Identifying Nonspecific Ligand Binding in Electrospray Ionization Mass Spectrometry Using the Reporter Molecule Method

The application of the reporter molecule (Mrep) method for identifying nonspecific complexes in the ES-MS analysis of protein–ligand and DNA–ligand interactions in vitro is described. To test the reliability of the method, it was applied to the ES-MS analysis of protein–carbohydrate complexes originating from specific interactions in solution and from nonspecific interactions in the ES process. These control experiments confirm the basic assumptions underlying the Mrep method, namely that nonspecific ligand binding is a random process, and that the ES droplet histories for specific and nonspecific complexes are distinct. The application of the Mrep method to the ES-MS analysis of the sequential binding of the ethidium cation, a DNA intercalator, to single and double strand oligodeoxynucleotides is also described, and highlights the general utility of the method

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism

Translocator protein in late stage Alzheimer\u27s disease and Dementia with Lewy bodies brains

OBJECTIVE: Increased translocator protein (TSPO), previously known as the peripheral benzodiazepine receptor (PBR), in glial cells of the brain has been used as a neuroinflammation marker in the early and middle stages of neurodegenerative diseases, such as Alzheimer\u27s disease (AD) and Dementia with Lewy Bodies (DLB). In this study, we investigated the changes in TSPO density with respect to late stage AD and DLB. METHODS: TSPO density was measured in multiple regions of postmortem human brains in 20 different cases: seven late stage AD cases (Braak amyloid average: C; Braak tangle average: VI; Aged 74-88, mean: 83 ± 5 years), five DLB cases (Braak amyloid average: C; Braak tangle average: V; Aged 79-91, mean: 84 ± 4 years), and eight age-matched normal control cases (3 males, 5 females: aged 77-92 years; mean: 87 ± 6 years). Measurements were taken by quantitative autoradiography using [ RESULTS: No significant changes were found in TSPO density of the frontal cortex, striatum, thalamus, or red nucleus of the AD and DLB brains. A significant reduction in TSPO density was found in the substantia nigra (SN) of the AD and DLB brains compared to that of age-matched healthy controls. INTERPRETATION: This distinct pattern of TSPO density change in late stage AD and DLB cases may imply the occurrence of microglia dystrophy in late stage neurodegeneration. Furthermore, TSPO may not only be a microglia activation marker in early stage AD and DLB, but TSPO may also be used to monitor microglia dysfunction in the late stage of these diseases

Development and characterisation of a novel three-dimensional inter-kingdom wound biofilm model

Chronic diabetic foot ulcers are frequently colonised and infected by polymicrobial biofilms that ultimately prevent healing. This study aimed to create a novel in vitro inter-kingdom wound biofilm model on complex hydrogel-based cellulose substrata to test commonly used topical wound treatments. Inter-kingdom triadic biofilms composed of Candida albicans, Pseudomonas aeruginosa, and Staphylococcus aureus were shown to be quantitatively greater in this model compared to a simple substratum when assessed by conventional culture, metabolic dye and live dead qPCR. These biofilms were both structurally complex and compositionally dynamic in response to topical therapy, so when treated with either chlorhexidine or povidone iodine, principal component analysis revealed that the 3-D cellulose model was minimally impacted compared to the simple substratum model. This study highlights the importance of biofilm substratum and inclusion of relevant polymicrobial and inter-kingdom components, as these impact penetration and efficacy of topical antiseptics

A UV to Mid-IR Study of AGN Selection

We classify the spectral energy distributions (SEDs) of 431,038 sources in the 9 sq. deg Bootes field of the NOAO Deep Wide-Field Survey (NDWFS). There are up to 17 bands of data available per source, including ultraviolet (GALEX), optical (NDWFS), near-IR (NEWFIRM), and mid-infrared (IRAC/MIPS) data, as well as spectroscopic redshifts for ~20,000 objects, primarily from the AGN and Galaxy Evolution Survey (AGES). We fit galaxy, AGN, stellar, and brown dwarf templates to the observed SEDs, which yield spectral classes for the Galactic sources and photometric redshifts and galaxy/AGN luminosities for the extragalactic sources. The photometric redshift precision of the galaxy and AGN samples are sigma/(1+z)=0.040 and sigma/(1+z)=0.169, respectively, with the worst 5% outliers excluded. Based on the reduced chi-squared of the SED fit for each SED model, we are able to distinguish between Galactic and extragalactic sources for sources brighter than I=23.5. We compare the SED fits for a galaxy-only model and a galaxy+AGN model. Using known X-ray and spectroscopic AGN samples, we confirm that SED fitting can be successfully used as a method to identify large populations of AGN, including spatially resolved AGN with significant contributions from the host galaxy and objects with the emission line ratios of "composite" spectra. We also use our results to compare to the X-ray, mid-IR, optical color and emission line ratio selection techniques. For an F-ratio threshold of F>10 we find 16,266 AGN candidates brighter than I=23.5 and a surface density of ~1900 AGN per deg^2.Comment: Submitted to ApJ, 35 pages, 17 figures, 2 table

Online Search with Predictions: Pareto-optimal Algorithm and its Applications in Energy Markets

This paper develops learning-augmented algorithms for energy trading in volatile electricity markets. The basic problem is to sell (or buy) $k$ units of energy for the highest revenue (lowest cost) over uncertain time-varying prices, which can framed as a classic online search problem in the literature of competitive analysis. State-of-the-art algorithms assume no knowledge about future market prices when they make trading decisions in each time slot, and aim for guaranteeing the performance for the worst-case price sequence. In practice, however, predictions about future prices become commonly available by leveraging machine learning. This paper aims to incorporate machine-learned predictions to design competitive algorithms for online search problems. An important property of our algorithms is that they achieve performances competitive with the offline algorithm in hindsight when the predictions are accurate (i.e., consistency) and also provide worst-case guarantees when the predictions are arbitrarily wrong (i.e., robustness). The proposed algorithms achieve the Pareto-optimal trade-off between consistency and robustness, where no other algorithms for online search can improve on the consistency for a given robustness. Further, we extend the basic online search problem to a more general inventory management setting that can capture storage-assisted energy trading in electricity markets. In empirical evaluations using traces from real-world applications, our learning-augmented algorithms improve the average empirical performance compared to benchmark algorithms, while also providing improved worst-case performance

A Semi-Analytical Method for Determining the Energy Release Rate of Cracks in Adhesively-Bonded Single-Lap Composite Joints

A semi-analytical method for determining the strain energy release rate due to a prescribed interface crack in an adhesively-bonded, single-lap composite joint subjected to axial tension is presented. The field equations in terms of displacements within the joint are formulated by using first-order shear deformable, laminated plate theory together with kinematic relations and force equilibrium conditions. The stress distributions for the adherends and adhesive are determined after the appropriate boundary and loading conditions are applied and the equations for the field displacements are solved. Based on the adhesive stress distributions, the forces at the crack tip are obtained and the strain energy release rate of the crack is determined by using the virtual crack closure technique (VCCT). Additionally, the test specimen geometry from both the ASTM D3165 and D1002 test standards are utilized during the derivation of the field equations in order to correlate analytical models with future test results. The system of second-order differential field equations is solved to provide the adherend and adhesive stress response using the symbolic computation tool, Maple 9. Finite element analyses using J-integral as well as VCCT were performed to verify the developed analytical model. The finite element analyses were conducted using the commercial finite element analysis software ABAQUS. The results determined using the analytical method correlated well with the results from the finite element analyses

Factitious Disorders and Cardiothoracic Surgery: The Ongoing Multidisciplinary Challenges of a Complex Case

Chronic factitious disorder, Munchausen's syndrome, can be challenging to manage—particularly when complaints and symptoms suggest medical or surgical emergencies. We present a patient whose problems have spanned many years and a great distance. Hopefully, with a greater awareness of this disease, as this patient continues to seek health care in many different hospitals, the implications of timely access to information, good histories and physical exams, and an index of suspicion can assist in potentially avoiding unnecessary, expensive, and invasive evaluations