bluuebunny/crossref_metadata_2025 huggingface dataset:
Pilot study of EVIDENCE: High diagnostic yield and clinical utility of whole exome sequencing using an automated interpretation system for patients with suspected genetic disorders
Authors: Seo Go Hun , Kim Taeho , Park Jung-young , Lee Jungsul , Kim Sehwan , Won Dhong-gun , Oh Arum , Lee Yena , Choi In Hee , Choi Jeongmin , Lee Hajeong , Kang Hee Gyung , Cho Hee Yeon , Cho Min Hyun , Kim Yoon Jeon , Yoon Young Hee , Eun Baik-Lin , Desnick Robert J , Keum Changwon , Lee Beom Hee
Published: May 2019

Purpose

EVIDENCE, an automated interpretation system, has been developed to facilitate the entire process of whole exome sequencing (WES) analyses. This study investigated the diagnostic yield of EVIDENCE in patients suspected genetic disorders.

Methods

DNA from 330 probands (age range, 0–68 years) with suspected genetic disorders were subjected to WES. Candidate variants were identified by EVIDENCE and confirmed by testing family members and/or clinical reassessments.

Results

The average number of overlapping organ categories per patient was 4.5 ± 5.0. EVIDENCE reported a total 244 variants in 215 (65.1%) of the 330 probands. After clinical reassessment and/or family member testing, 196 variants were identified in 171 probands (51.8%), including 115 novel variants. These variants were confirmed as being responsible for 146 genetic disorders. One hundred-seven (54.6%) of the 196 variants were categorized as pathogenic or likely pathogenic before, and 146 (74.6%) after, clinical assessment and/or family member testing. Factors associated with a variant being confirmed as causative include rules, such as PVS1, PS1, PM1, PM5, and PP5, and similar symptom scores between that variant and a patient’s phenotype.

Conclusion

This new, automated variant interpretation system facilitated the diagnosis of various genetic diseases with a 51% improvement in diagnostic yield.
Using selection by non-antibiotic stressors to sensitize bacteria to antibiotics
Authors: Maltas Jeff , Krasnick Brian , Wood Kevin B.
Published: May 2019

ABSTRACT

Bacterial resistance to one antibiotic is frequently accompanied by crossresistance to other drugs. Similarly, non-antibiotic selective forces, from biocides to osmotic stress, have been shown to decrease antibiotic susceptibility, often the result of shared, non-specific resistance mechanisms. On the other hand, evolved resistance to particular antibiotics may also be associated with increased sensitivity to other drugs, highlighting evolutionary constraints that could form the basis for novel anti-resistance strategies. While recent studies indicate this collateral sensitivity is common between antibiotics, much less is known about potentially sensitizing effects of non-antibiotic stressors. In this study, we use laboratory evolution to investigate adaptation of E. faecalis, an opportunistic bacterial pathogen, to a broad collection of environmental agents, ranging from antibiotics and biocides to extreme pH and osmotic stress. We find that non-antibiotic selection frequently leads to increased sensitivity to other conditions, including multiple antibiotics. Using population sequencing and whole genome sequencing of single isolates from the evolved populations, we identify multiple mutations in genes previously linked with resistance to the selecting conditions, including genes corresponding to known drug targets or multi-drug efflux systems previously tied to collateral sensitivity. Finally, we hypothesized based on the measured sensitivity profiles that sequential rounds of antibiotic and non-antibiotic selection may lead to hypersensitive populations by harnessing the orthogonal collateral effects of particular pairs of selective forces. To test this hypothesis, we show experimentally that populations evolved to a sequence of linezolid (an oxazolidinone antibiotic) and sodium benzoate (a common preservative) exhibit increased sensitivity to more stressors than adaptation to either condition alone. The results demonstrate how sequential adaptation to drug and non-drug environments can be used to sensitize bacterial to antibiotics and highlight new potential strategies for exploiting shared constraints governing adaptation to diverse environmental challenges.
Linking patterns of genetic variation to processes of diversification in Malaysian torrent frogs (Anura: Ranidae:Amolops): a landscape genomics approach
Authors: Chan Kin Onn , Brown Rafe M.
Published: May 2019

The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned, and distributed. This study investigates the role of spatial, environmental, and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow, and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide SNPs in conjunction with landscape variables derived from GIS, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-environment (IBE), and isolation-by-colonization (IBC). Our results demonstrated that IBE, contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.
Toffee – a highly efficient, lossless file format for DIA-MS
Authors: Tully Brett
Published: May 2019

The closed nature of vendor file formats in mass spectrometry is a significant barrier to progress in developing robust bioinformatics software. In response, the community has developed the open mzML format, implemented in XML and based on controlled vocabularies. Widely adopted, mzML is an important step forward; however, it suffers from two challenges that are particularly apparent as the field moves to high-throughput proteomics: large increase in file size, and a largely sequential I/O access pattern.

Described here is ‘toffee’, an open, random I/O format backed by HDF5, with lossless compression that gives file sizes similar to the original vendor format and can be reconverted back to mzML without penalty. It is shown that mzML and toffee are equivalent when processing data using OpenSWATH algorithms, in additional to novel applications that are enabled by new data access patterns. For instance, a peptide-centric deep-learning pipeline for peptide identification is proposed.

Documentation and examples are available at https://toffee.readthedocs.io, and all code is MIT licensed at https://bitbucket.org/cmriprocan/toffee.
The female urinary microbiota in relation to the reproductive tract microbiota
Authors: Chen Chen , Hao Lilan , Wei Weixia , Li Fei , Song Liju , Zhang Xiaowei , Dai Juanjuan , Jie Zhuye , Li Jiandong , Song Xiaolei , Wang Zirong , Zhang Zhe , Zeng Liping , Du Hui , Tang Huiru , Yang Huanming , Wang Jian , Kristiansen Karsten , Xu Xun , Wu Ruifang , Jia Huijue
Published: May 2019

Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. The potential link between female urine and reproductive tract microbial communities is currently not clear.

Here we collected the urine samples from 147 Chinese women of reproductive age, and explored the nature of colonization by 16S rRNA gene amplicon sequencing, real-time qPCR and live bacteria culture. To demonstrate utility intra-individual Spearman’s correlation was used to explore the relationship between urine and multi-sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Types of diverse, Streptococcus-dominated, and Lactobacillus-dominated were the three most common types in the cohort. Detailed comparison of the urinary microbiota to the multi-sites of reproductive tract microbiota demonstrated the urinary microbiota was more similar to the microbiota in the cervix and uterine cavity instead of vagina in the same women.

Our data demonstrates the potential connectivity of the microbiota in the female urogenital system and provided insight into the exploration of urethra and genital tract diseases.
Electrospun Ag-doped SnO2 hollow nanofibers with high antibacterial activity
Authors: Li Yang , Tang Xiaoning , Zhang Bin , Mao Huaming
Published: May 2019

With the continuous improvement in medical science in modern times, the spread of bacterial infection has become a matter of global concern. Therefore, the search for biological medical materials with antibacterial function has become a focus of intense research. In this work, pure SnO2 and Ag-doped SnO2 hollow nanofibers were fabricated by a combination of an electrospinning method and a calcination procedure, and the effects of the doped Ag on antibacterial activity were subsequently investigated. Through the process of high-temperature calcination, a high heating rate would lead to the formation of a hollow tubular structure in SnO2 fibers, and Ag2O would be reduced to Ag0 by a facile process with appropriate thermal treatment. Additionally, the existence of SnO2 as a tetragonal rutile structure was confirmed. On the basis of pure SnO2, doping with silver greatly improved the antibacterial activity of hollow nanofibers. The formation mechanism and the antibacterial mechanism of pure SnO2 and Ag-doped hollow nanofibers are also discussed. This study has broad application prospects for biological medicine.
Mycobacterium tuberculosis reactivates HIV via exosomes mediated resetting of cellular redox potential and bioenergetics
Authors: Tyagi Priyanka , Pal Virender Kumar , Srinivasan Sandhya , Singh Amit
Published: May 2019

The synergy betweenMycobacterium tuberculosis(Mtb) and HIV-1 interferes with therapy and facilitates pathogenesis of both human pathogens. Fundamental mechanisms by whichMtbexacerbates HIV-1 are not clear. Here, we show that exosomes secreted by macrophages infected withMtb, including drug-resistant clinical strains, reactivate HIV-1 by inducing oxidative stress. Mechanistically,Mtb-specific exosomes realign mitochondrial and non-mitochondrial oxygen consumption rate (OCR) and modulates the expression of genes mediating oxidative stress response, inflammation, and HIV-1 transactivation. Proteomics revealed the enrichment of several host factors (e.g.,HIF-1α, galectins, Hsp90) known to promote HIV-1 reactivation in theMtb-specific exosomes. Treatment with a known antioxidant, N-acetyl cysteine, or with the inhibitors of host factors galectins and Hsp90 attenuated HIV-1 reactivation byMtb-specific exosomes. Our findings uncovered new paradigms for understanding the redox and bioenergetics basis of HIV-TB co-infection, which will enable the design of effective therapeutic strategies.
Moss Kinesin-14 KCBP accelerates chromatid motility in anaphase
Authors: Yoshida Mari , Yamada Moé , Goshima Gohta
Published: May 2019

KCBP is a microtubule (MT) minus-end-directed kinesin widely conserved in plants. It was shown in Arabidopsis that KCBP controls trichome cell shape by orchestrating MT and actin cytoskeletons using its tail and motor domains. In contrast, the KCBP knockout (KO) line in the moss Physcomitrella patens showed a defect in nuclear and organelle positioning in apical stem cells. Moss KCBP is postulated to transport the nucleus and chloroplast via direct binding to their membranes, since it binds to and transports liposomes composed of phospholipids in vitro. However, domains required for cargo transport in vivo have not been mapped. Here, we performed a structure-function analysis of moss KCBP. We found that the FERM domain in the tail region, which is known to bind to lipids as well as other proteins, is essential for both nuclear and chloroplast positioning, whereas the proximal MyTH4 domain plays a supporting role in chloroplast transport. After anaphase but prior to nuclear envelope re-formation, KCBP accumulates on the chromosomes, in particular at the centromeric region in a FERM-dependent manner. In the KCBP knockout line, poleward chromosome motility in anaphase was reduced and lagging chromosomes occasionally appeared. These results suggest that KCBP binds to non-membranous naked chromosomes via an unidentified protein(s) for their transport. Finally, the liverwort orthologue of KCBP rescued the chromosome/chloroplast mis-positioning of the moss KCBP KO line, suggesting that the cargo transport function is conserved at least in bryophytes.
Draft Genome Sequence of Candida auris Strain LOM, a Human Clinical Isolate from Greater Metropolitan Houston, Texas
Authors: Long S. Wesley , Olsen Randall J. , Nguyen Hoang A. T. , Saavedra Matthew Ojeda , Musser James M.
Published: May 2019

Candida auris is an emerging pathogen with considerable public health importance. We present the draft genome sequence of a strain recently cultured from the urine of a patient hospitalized in the greater Houston metropolitan region. Two combined Oxford Nanopore sequencing runs provided sufficient data to rapidly generate a draft genome.
Evaluating the performance of 3-tissue constrained spherical deconvolution pipelines for within-tumor tractography
Authors: Aerts Hannelore , Dhollander Thijs , Marinazzo Daniele
Published: May 2019

The use of diffusion MRI (dMRI) for assisting in the planning of neurosurgery has become increasingly common practice, allowing to non-invasively map white matter pathways via tractography techniques. Limitations of earlier pipelines based on the diffusion tensor imaging (DTI) model have since been revealed and improvements were made possible by constrained spherical deconvolution (CSD) pipelines. CSD allows to resolve a full white matter (WM) fiber orientation distribution (FOD), which can describe so-called “crossing fibers”: complex local geometries of WM tracts, which DTI fails to model. This was found to have a profound impact on tractography results, with substantial implications for presurgical decision making and planning. More recently, CSD itself has been extended to allow for modeling of other tissue compartments in addition to the WM FOD, typically resulting in a 3-tissue CSD model. It seems likely this may improve the capability to resolve WM FODs in the presence of infiltrating tumor tissue. In this work, we evaluated the performance of 3-tissue CSD pipelines, with a focus on within-tumor tractography. We found that a technique named single-shell 3-tissue CSD (SS3T-CSD) successfully allowed tractography within infiltrating gliomas, without increasing existing single-shell dMRI acquisition requirements.
Organohalide-respiringDesulfolunaspecies isolated from marine environments
Authors: Peng Peng , Goris Tobias , Lu Yue , Nijsse Bart , Burrichter Anna , Schleheck David , Koehorst Jasper J. , Liu Jie , Sipkema Detmer , Sinninghe Damste Jaap S. , Stams Alfons J. M. , Häggblom Max M. , Smidt Hauke , Atashgahi Siavash
Published: May 2019

The genusDesulfolunacomprises two anaerobic sulfate-reducing strains,D. spongiiphilaAA1⊤andD. butyratoxydansMSL71⊤of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third member of this genus from marine intertidal sediment, designedD. spongiiphilastrain DBB. All threeDesulfolunastrains harbour three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes. Brominated but not chlorinated aromatic compounds were dehalogenated by all three strains. TheDesulfolunastrains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect OHR. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR (RT-qPCR) revealed differential induction ofrdhAgenes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed differential expression ofrdhA1with 1,4-dibromobenzene, and revealed a possible electron transport chain from lactate dehydrogenases and pyruvate oxidoreductase to RdhA1 via menaquinones and either RdhC, or Fix complex (electron transfer flavoproteins), or Qrc complex (Type-1 cytochrome c3:menaquinone oxidoreductase).
Why are education, socioeconomic position and intelligence genetically correlated?
Authors: Morris Tim T , Davies Neil M , Hemani Gibran , Smith George Davey
Published: May 2019

Genetic associations and correlations are perceived as confirmation that genotype influences one or more phenotypes respectively. However, genetic correlations can arise from non-biological or indirect mechanisms including population stratification, dynastic effects, and assortative mating. In this paper, we outline these mechanisms and demonstrate available tools and analytic methods that can be used to assess their presence in estimates of genetic correlations and genetic associations. Using educational attainment and parental socioeconomic position data as an exemplar, we demonstrate that both heritability and genetic correlation estimates may be inflated by these indirect mechanisms. The results highlight the limitations of between-individual estimates obtained from samples of unrelated individuals and the potential value of family-based studies. Use of the highlighted tools in combination with within-sibling or mother-father-offspring trio data may offer researchers greater opportunity to explore the underlying mechanisms behind genetic associations and correlations and identify the underlying causes of estimate inflation.
Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains
Authors: Sprague Daniel , Waters Shafagh A. , Kirk Jessime M. , Wang Jeremy R. , Samollow Paul B. , Waters Paul D. , Calabrese J. Mauro
Published: May 2019

The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analogue of eutherian Xist. Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity. However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of non-linear sequence similarity. Xist Repeats B, C and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k-mers corresponded to domain-specific enrichment of protein-binding motifs. Within individual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.
Association of simple renal cysts and chronic kidney disease with large abdominal aortic aneurysm
Authors: Miszczuk Milena , Müller Verena , Althoff Christian E. , Stroux Andrea , Widhalm Daniela , Dobberstein Andy , Greiner Andreas , Kuivaniemi Helena , Hinterseher Irene
Published: May 2019

Abdominal aortic aneurysms (AAA) primarily affect elderly men who often have many other diseases, with similar risk factors and pathobiological mechanisms to AAA. The aim of this study was to assess the prevalence of simple renal cysts (SRC), chronic kidney disease (CKD), and other kidney diseases (e.g. nephrolithiasis) among patients presenting with AAA. Two groups of patients (100/group), with and without AAA, from the Surgical Clinic Charité, Berlin, Germany, were selected for the study. The control group consisted of patients who were evaluated for a kidney donation (n = 14) and patients who were evaluated for an early detection of a melanoma recurrence (n = 86). The AAA and control groups were matched for age and sex. Medical records were analyzed and computed tomography scans were reviewed for the presence of SRC and nephrolithiasis. SRC (73% vs. 57%; p<0.001) and CKD (31% vs. 8%; p<0.001) were both more common among AAA than control group patients. On multivariate analysis, CKD, but not SRC, showed a strong association with AAA. Knowledge about pathobiological mechanisms and association between CKD and AAA could provide better diagnostic and therapeutic approaches for these patients.
An introduction to classical molecular dynamics simulation for experimental scattering users
Authors: McCluskey Andrew R. , Grant James , Symington Adam R. , Snow Tim , Doutch James , Morgan Benjamin J. , Parker Stephen C. , Edler Karen J.
Published: May 2019

Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a `black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.
Public management innovations in the United Arab Emirates: rationales, trends and outcomes
Authors: Khalid Saba , Sarker Abu Elias
Published: May 2019

Purpose

The purpose of this paper is to analyze the rationales for, the trends and the impacts of innovations in the public management system of the United Arab Emirates (UAE).

Design/methodology/approach

This study has adopted an interpretative and exploratory approach. To this end, extensive reviews have been made of government documents, reports of international organizations and relevant academic research articles.

Findings

The findings show that the UAE Government has embarked on a massive innovation program to bring dynamism and to feed the requirements of the UAE Vision 2021. As pressured by both external and internal forces, the directions of innovations in the UAE public management system correspond to the global trends. The results of innovations are positive in terms of the enhancement of efficiency, effectiveness, citizens’ satisfaction and citizens’ trust in public services.

Originality/value

This paper links theoretical insights from different sources to analyze the dynamics of public management innovations in the UAE which will be helpful for further comprehensive empirical research in the future.
Curriculum leadership and the enhancement of teacher education programs
Authors: Xiong Xi Bei , Lim Cher Ping , Liu Shi Qi
Published: May 2019

Purpose

Teacher education programmes are critical in developing pre-service teachers’ competencies during the apprenticeship phase (Lim et al., 2010), whereas there is evidence indicating that teacher education programmes depend on curriculum leadership (Robinson et al., 2008). The purpose of this paper is to explore the ways in which curriculum leaders enact their curriculum leadership to enhance teacher education programmes in a context of a normal university in Mainland China.

Design/methodology/approach

In this paper, three groups of curriculum leaders, from university, faculty and classroom level, respectively, are interviewed.

Findings

This study highlights the significance of curriculum leadership in teacher education programmes enhancement in China, particularly the significant impacts from curriculum leaders’ involvement on the programme processes of planning, implementation and evaluation.

Research limitations/implications

Implications for research include a conceptualization of curriculum leadership in teacher education and pre-service teachers’ training in China, and a theoretical integration of curriculum leadership and the enhancement of teacher education programmes.

Originality/value

Implications for practice regard to restructuring curriculum leadership system and informing curriculum leadership practices, not only in Asian countries, but might be able to shed light on the curriculum leadership development in a range of educational contexts either similar to or different from that of Mainland China. This study thus would contribute to several areas of research.
Promoting teachers’ agency and creative teaching through research
Authors: Cloonan Anne , Hutchison Kirsten , Paatsch Louise
Published: May 2019

Purpose

In response to threats to teacher autonomy and creativity by measurements of teacher quality through student performance on high-stakes test scores and standardised professional learning, this study aims to explore teacher collaborative research for opportunities for promotion of teacher agency.

Design/methodology/approach

The authors explore the following research question: How is agentic teacher research into English teaching that integrates information and communication technologies and creative and critical thinking enabled? Using ethnographic tools and an analytical lens influenced by ecological teacher agency, factors which enable teacher agency within teacher research are investigated.

Findings

Teachers’ experiences of, and insights into, collaborative research indicate the enabling of teacher agency through an interplay of personal and professional narratives and available cultural, structural and material resources. Intersections between teacher research and teaching for creativity and teacher agency are revealed.

Originality/value

Three separate fields of study including teacher agency, teacher research and teaching for creativity are brought together providing insight into how teacher research into teaching for creativity in literacy learning can enhance teacher collaboration, autonomy and agency.
To what extent does China’s aid in Africa affect traditional donors?
Authors: Deyassa Kassaye Gudeta
Published: May 2019

Purpose

The purpose of this paper is to examine whether the welfare and social policy ideas that characterize Chinese aid in Africa are influencing traditional donors and becoming global.

Design/methodology/approach

The paper utilised a qualitative study that has two main components: first, a comprehensive content analysis of over 50 key Sino–African, Chinese and Western policy documents from 2000 (since cooperation between Beijing and African countries first became institutionalised); and, second, there were semi-structured interviews with Chinese, African and Western stakeholders in Addis Ababa (Ethiopia), who were directly involved in the relationship between China and Africa and related development issues.

Findings

The results of documentation and interview analyses show that there are currently significant differences between Chinese and Western approaches. China has developed much stronger and more explicit links between development aid and economic activity than most Western donors. The aid is usually implemented through specific projects rather than broader programmes or policies.

Originality/value

It is reasonable to assume that the new developments initiated by the Agency’s international pioneers are likely to be a new emerging trend. As the conditions and processes of social policy design in developing countries are so closely linked with the ideas of international development institutions (if not predetermined), a possible change in the direction of travel of the ideas and activities of this community requires close coordination analysis and evaluation.
A multi-unit serial inspection robot for power transmission lines
Authors: Tao Guanghong , Fang Lijin
Published: May 2019

Purpose

The purpose of this paper is to introduce a robot mechanism designed for power transmission line inspection. The focus for this design is on obstacle-crossing ability with a goal to create a robot moving and crossing obstacle on not only the straight line but also the steering line.

Design/methodology/approach

A novel four-unit tri-arm serial robot mechanism is proposed. Every novel unit designed for pitching motion is based on parallelogram structure, which is driven by cables and only one motor. There is gripper-wheel compounding mechanism mounted on the arm. The prototype and obstacle environments are established, and the obstacle-crossing experiments are conducted.

Findings

The novel unit mechanism and robot prototype have been tested in the lab. The prototype has demonstrated the obstacle-crossing ability when moving and crossing fundamental obstacles on the line. The experimental results show that the robot mechanism meets the obstacle-crossing requirements.

Practical implications

The novel robot technology can be used for defect inspection of power transmission line by power companies.

Social implications

It stands to lower the intense and risk of inspection works and reduce the costs related to inspection.

Originality/value

Innovative features include its architecture, mobility and driving method.
Design and fabrication of a lower limb exoskeleton to assist in stair ascending
Authors: Joudzadeh Payman , Hadi Alireza , Tarvirdizadeh Bahram , Borooghani Danial , Alipour Khalil
Published: May 2019

Purpose

This paper aims to deal with the development of a novel lower limb exoskeleton to assist disabled people in stair ascending.

Design/methodology/approach

For this purpose, a novel design of a mixture of motors and cables has been proposed for users to wear them easily and show the application of the system in stair climbing.

Findings

One of the prominences of this study is the provided robot design where four joints are actuated with only two motors; each motor actuates either the knees or ankles. Another advantage of the designed system is that with motors placed in a backpack, the knee braces can be worn under clothes to be concealed. Finally, the system performance is evaluated using electromyography (EMG) signals showing 28 per cent reduction in energy consumption of related muscles.

Originality/value

This investigation deals with the development of a novel lower limb exoskeleton to assist disabled people in stair ascending.
Position/force control of robot manipulators using reinforcement learning
Authors: Perrusquía Adolfo , Yu Wen , Soria Alberto
Published: May 2019

Purpose

The position/force control of the robot needs the parameters of the impedance model and generates the desired position from the contact force in the environment. When the environment is unknown, learning algorithms are needed to estimate both the desired force and the parameters of the impedance model.

Design/methodology/approach

In this paper, the authors use reinforcement learning to learn only the desired force, then they use proportional-integral-derivative admittance control to generate the desired position. The results of the experiment are presented to verify their approach.

Findings

The position error is minimized without knowing the environment or the impedance parameters. Another advantage of this simplified position/force control is that the transformation of the Cartesian space to the joint space by inverse kinematics is avoided by the feedback control mechanism. The stability of the closed-loop system is proven.

Originality/value

The position error is minimized without knowing the environment or the impedance parameters. The stability of the closed-loop system is proven.
Efficient trajectory of a car-like mobile robot
Authors: Valero Francisco , Rubio Francisco , Besa Antonio José , Llopis-Albert Carlos
Published: May 2019

Purpose

The purpose is to create an algorithm that optimizes the trajectories that an autonomous vehicle must follow to reduce its energy consumption and reduce the emission of greenhouse gases.

Design/methodology/approach

An algorithm is presented that respects the dynamic constraints of the robot, including the characteristics of power delivery by the motor, the behaviour of the tires and the basic inertial parameters. Using quadratic sequential programming with distributed and non-monotonous search direction (Quadratic Programming Algorithm with Distributed and Non-Monotone Line Search), an optimization algorithm proposed and developed by Professor K. Schittkowski is implemented.

Findings

Relations between important operating variables have been obtained, such as the evolution of the autonomous vehicle’s velocity, the driving torque supplied by the engine and the forces acting on the tires. In a subsequent analysis, the aim is to analyse the relationship between trajectory made and energy consumed and calculate the reduction of greenhouse gas emissions. Also this method has been checked against another different methodology commented on in the references.

Research limitations/implications

The main limitation comes from the modelling that has been done. As greater is the mechanical systems analysed, more simplifying hypotheses should be introduced to solve the corresponding equations with the current computers. However, the solutions are obtained and they can be used qualitatively to draw conclusions.

Practical implications

One main objective is to obtain guidelines to reduce greenhouse gas emissions by reducing energy consumption in the realization of autonomous vehicles’ trajectories. The first step to achieve that is to obtain a good model of the autonomous vehicle that takes into account not only its kinematics but also its dynamic properties, and to propose an optimization process that allows to minimize the energy consumed. In this paper, important relationships between work variables have been obtained.

Social implications

The idea is to be friendly with nature and the environment. This algorithm can help by reducing an instance of greenhouse gases.

Originality/value

Originality comes from the fact that we not only look for the autonomous vehicle’s modelling, the simulation of its motion and the analysis of its working parameters, but also try to obtain from its working those guidelines that are useful to reduce the energy consumed and the contamination capability of these autonomous vehicles or car-like robots.
Effect of depositing torch angle on the first layer of wire arc additive manufacture using cold metal transfer (CMT)
Authors: Su Chuanchu , Chen Xizhang
Published: May 2019

Purpose

This paper aims to mainly report the impact of torch angle on the dynamic behavior of the weld pool which is recorded and monitored in real time with the aid of a high-speed camera system. The influence of depositing torch angle on the fluctuation behavior of weld pool and the quality of weld formation are compared and analyzed.

Design/methodology/approach

The FANUC controlled robotic manufacturing system comprised a Fronius cold metal transfer (CMT) Advanced 4000R power source, FANUC robot, water cooling system, wire feeding system and a gas shielding system. An infrared laser was used to illuminate the weld pool for high-speed imaging at 1,000 frames per second with CR600X2 high-speed camera. The high-speed camera was set up a 35 Â° angle with the deposition direction to investigate the weld pool flow patterns derived from high-speed video and the effect of torch angles on the first layer of wire additive manufacture-CMT.

Findings

The experimental results demonstrated that different torch angles significantly influence on the deposited morphology, porosity formation rate and weld pool flow.

Originality/value

With regard to the first layer of wire arc additive manufacture of aluminum alloys, the change of torch angle is critical. It is clear that different torch angles significantly influence on the weld morphology, porosity formation and weld pool flow. Furthermore, under different torch angles, the deposited beads will produce different defects. To get well deposited beads, 0-10° torch could be made away from the vertical position of the deposition direction, in which the formation of deposited beads were well and less porosity and other defects.
Litter movement pathways across terrestrial–aquatic ecosystem boundaries affect litter colonization and decomposition in streams
Authors: Abelho Manuela , Descals Enrique
Published: May 2019

Streams and their riparian zones are connected by spatial flows of organic matter and constitute a model example of a meta‐ecosystem. Fluxes of leaf litter from the riparian zone to the stream are a major energy source in stream food webs. Leaf litter can enter the stream vertically, falling from the tree and into the stream, or laterally, washing into the stream after a period of exposure in the terrestrial ecosystem. The latter can contribute up to 23% to the total amount of litterfall entering streams.

To determine if decomposition, microbial and invertebrate colonization of lateral litter inputs are similar to those of vertical inputs, we assessed leaf decomposition of alder, poplar and a 1:1 mixture of the two species in three scenarios across a gradient of terrestrial:aquatic exposures.

Overall, decomposition was explained by a negative exponential model and decreased with the increase in the period of terrestrial exposure in all cases. Invertebrate colonization tended to decrease with the increase in the period of terrestrial exposure, but total invertebrate richness and biomass were more affected by litter type than by the exposure scenario, attaining higher values in the mixture than in the species alone.

As the length of exposure in the terrestrial ecosystem increased, in‐stream decomposition rates of leaf litter decreased. Comparing leaf species treatments, alder decomposition rates were faster than poplar and the alder–poplar mixture.

The richness of the aquatic hyphomycete community colonizing leaf litter after submergence decreased, and sporulation rates were strongly inhibited with an increasing terrestrial exposure period. While fungi colonizing leaf litter exposed only in the stream invested in rapid reproduction, fungi colonizing litter with prior terrestrial exposure built up more biomass.

We conclude that the path taken by the litter fluxes has important effects on the functioning of the receiving ecosystem. Studies relying only on the fate of freshly abscissed leaf litter (vertical inputs) may not present a complete picture of the decomposition process in streams and may have been overestimating the overall richness and reproductive activity of the aquatic hyphomycetes colonizing leaf litter.
Experimental evidence of the long‐term effects of reindeer on Arctic vegetation greenness and species richness at a larger landscape scale
Authors: Sundqvist Maja K. , Moen Jon , Björk Robert G. , Vowles Tage , Kytöviita Minna‐Maarit , Parsons Malcolm A. , Olofsson Johan
Published: May 2019

Large herbivores influence plant community structure and ecosystem processes in many ecosystems. In large parts of the Arctic, reindeer (or caribou) are the only large herbivores present. Recent studies show that reindeer have the potential to mitigate recent warming‐induced shrub encroachment in the Arctic and the associated greening of high‐latitude ecosystems. This will potentially have large scale consequences for ecosystem productivity and carbon cycling.

To date, information on variation in the interactions between reindeer and plants across Arctic landscapes has been scarce. We utilized a network of experimental sites across a latitudinal gradient in the Scandinavian mountains where reindeer have been excluded from 59 study plots for at least 15 years. We used this study system to test the effect of long‐term exclusion of reindeer on the abundance of major plant functional groups, the greenness indexes Leaf Area Index (LAI) and Normalized Difference Vegetation Index (NDVI), soil mineral nitrogen (N) and phosphorous (P), and species richness, and to determine whether the effect of reindeer exclusion is dependent on reindeer density, productivity, soil fertility or climate.

We found that NDVI and LAI, lichen and deciduous shrub abundances were largely reduced while soil mineral N was enhanced by reindeer. The direction and amplitude of other plant functional group responses to reindeer exclusion differed between forest and tundra as well as shrub‐ and herbaceous‐dominated vegetation. Higher reindeer densities were related to decreased plant species richness in low‐productive sites and to increased species richness in productive sites.

The relative reduction in LAI and associated absolute reductions of deciduous shrubs in response to reindeer were positively related to reindeer density, while the relative reduction in NDVI was not. Further, relative reductions in LAI and NDVI in response to reindeer were unrelated to climate and soil fertility.

Synthesis. Our results provide long‐term experimental evidence highlighting the role of reindeer density in regulating plant species richness, global climate change induced greenness patterns and shrub encroachment at regional scales in the Arctic. These findings emphasize the need to consider reindeer in models predicting vegetation patterns and changes in high‐latitude ecosystems.
Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome
Authors: Pérez‐Izquierdo Leticia , Zabal‐Aguirre Mario , González‐Martínez Santiago C. , Buée Marc , Verdú Miguel , Rincón Ana , Goberna Marta
Published: May 2019

Plant genetic variation, through its phenotypic display, can determine the composition of below ground microbial communities. Variation within a species is increasingly acknowledged to have substantial ecological consequences, particularly through trophic cascades. We hypothesized that the intraspecific genotypic variation of the tree host might impact the phylogenetic composition of its rhizospheric microbial communities, by favouring particular clades, that might be further reflected in ecosystem process rates.

We tested whether the intraspecific genotypic variation of Pinus pinaster modulates nutrient cycling by determining the phylogenetic structure of its symbiotic ectomycorrhizal fungi and rhizospheric bacteria. We sequenced fungal and bacterial molecular markers and reconstructed phylogenies in the rhizosphere of P. pinaster trees belonging to three genotypic variants (Mediterranean, Atlantic, African) in three 45‐year‐old common garden experiments, and measured seven soil enzymatic activities.

Local effects, based on differences in elevation and soil conditions across sites, were strong predictors of the ectomycorrhizal and bacterial communities thriving in tree’s rhizosphere. Across‐site variation also explained differences in phosphorus cycling. We detected, however, a significant effect of the plant genotype on the phylogenetic structure of the root‐associated microbiota that was consistent across sites.

The most productive Mediterranean plant genotype sheltered the most distinct root microbiome, with the dominant Basidiomycetes and Proteobacteria having a strong influence on the phylogenetic microbial community structure and associating with an enhanced hydrolysis of celluloses, hemicelluloses and chitin. Beneath the less productive Atlantic genotype, the less abundant Ascomycetes and up to thirteen bacterial phyla shaped the phylogenetic microbial structure, and predicted the rates of peptidase. Ectomycorrhizal fungi explained the activity of cellulases and protease, and bacteria that of hemicellulases and chitinase, suggesting functional complementarity.

Synthesis. This is the first report using three‐replicated long‐term common gardens in mature forests to disentangle plant genotype‐ and site‐specific drivers of the rhizospheric microbiome and its enzymatic potential. We concluded that intraspecific variation in primary producers leaves a phylogenetic signature in mutualists and decomposers that further modulate key steps in carbon and nitrogen cycles. These results emphasize the ecological relevance of plant intraspecific diversity in determining essential plant–soil feedbacks that control ecosystem productivity and performance.
Adolescents' navigation of linguistic and nonlinguistic modes when reading a digital narrative
Authors: Karchmer‐Klein Rachel , Shinas Valerie Harlow
Published: May 2019

Background

The purpose of this study was to examine how skilled adolescent readers draw on their prior knowledge of multimodality and narrative text structure when navigating an intentionally designed digital narrative text. We know that skilled middle‐school readers have been taught narrative text structure and that adolescents who use the Internet regularly are aware of multimodality. However, we do not know if these same readers understand the purposes of multimodality in digital narratives, nor do we know how they navigate modes when they are used as both scaffolds and central to meaning making in the same text.

Methods

The participants were a purposeful sample of 10 skilled eighth‐grade readers who used the Internet regularly to search, locate and read content in and outside of school. Transcripts from think alouds, semistructured interviews and oral retellings were qualitatively analysed to identify patterns in participants' navigation of a digital narrative.

Results

Data analysis suggested that skilled readers who use the Internet regularly brought multiple layers of textual schema to the task of reading a digital multimodal narrative. Results also indicated these skilled readers relied on written language to learn story elements and interpreted the purpose of nonlinguistic modes was to set the tone of the story and present details. Additionally, participants reported utilising flexible approaches to navigating the text depending upon which modes were presented.

Conclusions

Literacy instruction must disrupt long‐held beliefs that privilege words over other modes in texts. It should include explicit teaching of multimodality and the flexibility required for reading in digital spaces.