Tip–sample interactions: Extraction of single molecular pair potentials from force curves

This article describes a method for extracting the true tip–sample potential from an experimental force curve in atomic force microscopy. This potential is not the negative integral of the force curve. Rather, the potential is a more complicated function of the force curve and cantilever spring constant. If information about the shape of the tip is known, a decorrelation may be performed to extract molecular pair potentials from the total tip–sample potential. Applications and limitations of this method are discussed

A Bayesian shifting method for uncertainty in the open-hole gamma-ray log around casing points

The wireline gamma-ray log is sensitive to open-hole conditions and, in particular, the diameter. This means that the log can jump at casing points. Although environmental corrections exist, they can fail at these points. We present a Bayesian method for deriving a new quantity – the shifted gamma–ray index – that takes these shifts into account by fitting a piecewise linear function to open-hole data in a depth window around the casing point. Because it is Bayesian, the method enables us to assess our uncertainty about its performance. This method requires very little knowledge of the borehole or drilling conditions but relies on the assumption that the lithology is consistent. Investigating the other wireline logs enables us to assess whether this assumption is valid. We demonstrate our method using well data from offshore mid-Norway

Using visualisation methods to analyse referral networks within community health care among patients aged 65 years and over

Community health care services are considered integral to overcoming future problems in health care. However, this sector faces its own challenges, such as how to organise services to provide coordinated care given: their physical distribution, patients using multiple services, increased patient use and differing patient needs. The aim of this work was to explore, analyse and understand patterns in community referrals for patients aged 65 years and over, and their use of multiple services through data visualisation. Working with a large community provider, these methods helped researchers and service managers to investigate questions that were otherwise difficult to answer from raw data. Each map focuses on a different characteristic of community referrals: patients reusing services, concurrent uses of different services and patterns of subsequent referrals. We apply these methods to routine patient data and discuss their implications in designing of a single point of access - a service for streamlining referrals

Sensitivity to parenting in adolescents with callous/unemotional traits: Observational and experimental findings

Children and adolescents with callous-unemotional (CU) traits have been distinguished as a subset of individuals with disruptive behavioral disorders who may be less sensitive to parenting influence; we test this hypothesis using multiple methods and assessment paradigms. Two hundred seventy-one adolescents (mean age 12.6 years) from 3 samples at elevated risk for disruptive behavior disorders were studied. Symptoms of CU behavior were derived from standard questionnaire; assessments of behavioral adjustment were derived from clinical interview with parent, and parent-report, teacher-report, and self-report questionnaire. Parent–child relationship quality was based on observational assessments in which adolescent and parent behaviors were rated in 3 interaction tasks: (a) low conflict planning task; (b) problem-solving conflict task; (c) puzzle challenge task; parent interview and parent-report and child-report questionnaires of parenting were also assessed. Results indicated that the associations between parent–child relationship quality and behavioral adjustment were comparable in adolescents with and without CU traits. More notably, observational data indicated that adolescents with elevated CU traits showed comparatively greater within-individual variability in observed angry/irritable behavior across interaction tasks, suggesting greater sensitivity to and emotional dysregulation in challenging interpersonal contexts. The findings suggest that adolescents with CU are not less sensitive to parental influence and may in contrast show greater context-sensitive disturbances in emotional regulation. The results have implications for family-based assessment and treatment for adolescents with disruptive behavior disorders

Protein flexibility is key to cisplatin crosslinking in calmodulin

Chemical crosslinking in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) has significant potential for studying protein structures and proteinprotein interactions. Previously, cisplatin has been shown to be a crosslinker and crosslinks multiple methionine (Met) residues in apo-calmodulin (apo-CaM). However, the inter-residue distances obtained from nuclear magnetic resonance structures are inconsistent with the measured distance constraints by crosslinking. Met residues lie too far apart to be crosslinked by cisplatin. Here, by combining FTICR MS with a novel computational flexibility analysis, the flexible nature of the CaM structure is found to be key to cisplatin crosslinking in CaM. It is found that the side chains of Met residues can be brought together by flexible motions in both apo-CaM and calcium-bound CaM (Ca4-CaM). The possibility of cisplatin crosslinking Ca4-CaM is then confirmed by MS data. Therefore, flexibility analysis as a fast and low-cost computational method can be a useful tool for predicting crosslinking pairs in protein crosslinking analysis and facilitating MS data analysis. Finally, flexibility analysis also indicates that the crosslinking of platinum to pairs of Met residues will effectively close the nonpolar groove and thus will likely interfere with the binding of CaM to its protein targets, as was proved by comparing assays for cisplatin-modified/unmodified CaM binding to melittin. Collectively, these results suggest that cisplatin crosslinking of apo-CaM or Ca4-CaM can inhibit the ability of CaM to recognize its target proteins, which may have important implications for understanding the mechanism of tumor resistance to platinum anticancer drugs

A sequential dynamic Bayesian network for pore pressure estimation with uncertainty quantification

Pore-pressure estimation is an important part of oil-well drilling, since drilling into unexpected highly pressured fluids can be costly and dangerous. However, standard estimation methods rarely account for the many sources of uncertainty, or for the multivariate nature of the system. We propose the pore pressure sequential dynamic Bayesian network (PP SDBN) as an appropriate solution to both these issues. The PP SDBN models the relationships between quantities in the pore pressure system, such as pressures, porosity, lithology and wireline log data, using conditional probability distributions based on geophysical relationships to capture our uncertainty about these variables and the relationships between them. When wireline log data is given to the PP SDBN, the probability distributions are updated, providing an estimate of pore pressure along with a probabilistic measure of uncertainty that reflects the data acquired and our understanding of the system. This is the advantage of a Bayesian approach. Our model provides a coherent statistical framework for modelling the pore pressure system. The specific geophysical relationships used can be changed to better suit a particular setting, or reflect geoscientists’ knowledge. We demonstrate the PP SDBN on an offshore well from West Africa. We also perform a sensitivity analysis, demonstrating how this can be used to better understand the working of the model and which parameters are the most influential. The dynamic nature of the model makes it suitable for real time estimation during logging while drilling. The PP SDBN models shale pore pressure in shale rich formations with mechanical compaction as the overriding source of overpressure. The PP SDBN improves on existing methods since it produces a probabilistic estimate that reflects the many sources of uncertainty present

Contrasting Ecosystem-Effects of Morphologically Similar Copepods

Organisms alter the biotic and abiotic conditions of ecosystems. They can modulate the availability of resources to other species (ecosystem engineering) and shape selection pressures on other organisms (niche construction). Very little is known about how the engineering effects of organisms vary among and within species, and, as a result, the ecosystem consequences of species diversification and phenotypic evolution are poorly understood. Here, using a common gardening experiment, we test whether morphologically similar species and populations of Diaptomidae copepods (Leptodiaptomus ashlandi, Hesperodiaptomus franciscanus, Skistodiaptomus oregonensis) have similar or different effects on the structure and function of freshwater ecosystems. We found that copepod species had contrasting effects on algal biomass, ammonium concentrations, and sedimentation rates, and that copepod populations had contrasting effects on prokaryote abundance, sedimentation rates, and gross primary productivity. The average size of ecosystem-effect contrasts between species was similar to those between populations, and was comparable to those between fish species and populations measured in previous common gardening experiments. Our results suggest that subtle morphological variation among and within species can cause multifarious and divergent ecosystem-effects. We conclude that using morphological trait variation to assess the functional similarity of organisms may underestimate the importance of species and population diversity for ecosystem functioning

Ischemic preconditioning in the liver is independent of regulatory T cell activity

Ischemic preconditioning (IPC) protects organs from ischemia reperfusion injury (IRI) through unknown mechanisms. Effector T cell populations have been implicated in the pathogenesis of IRI, and T regulatory cells (Treg) have become a putative therapeutic target, with suggested involvement in IPC. We explored the role of Treg in hepatic IRI and IPC in detail. IPC significantly reduced injury following ischemia reperfusion insults. Treg were mobilized rapidly to the circulation and liver after IRI, but IPC did not further increase Treg numbers, nor was it associated with modulation of circulating pro-inflammatory chemokine or cytokine profiles. We used two techniques to deplete Treg from mice prior to IRI. Neither Treg depleted FoxP3.LuciDTR mice, nor wildtyoe mice depleted of Tregs with PC61, were more susceptible to IRI compared with controls. Despite successful enrichment of Treg in the liver, by adoptive transfer of both iTreg and nTreg or by in vivo expansion of Treg with IL-2/anti-IL-2 complexes, no protection against IRI was observed.We have explored the role of Treg in IRI and IPC using a variety of techniques to deplete and enrich them within both the liver and systemically. This work represents an important negative finding that Treg are not implicated in IPC and are unlikely to have translational potential in hepatic IRI

Application of two-photon absorption laser induced fluorescence to validate actinometry measurements of absolute atomic oxygen number density based on improved EEDFs obtained from PIC simulations.

Actinometry is a non-invasive optical technique that allows absolute atomic oxygen density determination within a plasma provided certain conditions are met. However, the technique is sensitive to to the accuracy of the Electron Energy Distribution Function (EEDF). A Maxwellian distribution is often used for actinometry calculations, but this is typically just an approximation. A Particle in Cell (PIC) code is used to try and generate a more accurate EEDF to improve the actinometry results. To do this the electron density in the plasma is measured using a hairpin probe and compared to the electron density predicted by the PIC code. The code is adjusted to get a reasonable agreement with the hairpin probe electron densities. The corresponding EEDF from the PIC code is then used in the actinoometry model to calculate the atomic oxygen density in the plasma. The actinometry results are compared to oxygen density measurements made using Two-photon Absorption Laser Induced Fluorescence to validate the actinometry results

T-bet is essential for Th1-mediated, but not Th17-mediated, CNS autoimmune disease

T cells that produce both IL-17 and IFN-γ, and co-express ROR-γt and T-bet, are often found at sites of autoimmune inflammation. However, it is unknown whether this co-expression of T-bet with ROR-γt is a prerequisite for immunopathology. We show here that T-bet is not required for the development of Th17-driven experimental autoimmune encephalomyelitis (EAE). The disease was not impaired in T-bet(−/−) mice and was associated with low IFN-γ production and elevated IL-17 production among central nervous system (CNS) infiltrating CD4(+) T cells. T-bet(−/−) Th17 cells generated in the presence of IL-6/TGF-β/IL-1 and IL-23 produced GM-CSF and high levels of IL-17 and induced disease upon transfer to naïve mice. Unlike their WT counterparts, these T-bet(−/–) Th17 cells did not exhibit an IL-17→IFN-γ switch upon reencounter with antigen in the CNS, indicating that this functional change is not critical to disease development. In contrast, T-bet was absolutely required for the pathogenicity of myelin-responsive Th1 cells. T-bet-deficient Th1 cells failed to accumulate in the CNS upon transfer, despite being able to produce GM-CSF. Therefore, T-bet is essential for establishing Th1-mediated inflammation but is not required to drive IL-23-induced GM-CSF production, or Th17-mediated autoimmune inflammation