bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Laser Speckle Imaging
Authors: Postnov Dmitry D. , Tang Jianbo , Erdener Sefik Evren , Kılıç Kıvılcım , Boas David A.
Published: May 2019

Utilizing a high-speed camera and recording back-scattered laser light at more than 20,000 frames per second, we introduce the first wide-field dynamic laser speckle imaging (DLSI) in which we are able to quantify the laser speckleintensity temporal auto-correlation function g2(τ) for every pixel individually to obtain a quantitative image of the dynamics of the light scattering particles in the sample. The ability to directly and quantitatively measure the intensity auto-correlation function allows us to solve the problem of how to quantitatively interpret data measured by laser speckle contrast imaging (LSCI), multi-exposure laser speckle imaging (MESI) and laser Doppler flowmetry (LDF). The intensity auto-correlation function is related to the field temporal auto-correlation function g1(τ), which has been quantitatively related to the dynamics of the light scattering particles including flowing red blood cells. The form of g1(τ) depends on the amount of light scattering (i.e. single or multiple scattering) and the type of particle motion (i.e. ordered or unordered). Although these forms of the field correlation functions have been established for over 30 years, there is no agreement nor experimental support on what scattering and motion regimes are relevant for the varied biomedical applications. We thus apply DLSI to image cerebral blood flow in mouse through a cranial window and show that the generally accepted form of g1(τ), is applicable only to visible surface vessels of a specific size (20 – 200μm). We demonstrate that for flow in smaller vessels and in parenchymal regions that the proper g1(τ) form corresponds with multiple scattering light and unordered motion which was never considered to be relevant for these techniques. We show that the wrong assumption for the field auto-correlation model results in a severe underestimation of flow changes when measuring blood flow changes during ischemic stroke. Finally, we describe how DLSI can be integrated with other laser speckle methods to guide model selection, or how it can be used by itself as a quantitative blood flow imaging technique.
Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems
Authors: Guimarães Sales Naiara , McKenzie Maisie B. , Drake Joseph , Harper Lynsey R. , Browett Samuel S. , Coscia Ilaria , Wangensteen Owen S. , Baillie Charles , Bryce Emma , Dawson Deborah A. , Ochu Erinma , Hänfling Bernd , Handley Lori Lawson , Mariani Stefano , Lambin Xavier , Sutherland Christopher , McDevitt Allan D.
Published: May 2019

Environmental DNA (eDNA) metabarcoding has revolutionised biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relatively untested.

We first assess the efficiency of eDNA metabarcoding in detecting semi-aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, we evaluate the detection efficiency of eDNA samples compared to multiple conventional non-invasive survey methods (latrine surveys and camera trapping) using occupancy modelling.

eDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA in areas where authenticated records do not currently exist, but potential false positives were also identified for several non-native species.

Water-based eDNA samples provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole, and red deer) using occupancy models. The comparison between survey ‘effort’ to reach a detection probability of ≥0.95 revealed that 3-6 water replicates would be equivalent to 3-5 latrine surveys and 5-30 weeks of single camera deployment, depending on the species.

Synthesis and Applications. eDNA metabarcoding represents an extremely promising tool for monitoring mammals, allowing for the detection of multiple species simultaneously, and provides comparable results to widely-used conventional survey methods. eDNA from freshwater systems delivers a ‘terrestrial dividend’ by detecting both semi-aquatic and terrestrial mammalian communities, and provides a basis for future monitoring at a landscape level over larger spatial and temporal scales (i.e. long-term monitoring at national levels).
Rainfall as a significant contributing factor to butterfly seasonality along a climatic gradient in the neotropics
Authors: Checa María F. , Levy Elisa , Rodriguez Jaqueline , Willmott Keith
Published: May 2019

We analyzed the dynamics of multi-species butterfly communities along a climatic gradient with varying precipitation regimes for three consecutive years, and determine how climatic variables associate with observed butterfly seasonality. To provide a baseline for future studies of how climate change might affect these butterfly populations, we additionally explored the role of butterfly seasonality as a potential contributing factor for their susceptibility to climate variation. As far as we know, this represents the first study that simultaneously sampled and described seasonality patterns of tropical butterfly communities across ecosystems with varying climatic seasonality. A 3-year survey was carried out at three sites (i.e., wet, transition and dry forests) across a climatic gradient in western Ecuador. Butterflies were sampled using traps baited with rotting banana and prawn every two months from Nov 2010 to Sep 2013. Traps were set up at two heights, in the understory and canopy. In total, 7046 individuals of 212 species were sampled over 180 sampling days.

Butterfly communities exhibited conspicuous intra and inter-annual variation in temporal dynamics with certain elements (e.g., maximum abundance recorded) of seasonality patterns likely synchronized in seasonal forests (i.e., transition and dry forest) across years but not in aseasonal forests (i.e., wet forest). In addition, the highest numbers of species and individuals occurred during the wet season across all study sites and years; indeed, rainfall was significantly positively associated with temporal abundance. Likewise, butterfly species displaying stronger seasonality were significantly associated with higher rainfall periods in seasonal forests. Variation in precipitation regimes might significantly affect more seasonal species.
Aggregation of nontuberculous mycobacteria is regulated by carbon:nitrogen balance
Authors: DePas William H. , Bergkessel Megan , Newman Dianne K.
Published: May 2019

Nontuberculous mycobacteria (NTM) are emerging opportunistic pathogens that form biofilms in environmental reservoirs such as household water systems and aggregate into phagocytosis-resistant clusters during infection. NTM constitutively aggregatein vitro, a phenotype typically considered to be a by-product of the mycolic-acid-rich cell wall. While culturing a model NTM,Mycobacterium smegmatis, in rich medium, we fortuitously discovered that planktonic cells accumulated in the culture after ∼3 days. By providing selective pressure for bacteria that disperse earlier, we isolated a strain with two mutations in the oligopeptide permease operon (opp). A mutant lacking theoppoperon (Δopp) dispersed earlier and more completely than wildtype (WT). We show that Δopp’s aggregation defect was nutrient related; aggregation was restored by non-peptide carbon sources. Experiments with WTM. smegmatisrevealed that growth as aggregates is favored when carbon is replete, while dispersal can be induced by carbon starvation. In addition, under conditions of low available carbon relative to available nitrogen,M. smegmatisgrows as planktonic cells. By adjusting carbon and nitrogen sources in defined medium, we tuned the cellular C:N ratio such thatM. smegmatisgrows either as aggregates or planktonic cells. Lastly, we tested the effect of C:N balance on aggregation in clinically relevant NTM. Altogether, we show that NTM aggregation is a controlled process that is regulated by the relative availability of carbon and nitrogen for metabolism. Because NTM aggregation is correlated with increased virulence, these results may contribute to targeted anti-biofilm therapeutics.

Importance

Free-living bacteria can assemble into multicellular aggregates called biofilms. Biofilms help bacteria tolerate multiple stresses, including antibiotics and the host immune system. Differing environmental pressures have resulted in biofilm architecture and regulation varying among bacterial species and strains. Nontuberculous mycobacteria are a group of emerging opportunistic pathogens that utilize biofilms to adhere to household plumbing and showerheads and to avoid phagocytosis by host immune cells. Mycobacteria harbor a unique cell wall built chiefly of long chain mycolic acids that confers hydrophobicity and has been thought to cause constitutive aggregation in liquid media. Here we show that aggregation is instead a regulated process dictated by the balance of available carbon and nitrogen. Understanding that mycobacteria utilize metabolic cues to regulate the transition between planktonic and aggregated cells reveals an inroad to controlling aggregation through targeted therapeutics.
Multi-resolution localization of causal variants across the genome
Authors: Sesia Matteo , Katsevich Eugene , Bates Stephen , Candès Emmanuel , Sabatti Chiara
Published: May 2019

We presentKnockoffZoom, a flexible method for the genetic mapping of complex traits at multiple resolutions.KnockoffZoomlocalizes causal variants by testing the conditional associations of genetic segments of decreasing width while provably controlling the false discovery rate using artificial genotypes as negative controls. Our method is equally valid for quantitative and binary phenotypes, making no assumptions about their genetic architectures. Instead, we rely on well-established genetic models of linkage disequilibrium. We demonstrate that our method can detect more associations than mixed effects models and achieve fine-mapping precision, at comparable computational cost. Lastly, we applyKnockoffZoomto data from 350k subjects in the UK Biobank and report many new findings.
CENP-A drives asymmetric cell division and maintains stem identity
Authors: Dattoli Anna A. , Carty Ben L. , Kochendoerfer Antje M. , Walshe Annie E. , Dunleavy Elaine M.
Published: May 2019

Centromeres, chromosomal loci essential for genome integrity, are epigenetically defined by CENP-A-containing chromatin. Recent studies suggest that parental CENP-A is asymmetrically distributed upon stem cell asymmetric division. However, a direct link between centromeres and stem cell identity has not been demonstrated. We show thatDrosophilafemale germline stem cells (GSCs) and neuroblasts assemble centromeres between G2-phase and prophase, requiring CYCLIN A. Intriguingly, chromosomes that will be inherited by GSCs incorporate more CENP-A and capture more spindle fibers at pro-metaphase. Furthermore, over-expression of CAL1 (DrosophilaCENP-A assembly factor) causes GSC-like tumours, while over-expression of both CENP-A and CAL1 promotes stem cell self-renewal. Finally, once centromeres have been assembled in GSCs, continued CENP-A assembly is not required in differentiating cells outside of the niche and CAL1 becomes dispensable. According to our results CENP-A regulates stem cell identity/maintenance. Moreover, crucial centromere assembly occurs in the niche prior to oocyte meiosis.
Fluorescence assay for simultaneous quantification of CFTR ion-channel function and plasma membrane proximity
Authors: Prins Stella , Langron Emily , Hastings Cato , Hill Emily J. , Stefan Andra C. , Griffin Lewis D. , Vergani Paola
Published: May 2019

CFTR, a plasma membrane anion channel, plays a key role in controlling transepithelial fluid movement. Excessive activation results in intestinal fluid loss during secretory diarrhoeas, while CFTR mutations underlie cystic fibrosis (CF). Anion permeability depends both on how well CFTR channels work (permeation/gating) and on how many are present at the membrane (reflecting folding, trafficking, metabolic stability). Recently, treatments with two drug classes targeting CFTR – one boosting ion-channel function (potentiators), the other increasing plasma membrane density (correctors) – have provided significant health benefits to CF patients.

Here we present an image-based fluorescence assay that can rapidly and simultaneously estimate both CFTR ion-channel function and the protein’s proximity to the membrane. We monitor F508del-CFTR, the most common CF-causing variant, and confirm rescue by low temperature, CFTR-targeting drugs and second-site revertant mutation R1070W. In addition, we characterize a panel of 62 CF-causing mutations. Our measurements correlate well with published data (electrophysiology and biochemistry), further confirming validity of the assay.

Finally, we profile effects of acute treatment with approved potentiator drug VX-770 on the rare-mutation panel. Mapping the potentiation profile on CFTR structures raises mechanistic hypotheses on drug action, suggesting that VX-770 might allow an open-channel conformation with an alternative arrangement of domain interfaces around site 1.

The assay is a valuable tool for investigation of CFTR molecular mechanisms, allowing accurate inferences on gating/permeation. In addition, by providing a two-dimensional characterization of the CFTR protein, it could better inform development of single-drug and precision therapies addressing the root cause of CF disease.
Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells
Authors: Li Guoliang , Neuert Gregor
Published: May 2019

Transcript levels powerfully influence cell behavior and phenotype and are carefully regulated at several steps. Recently developed single cell approaches such as RNA single molecule fluorescence in-situ hybridization (smFISH) have produced advances in our understanding of how these steps work within the cell. In comparison to single-cell sequencing, smFISH provides more accurate quantification of RNA levels. Additionally, transcript subcellular localization is directly visualized, enabling the analysis of transcription (initiation and elongation), RNA export and degradation. As part of our efforts to investigate how this type of analysis can generate improved models of gene expression, we used smFISH to quantify the kinetic expression of STL1 and CTT1 mRNAs in single Saccharomyces cerevisiae cells upon 0.2 and 0.4M NaCl osmotic stress. In this Data Descriptor, we outline our procedure along with our data in the form of raw images and processed mRNA counts. We discuss how these data can be used to develop single cell modelling approaches, to study fundamental processes in transcription regulation and develop single cell image processing approaches.
Daily rhythms in lactate metabolism in the medial prefrontal cortex of mouse: Effects of light and aging
Authors: Wallace Naomi K. , Pollard Felicity , Savenkova Marina , Karatsoreos Ilia N.
Published: May 2019

Aging is associated with reduced circadian (daily) rhythm amplitude in physiology and behavior, and decreased function of the prefrontal cortex (PFC). Similar effects are seen in younger mice experiencing circadian desynchrony (CD) caused by exposure to 20h light-dark cycles (T20). Given changes in PFC structure/function, underlying metabolic functioning of the PFC may also occur. We aimed to determine whether there are similarities in neurometabolism between Aged and CD mice. Using enzymatic amperometric biosensors, we recorded lactate concentration changes in the medial PFC in freely-behaving mice. Young mice displayed a circadian rhythm of lactate, which was severely blunted by CD, while Aging only changed the rhythm in constant conditions. We simultaneously probed the relationship between arousal state and PFC lactate rhythms, showing relationships between arousal state and lactate concentration, and documenting changes that occurred in CD and aging. Finally, using RT-qPCR, we found changes in genes related to metabolism and plasticity in both Aged and CD mice. Together, these data suggest both Aging and light cycle manipulation can disrupt mPFC neurometabolism.

Highlights

Lactate recordings were taken in Aged and circadian desynchronized (CD) mice.

Lactate displayed a circadian rhythm in Control mice which was blunted in CD mice.

The sleep state/lactate relationship was influenced by Aging, CD, and light.

Both Aging and CD changed the expression of genes related to neurometabolism.
Phylogeography and Molecular Species Delimitation Reveal Cryptic and Incipient Speciation in Synchronous Flashing Fireflies (Coleoptera: Lampyridae) of Southeast Asia
Authors: Jusoh Wan F. A. , Ballantyne Lesley , Onn Chan Kin
Published: May 2019

Synchronous flashing fireflies of the genusPteroptyxare ubiquitous throughout Southeast Asia, yet, knowledge on its biodiversity and evolutionary history remains lacking. Recent studies have revealed notable population-level phylogeographic structure within theP. tenerandP. bearnigroups in Malaysia, suggesting that cryptic species may exist. Additionally, the close morphological and genetic affinity of the recently described speciesP. balingianatoP. malaccaehas raised questions about its validity. In this study, we assembled the most densely sampled genetic dataset onPteroptyxto-date to estimate a comprehensive phylogeny using mitochondrial and nuclear DNA and subsequently implemented a suite of distance-, phylogeny-, and coalescent-based species delimitation methods to characterize species boundaries within theP. tener,P. bearni, andP. balingiana/P. malaccaegroups. Using a total evidence approach from multiple lines of evidence, we showed that populations ofP. teneralong the west coast of Peninsular Malaysia are sufficiently divergent from populations from the east coast and Borneo to warrant specific recognition, despite the absence of morphological differentiation. Conversely, divergence ofP. bearnifrom Borneo and eastern Peninsular Malaysia, as well asP. balingianafromP. malaccaewere modest and their distinction as separate species were ambiguous; consistent with incipient species in the gray zone of speciation. Overall, this study contributes to the limited but growing body of genetic work on Southeast Asian fireflies and underscores the urgent need to increase the breadth and depth of geographic, taxonomic, and genetic sampling to provide a deeper understanding of their biodiversity and evolutionary history.
Analysis host-recognition mechanism of staphylococcal kayvirus ɸSA039 reveals a novel strategy that protects Staphylococcus aureus against infection by Staphylococcus pseudintermedius Siphoviridae phages
Authors: Azam Aa Haeruman , Kadoi Kenji , Miyanaga Kazuhiko , Usui Masaru , Tamura Yutaka , Cui Longzhu , Tanji Yasunori
Published: May 2019

Following the emergence of antibiotic resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP), phage therapy has attracted significant attention as an alternative to antibiotic treatment. Bacteriophages belonging to kayvirus (previously known as Twort-like phages) have broad host range and are strictly lytic in Staphylococcus spp. Previous work revealed that kayvirus ɸSA039 has a host-recognition mechanism distinct from those of other known kayviruses: most of kayviruses use the backbone of wall teichoic acid (WTA) as their receptor; by contrast, ɸSA039 uses the β-N-acetylglucosamine (β-GlcNAc) residue in WTA. In this study, we found that ɸSA039 could switch its receptor to be able to infect S. aureus lacking the β-GlcNAc residue by acquiring a spontaneous mutation in open reading frame (ORF) 100 and ORF102. Moreover, ɸSA039 could infect S. pseudintermedius, which has a different WTA structure than S. aureus. By comparison with newly isolated S. pseudintermedius–specific phage (SP phages), we determined that glycosylation in WTA of S. pseudintermedius is essential for adsorption of SP phages, but not ɸSA039. Finally, we describe a novel strategy of S. aureus which protects the bacteria from infection of SP phages. Notably, glycosylation of ribitol phosphate (RboP) WTA by TarM or/and TarS prevents infection of S. aureus by SP phages. These findings could help to establish a new strategy for treatment of S. aureus and S. pseudintermedius infection, as well as provide valuable insights into the biology of phage–host interactions.
A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation
Authors: Moradi Keivan , Ascoli Giorgio A.
Published: May 2019

The cellular and synaptic architecture of the rodent hippocampus has been described in thousands of peer-reviewed publications. However, no human- or machine-readable public catalog of synaptic electrophysiology data exists for this or any other neural system. Harnessing state of the art information technology, we have developed a cloud-based toolset for identifying empirical evidence from the scientific literature pertaining to synaptic electrophysiology, for extracting the experimental data of interest, and for linking each entry to relevant text or figure excerpts. Mining more than 1,200 published journal articles, we have identified eight different signal modalities quantified by 68 different methods to measure synaptic amplitude, kinetics, and plasticity in hippocampal neurons. We have designed a data structure that both reflects these variabilities and maintains the existing relations among experimental modalities. Moreover, we mapped every annotated experiment to identified “synapse types,” i.e. specific pairs of presynaptic and postsynaptic neuron types. To this aim, we leveraged Hippocampome.org, an open-access knowledge base of morphologically, electrophysiologically, and molecularly characterized neuron types in the rodent hippocampal formation. Specifically, we have implemented a computational pipeline to systematically translate neuron type properties into formal queries in order to find all compatible synapse types. With this system, we have collected nearly 40,000 synaptic data entities covering 88% of the 3,120 potential connections in Hippocampome.org. Correcting membrane potentials with respect to liquid junction potentials significantly reduced the difference between theoretical and experimental reversal potentials, thereby enabling the accurate conversion of all synaptic amplitudes to conductance. This dataset allows for large-scale hypothesis testing of the general rules governing synaptic signals. To illustrate these applications, we confirmed several expected correlations between synaptic measurements and their covariates while suggesting previously unreported ones. We release all data open source at Hippocampome.org in order to further research across disciplines.
Quantifying genetic regulatory variation in human populations improves transcriptome analysis in rare disease patients
Authors: Mohammadi Pejman , Castel Stephane E. , Cummings Beryl B. , Einson Jonah , Sousa Christina , Hoffman Paul , Donkervoort Sandra , Mohassel Payam , Foley Reghan , Wheeler Heather E. , Im Hae Kyung , Bonnemann Carsten G. , MacArthur Daniel G. , Lappalainen Tuuli
Published: May 2019

Transcriptome data holds substantial promise for better interpretation of rare genetic variants in basic research and clinical settings. Here, we introduce ANalysis of Expression VAriation (ANEVA) to quantify genetic variation in gene dosage from allelic expression (AE) data in a population. Application to GTEx data showed that this variance estimate is robust across datasets and is correlated with selective constraint in a gene. We next used ANEVA variance estimates in a Dosage Outlier Test (ANEVA-DOT) to identify genes in an individual that are affected by a rare regulatory variant with an unusually strong effect. Applying ANEVA-DOT to AE data form 70 Mendelian muscular disease patients showed high accuracy in detecting genes with pathogenic variants in previously resolved cases, and lead to one confirmed and several potential new diagnoses in cases previously unresolved. Using our reference estimates from GTEx data, ANEVA-DOT can be readily incorporated in rare disease diagnostic pipelines to better utilize RNA-seq data.

One Sentence Summary

New statistical framework for modelling allelic expression characterizes genetic regulatory variation in populations and informs diagnosis in rare disease patients
Transcriptome Profile Analysis of Twisted Leaf Disease Response in Susceptible Sugarcane with Narenga porphyrocoma Genetic Background
Authors: Wei Jinju , Xiu Zhihui , Ou Huiping , Chen Junhui , Jiang Huayan , Zhang Xiaoqiu , Zhang Ronghua , Zhou Hui , Gui Yiyun , Li Haibi , Li Yangrui , Yang Rongzhong , Huang Dongliang , Tan Hongwei , Liu Xihui
Published: May 2019

Sugarcane is an important industrial crop with a high sugar yield that has become a leading energy crop worldwide. It is widely cultivated in tropical and subtropical regions. Various diseases beset the cultivation of sugarcane. The molecular study of disease resistance in sugarcane is limited by its complicated genome. In our study, RNA-seq was employed to detect the mechanism of twisted leaf disease tolerance in modern cultivar sugarcane, which derived from Narenga porphyrocoma. We completed high-throughput transcriptomic sequencing of 12 samples, including three stages of a susceptible (NSBC1_T “H3-8”) and an unsusceptible cultivar (NSBC1_CK “H-19”) with two biological repeats, respectively. Using the Saccharum spontaneum genome as reference, the average mapping ratio of the clean data was over 70%. Among the differentially expressed genes between H3-8 and H3-19, we focused on the analysis of hormone pathways and resistance (R) genes. The results showed that twisted leaf disease triggers hormone networks and around 40% of R genes conditioned lower expression in the susceptible cultivar. One of the possible reasons for H3-8 being susceptible to twisted leaf disease might be the null/retarded response of R genes, especially in pre-onset stage (46% down-regulated) of pathogens infection.
Protein secondary structure prediction with context convolutional neural network
Authors: Long Shiyang , Tian Pu
Published: May 2019

Protein secondary structure (SS) prediction is important for studying protein structure and function. Both traditional machine learning methods and deep learning neural networks have been utilized and great progress has been achieved in approaching the theoretical limit. Convolutional and recurrent neural networks are two major types of deep leaning architectures with comparable prediction accuracy but different training procedures to achieve optimal performance. We are interested in seeking novel architectural style with competitive performance and in understanding performance of different architectures with similar training procedures.

Results

We constructed a context convolutional neural network (Contextnet) and compared its performance with popular models (e.g. convolutional neural network, recurrent neural network, conditional neural fields …) under similar training procedures on Jpred dataset. the Contextnet was proven to be highly competitive. Additionally, we retrained the network with the Cullpdb data set and compared with Jpred, ReportX and Spider3 server, the Contextnet was found to be more accurate on CASP13 dataset. Training procedures were found to have significant impact on the accuracy of the Contextnet.

Availability

The full source code and dataset have been uploaded at https://github.com/qzlshy/second_structure_model and https://github.com/qzlshy/ss_pssm_hhm.

Contact

tianpu@jlu.edu.cn
Environmental niche forecasts of globally threatened yellow-throated bulbul, Pycnonotus xantholaemus for conservation prospects in the Deccan peninsula, India
Authors: Jha Ashish , Vasudevan Karthikeyan
Published: May 2019

Yellow-throated Bulbul,Pycnonotus xantholaemusis an endemic, rare and threatened species with discontinuous distribution across Deccan peninsula. IUCN has enlisted surveys for newer populations as one of the conservation measures. We used maxent algorithm to generate environmental niche model for further surveys. We looked into climatic envelope at occurrence points and contrast it with background climatic envelope. We compared the model for current scenario and future scenario to assess change in extent of predicted niche over time. We used six variables: climatic, topographical and vegetation layers, and a final set of 102 verified presence locations to generate the model. Topographic ruggedness index and precipitation of wettest month (Bio13) were the strong predictors for Yellow-throated Bulbul niche. Model predicts highly discontinuous and small fragments totalling 7% area of peninsular India as suitable niche. Only 10 % of predicted niche falls within India’s protected area network. Loss of habitat due to granite quarrying and anthropogenic pressure will be a bigger threat than climate change.
A customizable tablet app for hand movement research outside the lab
Authors: Matic Adam , Gomez-Marin Alex
Published: May 2019

Background

Precise behavioral measurements allow the discovery of movement constraints that provide insights into sensory-motor processes and their underlying neural mechanisms. For instance, when humans draw an ellipse on a piece of paper, the instantaneous speed of the pen co-varies tightly with the local curvature of the path. Known as the speed-curvature power law, this phenomenon relates to fundamental questions of motor control.

New Method

We have developed a software app for displaying static curves or dynamic targets while recording finger or stylus movements on Android touch-screen tablets. Designed for human hand movement research, the app is free, ready-to-use, open-source and customizable.

Results

We provide a template experimental protocol, and detailed explanations to use it and flexibly modify the code for different kinds of tasks. Our validation of the app demonstrates laboratory-quality results outside the laboratory. We also provide raw data and analysis scripts.

Comparison with Existing Methods

Commonly used laboratory devices for recording hand movement trajectories are large, heavy and expensive. In turn, software apps are often not published, nor customizable. Our app running on tablets becomes an affordable, flexible, and portable tool suited for quantitative and robust behavioral studies with large number of participants and outside the laboratory (e.g. in a classroom, a hospital, or at home).

Conclusions

The affordability, flexibility, and resolution of our tablet app provide an effective tool to study behavior quantitatively in the real world.

Highlights

A free, ready-to-use, open source, and customizable app for Android tablets.

High-resolution measuring of finger movement during tracing, tracking & scribbling.

Fast and easy data collection and experimental design with affordable hardware.

Allowing for high-throughput experiments outside the lab (classroom, hospital, home).

Validated for state-of-the-art research (speed-curvature power law, drawing accuracy).
Operations Research Methods for Estimating the Population Size of Neuron Types
Authors: Attili Sarojini M. , Mackesey Sean , Ascoli Giorgio A.
Published: May 2019

Understanding brain computation requires assembling a complete catalog of its architectural components. Although the brain is organized into several anatomical and functional regions, it is ultimately the neurons in every region that are responsible for cognition and behavior. Thus, classifying neuron types through-out the brain and quantifying the population sizes of distinct classes in different regions is a key subject of research in the neuroscience community. Although the total number of neurons in the brain has been estimated for multiple species, the definition and population size of each neuron type are still open questions even in common model organisms: the so called cell census problem. We propose a methodology that uses operations research principles to estimate the number of neurons in each type based on available information on their distinguishing properties. Thus, assuming a set of neuron type definitions, we provide a solution to the issue of assessing their relative proportions. Specifically, we present a three-step approach that includes literature search, equation generation, and numerical optimization. Solving numerically the set of equations generated by literature mining yields best estimates or most likely ranges for the number of neurons in each type. While this strategy can be applied to any neural system, we illustrate its usage on the rodent hippocampus.
A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity
Authors: Leempoel Kevin , Hebert Trevor , Hadly Elizabeth A.
Published: May 2019

Environmental DNA (eDNA) is one of the most promising approaches to meet the demand for the fast and frequent monitoring of ecosystems needed to tackle the current decline in biodiversity. However, before eDNA can establish itself as a robust alternative for mammal monitoring, comparison with existing approaches is necessary, yet has not been done. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases.

To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed species observations from a long-term (∼9-yr) camera trapping study. At the same time, we considered multiple experimental parameters, including two sampling designs, two DNA extraction kits and two metabarcodes of different sizes.

All mammals consistently recorded with cameras were detected in eDNA. In addition, eDNA reported many small mammals not recorded by camera traps, but whose presence in the study area is otherwise documented. A long metabarcode (≈220bp) offering a high taxonomic resolution, achieved a similar efficiency as a shorter one (≈70bp) and a phosphate buffer-based extraction gave similar results as a total DNA extraction method for a fraction of the price. Our results support that eDNA-based monitoring should become a valuable part of terrestrial mammal surveys. Yet, the lack of coverage of mammal mitochondrial genomes in public databases must be addressed before eDNA can be used to its full potential.
5-{[(2-Hydroxyethyl)sulfanyl]methyl}quinolin-8-ol
Authors: Rbaa Mohamed , Ramli Youssef , Lakhrissi Younes , Mague Joel , Lakhrissi Brahim
Published: May 2019

In the title molecule, C12H13NO2S, the quinolinol unit is planar (r.m.s. deviation = 0.0128 Å). In the crystal, O—H...N and O—H...S hydrogen bonds together with π-stacking interactions form layers parallel to [100] that are associated through C—H...O hydrogen bonds.
The portrayal of early accountants in nineteenth century Portuguese literature
Authors: Leão Fernanda , Gomes Delfina , Carnegie Garry D.
Published: May 2019

Purpose

The purpose of this paper is to study the portrayal of early accountants in the unfamiliar site of Portugal by examining Portuguese-language realist literature from the second half of the nineteenth century.

Design/methodology/approach

Two popular literary works – Uma Família Inglesa (An English Family), written by Júlio Dinis and published in 1867, and Singularidades de uma Rapariga Loura (The Idiosyncrasies of a Young Blonde Woman), written by Eça de Queirós and published in 1873 – were examined through a qualitative content analysis.

Findings

The dimensions of the accounting stereotype discerned for the two early accounting practitioners featured in these works are portrayed as: modest; on-the-job trained practitioner; uncreative, conservative and unenergetic; honest financial manager; servant of the capitalist (i.e. merchant), and warm and sentimental. The accountant stereotype depicted from 1860s to 1870s period is similar to the conventional accountant stereotype, identified as the “traditional accountant” stereotype. Variations from this stereotype, however, are identified in the local, time-specific settings of Lisbon and Oporto.

Originality/value

The study’s portrayal of early accounting practitioners occurs during a period of transformation marked by liberalism. It augments an understanding of the image of early accounting practitioners, reflecting their social positioning at a time of significant social, economic, political and cultural changes, thereby contributing to an appreciation of the historical legacy of the accountant stereotype in continental Europe. Importantly, a taxonomy is proposed for content analysis that can be used and developed by future researchers.
An empirical analysis of stock market interdependence and volatility spillover in the stock markets of Africa and Middle East region
Authors: Panda Ajaya Kumar , Nanda Swagatika , Paital Rashmi Ranjan
Published: May 2019

Purpose

The purpose of this paper is to examine the short-term and long-term interdependence among the stock markets of Africa and Middle East region. It also attempts to analyze the pattern of volatility spillover among the regional stock markets.

Design/methodology/approach

The study has used Granger causality test, variance decomposition test of vector auto-regression (VAR) model, vector error correction model (VECM), multivariate generalized conditional heteroskedasticity (MGARCH-BEKK) models and Johansen and Juselius multivariate cointegration techniques.

Findings

The study finds that the interlinkages of the stock markets are not uniform across all the countries of the region. The stock market of Israel, South Africa and Jordan are found to be highly connected stock market of the region followed by Egypt and Botswana. The study also finds significant spillover of lagged standardized volatility across the stock markets of the region. But the magnitude of the response of volatility spillover and its persistence is very minimum. However, the stock markets are found to be co-integrated and expected to share long-run equilibrium relationships among each other.

Research limitations/implications

The study has the scope to be extended to capture the time-varying integration of market returns with transmission of monetary policy and exchange rate changes within the region. The results obtained from this study may assist the firm managers and international investors to understand the key drivers of market connectedness.

Originality/value

Empirically investigating the pattern of stock market connectedness in Africa and Middle East region with advanced methodology over a long study period is the originality of this study.
Do prestige and trust sustain knowledge-based communities? Evidence from Medical Ethics co-authorship networks in France
Authors: Kumar Sameer
Published: May 2019

Purpose

The purpose of this paper is to identify embedded communities among Medical Ethics scholars in France based on their position and strength of association in the social networks they form.

Design/methodology/approach

The author constructed a co-authorship network by linking two authors if they co-authored a paper. Once the co-authorship network was constructed, the author investigated the entire network quantitatively using standard research methods known as social network analysis. The author’s mechanism of community detection was via identification, i.e. communities were user-defined based on topological analysis.

Findings

The study identified that communities formed by trust (bonding or repeat connections) or by prestige (connection of well-connected scholars with those that are already well-connected) overlap each other, suggesting that trust and prestige may go hand in hand in sustaining communities. Structural holes within trust networks indicated that some actors played more of a broker role than did other actors.

Research limitations/implications

The study uses Web of Science field based category to extract data. Although thorough cleaning of data has been performed, author disambiguation over a three decade period remains a limitation.

Originality/value

Although there have been numerous studies on mapping co-authorship networks, there has been limited work investigating the underlying communities formed by author associations. The results of this study should be of immense benefit to those studying the science of science and S&T policy.
Exploring the impact of game framing and task framing on user participation in citizen science projects
Authors: Tang Jian , Prestopnik Nathan R.
Published: May 2019

Purpose

The purpose of this paper is to examine how game framing and task framing influence experienced meaningfulness (eudaimonia) and perceived enjoyment (hedonia), which, in turn, can account for user participation behavior in citizen science projects.

Design/methodology/approach

The authors designed and implemented a citizen science system, Citizen Sort, and used a survey method to investigate to what extent game framing and task framing influence participation behavior. PLS–SEM was used to test research hypotheses with 76 Citizen Sort participants.

Findings

Analysis confirmed that game framing and task framing have a significant impact on perceived enjoyment, but showed that only task framing has a direct effect on experienced meaningfulness. The effects of experienced meaningfulness on participation were fully mediated by perceived enjoyment. Content analysis of qualitative data revealed additional insights.

Research limitations/implications

This research is limited due to its sample size and considered as an exploratory study, in which PLS–SEM was used to identify the impact of game framing and task framing as well as support the theory development regarding the dual nature of citizen science games.

Practical implications

This research provided suggestions for scientists, designers and project initiators that game framing and task framing should be effectively integrated to provide enjoyable and meaningful experiences so as to promote user contribution.

Originality/value

This research is one of initial studies which explored the impact of dual nature of citizen science games. The findings of this study provide the groundwork for guidelines and strategies to facilitate user contribution in citizen science projects.
Application of Whitney elements for the reconstruction of electric arc current density in low-voltage circuit breakers
Authors: Dong Jinlong , Di Rienzo Luca , Chadebec Olivier , Wang Jianhua
Published: May 2019

Purpose

This paper aims to present the mathematical formulations of a magnetic inverse problem for the electric arc current density reconstruction in a simplified arc chamber of a low-voltage circuit breaker.

Design/methodology/approach

Considering that electric arc current density is a zero divergence vector field, the inverse problem can be solved in Whitney space W2 in terms of electric current density J with the zero divergence condition as a constraint or can be solved in Whitney space W1 in terms of electric vector potential T where the zero divergence condition naturally holds. Moreover, the tree gauging condition is applied to ensure a unique solution when solving for the vector potential in space W1. Tikhonov regularization is used to treat the ill-posedness of the inverse problem complemented with L-curve method for the selection of regularization parameters. A common mode approach is proposed, which solves for the reduced electric vector potential representing the internal current loops instead of solving for the total electric vector potential. The proposed inversion approaches are numerically tested starting from simulated magnetic field values.

Findings

With the common mode approach, the reconstruction of current density is significantly improved for both formulations using face elements in space W2 and using edge elements in space W1. When solving the inverse problem in space W1, the choice of the regularization operator has a key role to obtain a good reconstruction, where the discrete curl operator is a good option. The standard Tikhonov regularization obtains a good reconstruction with J-formulation, but fails in the case of T-formulation. The use of edge elements requires a tree-cotree gauging to ensure the uniqueness of T. Moreover, additional efforts have to be taken to find an optimal regularization operator and an optimal tree when using edge elements. In conclusion, the J-formulation is to be preferred.

Originality/value

The proposed approaches are able to reconstruct the three-dimensional electric arc current density from its magnetic field in a non-intrusive manner. The formulations enable us to incorporate a priori knowledge of the unknown current density into the solution of the inverse problem, including the zero divergence condition and the boundary conditions. A common mode approach is proposed, which can significantly improve the current density reconstruction.
Segmentation mapping and folding method of surfaces of revolution and its applications
Authors: Zhao Xiao-Shun , Yu Li , Yang Xue , Zhang Si-Yu
Published: May 2019

Purpose

The purpose of this study was to develop a new folding method for modeling complicated folded fabric with surfaces of revolution.

Design/methodology/approach

Irregular wrinkles and mesh distortions easily appear in the fold modeling of a complex curved surface. Aimed at this key technical problem, the segmentation mapping folding method (SMFM) is proposed in this paper. First, high-precision flattened planes were obtained by using segmentation mapping techniques. Second, the segmented planes were transformed into a folded and continuous geometric model by using matrix transformations. Finally, initial stress was used to modify the geometric folding errors, which ensured agreement with the inflated flexible fabric’s geometry and the original design.

Findings

Compared with the traditional folding method, SMFM has the advantages of good finite-element mesh quality, large radial compression rate, regular folds, etc. The surface area error and the volume error of the inflated single torus established by SMFM were only 1.2 per cent, showing that SMFM has high modeling accuracy. The numerical results of an inflatable re-entry vehicle are presented to demonstrate the reliability, feasibility and applicability of SMFM. Moreover, the stress modification reduced the problems of stress concentration and mesh distortions, improving the accuracy and stability of the numerical calculations.

Originality/value

In this paper, for the first time, a folding method for modeling complicated folded fabric is proposed. This methodology can be used to model the multidimensional compression and regular folds of complex surfaces of revolution that cannot be flattened and to improve the accuracy and stability of the numerical calculations.