bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites
Authors: Lee V Vern , Judd Louise M. , Jex Aaron R. , Holt Kathryn E. , Tonkin Christopher J. , Ralph. Stuart A. 
Published: February 2020

AbstractAlternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterised in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic features, such as the high AT content of Plasmodium RNA, but also the limitations of short read sequencing in deciphering complex splicing events. In this study, we utilised the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies (ONT) to survey the alternative splicing landscape ofToxoplasma gondiiandPlasmodium falciparum. We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or near full-length transcripts with comparable quantification to Illumina sequencing. By comparing this data with available gene models, we find widespread alternative splicing, particular intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic diversity, rather than expanding proteomic diversity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This work highlights a strategy in using long read sequencing to understand splicing events at the whole transcript level, and has implications in future interpretation of RNA-seq studies.
SAMHD1 limits the efficacy of forodesine in leukaemia by protecting cells against cytotoxicity of dGTP
Authors: Davenne Tamara , Klintman Jenny , Sharma Sushma , Rigby Rachel E. , Cursi Chiara , Bridgeman Anne , Dadonaite Bernadeta , Keersmaecker Kim De , Hillmen Peter , Chabes Andrei , Schuh Anna , Rehwinkel Jan 
Published: February 2020

SummaryThe anti-leukaemia agent forodesine causes cytotoxic overload of intracellular deoxyguanosine triphosphate (dGTP) but is efficacious only in a subset of patients. We report that SAMHD1, a phosphohydrolase degrading deoxyribonucleoside triphosphates (dNTPs), protected cells against the effects of dNTP imbalances. SAMHD1-deficient cells induced intrinsic apoptosis upon provision of deoxyribonucleosides, particularly deoxyguanosine (dG). Moreover, dG and forodesine acted synergistically to kill cells lacking SAMHD1. Using mass cytometry, we found that these compounds killed SAMHD1-deficient malignant cells from patients with chronic lymphocytic leukaemia (CLL). Normal cells and CLL cells from patients withoutSAMHD1mutation were unaffected. We therefore propose to use forodesine as a precision medicine for leukaemia, stratifying patients bySAMHD1genotype or expression.Supplementary Figure 5.Graphical AbstractHighlightsSAMHD1-deficient cells die upon exposure to deoxyribonucleosides (dNs)Deoxyguanosine (dG) is the most toxic dN, inducing apoptosis in cells lacking SAMHD1SAMHD1-mutated leukaemic cells can be killed by dG and the PNP-inhibitor forodesineIn BriefSAMHD1 degrades deoxyribonucleoside triphosphates (dNTPs), the building blocks of DNA. Davenne et al. found that SAMHD1 protects cells against dNTP imbalances. Exposure of SAMHD1-deficient cells to deoxyguanosine (dG) results in increased intracellular dGTP levels and subsequent apoptosis. This can be exploited to selectively kill cancer cells that acquiredSAMHD1mutations.
Temperature modulates stress response in anammox reactors
Authors: Niederdorfer Robert , Hausherr Damian , Palomo Alejandro , Wei Jing , Magyar Paul , Smets Barth F. , Joss Adriano , Bürgmann Helmut 
Published: February 2020

AbstractAutotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to oxygen shocks under favorable and cold temperature regimes. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of oxygen perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Temperature induced distinct transcriptional states in compositionally identical communities and transient pulses of dissolved oxygen resulted in the upregulation of stress-response only under favorable temperatures. Anammox species and other key biofilm taxa display different transcriptional responses to the induced stress regimes.
AncesTree: an interactive immunoglobulin lineage tree visualizer
Authors: Foglierini Mathilde , Pappas Leontios , Lanzavecchia Antonio , Corti Davide , Perez Laurent 
Published: February 2020

AbstractHigh-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. To complement Phylip algorithm, we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins (Ig) phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools (such as IMGT®). The GUI is a Java standalone application allowing interaction with Ig-tree that can run under Windows, Linux and Mac OS.
The separation of Antler Polypeptide and its effects on the proliferation and osteogenetic differentiation of Bone Marrow Mesenchymal Stem Cells
Authors: Ping Wang , Tie-Feng Sun , Gang Li , Hui-Min Zhang , Fan-jie Liu , Zhi-hui Gao , Sheng-nan Cao , Guo-dong Sun , Hai-tao Du , Cong-an Wang , Dan-dan Wang , Bin Shi , Ling Lin 
Published: February 2020

AbstractThe effects of antler polypeptide on rat bone marrow mesenchymal stem cells (BMSCs) were investigated. Antler polypeptide was separated from Colla Cornus Cervi by ultrafiltration into different samples according to molecular weight: A (molecular weight <800 Da), B (molecular weight 800-1500 Da) and C (molecular weight >1500 Da). The content of antler polypeptide in A, B and C solutions were quantified by high-performance liquid chromatography (HPLC). The effects of antler polypeptide at different concentrations on the proliferation, cell cycle, and osteogenesis of BMSCs were investigated. The highest cell proliferation rate (84.66%) was observed for antler polypeptide B at a concentration of 1.578 × 10−2g/mL. Antler polypeptide B significantly promoted the proliferation of BMSCs with a proliferation index of 38.68%, which was significantly higher than that of the other groups. Antler polypeptide B significantly enhanced the activity of alkaline phosphatase in BMSCs compared to that of blank group (P<0.001). Antler polypeptide B increased the BMP7 protein expression in BMSCs. Our data suggested that antler polypeptide may promote the proliferation and osteogenic differentiation of BMSCs.
Behavioral features of motivated response to alcohol inDrosophila
Authors: Catalano Jamie L. , Mei Nicholas , Azanchi Reza , Song Sophia , Blackwater Tyler , Heberlein Ulrike , Kaun Karla R. 
Published: February 2020

AbstractAnimals avoid predators and find the best food and mates by learning from the consequences of their behavior. However, reinforcers are not always uniquely appetitive or aversive but can have complex properties. Most intoxicating substances fall within this category; provoking aversive sensory and physiological reactions while simultaneously inducing overwhelming appetitive properties. Here we describe the subtle behavioral features associated with continued seeking for alcohol despite aversive consequences. We developed an automated runway apparatus to measure howDrosophilarespond to consecutive exposures of a volatilized substance. Behavior within this Behavioral Expression of Ethanol Reinforcement Runway (BEER Run) demonstrated a defined shift from aversive to appetitive responses to volatilized ethanol. Behavioral metrics attained by combining computer vision and machine learning methods, reveal that a subset of 9 classified behaviors and component behavioral features associate with this shift. We propose this combination of 9 behaviors can be used to navigate the complexities of operant learning to reveal motivated goal-seeking behavior.
Real-time resolution of short-read assembly graph using ONT long reads
Authors: Nguyen Son Hoang , Cao Minh Duc , Coin Lachlan 
Published: February 2020

AbstractA streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequencing resources and reducing time-to-result. A previous approach implemented innpScarfprovided an efficient streaming algorithm for hybrid assembly but was relatively prone to mis-assemblies compared to other graph-based methods. Here we presentnpGraph, a streaming hybrid assembly tool using the assembly graph instead of the separated pre-assembly contigs. It is able to produce more complete genome assembly by resolving the path finding problem on the assembly graph using long reads as the traversing guide. Application to synthetic and real data from bacterial isolate genomes show improved accuracy while still maintaining a low computational cost.npGraphalso provides a graphical user interface (GUI) which provides a real-time visualisation of the progress of assembly. The tool and source code is available athttps://github.com/hsnguyen/assembly.
An integrated approach for line balancing and AGV scheduling towards smart assembly systems
Authors: Rahman Humyun Fuad , Janardhanan Mukund Nilakantan , Nielsen Peter 
Published: February 2020

Purpose
Optimizing material handling within the factory is one of the key problems of modern assembly line systems. The purpose of this paper is to focus on simultaneously balancing a robotic assembly line and the scheduling of material handling required for the operation of such a system, a topic that has received limited attention in academia. Manufacturing industries focus on full autonomy because of the rapid advancements in different elements of Industry 4.0 such as the internet of things, big data and cloud computing. In smart assembly systems, this autonomy aims at the integration of automated material handling equipment such as automated guided vehicles (AGVs) to robotic assembly line systems to ensure a reliable and flexible production system.

Design/methodology/approach
This paper tackles the problem of designing a balanced robotic assembly line and the scheduling of AGVs to feed materials to these lines such that the cycle time and total tardiness of the assembly system are minimized. Because of the combination of two well-known complex problems such as line balancing and material handling and a heuristic- and metaheuristic-based integrated decision approach is proposed.

Findings
A detailed computational study demonstrates how an integrated decision approach can serve as an efficient managerial tool in designing/redesigning assembly line systems and support automated transportation infrastructure.

Originality/value
This study is beneficial for production managers in understanding the main decisional steps involved in the designing/redesigning of smart assembly systems and providing guidelines in decision-making. Moreover, this study explores the material distribution scheduling problems in assembly systems, which is not yet comprehensively explored in the literature.
Information, data, and knowledge in the cognitive system of the observer
Authors: Bosancic Boris 
Published: February 2020

PurposeIn line with the cognitive viewpoint on the phenomenon of information, the constructivist tradition based on Maturana and Varela's theory of knowing, and some aspects of Shannon's theory of communication, the purpose of this paper is to shed more light on the role of information, data, and knowledge in the cognitive system (domain) of the observer.Design/methodology/approachIn addition to the literature review, a proposed description of the communication and knowledge acquisition processes within the observer's cognitive system/domain is elaborated.FindingsThe paper recognizes communication and knowledge acquisition as separate processes based on two roles of information within the observer's cognitive system, which are emphasized. The first role is connected with the appropriate communication aspects of Shannon's theory related to encoding cognitive entities in the cognitive domain as data representations for calculating theirinformativeness. The second role involves establishing relations between cognitive entities encoded as data representations through the knowledge acquisition process in the observer's cognitive domain.Originality/valueIn this way, according to the cognitive viewpoint, communication and knowledge acquisition processes are recognized as important aspects of the cognitive process as a whole. In line with such a theoretical approach, the paper seeks to provide an extension of Shannon's original idea, intending to involve the observer's knowledge structure as an important framework for the deepening of information theory.
The diffusion and influence of theoretical models of information behaviour. The case of Savolainen's ELIS model
Authors: González-Teruel Aurora , Pérez-Pulido Margarita 
Published: February 2020

PurposeTo ascertain the diffusion and influence of Savolainen's ELIS model and its use as a theoretical and/or methodological basis for research.Design/methodology/approachA context citation analysis was made of the work where this researcher published his model. Analysis covered the year of publication, the type of work and the subject matter of the citing documents concerned. In-context citations were analysed for their frequency in each citing text, style, location and content cited.FindingsThe ELIS model received 18.5 cites/year. 20.2 per cent of them corresponded to papers published in journals in other areas, mainly computer science. The average of cites per paper was 1.8; 64.5 percent of the citing works cited them only once. 60 per cent of the cites were considered essential. Only 13.7 per cent of these cites appear in theory or methods. 37 per cent of the citing documents contained no concept relating to the model.Research limitations/implicationsThe method used focuses on the most direct context of a cite (sentence or paragraph), but isolates it from the general context (full document, other documents by the author or their social capital). It has, however, allowed this research issue to be dealt with under laboratory conditions and revealed nuances hidden by the absolute number of cites.Originality/valueIt has become evident that the dissemination and influence of the ELIS model are less than what the total number of cites indicates and that it has scarcely been incorporated into research design. Despite its popularity, it is not being validated and/or refuted by way of empirical data.
How can scientists and engineers contribute to organisational sustainability reform?
Authors: Gia Hoang Thinh , Hoang Cuong Van , Vu Nam Hai , Nguyen Giang Tinh Ngo , Nguyen Thanh Thi Huong 
Published: February 2020

PurposeThis paper aims to explore how research and development (R&D) scientists and engineers can contribute to sustainability initiatives in their organisations.Design/methodology/approachThis paper uses a critical case study methodology, focussed on a large Vietnamese company in which business leaders sought to engage R&D scientists and engineers in sustainability initiatives focussed on eco-innovation and eco-efficiency. Bourdieu’s theoretical lens of habitus, capitals and field facilitates a relational analysis of the findings.FindingsWhile R&D scientists and engineers adapted well to early changes aligned with eco-innovation, they struggled to engage with sustainability initiatives in the case firm. This study explains adaptions and constraints as scientists and engineers’ professional habitus and capitals, and their broader organisational field.Practical implicationsThis paper provides insight into how organisations might integrate professional acculturation and appropriate facilitators to promote the additional contribution of scientists and engineers to sustainability initiatives in the context of an organisation.Social implicationsAlthough eco-innovation and eco-efficiency are only potential dimensions of comprehensive organisational sustainability reform, this research provides insight into how engaging scientists and engineers with a broader social sustainability agenda might be advanced.Originality/valueThe study addresses calls for empirical insights into ways that scientists and engineers can commit to organisational sustainability practices based on the configurations of habitus, capital and organisational field.
Longitudinal relationships between syntactic skills and Chinese written composition in Grades 3 to 6
Authors: Yeung Pui‐sze , Ho Connie Suk‐han , Chan David Wai‐ock , Chung Kevin Kien‐hoa 
Published: February 2020

BackgroundStudies have shown that word dictation and syntactic skills are significant predictors of written composition performance among Chinese children in elementary grades. However, there is a paucity of research on the bidirectional relationships between these two cognitive‐linguistic skills (i.e., word dictation and syntactic skills) and Chinese writing skills.MethodsThis paper reports the findings of a 1‐year longitudinal study tracking the developmental patterns of Chinese writing among students in Grades 3 and 5 in Hong Kong. The participants were administered tasks involving cognitive‐linguistic skills (working memory, word dictation and syntactic skills) and writing skills (narrative writing and expository writing).ResultsMultiple regression analysis revealed that word dictation and syntactic skills in Grades 3 and 5 were significant longitudinal predictors of Chinese written composition performance in Grade 4 and Grade 6. Syntactic skills, but not word dictation, contributed a significant amount of unique variance to writing performance after controlling for the autoregressor effect of writing. The results also showed that written composition performance in Grades 3 and 5 contributed unique variance to individual differences in syntactic skills in Grades 4 and 6, after controlling for syntactic skills in the preceding year and other cognitive‐linguistic variables.ConclusionThe patterns of results underscore the significance of syntactic skills in Chinese written composition in upper elementary grades and the bidirectional relationship between syntactic skills and written composition in Chinese.HighlightsWhat is already known about this topicChinese word dictation, syntactic skills and verbal working memory are the major types of developmental skills important in Chinese writing among children in elementary grades.What this paper addsThe longitudinal contribution of word dictation to writing performance across grades was mediated by the contribution of word dictation to concurrent writing performance.Syntactic skills contributed a unique amount of variance to writing performance across grades even after controlling for the autoregressor effect of writing.The longitudinal relationships between syntactic skills and written composition were bidirectional.Implications for theory, policy or practiceAn emphasis on grammar teaching in the context of writing may benefit both writing and syntactic skills development.Combined word dictation and composing instruction, rather than teaching word dictation alone or composing instruction alone, may enhance composing skills.
Relative Poverty in Great Britain and the United States, 1979–2017
Authors: Joyce Robert , Ziliak James P. 
Published: February 2020

AbstractThis paper examines the major changes to the face of poverty in Great Britain over the past few decades, assessing the role of policy, and compares and contrasts this with the patterns seen in the United States, using harmonised household survey data. There are various commonalities between the countries, including a shift in the composition of those in poverty towards working‐age households without children, who have not been the focus of policy attention. There are also big differences, with a steadily increasing share of poverty in Great Britain – but a stable share in the United States – found in households with an adult in paid work. This perhaps explains why the anti‐poverty focus in Great Britain is now squarely on the plight of working households, while in the United States it is focused on labour force participation among the low skilled – even though, as we show, the United States has, for decades, been accustomed to in‐work poverty comprising a significantly higher proportion of overall poverty than in Great Britain.
In‐Work Credits in the UK and the US
Authors: Brewer Mike , Hoynes Hilary 
Published: February 2020

AbstractIn‐work credits grew in popularity worldwide during the late 1990s and 2000s as a means of reforming welfare systems in ways that could both encourage work and reduce poverty. This paper reviews the role of in‐work tax credits in the UK and the US, what is known and remains to be known about their impacts and distributional consequences, and the possibilities for reform. Evidence is clear that in‐work credits reduce poverty and can encourage lone parents to work, but have minimal impacts, in aggregate, on second earners. Spending on in‐work credits has grown in the UK, but there have been two major overhauls of the way these are structured so that, on current plans, the UK will not have an identifiable in‐work credit by 2023. In the US, in‐work assistance has grown in generosity and reach since the 1980s, thanks to broad political support for the Earned Income Tax Credit (EITC) and the (less‐targeted) Child Tax Credit. Future debates in the UK should focus on the rise of in‐work poverty, particularly amongst couples, with some needed focus on the design of in‐work benefits, a debate where economic analysis and evidence should have a major role to play. In the US, the policy discussion should be about whether to increase substantially the EITC for those without children, and how best to maintain or expand the credit's generosity for those with children.