STXMPy: a new software package for automated region of interest selection and statistical analysis of XANES data

<p>Abstract</p> <p>Background</p> <p>Soft X-ray spectromicroscopy based absorption near-edge structure analysis, is a spectroscopic technique useful for investigating sample composition at a nanoscale of resolution. While the technique holds great promise for analysis of biological samples, current methodologies are challenged by a lack of automatic analysis software e. g. for selection of regions of interest and statistical comparisons of sample variability.</p> <p>Results</p> <p>We have implemented a set of functions and scripts in Python to provide a semiautomatic treatment of data obtained using scanning transmission X-ray microscopy. The toolkit includes a novel line-by-line absorption conversion and data filtering automatically identifying image components with significant absorption. Results are provided to the user by direct graphical output to the screen and by output images and data files, including the average and standard deviation of the X-ray absorption spectrum. Using isolated mouse melanosomes as a sample biological tissue, application of STXMPy in analysis of biological tissues is illustrated.</p> <p>Conclusion</p> <p>The STXMPy package allows both interactive and automated batch processing of scanning transmission X-ray microscopic data. It is open source, cross platform, and offers rapid script development using the interpreted Python language.</p

MRI: ID-Development of a Hybrid Scanning Fluorescence and Sum Frequency Spectroscopy Imaging Microscope

With this award from the Major Research Instrumentation program (MRI), Michael Mason and colleagues from the Department of Chemistry at the University of Maine will develop a hybrid scanning fluorescence (FL) and sum frequency (SF) spectroscopy imaging microscope. The instrument will be constructed by the addition of sample scanning and FL capability to an existing broadband SF spectrometer. The SF NIR pump source will be used to excite SF at the sample interface, while a modulated Argon ion CW laser will excite FL. These collinear sources will give rise to spatially and temporally correlated SF and FL signals which will be separated and individually detected. The instrument will simultaneously measure the fluorescence and sum frequency to yield information about the localized dynamics of a single particle, i.e. protein, and spatially correlated structural information about the bulk material containing the particle. This yields information about the interaction between the particle and the bulk not accessible by any other method. The proposal will initially investigate test projects including the study of membrane domain structure and membrane-membrane interactions, e,g., correlation of the structure and dynamics of lipid and protein molecules within planar supported lipid bilayers. Successful development of this instrument could lead to major breakthroughs in several fields ranging from surface chemistry and biophysics to nanotechnology and cellular biology

Droplet‐Microarray: Miniaturized Platform for High‐Throughput Screening of Antimicrobial Compounds

Currently, there are no time-saving and cost-effective high-throughput screening methods for the evaluation of bacterial drug-resistance. In this study, a droplet microarray (DMA) system is established as a miniaturized platform for high-throughput screening of antibacterial compounds using the emerging, opportunistic human pathogen Pseudomonas aeruginosa (P. aeruginosa) as a target. Based on the differences in wettability of DMA slides, a rapid method for generating microarrays of nanoliter-sized droplets containing bacteria is developed. The bacterial growth in droplets is evaluated using fluorescence. The new method enables immediate screening with libraries of antibiotics. A novel simple colorimetric readout method compatible with the nanoliter size of the droplets is established. Furthermore, the drug-resistance of P. aeruginosa 49, a multi-resistant strain from an environmental isolate, is investigated. This study demonstrates the potential of the DMA platform for the rapid formation of microarrays of bacteria for high-throughput drug screening

Establishing Research Competitiveness in Biophysical Sciences in Maine

The Maine EPSCoR Research Infrastructure Improvement award is designed to enhance Maine\u27s competitiveness in molecular biophysical sciences through a partnership between the University of Maine and Maine\u27s non-profit research organizations. The proposed Biophysical Sciences Institute brings together University of Maine faculty in physics, chemistry, biology, mathematics, and spatial engineering, with biomedical researchers at the Jackson Laboratory and Maine Medical Center Research Institute. Maine EPSCoR proposes to hire additional tenure-track faculty in the fields of biophysics and advanced optics, biochemistry, structural biology, applied mathematics, computer science, image analysis and visualization, and material science. The new and existing investigators will form research teams to develop new measurement techniques, new sensors, and innovative approaches to data processing and interpretation in intracellular structures and dynamics, functional materials as a means to manipulate cellular reactions, and biocomputing. In addition to establishing the institute, Maine EPSCoR will integrate research and education through improvements to graduate training

Direct three-dimensional imaging of polymer-water interfaces by nanoscale hard X-ray phase tomography

We report three-dimensional (3D) direct imaging of complex surface-liquid interfaces by hard X-ray phase contrast tomography as a non-destructive approach for the morphological characterization of surfaces at the micro- and nanoscale in contact with water. Specifically{,} we apply this method to study the solid-air-water interface in hydrophobic macroporous polymethacrylate surfaces{,} and the solid-oil-water interface in slippery liquid-infused porous surfaces (SLIPS). Varying the isotropic spatial resolution allows the 3D quantitative characterization of individual polymer globules{,} globular clusters (porosity) as well as the infused lubricant layer on SLIPS. Surface defects were resolved at the globular level. We show the first application of X-ray nanotomography to hydrated surface characterizations and we anticipate that X-ray nanoscale imaging will open new ways for various surface/interface studies

Adherent cells avoid polarization gradients on periodically poled LiTaO\u3csub\u3e3\u3c/sub\u3e ferroelectrics

The response of fibroblast cells to periodically poled LiTaO3 ferroelectric crystals has been studied. While fibroblast cells do not show morphological differences on the two polarization directions, they show a tendency to avoid the field gradients that occur between polarization domains of the ferroelectric. The response to the field gradients is fully established after one hour, a time at which fibroblasts form their first focal contacts. If suspension cells, with a lower tendency to establish strong surface contacts are used, no influence of the field gradients is observed

Adherent cells avoid polarization gradients on periodically poled LiTaO\u3csub\u3e3\u3c/sub\u3e ferroelectrics

The response of fibroblast cells to periodically poled LiTaO3 ferroelectric crystals has been studied. While fibroblast cells do not show morphological differences on the two polarization directions, they show a tendency to avoid the field gradients that occur between polarization domains of the ferroelectric. The response to the field gradients is fully established after one hour, a time at which fibroblasts form their first focal contacts. If suspension cells, with a lower tendency to establish strong surface contacts are used, no influence of the field gradients is observed

More illness in offspring of bipolar patients from the U.S. compared to Europe.

Background Evidence suggests that patients with bipolar disorder from the United States have an earlier age of onset and a more difficult course of illness than those from Germany and the Netherlands. These characteristics were related to a greater family burden of psychiatric illness and the experience of more psychosocial adversity in childhood. We hypothesized that this greater illness burden would extend to the offspring of the US patients. Methods 968 outpatients (average age 41) with bipolar illness gave informed consent for participation in a treatment outcome network and filled out a detailed questionnaire about their illness and family history of illness, including whether their offspring had a diagnosis of depression, bipolar disorder, alcohol or substance abuse, suicide attempt or “other” illness. Of those with children, 356 were from the US and 132 were from Europe. Results Compared to the Europeans, offspring of patients from the US had significantly (p\u3c0.001) more depression, bipolar disorder, drug abuse, and “other” illnesses. The number of illnesses in the offspring was related to the bipolar parent being from the US, having had childhood adversity, more than 20 prior episodes, and more parental psychiatric illness. Conclusions While the findings are limited by their basis on self report, the distribution of the percentages in the US offspring are similar to those of Axelson et al. (2015) who used direct interviews. The higher burden of illness in the offspring and their in directprogenitors from the US compared to Europe warrant new attempts at better treatment and prevention

UV-triggered dopamine polymerization: Control of polymerization, surface coating, and photopatterning

UV irradiation is demonstrated to initiate dopamine polymerization and deposition on different surfaces under both acidic and basic pH. The observed acceleration of the dopamine polymerization is explained by the UV-induced formation of reactive oxygen species that trigger dopamine polymerization. The UV-induced dopamine polymerization leads to a better control over polydopamine deposition and formation of functional polydopamine micropatterns

Relationship of comorbid personality disorders to prospective outcome in bipolar disorder

Introduction There is a high incidence of Axis II personality disorders (PDs) in patients with bipolar illness, but their influence on the prospectively measured course of bipolar disorder has been less well explicated. Methods 392 outpatients with bipolar disorder gave informed consent, completed the PDQ4 99 item personality disorder rating, and where clinically rated during at least one year of prospective naturalistic treatment. They were classified as Well on admission (N = 64) or Responders (N = 146) or Non-responders (N = 182) to treatment for at least six months. Results Patients who were positive for PDs were very infrequently represented in the category of Well on admission. In addition, patients with borderline, depressive, and schizoid PDs were significantly more likely to be Non-responders compared to Responders upon prospective naturalistic treatment in the network. Conclusions Patients with bipolar disorder and comorbid PDs were in general less likely to be Well from treatment in the community at network entry or to be a Responder to prospective treatment in the network. Therapeutic approaches to patients with PDs deserve specific study in an attempt to achieve a better long-term course of bipolar disorder