bluuebunny/crossref_metadata_2025 huggingface dataset:
The most primitive extant ancestor of organisms and discovery of definitive evolutionary equations
Authors: Sorimachi Kenji
Published: July 2018

Organisms are classified into three domains, Prokaryota, Archaea, and Eukaryota, and their evolutionary divergence has been characterized based on morphological and molecular features using rationale based on Darwin’s theory of natural selection. However, universal rules that govern genome evolution have not been identified. Here, a simple, innovative approach has been developed to evaluate biological evolution initiating the origin of life: whole genomes were divided into several fragments, and then differences in normalized nucleotide content between nucleotide pairs were compared. Based on nucleotide content structures, Monosiga brevicollis mitochondria may be the most primitive extant ancestor of the species examined here. The two normalized nucleotide contents are universally expressed by a linear regression line, (X − Y)/(X + Y) = a (X − Y) + b, where X and Y are nucleotide contents and (a) and (b) are constants. The value of (G + C), (G + A), (G + T), (C + A), (C + T) and (A + T) was ~0.5. Plotting (X − Y)/(X + Y) against X/Y showed a logarithmic function (X − Y)/(X + Y) = a ln X/Y + b, where (a) and (b) are constant. Nucleotide content changes are expressed by a definitive equation, (X − Y) ≈ 0.25 ln(X/Y).
Native Mass Spectrometry Reveals the Conformational Diversity of the UVR8 Photoreceptor
Authors: Camacho Inês S. , Theisen Alina , Johannissen Linus O. , Díaz-Ramos L. Aranzazú , Christie John M. , Jenkins Gareth I. , Bellina Bruno , Barran Perdita , Jones Alex R.
Published: July 2018

UVR8 is a plant photoreceptor protein that regulates photomorphogenic and protective responses to UV light. The inactive, homodimeric state absorbs UV-B light resulting in dissociation into monomers, which are considered to be the active state and comprise a β-propeller core domain and intrinsically disordered N- and C-terminal tails. The C-terminus is required for functional binding to signalling partner COP1. To date, however, structural studies have only been conducted with the core domain where the terminal tails have been truncated. Here, we report structural investigations of full-length UVR8 using native ion mobility mass spectrometry adapted for photo-activation. We show that, whilst truncated UVR8 photo-converts from a single conformation of dimers to a single monomer conformation, the full-length protein exist in numerous conformational families. The full-length dimer adopts both a compact state and an extended state where the C-terminus is primed for activation. In the monomer the extended C-terminus destabilises the core domain to produce highly extended yet stable conformations, which we propose are the fully active states that bind COP1. Our results reveal the conformational diversity of full-length UVR8. We also demonstrate the potential power of native mass spectrometry to probe functionally important structural dynamics of photoreceptor proteins throughout nature.

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Skull base invasive low-grade meningiomas, a distinct genetic subgroup: A microarray gene expression profile analysis
Authors: Sakuma Jun , Fujii Masazumi , Kishida Yugo , Iwami Kenichiro , Oda Keiko , Iwatate Kensho , Ichikawa Masahiro , Bakhit Mudathir , Sato Taku , Waguri Satoshi , Watanabe Shinya , Saito Kiyoshi
Published: July 2018

Introduction

Meningioma is the most common adult primary brain tumor originating from meningeal coverings of the brain and spinal cord. Commonly, World Health Organization (WHO) grade-I meningiomas are slowly growing and surgically curative, some present with clinically aggressive behavior, invading the skull base bone and soft tissues by extending into the extracranial spaces.

Methods

To detect the genetic background of the Skull Base Invasive Low-grade Meningioma (SBILM), we conducted a comprehensive analysis of gene expression was conducted on 32 meningioma samples.

Results

The cluster analysis of the gene expression profile demonstrated a distinctive clustering pattern of the SBILM. Based on the clinical behavior and the microarray findings, they might be a distinct subgroup of meningiomas.

Conclusion

Further studies on characterization of genes specifically expressed by the SBILM could lead to the development of diagnostic tools, differentiating it from other WHO grade-I meningiomas and assist in the appropriate management and follow-up strategy, and open the door for development of pharmacological therapies.
Zebrafishduoxmutations provide a model for human congenital hypothyroidism
Authors: Chopra Kunal , Ishibashi Shoko , Amaya Enrique
Published: July 2018

Thyroid dyshormonogenesis is a leading cause of congenital hypothyroidism, a highly prevalent but treatable condition. Thyroid hormone synthesis is dependent on the formation of reactive oxygen species (ROS). In humans, the primary sources for ROS production during thyroid hormone synthesis are the NADPH oxidase, DUOX1 and DUOX2. Indeed mutations inDUOX1andDUOX2have been linked with congenital hypothyroidism. Unlike humans, zebrafish has a single orthologue forDUOX1andDUOX2. In this study, we investigated the phenotypes associated with two nonsense mutant alleles of the singleduoxgene in zebrafish,sa9892andsa13017. Both alleles gave rise to readily observable phenotypes reminiscent of congenital hypothyroidism, from the larval stages through to adulthood. By using various methods to examine the external and internal phenotypes, we discovered a strong correlation between TH synthesis andduoxfunction, beginning from the early larval stage, when T4levels are already noticeably absent in the mutants. Loss of T4production resulted in growth retardation, pigmentation defects, ragged fins, thyroid hyperplasia / external goiter, and infertility. Remarkably all of these defects associated with chronic congenital hypothyroidism could be rescued with T4treatment, even when initiated when the fish had already reached adulthood. Our work suggests that these zebrafishduoxmutants may provide a powerful model to understand the aetiology of untreated and treated congenital hypothyroidism even in advance stages of development.
HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism
Authors: Mills Benjamin B. , Thomas Andrew D. , Riddle Nicole C.
Published: July 2018

Heterochromatin Protein 1 (HP1) proteins are an important family of chromosomal proteins conserved among all major eukaryotic lineages. While HP1 proteins are best known for their role in heterochromatin, many HP1 proteins function in euchromatin as well. As a group, HP1 proteins carry out diverse functions, playing roles in the regulation of gene expression, genome stability, chromatin structure, and DNA repair. While the heterochromatic HP1 proteins are well studied, our knowledge of HP1 proteins with euchromatic distribution is lagging behind. We have created the first mutations in HP1B, a Drosophila HP1 protein with euchromatic function, and the Drosophila homolog most closely related to mammalian HP1α, HP1β, and HP1γ. We find that HP1B is a non-essential protein in Drosophila, with mutations affecting fertility and animal activity levels. In addition, animals lacking HP1B show altered food intake and higher body fat levels. Gene expression analysis of animals lacking HP1B demonstrates that genes with functions in various metabolic processes are affected primarily by HP1B loss. Our findings suggest that there is a link between the chromatin protein HP1B and the regulation of metabolism.
Information theoretic analysis of hyperspectral imaging systems with applications to fluorescence microscopy
Authors: Ram Sripad
Published: July 2018

We present a general stochastic model for hyperspectral imaging data and derive analytical expressions for the Fisher information matrix for the underlying spectral unmixing problem. We investigate the linear mixing model as a special case and define a linear unmixing performance bound by using the Cramer-Rao inequality. As an application, we consider fluorescence imaging and show how the performance bound provides a spectral resolution limit that predicts how accurately a pair of spectrally similar fluorescent labels can be spectrally unmixed. We also report a novel result that shows how the spectral resolution limit can be overcome by exploiting the phenomenon of anti-Stokes shift fluorescence. In addition, we investigate how photon statistics, channel addition and channel splitting affect the performance bound. Finally by using the performance bound as a benchmark, we compare the performance of the least squares and the maximum likelihood estimators for spectral unmixing. For the imaging conditions tested here, our analysis shows that both estimators are unbiased and that the standard deviation of the maximum likelihood estimator is consistently closer to the performance bound than that of the least squares estimator. The results presented here are based on broad assumptions regarding the underlying data model and are applicable to hyperspectral data acquired with point detectors, sCMOS, CCD and EMCCD imaging detectors.

EDICS: ELI-COL, COI-MCI.
Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution
Authors: Gao Ruixuan , Asano Shoh M. , Upadhyayula Srigokul , Igor Pisarev , Milkie Daniel E. , Liu Tsung-Li , Ved Singh , Austin Graves , Huynh Grace H. , Zhao Yongxin , Bogovic John , Colonell Jennifer , Ott Carolyn M. , Zugates Christopher , Tappan Susan , Rodriguez Alfredo , Mosaliganti Kishore R. , Megason Sean G. , Lippincott-Schwartz Jennifer , Hantman Adam , Rubin Gerald M. , Kirchhausen Tom , Saalfeld Stephan , Aso Yoshinori , Boyden Edward S. , Betzig Eric
Published: July 2018

Optical and electron microscopy have made tremendous inroads in understanding the complexity of the brain, but the former offers insufficient resolution to reveal subcellular details and the latter lacks the throughput and molecular contrast to visualize specific molecular constituents over mm-scale or larger dimensions. We combined expansion microscopy and lattice light sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entireDrosophilabrain, including synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly neuropil domain. The technology should enable statistically rich, large scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.

One Sentence Summary

Combined expansion and lattice light sheet microscopy enables high speed, nanoscale molecular imaging of neural circuits over large volumes.
Thresholding of cryo-EM density maps by false discovery rate control
Authors: Beckers Maximilian , Jakobi Arjen J. , Sachse Carsten
Published: July 2018

Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task due to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, we developed a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control. In this way, 3D confidence maps contain separated signal from background noise in the form of local detection rates of EM density values. We demonstrate that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures due to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions to the structure.
Comparison of human and murine enteroendocrine cells by transcriptomic and peptidomic profiling
Authors: Roberts Geoffrey P , Larraufie Pierre , Richards Paul , Kay Richard G , Galvin Sam G , Miedzybrodzka Emily L , Leiter Andrew , Joyce Li H. , Glass Leslie L , Ma Marcella KL , Lam Brian , Yeo Giles SH , Scharfmann Raphaël , Chiarugi Davide , Hardwick Richard H , Reimann Frank , Gribble Fiona M
Published: July 2018

Enteroendocrine cells (EECs) produce hormones that regulate food absorption, insulin secretion and appetite. Both EECs and their peptide products are foci of drug discovery programmes for diabetes and obesity. We compared the human and mouse EEC transcriptome and peptidome to validate mouse as a model of the human enteroendocrine axis. We present the first RNA sequencing analysis of human EECs, and demonstrate strong correlation with mouse, although with outliers including some low abundance G-protein coupled receptors. Liquid chromatography mass spectrometry (LC-MS) identified peptide hormone gradients along the human and mouse gut that should enhance progress in gut physiology and therapeutics.
Free-ranging dogs understand human intentions and adjust their behavioral responses accordingly
Authors: Bhattacharjee Debottam , Sau Shubhra , Bhadra Anindita
Published: July 2018

Domestic dogs (Canis lupus familiaris) are remarkably sensitive and responsive while interacting with humans. Pet dogs are known to have social skills and abilities to display situation-specific responses, but there is lack of information regarding free-ranging dogs which constitute majority of the world’s dog population. Free-ranging dogs found in most of the developing countries interact constantly with familiar and unfamiliar humans receiving both positive and negative behavior. Thus, understanding human intentions and subsequent behavioral adjustments are crucial for dogs that share habitats with humans. Here we subjected free-ranging dogs to different human social communicative cues (friendly and threatening – low and high), followed by a food provisioning phase and tested their responsiveness. Dogs exhibited higher proximity seeking behavior as a reaction to friendly gesture whereas, they were prompted to maintain distance depending on the impact of the threatening cues. Interestingly, only the high-impact threatening showed to have a persistent effect which also remained during the subsequent food provisioning phase. An elevated approach in the food provisioning phase elicited the dependency of free-ranging dogs on humans for sustenance. Our findings suggest that free-ranging dogs demonstrate behavioral plasticity on interacting with humans; which provides significant insights into the establishment of the dog-human relationship on streets.
The wheatSr22,Sr33,Sr35andSr45genes confer resistance against stem rust in barley
Authors: Asyraf Md. Hatta M. , Johnson Ryan , Matny Oadi , Smedley Mark A. , Yu Guotai , Chakraborty Soma , Bhatt Dhara , Xia Xiaodi , Arora Sanu , Steuernagel Burkhard , Richardson Terese , Mago Rohit , Lagudah Evans S. , Patron Nicola , Ayliffe Mick , Rouse Matthew N. , Harwood Wendy A. , Periyannan Sambasivam K. , Steffenson Brian J. , Wulff Brande B. H.
Published: July 2018

In the last 20 years, stem rust caused by the fungusPuccinia graminisf. sp.tritici(Pgt), has re-emerged as a major threat to wheat and barley cultivation in Africa and Europe. In contrast to wheat with 82 designated stem rust (Sr) resistance genes, barley’s genetic variation for stem rust resistance is very narrow with only seven resistance genes genetically identified. Of these, only one locus consisting of two genes is effective against Ug99, a strain ofPgtwhich emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheatSrgenes effective against Ug99.Sr22,Sr33,Sr35andSr45were transformed into barley cv. Golden Promise usingAgrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogenPuccinia hordei, indicating that the resistance conferred by these wheatSrgenes was specific forPgt. ClonedSrgenes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
Long non-coding RNAs are largely dispensable for zebrafish embryogenesis, viability and fertility
Authors: Goudarzi Mehdi , Berg Kathryn , Pieper Lindsey M. , Schier Alexander F.
Published: July 2018

Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyranoandsquint) and other conserved lncRNAs (gas5andlnc-setd1ba)were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs are dispensable for embryogenesis, viability and fertility.
Highly efficient scarless knock-in of reporter genes into human and mouse pluripotent stem cells via transient antibiotic selection
Authors: Sluch Valentin M. , Chamling Xitiz , Wenger Claire , Duan Yukan , Rice Dennis S. , Zack Donald J.
Published: July 2018

Pluripotent stem cells (PSCs) edited with genetic reporters are useful tools for differentiation analysis and for isolation of specific cell populations for study. Reporter integration into the genome is now commonly achieved by targeted DNA nuclease-enhanced homology directed repair (HDR). However, human PSCs are known to have a low frequency of gene knock-in (KI) by HDR, making reporter line generation an arduous process. Here, we report a methodology for scarless KI of large fluorescent reporter genes into PSCs by transient selection with puromycin or zeocin. With this method, we can perform targeted KI of a single reporter gene with up to 65% efficiency, as well as simultaneous KI of two reporter genes into different loci with up to 11% efficiency. Additionally, we demonstrate that this method also works in mouse PSCs.
Sulci of the canine brain: a review of terminology
Authors: Czeibert Kálmán , Piotti Patrizia , Petneházy Örs , Kubinyi Enikő
Published: July 2018

Over the last decades there have been several publications of anatomical and neurological textbooks, which include descriptions about the dogs’ brain. However, the terminology used is inconsistent, partly due to individual differences in neocortical gyration and partly due to the common practice of adapting terms from human and murine anatomy. In order to identify such incongruences, in Study 1, we reviewed the existing literature and identified the common terms used as well as any discrepancies between textbooks. Three main forms of inconsistencies were found; a) the use of terms that are not included in the Nomina Anatomica Veterinaria (NAV), b) the inclusion of structures that are listed as not canine-specific, and c) the use of similar names to identify potentially different anatomical structures. To address these issues, in Study 2 we investigated the consistency in appearance of the cerebral sulci, performing a macroscopical examination on 79 canine brains obtained through the Canine Brain and Tissue Bank (CBTB). We then evaluated whether sulci on the frontal regions of brachycephalic breeds differed from those of mesocephalic and dolichocephalic groups, as frontal and olfactory regions are subjected to the most extreme modifications following the shortening of the skull. The statistical analysis showed no difference across the skull length types regarding the occurrence of these sulci, although furrows on the lateral side of the brain proved to be more stable than those on the medial side. In Study 3, we summarized the findings in accordance with the NAV to produce a definitive index of the terms that we recommend be used for each identified sulci. Such an index is beneficial for educational, clinical use, and research (e.g. neuroscience) purposes. The dog is emerging as a pioneering and exceptional model in comparative neuroscience, and therefore the implications for canine neuroscience research should not be underestimated.
HOPS-dependent endosomal fusion required for efficient cytosolic delivery of therapeutic peptides and small proteins
Authors: Steinauer Angela , LaRochelle Jonathan R. , Wissner Rebecca , Berry Samuel , Schepartz Alanna
Published: July 2018

Protein therapeutics represent a significant and growing component of the modern pharmacopeia, but their potential to treat human disease is limited because most proteins fail to traffic across biological membranes. Recently, we discovered that cell-permeant miniature proteins (CPMPs) containing a precisely defined, penta-arginine motif traffic readily to the cytosol and nucleus with efficiencies that rival those of hydrocarbon-stapled peptides active in animals and man. Like many cell-penetrating peptides (CPPs), CPMPs enter the endocytic pathway; the difference is that CPMPs are released efficiently from endosomes while other CPPs are not. Here, we seek to understand how CPMPs traffic from endosomes into the cytosol and what factors contribute to the efficiency of endosomal release. First, using two complementary cell-based assays, we exclude endosomal rupture as the primary means of endosomal escape. Next, using a broad spectrum of techniques, including an RNA interference (RNAi) screen, fluorescence correlation spectroscopy (FCS), and confocal imaging, we identify VPS39—a gene encoding a subunit of the homotypic fusion and protein sorting (HOPS) complex—as a critical determinant in the trafficking of CPMPs and hydrocarbon-stapled peptides to the cytosol. Although CPMPs neither inhibit nor activate HOPS function, HOPS activity is essential to efficiently deliver CPMPs to the cytosol. Subsequent multi-color confocal imaging studies identify CPMPs within the endosomal lumen, particularly within the intraluminal vesicles (ILVs) of Rab7+and Lamp1+endosomes that are the products of HOPS-mediated fusion. These results suggest that CPMPs require HOPS to reach ILVs—an environment that serves as a prerequisite for efficient endosomal escape.
FIFO ATP synthase responds to glycolysis inhibition by localization into the inner boundary membrane
Authors: Zalyevskiy K. , Hager F. , Richter C. P. , Psathaki K. , Appelhans T. , Busch K.B.
Published: July 2018

Mitochondrial F1F0ATP synthase is the key enzyme to fuel the cell with essential ATP. Strong indications exist that the respiratory chain and the ATP synthase are physically separated within cristae. How static this organization is, is largely unknown. Here, we investigated the effect of substrate restriction on mitochondrial respiration and the spatio-temporal organization of ATP synthase. By superresolution microscopy, the localization and mobility of single labelled mitochondrial ATP synthase was determined in live cells. We found, that the ATP synthase under oxidative respiration displayed a clear localization and confined mobility in cristae. Trajectories of individual ATP synthase proteins show a perpendicular course to the longitudinal axis of the respective mitochondrion, exactly following the ultrastructure of cristae. When substrate for TCA cycle and respiration was limited, a significant proportion of ATP synthase localized from cristae to the inner boundary membrane, and only less mobile ATP synthase remained in cristae. These observations showing the plasticity of the spatio-temporal organisation of ATP synthase can explain why ATP synthase show interactions with proteins in distinct mitochondrial subcompartments such as inner boundary membrane, cristae junctions and cristae.
Modulating hinge flexibility in the APP transmembrane domain alters γ-secretase cleavage
Authors: Götz Alexander , Mylonas Nadine , Högel Philipp , Silber Mara , Heinel Hannes , Menig Simon , Vogel Alexander , Feyrer Hannes , Huster Daniel , Luy Burkhard , Langosch Dieter , Scharnagl Christina , Muhle-Goll Claudia , Kamp Frits , Steiner Harald
Published: July 2018

Intramembrane cleavage of the β-amyloid precursor protein C99 substrate by γ-secretase is implicated in Alzheimer’s disease pathogenesis. Since conformational flexibility of a di-glycine hinge in the C99 transmembrane domain (TMD) might be critical for γ-secretase cleavage, we mutated one of the glycine residues, G38, to a helix-stabilizing leucine and to a helix-distorting proline. CD, NMR and hydrogen/deuterium exchange measurements as well as MD simulations showed that the mutations distinctly altered the intrinsic structural and dynamical properties of the TMD. However, although helix destabilization/unfolding was not observed at the initial ε-cleavage sites of C99, both mutants impaired γ-secretase cleavage and altered its cleavage specificity. Moreover, helix flexibility enabled by the di-glycine hinge translated to motions of other helix parts. Our data suggest that both local helix stabilization and destabilization in the di-glycine hinge may decrease the occurrence of enzyme-substrate complex conformations required for normal catalysis and that hinge mobility can be conducive for productive substrate-enzyme interactions.
Improving Whole-Brain Neural Decoding of fMRI with Domain Adaptation
Authors: Zhou Shuo , Cox Christopher R. , Lu Haiping
Published: July 2018

In neural decoding, there has been a growing interest in machine learning on whole-brain functional magnetic resonance imaging (fMRI). However, the size discrepancy between the feature space and the training set poses serious challenges. Simply increasing the number of training examples is infeasible and costly. In this paper, we proposed a domain adaptation framework for whole-brain fMRI (DawfMRI) to improve whole-brain neural decoding on target data leveraging pre-existing source data. DawfMRI consists of three steps: 1) feature extraction from whole-brain fMRI, 2) source and target feature adaptation, and 3) source and target classifier adaptation. We evaluated its eight possible variations, including two non-adaptation and six adaptation algorithms, using a collection of seven task-based fMRI datasets (129 unique subjects and 11 cognitive tasks in total) from the OpenNeuro project. The results demonstrated that appropriate source domain can help improve neural decoding accuracy for challenging classification tasks. The best-case improvement is 8.94% (from 78.64% to 87.58%). Moreover, we discovered a plausible relationship between psychological similarity and adaptation effectiveness. Finally, visualizing and interpreting voxel weights showed that the adaptation can provide additional insights into neural decoding.
Perspective: Genomic inference using diffusion models and the allele frequency spectrum
Authors: Ragsdale Aaron P. , Moreau Claudia , Gravel Simon
Published: July 2018

Evolutionary, biological, and demographic processes combine to shape the variation observed in populations. Understanding how these processes are expected to influence variation allows us to infer past demographic events and the nature of selection in human populations. Forward models such as the diffusion approximation provide a powerful tool for analyzing the distribution of allele frequencies in contemporary populations due to their computational tractability and model flexibility. Here, we discuss recent computational developments and their application to reconstructing human demographic history and patterns of selection at new mutations. We also reexamine how some classical assumptions that are still commonly used in inference studies fare when applied to modern data. We use whole-genome sequence data for 797 French Canadian individuals to examine the neutrality of synonymous sites. We find that selection can lead to strong biases in the inferred demography, mutation rate, and distributions of fitness effects. We use these distributions of fitness effects together with demographic and phenotype-fitness models to predict the relationship between effect size and allele frequency, and contrast those predictions to commonly used models in statistical genetics. Thus the simple evolutionary models investigated by Kimura and Ohta still provide important insight into modern genetic research.
Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF
Authors: Correia Kevin , Ho Hanchen , Mahadevan Radhakrishnan
Published: July 2018

Background

Organohalide-respiring bacteria (OHRB) play an important role in the global halogen cycle and bioremediation of industrial sites contaminated with chlorinated organics. One notable OHRB is Dehalobacter restrictus strain CF, which is capable of respiring chloroform to dichloromethane. Improved bioremediation strategies could be employed with a greater understanding of D. restrictus’ metabolism in isolate and community cultures. To this end, we reconstructed the genome-scale metabolic network of D. restrictus to study its metabolism in future studies using flux balance analysis.

Method

The RAST annotation server and Model SEED framework were used to obtain a draft metabolic network reconstruction. Additional curation was required for its acetyl-CoA sources, the Wood-Ljungdahl pathway, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes.

Results

iHH623 is the first curated genome-scale metabolic model in the Peptococcaceae family. It spans 1087 reactions and 983 metabolites, covering 623 genes (21% of all ORF’s). Its potential sources of acetyl-CoA are pyruvate ferredoxin oxidoreductase, pyruvate formate lyase, acetyl-CoA synthetase, phosphate acetyltransferase, and CO-methylating acetyl-CoA synthase. NADPH may be regenerated by isocitrate dehydrogenase, malic enzyme, NADP-reducing hydrogenase, cytosolic formate dehydrogenase, ferredoxin-dependent bifurcating transhydrogenase, 5-methyltetrahydrofolate dehydrogenase, and 5-10-methylenetetrahydrofolate. Additional reactions that were added or removed to the D. restrictus reconstruction are discussed.

Conclusions

We reconstructed the genome-scale metabolic network of D. restricus by obtaining an initial draft with the RAST server and Model SEED framework. Curation was required for D. restricus’ acetyl-CoA sources, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes. This metabolic model can be used to decipher D. restrictus’ metabolism in isolate and community cultures in future studies, or as a template to reconstruct the metabolic network of other Peptococcaceae species. The extensive curation of the draft metabolic network reconstruction highlights the need to be cautious of automated metabolic network reconstruction.
Determination of temperature-dependent crystallographic parameters of Al–Si alloys using in situ neutron diffraction
Authors: Vandersluis Eli , Sediako Dimitry , Emadi Payam , Ravindran Comondore , Elsayed Abdallah , Byczynski Glenn
Published: July 2018

Accurate evaluation of temperature-dependent lattice spacings of individual phases in complex engineering alloys enables analysis and design of enhanced components for high-temperature applications. However, typical characterization techniques are limited to measurements at temperatures at which the alloy is completely solid state. In this study, in situ neutron diffraction was performed to determine the crystallographic parameters of several phases in unmodified and Sr-modified Al–6 wt% Si and A319 alloys from the start of solidification to 423 K. Approximately linear correlations were found for the interplanar spacings and lattice parameters of Al, Si, Al5Mg8Cu2Si6 and Al15(Fe,Mn)3Si2 phases with temperature for the entire measured range. The greater concentration of lattice-contracting elements dissolved in the A319 solid solutions resulted in smaller lattice spacings and larger coefficients of thermal expansion than the same phases in Al–6 wt% Si, yet eutectic modification with Sr did not produce noticeable changes in the crystallographic parameters. The Si phase was found to have the largest thermal expansion coefficient misfit with the Al matrix. These findings offer significant insight into the development and mitigation of thermal stresses in the processing and operation of engineering components.
Making an order: the concerted alignment of [MOF5]2− (M = Nb and Ta) dipolar anions in one-dimensional coordination chains sustained by tris(3,4,5-trimethyl-1H-pyrazole)copper(II)
Authors: Sharko Anastasiya V. , Erhart Oliver , Krautscheid Harald , Domasevitch Kostiantyn V.
Published: July 2018

Electronic distortions, which are inherent in the oxide fluoride anions [MOF5]2− (M = Nb and Ta), provide an origin of polar molecular arrangements for the development of new polar second-harmonic-generating, piezo-, pyro- and ferroelectric materials. It is still a challenge to expand this approach to the realm of metal–organic polymers, while insufficient control over the environment of the [MOF5]2− units results in their orientational disorder and loss of polarity. The structures of catena-poly[[tris(3,4,5-trimethyl-1H-pyrazole-κN
2)copper(II)]-μ-oxido-[tetrafluoridoniobium(V)]-μ-fluorido], [CuNbF5O(C6H10N2)3]
n
, (I), and its isostructural pentafluoridooxidotantalate(V) analogue, catena-poly[[tris(3,4,5-trimethyl-1H-pyrazole-κN
2)copper(II)]-μ-oxido-[tetrafluoridotantalum(V)]-μ-fluorido], [CuTaF5O(C6H10N2)3]
n
, (II), are the first examples of the strict orientational order of [MOF5]2− (M = Nb and Ta) in one-dimensional coordination chains. A primary factor for the exact discrimination of one orientation of the anion over the other is strong and shape-selective multiple interactions of [MOF5]2− with the inherently acentric CuL
3
2+ platform, with a set of two coordination and three N—H...F hydrogen bonds. In (I) and (II), the Cu2+ ions exhibit distorted square-pyramidal fivefold coordination formed by three pyrazole N atoms and the oxide O atom, defining the equatorial plane, and the anionic bridging F atom (which is trans with respect to the M—O bond) residing in the apical position. The inorganic bridges connect CuL
3
2+ moieties into polar zigzag chains; the bulk polarity of the structure is eliminated by an antiparallel alignment of the individual chains. These chains are further connected through C—H...F hydrogen bonding and very weak C—H...π interactions of the organic ligands.
Thermal insulation and morphology of natural and synthetic filled outdoor sportswear by repeated water washing and dry cleaning
Authors: Kim Sunyoung , Kim Eunae , Park Youngmi
Published: July 2018

Purpose

The purpose of this paper is to examine the thermal insulation and water vapor transmission rate (WVTR) according to the type of the filling material, and compared the thermal insulation in the dynamic state considering actual wearing conditions.

Design/methodology/approach

The thermal insulation and WVTR were evaluated in a standard state depending on the type of filling material (goose down (GD), duck down (DD), Thinsulate700 (T700), Thinsulate600 (T600) and Polyester (PET)), and the changes in thermal insulation were examined by measuring the microclimate in the case of an environmental change from a high temperature to a low temperature. In addition, the clumping of filling material and the changes in the thickness/weight depending on the laundry process were observed, and the relationships with the thermal insulation were analyzed.

Findings

The results showed that for natural filling materials (GD and DD), the thermal insulation deteriorated significantly due to changes in the thickness/weight after laundering ten times, and water washing was more appropriate than the dry cleaning. On the other hand, the artificial filling materials (T700, T600 and PET) showed a relatively smaller difference, except for clumping, when they went through more dry cleaning or water washing cycles compared to the natural filling materials.

Originality/value

The results showed that the laundry methods have different effects on the damage to the filling material, the change in thermal insulation, and the change in the comfort-related physical property. Therefore, it is important to select the optimal laundry method depending on the filling material.
Dynamic thermal transfer of textiles in rotational motions
Authors: Li Wenbin , Xu Weilin , Wang Xin
Published: July 2018

Purpose

Clothing is subject to a dynamic thermal transport process in its routine service in which the apparel and human body together with environment interact with each other. Understanding of the thermal transfer in this case should take the variations of human body and environment together with clothing attributes into consideration. The paper aims to discuss these issues.

Design/methodology/approach

Based on the purpose-built dynamic thermal and moisture tester, this study focuses on the thermal transfer of fabrics in different rotational motions. The energy consumption and power of the simulated human skin, the temperature and the thermal retention rate were monitored in the process of rotation of the testing platform with gradually increased rotating speed.

Findings

It has been found that the thermal transfer of a rotating fabric is greatly affected by the rotating speed, the angle of the fabric toward the moving direction and the attributes of the fabric such as its thickness, layers, structure and its fiber composition.

Practical implications

This study will benefit the understanding of the dynamic thermal interaction of human with the environment, and the designing of clothing with excellent thermal comfort.

Originality/value

This work reveals the dynamic thermal transfer of fabrics in rotational motions. It provides a platform to study the dynamic thermal behavior of clothing in daily use.
What made base erosion and profit shifting project possible?
Authors: Matsuoka Akira
Published: July 2018

Purpose

The purpose of this paper is to unveil the true background of the Base Erosion and Profit Shifting (BEPS) Project and to suggest crucial indexes for bringing a movement into a future ceiling causing a struggle of the international tax system.

Design/methodology/approach

This paper looks into the historical context of this project before and after Starbucks’ scandal, comparing to other contexts of the international tax system. Also, this paper partially reviews BEPS from a legal perspective.

Findings

The key factors for building momentum of reform of international taxation are a country having a government willing to embrace the cause of reform, unfairness felt toward entities using tax avoidance schemes which other comparable entities could not be use, grass-roots pressure for the reform, effective places to negotiate cooperation among major countries for the reform, solid cooperation among many countries in the world to implement standards and rhetoric of slogan with less opposition.

Originality/value

The momentum of the reform of international taxation was analyzed before. But the BEPS Project has involved some unique events as compared with the Organization for Economic Cooperation and Development’s project on harmful tax practices, such as initiation of NGOs and boycott by consumers. Additionally, this paper will discuss insights, which the former research did not do.
TBML suspicious activity reports – a financial intelligence unit perspective
Authors: Naheem Mohammed Ahmad
Published: July 2018

Purpose

The purpose of this paper is to share research data from the Financial Intelligence sector on trade-based money laundering (TBML), as a way to better inform banking risk assessment and the submission of suspicious activity reports (SARs).

Design/methodology/approach

The research data formed part of a bigger project on TBML banking risk assessment for improving the detection of TBML activity. This paper analysed the data from an online survey carried out among the financial intelligence staff from financial intelligence units (FIUs) and some external financial intelligence agencies. The aim was to determine which areas of banking SARs needed to be improved or enhanced to support FIU investigations.

Findings

The research found that FIUs do use the data supplied to them, in particular the SARs. The research also found that more data would be appreciated from banks especially in relation to beneficial ownership information and politically exposed persons data. The findings highlighted that contact between banks and FIUs was limited and restricted to a couple of key individuals, whereas the increased requirement for intelligence and more data would suggest that this relationship needs to be expanded and strengthened.

Research limitations/implications

The main limitation was the restricted scope of the survey (only focussed on TBML) and was broad in depth, and perhaps a local FIU survey would be useful to look at specific country recommendations. Similar research also needs to be conducted on other forms of ML activity. The research identified the need for more information on beneficial ownership information; however, other work needs to be done on how exactly banks can access this data.

Practical implications

The main outcome from the research was the need for SARs to contain more detailed information on beneficial ownership and politically exposed persons data. This needs to be incorporated into a specific risk assessment tool for TBML that considers not only the client but also relevant business partners and silent partners/shell companies used by the client. This research is part of a bigger research project that has developed a risk matrix tool for TBML and can be linked into this work.

Originality/value

The paper used original data collected by the researcher from 49 FIU and financial intelligence staff across the globe. The timely presentation of the results and the nature of the sample means that this is relevant and useful data to be presented to the banking sector.
Organizational ambidexterity in public non-profit organizations: interest and limits
Authors: Peng Hongxia
Published: July 2018

Purpose

The purpose of this paper is to study the potential interest in and the possible limits of the concept of organizational ambidexterity (Duncan, 1976; Tushman and O’Reilly, 1996) in the context of public non-profit organizations (PNPOs), a concept that is frequently studied in the private sector.

Design/methodology/approach

From an inductive and qualitative approach, this research is based on observations of ambidextrous innovation processes implemented in a French PNPO in charge of job search and unemployment compensation operations.

Findings

This research shows that the concept of organizational ambidexterity might provide some strategic leads for balancing the possible paradoxes within different kinds of expectations of the stakeholders of PNPOs. It might also facilitate the combination of the stability of public service deliverance and organizational transformation. Beyond its interest, this study identifies the limits of the concept in the context of PNPOs. For overcoming its limits, the study suggests a renewed understanding of organizational ambidexterity by taking account of PNPOs’ specificities, especially in terms of the regulation of the different tensions generated by ambidextrous organizational change.

Research limitations/implications

This research proposes a conceptual framework built with the integration of sectorial and organizational characteristics of the public non-profit sector for understanding the organizational ambidexterity and its possible strategic, organizational and management implications in this sector. The results are limited to the context the author studied because of several sectorial, national, organizational and cultural specificities.

Practical implications

The results might inspire management practices in PNPOs and potentially in private non-profit organizations or in voluntary organizations, since these three types of organizations could have certain similar organizational characteristics and might encounter similar questions in terms of strategy and innovation management.

Originality/value

This research suggests a renewed understanding of the concept of organizational ambidexterity in a sector in which the complexities, tensions and paradoxes generated by different stakeholders’ expectations are probably more present but less explicit than other organizations.
Developing primary health care in Thailand
Authors: Tejativaddhana Phudit , Briggs David , Singhadej Orapin , Hinoguin Reggie
Published: July 2018

Purpose

The purpose of this paper is to describe progress in an across sectorial approach to primary health care at the district health service (DHS) level in Thailand in response to recent innovative national public policy directions which have been enshrined in constitutional doctrine and publicly endorsed by the Prime Minister. This paper describes one response to the Prime Minister’s challenge for Thailand to become the centre of learning in the sub-region in health management.

Design/methodology/approach

The authors utilised a descriptive case study approach utilising an analysis of the Naresuan University initiative of establishing the College of Health Systems Management (NUCHSM). Within that case study, there is a focus on challenges relevant to the socio-economic determinants of health (SOED) and an emphasis on utilising Sustainable Development Goals (SDGs) within the DHS structure.

Findings

The findings describe the establishment of the NUCHSM. A Master of Science (Health Systems Management) by research and a PhD degree have been created and supported by an international faculty. The Thailand International Cooperation Agency recognised NUCHSM by providing scholarships. International students are from Bangladesh, Bhutan, Kenya, Malawi and Timor Leste. Research consultancy projects include two in Lao People’s Democratic Republic; plus, a prototype DHS management system responsive to SDG attainment; and a project to establish a sustainable Ageing Society philosophy for a Thai municipality.

Originality/value

The case study on NUCHSM and its antecedents in its development have demonstrated originality in a long-standing international collaboration, and it has been recognised by the national government to provide scholarships to citizens of the countries in the sub-region to undertake postgraduate studies in health management. The concept of learning from each other and together, simultaneously as a group, through action research projects funded to enhance the evolution of DHSs is innovative.