bluuebunny/crossref_metadata_2025 huggingface dataset:
Plastic limit bearing calculation of blasting-roof in deep hole mining and its applications
Authors: Wang Wei , Luo Zhouquan , Qin Yaguang , Xiang Jun
Published: July 2019

A plastic bearing calculation method for a blasting-roof is proposed to solve the problem of determining the blasting-roof thickness in deep hole mining. A mechanical analysis model for the plastic bearing was built for the typical boundary conditions of blasting-roofs. The external and internal work of the blasting-roof are equal under the plastic limit state through calculation. The limit bearing formulae of blasting-roofs under various boundary conditions were derived based on the principle of virtual work. A Vertical Crater Retreat stope was taken as the object, and the safe blasting-roof thickness was determined to be 6 m using the derived formula (considering the safety coefficient). A numerical model of stope was constructed using the Surpac-Flac3D technique, while the blasting-roof stability was simulated under different thicknesses. Variations in the simulated indexes (stress and plastic zone volume) prove that the theoretical calculations are reliable. The plastic bearing calculation method can provide a new method to determine the blasting-roof thickness in deep hole mining.
Aβ42 fibril formation from predominantly oligomeric samples suggests a link between oligomer heterogeneity and fibril polymorphism
Authors: Xue Christine , Tran Joyce , Wang Hongsu , Park Giovanna , Hsu Frederick , Guo Zhefeng
Published: July 2019

Amyloid-β (Aβ) oligomers play a central role in the pathogenesis of Alzheimer's disease. Oligomers of different sizes, morphology and structures have been reported in both
in vivo
and
in vitro
studies, but there is a general lack of understanding about where to place these oligomers in the overall process of Aβ aggregation and fibrillization. Here, we show that Aβ42 spontaneously forms oligomers with a wide range of sizes in the same sample. These Aβ42 samples contain predominantly oligomers, and they quickly form fibrils upon incubation at 37°C. When fractionated using ultrafiltration filters, the samples enriched with smaller oligomers form fibrils at a faster rate than the samples enriched with larger oligomers, with both a shorter lag time and faster fibril growth rate. This observation is independent of Aβ42 batches and hexafluoroisopropanol treatment. Furthermore, the fibrils formed by the samples enriched with larger oligomers are more readily solubilized by epigallocatechin gallate, a main catechin component of green tea. These results suggest that the fibrils formed by larger oligomers may adopt a different structure from fibrils formed by smaller oligomers, pointing to a link between oligomer heterogeneity and fibril polymorphism.
Open science and modified funding lotteries can impede the natural selection of bad science
Authors: Smaldino Paul E. , Turner Matthew A. , Contreras Kallens Pablo A.
Published: July 2019

Assessing scientists using exploitable metrics can lead to the degradation of research methods even without any strategic behaviour on the part of individuals, via ‘the natural selection of bad science.’ Institutional incentives to maximize metrics like publication quantity and impact drive this dynamic. Removing these incentives is necessary, but institutional change is slow. However, recent developments suggest possible solutions with more rapid onsets. These include what we call
open science improvements
, which can reduce publication bias and improve the efficacy of peer review. In addition, there have been increasing calls for funders to move away from prestige- or innovation-based approaches in favour of lotteries. We investigated whether such changes are likely to improve the reproducibility of science even in the presence of persistent incentives for publication quantity through computational modelling. We found that modified lotteries, which allocate funding randomly among proposals that pass a threshold for methodological rigour, effectively reduce the rate of false discoveries, particularly when paired with open science improvements that increase the publication of negative results and improve the quality of peer review. In the absence of funding that targets rigour, open science improvements can still reduce false discoveries in the published literature but are less likely to improve the overall culture of research practices that underlie those publications.
Degradation of methylene blue by natural manganese oxides: kinetics and transformation products
Authors: Zhou Shuangxi , Du Zhiling , Li Xiuwen , Zhang Yunhai , He Yide , Zhang Yongjun
Published: July 2019

In this study, natural manganese oxides (MnO

x

), an environmental material with high redox potential, were used as a promising low-cost oxidant to degrade the widely used dyestuff methylene blue (MB) in aqueous solution. Although the surface area of MnO

x

was only 7.17 m
2
g
−1
, it performed well in the degradation of MB with a removal percentage of 85.6% at pH 4. It was found that MB was chemically degraded in a low-pH reaction system and the degradation efficiency correlated negatively with the pH value (4–8) and initial concentration of MB (10–50 mg l
−1
), but positively with the dosage of MnO

x

(1–5 g l
−1
). The degradation of MB fitted well with the second-order kinetics. Mathematical models were also built for the correlation of the kinetic constants with the pH value, the initial concentration of MB and the dosage of MnO

x

. Furthermore, several transformation products of MB were identified with HPLC-MS, which was linked with the bond energy theory to reveal that the degradation was initiated with demethylation.
Leading-edge vortices over swept-back wings with varying sweep geometries
Authors: Lambert William B. , Stanek Mathew J. , Gurka Roi , Hackett Erin E.
Published: July 2019

Micro air vehicles are used in a myriad of applications, such as transportation and surveying. Their performance can be improved through the study of wing designs and lift generation techniques including leading-edge vortices (LEVs). Observation of natural fliers, e.g. birds and bats, has shown that LEVs are a major contributor to lift during flapping flight, and the common swift (
Apus apus
) has been observed to generate LEVs during gliding flight. We hypothesize that nonlinear swept-back wings generate a vortex in the leading-edge region, which can augment the lift in a similar manner to linear swept-back wings (i.e. delta wing) during gliding flight. Particle image velocimetry experiments were performed in a water flume to compare flow over two wing geometries: one with a nonlinear sweep (swift-like wing) and one with a linear sweep (delta wing). Experiments were performed at three spanwise planes and three angles of attack at a chord-based Reynolds number of 26 000. Streamlines, vorticity, swirling strength, and
Q
-criterion were used to identify LEVs. The results show similar LEV characteristics for delta and swift-like wing geometries. These similarities suggest that sweep geometries other than a linear sweep (i.e. delta wing) are capable of creating LEVs during gliding flight.
LncRNA GUARDIN suppresses cellular senescence through a LRP130-PGC1α-FOXO4-p21-dependent signaling axis
Authors: Sun Xuedan , FrancisThorne Rick , Zhang Xu Dong , He Miao , Feng Shanshan , Liu Xiaoying , Wu Mian
Published: July 2019

The long non-coding RNA GUARDIN functions to protect genome stability. Inhibiting GUARDIN expression can alter cell fate decisions towards senescence or apoptosis, but the underlying molecular signals are unknown. Here we show that GUARDIN is an essential component of a transcriptional repressor complex involving LRP130 and PGC1α which suppresses FOXO4 expression. GUARDIN acts as a scaffold to stabilize LRP130/PGC1α heterodimers and their occupancy at the FOXO4 promotor. Destabilizing this complex by silencing of GUARDIN, LRP130 or PGC1α leads to FOXO4-dependent upregulation of p21, thereby driving cells into senescence. We also found that GUARDIN expression was induced by rapamycin, a senolytic agent that suppresses cell senescence. FOS-Like Antigen 2 (FOSL2) acts as a transcriptional repressor of GUARDIN with increased levels in the presence of rapamycin resulting from downregulation of FOSL2. Together, these results demonstrate that GUARDIN inhibits p21-dependent senescence through a LRP130-PGC1α-FOXO4 signaling axis and moreover, GUARDIN contributes to the anti-senolytic activities of rapamycin.
TGFβ restricts T cell function and bacterial control within the tuberculous granuloma
Authors: Gern Benjamin H , Adams Kristin N , Plumlee Courtney R , Stoltzfus Caleb R , Shehata Laila , Busman-Sahay Kathleen , Hansen Scott G , Axthelm Michael K , Picker Louis J , Estes Jacob D , Urdahl Kevin B , Gerner Michael Y
Published: July 2019

Interferon gamma (IFNγ) produced by CD4 T cells is required for immune containment ofMycobacterium tuberculosis(Mtb) infection. Despite this, IFNγ plays a minor role in CD4 T cell-mediated immunity within the lung. In this study, we use a recently-developed murine model of physiologic Mtb infection coupled with advanced quantitative imaging to demonstrate that IFNγ production by Mtb-specific T cells is rapidly extinguished within the granuloma, but not in unaffected areas of the lung. This is mediated via localized immunosuppression through cell-intrinsic TGFβ signaling in effector T helper 1 cells within the granuloma, and blockade of TGFβ signaling in T cells results in improved immune cell function and decreased pulmonary bacterial burden. These findings uncover a potent immunosuppressive mechanism associated with Mtb infection and provide potential targets for host-directed therapy.
Inference of selection from genetic time series using various parametric approximations to the Wright-Fisher model
Authors: Paris Cyriel , Servin Bertrand , Boitard Simon
Published: July 2019

Detecting genomic regions under selection is an important objective of population genetics. Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but rapid advances in DNA sequencing have increased the availability of time series genomic data. A common approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain. Based on this principle, several methods have been proposed to infer selection intensity. One of their differences lies in how they model the transition probabilities of the Markoiv chain. Using the Wright-Fisher model is a natural choice but its computational cost is prohibitive for large population sizes so approximations to this model based on parametric distributions have been proposed. Here, we compared the performance of some of these approximations with respect to their power to detect selection and estimation of the selection coefficient. We developped a new generic Hidden Markov Model likelihood calculator and applied it on genetic time series simulated under various evolutionary scenarios. The Beta-with-Spikes approximation, which combines discrete fixation probabilities with a continuous Beta distribution, was found to perform consistently better than the others. This distribution provides an almost perfect fit to the Wright-Fisher model in terms of selection inference, for a computational cost that does not increase with population size. We further evaluate this model for population sizes not accessible to the Wright-Fisher model and illustrate its performance on a dataset of two divergently selected chicken populations.
Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins
Authors: Erlendsson Simon , Morado Dustin R. , Shepherd Jason D. , Briggs John A. G.
Published: July 2019

The neuronal protein Arc is a critical mediator of synaptic plasticity. Arc originated in tetrapods and flies through domestication of retrotransposon Gag genes. Recent studies have suggested that Arc mediates intercellular mRNA transfer and like Gag, can form capsid-like structures. Here we report that Drosophila proteins dArc1 and dArc2 assemble virus-like capsids. We determine the capsid structures to 2.8 Å and 3.7 Å resolution, respectively, finding similarity to capsids of retroviruses and retrotransposons. Differences between dArc1 and dArc2 capsids, including the presence of a structured zinc-finger pair in dArc1, are consistent with differential RNA-binding specificity. Our data support a model in which ancestral capsid-forming and RNA-binding properties of Arc remain under positive selection pressure and have been repurposed to function in neuronal signalling.
Dyslexic children show altered temporal structure of the nonlinear VEP
Authors: Crewther Sheila , Rutkowski Jacqueline , Crewther David
Published: July 2019

The neural basis of dyslexia remains unresolved, despite many theories relating dyslexia to dysfunction in visual magnocellular and auditory temporal processing, cerebellar dysfunction, attentional deficits, as well as excessive neural noise. Recent research identifies perceptual speed as a common factor, integrating several of these systems. Optimal perceptual speed invokes transient attention as a necessary component, and change detection in gap paradigm tasks is impaired in those with dyslexia. This research has also identified an overall better change detection for targets presented in the upper compared with lower visual fields. Despite the magnocellular visual pathway being implicated in the aetiology of dyslexia over 30 years ago, objective physiological measures have been lacking. Thus, we employed nonlinear visual evoked potential (VEP) techniques which generate second order kernel terms specific for magno and parvocellular processing as a means to assessing the physiological status of poor readers (PR, n=12) compared with good readers (GR, n=16) selected from children with a mean age of 10yr. The first and second order Wiener kernels using multifocal VEP were recorded from a 4° foveal stimulus patch as well as for upper and lower visual field peripheral arcs. Foveal responses showed little difference between GR and PR for low contrast stimulation, except for the second slice of the second order kernel where lower peak amplitudes were recorded for PR vs GR. At high contrast, there was a trend to smaller first order kernel amplitudes for short latency peaks of the PR vs GR. In addition, there were significant latency differences for the first negativity in the first two slices of the second order kernel. In terms of peripheral stimulation, lower visual field response amplitudes were larger compared with upper visual field responses, for both PR and GR. A trend to larger second/first order ratio for magnocellularly driven responses suggests the possibility of lesser neural efficiency in the periphery for the PR compared with the GR. Stronger lower field peripheral response may relate to better upper visual field change detection performance when target visibility is controlled through flicking masks. In conclusion, early cortical magnocellular processing at low contrast was normal in those with dyslexia, while cortical activity related to parvocellular afferents was reduced. In addition, the study demonstrated a physiological basis for upper versus lower visual field differences related to magnocellular function.
Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem
Authors: Qiu Yutong , Ma Cong , Xie Han , Kingsford Carl
Published: July 2019

Transcriptomic structural variants (TSVs) — structural variants that affect expressed regions — are common, especially in cancer. Detecting TSVs is a challenging computational problem. Sample heterogeneity (including differences between alleles in diploid organisms) is a critical confounding factor when identifying TSVs. To improve TSV detection in heterogeneous RNA-seq samples, we introduce the MULTIPLECOMPATIBLEARRANGEMENTPROBLEM(MCAP), which seekskgenome rearrangements to maximize the number of reads that are concordant with at least one rearrangement. This directly models the situation of a heterogeneous or diploid sample. We prove that MCAP is NP-hard and provide a-approximation algorithm fork= 1 and a-approximation algorithm for the diploid case (k= 2) assuming an oracle fork= 1. Combining these, we obtain a-approximation algorithm for MCAP whenk= 2 (without an oracle). We also present an integer linear programming formulation for generalk. We completely characterize the graph structures that requirek> 1 to satisfy all edges and show such structures are prevalent in cancer samples. We evaluate our algorithms on 381 TCGA samples and 2 cancer cell lines and show improved performance compared to the state-of-the-art TSV-calling tool, SQUID.
Genomic analysis on broiler-associated Clostridium perfringens strains and caecal microbiome profiling reveals key factors linked to poultry Necrotic Enteritis
Authors: Kiu Raymond , Brown Joseph , Bedwell Harley , Leclaire Charlotte , Caim Shabhonam , Pickard Derek , Dougan Gordon , Dixon Ronald A , Hall Lindsay J
Published: July 2019

Background

Clostridium perfringens is a key pathogen in poultry-associated necrotic enteritis (NE). To date there are limited Whole Genome Sequencing based studies describing broiler-associated C. perfringens in healthy and diseased birds. Moreover, changes in the caecal microbiome during NE is currently not well characterised. Thus, the aim of this present study was to investigate C. perfringens virulence factors linked to health and diseased chickens, including identifying caecal microbiota signatures associated with NE.

Results

We analysed 88 broiler chicken C. perfringens genomes (representing 66 publicly available genomes and 22 newly sequenced genomes) using different phylogenomics approaches and identified a potential hypervirulent and globally-distributed clone spanning 20-year time-frame (1993-2013). These isolates harbored a greater number of virulence genes (including toxin and collagen adhesin genes) when compared to other isolates. Further genomic analysis indicated exclusive and overabundant presence of important NE-linked toxin genes including netB and tpeL in NE-associated broiler isolates. Secondary virulence genes including pfoA, cpb2, and collagen adhesin genes cna, cnaA and cnaD were also enriched in the NE-linked C. perfringens genomes. Moreover, an environmental isolate obtained from farm animal feeds was found to encode netB, suggesting potential reservoirs of NetB-positive C. perfringens strains (toxinotype G). We also analysed caecal samples from a sub-set of 11 diseased and healthy broilers using 16S rRNA amplicon sequencing, which indicated a significant and positive correlation in genus Clostridium within the wider microbiota of those broilers diagnosed with NE, alongside reductions in beneficial microbiota members.

Conclusions

These data indicate a positive association of virulence genes including netB, pfoA, cpb2, tpeL and cna variants linked to NE-linked isolates. Potential global dissemination of specific hypervirulent lineage, coupled with distinctive microbiome profiles, highlights the need for further investigations, which will require a large worldwide sample collection from healthy and NE-associated birds.
64-Channel Carbon Fiber Electrode Arrays for Chronic Electrophysiology
Authors: Guitchounts Grigori , Cox David
Published: July 2019

A chief goal in neuroscience is to understand how neuronal activity relates to behavior, perception, and cognition. However, monitoring neuronal activity over long periods of time is technically challenging, and limited, in part, by the invasive nature of recording tools. While electrodes allow for recording in freely-behaving animals, they tend to be bulky and stiff, causing damage to the tissue they are implanted in. One solution to this invasiveness problem may be probes that are small enough to fly under the immune system’s radar. Carbon fiber (CF) electrodes are thinner and more flexible than typical metal or silicon electrodes, but the arrays described in previous reports had low channel counts and required time-consuming manual assembly. Here we report the design of an expanded-channel-count carbon fiber electrode array (CFEA) as well as a method for fast preparation of the recording sites using acid etching and electroplating with PEDOT-TFB, and demonstrate the ability of the 64-channel CFEA to record from rat visual cortex. We include designs for interfacing the system with micro-drives or flex-PCB cables for recording from multiple brain regions, as well as a facilitated method for coating CFs with the insulator Parylene-C. High-channel-count CFEAs may thus be an alternative to traditional microwire-based electrodes and a practical tool for exploring the neural code.
Classification of hospital and urban wastewater resistome and microbiota over time and their relationship to the eco-exposome
Authors: Buelow Elena , Rico Andreu , Gaschet Margaux , Lourenço José , Kennedy Sean P. , Wiest Laure , Ploy Marie-Cecile , Dagot Christophe
Published: July 2019

Wastewaters (WW) are important sources for the dissemination of antimicrobial resistance (AMR) into the environment. Hospital WW (HWW) contain higher loads of micro-pollutants and AMR markers than urban WW (UWW). Little is known about the long-term dynamics of H and U WW and the impact of their joined treatment on the general burden of AMR. Here, we characterized the resistome, microbiota and eco-exposome signature of 126 H and U WW samples treated separately for three years, and then mixed, over one year. Multi-variate analysis and machine learning revealed a robust signature for each WW with no significant variation over time before mixing, and once mixed, both WW closely resembled U signatures. We demonstrated a significant impact of pharmaceuticals and surfactants on the resistome and microbiota of H and U WW. Our results present considerable targets for AMR related risk assessment of WW.
Mozambican genetic variation provides new insights into the Bantu expansion
Authors: Semo Armando , Gayà-Vidal Magdalena , Fortes-Lima Cesar , Alard Bérénice , Oliveira Sandra , Almeida João , Prista António , Damasceno Albertino , Fehn Anne-Maria , Schlebusch Carina , Rocha Jorge
Published: July 2019

The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ∼1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a “late split” between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.
C. elegans LIN-28 controls temporal cell-fate progression by regulating LIN-46 expression via the 5’UTR of lin-46 mRNA
Authors: Ilbay Orkan , Nelson Charles , Ambros Victor
Published: July 2019

Human Lin28 is a conserved RNA-binding protein that promotes proliferation and pluripotency and can be oncogenic. Lin28 and C. elegans LIN-28 bind to precursor RNAs of the conserved, cellular differentiation-promoting, microRNA let-7 and inhibits production of mature let-7 microRNA. Lin28/LIN-28 also binds to and regulates many mRNAs in various cell types. However, the determinants and consequences of these LIN-28-mRNA interactions are not well understood. Here, we report that LIN-28 in C. elegans represses the expression of LIN-46, a downstream protein in the heterochronic pathway, via the 5’ UTR of the lin-46 mRNA. We show that both LIN-28 and the 5’UTR of lin-46 are required to prevent LIN-46 expression in the L1 and L2 stages, and that precocious LIN-46 expression is sufficient to skip L2 stage proliferative cell-fates, resulting in heterochronic defects similar to the ones observed in lin-28(0) animals. We propose that the lin-46 5’UTR mediates LIN-28 binding to and repression of the lin-46 mRNA. Our results demonstrate that precocious LIN-46 expression alone can account for lin-28(0) phenotypes, demonstrating the biological importance of regulation of individual target mRNAs by LIN-28.
An analysis of respiratory function and mitochondrial morphology in Candida albicans
Authors: Duvenage Lucian , Pentland Daniel R. , Munro Carol A. , Gourlay Campbell W.
Published: July 2019

Respiratory function and mitochondrial dynamics have been well characterised in a number of cell types, including the model yeast Saccharomyces cerevisiae, but remain under-researched in fungal pathogens such as Candida albicans. An understanding of mitochondrial activity and morphology is important if we are to understand the role that this organelle plays in adaption and response to stress. Here we examine the respiratory profiles of several prominent pathogenic Candida species and present a useful GFP probe for the study of mitochondrial morphology. We examine mitochondrial morphology under a variety of conditions that Candida species may encounter within the host, such as acidic pH, respiratory and oxidative stress. The GFP probe also allowed for the visualisation of mitochondria during hyphal development, during growth following macrophage engulfment and distribution within biofilms. These data demonstrate that the mitochondrial network of C. albicans is highly responsive to both environmental conditions and developmental cues, suggesting important roles for this organelle in environmental adaption.
Neurotensin receptor 1 deletion suppresses methamphetamine self-administration and the associated reduction in dopamine cell firing
Authors: Dominguez-Lopez Sergio , Sharma Ramaswamy , Beckstead Michael J.
Published: July 2019

We previously reported that pharmacological blockade of neurotensin receptors in the ventral tegmental area (VTA) decreases methamphetamine (METH) self-administration in mice. Here we explored the consequences of genetic deletion of neurotensin receptor 1 (NtsR1) in METH self-administration and VTA dopamine neuron firing activity. We implanted mice with an indwelling jugular catheter and trained them to nose-poke for intravenous infusions of METH. Mice with NtsR1 deletion (KO) acquired selfadministration similar to wildtype (WT) and heterozygous (HET) littermates. However, in NtsR1 KO and HET mice, METH intake and motivated METH seeking decreased when the response requirement was increased to a fixed ratio 3 and when mice were tested on a progressive ratio protocol. After completion of METH self-administration, single cell in vivo extracellular recordings of dopamine firing activity in the VTA were obtained in anesthetized mice. In WT METH-experienced mice, dopamine cell firing frequency dramatically decreases compared to WT drug-naïve mice. NtsR1 KO and HET mice did not exhibit this decline of dopamine cell firing activity after prolonged METH selfadministration. We also observed an increase in population activity following METH selfadministration that was strongest in the WT group. Our results suggest a role for NtsR1 in METH-seeking behavior, and ablation of NtsR1 receptors prevents the detrimental effects of prolonged METH self-administration on VTA dopamine cell firing frequency.
The mechanical basis for snapping of the Venus flytrap, Darwin’s ‘most wonderful plant in the world’
Authors: Burri Jan T. , Saikia Eashan , Läubli Nino F. , Vogler Hannes , Wittel Falk K. , Rüggeberg Markus , Herrmann Hans J. , Burgert Ingo , Nelson Bradley J. , Grossniklaus Ueli
Published: July 2019

The carnivorous Venus flytrap catches prey by an ingenious snapping mechanism. Based on work over the past 190 years, it has become generally accepted that two touches of the trap’s sensory hairs within 30 seconds, each one generating an action potential, are required to trigger closure of the trap. We developed an electromechanical model which, however, suggests that under certain circumstances one touch is sufficient to generate two action potentials. Using a force-sensing microrobotics system, we precisely quantified the sensory hair deflection parameters necessary to trigger trap closure, and correlated them with the elicited action potentials in vivo. Our results confirm the model’s predictions, suggesting that the Venus flytrap may be adapted to a wider range of prey movement than previously assumed.
Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island
Authors: Choi Jae Young , Purugganan Michael , Stacy Elizabeth A.
Published: July 2019

A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within HawaiianMetrosideros, a hyper-variable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin ofMetrosideros polymorphavar.newellii(newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wideM. polymorphavar.glaberrima(glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii’s origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 million years. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e.secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e.primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.

Author summary

A long-standing question in evolution is whether or not new species can arise in the presence of gene flow, which is expected to inhibit the formation of reproductive isolating barriers. We investigated the genomics underlying the origin of a Hawaii Island-endemic riparian tree and purported case of incipient sympatric speciation due to disruptive selection across a sharp forest-riparian ecotone. We find extensive evidence of ongoing gene flow between the riparian tree and its closest relative along with local genomic regions resistant to admixture that likely formed through selection on genes for ecological adaptation and/or reproductive isolation. These results strongly suggest that where disruptive selection is strong, incipient speciation with gene flow is possible even in long-lived, highly dispersible trees.
Functional activity of antisera against recombinant Zika virus envelope protein subunits expressed in Escherichia coli
Authors: Tham Hong-Yun , Ooi Man Kwan , Balasubramaniam Vinod RMT , Hassan Sharifah Syed , Tham Hong-Wai
Published: July 2019

The global Zika virus (ZIKV) outbreak across continents has been drawing research attentions to researchers and healthcare professionals. It highlights the urgent development of ZIKV vaccines that offer rapid, precise and specific protection to those living in the high-risk regions - the tropical and subtropical regions. As a public health priority, there is a progressive development in the discovery of vaccine candidates and design in recent years. Many efforts have been placed in the in vitro development of ZIKV subunits as the vaccine candidate in various protein expression systems, including bacteria, yeast, plant cells, insect cells and mammalian cells. However, due to the lack of knowledge on humoral and cellular immune responses against virus vaccines, a commercialised vaccine against Dengue virus (DENV) has been suspended due to a health scare in Philippines. Moreover, the closely-related DENV and ZIKV has indicated serological cross-reactivity between both viruses. This has led to greater attentions to precautions needed during the design of ZIKV and DENV vaccines. In this study, we pre-selected, synthesised and expressed the domain III of ZIKV envelope protein (namely rEDIII) based on a previously-established report (GenBank: AMC13911.1). The characteristics of purified ZIKV rEDIII was tested using SDS-PAGE, Western blotting and LC-MS/MS. Since the ZIKV rEDIII has been well reported as a potential protein candidate in ZIKV vaccine development, we assessed the possible outcome of preexisting immunity against the rEDIII proteins by conducting dot-blotting assays using mice antisera pre-immunised with ZIKV particles (ZIKV strain: MRS_OPY_Martinique_PaRi_2015, GenBank: KU647676) . Surprisingly, the antisera was able to recognise the rEDIII of a different ZIKV strain (GenBank: AMC13911.1). Despite its great antigenicity in eliciting humoral and cellular immunity against ZIKV infection, our finding calls for greater attention to evaluate the details of ZIKV rEDIII as a stand-alone vaccine candidate.
Production, purification and evaluation of biodegrading potential of PHB depolymerase ofStenotrophomonassp. RZS 7
Authors: Sayyed R. Z. , Wani S. J. , Al-Harthi Helal F. , Syed Asad , El-Enshasy Hesham Ali
Published: July 2019

There are numerous reports on PHB depolymerases produced by a wide variety of microorganisms isolated from various habitats, however, reports on PHB depolymerase isolated from plastic contaminated sites are scares. Thermophilic PHB polymerase produced by isolates obtained from plastic contaminated sites is expected to have better relevance for its application in plastic/bioplastic degradation. Although PHB has attracted commercial significance, the inefficient production and recovery methods, inefficient purification of PHB depolymerase and lack of ample knowledge on PHB degradation by PHB depolymerase have hampered its large scale commercialization. Therefore, to ensure the biodegradability of biopolymers, it becomes imperative to study the purification of the biodegrading enzyme system. We report the production, purification, and characterization of extracellular PHB depolymerase fromStenotrophomonassp. RZS 7 isolated from a plastic contaminated site. The isolate produced extracellular poly-β-hydroxybutyrate (PHB) depolymerase in the mineral salt medium at 30oC during 4 days of incubation under shake flask condition. Purification of the enzyme was carried out by three different methods using PHB as a substrate. Purification of PHB depolymerase by ammonium salt precipitation, column chromatography, and solvent purification method was successfully carried out. Among the purification method tested, the enzyme was best purified by column chromatography on Octyl-Sepharose CL-4B column with maximum (0.7993 U mg-1ml-1) purification yield. The molecular weight of purified PHB depolymerase (40 kDa) closely resembled with PHB depolymerase ofAureobacterium saperdae. Experiments on assessment of biodegradation of PHB in liquid culture medium and under natural soil conditions confirmed PHB biodegradation potential ofStenotrophomonassp. RZS 7. The results obtained in FTIR analysis, HPLC study and GC-MS analysis confirmed the biodegradation attempt in liquid medium byStenotrophomonassp. RZS 7. Changes in surface morphology of PHB film in soil burial as observed in FE SEM analysis confirmed the biodegradation of PHB. The isolate was capable of degrading PHB and resulted in 87.74% degradation. Higher rate of degradation under natural soil condition is the result of activity of soil microbes that complemented the degradation byStenotrophomonassp. RZS 7.
Modelling vegetation understory cover using LiDAR metrics
Authors: Venier Lisa A. , Swystun Tom , Mazerolle Marc J. , Kreutzweiser David P. , Wainio-Keizer Kerrie L. , McIlwrick Ken A. , Woods Murray E. , Wang Xianli
Published: July 2019

Forest understory vegetation is an important feature of wildlife habitat among other things. Predicting and mapping understory is a critical need for forest management and conservation planning, but it has proved difficult. LiDAR has the potential to generate remotely sensed forest understory structure data, yet this potential has to be fully validated. Our objective was to examine the capacity of LiDAR point cloud data to predict forest understory cover. We modeled ground-based observations of understory structure in three vertical strata (0.5 m to < 1.5 m, 1.5 m to < 2.5 m, 2.5 m to < 3.5 m) as a function of a variety of LiDAR metrics using both mixed-effects and Random Forest models. We compared four understory LiDAR metrics designed to control for the spatial heterogeneity of sampling density. The four metrics were highly correlated and they all produced high values of variance explained in mixed-effects models. The top-ranked model used a voxel-based understory metric along with vertical stratum (Akaike weight = 1, explained variance = 87%, SMAPE=15.6%). We found evidence of occlusion of LiDAR pulses in the lowest stratum but no evidence that the occlusion influenced the predictability of understory structure. The Random Forest model results were consistent with those of the mixed-effects models, in that all four understory LiDAR metrics were identified as important, along with vertical stratum. The Random Forest model explained 74.4% of the variance, but had a lower cross-validation error of 12.9%. Based on these results, we conclude that the best approach to predict understory structure is using the mixed-effects model with the voxel-based understory LiDAR metric along with vertical stratum, but that other understory LiDAR metrics (fractional cover, normalized cover and leaf area density) would still be effective in mixed-effects and Random Forest modelling approaches.
What are the driving factors of pesticide overuse in vegetable production? Evidence from Chinese farmers
Authors: Yang Mansha , Zhao Xia , Meng Ting
Published: July 2019

Purpose

Pesticide overuse has caused a series of negative impacts on environment and human health. The purpose of this paper is to examine the farmers’ behavior of pesticide overuse and to identify the underlying determinants, based on the survey data from Shandong Province, China.

Design/methodology/approach

A two-stage semiparametric approach and the binary probit model were employed in this study to analyze the marginal pesticide productivity and investigate the determinants of the pesticide overuse.

Findings

Results suggest that the marginal pesticide productivity is negative, indicating a serious overuse of pesticides in the surveyed area. Both market factors and government regulation have impacts on farmers’ use of pesticides.

Originality/value

This study estimates marginal pesticide productivity with an innovative methodology, and explores the role of market factors and government regulation in regulating farmers’ behavior of pesticide use, especially in a typical vegetable growing area and targeting a specific type of vegetable.
Return and volatility spillovers between Bitcoin and other asset classes in Turkey
Authors: Vardar Gulin , Aydogan Berna
Published: July 2019

Purpose

With a substantial return and volatility characteristic of Bitcoin, which may be seen as a new category of investment assets, better understanding of the nature of return and volatility spillover can help investors and regulators in achieving the potential goal from portfolio diversification. The paper aims to discuss these issues.

Design/methodology/approach

This paper explores the return and volatility transmission between the Bitcoin, as the largest cryptocurrency, and other traditional asset classes, namely stock, bond and currencies from the standpoint of Turkey over the period July, 2010–June, 2018 using the newly developed multivariate econometric technique, VAR–GARCH, in mean framework with the BEKK representation.

Findings

The empirical results reveal the existence of the positive unilateral return spillovers from the bond market to Bitcoin market. Regarding the results of shock and volatility spillovers, there exists strong evidence of bidirectional cross-market shock and volatility spillover effects between Bitcoin and all other financial asset classes, except US Dollar exchange rate.

Originality/value

The important extention is the adoption of a newly developed multivariate econometric technique, VAR–GARCH, in mean framework with the BEKK representation, proposed by Engle and Kroner (1995), which is employed for the first time specifically to examine the extent of integration in terms of volatility and return between Bitcoin and key asset classes. Second, Bitcoin has experienced a rapid growth since around a decade and a number of investors are showing interest in its potential as an integrative part of portfolio diversification. The information provided by empirical results gives empirical bases from which to address topics concerning hedging purposes and optimal portfolio allocation. It is also increasingly important to analyze the current behavior of Bitcoin in relation to other assets to provide policy makers and regulatory bodies with guidance on the role of the Bitcoin as an investment asset in Turkey. Thus, this is the first serious attempt at exploring the potential for Bitcoin to offer diversification opportunities in the context of Turkey.
Does hotel cleanliness correlate with surfaces guests contact?
Authors: Park Haeik , Kline Sheryl Fried , Kim Jooho , Almanza Barbara , Ma Jing
Published: July 2019

Purpose

This study aims to strengthen implications about hotel cleaning outcomes by comparing guests’ perception of the amount of contact they have with cleanliness of hotel surfaces.

Design/methodology/approach

This study used two data-collection methods, a survey and an adenosine triphosphate (ATP) test. Data were collected from recent hotel guests using Amazon Mechanical Turk. Guests were asked to identify hotel surfaces that they touch most frequently. Actual hotel cleanliness was measured using empirical data collected with ATP meters. The two data sets were used to compare guests’ perceptions about the amount of contact they have with actual cleanliness measurements of those hotel surfaces.

Findings

This study found that amount of guest contact was related to cleanliness of surfaces in guestrooms. Significant differences were found in guest perception between high- and low-touch areas and between guestrooms and hotel public areas. More high-touch areas and higher ATP readings were found in guestrooms than in hotel public areas.

Originality/value

To the best of the authors’ knowledge this study is the first to compare guest contact with hotel surfaces to a scientific measure of hotel cleanliness. In addition, this study is unique because it assesses guest contact and cleanliness of public areas to provide a holistic view of hotel-cleaning needs. The study offers industry empirically based results from guest perception and scientifically based data that can be used to improve hotel housekeeping programs.
Investigating green supply chain management practices and performance
Authors: Cousins Paul D. , Lawson Benn , Petersen Kenneth J. , Fugate Brian
Published: July 2019

Purpose

Sustainable supply chain management has become an increasingly important driver of business performance. Understanding the contingent nature of how performance is improved in this context is therefore a critical task for management. The purpose of this paper is to explore the moderating effects of two practices unique to sustainable supply chain – ecocentricity and supply chain traceability – on a firm’s environmental and operating cost performance.

Design/methodology/approach

Survey data were collected from 248 UK manufacturing firms and analyzed using moderated hierarchical regression.

Findings

The results suggest that green supply chain management (GSCM) practices are associated with improvements in both environmental and cost-based performance. Further, higher levels of ecocentricity and supply chain traceability are associated with stronger relationships between GSCM practices and cost performance. Contrary to expectations, high levels of supply chain traceability were found to negatively moderate the relationship between GSCM practices and environmental performance.

Research limitations/implications

The research design was survey-based and cross-sectional. Future studies would benefit from longitudinal research designs that capture the effects of GSCM practices on performance over an extended period. The survey data is also perceptual; using secondary data to capture environmental performance outcomes, for example, would be another opportunity for future research.

Practical implications

The authors provide additional support to findings that GSCM practices benefit both environmental and cost performance dimensions. In this context, the authors show that investments by firms in working with a broader set of eco-system partners (ecocentricity) and building supply chain traceability and leads to improved environmental sustainability outcomes. The authors encourage managers to carefully consider how they conceptualize and monitor their supply chains.

Originality/value

This paper offers several contributions to the research in this area. First, the authors develop and validate a measurement scale for ecocentricity and supply chain traceability. Second, the authors show how these two variables – unique to sustainable supply chains – can positively influence firm and environmental performance.