Quantitative 3D strain analysis in analogue experiments: Integration of X-ray computed tomography and digital volume correlation techniques

The combination of scaled analogue experiments, material mechanics, X-ray computed tomography (XRCT) and Digital Volume Correlation techniques (DVC) is a powerful new tool not only to examine the 3 dimensional structure and kinematic evolution of complex deformation structures in scaled analogue experiments, but also to fully quantify their spatial strain distribution and complete strain history. Digital image correlation (DIC) is an important advance in quantitative physical modelling and helps to understand non-linear deformation processes. Optical non-intrusive (DIC) techniques enable the quantification of localised and distributed deformation in analogue experiments based either on images taken through transparent sidewalls (2D DIC) or on surface views (3D DIC). X-ray computed tomography (XRCT) analysis permits the non-destructive visualisation of the internal structure and kinematic evolution of scaled analogue experiments simulating tectonic evolution of complex geological structures. The combination of XRCT sectional image data of analogue experiments with 2D DIC only allows quantification of 2D displacement and strain components in section direction. This completely omits the potential of CT experiments for full 3D strain analysis of complex, non-cylindrical deformation structures. In this study, we apply digital volume correlation (DVC) techniques on XRCT scan data of “solid” analogue experiments to fully quantify the internal displacement and strain in 3 dimensions over time. Our first results indicate that the application of DVC techniques on XRCT volume data can successfully be used to quantify the 3D spatial and temporal strain patterns inside analogue experiments. We demonstrate the potential of combining DVC techniques and XRCT volume imaging for 3D strain analysis of a contractional experiment simulating the development of a non-cylindrical pop-up structure. Furthermore, we discuss various options for optimisation of granular materials, pattern generation, and data acquisition for increased resolution and accuracy of the strain results. Three-dimensional strain analysis of analogue models is of particular interest for geological and seismic interpretations of complex, non-cylindrical geological structures. The volume strain data enable the analysis of the large-scale and small-scale strain history of geological structures.

Fluorinated olefinic peptide nucleic acid: synthesis and pairing properties with complementary DNA

The fluorinated olefinic peptide nucleic acid (F-OPA) system was designed as a peptide nucleic acid (PNA) analogue in which the base carrying amide moiety was replaced by an isostructural and isoelectrostatic fluorinated C-C double bond, locking the nucleobases in one of the two possible rotameric forms. By comparison of the base-pairing properties of this analogue with its nonfluorinated analogue OPA and PNA, we aimed at a closer understanding of the role of this amide function in complementary DNA recognition. Here we present the synthesis of the F-OPA monomer building blocks containing the nucleobases A, T, and G according to the MMTr/Acyl protecting group scheme. Key steps are a selective desymmetrization of the double bond in the monomer precursor via lactonization as well as a highly regioselective Mitsunobu reaction for the introduction of the bases. PNA decamers containing single F-OPA mutations and fully modified F-OPA decamers and pentadecamers containing the bases A and T were synthesized by solid-phase peptide chemistry, and their hybridization properties with complementary parallel and antiparallel DNA were assessed by UV melting curves and CD spectroscopic methods. The stability of the duplexes formed by the decamers containing single (Z)-F-OPA modifications with parallel and antiparallel DNA was found to be strongly dependent on their position in the sequence with T(m) values ranging from +2.4 to -8.1 degrees C/modification as compared to PNA. Fully modified F-OPA decamers and pentadecamers were found to form parallel duplexes with complementary DNA with reduced stability compared to PNA or OPA. An asymmetric F-OPA pentadecamer was found to form a stable self-complex (T(m) approximately 65 degrees C) of unknown structure. The generally reduced affinity to DNA may therefore be due to an increased propensity for self-aggregation

Exploring Hoogsteen and reversed-Hoogsteen duplex and triplex formation with tricyclo-DNA purine sequences

The duplex- and triplex-formation properties of the tricyclo-DNA purine decamer 5'p-gagaaggaaa-3' as a single strand or as part of a hairpin duplex with corresponding parallel and antiparallel pyrimidine DNA and RNA complements, as well as with antiparallel purine DNA and RNA complements, were investigated by UV melting curve analysis, circular dichroism spectroscopy, and gel mobility shift experiments. It was found that tricyclo-DNA forms very stable duplexes with the pyrimidine RNA and DNA complements not only in the Watson-Crick pairing mode, but also in the Hoogsteen one. Below pH 6.0, the tc-DNA/DNA and tc-DNA/RNA Hoogsteen duplexes were found to be more stable than the corresponding Watson-Crick DNA duplexes. Triplexes of the hairpin structure with parallel pyrimidine complements revealed even stronger Hoogsteen pairing relative to the duplexes, presumably due to structural preorganization phenomena. Triplex formation with antiparallel pyrimidine and purine third strands (reversed-Hoogsteen motif) could not be observed and seem to be unstable

International Clostridium difficile animal strain collection and large diversity of animal associated strains

BACKGROUND Clostridium difficile is an important cause of intestinal infections in some animal species and animals might be a reservoir for community associated human infections. Here we describe a collection of animal associated C. difficile strains from 12 countries based on inclusion criteria of one strain (PCR ribotype) per animal species per laboratory. RESULTS Altogether 112 isolates were collected and distributed into 38 PCR ribotypes with agarose based approach and 50 PCR ribotypes with sequencer based approach. Four PCR ribotypes were most prevalent in terms of number of isolates as well as in terms of number of different host species: 078 (14.3% of isolates; 4 hosts), 014/020 (11.6%; 8 hosts); 002 (5.4%; 4 hosts) and 012 (5.4%; 5 hosts). Two animal hosts were best represented; cattle with 31 isolates (20 PCR ribotypes; 7 countries) and pigs with 31 isolates (16 PCR ribotypes; 10 countries). CONCLUSIONS This results show that although PCR ribotype 078 is often reported as the major animal C. difficile type, especially in pigs, the variability of strains in pigs and other animal hosts is substantial. Most common human PCR ribotypes (014/020 and 002) are also among most prevalent animal associated C. difficile strains worldwide. The widespread dissemination of toxigenic C. difficile and the considerable overlap in strain distribution between species furthers concerns about interspecies, including zoonotic, transmission of this critically important pathogen.

An initiative for participatory monitoring of large scale acquisitions: Opportunities and results thus far

Increasing commercial pressures on land are provoking fundamental and far-reaching changes in the relationships between people and land. Much knowledge on land-oriented investments projects currently comes from the media. Although this provides a good starting point, lack of transparency and rapidly changing contexts mean that this is often unreliable. The International Land Coalition, in partnership with Oxfam Novib, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), University of Pretoria, Centre for Development and Environment of the University of Bern (CDE), and GIZ, started to compile an inventory of land-related investments. This project aims to better understand the extent, trends and impacts of land-related investments by supporting an ongoing and systematic stocktaking exercise of the various investment projects currently taking place worldwide. It involves a large number of organizations and individuals working in areas where land transactions are being made, and able to provide details of such investments. The project monitors land transactions in rural areas that imply a transformation of land use rights from communities and smallholders to commercial use, and are made both by domestic and foreign investors (private actors, governments, government-back private investors). The focus is on investments for food or agrofuel production, timber extraction, carbon trading, mineral extraction, conservation and tourism. A novel way of using ITC to document land acquisitions in a spatially explicit way and by using an approach called “crowdsourcing” is being developed. This approach will allow actors to share information and knowledge directly and at any time on a public platform, where it will be scrutinized in terms of reliability and cross checked with other sources. Up to now, over 1200 deals have been recorded across 96 countries. Details of such transactions have been classified in a matrix and distributed to over 350 contacts worldwide for verification. The verified information has been geo-referenced and represented in two global maps. This is an open database enabling a continued monitoring exercise and the improvement of data accuracy. More information will be released over time. The opportunities arise from overcoming constraints by incomplete information by proposing a new way of collecting, enhancing and sharing information and knowledge in a more democratic and transparent manner. The intention is to develop interactive knowledge platform where any interested person can share and access information on land deals, their link to involved stakeholders, and their embedding into a geographical context. By making use of new ICT technologies that are more and more in the reach of local stakeholders, as well as open access and web-based spatial information systems, it will become possible to create a dynamic database containing spatial explicit data. Feeding in data by a large number of stakeholders, increasingly also by means of new mobile ITC technologies, will open up new opportunities to analyse, monitor and assess highly dynamic trends of land acquisition and rural transformation.

The elusive S2 state, the S1/S2 splitting, and the excimer states of the benzene dimer

We observe the weak S 0 → S 2 transitions of the T-shaped benzene dimers (Bz)2 and (Bz-d 6)2 about 250 cm−1 and 220 cm−1 above their respective S 0 → S 1 electronic origins using two-color resonant two-photon ionization spectroscopy. Spin-component scaled (SCS) second-order approximate coupled-cluster (CC2) calculations predict that for the tipped T-shaped geometry, the S 0 → S 2 electronic oscillator strength f el (S 2) is ∼10 times smaller than f el (S 1) and the S 2 state lies ∼240 cm−1 above S 1, in excellent agreement with experiment. The S 0 → S 1 (ππ ∗) transition is mainly localized on the “stem” benzene, with a minor stem → cap charge-transfer contribution; the S 0 → S 2 transition is mainly localized on the “cap” benzene. The orbitals, electronic oscillator strengths f el (S 1) and f el (S 2), and transition frequencies depend strongly on the tipping angle ω between the two Bz moieties. The SCS-CC2 calculated S 1 and S 2 excitation energies at different T-shaped, stacked-parallel and parallel-displaced stationary points of the (Bz)2 ground-state surface allow to construct approximate S 1 and S 2 potential energy surfaces and reveal their relation to the “excimer” states at the stacked-parallel geometry. The f el (S 1) and f el (S 2) transition dipole moments at the C 2v -symmetric T-shape, parallel-displaced and stacked-parallel geometries are either zero or ∼10 times smaller than at the tipped T-shaped geometry. This unusual property of the S 0 → S 1 and S 0 → S 2 transition-dipole moment surfaces of (Bz)2 restricts its observation by electronic spectroscopy to the tipped and tilted T-shaped geometries; the other ground-state geometries are impossible or extremely difficult to observe. The S 0 → S 1/S 2 spectra of (Bz)2 are compared to those of imidazole ⋅ (Bz)2, which has a rigid triangular structure with a tilted (Bz)2 subunit. The S 0 → S 1/ S 2 transitions of imidazole-(benzene)2 lie at similar energies as those of (Bz)2, confirming our assignment of the (Bz)2 S 0 → S 2 transition.

Barriers to cross-border research projects: A prelude to improving professional collaborations between the United States and Mexico

Study objective. This was a secondary data analysis of a study designed and executed in two phases in order to investigate several questions: Why aren't more investigators conducting successful cross-border research on human health issues? What are the barriers to conducting this research? What interventions might facilitate cross-border research? ^ Methods. Key informant interviews and focus groups were used in Phase One, and structured questionnaires in Phase Two. A multi-question survey was created based on the findings of focus groups and distributed to a wider circle of researchers and academics for completion. The data was entered and analyzed using SPSS software. ^ Setting. El Paso, TX located on the U.S-Mexico Border. ^ Participants. Individuals from local academic institutions and the State Department of Health. ^ Results. From the transcribed data of the focus groups, eight major themes emerged: Political Barriers, Language/Cultural Barriers, Differing Goals, Geographic Issues, Legal Barriers, Technology/Material Issues, Financial Barriers, and Trust Issues. Using these themes, the questionnaire was created. ^ The response rate for the questionnaires was 47%. The largest obstacles revealed by this study were identifying a funding source for the project (47% agreeing or strongly agreeing), difficulties paying a foreign counterpart (33% agreeing or strongly agreeing) and administrative changes in Mexico (31% agreeing or strongly agreeing). ^ Conclusions. Many U.S. investigators interested in cross-border research have been discouraged in their efforts by varying barriers. The majority of respondents in the survey felt financial issues and changes in Mexican governments were the most significant obstacles. While some of these barriers can be overcome simply by collaboration among motivated groups, other barriers may be more difficult to remove. Although more evaluation of this research question is warranted, the information obtained through this study is sufficient to support creation of a Cross-Border Research Resource Manual to be used by individuals interested in conducting research with Mexico. ^

Design and Optimization of Four-dimensional Cone-beam Computed Tomography in Image-guided Radiation Therapy

The influence of respiratory motion on patient anatomy poses a challenge to accurate radiation therapy, especially in lung cancer treatment. Modern radiation therapy planning uses models of tumor respiratory motion to account for target motion in targeting. The tumor motion model can be verified on a per-treatment session basis with four-dimensional cone-beam computed tomography (4D-CBCT), which acquires an image set of the dynamic target throughout the respiratory cycle during the therapy session. 4D-CBCT is undersampled if the scan time is too short. However, short scan time is desirable in clinical practice to reduce patient setup time. This dissertation presents the design and optimization of 4D-CBCT to reduce the impact of undersampling artifacts with short scan times. This work measures the impact of undersampling artifacts on the accuracy of target motion measurement under different sampling conditions and for various object sizes and motions. The results provide a minimum scan time such that the target tracking error is less than a specified tolerance. This work also presents new image reconstruction algorithms for reducing undersampling artifacts in undersampled datasets by taking advantage of the assumption that the relevant motion of interest is contained within a volume-of-interest (VOI). It is shown that the VOI-based reconstruction provides more accurate image intensity than standard reconstruction. The VOI-based reconstruction produced 43% fewer least-squares error inside the VOI and 84% fewer error throughout the image in a study designed to simulate target motion. The VOI-based reconstruction approach can reduce acquisition time and improve image quality in 4D-CBCT.

Family Preservation Conference Participants and the Internet: Opinions about On-Line Continuing Education

Development of distance and distributed learning continuing education (CE) opportunities for human services workers requires existence of such CE offerings, participant access to the Internet, knowledge of the Internet's use, and willingness to enroll in such programs. A survey of human services professionals who attended the Family Preservation Annual Conferences in 2000 (N = 230) and 2002 (N - 197) revealed that 92% (n = 206) of 2000 survey participants and 98% (192) of 2002 survey participants have used the Internet, while 76% of 2000 and 56% of 2002 respondents reported no formal training in the use of the Internet and its features. Findings are reported that reveal substantial interest among subjects in the Internet as a medium for continuing education programs for professional development.

Renal Cryoablation: Investigation of Periprocedural Visualization Tools and Treatment Response Quantification

Cryoablation for small renal tumors has demonstrated sufficient clinical efficacy over the past decade as a non-surgical nephron-sparing approach for treating renal masses for patients who are not surgical candidates. Minimally invasive percutaneous cryoablations have been performed with image guidance from CT, ultrasound, and MRI. During the MRI-guided cryoablation procedure, the interventional radiologist visually compares the iceball size on monitoring images with respect to the original tumor on separate planning images. The comparisons made during the monitoring step are time consuming, inefficient and sometimes lack the precision needed for decision making, requiring the radiologist to make further changes later in the procedure. This study sought to mitigate uncertainty in these visual comparisons by quantifying tissue response to cryoablation and providing visualization of the response during the procedure. Based on retrospective analysis of MR-guided cryoablation patient data, registration and segmentation algorithms were investigated and implemented for periprocedural visualization to deliver iceball position/size with respect to planning images registered within 3.3mm with at least 70% overlap and a quantitative logit model was developed to relate perfusion deficit in renal parenchyma visualized in verification images as a result of iceball size visualized in monitoring images. Through retrospective study of 20 patient cases, the relationship between likelihood of perfusion loss in renal parenchyma and distance within iceball was quantified and iteratively fit to a logit curve. Using the parameters from the logit fit, the margin for 95% perfusion loss likelihood was found to be 4.28 mm within the iceball. The observed margin corresponds well with the clinically accepted margin of 3-5mm within the iceball. In order to display the iceball position and perfusion loss likelihood to the radiologist, algorithms were implemented to create a fast segmentation and registration module which executed in under 2 minutes, within the clinically-relevant 3 minute monitoring period. Using 16 patient cases, the average Hausdorff distance was reduced from 10.1mm to 3.21 mm with average DSC increased from 46.6% to 82.6% before and after registration.

Anisotropy and acoustic properties at DSDP Holes 62-463 and 62-465A

Variations of acoustic properties within the sediment column may significantly affect the propagation of acoustic energy in the upper portion of the oceanic crust. Moreover, the acoustic properties of sediments reflect their mineral compositions, fabrics, and degrees of compaction and cementation. Hence, the physical properties of indurated deep-sea sediments are of considerable geophysical and geological interest. Chalks and limestones are particularly important because substantial accumulations of biogenic carbonates are generally present at the base of the deep-sea sediment column, and high-standing features such as Hess Rise are capped by calcareous deposits. This paper constitutes a preliminary report of the compressional-wave velocities and densities of 31 indurated calcareous sediment samples recovered at DSDP Sites 463 and 465, in the Mid-Pacific Mountains and on Hess Rise, respectively. The sample set includes nine pairs of samples in which velocities were measured parallel and perpendicular to bedding to determine the velocity anisotropy of the sediment. This research is part of an ongoing study of the seismic properties of indurated deep-sea carbonates.

Growth rates and biometric measurements of coccolithophores (Coccolithus pelagicus, Coccolithus braarudii, Emiliania huxleyi) during experiments

Coccolithophores, a diverse group of phytoplankton, make important contributions to pelagic calcite production and export, yet the comparative biogeochemical role of species other than the ubiquitous Emiliania huxleyi is poorly understood. Here we examined the relative importance of E. huxleyi and two Coccolithus species (Coccolithus pelagicus and Coccolithus braarudii), in terms of daily calcite production, by culturing E. huxleyi and Coccolithus in parallel, and comparing growth rates and biometrically determined cellular carbon calcite quotas. Biometric measurements of Coccolithus species, and E. huxleyi cell diameters, were performed using polarised light microscopy. Scanning electron microscopy was used for all other biometric measurements of E. huxleyi.

Seismic velocities and elastic properties of gabbroic rocks from ODP Hole 118-735B

The nearly continuous recovery of 0.5 km of generally fresh, layer 3 gabbroic rocks at Hole 735B, especially near the bottom of the section, presents scientists an unusual opportunity to study the detailed elastic properties of the lower oceanic crust. Extending compressional-wave and density shipboard measurements at room pressure, Vp and Vs were measured at pressures from 20 to 200 MPa using the pulse transmission method. All of the rocks exhibit significant increases in velocity with increasing pressure up to about 150 MPa, a feature attributed to the closing of microcrack porosity. Measured velocities reflect the mineralogical makeup and microstructures acquired during the tectonic history of Hole 735B. Most of the undeformed and unaltered gabbros are approximately 65:35 plagioclase/clinopyroxene rocks plus olivine or oxide minerals, and the observed densities and velocities are fully consistent with the Voigt-Reuss-Hill (VRH) averages of the component minerals and their proportions. Depending on their olivine content, the predominant olivine gabbros at 200 MPa have average Vp = 7.1 ± 0.2 km/s, Vs = 3.9 ± 0.1 km/s, and grain densities of 2.95 ± 0.5 g/cm3. The less abundant iron-titanium (Fe-Ti) oxide gabbros average Vp = 6.75 ± 0.15 km/s, Vs = 3.70 ± 0.1 km/s, and grain densities of 3.22 ± 0.05 g/cm3, reflecting the higher densities and lower velocities of oxide minerals compared to olivine. About 30% of the core is plastically deformed, and the densities and directionally averaged velocities of these shear-zone tectonites are generally consistent with those of the gabbros, their protoliths. Three sets of observations indicate that the shear-zone metagabbros are elastically anisotropic: (1) directional variations in Vp, both vertical and horizontal and with respect to foliation and lineation; (2) discrepancies among Vp values for the horizontal cores and the VRH averages of the component minerals and their mineral proportions, suggesting preferred crystallographic orientations of anisotropic minerals; and (3) variations of Vs of up to 7%, with polarization directions parallel and perpendicular to foliation. Optical inspection of thin sections of the same samples indicates that plagioclase feldspar, clinopyroxene, and amphibole typically display crystallographic-preferred orientations, and this, plus the elastic anisotropy of these minerals, suggests that preferred orientations are responsible for much of the observed anisotropy, particularly at high pressure. Alteration tends to be localized to brittle faults and brecciated zones, and typical alteration minerals are amphibole and secondary plagioclase, which do not significantly change the velocity-density relationships.

Artificial oxygen fluxes measured by the eddy correlation method using stirring-sensitive oxygen microsensor and oxygen optodes in a flume experiment

In the last decade, the aquatic eddy correlation (EC) technique has proven to be a powerful approach for non-invasive measurements of oxygen fluxes across the sediment water interface. Fundamental to the EC approach is the correlation of turbulent velocity and oxygen concentration fluctuations measured with high frequencies in the same sampling volume. Oxygen concentrations are commonly measured with fast responding electrochemical microsensors. However, due to their own oxygen consumption, electrochemical microsensors are sensitive to changes of the diffusive boundary layer surrounding the probe and thus to changes in the ambient flow velocity. The so-called stirring sensitivity of microsensors constitutes an inherent correlation of flow velocity and oxygen sensing and thus an artificial flux which can confound the benthic flux determination. To assess the artificial flux we measured the correlation between the turbulent flow velocity and the signal of oxygen microsensors in a sealed annular flume without any oxygen sinks and sources. Experiments revealed significant correlations, even for sensors designed to have low stirring sensitivities of ~0.7%. The artificial fluxes depended on ambient flow conditions and, counter intuitively, increased at higher velocities because of the nonlinear contribution of turbulent velocity fluctuations. The measured artificial fluxes ranged from 2 - 70 mmol m**-2 d**-1 for weak and very strong turbulent flow, respectively. Further, the stirring sensitivity depended on the sensor orientation towards the flow. Optical microsensors (optodes) that should not exhibit a stirring sensitivity were tested in parallel and did not show any significant correlation between O2 signals and turbulent flow. In conclusion, EC data obtained with electrochemical sensors can be affected by artificial flux and we recommend using optical microsensors in future EC-studies. Flume experiments were conducted in February 2013 at the Institute for Environmental Sciences, University of Koblenz-Landau Landau. Experiments were performed in a closed oval-shaped acrylic glass flume with cross-sectional width of 4 cm and height of 10 cm and total length of 54 cm. The fluid flow was induced by a propeller driven by a motor and mean flow velocities of up to 20 cm s-1 were generated by applying voltages between 0 V and 4 V DC. The flume was completely sealed with an acrylic glass cover. Oxygen sensors were inserted through rubber seal fittings and allowed positioning the sensors with inclinations to the main flow direction of ~60°, ~95° and ~135°. A Clark type electrochemical O2 microsensor with a low stirring sensitivity (0.7%) was tested and a fast-responding needle-type O2 optode (PyroScience GmbH, Germany) was used as reference as optodes should not be stirring sensitive. Instantaneous three-dimensional flow velocities were measured at 7.4 Hz using stereoscopic particle image velocimetry (PIV). The velocity at the sensor tip was extracted. The correlation of the fluctuating O2 sensor signals and the fluctuating velocities was quantified with a cross-correlation analysis. A significant cross-correlation is equivalent to a significant artificial flux. For a total of 18 experiments the flow velocity was adjusted between 1.7 and 19.2 cm s**-1, and 3 different orientations of the electrochemical sensor were tested with inclination angles of ~60°, ~95° and ~135° with respect to the main flow direction. In experiments 16-18, wavelike flow was induced, whereas in all other experiments the motor was driven by constant voltages. In 7 experiments, O2 was additionally measured by optodes. Although performed simultaneously with the electrochemical sensor, optode measurements are listed as separate experiments (denoted by the attached 'op' in the filename), because the velocity time series was extracted at the optode tip, located at a different position in the flume.

Major and trace element data for the Mehmetalan (ME), Mollatopuz (MO), and Alabayir (C) diabase dykes in turkey

The diabases cut across the ophiolites as parallel and variably thick dyke-swarms. Geochemistry of the diabases reveals three distinct groups, including a) supra-subduction zone (SSZ) type, which is characterized by marked Nb-anomaly and normal mid-ocean ridge basalt (N-MORB) like HFSE distribution, b) enriched MORB (E-MORB) type, showing some degree of enrichment relative to N-MORB, c) oceanic-island basalt (OIB) type with characteristic hump-backed trace element patterns, coupled with fractionated REE distribution.