bluuebunny/crossref_metadata_2025 huggingface dataset:
Collisions involving antiprotons and antihydrogen: an overview
Authors: Jonsell S.
Published: February 2018

I give an overview of experimental and theoretical results for antiproton and antihydrogen scattering with atoms and molecules (in particular H, He). At low energies (

1 keV) there are practically no experimental data available. Instead I compare the results from different theoretical calculations, of various degrees of sophistication. At energies up to a few tens of eV, I focus on simple approximations that give reasonably accurate results, as these allow quick estimates of collision rates without embarking on a research project.

This article is part of the Theo Murphy meeting issue ‘Antiproton physics in the ELENA era’.
Theoretical aspects of antimatter and gravity
Authors: Blas Diego
Published: February 2018

In this short contribution, I review the physical case of studying the gravitational properties of antimatter from a theoretical perspective. I first discuss which elements are desirable for any theory where the long-range interactions between matter and antimatter differ from those of matter with itself. Afterwards I describe the standard way to hide the effects of new forces in matter–matter interactions which still allows one to generate ponderable matter–antimatter interactions. Finally, I comment on some recent ideas and propose some possible future directions.

This article is part of the Theo Murphy meeting issue ‘Antiproton physics in the ELENA era’.
Detection of Plasmodium berghei infected Anopheles stephensi using near-infrared spectroscopy
Authors: Esperança Pedro M. , Blagborough Andrew M. , Da Dari F. , Dowell Floyd E. , Churcher Thomas S.
Published: February 2018

Background

The proportion of mosquitoes infected with malaria is an important entomological metric used to assess the intensity of transmission and the impact of vector control interventions. Currently the prevalence of mosquitoes with salivary gland sporozoites is estimated by dissecting mosquitoes under a microscope or using molecular methods. These techniques are laborious, subjective, and require either expensive equipment or training. This study evaluates the potential of near infra-red spectroscopy (NIRS) to identify laboratory reared mosquitoes infected with rodent malaria.

Methods

Anopheles stephensimosquitoes were reared in the laboratory and fed onPlasmodium bergheiinfected blood. After 12 and 21 days post-feeding mosquitoes were killed, scanned and analysed using NIRS and immediately dissected by microscopy to determine the number of oocysts on the midgut wall or sporozoites in the salivary glands. A predictive classification model was used to determine parasite prevalence and intensity status from spectra.

Results

The predictive model correctly classifies infectious and uninfectious mosquitoes with an overall accuracy of 72%. The false negative and false positive rates are, respectively, 30% and 26%. While NIRS was able to differentiate between uninfectious and highly infectious mosquitoes, differentiating between mid-range infectious groups was less accurate. Multiple scans of the same specimen, with repositioning the mosquito between scans, is shown to improve accuracy. On a smaller dataset NIRS was unable to predict whether mosquitoes harboured oocysts.

Conclusions

We provide the first evidence that NIRS can differentiate between infectious and uninfectious mosquitoes. Currently the method has moderate accuracy and distinguishing between different intensities of infection is challenging. The classification model provides a flexible framework and allows for different error rates to be optimised, enabling the sensitivity and specificity of the technique to be varied according to requirements.
Changes in the neuropeptide complement correlate with nervous system architectures in xenacoelomorphs
Authors: Thiel Daniel , Franz-Wachtel Mirita , Aguilera Felipe , Hejnol Andreas
Published: February 2018

Neuropeptides are essential neurosecretory signaling molecules common in protostomes and deuterostomes (together Nephrozoa). Not much, however, is known about the neuropeptide complement of the sister group Xenacoelomorpha. This group is comprised of the three cladesXenoturbella, Nemertodermatida, and Acoela, which differ strongly in their nervous system anatomy. In order to reconstruct the ancestral bilaterian neuropeptide complement and gain insights into neuropeptide evolution within Xenacoelomorpha, we analyzed transcriptomes of 13 acoels, nemertodermatids, andXenoturbellaspecies. Together with motif searches, similarity searches, mass spectrometry and phylogenetic analyses of neuropeptide precursors and neuropeptide receptors, we reconstruct the xenacoelomorph neuropeptide complement. Our comparison of xenacoelomorph GPCRs with cnidarian and nephrozoan neuropeptide receptors shows that the neuropeptide signaling diversified into at least 20 ancestral peptidergic systems in the lineage to Bilateria. We find thatXenoturbellaspecies possess many of the ancestral bilaterian peptidergic systems and only a few clade-specific neuropeptides. Nemertodermatids seem to have nearly the complete complement of ancestral bilaterian systems and several novel neuropeptides. Acoels show an extensive loss of conserved bilaterian systems, but gained the highest number of novel and group-specific neuropeptides. While it is difficult to correlate the emergence of the bilaterian neuropeptide complement with the evolution of centralized nervous systems, we find a correlation between nervous system novelties and the expansion of taxon-specific neuropeptides in Xenacoelomorpha.
Phosphorylation of the exocyst subunit Exo70B2 contributes to the regulation of its function
Authors: Teh Ooi-Kock , Lee Chil-Woo , Ditengou Franck Anicet , Klecker Till , Furlan Giulia , Zietz Marco , Hause Gerd , Eschen-Lippol Lennart , Hoehenwarter Wolfgang , Lee Justin , Ott Thomas , Trujillo Marco
Published: February 2018

The exocyst is a conserved hetero-octameric complex that mediates early tethering of post-Golgi vesicles during exocytosis. Its Exo70 subunit functions as a spatiotemporal regulator by mediating numerous interactions with proteins and lipids. However, a molecular understanding of the exocyst functions remains challenging. Exo70B2 localized to dynamic foci at the plasma membrane and transited through Brefeldin A (BFA)-sensitive compartments, indicating that it participates in conventional secretion. Conversely, treatment with the immunogenic peptide flg22 or the salicylic acid (SA) defence hormone analogue Benzothiadiazole (BTH), induced Exo70B2 transport into the vacuole where it colocalized with autophagic markers AUTOPHAGY-RELATED PROTEIN 8 (ATG8) and NEIGHBOR OF BRCA1 GENE 1 (NBR1). According with its role in immunity, we discovered that Exo70B2 interacts with and is phosphorylated by the MITOGEN-ACTIVATED PROTEIN KINASE 3 (MPK3). Mimicking phosphorylation inhibited Exo70B2 localization at sites of active secretion. By contrast, lines expressing phosphonull variants displayed higher Effector-Triggered Immunity and were hypersensitive to BTH, conditions known to induce the secretory pathway. Our results suggest a molecular mechanism by which phosphorylation of Exo70B2 regulates interaction with the plasma membrane, and couples the secretory pathway with cellular signalling.
Revisiting the evolutionary analysis of mammalian CRISPs reveals positive selection
Authors: Vicens Alberto , Treviño Claudia
Published: February 2018

Cysteine-rich secretory proteins (CRISPs) constitute a versatile family, with functions that include being components of reptilian venom and participation in mammalian reproduction. While non-mammalian vertebrates express a single CRISP gene, mammals generally express three CRISP paralogs. A previous study assessing the molecular evolution of vertebrate CRISPs revealed strong positive selection in reptilian CRISP and negative selection in mammalian CRISPs. In this study, we re-assessed molecular adaptation of mammalian CRISPs through an analysis of larger sequence datasets that represent mammalian diversity. Our analyses show evidence of recent episodes of positive selection for all mammalian CRISPs. Intensity of positive selection was heterogeneous both among CRISP paralogs (being stronger in CRISP3 than in CRISP1 and CRISP2) and across functional domains (having more impact on CRD or PR-1 domain). Analysis of episodic selection did not yield strong signatures of adaptive evolution in any particular mammalian group, suggesting that positive selection was more pervasive on mammalian CRISPs. Our findings provide evidence of adaptive evolution in a family of reproduction-related proteins, and offer interesting insights regarding the role of mammalian CRISPs in fertility and speciation.
Gender balance in time-keeping at life science conferences
Authors: Edlund Petra , Tranfield Erin M. , van Noort Vera , Siu Ting Karen , Tapani Sofia , Hoog Johanna L.
Published: February 2018

Scientific conferences are biased against women when selecting speakers, but recent studies showed a positive trend where the ratio of invited female speakers had increased. We have recorded speaking times at 11 different conferences during 2016-2017 to analyze which factors influenced a speaker’s time keeping. Men and women went over time 47% and 41% of the talks, respectively. In a regression analysis, it was found that the most important factors that influences how long a presenter spoke was 1) their allocated time, 2) their career stage and 3) the level of time keeping enforcement. It was also found that gender and the size of the conference contributed significantly towards the speaker’s timing. Male speakers exceeded their allocated time more frequently than female speakers, especially at large conferences (60% vs 49%). Since conferences are an important arena for science dissemination this might have a negative impact on female scientist’s careers.
Food hardness and stone tool weight in wild primate nut-cracking
Authors: Haslam Michael
Published: February 2018

This study presents data on average stone tool weights and the hardness of foods processed by the three known stone-tool-using primate species: Burmese long-tailed macaques (Macaca fascicularis aurea), bearded capuchins (Sapajus libidinosus) and Western chimpanzees (Pan troglodytes verus). Each of these primates uses stone hammers to crack open nuts in the wild, making them suitable for inter-species behavioural comparison. This work draws on published results to identify a distinct difference in the tool weight/food hardness curve between chimpanzees and the two monkey taxa, with the latter reaching an asymptote in mean tool weight of just over 1 kg regardless of increasing food hardness. In contrast, chimpanzees rapidly increase their tool weight in response to increasing hardness, selecting average masses over 5 kg to process the hardest nuts. Species overlap in their preference for tools of 0.8-1 kg for opening foods of hardness 2-3 kN, suggesting that this conjunction may represent a primate stone-tool-use optimum.
Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence repair outcome
Authors: Kallimasioti-Pazi Eirini M , Thelakkad Chathoth Keerthi , Taylor Gillian C , Meynert Alison , Ballinger Tracy , Kelder Martijn , Lalevée Sébastien , Sanli Ildem , Feil Robert , Wood Andrew J
Published: February 2018

CRISPR-Cas9 genome editing occurs in the context of chromatin, which is heterogeneous in structure and function across the genome. Chromatin heterogeneity is thought to affect genome editing efficiency, but this has been challenging to quantify due to the presence of confounding variables. Here, we develop a method that exploits the allele-specific chromatin status of imprinted genes in order to address this problem. Because maternal and paternal alleles of imprinted genes have identical DNA sequence and are situated in the same nucleus, allele-specific differences in the frequency and spectrum of Cas9-induced mutations can be attributed unequivocally to epigenetic mechanisms. We found that heterochromatin can impede mutagenesis, but to a degree that depends on other key experimental parameters. Mutagenesis was impeded by up to 7-fold when Cas9 exposure was brief and when intracellular Cas9 expression was low. Surprisingly, the outcome of mutagenic DNA repair was independent of chromatin state, with similar efficiencies of homology directed repair and deletion spectra on maternal and paternal chromosomes. Combined, our data show that heterochromatin imposes a permeable barrier that influences the kinetics, but not the endpoint of CRISPR-Cas9 genome editing, and suggest that therapeutic applications involving low-level Cas9 exposure will be particularly affected by chromatin status.
Understanding policing as a mechanism of cheater control in cooperating bacteria
Authors: Wechsler Tobias , Kümmerli Rolf , Dobay Akos
Published: February 2018

Policing occurs in insect, animal and human societies, where it is used as a conditional strategy to prevent cheating and enforce cooperation. Recently, it has been suggested that policing might even be relevant in enforcing cooperation in much simpler organisms such as bacteria. Here, we used individual-based modelling to develop an evolutionary concept for policing in bacteria, and identify the conditions under which it can be adaptive. We modelled interactions between cooperators, producing a beneficial public good, cheaters exploiting the public good without contributing to it, and public good producing policers that secrete a toxin to selectively target cheaters. We found that toxin-mediated policing is favored when (i) toxins are potent and durable, (ii) cheap to produce, (iii) cell and public good diffusion is intermediate, and (iv) toxins diffuse farther than the public good. Overall, we show that toxin-mediated policing can enforce cooperation, but the parameter space where it is beneficial seems quite narrow. Moreover, we found that policing decays when the genetic linkage between public good and toxin production breaks. This is because policing is itself a public good, offering protection to toxin-resistant mutants that still produce public goods, yet no longer invest in toxins. Our work suggests that very specific environmental conditions are required for genetically fixed policing mechanisms to evolve in bacteria, and offers empirically testable predictions for their evolutionary stability.
Cell atlas of human uterus
Authors: Wu Bingbing , Li Yu , Liu Yanshan , Jin Kaixiu , Zhao Kun , An Chengrui , Li Qikai , Gong Lin , Zhao Wei , Hu Jinghui , Qian Jianhua , Ouyang HongWei , Zou XiaoHui
Published: February 2018

The human uterus is a highly dynamic tissue that undergoes repeated damage repair and regeneration during the menstrual cycle, which make it ideal model to study tissue regeneration and pathological process. Stem/progenitors were speculated to be involved in the regeneration of endometrial epithelial and pathogenesis of endometriosis. But the identity, microenvironment and regulatory mechanisms of the uterus epithelial stem/progenitors in vivo remain unclear. Here, we dissected the cell heterogeneities of the full-thickness human uterus epithelial cells (11 clusters), stroma cells (6 clusters), endothelial cells (5 clusters), smooth muscle cells (2 clusters), myofibroblasts (2 clusters) and immune cells (6 clusters) from 2735 single cell by single cell RNA-seq. Further analysis identified a unique ciliated epithelial cell cluster showing characteristics of stem/progenitors with properties of epithelial-mesenchymal transition (EMT) that mainly localized in the upper functionalis of the endometrium. Ordering the cell subpopulations along the pseudo-space revealed cell clusters possess cellular states of stress, inflammation and apoptosis in the upper functionalis cellular ecosystem of the endometrium. Connectivity map between the human uterus subpopulations revealed potential inflammatory (cytokines and chemokines) and developmental (WNT, FGF, VEGF) signals within the upper functionalis cellular ecosystem of the endometrium, especially from other epithelial clusters, regulating cell plasticity of the EMT-epithelial clusters. This study reconstructed the heterogeneities, space-specific distribution and connectivity map of human uterus atlas, which would provide insight in the regeneration of uterus endometria and reference for the pathogenesis of uterus.
C3: An R package for cross-species compendium-based cell-type identification
Authors: Kabir Md Humayun , Djordjevic Djordje , O’Connor Michael D. , Ho Joshua W. K.
Published: February 2018

Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples because a large volume of data exists for these organisms. However, such rich data repositories often do not exist for most non-model organisms. This makes transcriptome-based sample classification in these species challenging. We propose to overcome this challenge by performing a cross-species compendium comparison. The key is to utilise a recently published cross-species gene set analysis (XGSA) framework to correct for biases that may arise due to potentially complex homologous gene mapping between two species. The framework is implemented as an open source R package called C3. We have evaluated the performance of C3 using a variety of public data in NCBI Gene Expression Omnibus. We also compared the functionality and performance of C3 against some similar gene expression profile matching tools. Our evaluation shows that C3 is a simple and effective method for cell type identification. C3 is available at https://github.com/VCCRI/C3.
Human cortical pyramidal neurons: From spines to spikes via models
Authors: Eyal Guy , Verhoog Matthias B. , Testa-Silva Guilherme , Deitcher Yair , Benavides-Piccione Ruth , DeFelipe Javier , de Kock Christiaan P.J. , Mansvelder Huibert D. , Segev Idan
Published: February 2018

We present the first-ever detailed models of pyramidal cells from human neocortex, including models on their excitatory synapses, dendritic spines, dendritic NMDA- and somatic/axonal- Na+ spikes that provided new insights into signal processing and computational capabilities of these principal cells. Six human layer 2 and layer 3 pyramidal cells (HL2/L3 PCs) were modeled, integrating detailed anatomical and physiological data from both fresh and post mortem tissues from human temporal cortex. The models predicted particularly large AMPA- and NMDA- conductances per synaptic contact (0.88 nS and 1.31nS, respectively) and a steep dependence of the NMDA-conductance on voltage. These estimates were based on intracellular recordings from synaptically-connected HL2/L3 pairs, combined with extra-cellular current injections and use of synaptic blockers. A large dataset of high-resolution reconstructed HL2/L3 dendritic spines provided estimates for the EPSPs at the spine head (12.7 ± 4.6 mV), spine base (9.7 ± 5.0 mV) and soma (0.3 ± 0.1 mV), and for the spine neck resistance (50 – 80 MΩ). Matching the shape and firing pattern of experimental somatic Na+-spikes provided estimates for the density of the somatic/axonal excitable membrane ion channels, predicting that 134 ± 28 simultaneously activated HL2/L3- HL2/L3 synapses are required for generating (with 50% probability) a somatic Na+ spike. Dendritic NMDA spikes were triggered in the model when 20 ± 10 excitatory spinous synapses were simultaneously activated on individual dendritic branches. The particularly large number of basal dendrites in HL2/L3 PCs and the distinctive cable elongation of their terminals imply that ~25 NMDA- spikes could be generated independently and simultaneously in these cells, as compared to ~14 in L2/3 PCs from the rat temporal cortex. These multi-sites nonlinear signals, together with the large (~30,000) excitatory synapses/cell, equip human L2/L3 PCs with enhanced computational capabilities. Our study provides the most comprehensive model of any human neuron to-date demonstrating the biophysical and computational distinctiveness of human cortical neurons.
STAG: Species Tree Inference from All Genes
Authors: Emms D.M. , Kelly S.
Published: February 2018

Species tree inference is fundamental to our understanding of the evolution of life on earth. However, species tree inference from molecular sequence data is complicated by gene duplication events that limit the availably of suitable data for phylogenetic reconstruction. Here we propose a novel method for species tree inference called STAG that is specifically designed to leverage data from multi-copy gene families. By application to 12 real species datasets sampled from across the eukaryotic domain we demonstrate that species trees inferred from multi-copy gene families are comparable in accuracy to species trees inferred from single-copy orthologues. We further show that the ability to utilise data from multi-copy gene families increases the amount of data available for species tree inference by an average of 8 fold. We reveal that on real species datasets STAG has higher accuracy than other leading methods for species tree inference; including concatenated alignments of protein sequences, ASTRAL & NJst. Finally we show that STAG is fast, memory efficient and scalable and thus suitable for analysis of large multispecies datasets.
Evolution of subgenomic RNA shapes dengue virus adaptation and epidemiological fitness
Authors: Finol Esteban , Ooi Eng Eong
Published: February 2018

Genetic changes in the dengue virus (DENV) genome affects viral fitness both clinically and epidemiologically. Even in the 3’ untranslated region (3’UTR), mutations could impact the formation of subgenomic flaviviral RNA (sfRNA) and the specificity of sfRNA in inhibiting host proteins necessary for successful viral replication. Indeed, we have recently shown that mutations in the 3’UTR of DENV2 affected its ability to inhibit TRIM25 E3 ligase activity to reduce interferon (IFN) expression, which potentially contributed to the emergence of a new viral clade during the 1994 dengue epidemic in Puerto Rico. However, whether differences in 3’UTRs shaped DENV evolution on a larger scale remains incompletely understood. Herein, we combined RNA phylogeny with phylogenetics to gain insights on sfRNA evolution. We found that sfRNA structures are under purifying selection and highly conserved despite sequence divergence. Interestingly, only the second flaviviral Nuclease-resistant RNA (fNR2) structure of DENV-2 has undergone strong positive selection. Epidemiological reports also suggest that nucleotide substitutions in fNR2 may drive DENV-2 epidemiological fitness, possibly through sfRNA-protein interactions. Collectively, our findings indicate that 3’UTRs are important determinants of DENV fitness in human-mosquito cycles.

Highlights

Dengue viruses (DENV) preserve RNA elements in their 3’ untranslated region (UTR).

Site-specific quantification of natural selection revealed positive selection on DENV2 sfRNA.

Flaviviral nuclease-resistant RNA (fNR) structures in DENV 3’UTRs contribute to DENV speciation.

A highly evolving fNR structure appears to increase DENV-2 epidemiological fitness.
Exosomes and exosomal miRNAs from muscle-derived fibroblasts promote skeletal muscle fibrosis
Authors: Zanotti Simona , Gibertini Sara , Blasevich Flavia , Bragato Cinzia , Ruggieri Alessandra , Saredi Simona , Introna Clelia , Bernasconi Pia , Maggi Lorenzo , Mantegazza Renato , Mora Marina
Published: February 2018

We investigated in vitro and in vivo the pro-fibrotic role of exosomes released by muscle-derived fibroblasts of Duchenne muscular dystrophy (DMD) patients, and of miRNAs carried by exosomes. We found that exosomes from DMD fibroblasts, but not from myoblasts, had significantly higher levels of miR-199a-5p, a miRNA up-regulated in fibrotic conditions, compared to control exosomes. In control fibroblasts, exposure to DMD fibroblast-derived exosomes induced a myofibroblastic phenotype with increase in α-smooth actin, collagen and fibronectin transcript and protein expression, soluble collagen production and deposition, cell proliferation, and activation of Akt and ERK signalling, while exposure to control exosomes did not. These findings were related to transfer of high levels of miR-199a-5p and to reduction of its target caveolin-1. Finally, injection of DMD fibroblast-derived exosomes into mouse tibialis anterior muscle after cardiotoxin-induced necrosis, produced greater fibrosis than control exosomes.

Our findings indicate that exosomes produced by local fibroblasts in the DMD muscle are able to induce phenotypic conversion of normal fibroblasts to myofibroblasts thereby increasing the fibrotic response; and suggest miR-199a-5p and caveolin-1as potential therapeutic targets.
Probing the limits of alpha power lateralization as a neural marker of selective attention in middle-aged and older listeners
Authors: Tune Sarah , Wöstmann Malte , Obleser Jonas
Published: February 2018

In recent years, hemispheric lateralization of alpha power has emerged as a neural mechanism thought to underpin spatial attention across sensory modalities. Yet, how healthy aging, beginning in middle adulthood, impacts the modulation of lateralized alpha power supporting auditory attention remains poorly understood. In the current electroencephalography (EEG) study, middle-aged and older adults (N= 29; ~40-70 years) performed a dichotic listening task that simulates a challenging, multi-talker scenario. We examined the extent to which the modulation of 8-12 Hz alpha power would serve as neural marker of listening success across age. With respect to the increase in inter-individual variability with age, we examined an extensive battery of behavioral, perceptual, and neural measures. Similar to findings on younger adults, middle-aged and older listeners′ auditory spatial attention induced robust lateralization of alpha power, which synchronized with the speech rate. Notably, the observed relationship between this alpha lateralization and task performance did not co-vary with age. Instead, task performance was strongly related to an individual’s attentional and working memory capacity. Multivariate analyses revealed a separation of neural and behavioral variables independent of age. Our results suggest that in age-varying samples as the present one, the lateralization of alpha power is neither a sufficient nor necessary neural strategy for an individual’s auditory spatial attention, as higher age might come with increased use of alternative, compensatory mechanisms. Our findings emphasize that explaining inter-individual variability will be key to understanding the role of alpha oscillations in auditory attention in the aging listener.
Population Turnover in Remote Oceania Shortly After Initial Settlement
Authors: Lipson Mark , Skoglund Pontus , Spriggs Matthew , Valentin Frederique , Bedford Stuart , Shing Richard , Buckley Hallie , Phillip Iarawai , Ward Graeme K. , Mallick Swapan , Rohland Nadin , Broomandkhoshbacht Nasreen , Cheronet Olivia , Ferry Matthew , Harper Thomas K. , Michel Megan , Oppenheimer Jonas , Sirak Kendra , Stewardson Kristin , Auckland Kathryn , Hill Adrian V.S. , Maitland Kathryn , Oppenheimer Stephen J. , Parks Tom , Robson Kathryn , Williams Thomas N. , Kennett Douglas J. , Mentzer Alexander J. , Pinhasi Ron , Reich David
Published: February 2018

Ancient DNA analysis of three individuals dated to ~3000 years before present (BP) from Vanuatu and one ~2600 BP individual from Tonga has revealed that the first inhabitants of Remote Oceania (“First Remote Oceanians”) were almost entirely of East Asian ancestry, and thus their ancestors passed New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture with the Papuan groups they encountered [1]. However, all present-day populations in Near and Remote Oceania harbor 25-100% Papuan ancestry, implying that there must have been at least one later stream of migration eastward from Near Oceania. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu ranging from 3,000-150 BP, along with 185 present-day Vanuatu individuals from 18 islands. We show that people of almost entirely Papuan ancestry had arrived in Vanuatu by 2400 BP, an event that coincided with the end of the Lapita cultural period, changes in skeletal morphology, and the cessation of long-distance trade between Near and Remote Oceania [2]. First Remote Oceanian ancestry subsequently increased via admixture but remains at 10-20% in most islands. Through a fine-grained comparison of ancestry profiles in Vanuatu and Polynesia with diverse groups in Near Oceania, we find that Papuan ancestry in Vanuatu is consistent with deriving from the Bismarck Archipelago instead of the geographically closer Solomon Islands. Papuan ancestry in Polynesia also shows connections to the ancestry profiles present in the Bismarck Archipelago but is more similar to Tolai from New Britain and Tutuba from Vanuatu than to the ancient Vanuatu individuals and the great majority of present-day Vanuatu populations. This suggests a third eastward stream of migration from Near to Remote Oceania bringing a different type of Papuan ancestry.
Human noise blindness drives suboptimal cognitive inference
Authors: Castañón Santiago Herce , Bang Dan , Moran Rani , Ding Jacqueline , Egner Tobias , Summerfield Christopher
Published: February 2018

Humans typically make near-optimal sensorimotor judgments but show systematic biases when making more cognitive judgments. Here we test the hypothesis that, while humans are sensitive to the noise present during early sensory processing, the “optimality gap” arises because they are blind to noise introduced by later cognitive integration of variable or discordant pieces of information. In six psychophysical experiments, human observers judged the average orientation of an array of contrast gratings. We varied the stimulus contrast (encoding noise) and orientation variability (integration noise) of the array. Participants adapted near-optimally to changes in encoding noise, but, under increased integration noise, displayed a range of suboptimal behaviours: they ignored stimulus base rates, reported excessive confidence in their choices, and refrained from opting out of objectively difficult trials. These overconfident behaviours were captured by a Bayesian model which is blind to integration noise. Our study provides a computationally grounded explanation of suboptimal cognitive inferences.
Shifting patterns of seasonal influenza epidemics
Authors: Coletti Pietro , Poletto Chiara , Turbelin Clément , Blanchon Thierry , Colizza Vittoria
Published: February 2018

Seasonal waves of influenza display a complex spatiotemporal pattern resulting from the interplay of biological, socio-demographic, and environmental factors. At country level many studies characterized the robust properties of annual epidemics, depicting a typical season. Here we analyzed season-by-season variability, introducing a clustering approach to assess the deviations from typical spreading patterns. The classification is performed on the similarity of temporal configurations of onset and peak times of regional epidemics, based on influenza-like-illness time-series in France from 1984 to 2014. We observed a larger variability in the onset compared to the peak. Two relevant classes of clusters emerge: groups of seasons sharing similar recurrent spreading patterns (clustered seasons) and single seasons displaying unique patterns (monoids). Recurrent patterns exhibit a more pronounced spatial signature than unique patterns. We assessed how seasons shift between these classes from onset to peak depending on epidemiological, environmental, and socio-demographic variables. We found that the spatial dynamics of influenza and its association with commuting, previously observed as a general property of French influenza epidemics, applies only to seasons exhibiting recurrent patterns. The proposed methodology is successful in providing new insights on influenza spread and can be applied to incidence time-series of different countries and different diseases.
From spiral cleavage to bilateral symmetry: The developmental cell lineage of the annelid brain
Authors: Vopalensky Pavel , Tosches Maria Antonietta , Achim Kaia , Handberg-Thorsager Mette , Arendt Detlev
Published: February 2018

The spiral cleavage pattern is characteristic for Spiralia (Lophotrochozoa), a large assembly of marine invertebrates. In most cases, spiral cleavage produces freely swimming, trochophora-type larvae with a simple nervous system that controls ciliary locomotion. These larvae acquire bilateral symmetry, as manifested for example in the larval brain. The transition from the rotational symmetry of spiral cleavage into the bilateral adult body has not yet been understood. Here, we present the developmental cell lineage of the brain of the annelidPlatynereis dumeriliifrom the zygote until the mid-trochophore stage (~30 hpf), in combination with a gene expression atlas for several embryonic and larval stages. Comparison of multiple embryos reveals a highly stereotypical development and an invariant cell lineage of the differentiated cell types. In addition, we observe a fundamental subdivision of the larval brain into a highly proliferative dorsolateral region and an early differentiating ventromedial region that gives rise to the apical nervous system. The transition from rotational to bilateral symmetry progresses gradually from the lateral to the central regions. Strikingly, the spiral-to-bilateral transition does not involve extensive cell migration. Rather, corresponding cells in different spiral quadrants acquire highly divergent identities in line with their bilateral position.
Characterization of a quadrant diamond transmission X-ray detector including a precise determination of the mean electron–hole pair creation energy
Authors: Keister Jeffrey W. , Cibik Levent , Schreiber Swenja , Krumrey Michael
Published: February 2018

Precise monitoring of the incoming photon flux is crucial for many experiments using synchrotron radiation. For photon energies above a few keV, thin semiconductor photodiodes can be operated in transmission for this purpose. Diamond is a particularly attractive material as a result of its low absorption. The responsivity of a state-of-the art diamond quadrant transmission detector has been determined, with relative uncertainties below 1% by direct calibration against an electrical substitution radiometer. From these data and the measured transmittance, the thickness of the involved layers as well as the mean electron–hole pair creation energy were determined, the latter with an unprecedented relative uncertainty of 1%. The linearity and X-ray scattering properties of the device are also described.
Solid energy calibration standards for PK-edge XANES: electronic structure analysis of PPh4Br
Authors: Blake Anastasia V. , Wei Haochuan , Donahue Courtney M. , Lee Kyounghoon , Keith Jason M. , Daly Scott R.
Published: February 2018

PK-edge X-ray absorption near-edge structure (XANES) spectroscopy is a powerful method for analyzing the electronic structure of organic and inorganic phosphorus compounds. Like all XANES experiments, PK-edge XANES requires well defined and readily accessible calibration standards for energy referencing so that spectra collected at different beamlines or under different conditions can be compared. This is especially true for ligandK-edge X-ray absorption spectroscopy, which has well established energy calibration standards for Cl (Cs2CuCl4) and S (Na2S2O3·5H2O), but not neighboring P. This paper presents a review of common PK-edge XANES energy calibration standards and analysis of PPh4Br as a potential alternative. The PK-edge XANES region of commercially available PPh4Br revealed a single, highly resolved pre-edge feature with a maximum at 2146.96 eV. PPh4Br also showed no evidence of photodecomposition when repeatedly scanned over the course of several days. In contrast, we found that PPh3rapidly decomposes under identical conditions. Density functional theory calculations performed on PPh3and PPh4+revealed large differences in the molecular orbital energies that were ascribed to differences in the phosphorus oxidation state (IIIversusV) and molecular charge (neutralversus+1). Time-dependent density functional theory calculations corroborated the experimental data and allowed the spectral features to be assigned. The first pre-edge feature in the PK-edge XANES spectrum of PPh4Br was assigned to P 1s → P-C π* transitions, whereas those at higher energy were P 1s → P-C σ*. Overall, the analysis suggests that PPh4Br is an excellent alternative to other solid energy calibration standards commonly used in PK-edge XANES experiments.
X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery
Authors: Amporndanai Kangsa , Johnson Rachel M. , O'Neill Paul M. , Fishwick Colin W. G. , Jamson Alexander H. , Rawson Shaun , Muench Stephen P. , Hasnain S. Samar , Antonyuk Svetlana V.
Published: February 2018

Cytochromebc1, a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochromebc1from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochromebc1that may be available from parasites, all efforts have been focused on homologous cytochromebc1complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochromebc1is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.
Crystal structures of two 2,3-diaryl-2,3-dihydro-4H-1,3-benzothiazin-4-ones
Authors: Yennawar Hemant P. , Buchwalter Michaela J. , Colburn Baylee K. , Silverberg Lee J.
Published: February 2018

The syntheses and crystal structures of 2,3-bis[3-(trifluoromethyl)phenyl]-2,3-dihydro-4H-1,3-benzothiazin-4-one (di-m-CF3; C22H13F6NOS) (1) and 2,3-bis(4-methylphenyl)-2,3-dihydro-4H-1,3-benzothiazin-4-one (di-p-CH3; C22H19NOS) (2) are reported. Each structure is racemic: the asymmetric unit of2consists of two molecules. In both1and2, the six-membered 1,3-thiazine ring is close to an envelope conformation with the chiral C atom forming the flap. In1, the 2-aryl group is pseudo-equatorial, while in2it is pseudo-axial. In1, the pendant aryl rings form a V shape with an inter-centroid distance of 3.938 (3) Å and an acute dihedral angle of 48.3 (2)° between them. Both CF3groups are disordered over two orientations in 0.687 (19):0.313 (19) and 0.667 (16):0.33 (16) ratios. In each of the independent molecules of2, the aryl rings are almost orthogonal to each other [dihedral angles = 85.50 (12) and 86.07 (11)°]. In both structures, the chiral C atom and the O atoms participate in C—H...O-type hydrogen bonding between symmetry-related molecules of1or the independent enantiomers in2, forming chains along thec-axis direction in1and theb-axis direction in2. Additionally, in1, π–π contacts of both face-to-face and edge-to-face type, as well as π-H...O and π-H...F interactions are observed. In2, a racemic mixture of molecules forms layers in theacplane linked by weak π–π and C—H...π interactions.
(4-Methylphenyl)methanaminium bromide hemihydrate
Authors: Aarthi R , Thiruvalluvar A , Ramachandra Raja C
Published: February 2018

In the title hydrated salt, C8H12N+·Br−·0.5H2O, which is isostructural with its chloride congener, the water O atom lies on a crystallographic twofold axis. In the crystal, the components are linkedviaC—H...Br, O—H...Br, N—H...Br and N—H...O hydrogen bonds to generate (100) sheets. The sheets are linked by two weak C—H...π interactions, generating a three-dimensional network.
Quandary of a social entrepreneur
Authors: Sharma Shalaghya , Singh Anjani K.
Published: February 2018

Subject area

Social entrepreneurship

Study level/applicability

The case can be a learning resource for management students and budding entrepreneurs with aspirations for a career in the field of social entrepreneurship.

Case overview

This case examines the organizational change and dilemmas social entrepreneurs have to face when enterprises grow. The organization under study “Action for Children Today” (ACT) aimed to help under privileged children. The organization was the brain child of young, energetic, media professional Ananthi Subramanian. Ananthi had never dreamt of being a social entrepreneur, but her mission of inclusion for underprivileged orphans in mainstream society by educating and inculcating skills, took her towards a new life and career. The endeavour began as a shelter for homeless children, but Ananthi came across other issues faced by the children, so new ventures were added under the umbrella of ACT. Although it was never an easy journey, Ananthi’s commitment kept her motivated to work for the cause and the organization that started with just one child has been home to more than 300 children up to the present day. ACT had its share of ups and downs through its journey and the case is based on certain issues and challenges that the organization had to face and how it overcame those hurdles.

Expected learning outcomes

Expected learning outcomes are as follows: a better understanding of different forms of social entrepreneurship; an understanding of problems and challenges faced by social entrepreneurs; and an understanding of how to implement new business models.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS: 3 Entrepreneurship
Risk interaction identification in international supply chain logistics
Authors: Kwak Dong-Wook , Rodrigues Vasco Sanchez , Mason Robert , Pettit Stephen , Beresford Anthony
Published: February 2018

Purpose

International supply chains can be severely disrupted by failures in international logistics processes. Therefore, an understanding of international logistics risks, or causes of failure, how these may interact with each other and how they can be mitigated are imperatives for the smooth operation of international supply chains. The purpose of this paper is to specifically investigate the interactions between international logistics risks within the prevailing structures of international supply chains and highlights how these risks may be inter-connected and amplified. A new dynamic supply chain logistics risk analysis model is proposed which is novel as it provides a holistic understanding of the risk event interactivity.

Design/methodology/approach

The paper applies interpretive structural modelling to data collected from a survey of leading supply chain practitioners, in order to analyse their perspectives of risk elements and interactions. The risk elements and their contextual relationship were derived empirically through the use of focus groups and subsequent Delphi study. The two stages of the research rely on experts’ views on risk events and clusters and the level of interactions among those clusters.

Findings

A key finding of this research is that supply chain practitioner’s perception of risk consists of inter-connected four levels: value streams risks; information and relationship risks; risks in international supply chain activities; and external environment. In particular, since level 2 risk creates feedback loops of risks, risk management at level 2 can dampen the amplification effect and the strength of the interactions.

Practical implications

Several managerial implications are drawn. First, the research guides managers in the identification and evaluation of risk events which can impact the performance of their international logistics supply chain operations. Second, evidence is presented that supports the proposition that the relationships with trading partners and LSPs, and the degree of logistics information exchange, are critical to prevent, or at least mitigate, logistics risks which can substantially affect the responsiveness of the international supply chain.

Originality/value

The main contribution to knowledge that this study offers to the literature on supply chain risk management is the development of a supply chain logistics risk analysis model which includes both risk elements and interactions. The research demonstrates the importance of taking into account risk interactions in the process of identification and evaluation of risk events.
Giving sense and changing perceptions in the implementation of the performance management system in public sector organisations in developing countries
Authors: Ohemeng Frank Louis Kwaku , Amoako Asiedu Emelia , Obuobisa-Darko Theresa
Published: February 2018

Purpose

Change in public organisations has become inevitable in modern times. Yet, implementing change continues to be problematic, especially the attempt to introduce performance management (PM) in the sector. The purpose of this paper is to examine how HR managers are using sensegiving processes to attempt to institutionalise PM in public organisations in Ghana PM in public organisations in Ghana.

Design/methodology/approach

The paper utilises the mixed methods approach to examine the process of sensegiving. In using this method, the authors used focus group, as well as individual interview techniques and a quantitative survey of some selected organisations in the public sector.

Findings

The results of the study show that, four main activities, i.e. workshops, seminars and training, one-on-one communication, and unit meetings are employed in the process. The analysis indicates that these activities have become quite effective in the quest to change perceptions about PM in the sector.

Research limitations/implications

The research was limited to a few organisations. Hence, it will be necessary to expand it, if possible to the entire public sector to see if the same results will be obtained.

Practical implications

It shows that reformers must be cognisant of the views of employees in developing and implementing reforms that focus on changing both individual orientations and organisational and culture.

Originality/value

This is the first time such a study has been done in Ghana. Furthermore, studies on PM institutionalisation and implementation have either been qualitative or quantitative in nature. Studies using the mixed methods approach are rare, with those we know coming mostly from the Western World. Thus, this paper is one of the few to examine this issue using the mixed methods approach and more so from a developing country’s perspective.