Inferring the dynamics of ionic currents from recursive piecewise data assimilation of approximate neuron models

We construct neuron models from data by transferring information from an observed time series to the state variables and parameters of Hodgkin-Huxley models. When the learning period completes, the model will predict additional observations and its parameters uniquely characterise the complement of ion channels. However, the assimilation of biological data, as opposed to model data, is complicated by the lack of knowledge of the true neuron equations. Reliance on guessed conductance models is plagued with multi-valued parameter solutions. Here, we report on the distributions of parameters and currents predicted with intentionally erroneous models, over-specified models, and an approximate model fitting hippocampal neuron data. We introduce a recursive piecewise data assimilation (RPDA) algorithm that converges with near-perfect reliability when the model is known. When the model is unknown, we show model error introduces correlations between certain parameters. The ionic currents reconstructed from these parameters are excellent predictors of true currents and carry a higher degree of confidence, >95.5%, than underlying parameters, >53%. Unexpressed ionic currents are correctly filtered out even in the presence of mild model error. When the model is unknown, the covariance eigenvalues of parameter estimates are found to be a good gauge of model error. Our results suggest that biological information may be retrieved from data by focussing on current estimates rather than parameters

Field Tests of Some Liming Treatments for Growing Burley Tobacco on Acid Soils

A major problem in the production of tobacco on acid soils in Kentucky is manganese toxicity, despite the fact that it can be easily prevented. Since manganese toxicity is caused by high levels of soil acidity, prevention of soil acidity by liming is the best method of control. And soil testing is the only way to determine how acid a field has become

Ion-neutral sympathetic cooling in a hybrid linear rf Paul and magneto-optical trap

Long range polarization forces between ions and neutral atoms result in large elastic scattering cross sections, e.g., 10^6 a.u. for Na+ on Na or Ca+ on Na at cold and ultracold temperatures. This suggests that a hybrid ion-neutral trap should offer a general means for significant sympathetic cooling of atomic or molecular ions. We present SIMION 7.0 simulation results concerning the advantages and limitations of sympathetic cooling within a hybrid trap apparatus, consisting of a linear rf Paul trap concentric with a Na magneto-optical trap (MOT). This paper explores the impact of various heating mechanisms on the hybrid system and how parameters related to the MOT, Paul trap, number of ions, and ion species affect the efficiency of the sympathetic cooling

Dynamics of a deep-water seagrass population on the Great Barrier Reef: annual occurrence and response to a major dredging program

Global seagrass research efforts have focused on shallow coastal and estuarine seagrass populations where alarming declines have been recorded. Comparatively little is known about the dynamics of deep-water seagrasses despite evidence that they form extensive meadows in some parts of the world. Deep-water seagrasses are subject to similar anthropogenic threats as shallow meadows, particularly along the Great Barrier Reef lagoon where they occur close to major population centres. We examine the dynamics of a deep-water seagrass population in the GBR over an 8 year period during which time a major capital dredging project occurred. Seasonal and inter-annual changes in seagrasses were assessed as well as the impact of dredging. The seagrass population was found to occur annually, generally present between July and December each year. Extensive and persistent turbid plumes from a large dredging program over an 8 month period resulted in a failure of the seagrasses to establish in 2006, however recruitment occurred the following year and the regular annual cycle was re-established. Results show that despite considerable inter annual variability, deep-water seagrasses had a regular annual pattern of occurrence, low resistance to reduced water quality but a capacity for rapid recolonisation on the cessation of impacts

Are megaquakes clustered?

We study statistical properties of the number of large earthquakes over the past century. We analyze the cumulative distribution of the number of earthquakes with magnitude larger than threshold M in time interval T, and quantify the statistical significance of these results by simulating a large number of synthetic random catalogs. We find that in general, the earthquake record cannot be distinguished from a process that is random in time. This conclusion holds whether aftershocks are removed or not, except at magnitudes below M = 7.3. At long time intervals (T = 2-5 years), we find that statistically significant clustering is present in the catalog for lower magnitude thresholds (M = 7-7.2). However, this clustering is due to a large number of earthquakes on record in the early part of the 20th century, when magnitudes are less certain.Comment: 5 pages, 5 figure

Hip Preservation Surgery in Patients With Femoroacetabular Impingement Syndrome and Acetabular Dysplasia Improves Functional Measures and Pain Catastrophizing

Background Chronic hip pain is a debilitating condition that severely reduces one\u27s quality of life. Prior studies uncovered a link between hip pathologies and pain catastrophizing, anxiety, and depression. The purpose of this study was to investigate whether hip preservation surgery in patients with femoroacetabular impingement syndrome (FAIS) and acetabular dysplasia (AD) improves functional outcomes and pain catastrophizing. Methods Patients with FAIS and AD were requested to complete a hip questionnaire both preoperatively and postoperatively at a single academic center (University of Texas Southwestern Medical Center, Dallas, Texas, USA). Pain catastrophizing was evaluated using the pain catastrophizing scale, and pain level was assessed using the visual analog scale. Assessments of hip functional outcomes included the hip outcome score (HOS) and the hip disability and osteoarthritis outcome score (HOOS). Outcome measures before and after treatment were compared using the dependent samples t-test. A correlation analysis, using the Spearman partial correlation coefficient (rs), was conducted to evaluate the relationship between variables. Results The results indicated a clinically significant improvement in functional measures and pain catastrophizing in patients who underwent hip preservation surgery. The most significant discovery was an inverse relationship between both HOOS quality of life (rs=-0.293, p=0.0065, false discovery rate (FDR)=0.0210) and HOS activities of daily living (rs=-0.242, p=0.0254, FDR=0.0423) and pain catastrophizing; however, similar improvements were seen in pain catastrophizing with improvements in other functional outcomes. Conclusion Undergoing hip preservation surgery for patients with AD or FAIS improved their hip functional measures and decreased pain catastrophizing postoperatively. The improvement of hip function, quality of life, and pain catastrophizing reveals an intricate link between the functional outcomes of hip preservation surgery and pain catastrophizing

Remobilization of Tol2 transposons in Xenopus tropicalis

<p>Abstract</p> <p>Background</p> <p>The Class II DNA transposons are mobile genetic elements that move DNA sequence from one position in the genome to another. We have previously demonstrated that the naturally occurring <it>Tol2 </it>element from <it>Oryzias latipes </it>efficiently integrates its corresponding non-autonomous transposable element into the genome of the diploid frog, <it>Xenopus tropicalis. Tol2 </it>transposons are stable in the frog genome and are transmitted to the offspring at the expected Mendelian frequency.</p> <p>Results</p> <p>To test whether <it>Tol2 </it>transposons integrated in the <it>Xenopus tropicalis </it>genome are substrates for remobilization, we injected <it>in vitro </it>transcribed <it>Tol2 </it>mRNA into one-cell embryos harbouring a single copy of a <it>Tol2 </it>transposon. Integration site analysis of injected embryos from two founder lines showed at least one somatic remobilization event per embryo. We also demonstrate that the remobilized transposons are transmitted through the germline and re-integration can result in the generation of novel GFP expression patterns in the developing tadpole. Although the parental line contained a single <it>Tol2 </it>transposon, the resulting remobilized tadpoles frequently inherit multiple copies of the transposon. This is likely to be due to the <it>Tol2 </it>transposase acting in discrete blastomeres of the developing injected embryo during the cell cycle after DNA synthesis but prior to mitosis.</p> <p>Conclusions</p> <p>In this study, we demonstrate that single copy <it>Tol2 </it>transposons integrated into the <it>Xenopus tropicalis </it>genome are effective substrates for excision and random re-integration and that the remobilized transposons are transmitted through the germline. This is an important step in the development of 'transposon hopping' strategies for insertional mutagenesis, gene trap and enhancer trap screens in this highly tractable developmental model organism.</p

SDSS J134441.83+204408.3: A Highly Asynchronous Short-period Magnetic Cataclysmic Variable with a 56 MG Field Strength

When the accreting white dwarf in a magnetic cataclysmic variable star (mCV) has a field strength in excess of 10 MG, it is expected to synchronize its rotational frequency to the binary orbit frequency, particularly at small binary separations, due to the steep radial dependence of the magnetic field. We report the discovery of an mCV (SDSS J134441.83+204408.3, hereafter J1344) that defies this expectation by displaying asynchronous rotation (Pspin/Porb = 0.893) in spite of a high surface field strength (B = 56 MG) and a short orbital period (114 minutes). Previously misidentified as a synchronously rotating mCV, J1344 was observed by Transiting Exoplanet Survey Satellite during sector 50, and the resulting power spectrum shows distinct spin and orbital frequencies, along with various sidebands and harmonics. Although there are several other asynchronous mCVs at short orbital periods, the presence of cyclotron humps in J1344's Sloan Digital Sky Survey spectrum makes it possible to directly measure the field strength in the cyclotron-emitting region, and while a previously study estimated 65 MG based on its identification of two cyclotron humps, we revise this to 56 ± 2 MG based on the detection of a third hump and on our modeling of the cyclotron spectrum. Short-period mCVs with field strengths above 10 MG are normally expected to be synchronous, so the highly asynchronous rotation in J1344 presents an interesting challenge for theoretical studies of spin-period evolution

Open source drug discovery - A limited tutorial

Open science is a new concept for the practice of experimental laboratory-based research, such as drug discovery. The authors have recently gained experience in how to run such projects and here describe some straightforward steps others may wish to take towards more openness in their own research programmes. Existing and inexpensive online tools can solve many challenges, while some psychological barriers to the free sharing of all data and ideas are more substantia