadjusted analyses, CDDC participants had signifi cantly more rapid relapse to opioid use post-release compared with VTC participants (median time to relapse 31 days [IQR 26–32] vs 352 days [256–unestimable], log rank test, p<0·0001). VTC participants had an 84% (95% CI 75–90) decreased risk of opioid relapse after adjustment for control variables and inverse propensity of treatment weights. Time-varying eff ect modelling revealed the largest hazard ratio reduction, at 91% (95% CI 83–96), occurs during the fi rst 50 days in the community. Interpretation Opioid-dependent individuals in CDDCs are signifi cantly more likely to relapse to opioid use after release, and sooner, than those treated with evidence-based treatments such as methadone, suggesting that CDDCs have no role in the treatment of opioid-use disorders

Investigating Dielectric and Metamaterial Effects in a Terahertz Traveling-Wave Tube Amplifier

Adding material enhancements to a terahertz traveling-wave tube amplifier is investigated. Isotropic dielectrics, negative-index metamaterials, and anisotropic crystals are simulated, and plans to increase the efficiency of the device are discussed. Early results indicate that adding dielectric to the curved sections of the serpentine-shaped slow-wave circuit produce optimal changes in the cold-test characteristics of the device and a minimal drop in operating frequency. Additional results suggest that materials with simultaneously small relative permittivities and electrical conductivities are best suited for increasing the efficiency of the device. More research is required on the subject, and recommendations are given to determine the direction

Shear-Wave Splitting and Mantle Flow Beneath the Colorado Plateau and its Boundary with the Great Basin

Shear-wave splitting measurements from SKS and SKKS phases show fast polarization azimuths that are subparallel to North American absolute plate motion within the central Rio Grande Rift (RGR) and Colorado Plateau (CP) through to the western rim of the CP, with anisotropy beneath the CP and central RGR showing a remarkably consistent pattern with a mean fast azimuth of 4 degrees +/- degrees 6 E of N. Approaching the rim from the southeast, fast anisotropic directions become north-northeast-south-southwest (NNE-SSW), rotate counter clockwise to north-south in the CP-GB transition, and then to NNW-SSE in the western Great Basin ( GB). This change is coincident with uppermost mantle S-wave velocity perturbations that vary from +4% beneath the western CP and the eastern edge of the Marysvale volcanic field to about -8% beneath the GB. Corresponding delay times average 1.5 sec beneath the central CP, decrease to approximately 0.8 sec near the CP-GB transition, and increase to about 1.2 sec beneath the GB. For the central CP, we suggest anisotropy predominantly controlled by North American plate motion above the asthenosphere. The observed pattern of westward-rotating anisotropy from the western CP through the CP-GB transition may be influenced to asthenospheric flow around a CP lithospheric keel and/or by vertical flow arising from edge-driven small-scale convection. The anisotropic transition from the CP to the GB thus marks a first-order change from absolute plate motion dominated lithosphere-asthenosphere shear to a new regime controlled by regional flow processes. The NNW-SSE anisotropic fast directions of split SKS waves in the eastern GB area are part of a broad circular pattern of seismic anisotropic fast direction in the central GB that has recently been hypothesized to be due to toroidal flow around the sinking Juan de Fuca-Gorda slab.National Science Foundation EAR 9706094, 9707188, 9707190, 0207812Los Alamos National Laboratory Institute of Geophysics and Planetary PhysicsNational Science Foundation Cooperative EAR-000430Department of Energy National Nuclear Security AdministrationGeological Science

Quantifying subtropical North Pacific gyre mixed layer primary productivity from Seaglider observations of diel oxygen cycles

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geophysical Research Letters 42 (2015): 4032–4039, doi:10.1002/2015GL063065.Using autonomous underwater gliders, we quantified diurnal periodicity in dissolved oxygen, chlorophyll, and temperature in the subtropical North Pacific near the Hawaii Ocean Time-series (HOT) Station ALOHA during summer 2012. Oxygen optodes provided sufficient stability and precision to quantify diel cycles of average amplitude of 0.6 µmol kg−1. A theoretical diel curve was fit to daily observations to infer an average mixed layer gross primary productivity (GPP) of 1.8 mmol O2 m−3 d−1. Cumulative net community production (NCP) over 110 days was 500 mmol O2 m−2 for the mixed layer, which averaged 57 m in depth. Both GPP and NCP estimates indicated a significant period of below-average productivity at Station ALOHA in 2012, an observation confirmed by 14C productivity incubations and O2/Ar ratios. Given our success in an oligotrophic gyre where biological signals are small, our diel GPP approach holds promise for remote characterization of productivity across the spectrum of marine environments.The authors acknowledge support from the National Science Foundation (NSF) through an NSF Science and Technology Center, the Center for Microbial Oceanography Research and Education (C-MORE; NSF EF-0424599). D.N. also was supported by NSF (OCE-1129644) and an Independent Study Award from the Woods Hole Oceanographic Institution (WHOI). D.M.K. was also supported by the Gordon and Betty Moore Foundation. WHOI Summer Student Fellow Cole Stites-Clayton, Stanford University, contributed to early stages of Seaglider data analysis and was supported by an NSF REU grant to WHOI (OCE-1156952)