Estimation of subsurface porosities and thermal conductivities of polygonal tundra by coupled inversion of electrical resistivity, temperature, and moisture content data

Studies indicate greenhouse gas emissions following permafrost thaw will amplify current rates of atmospheric warming, a process referred to as the permafrost carbon feedback. However, large uncertainties exist regarding the timing and magnitude of the permafrost carbon feedback, in part due to uncertainties associated with subsurface permafrost parameterization and structure. Development of robust parameter estimation methods for permafrost-rich soils is becoming urgent under accelerated warming of the Arctic. Improved parameterization of the subsurface properties in land system models would lead to improved predictions and a reduction of modeling uncertainty. In this work we set the groundwork for future parameter estimation (PE) studies by developing and evaluating a joint PE algorithm that estimates soil porosities and thermal conductivities from time series of soil temperature and moisture measurements and discrete in-time electrical resistivity measurements. The algorithm utilizes the Model-Independent Parameter Estimation and Uncertainty Analysis toolbox and coupled hydrological-thermal-geophysical modeling. We test the PE algorithm against synthetic data, providing a proof of concept for the approach. We use specified subsurface porosities and thermal conductivities and coupled models to set up a synthetic state, perturb the parameters, and then verify that our PE method is able to recover the parameters and synthetic state. To evaluate the accuracy and robustness of the approach we perform multiple tests for a perturbed set of initial starting parameter combinations. In addition, we varied types and quantities of data to better understand the optimal dataset needed to improve the PE method. The results of the PE tests suggest that using multiple types of data improve the overall robustness of the method. Our numerical experiments indicate that special care needs to be taken during the field experiment setup so that (1) the vertical distance between adjacent measurement sensors allows the signal variability in space to be resolved and (2) the longer time interval between resistivity snapshots allows signal variability in time to be resolved

Onshore to offshore trends in carbonate sequence development, diagenesis and reservoir quality across a land-attached shelf in SE Asia

Although isolated Miocene buildups in SE Asia commonly form prolific hydrocarbon reservoirs, their equivalents on clastic-dominated land-attached shelves remain poorly known and underexplored. Here, onshore to offshore trends in carbonate development and reservoir quality are assessed across the NW Borneo shelf through study of surface outcrops and subsurface wells. A multidisciplinary programme of fieldwork, petrography and geochemical analyses allowed evaluation of spatio-temporal variations in deposition, diagenesis and pore system development, together with an assessment of controlling influences. In addition to field logging and sample collection >200 samples were studied via transmitted light, cathodoluminescent and scanning electron microscopy together with stable isotopic characterisation (O, C and Sr).Carbonates developed as localised low-, and higher-relief buildups, as well as more continuous sheet-like deposits in near-coast to shelf margin positions. Molluscs, corals, larger benthic foraminifera and coralline algae are common constituents. Most samples show evidence for marine micritisation, and just in shelf margin positions isopachous cements. However, burial diagenesis predominates in the form of compaction, neomorphism, fracturing, late leaching and dolomitisation. Near-coastal carbonates commonly contain siliciclastics, as do some shelf margin deposits that interdigitate with, or are covered in siliciclastics. Some early, probable meteoric leaching affected inner shelf deposits prior to pervasive neomorphic to blocky/poikilotopic calcite cement formation. On the basis of δ 18 O V-PDB values of −4.5 to −7.9‰ equivalent to δ 18 O V-SMOW values of 0 to −4‰ at 25–40 °C and δ 13 C V-PDB values of −0.6 to +1.6‰ cementation probably reflects alteration from terrestrial groundwaters in meteoric aquifers derived from the humid landmass of Borneo. Despite this cementation, moderate energy inner- to mid-shelf grainstones from the core of mounded carbonates still retain, or have enhanced porosity (<8%) over their lower energy counterparts (<4% porosity). Retention of primary porosity and/or late burial dissolution (often associated with saddle dolomite formation) enhancing predominantly primary and minor secondary porosity is key to reservoir quality development in outer-shelf deposits. Best porosity (<20–35%) is in high energy grainstones and rudstones from outer-shelf to shelf-margin positions that experienced minimal clastic influx, most commonly from backstepping to aggradational carbonate sequences.Although stable isotopes for shelf margin calcite cements are consistent with precipitation from marine-derived fluids (δ18O V-PDB values of −3.6 to −5.4‰), those for the late dolomites are suggestive of fluids of meteoric origin (δ18O V-PDB values of −5.2 to −7.4‰ equivalent to values of −0.3 to −6.3‰ V-SMOW at 40–60 °C). Critical factors for reservoir quality development in carbonates from siliciclastic-dominated shelves in the equatorial tropics are: (1) development and preservation of primary porosity, (2) cementation associated with meteoric aquifers draining large humid equatorial landmasses, and (3) burial leaching and fluid pathways

ciliaFA : a research tool for automated, high-throughput measurement of ciliary beat frequency using freely available software

Background: Analysis of ciliary function for assessment of patients suspected of primary ciliary dyskinesia (PCD) and for research studies of respiratory and ependymal cilia requires assessment of both ciliary beat pattern and beat frequency. While direct measurement of beat frequency from high-speed video recordings is the most accurate and reproducible technique it is extremely time consuming. The aim of this study was to develop a freely available automated method of ciliary beat frequency analysis from digital video (AVI) files that runs on open-source software (ImageJ) coupled to Microsoft Excel, and to validate this by comparison to the direct measuring high-speed video recordings of respiratory and ependymal cilia. These models allowed comparison to cilia beating between 3 and 52 Hz. Methods: Digital video files of motile ciliated ependymal (frequency range 34 to 52 Hz) and respiratory epithelial cells (frequency 3 to 18 Hz) were captured using a high-speed digital video recorder. To cover the range above between 18 and 37 Hz the frequency of ependymal cilia were slowed by the addition of the pneumococcal toxin pneumolysin. Measurements made directly by timing a given number of individual ciliary beat cycles were compared with those obtained using the automated ciliaFA system. Results: The overall mean difference (± SD) between the ciliaFA and direct measurement high-speed digital imaging methods was −0.05 ± 1.25 Hz, the correlation coefficient was shown to be 0.991 and the Bland-Altman limits of agreement were from −1.99 to 1.49 Hz for respiratory and from −2.55 to 3.25 Hz for ependymal cilia. Conclusions: A plugin for ImageJ was developed that extracts pixel intensities and performs fast Fourier transformation (FFT) using Microsoft Excel. The ciliaFA software allowed automated, high throughput measurement of respiratory and ependymal ciliary beat frequency (range 3 to 52 Hz) and avoids operator error due to selection bias. We have included free access to the ciliaFA plugin and installation instructions in Additional file 1 accompanying this manuscript that other researchers may use

Visualizing and trapping transient oligomers in amyloid assembly pathways

Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease

Behavioral and psychological symptoms of dementia: The effects of physical activity at adult day service centers

Adult day services (ADS) are an increasingly popular option for caregivers of people with dementia, but there is little research on the effects of activities on the behavior and mood of the client. This study examines participation by 94 individuals in different types of adult day-care activities and their association with changes in behavior and psychological symptoms of dementia (BPSD) for the client during a three-month span. Three domains of BPSD were examined: restless behaviors, mood behaviors, and positive behaviors. Using growth curve modeling, results show that the restless and mood behavior domains, on average, were stable over three months, whereas positive behaviors increased. For all three behavior domains there were individual differences in average level of BPSD. Average rate of change for individuals also varied from the mean for restless and mood behaviors. Physical activities, social activities, engaging activities, and watching and listening activities, along with a day-care dosage variable, were used as covariates to explain these individual differences in change. Engaging activities explained some of the individual variance for restless behaviors; as individuals increased one increment in engaging activities, they had fewer restless behavior problems over time. These results suggest that some features of programming may be related to improvements in restless behavior

Fast Multiplane Functional Imaging Combining Acousto-optic Switching and Remote Focusing

Networks of neurons are inherently three-dimensional in nature, whereas conventional imaging methods, such as laser scanning two-photon microscopy, usually provide only fast two-dimensional imaging. Rapid volumetric imaging would however be preferable for imaging neurons. To get a more complete picture of the dynamics of the neuron-to-neuron interactions, we have developed a pseudo-parallelised multi-plane two-photon excitation imaging system through the incorporation of an acousto-optic switching and a remote focusing technique into a resonant scanning microscope. This permits the recording of millisecond scale fluorescence transients of calcium indicators from large populations of neurons upon neural firing events at multiple chosen axial planes in very short time frame. While the remote focusing system offers aberration-free axial scanning over a few hundreds of micrometres of depth, the acousto-optic deflector provides high speed optical switching between different laser beam paths in sub-microsecond timescale which in turn, controls the axial focal plane to be targeted. Here, we report on the development of the high temporal resolution multi-plane targeted microscope and its potential application

Cognitive and behavioral predictors of light therapy use

Objective: Although light therapy is effective in the treatment of seasonal affective disorder (SAD) and other mood disorders, only 53-79% of individuals with SAD meet remission criteria after light therapy. Perhaps more importantly, only 12-41% of individuals with SAD continue to use the treatment even after a previous winter of successful treatment. Method: Participants completed surveys regarding (1) social, cognitive, and behavioral variables used to evaluate treatment adherence for other health-related issues, expectations and credibility of light therapy, (2) a depression symptoms scale, and (3) self-reported light therapy use. Results: Individuals age 18 or older responded (n = 40), all reporting having been diagnosed with a mood disorder for which light therapy is indicated. Social support and self-efficacy scores were predictive of light therapy use (p's<.05). Conclusion: The findings suggest that testing social support and self-efficacy in a diagnosed patient population may identify factors related to the decision to use light therapy. Treatments that impact social support and self-efficacy may improve treatment response to light therapy in SAD. © 2012 Roecklein et al

Extending Construal Level Theory to Distributed Teams: Perception and Evaluation of Distant Others

Building on prior research on distributed teams that has identified physical and temporal distance as impediments to collaboration and relationship development, this paper explores how and why we treat geographically distant others differently from those who are proximal. According to construal level theory, physically- or temporally-distant events or objects are more psychologically distant and are more likely to be described in terms of their more general characteristics, while views of more proximal events or objects will be more detailed and nuanced. We extend construal level theory to the distributed team context by advancing propositions about how group members perceive and evaluate distant others in contrast to proximal others. By comparing to alternative computer-mediated communication and social psychological theories that have been applied to this phenomenon, we show that construal level theory offers parsimonious explanations as well as novel predictions about how and why we perceive and evaluate distant others differently. The paper then considers theoretical, methodological, and practical implications of construal level theory for distributed teams and other virtual settings

Assisted evolution enables HIV-1 to overcome a high trim5α-imposed genetic barrier to rhesus macaque tropism

Diversification of antiretroviral factors during host evolution has erected formidable barriers to cross-species retrovirus transmission. This phenomenon likely protects humans from infection by many modern retroviruses, but it has also impaired the development of primate models of HIV-1 infection. Indeed, rhesus macaques are resistant to HIV-1, in part due to restriction imposed by the TRIM5α protein (rhTRIM5α). Initially, we attempted to derive rhTRIM5α-resistant HIV-1 strains using two strategies. First, HIV-1 was passaged in engineered human cells expressing rhTRIM5α. Second, a library of randomly mutagenized capsid protein (CA) sequences was screened for mutations that reduced rhTRIM5α sensitivity. Both approaches identified several individual mutations in CA that reduced rhTRIM5α sensitivity. However, neither approach yielded mutants that were fully resistant, perhaps because the locations of the mutations suggested that TRIM5α recognizes multiple determinants on the capsid surface. Moreover, even though additive effects of various CA mutations on HIV-1 resistance to rhTRIM5α were observed, combinations that gave full resistance were highly detrimental to fitness. Therefore, we employed an 'assisted evolution' approach in which individual CA mutations that reduced rhTRIM5α sensitivity without fitness penalties were randomly assorted in a library of viral clones containing synthetic CA sequences. Subsequent passage of the viral library in rhTRIM5α-expressing cells resulted in the selection of individual viral species that were fully fit and resistant to rhTRIM5α. These viruses encoded combinations of five mutations in CA that conferred complete or near complete resistance to the disruptive effects of rhTRIM5α on incoming viral cores, by abolishing recognition of the viral capsid. Importantly, HIV-1 variants encoding these CA substitutions and SIVmac239 Vif replicated efficiently in primary rhesus macaque lymphocytes. These findings demonstrate that rhTRIM5α is difficult to but not impossible to evade, and doing so should facilitate the development of primate models of HIV-1 infection

Multi-Timescale Perceptual History Resolves Visual Ambiguity

When visual input is inconclusive, does previous experience aid the visual system in attaining an accurate perceptual interpretation? Prolonged viewing of a visually ambiguous stimulus causes perception to alternate between conflicting interpretations. When viewed intermittently, however, ambiguous stimuli tend to evoke the same percept on many consecutive presentations. This perceptual stabilization has been suggested to reflect persistence of the most recent percept throughout the blank that separates two presentations. Here we show that the memory trace that causes stabilization reflects not just the latest percept, but perception during a much longer period. That is, the choice between competing percepts at stimulus reappearance is determined by an elaborate history of prior perception. Specifically, we demonstrate a seconds-long influence of the latest percept, as well as a more persistent influence based on the relative proportion of dominance during a preceding period of at least one minute. In case short-term perceptual history and long-term perceptual history are opposed (because perception has recently switched after prolonged stabilization), the long-term influence recovers after the effect of the latest percept has worn off, indicating independence between time scales. We accommodate these results by adding two positive adaptation terms, one with a short time constant and one with a long time constant, to a standard model of perceptual switching