bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent advances in headache neuroimaging
Authors: Messina Roberta , Filippi Massimo , Goadsby Peter J.
Published: June 2018

Purpose of review

Primary headaches, such as migraine and cluster headache, are one of the most common and disabling neurological diseases worldwide. Neuroimaging studies have changed the way we understand these diseases and have enriched our knowledge of the mechanisms of actions of currently available therapies.

Recent findings

The present review highlights the major findings reported in migraine and cluster headache neuroimaging over the last year. Widespread structural and functional abnormalities in cortical and subcortical areas involved in multisensory, including pain, processing have been shown in migraine and cluster headache patients during different phases of the disease. Beyond the involvement of single brain areas, dysfunctional brain networks contribute to their pathophysiology. New central mechanisms of action of headache preventive treatments have also been explored.

A better understanding of migraine and cluster headache biology has paved the way for the development of new improved treatments for both these conditions. Although significant advances have been made over the last year, there are still many unsolved questions to address.
Harnessing formal concepts of biological mechanism to analyze human disease
Authors: Darden Lindley , Kundu Kunal , Pal Lipika R. , Moult John
Published: June 2018

Mechanism is a widely used concept in biology: in 2017 more than 10% of PubMed abstracts used the term. Thus, searching for and reasoning about mechanisms is fundamental to much of biomedical research, but until now there has been almost no computational infrastructure for this purpose. Recent work in the philosophy of science has explored the central role that the search for mechanistic accounts of biological phenomena plays in biomedical research, providing a conceptual basis for representing and analyzing biological mechanism. The foundational categories for components of mechanisms - entities and activities - guide the development of general, abstract types of biological mechanism parts. Building on that analysis, we have developed a formal framework for describing and representing biological mechanism, MecCog, and applied it to describing mechanisms underlying human genetic disease. Mechanisms are depicted using a graphical notation. Key features are assignment of mechanism components to stages of biological organization and classes; visual representation of uncertainty, ignorance, and ambiguity; and tight integration with literature sources. The MecCog framework facilitates analysis of many aspects of disease mechanism, including the prioritization of future experiments, probing of gene-drug and gene-environment interactions, identification of possible new drug targets, personalized drug choice, analysis of non-linear interactions between relevant genetic loci, and classification of disease based on mechanism.
Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty
Authors: Escorcia-Rodríguez Juan M. , Esposito Mario , Freyre-González Julio A. , Moreno-Hagelsieb Gabriel
Published: June 2018

Orthologs diverge after lineage separation events and paralogs after gene duplications. Thus, orthologs are expected to remain more functionally coherent across lineages, while paralogs have been proposed as a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS), as proxy for functional divergence. We used five working definitions of orthology, including reciprocal best hits (RBH), among other definitions based on network analyses and clustering. The results showed that orthologs, by all definitions tested, had values of dN/dS noticeably lower than those of paralogs, suggesting that, as a group, orthologs tend to be more functionally stable than paralogs. The differences in dN/dS ratios remained suggesting the functional stability of orthologs after eliminating gene comparisons with potential problems, such as genes with high codon usage biases, low coverage of either of the aligned sequences, or sequences with very high similarities. Separation by percent identity of the encoded proteins showed that the differences between the dN/dS ratios of orthologs and paralogs were more evident at high sequence identity, less so as identity dropped. While the last results partially explained the differences between dN/dS ratios of the two groups as being related to differences in protein identity, they also suggested that paralogs undergo functional divergence relatively early after duplication. Our analyses indicate that choosing orthologs as probably functionally coherent remains the right approach in comparative genomics.
Evidence that recurrent circuits are critical to the ventral stream’s execution of core object recognition behavior
Authors: Kohitij Kar , Jonas Kubilius , Kailyn Schmidt , Issa Elias B. , DiCarlo James J.
Published: June 2018

Non-recurrent deep convolutional neural networks (DCNNs) are currently the best models of core object recognition; a behavior supported by the densely recurrent primate ventral stream, culminating in the inferior temporal (IT) cortex. Are these recurrent circuits critical to ventral stream’s execution of this behavior? We reasoned that, if recurrence is critical, then primates should outperform feedforward-only DCNNs for some images, and that these images should require additional processing time beyond the feedforward IT response. Here we first used behavioral methods to discover hundreds of these “challenge” images. Second, using large-scale IT electrophysiology in animals performing core recognition tasks, we observed that behaviorally-sufficient, linearly-decodable object identity solutions emerged ~30ms (on average) later in IT for challenge images compared to DCNN and primate performance-matched “control” images. We observed these same late solutions even during passive viewing. Third, consistent with a failure of feedforward computations, the behaviorally-critical late-phase IT population response patterns evoked by the challenge images were poorly predicted by DCNN activations. Interestingly, deeper CNNs better predicted these late IT responses, suggesting a functional equivalence between recurrence and additional nonlinear transformations. Our results argue that automatically-evoked recurrent circuits are critical even for rapid object identification. By precisely comparing current DCNNs, primate behavior and IT population dynamics, we provide guidance for future recurrent model development.
ΦCrAss001, a member of the most abundant bacteriophage family in the human gut, infects Bacteroides
Authors: Shkoporov Andrey N. , Khokhlova Ekaterina V. , Fitzgerald C. Brian , Stockdale Stephen R. , Draper Lorraine A. , Ross R. Paul , Hill Colin
Published: June 2018

ΦCrAss001, isolated from human faecal material, is the first member of the extensive crAssphage family to be grown in pure culture. The bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming in silico predictions of the likely host. Genome analysis demonstrated that the phage DNA is 102 kb in size, has an unusual genome organisation and does not possess any obvious genes for lysogeny. In addition, electron microscopy confirms that φcrAss001 has a podovirus-like morphology. Despite the absence of lysogeny genes, φcrAss001 replicates in a way that does not disrupt proliferation of the host bacterium and is able to maintain itself in continuous host culture.
Concurrent Spatiotemporal Daily Land Use Regression Modeling and Missing Data Imputation of Fine Particulate Matter Using Distributed Space Time Expectation Maximization
Authors: Taghavi-Shahri Seyed Mahmood , Fassò Alessandro , Mahaki Behzad , Amini Heresh
Published: June 2018

Graphical Abstract

Land use regression (LUR) has been widely applied in epidemiologic research for exposure assessment. In this study, for the first time, we aimed to develop a spatiotemporal LUR model using Distributed Space Time Expectation Maximization (D-STEM). This spatiotemporal LUR model examined with daily particulate matter ≤ 2.5 μm (PM2.5) within the megacity of Tehran, capital of Iran. Moreover, D-STEM missing data imputation was compared with mean substitution in each monitoring station, as it is equivalent to ignoring of missing data, which is common in LUR studies that employ regulatory monitoring stations’ data. The amount of missing data was 28% of the total number of observations, in Tehran in 2015. The annual mean of PM2.5 concentrations was 33 μg/m3. Spatiotemporal R-squared of the D-STEM final daily LUR model was 78%, and leave-one-out cross-validation (LOOCV) R-squared was 66%. Spatial R-squared and LOOCV R-squared were 89% and 72%, respectively. Temporal R-squared and LOOCV R-squared were 99.5% and 99.3%, respectively. Mean absolute error decreased 26% in imputation of missing data by using the D-STEM final LUR model instead of mean substitution. This study reveals competence of the D-STEM software in spatiotemporal missing data imputation, estimation of temporal trend, and mapping of small scale (20 × 20 meters) within-city spatial variations, in the LUR context. The estimated PM2.5 concentrations maps could be used in future studies on short- and/or long-term health effects. Overall, we suggest using D-STEM capabilities in increasing LUR studies that employ data of regulatory network monitoring stations.

Highlights

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First Land Use Regression using D-STEM, a recently introduced statistical software

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Assess D-STEM in spatiotemporal modeling, mapping, and missing data imputation

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Estimate high resolution (20×20 m) daily maps for exposure assessment in a megacity

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Provide both short- and long-term exposure assessment for epidemiological studies
Neural Responses in Dorsal Prefrontal Cortex Reflect Proactive Interference during an Auditory Reversal Task
Authors: Francis Nikolas A. , Radtke-Schuller Susanne , Fritz Jonathan B. , Shamma Shihab A.
Published: June 2018

Task-related plasticity in the brain is triggered by changes in the behavioral meaning of sounds. We investigated plasticity in ferret dorsolateral frontal cortex (dlFC) during an auditory reversal task to study the neural correlates of proactive interference, i.e., perseveration of previously learned behavioral meanings that are no longer task-appropriate. Although the animals learned the task, target recognition decreased after reversals, indicating proactive interference. Frontal cortex responsiveness was consistent with previous findings that dlFC encodes the behavioral meaning of sounds. However, the neural responses observed here were more complex. For example, target responses were strongly enhanced, while responses to non-target tones and noises were weakly enhanced and strongly suppressed, respectively. Moreover, dlFC responsiveness reflected the proactive interference observed in behavior: target responses decreased after reversals, most significantly during incorrect behavioral responses. These findings suggest that the weak representation of behavioral meaning in dlFC may be a neural correlate of proactive interference.

Significance Statement

Neural activity in prefrontal cortex (PFC) is believed to enable cognitive flexibility during sensory-guided behavior. Since PFC encodes the behavioral meaning of sensory events, we hypothesized that weak representation of behavioral meaning in PFC may limit cognitive flexibility. To test this hypothesis, we recorded neural activity in ferret PFC, while ferrets performed an auditory reversal task in which the behavioral meanings of sounds were reversed during experiments. The reversal task enabled us study PFC responses during proactive interference, i.e. perseveration of previously learned behavioral meanings that are no longer task-appropriate. We found that task performance errors increased after reversals while PFC representation of behavioral meaning diminished. Our findings suggest that proactive interference may occur when PFC forms weak sensory-cognitive associations.
Career Choice, Gender, and Mentor Impact: Results of the U.S. National Postdoc Survey
Authors: McConnell Sean C. , Westerman Erica L. , Pierre Joseph F. , Heckler Erin J. , Schwartz Nancy B.
Published: June 2018

The postdoctoral community is an essential component of the academic and scientific workforce. As economic and political pressures impacting these enterprises continue to change, the postdoc experience has evolved from short, focused periods of training into often multidisciplinary, extended positions with less clear outcomes. As efforts are underway to amend U.S. federally funded research policies, the paucity of postdoc data has made evaluating the impact of policy recommendations challenging. Here we present comprehensive survey results from over 7,600 postdocs based at 351 academic and non-academic U.S. institutions in 2016. In addition to demographic and salary information, we present multivariate analyses on the factors that influence postdoc career plans and mentorship satisfaction in this population. We further analyze gender dynamics and expose wage disparities and career choice differences. Academic research positions remain the predominant career choice of postdocs in the U.S., although unequally between postdocs based on gender and residency status. Receiving mentorship training during the postdoctoral period has a large, positive effect on postdoc mentorship satisfaction. Strikingly, the quality of and satisfaction with postdoc mentorship appears to also heavily influence career choice. The data presented here are the most comprehensive data on the U.S. postdoc population to date. These results provide an evidence basis for informing government and institutional policies, and establish a critical cornerstone for quantifying the effects of future legislation aimed at the academic and scientific workforce.
A somatic evolutionary model of the dynamics of aneuploid cells during hematopoietic reconstitution
Authors: Rozhok Andrii I. , Silberman Rebecca E. , Amon Angelika , DeGregori James
Published: June 2018

Aneuploidy is associated with many cancers. Recent studies demonstrate that in thehematopoietic stem and progenitor cell (HSPC) compartment aneuploid cells havereduced fitness and are efficiently purged from the bone marrow. However, early phasesof hematopoietic reconstitution following bone marrow transplantation provide awindow of opportunity whereby aneuploid cells rise in frequency, only to decline to basallevels thereafter. Here we demonstrate by Monte Carlo modeling that two mechanismscould underlie this aneuploidy peak: rapid expansion of the engrafted HSPC populationand bone marrow microenvironment degradation caused by pre-transplantationradiation treatment. Both mechanisms reduce the strength of purifying selection actingin early post-transplantation bone marrow. We explore the contribution of other factorssuch as alterations in cell division rates that affect the strength of purifying selection, thebalance of drift and selection imposed by the HSPC population size, and the mutationselectionbalance dependent on the rate of aneuploidy generation per cell division. Wepropose a somatic evolutionary model for the dynamics of cells with aneuploidy or otherfitness-reducing mutations during hematopoietic reconstitution following bone marrowtransplantation.

Significance

Bone marrow transplantations (BMT) following ablative irradiation pose a great health risk. It’s been shown that additionally the bone microenvironment is conducive to elevated frequencies of aneuploid cells in mice during bone marrow reconstitution post-BMT. As aneuploidy is linked with many cancers, we explore the reasons of such aberrant cell frequency peaks by Monte Carlo modeling. We demonstrate that elevated rates of aneuploidy early post-BMT are likely to be caused by reduced purifying somatic selection resulting from the expansion of the reconstituting population and the damage to stem cell niches caused by ablative radiation
Susceptibility of European freshwater fish to climate change: species profiling based on life-history and environmental characteristics
Authors: Jarić Ivan , Lennox Robert J. , Kalinkat Gregor , Cvijanović Gorčin , Radinger Johannes
Published: June 2018

Climate change is expected to strongly affect freshwater fish communities. Combined with other anthropogenic impacts, the impacts will alter species distributions and contribute to population declines and local extinctions. To provide timely management and conservation of fishes, it is relevant to identify species that will be most impacted by climate change and those that will be resilient. Species traits are considered a promising source of information on characteristics that influence resilience to various environmental conditions and impacts. We collated life history traits and climatic niches of 443 European freshwater fish species and compared those identified as susceptible to climate change to those that are considered to be resilient. Significant differences were observed between the two groups in their distribution, life-history and climatic niches, with climate-change susceptible species being distributed more southwardly within Europe, and being characterized by higher threat levels, lower commercial relevance, lower vulnerability to fishing, smaller body size and warmer thermal envelopes. We establish a list of species revealed to be of highest priority for further research and monitoring regarding climate change susceptibility within Europe. The presented approach represents a promising tool, to quickly assess large groups of species regarding their susceptibility to climate change and other threats, and to identify research and management priorities.
Comparative genomics analyses indicate differential methylated amine utilisation trait within members of the genusGemmobacter
Authors: Kröber E. , Peixoto J , Cunningham MR , Spurgin L. , Wischer D , Kruger R , Kumaresan D.
Published: June 2018

Methylated amines are ubiquitous in the environment and play a role in regulating the earth’s climate via a set of complex biological and chemical reactions. Microbial degradation of these compounds is thought to be a major sink. Recently we isolated a facultative methylotroph,Gemmobactersp. LW-1, an isolate from the unique environment Movile Cave, Romania, which is capable of methylated amine utilisation as a carbon source. Here, using a comparative genomics approach, we investigate how widespread methylated amine utilisation trait is within the member of the bacterial genusGemmobacter. Five genomes of differentGemmobacterspecies isolated from diverse environments, such as activated sludge, fresh water, sulphuric cave waters (Movile Cave) and the marine environment were available from the public repositories and used for the analysis. Our results indicate that some members of the genusGemmobacter, namelyG. aquatilis, G. caeniandG. sp. LW-1 have the genetic potential of methylated amine utilisation while others (G. megateriumandG. nectariphilus) have not.
Gut segments outweigh the diet in shaping the intestinal microbiome composition in grass carp Ctenopharyngodon idellus
Authors: Feng Wenwen , Zhang Jing , Jakovlić Ivan , Xiong Fan , Wu Shangong , Zou Hong , Li Wenxiang , Li Ming , Wang Guitang
Published: June 2018

Although dynamics of the complex microbial ecosystem populating the gastrointestinal tract of animals has profound and multifaceted impacts on host’s metabolism and health, it remains unclear whether it is the intrinsic or extrinsic factors that play a more dominant role in mediating variations in the composition of intestinal microbiota. To address this, two strikingly different diets were studied: a high-protein, low-fiber formula feed (FF), and low-protein, high-fiber Sudan grass (SG). After a 16-week feeding trial on a herbivorous fish, grass carp, microbial profiles of midgut (M) and hindgut (H) segments of both groups were compared. Bacteroidetes were more abundant in the hindgut (T=-7.246, p<0.001), and Proteobacteria in the midgut (T=4.383, p<0.001). Fusobacteria were more abundant in the FF group (compared to the SG group, T=2.927, p<0.001). Bacterial composition was different (p<0.05) between the midguts of formula feed (M-FF) and Sudan grass (M-SG) groups, but not between the hindguts of two groups (H-FF and H-SG; p=0.269). PerMANOVA and VPA indicated that the gut segment contributed 19.8% (p<0.001) and 28% (p<0.001) of the variation of microbial communities, whereas diet contributed only 8.0% (p<0.001) and 14% (p<0.001), respectively. Overall, results suggest that intestinal compartments are a stronger determinant than diet in shaping the intestinal microbiota. Specifically, whereas diet has a strong impact on the microbiome composition in proximal gut compartments, this impact is much less pronounced distally, which is likely to be a reflection of a limited ability of some microbial taxa to thrive in the anoxic environment in distal segments.

IMPORTANCE

The impact of compositional dynamics of gut microbiota on host’s metabolism and health is so profound that the traditional idea of biological individual is increasingly replaced with "holobiont", comprising both the host and its microbiome. Composition of gut microbiota is strongly influenced by extrinsic (such as diet) and intrinsic (such as gut compartment) factors. Despite ample scientific attention both of these factors have received individually, their relative contributions in mediating the dynamics of the microbiome remain unknown. Given the importance of this issue, we set out to disentangle their individual contributions in a herbivorous fish, grass carp. We found that intestinal compartments are a stronger determinant than diet in shaping the intestinal microbiota. Whereas the impact of diet is strongly pronounced in proximal gut compartments, it appears that limited ability of some microbial taxa to thrive in the anoxic environment in distal segments strongly reduces the impact of diet distally.
The multifurcating skyline plot
Authors: Hoscheit Patrick , Pybus Oliver G.
Published: June 2018

A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The “skyline plot” and related approaches are commonly employed as exible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalised skyline plot methods to phylogenies that contain one or more multifurcations (i.e.hard polytomies). We use the theory of Λ-coalescents (specifically, Beta(2α,α)-coalescents) to develop the “multifurcating skyline plot”, which estimates a piecewise constant function of effective population size through time, conditional on a time-scaled multifurcating phylogeny. We implement a smoothing procedure and extend the method to serially-sampled (heterochronous) data, but we do not address here the problem of estimating trees with multifurcations from gene sequence alignments. We validate our estimator on simulated data using maximum likelihood and find that parameters of the Beta(2α,α)-coalescent process can be estimated accurately. Lastly we apply the multifurcating skyline plot to a molecular clock phylogeny of 1,610 Ebola virus sequences from the 2014-2016 West African outbreak. We artificially collapse short branches in this empirical phylogeny in order to mimic different levels of multifurcation and show that variance in the reproductive success of the pathogen through time can be estimated by combining the skyline plot with epidemiological case count data.
Ras inhibition by trametinib treatment in Drosophila attenuates gut pathology in females and extends lifespan in both sexes
Authors: Regan Jennifer C , Lu Yu-Xuan , Bolukbasi Ekin , Khericha Mobina , Partridge Linda
Published: June 2018

Females of most species live longer than do males. Furthermore, lifespan-extending
interventions in laboratory model organisms are often more effective in females (Regan and Partridge 2013). For instance, genetic and pharmacological suppression of activity of the insulin/insulin-like signalling - target of rapamycin (IIS-TOR) network generally extends female lifespan more than that of males in both Drosophila and mice (Clancy et al. 2001; Selman et al. 2009). We previously showed that attenuation of Ras-dependent IIS signalling by treatment with the FDA-approved MEK inhibitor, trametinib extends lifespan in females (Slack et al. 2015). Here, we demonstrate that trametinib treatment has beneficial effects on female-specific, age-related gut pathologies, similar to those obtained through dietary restriction (Regan et al. 2016). Importantly, we identify Ras inhibition as an effective lifespan-extending manipulation in males as well as females, pointing to parallel mechanisms of lifespan extension by trametinib in both sexes.
SPHIRE-crYOLO: A fast and accurate fully automated particle picker for cryo-EM
Authors: Wagner Thorsten , Merino Felipe , Stabrin Markus , Moriya Toshio , Antoni Claudia , Apelbaum Amir , Hagel Philine , Sitsel Oleg , Raisch Tobias , Prumbaum Daniel , Quentin Dennis , Roderer Daniel , Tacke Sebastian , Siebolds Birte , Schubert Evelyn , Shaikh Tanvir R. , Lill Pascal , Gatsogiannis Christos , Raunser Stefan
Published: June 2018

Selecting particles from digital micrographs is an essential step in single particle electron cryomicroscopy (cryo-EM). Since manual selection of complete datasets typically comprising many thousands of particles is a tedious and time-consuming process, many automatic particle pickers have been developed in the past few decades. However, non-ideal datasets pose a challenge to particle picking. Here, we present a novel automated particle picking software called crYOLO, which is based on the deep learning object detection system “You Only Look Once” (YOLO). After training the network with 500 – 2,500 particles per dataset, it automatically recognizes particles with high recall and precision reaching a speed of up to five micrographs per second. Importantly, we demonstrate a powerful general network trained on more than 40 datasets to select previously unseen datasets, thus paving the way for completely automated “on-the-fly” cryo-EM data pre-processing during data acquisition. CrYOLO is available as a standalone program underhttp://sphire.mpg.de/and will be part of the image processing workflow in SPHIRE.
An atlas of chromatin accessibility in the adult human brain
Authors: Fullard John F. , Hauberg Mads E. , Bendl Jaroslav , Egervari Gabor , Cirnaru Maria-Daniela , Reach Sarah M. , Motl Jan , Ehrlich Michelle E. , Hurd Yasmin L. , Roussos Panos
Published: June 2018

Most common genetic risk variants associated with neuropsychiatric disease are noncoding and are thought to exert their effects by disrupting the function of cis regulatory elements (CREs), including promoters and enhancers. Within each cell, chromatin is arranged in specific patterns to expose the repertoire of CREs required for optimal spatiotemporal regulation of gene expression. To further understand the complex mechanisms that modulate transcription in the brain, we used frozen postmortem samples to generate the largest human brain and cell-type–specific open chromatin data set to date. Using the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq), we created maps of chromatin accessibility in two cell types (neurons and non-neurons) across 14 distinct brain regions of five individuals. Chromatin structure varies markedly by cell type, with neuronal chromatin displaying higher regional variability than that of non-neurons. Among our findings is an open chromatin region (OCR) specific to neurons of the striatum. When placed in the mouse, a human sequence derived from this OCR recapitulates the cell type and regional expression pattern predicted by our ATAC-seq experiments. Furthermore, differentially accessible chromatin overlaps with the genetic architecture of neuropsychiatric traits and identifies differences in molecular pathways and biological functions. By leveraging transcription factor binding analysis, we identify protein-coding and long noncoding RNAs (lncRNAs) with cell-type and brain region specificity. Our data provide a valuable resource to the research community and we provide this human brain chromatin accessibility atlas as an online database “Brain Open Chromatin Atlas (BOCA)” to facilitate interpretation.
Reclassification of the BRAF p.Ile208Val variant by case-level data sharing
Authors: Grant Andrew R. , Hemphill Sarah E. , Vincent Lisa M. , Rehm Heidi L.
Published: June 2018

The ClinVar database is a useful tool for patients and physicians to view variant interpretations submitted by clinical and nonclinical labs. However, variants of uncertain significance (VUS) in ClinVar can pose a significant burden on patients. If possible, it is important to resolve discrepancies and uncertainties surrounding interpreted variants. Here we highlight a case of a family who received a report of a variant (c.622A>G, p.Ile208Val) in BRAF following prenatal RASopathy testing. The variant had been previously classified by our laboratory as a VUS, so the mother contacted our laboratory via ClinVar for further information, which prompted reevaluation of the variant. Multiple sources of case-level data as well as the presence of the variant in the general population yielded sufficient evidence to reclassify the variant as likely benign. This reclassification alleviated significant concern for the family, and the child was born healthy with no clinical manifestations of Noonan syndrome or a RASopathy.
Improving the detection efficiency and modulation transfer function of lens-coupled indirect X-ray imaging detectors based on point spread functions simulated according to lens performance parameters
Authors: Wang Yanping , Li Gang , Zhang Jie , Yi Qiru , Zhao Yue , Li Kun , Zhu Ye , Jiang Xiaoming
Published: June 2018

Lens-coupled indirect X-ray imaging detectors have the advantage of high resolution and the disadvantage of low detection efficiency. Using thicker single-crystalline films (SCFs) can improve the detection efficiency. However, the image quality will become worse due to the degradation of the point spread function (PSF) and modulation transfer function (MTF). This disadvantage can be improved by deconvolution with the PSF, which is unknown. In this article, a method was established to acquire the PSF based on a simulation of the imaging process for a lens-coupled indirect X-ray imaging detector. Because the structural parameters of commercial lenses cannot usually be obtained, the PSFs were calculated from lens performance parameters. PSFs were calculated using the conditions of 12 keV X-ray energy, 10× and 40× magnification objectives and 4.6 µm- and 20 µm-thick GGG:Tb scintillators. These were then used to deconvolve images of an Xradia resolution test pattern taken under the same conditions. The results show that after deconvolution the MTF had been clearly improved for both the 4.6 µm- and 20 µm-thick SCFs, indicating that the image has better quality than before deconvolution. Furthermore, a PSF deconvolution was performed on mouse brain tissue projection images, and the original and deconvolution projection images were used to perform computed-tomography reconstruction; the result proved that the method was effective for improving the image quality of low-contrast samples. Therefore, this method shows promise in allowing the use of thick SCFs to improve the detection efficiency while maintaining good image quality.
Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions
Authors: Schroer Martin A. , Blanchet Clement E. , Gruzinov Andrey Yu. , Gräwert Melissa A. , Brennich Martha E. , Hajizadeh Nelly R. , Jeffries Cy M. , Svergun Dmitri I.
Published: June 2018

Radiation damage by intense X-ray beams at modern synchrotron facilities is one of the major complications for biological small-angle X-ray scattering (SAXS) investigations of macromolecules in solution. To limit the damage, samples are typically measured under a laminar flow through a cell (typically a capillary) such that fresh solution is continuously exposed to the beam during measurement. The diameter of the capillary that optimizes the scattering-to-absorption ratio at a given X-ray wavelength can be calculated a priori based on fundamental physical properties. However, these well established scattering and absorption principles do not take into account the radiation susceptibility of the sample or the often very limited amounts of precious biological material available for an experiment. Here it is shown that, for biological solution SAXS, capillaries with smaller diameters than those calculated from simple scattering/absorption criteria allow for a better utilization of the available volumes of radiation-sensitive samples. This is demonstrated by comparing two capillary diameters d
i (d
i = 1.7 mm, close to optimal for 10 keV; and d
i = 0.9 mm, which is nominally sub-optimal) applied to study different protein solutions at various flow rates. The use of the smaller capillaries ultimately allows one to collect higher-quality SAXS data from the limited amounts of purified biological macromolecules.
Crystal structure of 2-[2-(pyridin-3-yl)diazen-1-yl]aniline
Authors: Peters Morten K. , Näther Christian , Herges Rainer
Published: June 2018

The crystal structure of the title compound, C11H10N4, comprises molecules in a trans conformation for which all the atoms are located in general positions. The six-membered rings are coplanar and this arrangement might be stabilized by intramolecular N—H...N hydrogen bonding. In the crystal, the molecules are linked into helical chains parallel to the b axis via N—H...N hydrogen bonding. The molecular packing shows a herringbone-like pattern along the a axis. Comparison of the X-ray powder diffraction with that calculated from single crystal data proves that a pure crystalline phase was obtained and UV–Vis measurements reveal that only the trans isomer is present.
Big data for big pharma
Authors: Festa Giuseppe , Safraou Imen , Cuomo Maria Teresa , Solima Ludovico
Published: June 2018

Purpose

Big pharma, which comprise the most important companies in the pharmaceutical sector, are ambidextrous organizations by nature. Big data can heavily influence this characteristic by simultaneously requiring adequate business process management. In fact, the impact of big data on business process management can assist big pharma in increasing process efficiency (which is related to the research and development pipeline) and process efficacy (related to product portfolio management). The purpose of this paper is to investigate this possibility and opportunity.

Design/methodology/approach

In the absence of specific scientific studies, as indicated by a review of the existing literature, the authors have adopted a grounded theory approach. This research has observed multiple cases (the 15 most important big pharma companies worldwide) through an electronic survey conducted on secondary data. The study has allowed the generation of a theoretical framework based on the (direct) relationship between knowledge process standardization (as the dependent variable) and big data (as the independent variable) in organizations oriented toward ambidexterity, such as big pharma in the specific scope of this research.

Findings

As big data utilization becomes widespread along the pipeline (or even along the value chain/supply chain), business process management increasingly uses (or tends to use) standardization, adopting process standardization as the main coordination mechanism to manage big knowledge. This theory is even more true when considering the moderating role of ambidexterity. An enterprise oriented toward structural ambidexterity (such as big pharma) that uses big data will require increased process standardization to manage big knowledge. Alternatively, an enterprise oriented toward contextual ambidexterity that uses big data will require increased output standardization.

Originality/value

Based on an analytical literature review, no research to date has focused strict attention on the influence that big data can have on business process management to improve the natural ambidexterity of big pharma. The main unique feature of this research relies on this point. The main value of the research originates from the theoretical framework reconstructed by grounded theory, which constitutes a powerful strategic tool to support executives and managers of big pharma in organizing business process management for their ambidextrous organizations using big data.
Speed of adjustment over entry and exit dynamics
Authors: Outla Adil , Hamzaoui Moustapha
Published: June 2018

Purpose

This paper aims to provide a theoretical conception that establishes growth rate dynamics for co-operatives and studies Moroccan co-operatives’ start-ups and closures, by analyzing the co-operatives’ growth rate speed of adjustment (SOA).

Design/methodology/approach

This paper documents the basic patterns of entry and exit flow for agricultural, artisanal, housing and fishery co-operatives; highlights, with econometric tests, whether co-operatives’ growth rate is mean reverting or a unit root random walk; and estimates the growth rate adjustment speed, using a quadratic interval reverting model to capture both the upward and downward speeds of adjustment.

Findings

The empirical results indicate that co-operatives’ growth rate is significantly mean reverting for all sectors. Also, it concludes that the upward and downward adjustment speeds are significantly different within and between sectors, with negative indicator for artisanal co-operatives. The paper discusses these results, which are of interest to academics and policymakers.

Research limitations/implications

The study does not investigate the causes of the growth rate SOA. Further, in-depth work with the results of this study would help scholars and policymakers to get close to the accurate research questions that characterize the mean reverting and affects the adjustment processes for Moroccan co-operatives.

Practical implications

The suggested model – with upward and downward adjustment speeds– could be valuable for policymakers’ strategies on co-operatives’ emergence.

Social implications

The paper moves policymakers closer to social work and socio-economic trends to explain the empirical regularities of co-operatives’ dynamics. The model could be of value to avoid a volatile rate of entries and exits, to ensure continuity, to avoid fast failure of co-operative memberships and then to achieve the social inclusion.

Originality/value

The paper provides empirical evidence and results for co-operatives’ start-ups and closures adjustment speed and determines the conditions in which government policy must be clarified and specified. To the best of the authors’ knowledge, this paper is the first empirical analysis for the co-operatives’ SOA over entry and exit dynamics.
Recruitment messaging, environmental fit and public service motivation
Authors: Asseburg Julia , Homberg Fabian , Vogel Rick
Published: June 2018

Purpose

Public organisations face increasing challenges to attract young and highly qualified staff. Previous studies have shown that public service motivation (PSM) is associated with a higher propensity to apply for public sector jobs, but the implications from these findings for the design of the recruitment process are still unclear. The purpose of this paper is to investigate how differently framed recruitment messages (i.e. inspirational and rational) affect perceptions of person-job (PJ) and person-organisation (PO) fit, how these associations are moderated by PSM and how they translate into application intentions.

Design/methodology/approach

The authors conducted a survey experiment and tested the hypotheses in a sample of 600 students in Germany. The experimental stimuli were hypothetical job advertisements in which inspirational and rational messages on organisational missions and job tasks were varied.

Findings

Results show that recruitment messaging, as mediated by perceived PJ and PO fit, can increase application intentions depending on the framing of the messages. Inspirational framings are more effective in attracting personnel than rational framings, especially when such messages convey specific and extensive information about job tasks. The extent to which recruitment messages translate into perceptions of fit depends, in part, on the level of the applicant’s PSM.

Originality/value

By focusing on recruitment messages and their framings, this study is among the few that explore how human resource management can capitalise on previous findings of research on PSM. The findings have implications for the selection and presentation of information on organisational missions and job tasks in the recruitment process. In a more theoretical vein, results contribute to the emerging consensus on the role of perceived PJ and PO fit in the attraction to public sector jobs. The authors deepen this reasoning by introducing self-discrepancy theory to the field of public management.
Optimizations of RZ5-TiC magnesium matrix composite wear parameters using Taguchi approach
Authors: Mehra Deepak , Mahapatra Manas Mohan , Harsha Suraj Prakash
Published: June 2018

Purpose

The advancement in modern manufacturing technology generated the need to develop new materials for better wear resistance. The purpose of this paper is to use the Taguchi optimization approach to examine which wear parameter significantly affects weight loss and coefficient of friction for RZ5-TiC composite. It is a simple and efficient method to find performance of wear parameter using minimum experimental runs.

Design/methodology/approach

RZ5-TiC composites were prepared using RZ5 as matrix, reinforced with TiC through self-propagating high-temperature synthesis technique. In the present work, an attempt has been made to study the influence of wear parameters like applied load (AL), sliding distance (SD) and Wt.% of TiC (WTC) on responses like weight loss and coefficient of friction of RZ5/TiCp composites. The pin-on-disc apparatus used to conduct abrasive wear test. The wear process parameters are optimized for minimum wear based on L27 Taguchi orthogonal design. The Taguchi technique using design of experiments (DOE) is used to obtain the data. The ANOVA and an orthogonal array are used to examine the influence of wear parameters on responses. The purpose is to examine parametric significances which affect responses.

Findings

It observed that wear parameters have the significant influence on responses of RZ5/TiCp composites. The interaction of sliding distance/Wt.% of TiC is observed and found significant influence on both responses. The optimum level of the significant wear parameters is achieved based on the maximum S/N ratio for RZ5/TiCp composites. The optimal interaction for weight loss and coefficient of friction is AL1-SD1-WTC3 and AL3-SD1-WTC3, respectively. Finally, the confirmation test is conducted and the results are obtained within the confidence interval.

Originality/value

The current manuscript provides an optimization of wear parameters using Taguchi approach. The extensive experimental data are used for this purpose and effects of wear parameters on responses are analyzed from the presented results. The results obtained are useful in improving the wear resistance of the RZ5-TiC composite.
Tribological characteristics comparison of formulated palm trimethylolpropane ester and polyalphaolefin for cam/tappet interface of direct acting valve train system
Authors: Zahid Rehan , Hj. Hassan Masjuki , Alabdulkarem Abdullah , Varman Mahendra , Kalam Md. Abul , Mufti Riaz Ahmad , Mohd Zulkifli Nurin Wahidah , Gulzar Mubashir , Bhutta Muhammad Usman , Ali Mian Ashfaq , Abdullah Usman , Yunus Robiah H.
Published: June 2018

Purpose

There is a continuous drive in automotive sector to shift from conventional lubricants to environmental friendly ones without adversely affecting critical tribological performance parameters. Because of their favorable tribological properties, chemically modified vegetable oils such as palm trimethylolpropane ester (TMP) are one of the potential candidates for the said role. To prove the suitability of TMP for applications involving boundary-lubrication regime such as cam/tappet interface of direct acting valve train system, a logical step forward is to investigate their compatibility with conventional lubricant additives.

Design/methodology/approach

In this study, extreme pressure and tribological characteristics of TMP, formulated with glycerol mono-oleate (GMO), molybdenum dithiocarbamate (MoDTC) and zinc dialkyldithiophosphate (ZDDP), has been investigated using four-ball wear tester and valve train test rig. For comparison, additive-free and formulated versions of polyalphaolefin (PAO) were used as reference. Moreover, various surface characterization techniques were deployed to investigate mechanisms responsible for a particular tribological behavior.

Findings

In additive-free form, TMP demonstrated better extreme pressure characteristics compared to PAO and lubricant additives which are actually optimized for conventional base-oils such as PAO, are also proved to be compatible with TMP to some extent, especially ZDDP. During cylinder head tests, additive-free TMP proved to be more effective compared to PAO in reducing friction of cam/tappet interface, but opposite behavior was seen when formulated lubricants were used. Therefore, there is a need to synthesize specialized friction modifiers, anti-wear and extreme pressure additives for TMP before using it as engine lubricant base-oil.

Originality/value

In this study, additive-free and formulated versions of bio-lubricant are tested for cam/tappet interface of direct acting valve train system of commercial passenger car diesel engine for the very test time. Another important aspect of this research was comparison of important tribological performance parameters (friction torque, wear, rotational speed of tappet) of TMP-based lubricants with conventional lubricant base oil, that is, PAO and its formulated version.