bluuebunny/crossref_metadata_2025 huggingface dataset:
A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation inArabidopsis thaliana
Authors: Ghoshal Basudev , Vong Brandon , Picard Colette L. , Suhua Feng , Tam Janet May , Jacobsen Steven E.
Published: July 2020

Plant RNA viruses are used as delivery vectors for their high level of accumulation and efficient spread during virus multiplication and movement. Utilizing this concept, several viral-based guide RNA delivery platforms for CRISPR-Cas9 genome editing have been developed. The CRISPR-Cas9 system has also been adapted for epigenome editing. While systems have been developed for CRISPR-Cas9 based gene activation or site-specific DNA demethylation, viral delivery of guide RNAs remains to be developed for these purposes. To address this gap we have developed a tobacco rattle virus (TRV)-based single guide RNA delivery system for epigenome editing inArabidopsis thaliana. Because tRNA-like sequences have been shown to facilitate the cell-to-cell movement of RNAs in plants, we used the tRNA-guide RNA expression system to express guide RNAs from the viral genome to promote heritable epigenome editing. We demonstrate that the tRNA-gRNA system with TRV can be used for both transcriptional activation and targeted DNA demethylation in Arabidopsis. We achieved up to ~8% heritability of the induced demethylation phenotype in the progeny of virus inoculated plants. We did not detect the virus in the next generation, indicating effective clearance of the virus from plant tissues. Thus, TRV delivery, combined with a specific tRNA-gRNA architecture, provides for fast and effective epigenome editing.

Author summary

The discovery of CRISPR-CAS9 and its non-catalytic variants have provided enormous capacity for crop improvement and basic research by modifying the genome and the epigenome. The standard methods for delivering genome and epigenome editing reagents to plants consist of generating stable transgenic lines through tissue culture processes, which have several drawbacks including the need for plant regeneration and crossing. To overcome some of these challenges, plant virus-based platforms are being developed for genome editing. Although viruses have a limited cargo capacity, limiting the use of viruses to encode entire editing systems, guide RNAs have been successfully delivered to transgenic CAS9 expressing plants for genome editing. However, the use of viruses for CRISPR-based epigenome editing and transcriptional activation have not yet been explored. In this study we show that viral delivery of guide RNAs using a modified tobacco rattle virus can be used for transcriptional activation and heritable epigenome editing. This study advances the use of plant RNA viruses as delivery agents for epigenome editing.
Screening and testing for a suitable untransfected cell line for SARS-CoV-2 studies
Authors: Pommerenke Claudia , Rand Ulfert , Uphoff Cord C. , Nagel Stefan , Zaborski Margarete , Hauer Vivian , Kaufmann Maren , Meyer Corinna , Denkmann Sabine A. , Riese Peggy , Eschke Kathrin , Kim Yeonsu , Safranko Zeljka Macak , Kurolt Ivan-Christian , Markotic Alemka , Brunotte Linda , Ludwig Stephan , Cicin-Sain Luka , Steenpaß Laura
Published: July 2020

At present, the novel pandemic coronavirus SARS-CoV-2 is a major global threat to human health and hence demands united research activities at different levels. Finding appropriate cell systems for drug screening and testing molecular interactions of the virus with the host cell is mandatory for drug development and understanding the mechanisms of viral entry and replication. For this, we selected human cell lines represented in the Cancer Cell Line Encyclopedia (CCLE) based on RNA-seq data determined transcript levels of ACE2 and TMPRSS2, two membrane proteins that have been identified to aid SARS-CoV-2 entry into the host cell. mRNA and protein expression of these host factors were verified via RQ-PCR and western blot. We then tested permissiveness of these cell lines towards SARS-CoV-2 infection, cytopathic effect, and viral replication finding limited correlation between receptor expression and infectability. One of the candidate cancer cell lines, the human colon cancer cell line CL-14, tested positive for SARS-CoV-2 infection. Our data argue that SARS-CoV-2 in vitro infection models need careful selection and validation since ACE2/TMPRSS2 receptor expression on its own does not guarantee permissiveness to the virus.

Author summary

In the midst of the pandemic outbreak of corona-virus SARS-CoV-2 therapeutics for disease treatment are still to be tested and the virus-host-interactions are to be elucidated. Drug testing and viral studies are commonly conducted with genetically manipulated cells. In order to find a cell model system without genetic modification we screened human cell lines for two proteins known to facilitate entry of SARS-CoV-2. We confirmed and quantified permissiveness of current cell line infection models, but dismissed a number of receptor-positive cell lines that did not support viral replication. Importantly, ACE2/TMPRSS2 co-expression seems to be necessary for viral entry but is not sufficient to predict permissiveness of various cancer cell lines. Moreover, the expression of specific splice variants and the absence of missense mutations of the host factors might hint on successful infection and virus replication of the cell lines.
Gradual Compaction of the Central Spindle Decreases its Dynamicity as Revealed in PRC1 and EB1 Gene-Edited Human Cells
Authors: Asthana Jayant , Cade Nicholas I. , Normanno Davide , Lim Wei Ming , Surrey Thomas
Published: July 2020

During mitosis the spindle undergoes morphological and dynamic changes. It reorganizes at the onset of anaphase when the antiparallel bundler PRC1 accumulates and recruits central spindle proteins to the midzone. Little is known about how the dynamic properties of the central spindle change during its morphological changes in human cells. Using gene editing, we generated human cells that express from their endogenous locus fluorescent PRC1 and EB1 to quantify their native spindle distribution and binding/unbinding turnover. EB1 plus end tracking revealed a general slowdown of microtubule growth, while PRC1, similar to its yeast orthologue Ase1, binds increasingly strongly to compacting antiparallel microtubule overlaps. KIF4A and CLASP1 bind more dynamically to the central spindle, but also show slowing down turnover. These results show that the central spindle gradually becomes more stable during mitosis, in agreement with a recent ‘bundling, sliding and compaction’ model of antiparallel midzone bundle formation in the central spindle during late mitosis.
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench
Authors: Emms D.M. , Kelly S.
Published: July 2020

Orthobench is the standard benchmark to assess the accuracy of orthogroup inference methods. It contains 70 expert curated reference orthogroups (RefOGs) that span the Bilateria and cover a range of different challenges for orthogroup inference. Here we leveraged improvements in tree inference algorithms and computational resources to re-interrogate these RefOGs and carry out an extensive phylogenetic delineation of their composition. This phylogenetic revision altered the membership of 31 of the 70 RefOGs, with 24 subject to extensive revision and a further 7 that required minor changes. We further used these revised and updated RefOGs to provide an assessment of the orthogroup inference accuracy of widely used orthogroup inference methods. Finally, we provide an open-source benchmarking suite to support the future development and use of the Orthobench benchmark.

Significance statement

Orthogroup inference forms the foundation of comparative genomic analysis. Benchmarks to evaluate performance are essential to enable these methods to be compared and stimulate further method development. Here we present an update to the orthobench benchmark database and provide a comparative performance evaluation of commonly used orthogroup inference methods.
Transcriptomically-inferred PI3K activity and stemness show a counterintuitive correlation withPIK3CAgenotype in breast cancer
Authors: Madsen Ralitsa R. , Rueda Oscar M. , Robin Xavier , Caldas Carlos , Semple Robert K. , Vanhaesebroeck Bart
Published: July 2020

A PI3Kα-selective inhibitor has recently been approved for use in breast tumours harbouring mutations inPIK3CA, the gene encoding PI3Kα. Preclinical studies have suggested that the PI3K/AKT/mTORC1 signalling pathway influences stemness, a dedifferentiation-related cellular phenotype associated with aggressive cancer. No direct evidence for such a correlation has been demonstrated to date in human tumours. In two independent human breast cancer cohorts, encompassing nearly 3,000 tumour samples, transcriptional footprint-based analysis uncovered a positive linear association between transcriptionally-inferred PI3K signalling scores and stemness scores. Unexpectedly, stratification of tumours according toPIK3CAgenotype revealed a “biphasic” relationship of mutantPIK3CAallele dosage with these scores. Relative to tumour samples withoutPIK3CAmutations, the presence of a single copy of a hotspotPIK3CAvariant was associated with lower PI3K signalling and stemness scores, whereas tumours with multiple copies ofPIK3CAhotspot mutations showed higher PI3K signalling and stemness scores. This observation was recapitulated in a human cell model of heterozygous and homozygousPIK3CAH1047Rexpression. Collectively, our analysis provides evidence for a signalling strength-dependent PI3K-stemness relationship in human breast cancer, which may aid future patient stratification for PI3K-targeted therapies.
Excitation-contraction coupling and its relation to synaptic dysfunction in Drosophila
Authors: Ormerod Kiel G. , Scibelli Anthony E. , Littleton J. Troy
Published: July 2020

The Drosophila neuromuscular system is widely used to characterize synaptic development and function. However, little is known about how specific synaptic deficits alter neuromuscular transduction and muscle contractility that ultimately dictate behavioural output. Here we develop a system for detailed characterization of excitation-contraction coupling at Drosophila larval NMJs and demonstrate how specific synaptic and neuronal manipulations disrupt muscle contractility. Muscle contraction force increases with motoneuron stimulation frequency and duration, showing considerable plasticity between 5-40 Hz, while saturating above 50 Hz. Temperature is negatively correlated with muscle performance and enhanced at lower temperatures. A screen for modulators of muscle contractility led to the identification and characterization of the molecular and cellular pathway by which a specific FMRFa peptide, TPAEDFMRFa, increases muscle performance. These findings indicateDrosophilaNMJs provide a robust system to relate synaptic dysfunction to alterations in excitation-contraction coupling.
Crash simulation of fuselage section in the rebound process and the secondary-impact process
Authors: Jin Zibo , Li Daochun , Xiang Jinwu
Published: July 2020

Purpose

This paper aims to investigate the rebound process and the secondary-impact process of the fuselage section that occurs in the actual crash events.

Design/methodology/approach

A full-scale three-dimensional finite element model of the fuselage section was developed to carry out the dynamic simulations. The rebound process was simulated by removing the impact surface at a certain point, while the secondary-impact process was simulated by striking the impact surface against the fuselage bottom after the first impact.

Findings

For the rebound process, the fuselage structure restores deformation due to the springback of the fuselage bottom, and it results in structural vibration of the fuselage section. For the secondary-impact process, the fuselage deformation is similar with that of the single impact process, indicating that the intermittent impact loading has little influence on the overall deformation of the fuselage section. The strut failure is the determining factor to the acceleration responses for both the rebound process and the secondary-impact process.

Practical implications

The rebound process and the secondary-impact process, which is difficult to study by experiments, was investigated by finite element simulations. The structure deformations and acceleration responses were obtained, and they can provide guidance for the crashworthy design of fuselage structures.

Originality/value

This research first investigated the rebound process and the secondary-impact process of the fuselage section. The absence of the ground load and the secondary-impact was simulated by controlling the impact surface, which is a new simulating method and has not been used in the previous research.
Deregulation, technical efficiency and production risk in rice farming: evidence from Zhejiang Province, China
Authors: Wang Juanli , Etienne Xiaoli , Ma Yongxi
Published: July 2020

Purpose

The purpose of this paper is to evaluate the technical efficiency and production risk in China's rice production and examine the effect of factor market reform on these two agricultural performance metrics.

Design/methodology/approach

Using an unbalanced farm-level panel data with 2,193 observations on 329 rice farms from 2004 to 2016, the authors estimate a translog stochastic production frontier model that accounts for both technical inefficiency and production risk. A one-step procedure through the maximum likelihood method that combines the stochastic production frontier, technical inefficiency and production risk functions is used to circumvent the bias problem often found in the conventional two-step model.

Findings

Estimation results show that both land and labor market reforms significantly improved the level of technical efficiency over the years, although the effect of land market deregulation is of a much higher magnitude compared to the latter. The land market reform, however, has also increased the risk of production. The authors further find that a higher proportion of hired labor in total labor cost helps lower production risk, while also acting to decrease technical efficiency. Additionally, agricultural subsidies not only increased the output variability but also lowered technical efficiency

Originality/value

First, the authors evaluate the effect of market deregulation on technical efficiency and production risk under a stochastic frontier framework that simultaneously accounts for both production performance metrics, which is important from a statistical point of view. Further, the authors exploit both cross-sectional and time-series variations in a panel setting to more accurately estimate the technical inefficiency scores and production risk for individual farmers, and investigate how the exogenous land and labor market reforms influence these two production performance measures in China's rice farming. This is the first study in the literature to analyze these questions under a panel framework.
Supervisees’ reactions to a concatenation of supervisors’ resource drain, ego depletion and abusive supervision
Authors: Malik Annam Hanif , Iqbal Muhammad Zahid , Ul Haq Mian Imran
Published: July 2020

Purpose

While integrating resource drain theory with ego depletion theory, this paper aims to understand the mechanism underlying the relationship between research supervisors’ interrole conflicts and their supervisees’ reactions. Specifically, this paper makes a case for supervisors’ ego depletion and supervisees’ perception of abusive supervision to mediate the relationship between supervisors’ work and family conflicts and supervisees’ satisfaction with research supervision.

Design/methodology/approach

The study uses data collected in three waves from 306 research supervisees (Level 1) nested in 100 research supervisors (Level 2), involved in MS/PhD research theses at different Pakistani universities.

Findings

Based on multilevel modeling, the study finds that supervisors’ interrole conflicts negatively predict supervisees’ satisfaction with supervision. Moreover, supervisors’ ego depletion and supervisees’ perception of abusive supervision mediate the above relationship, both singly and serially. Notably, supervisors’ family–work conflict predicts supervisees’ satisfaction with supervision more negatively than work–family conflict.

Originality/value

This study is unique in that unlike previous research studies on abusive supervision which used victimization approach the present study uses the perpetration approach.
A generalized framework for AMOVA with multiple hierarchies and ploidies
Authors: HUANG Kang , WANG Tiantian , DUNN Derek W. , ZHANG Pei , SUN Hongjuan , LI Baoguo
Published: July 2020

The analysis of molecular variance (AMOVA) is a widely used statistical method in population genetics and molecular ecology. The classic framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in extant species. The ploidy level may even vary within the same species, and/or within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for data that are multilocus genotypic and allelic phenotypic (with unknown allele dosage). We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a new software package, polygene, which is freely available at https://github.com/huangkang1987/polygene.
Development of an App to Facilitate Communication and Shared Decision‐making With Parents of Febrile Infants ≤ 60 Days Old
Authors: Aronson Paul L. , Politi Mary C. , Schaeffer Paula , Fleischer Eduardo , Shapiro Eugene D. , Niccolai Linda M. , Alpern Elizabeth R. , Bernstein Steven L. , Fraenkel Liana
Published: July 2020

Objectives

We aimed to develop and test a tool to engage parents of febrile infants ≤ 60 days of age evaluated in the emergency department (ED). The tool was designed to improve communication for all parents and to support shared decision‐making (SDM) about whether to perform a lumbar puncture (LP) for infants 29 to 60 days of age.

Methods

We conducted a multiphase development and testing process: 1) individual, semistructured interviews with parents and clinicians (pediatric and general emergency medicine [EM] physicians and pediatric EM nurses) to learn their preferences for a communication and SDM tool; 2) design of a “storyboard” of the tool with design impression testing; 3) development of a software application (i.e., app) prototype, called e‐Care; and 4) usability testing of e‐Care, using qualitative assessment and the system usability scale (SUS).

Results

We interviewed 27 parents and 23 clinicians. Interviews revealed several themes, including that a communication tool should augment but not replace verbal communication; a Web‐based format was preferred; and information about infections and testing, including the rationales for specific tests, would be valuable. We then developed separate versions of e‐Care for infants ≤ 28 days and 29 to 60 days of age, in both English and Spanish. The e‐Care app includes four sections: 1) homepage; 2) why testing is done; 3) what tests are done; and 4) what happens after testing, including a table for parents of infants 29 to 60 days of age to compare the risks/benefits of LP in preparation for an SDM conversation. Parents and clinicians reported that e‐Care was understandable and helpful. The mean SUS score was 90.3 (95% confidence interval = 84 to 96.6), representing “excellent” usability.

Conclusions

The e‐Care app is a useable and understandable tool to support communication and SDM with parents of febrile infants ≤ 60 days of age in the ED.
Prevalence and correlates of receipt by smokers of general practitioner advice on smoking cessation in England: a cross‐sectional survey of adults
Authors: Jackson Sarah E. , Garnett Claire , Brown Jamie
Published: July 2020

Background and Aims

Advice from a general practitioner (GP) can encourage smokers to quit. This study aimed to estimate the prevalence and correlates of receipt of GP advice on smoking, what type of advice and support was offered and characteristics and quitting activity associated with different types of advice.

Design/setting

Data were collected between 2016 and 2019 in a series of monthly cross‐sectional surveys of representative samples of the adult population in England.

Participants

A total of 11 588 past‐year smokers.

Measurements

Participants reported whether they had received advice or offer of support for smoking cessation from their GP in the last year. Socio‐demographic and behavioural characteristics and past‐year quit attempts and cessation were also recorded.

Findings

One in two [47.2%, 95% confidence interval (CI) = 46.1–48.3%] past‐year smokers who reported visiting their GP in the last year recalled receiving advice on smoking, and one in three (30.1%, 95% CI = 29.1–31.1%) reported being offered cessation support. The most common form of support offered was stop smoking services (16.5%, 95% CI = 15.7–17.3%) followed by prescription medication (8.1%, 95% CI = 7.5–8.7%); 3.7% (95% CI = 3.3–4.1%) reported having been recommended to use e‐cigarettes. Smokers who were older, non‐white, more addicted, and smoked five or more cigarettes/day had consistently higher odds of receiving advice or support. There were some differences by region, housing tenure, presence of children in the home and high‐risk drinking in the types of advice/support received. There were no significant differences by sex, occupational social grade, disability, type of cigarettes smoked, or survey year. Advice with any offer of support was associated with higher odds of attempting to quit than advice alone [adjusted odds ratio (ORadj) = 1.52, 95% CI = 1.30–1.76]. Advice alone was associated with higher odds of quit attempts than no advice in smokers with higher (ORadj = 1.34, 95% CI = 1.10–1.64) but not lower occupational social grade (ORadj = 0.90, 95% CI = 0.75–1.08).

Conclusions

In England, a minority of smokers receive support from their GP to stop smoking. Those who do are more likely to be older, non‐white and more addicted to cigarettes. Advice plus offer of support appears to be associated with increased odds of making a quit attempt, while advice without offer of support appears only to be associated with increased odds of making a quit attempt in higher occupational social grade smokers.
Dual‐trajectories of opioid and gabapentinoid use and risk of subsequent drug overdose among Medicare beneficiaries in the United States: a retrospective cohort study
Authors: Zhou Lili , Bhattacharjee Sandipan , Kwoh C. Kent , Tighe Patrick J. , Reisfield Gary M. , Malone Daniel C. , Slack Marion , Wilson Debbie L. , Chang Ching‐Yuan , Lo‐Ciganic Wei‐Hsuan
Published: July 2020

Background and aims

Little is known about opioid and gabapentinoid (OPI‐GABA) use duration and dose patterns’ associations with adverse outcome risks. We examined associations between OPI‐GABA dose and duration trajectories and subsequent drug overdose.

Design

Retrospective cohort study.

Setting

US Medicare.

Participants

Using a 5% sample (2011–16), we identified 71 005 fee‐for‐service Medicare beneficiaries with fibromyalgia, low back pain, neuropathy and/or osteoarthritis initiating OPIs and/or GABAs [mean age ± standard deviation (SD) = 65.5 ± 14.5 years, female = 68.1%, white = 76.8%].

Measurements

Group‐based multi‐trajectory models identified distinct OPI‐GABA use patterns during the year of OPI and/or GABA initiation, based on weekly average standardized daily dose (i.e. OPIs = morphine milligram equivalent, GABAs = minimum effective daily dose). We estimated models with three to 12 trajectories and selected the best model based on Bayesian information criterion (BIC) and Nagin's criteria. We estimated risk of time to first drug overdose diagnosis within 12 months following the index year, adjusting for socio‐demographic and health factors using inverse probability of treatment weighted multivariable Cox proportional hazards models.

Findings

We identified 10 distinct trajectories (BIC = –1 176 954; OPI‐only = 3, GABA‐only = 3, OPI‐GABA = 4). Compared with OPI‐only early discontinuers (40.6% of the cohort), 1‐year drug overdose risk varied by trajectory group: consistent low‐dose OPI‐only users [16.6%; hazard ratio (HR) = 1.47, 95% confidence interval (CI) = 1.19–1.82], consistent high‐dose OPI‐only users (1.8%; HR = 4.57, 95% CI = 2.99–6.98), GABA‐only early discontinuers (12.5%; HR = 1.39, 95% CI = 1.09–1.77), consistent low‐dose GABA‐only users (11.0%; HR = 1.44, 95% CI = 1.12–1.85), consistent high‐dose GABA‐only users (3.1%; HR = 1.43, 95% CI = 0.94–2.17), early discontinuation of OPIs and consistent low‐dose GABA users (6.9%; HR = 1.24, 95% CI = 0.90–1.69), consistent low‐dose OPI‐GABA users (3.4%; HR = 2.49, 95% CI = 1.76–3.52), consistent low‐dose OPI and high‐dose GABA users (3.2%; HR = 2.46, 95% CI = 1.71–3.53) and consistent high‐dose OPI and moderate‐dose GABA users (0.9%; HR = 7.22, 95% CI = 4.46–11.69).

Conclusions

Risk of drug overdose varied substantially among US Medicare beneficiaries on different use trajectories of opioids and gabapentinoids. High‐dose opioid‐only users and all consistent opioid and gabapentinoid users (regardless of doses) had more than double the risk of subsequent drug overdose compared with opioid‐only early discontinuers.
Brefeldin A inhibits clathrin‐dependent endocytosis and ion transport in Chara internodal cells
Authors: Foissner Ilse , Hoeftberger Margit , Hoepflinger Marion C. , Sommer Aniela , Bulychev Alexander A.
Published: July 2020

Background

The Characeae are multicellular green algae, which are closely related to higher plants. Their internodal cells are a convenient model to study membrane transport and organelle interactions.

Results

In this study, we report on the effect of brefeldin A (BFA), an inhibitor of vesicle trafficking, on internodal cells of Chara australis. BFA induced the commonly observed agglomeration of Golgi bodies and trans Golgi network into ‘brefeldin compartments’ at concentrations between 6 and 500 μM and within 30–120 min treatment. In contrast to most other cells, however, BFA inhibited endocytosis and significantly decreased the number of clathrin‐coated pits and clathrin‐coated vesicles at the plasma membrane. BFA did not inhibit secretion of organelles at wounds induced by puncturing or local light damage but prevented the formation of cellulosic wound walls probably because of insufficient membrane recycling. We also found that BFA inhibited the formation of alkaline and acid regions along the cell surface (‘pH banding pattern’) which facilitates carbon uptake required for photosynthesis; we hypothesise that this is due to insufficient recycling of ion transporters. During long‐term treatments over several days, BFA delayed the formation of complex 3D plasma membranes (charasomes). Interestingly, BFA had no detectable effect on clathrin‐dependent charasome degradation. Protein sequence analysis suggests that the peculiar effects of BFA in Chara internodal cells are due to a mutation in the guanine‐nucleotide exchange factor GNOM required for recruitment of membrane coats via activation of ADP‐ribosylation factor proteins.

Conclusions and Significance

This work provides an overview on the effects of BFA on different processes in C. australis. It revealed similarities but also distinct differences in vesicle trafficking between higher plant and algal cells. It shows that characean internodal cells are a promising model to study interactions between seemingly distant metabolic pathways.
Effective ecosystem monitoring requires a multi‐scaled approach
Authors: Sparrow Ben D. , Edwards Will , Munroe Samantha E.M. , Wardle Glenda M. , Guerin Greg R. , Bastin Jean‐Francois , Morris Beryl , Christensen Rebekah , Phinn Stuart , Lowe Andrew J.
Published: July 2020

Ecosystem monitoring is fundamental to our understanding of how ecosystem change is impacting our natural resources and is vital for developing evidence‐based policy and management. However, the different types of ecosystem monitoring, along with their recommended applications, are often poorly understood and contentious. Varying definitions and strict adherence to a specific monitoring type can inhibit effective ecosystem monitoring, leading to poor program development, implementation and outcomes. In an effort to develop a more consistent and clear understanding of ecosystem monitoring programs, we here review the main types of monitoring and recommend the widespread adoption of three classifications of monitoring, namely, targeted, surveillance and landscape monitoring. Landscape monitoring is conducted over large areas, provides spatial data, and enables questions relating to where and when ecosystem change is occurring to be addressed. Surveillance monitoring uses standardised field methods to inform on what is changing in our environments and the direction and magnitude of that change, whilst targeted monitoring is designed around testable hypotheses over defined areas and is the best approach for determining the causes of ecosystem change. The classification system is flexible and can incorporate different interests, objectives, targets and characteristics as well as different spatial scales and temporal frequencies, while also providing valuable structure and consistency across distinct ecosystem monitoring programs. To support our argument, we examine the ability of each monitoring type to inform on six key types of questions that are routinely posed for ecosystem monitoring programs, such as where and when change is occurring, what is the magnitude of change, and how can the change be managed? As we demonstrate, each type of ecosystem monitoring has its own strengths and weaknesses, which should be carefully considered relative to the desired results. Using this scheme, scientists and land managers can design programs best suited to their needs. Finally, we assert that for our most serious environmental challenges, it is essential that we include information from each of these monitoring scales to inform on all facets of ecosystem change, and this is best achieved through close collaboration between the scales. With a renewed understanding of the importance of each monitoring type, along with greater commitment to monitor cooperatively, we will be well placed to address some of our greatest environmental challenges.
Strength prediction of paste filling material based on convolutional neural network
Authors: Cheng Haigen , Hu Junjian , Hu Chen , Deng Fangming
Published: July 2020

The common backfill mining technology in the green mining industry can be used for the secondary utilization of construction waste in smart cities. This measure has the advantages of low cost, fast results, and less environmental pollution. Over the past few decades, with the continuous advancement of global urbanization, the effective and environmentally friendly construction waste disposal and emission are very important for the development of urban green construction. Construction waste can be prepared as paste filling material, as one of the raw materials for backfill mining. This paper proposes a new method that can quickly and accurately predict the strength of paste filling materials with different compositions. A deep connected convolutional neural network (CNN) that can extract input parameters is used to build a prediction model. The coarse aggregate, fine aggregate, and cementing material are employed as the input variables of the CNN model, and five indicators which are generally used to evaluate the strength of filling material are selected as the output results. The experimental results show that the proposed prediction approach can obtain robust prediction results and high prediction accuracy and speed.
Verification of differentially expressed genes in relation to hydrostatic pressure in the brain of two wrasse species with high‐tide preference in spawning
Authors: Udagawa Shingo , Hur Sung‐Pyo , Byun Jun‐Hwan , Takekata Hiroki , Takeuchi Yuki , Takemura Akihiro
Published: July 2020

Fish that inhabit shallow water are exposed to periodic changes in tidal cues, including hydrostatic pressure (HP). The present study aimed at verifying differentially expressed genes (DEGs) in the brain of the threespot wrasse Halichoeres trimaculatus (tropical species) and the honbera wrasse Halichoeres tenuispinis (temperate species), both of which were exposed to HP at 30 kPa (possible high‐tide stimuli in the field) or 1 kPa (low tide) for 3 or 6 h. A de novo assembly yielded 174,710 contigs (63,530 contigs were annotated) from the brain of threespot wrasse. Following RNA sequencing, quantitative PCR confirmed DEGs that were upregulated [AT atypical cadherin 2 (FAT2)] and downregulated [neuronal leucine‐rich repeat protein 3 (LRRN3), dual specificity tyrosine phosphorylation‐regulated kinase 1 (DYRK), mitogen‐activated protein kinase kinase 1 (MAP2K1) and phosphoinositide 3 kinase (PI3K)]. The effect of HP on the transcription of these DEGs (except for MAP2K1) disappeared within 6 h, suggesting that HP is a transitory stimulus occurring at the beginning of the tidal cycle. Similar DEG transcription was observed in the brain of honbera wrasse maintained under HP for 6 h. In situ hybridization of the brain of the threespot wrasse revealed that strong signals of MPA2K1 were seen in the telencephalon, diencephalon and pituitary, whereas those of PI3K were seen in the telencephalon, diencephalon and medulla oblongata. This result suggests that these kinases are involved in sensory function (telencephalon), somatic and visceral function (medullar oblongata) and the neuroendocrine system (diencephalon and pituitary), all of which were related to changes in HP stimuli. Following HP exposure, the transcription of c‐fos increased in the pituitary of honbera wrasse, suggesting that external stimuli directly or indirectly activate hormone synthesis at the hypothalamic–pituitary–gonadal axis. It is concluded that HP alters gene expression in relation to neural development and function in the central nervous system and plays a role in exerting tidal‐related reproduction and feeding in wrasses.
Three‐finger proteins from snakes and humans acting on nicotinic receptors: Old and new
Authors: Tsetlin Victor I. , Kasheverov Igor E. , Utkin Yuri N.
Published: July 2020

The first toxin to give rise to the three‐finger protein (TFP) family was α‐bungarotoxin (α‐Bgt) from Bungarus multicinctus krait venom. α‐Bgt was crucial for research on nicotinic acetylcholine receptors (nAChRs), and in this Review article we focus on present data for snake venom TFPs and those of the Ly6/uPAR family from mammalians (membrane‐bound Lynx1 and secreted SLURP‐1) interacting with nAChRs. Recently isolated from Bungarus candidus venom, αδ‐bungarotoxins differ from α‐Bgt: they bind more reversibly and distinguish two binding sites in Torpedo californica nAChR. Naja kaouthia α‐cobratoxin, classical blocker of nAChRs, was shown to inhibit certain GABA‐A receptor subtypes, whereas α‐cobratoxin dimer with 2 intermolecular disulfides has a novel type of 3D structure. Non‐conventional toxin WTX has additional 5th disulfide not in the central loop, as α‐Bgt, but in the N‐terminal loop, like all Ly6/uPAR proteins, and inhibits α7 and Torpedo nAChRs. A water‐soluble form of Lynx1, ws‐Lynx1, was expressed in E. coli, its 1H‐NMR structure and binding to several nAChRs determined. For SLURP‐1, similar information was obtained with its recombinant analogue rSLURP‐1. A common feature of ws‐Lynx1, rSLURP‐1, and WTX is their activity against nAChRs and muscarinic acetylcholine receptors. Synthetic SLURP‐1, identical to the natural protein, demonstrated some differences from rSLURP‐1 in distinguishing nAChR subtypes. The loop II fragment of the Lynx1 was synthesized having the same µM affinity for the Torpedo nAChR as ws‐Lynx1. This review illustrates the productivity of parallel research of nAChR interactions with the two TFP groups.

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Inalienable Customer Capital, Corporate Liquidity, and Stock Returns
Authors: DOU WINSTON WEI , JI YAN , REIBSTEIN DAVID , WU WEI
Published: July 2020

We develop a model in which customer capital depends on key talents' contribution and pure brand recognition. Customer capital guarantees stable demand but is fragile to financial constraints risk if retained mainly by talents, who tend to quit financially constrained firms, damaging customer capital. Using a proprietary, granular brand‐perception survey, we construct a firm‐level measure of the inalienability of customer capital (ICC) that captures the degree to which customer capital depends on talents. Firms with higher ICC have higher average returns, higher talent turnover, and more precautionary financial policies. The ICC‐sorted long‐short portfolio's spread comoves with financial constraints factor.
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Authors: Chiang Ka‐Yan , Lui Macy Mei‐Sze
Published: July 2020

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Arresting Confidence: Mass Incarceration and Black–White Differences in Perceptions of Legal Authorities
Authors: O'Brien Timothy L.
Published: July 2020

Objective

This article investigates changes in confidence in legal authorities associated with mass incarceration.

Methods

Binary logistic regression models are used to analyze five waves of data from a national survey of U.S. adults collected between 1981 and 2011 (n= 8,548). Predicted probabilities and discrete change coefficients are calculated to examine changes in blacks’ and whites’ attitudes about police and courts associated with changes in the incarceration rate.

Results

As the incarceration rate grew, blacks’ confidence in police declined substantially, while whites’ was unchanged. Blacks and whites each lost confidence in courts as incarceration increased. However, the loss was significantly greater among blacks than whites.

Conclusions

The growing incarceration rate was accompanied by distinctive shifts in blacks’ and whites’ confidence in legal authorities. This article underscores the importance of macro legal contexts for understanding race differences in legal confidence.
Effect of Chitosan Microparticles on the Uterine Microbiome of Dairy Cows with Metritis
Authors: Galvão Klibs N. , de Oliveira Eduardo B. , Cunha Federico , Daetz Rodolfo , Jones Kristi , Ma Zhengxin , Jeong Kwangcheol C. , Bicalho Rodrigo C. , Higgins Catherine H. , Rodrigues Marjory X. , Gonzalez Moreno Candelaria , Jeon Soojin
Published: July 2020

Third-generation cephalosporins, such as ceftiofur, are commonly used to treat metritis in dairy cows. Chitosan microparticles has been shown to have a broad spectrum of activity
in vitro
and to be effective against uterine pathogens
in vivo
; therefore, they have been hailed as a possible alternative to traditional antibiotics. Nonetheless, in the present study, we saw that chitosan microparticle treatment slowed the progression of the uterine microbiome of cows with metritis toward a healthy state, whereas ceftiofur treatment hastened the progression toward a healthy state. Given the lack of an effective alternative to traditional antibiotics and an increased concern about antimicrobial resistance, a greater effort should be devoted to the prevention of metritis in dairy cows.
Oral or Topical Exposure to Glyphosate in Herbicide Formulation Impacts the Gut Microbiota and Survival Rates of Honey Bees
Authors: Motta Erick V. S. , Mak Myra , De Jong Tyler K. , Powell J. Elijah , O'Donnell Angela , Suhr Kristin J. , Riddington Ian M. , Moran Nancy A.
Published: July 2020

The honey bee gut microbial community plays a vital role in immune response and defense against opportunistic pathogens. Environmental stressors, such as the herbicide glyphosate, may affect the gut microbiota, with negative consequences for bee health. Glyphosate is usually sprayed in the field mixed with adjuvants, which enhance herbicidal activity. These adjuvants may also enhance undesired effects in nontargeted organisms. This seems to be the case for glyphosate-based herbicide on honey bees. As we show in this study, oral exposure to either pure glyphosate or glyphosate in a commercial herbicide formulation perturbs the gut microbiota of honey bees, and topical exposure to the formulation also has a direct effect on honey bee health, increasing mortality in a dose-dependent way and leaving surviving bees with a perturbed microbiota. Understanding the effects of herbicide formulations on honey bees may help to protect these important agricultural pollinators.
Immunization against Anaplasma phagocytophilum Adhesin Binding Domains Confers Protection against Infection in the Mouse Model
Authors: Naimi Waheeda A. , Gumpf Jacob J. , Green Ryan S. , Izac Jerilyn R. , Zellner Matthew P. , Conrad Daniel H. , Marconi Richard T. , Martin Rebecca K. , Carlyon Jason A.
Published: July 2020

Anaplasma phagocytophilum
causes granulocytic anaplasmosis, a debilitating infection that can be fatal in the immunocompromised. It also afflicts animals, including dogs, horses, and sheep. No granulocytic anaplasmosis vaccine exists. Because
A. phagocytophilum
is an obligate intracellular bacterium, inhibiting microbe-host cell interactions that facilitate invasion can disrupt infection. The binding domains of
A. phagocytophilum
adhesins
A. phagocytophilum
invasion protein A (AipA),
A. phagocytophilum
surface protein (Asp14), and outer membrane protein A (OmpA) are essential for optimal bacterial entry into host cells, but their relevance to infection
in vivo
is undefined.
The Great ESKAPE: Exploring the Crossroads of Bile and Antibiotic Resistance in Bacterial Pathogens
Authors: Gipson Kevin S. , Nickerson Kourtney P. , Drenkard Eliana , Llanos-Chea Alejandro , Dogiparthi Snaha Krishna , Lanter Bernard B. , Hibbler Rhianna M. , Yonker Lael M. , Hurley Bryan P. , Faherty Christina S.
Published: July 2020

Throughout the course of infection, many pathogens encounter bactericidal conditions that threaten the viability of the bacteria and impede the establishment of infection. Bile is one of the most innately bactericidal compounds present in humans, functioning to reduce the bacterial burden in the gastrointestinal tract while also aiding in digestion. It is becoming increasingly apparent that pathogens successfully resist the bactericidal conditions of bile, including bacteria that do not normally cause gastrointestinal infections.
Dural arteriovenous fistula presenting with dementia and bulbar symptoms
Authors: Hall Christiana Avye , Swienton David , Taleti Esteban Luis
Published: July 2020

Dural arteriovenous fistulas are relatively rare. Some cases are difficult to diagnose, leading to unnecessary investigations, treatments and delays, particularly if the presentation is atypical. We report a case of a man who presented with progressive dementia and bulbar symptoms, both under-recognised non-haemorrhagic neurological deficits, caused by cortical venous hypertension. Brain imaging showed unusual bilateral thalamic, tectal plate and midbrain oedema. The patient was investigated and treated for alternative aetiologies, before being correctly diagnosed and managed using angiographic embolisation. His clinical and radiological signs improved significantly following treatment, reducing his risk of neurological morbidity and mortality.
Evidence of genetic differentiation in cigar wrasseCheilio inermis(Labridae) within the western Indian Ocean
Authors: Mayekiso Sisanda , Gouws Gavin , Mwale Monica , Gon Ofer
Published: July 2020

Patterns of genetic structure and connectivity of the monotypic cigar wrasse Cheilio inermis within western Indian Ocean (WIO) are poorly understood. Whether the species exists as a single panmictic population across the WIO is unclear. Sequence data were generated from two mitochondrial genes (cytochrome b and ATPase 6) and one nuclear intron (S7 intron I). High levels of haplotype and allelic diversity (h = 0.88–0.98; A = 0.95–0.98), along with low nucleotide diversities were observed across all markers. The pairwise ΦSTvalues indicated differentiation of Tanga from the four WIO localities (Inhaca, Nosy Bé, Gazi, and Shimoni), as well as differentiation between the northernmost WIO localities. AMOVAs indicated high differentiation among defined locality groups, whereas nuclear gene analysis found little differentiation among groups. The observed genetic differentiation in C. inermis could be caused by oceanic barriers, and by limited larval dispersal with the pelagic larvae possibly settling near their parental origin and promoting differentiation.
Prediction of peak and termination of novel coronavirus COVID-19 epidemic in Iran
Authors: Rafieenasab Sepehr , Zahiri Amir-Pouyan , Roohi Ehsan
Published: July 2020

The growth and development of COVID-19 transmission have significantly attracted the attention of many societies, particularly Iran, that have been struggling with this contagious, infectious disease since late February 2020. In this study, the known “Susceptible-Infectious-Recovered (SIR)” and some other mathematical approaches were used to investigate the dynamics of the COVID-19 epidemic to provide a suitable assessment of the COVID-19 virus epidemic in Iran. The epidemic curve and SIR model parameters were obtained with the use of Iran’s official data. The recovered people were considered alongside the official number of confirmed victims as the reliable long-time statistical data. The results offer important predictions of the COVID-19 virus epidemic such as the realistic number of victims, infection rate, peak time and other characteristics. Besides, the effectiveness of infection and immunization rates to the number of infected people and epidemic end time are reported. Finally, different suggestions for decreasing victims are offered.
COVID-19 cases in countries and territories at onset days as function of external tourism inflows
Authors: Hernández-Casildo J. , Hernández-Ramírez E. , del Castillo-Escribano M. , Ruiz-Gayosso J. A. , del Castillo-Mussot M. , Riascos A. P.
Published: July 2020

In every country except China, COVID-19 first infection cases were imported by travelers, which are either people coming back to their own country or visiting foreigners (international or external tourists). In a global and regional phenomenological analysis of COVID-19 spread, we assume that tourism inflow is a trigger mechanism of worldwide dissemination at the pandemic onset days. Taking into account all countries, a convenient common-time origin timeline was employed as if the beginning of the epidemic would have occurred simultaneously in every country. We obtained very good statistical Pearson and Spearman correlations between accumulated infected cases by country and a positive power of the product [Formula: see text], where [Formula: see text] is the tourism inflow before the pandemic and [Formula: see text] is the country population.
Molecular simulation of the adsorption characteristics of H2S in calcite slit-like pores
Authors: Yan Fei , Que Yi , Li Mao-Xiang , Wang Qiang
Published: July 2020

Hydrogen sulfide (H2S) in acid gas reservoirs is an important source of sulfur deposition in rock reservoirs. Studying the adsorption behavior of H2S in calcite slit-like pore is of great significance for predicting the amount of sulfur in natural gas. In this paper, the grand canonical Monte Carlo (GCMC) method is used to investigate the adsorption of H2S in calcite with slit-like pore. Moreover, the effects of different pressures, temperatures and pore sizes on the adsorption characteristics are discussed. The results showed that the adsorption of H2S goes up with the increasing of the pressure and gradually reaches a saturation level. And the adsorption of H2S decreases with the increasing of the temperature. The excess adsorption of H2S first increases and then decreases with the increasing of the pressure. The effect of the size on the excess adsorption capacity changes with the pressure. Meanwhile, the peak of the adsorbate near the surface of the adsorbent shows a nonmonotonic trend with the pressure.