Magnetic tests for magnetosome chains in Martian meteorite ALH84001

Transmission electron microscopy studies have been used to argue that magnetite crystals in carbonate from Martian meteorite ALH84001 have a composition and morphology indistinguishable from that of magnetotactic bacteria. It has even been claimed from scanning electron microscopy imaging that some ALH84001 magnetite crystals are aligned in chains. Alignment of magnetosomes in chains is perhaps the most distinctive of the six crystallographic properties thought to be collectively unique to magnetofossils. Here we use three rock magnetic techniques, low-temperature cycling, the Moskowitz test, and ferromagnetic resonance, to sense the bulk composition and crystallography of millions of ALH84001 magnetite crystals. The magnetic data demonstrate that although the magnetite is unusually pure and fine-grained in a manner similar to terrestrial magnetofossils, most or all of the crystals are not arranged in chains

Local structural studies of Ba1−x_{1-x}Kx_xFe2_2As2_2 using atomic pair distribution function analysis

Systematic local structural studies of Ba$_{1-x}$K$_x$Fe$_2$As$_2$ system are undertaken at room temperature using atomic pair distribution function (PDF) analysis. The local structure of the Ba$_{1-x}$K$_x$Fe$_2$As$_2$ is found to be well described by the long-range structure extracted from the diffraction experiments, but with anisotropic atomic vibrations of the constituent atoms ($U_{11}$ = $U_{22} \ne U_{33}$). The crystal unit cell parameters, the FeAs$_4$ tetrahedral angle and the pnictogen height above the Fe-plane are seen to show systematic evolution with K doping, underlining the importance of the structural changes, in addition to the charge doping, in determining the properties of Ba$_{1-x}$K$_x$Fe$_2$As$_2$

Improved methods for magnetic purification of malaria parasites and haemozoin

<p>Abstract</p> <p>Background</p> <p>Malaria parasites generate free haem upon catabolism of host haemoglobin during their intraerythrocytic growth cycle. In order to minimize oxidative toxicity of the ferric iron, the free haem molecules are polymerized into the biomineral beta-haematin (commonly referred to as haemozoin). Haemozoin crystals are paramagnetic, and this property can be exploited for the purification of late stage parasites as they contain larger haemozoin crystals than early stage parasites and uninfected cells. Commercially available magnets that were originally developed for the purpose of antibody-mediated cell purification are widely used for this purpose. As these methods are not necessarily optimized for parasite purification, the relationship between magnetic field strength and the quantity and quality of yield during parasite purification was explored.</p> <p>Methods</p> <p>Inexpensive rare-earth neodymium magnets with commercially available disposable columns were employed to explore the relationship between magnetic field strength and recovery of free haemozoin and infected erythrocytes (iRBCs).</p> <p>Results</p> <p>Yields of free haemozoin increased nearly linearly with increasing magnetic field strength to the strongest fields tested (8,500 Gauss). Stronger magnetic fields also improved the recovery of iRBCs with no detrimental effects on parasite viability. An in-house constructed magnetic stand, built for $75 in materials, produced superior results when compared with much more expensive commercial products.</p> <p>Conclusions</p> <p>Existing protocols for the magnetic purification of free haemozoin and iRBCs result in sub-optimal yields. Inexpensive high-strength neodymium magnets offer a better option, resulting in higher yields with no detrimental effects on parasite viability.</p

Simultaneous development of the Pediatric GERD Caregiver Impact Questionnaire (PGCIQ) in American English and American Spanish

BACKGROUND: The objective of this study was to develop simultaneously a new questionnaire, the Pediatric GERD Caregiver Impact Questionnaire (PGCIQ), in American English and American Spanish in order to elucidate the impact of caring for a child with GERD. METHODS: Two focus group discussions were conducted in American English and American Spanish to develop a relevant conceptual model. Focus group participants were the primary caregivers of children with GERD (newborn through 12 years of age). Participant responses were qualitatively analyzed to identify potential differences in caregiver perspectives by the caregiver's language, socio-economic status and demographic profile as well as the child's age and disease severity level. Items in the PGCIQ were generated simultaneously in English and Spanish by reviewing results of qualitative analysis from focus groups in each language. The PGCIQ was finalized in both languages after testing content validity and conducting an in-depth translatability assessment. RESULTS: Analysis of focus group comments resulted in the development of a first draft questionnaire consisting of 58 items in 10 domains. Content validity testing and an in-depth translatability assessment resulted in wording modification of 37 items, deletion of 14 items and the addition of a domain with five items. Feedback from the content validity testing interviews indicated that the instrument is conceptually relevant in both American English and American Spanish, clear, comprehensive and easy to complete within 10 minutes. The final version of the PGCIQ contains 49 items assessing ten domains. An optional module with nine items is available for investigative research purposes and for use only at baseline. CONCLUSION: The PGCIQ was developed using simultaneous item generation, a process that allows for consideration of concept relevance in all stages of development and in all languages being developed. The PGCIQ is the first questionnaire to document the multidimensional impact of caring for an infant or young child with GERD. Linguistic adaptation of the PGCIQ in multiple languages is ongoing. A validation study of the PGCIQ is needed to examine its psychometric properties, further refine the items and develop an appropriate scoring model

Creep Behavior of Passive Bovine Extraocular Muscle

This paper characterized bovine extraocular muscles (EOMs) using creep, which represents long-term stretching induced by a constant force. After preliminary optimization of testing conditions, 20 fresh EOM samples were subjected to four different loading rates of 1.67, 3.33, 8.33, and 16.67%/s, after which creep was observed for 1,500 s. A published quasilinear viscoelastic (QLV) relaxation function was transformed to a creep function that was compared with data. Repeatable creep was observed for each loading rate and was similar among all six anatomical EOMs. The mean creep coefficient after 1,500 seconds for a wide range of initial loading rates was at 1.37 ± 0.03 (standard deviation, SD). The creep function derived from the relaxation-based QLV model agreed with observed creep to within 2.7% following 16.67%/s ramp loading. Measured creep agrees closely with a derived QLV model of EOM relaxation, validating a previous QLV model for characterization of EOM biomechanics

GPU-based Acceleration of Symbol Timng Recovery

This paper presents a novel implementation of graphics processing unit (GPU) based symbol timing recovery using polyphase interpolators to detect symbol timing error. Symbol timing recovery is a compute intensive procedure that detects and corrects the timing error in a coherent receiver. We provide optimal sample-time timing recovery using a maximum likelihood (ML) estimator to minimize the timing error. This is an iterative and adaptive system that relies on feedback, therefore, we present an accelerated implementation design by using a GPU for timing error detection (TED), enabling fast error detection by exploiting the 2D filter structure found in the polyphase interpolator. We present this hybrid/ heterogeneous CPU and GPU architecture by computing a low complexity and low noise matched filter (MF) while simultaneously performing TED. We then compare the performance of the CPU vs. GPU based timing recovery for different interpolation rates to minimize the error and improve the detection by up to a factor of 35. We further improve the process by utilizing GPU optimization and performing block processing to improve the throughput even more, all while maintaining the lowest possible sampling rate.Laboratory for Telecommunications SciencesNational Science Foundation (NSF

Statistical Workflow for Feature Selection in Human Metabolomics Data.

High-throughput metabolomics investigations, when conducted in large human cohorts, represent a potentially powerful tool for elucidating the biochemical diversity underlying human health and disease. Large-scale metabolomics data sources, generated using either targeted or nontargeted platforms, are becoming more common. Appropriate statistical analysis of these complex high-dimensional data will be critical for extracting meaningful results from such large-scale human metabolomics studies. Therefore, we consider the statistical analytical approaches that have been employed in prior human metabolomics studies. Based on the lessons learned and collective experience to date in the field, we offer a step-by-step framework for pursuing statistical analyses of cohort-based human metabolomics data, with a focus on feature selection. We discuss the range of options and approaches that may be employed at each stage of data management, analysis, and interpretation and offer guidance on the analytical decisions that need to be considered over the course of implementing a data analysis workflow. Certain pervasive analytical challenges facing the field warrant ongoing focused research. Addressing these challenges, particularly those related to analyzing human metabolomics data, will allow for more standardization of as well as advances in how research in the field is practiced. In turn, such major analytical advances will lead to substantial improvements in the overall contributions of human metabolomics investigations

Chemokine CXCL12 activates dual CXCR4 and CXCR7-mediated signaling pathways in pancreatic cancer cells

<p>Abstract</p> <p>Background</p> <p>Previously assumed to be a select ligand for chemokine receptor CXCR4, chemokine CXCL12 is now known to activate both CXCR4 and CXCR7. However, very little is known about the co-expression of these receptors in cancer cells.</p> <p>Methods</p> <p>We used immunohistochemistry to determine the extent of co-expression in pancreatic cancer tissue samples and immunoblotting to verify expression in pancreatic cancer cell lines. In cell culture studies, siRNA was used to knock down expression of CXCR4, CXCR7, K-Ras and β-arrestin -2 prior to stimulating the cells with CXCL12. Activation of the mitogen-activated protein kinase pathway (MAPK) was assessed using both a Raf-pull down assay and western blotting. The involvement of the receptors in CXCL12-mediated increases in cell proliferation was examined via an ATP-based proliferation assay.</p> <p>Results</p> <p>First, we discovered frequent CXCR4/CXCR7 co-expression in human pancreatic cancer tissues and cell lines. Next, we observed consistent increases in ERK1/2 phosphorylation after exposure to CXCL12 or CXCL11, a CXCR7 agonist, in pancreatic cancer cell lines co-expressing CXCR4/CXCR7. To better characterize the receptor-mediated pathway(s), we knocked down CXCR4 or CXCR7, exposed the cells to CXCL12 and examined subsequent effects on ERK1/2. We observed that CXCR7 mediates the CXCL12-driven increase in ERK1/2 phosphorylation. Knockdown of CXCR4 expression however, decreased levels of K-Ras activity. Conversely, KRAS knockdown greatly reduced CXCL12-mediated increases in ERK1/2 phosphorylation. We then evaluated the role of β-arrestin-2, a protein directly recruited by chemokine receptors. We observed that β-arrestin-2 knockdown also inhibited increases in ERK1/2 phosphorylation mediated by both CXCR4 and CXCR7. Finally, we investigated the mechanism for CXCL12-enhanced cell proliferation and found that either receptor can modulate cell proliferation.</p> <p>Conclusions</p> <p>In summary, our data demonstrate that CXCR4 and CXCR7 are frequently co-expressed in human pancreatic cancer tissues and cell lines. We show that β-arrestin-2 and K-Ras dependent pathways coordinate the transduction of CXCL12 signals. Our results suggest that the development of therapies based on inhibiting CXCL12 signaling to halt the growth of pancreatic cancer should be focused at the ligand level in order to account for the contributions of both receptors to this signaling pathway.</p

A Single Visualization Technique for Displaying Multiple Metabolite-Phenotype Associations.

To assist with management and interpretation of human metabolomics data, which are rapidly increasing in quantity and complexity, we need better visualization tools. Using a dataset of several hundred metabolite measures profiled in a cohort of ~1500 individuals sampled from a population-based community study, we performed association analyses with eight demographic and clinical traits and outcomes. We compared frequently used existing graphical approaches with a novel 'rain plot' approach to display the results of these analyses. The 'rain plot' combines features of a raindrop plot and a conventional heatmap to convey results of multiple association analyses. A rain plot can simultaneously indicate effect size, directionality, and statistical significance of associations between metabolites and several traits. This approach enables visual comparison features of all metabolites examined with a given trait. The rain plot extends prior approaches and offers complementary information for data interpretation. Additional work is needed in data visualizations for metabolomics to assist investigators in the process of understanding and convey large-scale analysis results effectively, feasibly, and practically