A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse

Does pathway analysis make it easier for common variants to tag rare ones?

Analyzing sequencing data is difficult because of the low frequency of rare variants, which may result in low power to detect associations. We consider pathway analysis to detect multiple common and rare variants jointly and to investigate whether analysis at the pathway level provides an alternative strategy for identifying susceptibility genes. Available pathway analysis methods for data from genome-wide association studies might not be efficient because these methods are designed to detect common variants. Here, we investigate the performance of several existing pathway analysis methods for sequencing data. In particular, we consider the global test, which does not consider linkage disequilibrium between the variants in a gene. We improve the performance of the global test by assigning larger weights to rare variants, as proposed in the weighted-sum approach. Our conclusion is that straightforward application of pathway analysis is not satisfactory; hence, when common and rare variants are jointly analyzed, larger weights should be assigned to rare variants

Auditory temporal resolution and evoked responses to pulsed sounds for the Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis)

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology 197 (2011): 1149-1158, doi:10.1007/s00359-011-0677-y.Temporal cues are important for some forms of auditory processing, such as echolocation. Among odontocetes (toothed whales, dolphins, and porpoises), it has been suggested that porpoises may have temporal processing abilities which differ from other odontocetes because of their relatively narrow auditory filters and longer duration echolocation signals. This study examined auditory temporal resolution in two Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis) using auditory evoked potentials (AEPs) to measure: (i) rate following responses and modulation rate transfer function for 100 kHz centered pulse sounds and (ii) hearing thresholds and response amplitudes generated by individual pulses of different durations. The animals followed pulses well at modulation rates up to 1250 Hz, after which response amplitudes declined until extinguished beyond 2500 Hz. The subjects had significantly better hearing thresholds for longer, narrower-band pulses similar to porpoise echolocation signals compared to brief, broadband sounds resembling dolphin clicks. Results indicate that the Yangtze finless porpoise follows individual acoustic signals at rates similar to other odontocetes tested. Relatively good sensitivity for longer duration, narrow-band signals suggests that finless porpoise hearing is well-suited to detect their unique echolocation signals.The work was supported by the Office of Naval Research, a WHOI Mellon Joint Initiatives Award , the Chinese National Natural Science Foundation (grant No: 30730018) and the Institute of Hydrobiology of the Chinese Academy of Sciences2012-09-1

Measuring Flexicurity: Precautionary Notes, a New Framework, and an Empirical Example

Recently, there has been an increase and abundance of literature measuring flexicurity across countries. However, there is yet to be any agreement on the definition of the key concepts of flexicurity as well as the framework in which to base one’s research. Due to this, the outcomes found in the existing studies are rather diverse, far from reaching a consensus, and can be misleading. This paper addresses the issues by first introducing a framework, namely, the various levels and stages of flexicurity, as well as introducing some key issues that should be addressed when doing flexicurity indicators research. In addition, an empirical example is given to show how the framework derived can be used to carry out flexicurity research, and to show how by not regarding these frameworks one can come to misleading outcomes

Probabilistic 3D surface reconstruction from sparse MRI information

Surface reconstruction from magnetic resonance (MR) imaging data is indispensable in medical image analysis and clinical research. A reliable and effective reconstruction tool should: be fast in prediction of accurate well localised and high resolution models, evaluate prediction uncertainty, work with as little input data as possible. Current deep learning state of the art (SOTA) 3D reconstruction methods, however, often only produce shapes of limited variability positioned in a canonical position or lack uncertainty evaluation. In this paper, we present a novel probabilistic deep learning approach for concurrent 3D surface reconstruction from sparse 2D MR image data and aleatoric uncertainty prediction. Our method is capable of reconstructing large surface meshes from three quasi-orthogonal MR imaging slices from limited training sets whilst modelling the location of each mesh vertex through a Gaussian distribution. Prior shape information is encoded using a built-in linear principal component analysis (PCA) model. Extensive experiments on cardiac MR data show that our probabilistic approach successfully assesses prediction uncertainty while at the same time qualitatively and quantitatively outperforms SOTA methods in shape prediction. Compared to SOTA, we are capable of properly localising and orientating the prediction via the use of a spatially aware neural network.Comment: MICCAI 202

Effect of Hydrogen Peroxide on Immersion Challenge of Rainbow Trout Fry with Flavobacterium psychrophilum

An experimental model for immersion challenge of rainbow trout fry (Oncorhynchus mykiss) with Flavobacterium psychrophilum, the causative agent of rainbow trout fry syndrome and bacterial cold water disease was established in the present study. Although injection-based infection models are reliable and produce high levels of mortality attempts to establish a reproducible immersion model have been less successful. Various concentrations of hydrogen peroxide (H₂O₂) were evaluated before being used as a pre-treatment stressor prior to immersion exposure to F. psychrophilum. H₂O₂ accelerated the onset of mortality and increased mortality approximately two-fold; from 9.1% to 19.2% and from 14.7% to 30.3% in two separate experiments. Clinical signs observed in the infected fish corresponded to symptoms characteristically seen during natural outbreaks. These findings indicate that pre-treatment with H₂O₂ can increase the level of mortality in rainbow trout fry after exposure to F. psychrophilum

The host metabolite D-serine contributes to bacterial niche specificity through gene selection

Escherichia coli comprise a diverse array of both commensals and niche-specific pathotypes. The ability to cause disease results from both carriage of specific virulence factors and regulatory control of these via environmental stimuli. Moreover, host metabolites further refine the response of bacteria to their environment and can dramatically affect the outcome of the host–pathogen interaction. Here, we demonstrate that the host metabolite, D-serine, selectively affects gene expression in E. coli O157:H7. Transcriptomic profiling showed exposure to D-serine results in activation of the SOS response and suppresses expression of the Type 3 Secretion System (T3SS) used to attach to host cells. We also show that concurrent carriage of both the D-serine tolerance locus (dsdCXA) and the locus of enterocyte effacement pathogenicity island encoding a T3SS is extremely rare, a genotype that we attribute to an ‘evolutionary incompatibility’ between the two loci. This study demonstrates the importance of co-operation between both core and pathogenic genetic elements in defining niche specificity

Use of interrupter technique in assessment of bronchial responsiveness in normal subjects

BACKGROUND: A number of subjects, especially the very young and the elderly, are unable to cooperate and to perform forced expiratory manoeuvres in the evaluation of bronchial hyperresponsiveness (BHR). The objective of our study was to investigate the use of the interrupter technique as a method to measure the response to provocation and to compare it with the conventional PD(20 )FEV(1). METHODS: We studied 170 normal subjects, 100 male and 70 female (mean ± SD age, 38 ± 8.5 and 35 ± 7.5 years, respectively), non-smoking from healthy families. These subjects had no respiratory symptoms, rhinitis or atopic history. A dosimetric cumulative inhalation of methacholine was used and the response was measured by the dose which increases baseline end interruption resistance by 100% (PD(100)Rint, EI) as well as by percent dose response ratio (DRR). RESULTS: BHR at a cut-off level of 0.8 mg methacholine exhibited 31 (18%) of the subjects (specificity 81.2%), 21 male and 10 female, while 3% showed a response in the asthmatic range. The method was reproducible and showed good correlation with PD(20)FEV(1 )(r = 0.76, p < 0.005), with relatively narrow limits of agreement at -1.39 μmol and 1.27 μmol methacholine, respectively, but the interrupter methodology proved more sensitive than FEV(1 )in terms of reactivity (DRR). CONCLUSIONS: Interrupter methodology is clinically useful and may be used to evaluate bronchial responsiveness in normal subjects and in situations when forced expirations cannot be performed

Fishery Discards: Factors Affecting Their Variability within a Demersal Trawl Fishery

Discards represent one of the most important issues within current commercial fishing. It occurs for a range of reasons and is influenced by an even more complex array of factors. We address this issue by examining the data collected within the Danish discard observer program and describe the factors that influence discarding within the Danish Kattegat demersal fleet over the period 1997 to 2008. Generalised additive models were used to assess how discards of the 3 main target species, Norway lobster, cod and plaice, and their subcomponents (under and over minimum landings size) are influenced by important factors and their potential relevance to management. Our results show that discards are influenced by a range of different factors that are different for each species and portion of discards. We argue that knowledge about the factors influential to discarding and their use in relation to potential mitigation measures are essential for future fisheries management strategies