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Depth of field

Mónica Rouco, Sheean T Haley, Harriet Alexander, Samuel T Wilson, David M Karl, Sonya T Dyhrman
Populations of nitrogen-fixing cyanobacteria in the genus Trichodesmium are critical to ocean ecosystems, yet predicting patterns of Trichodesmium distribution and their role in ocean biogeochemistry is an ongoing challenge. This may, in part, be due to differences in the physiological ecology of Trichodesmium species, which are not typically considered independently in field studies. In this study, the abundance of the two dominant Trichodesmium clades (Clade I and Clade III) was investigated during a survey at Station ALOHA in the North Pacific Subtropical Gyre (NPSG) using a clade-specific qPCR approach...
October 18, 2016: Environmental Microbiology Reports
David R Diercks, Brian P Gorman, Johannes J L Mulders
Six precursors were evaluated for use as in situ electron beam-induced deposition capping layers in the preparation of atom probe tomography specimens with a focus on near-surface features where some of the deposition is retained at the specimen apex. Specimens were prepared by deposition of each precursor onto silicon posts and shaped into sub-70-nm radii needles using a focused ion beam. The utility of the depositions was assessed using several criteria including composition and uniformity, evaporation behavior and evaporation fields, and depth of Ga+ ion penetration...
October 17, 2016: Microscopy and Microanalysis
Chris Jeynes, Julien L Colaux
The analysis of thin films is of central importance for functional materials, including the very large and active field of nanomaterials. Quantitative elemental depth profiling is basic to analysis, and many techniques exist, but all have limitations and quantitation is always an issue. We here review recent significant advances in ion beam analysis (IBA) which now merit it a standard place in the analyst's toolbox. Rutherford backscattering spectrometry (RBS) has been in use for half a century to obtain elemental depth profiles non-destructively from the first fraction of a micron from the surface of materials: more generally, "IBA" refers to the cluster of methods including elastic scattering (RBS; elastic recoil detection, ERD; and non-Rutherford elastic backscattering, EBS), nuclear reaction analysis (NRA: including particle-induced gamma-ray emission, PIGE), and also particle-induced X-ray emission (PIXE)...
October 17, 2016: Analyst
John E Stone, William R Sherman, Klaus Schulten
Immersive molecular visualization provides the viewer with intuitive perception of complex structures and spatial relationships that are of critical interest to structural biologists. The recent availability of commodity head mounted displays (HMDs) provides a compelling opportunity for widespread adoption of immersive visualization by molecular scientists, but HMDs pose additional challenges due to the need for low-latency, high-frame-rate rendering. State-of-the-art molecular dynamics simulations produce terabytes of data that can be impractical to transfer from remote supercomputers, necessitating routine use of remote visualization...
May 2016: IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum: [proceedings]
Jian Huang
Helicoverpa armigera causes serious damage to most crops around the world. However, the impacts of snow thickness on the H. armigera overwintering pupae are little known. A field experiment was employed in 2012-2015 at Urumqi, China. At soil depths of 5, 10, and 15 cm, overwintering pupae were embedded with four treatments: no snow cover (NSC), snow cover (SC), increasing snow thickness to 1.5 times the thickness of SC (ISSC-1), and to two times the thickness of SC (ISSC-2). Results suggested that snow cover and increasing snow thickness both significantly increased soil temperatures, which helped to decrease the mortality of overwintering pupae (MOP) of H...
October 15, 2016: International Journal of Biometeorology
Giuseppe Roberto Pisaturo, Maurizio Righetti, Michael Dumbser, Markus Noack, Matthias Schneider, Valentina Cavedon
One way to study ecological implications induced by hydropeaking represents the coupling of hydrodynamic models with habitat suitability models, in which hydrodynamic parameters are typically used to describe the physical habitat of indicator species. This article discusses the differences in habitat suitability assessment between 2D and 3D CFD modelling as input for the habitat simulation tool CASiMiR. In the first part of the article, the accuracy of the hydraulic model is evaluated by comparing the model results with laboratory (model of a laboratory channel with erodible bed) and field measurements (Valsura River, Bolzano, Italy)...
October 12, 2016: Science of the Total Environment
Jonathan C Niclis, Carlos W Gantner, Walaa F Alsanie, Stuart J McDougall, Chris R Bye, Andrew G Elefanty, Edouard G Stanley, John M Haynes, Colin W Pouton, Lachlan H Thompson, Clare L Parish
: : Recent studies have shown evidence for the functional integration of human pluripotent stem cell (hPSC)-derived ventral midbrain dopamine (vmDA) neurons in animal models of Parkinson's disease. Although these cells present a sustainable alternative to fetal mesencephalic grafts, a number of hurdles require attention prior to clinical translation. These include the persistent use of xenogeneic reagents and challenges associated with scalability and storage of differentiated cells. In this study, we describe the first fully defined feeder- and xenogeneic-free protocol for the generation of vmDA neurons from hPSCs and utilize two novel reporter knock-in lines (LMX1A-eGFP and PITX3-eGFP) for in-depth in vitro and in vivo tracking...
October 14, 2016: Stem Cells Translational Medicine
Juan D Rojas, Paul A Dayton
Sub-micron phase-change contrast agents consist of a liquid perfluorocarbon core that can be vaporized by ultrasound (acoustic droplet vaporization) to generate contrast with excellent spatial and temporal control. When these agents, commonly referred to as nanodroplets, are formulated with cores of low boiling-point perfluorocarbons such as decafluorobutane and octafluoropropane, they can be activated with lowmechanical index imaging pulses for diagnostic applications. Since the utilization of minimum mechanical index is often desirable to avoid unnecessary biological effects, enabling consistent activation of these agents in an acoustic field is a challenge because the energy that must be delivered to achieve the vaporization threshold increases with depth due to attenuation...
October 12, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
Alexander A Doinikov, Thomas Combriat, Pierre Thibault, Philippe Marmottant
A theoretical model is developed for acoustic streaming generated by a cylindrical bubble confined in a fluid channel between two planar elastic walls. The bubble is assumed to undergo volume and translational oscillations. The volume oscillation is caused by an imposed acoustic pressure field and generates the bulk scattered wave in the fluid gap and Lamb-type surface waves propagating along the fluid-wall interfaces. The translational oscillation is induced by the velocity field of an external sound source such as another bubble or an oscillatory fluid flow...
September 2016: Physical Review. E
Damianos Chatzievangelou, Carolina Doya, Laurenz Thomsen, Autun Purser, Jacopo Aguzzi
Three benthic megafaunal species (i.e. sablefish Anoplopoma fimbria; pacific hagfish Eptatretus stoutii and a group of juvenile crabs) were tested for diel behavioral patterns at the methane hydrates site of Barkley Canyon (890 m depth), off Vancouver Island (BC, Canada). Fluctuations of animal counts in linear video-transects conducted with the Internet Operated Deep-Sea Crawler "Wally" in June, July and December of 2013, were used as proxy of population activity rhythms. Count time series and environmental parameters were analyzed under the hypothesis that the environmental conditioning of activity rhythms depends on the life habits of particular species (i...
2016: PloS One
Ziad El Rassi, Chanida Puangpila
This review article is an update of our previous one by C. Puangpila, E. Mayadunne and Z. El Rassi, Electrophoresis 2015, 36, 238-252. Similarly to the previous article, this review has two main topics, including (i) proteomic sample preparation (e.g., depletion of high abundance proteins, reduction of the protein dynamic concentration range and enrichment of a particular sub-proteome), and (ii) the subsequent chromatographic and/or electrophoretic pre-fractionation prior to protein separation and identification by LC-MS/MS...
October 12, 2016: Electrophoresis
Ekaterina Rostova, Carine Ben Adiba, Giovanni Dietler, Sergey K Sekatskii
Optical biosensors based on photonic crystal surface waves (PC SWs) offer a possibility to study binding interactions with living cells, overcoming the limitation of rather small evanescent field penetration depth into a sample medium that is characteristic for typical optical biosensors. Besides this, simultaneous excitation of s- and p-polarized surface waves with different penetration depths is realized here, permitting unambiguous separation of surface and volume contributions to the measured signal. PC-based biosensors do not require a bulk signal correction, compared to widely used surface plasmon resonance-based devices...
October 11, 2016: Biosensors
Steven E Massey
Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis...
August 2016: Microbiology Spectrum
Mohammadkarim Bahadori, Hamid Reza Khankeh, Rouhollah Zaboli, Ramin Ravangard, Isa Malmir
OBJECTIVE: Coordination is a major challenge in the field of health in disasters, mostly because of the complex nature of health-related activities. METHODS: This was a qualitative study based on the grounded theory approach. A total of 22 experts in the field of health in disasters participated in the study. The data were collected through in-depth interviews and literature review. The collected data were then analyzed by use of MAXQDA 2010 software (VERBI Software GmbH)...
October 11, 2016: Disaster Medicine and Public Health Preparedness
Simone Orlowski, Sharon Lawn, Ben Matthews, Anthony Venning, Kaisha Wyld, Gabrielle Jones, Megan Winsall, Gaston Antezana, Geoffrey Schrader, Niranjan Bidargaddi
BACKGROUND: Digital technologies show promise for reversing poor engagement of youth (16-24 years) with mental health services. In particular, mobile and internet based applications with communication capabilities can augment face-to-face mental health service provision. The literature in this field, however, fails to adequately capture the perspectives of the youth mental health workforce regarding utility and acceptability of technology for this purpose. METHODS: This paper describes results of in-depth qualitative data drawn from various stakeholders involved in provision of youth mental health services in one Australian rural region...
October 10, 2016: BMC Health Services Research
S Somanadhan, P J Larkin
BACKGROUND: Many rare diseases of childhood are life-threatening and chronically debilitating, so living with a rare disease is an on-going challenge for patients and their families. MPS is one of a range of rare inherited metabolic disorders (IMDs) that come under category 3 of life-limiting conditions, where there is no curative treatment available at present. Although the study of rare diseases is increasingly novel, and of clinical importance to the population, the lack of empirical data in the field to support policy and strategy development is a compelling argument for further research to be sought...
October 10, 2016: Orphanet Journal of Rare Diseases
Sindhu Ghanta, Michael I Jordan, Kivanc Kose, Dana H Brooks, Milind Rajadhyaksha, Jennifer G Dy
Segmenting objects of interest from 3D datasets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging...
October 5, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Bettina L Love
Through narrative inquiry, utilizing in-depth interviews and field observations, the goal of this research is to begin a dialogue within the field of education and mentoring scholarship that expands the mentoring of Black males beyond traditional norms of sex and gender identities/performances to reimagine the ways in which Black female masculinity can be a site of mentoring for Black and Brown boys.
October 10, 2016: Journal of Lesbian Studies
Xiao Li, Julio C Armas-Perez, Jose A Martinez-Gonzalez, Xiaoying Liu, Helou Xie, Camille Bishop, Juan P Hernandez-Ortiz, Rui Zhang, Juan J de Pablo, Paul F Nealey
The morphology and through-film optical properties of nematic liquid crystals (LCs) confined between two surfaces may be engineered to create switches that respond to external electric fields, thereby enabling applications in optoelectronics that require fast responses and low power. Interfacial properties between the confining surfaces and the LC play a central role in device design and performance. Here we investigate the morphology of LCs confined in hybrid cells with a top surface that exhibits uniform homeotropic anchoring and a bottom surface that is chemically patterned with sub-micron and micron- wide planar anchoring stripes in a background of homeotropic anchoring...
September 27, 2016: Soft Matter
Brent A Bell, Alex Yuan, Rose M Dicicco, Joseph Fogerty, Emma M Lessieur, Brian D Perkins
Non-invasive imaging is an invaluable diagnostic tool in ophthalmology. Two imaging devices, the scanning laser ophthalmoscope (SLO) and spectral domain optical coherence tomography (SDOCT), emerged from the clinical realm to provide research scientists with a real-time view of ocular morphology in living animals. We utilized these two independent imaging modalities in a complementary manner to perform in vivo optical sectioning of the adult zebrafish retina. Due to the very high optical power of the zebrafish lens, the confocal depth of field is narrow, allowing for detailed en face views of specific retinal layers, including the cone mosaic...
October 6, 2016: Experimental Eye Research
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