bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallelisation strategies for agent based simulation of immune systems
Authors: Kabiri Chimeh Mozhgan , Heywood Peter , Pennisi Marzio , Pappalardo Francesco , Richmond Paul 
Published: December 2019

Abstract
Background
In recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological domain due to high demand for a large scale analysis tools for the collection and interpretation of information to solve biological problems. Simulating massive multi-agent systems (i.e. simulations containing a large number of agents/entities) requires major computational effort which is only achievable through the use of parallel computing approaches.

Results
This paper explores different approaches to parallelising the key component of biological and immune system models within an ABM model: pairwise interactions. The focus of this paper is on the performance and algorithmic design choices of cell interactions in continuous and discrete space where agents/entities are competing to interact with one another within a parallel environment.

Conclusions
Our performance results demonstrate the applicability of these methods to a broader class of biological systems exhibiting typical cell to cell interactions. The advantage and disadvantage of each implementation is discussed showing each can be used as the basis for developing complete immune system models on parallel hardware.
Toward computational modelling on immune system function
Authors: Pappalardo Francesco , Pennisi Marzio , Reche Pedro A. , Russo Giulia 
Published: December 2019

AbstractThe 2nd Computational Methods for the Immune System function Workshop has been held in Madrid in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018) in Madrid, Spain, from December 3 to 6, 2018. The workshop has been obtained 100% more submissions in respect to the first edition, highlighting a growing interest for the treated topics. The best papers (9) have been selected for extension in this special issue, with themes about immune system and disease simulation, computer-aided design of novel candidate vaccines, methods for the analysis of immune system involved diseases based on statistical methods, meta-heuristics and game theory, and modelling strategies for improving the simulation of the immune system dynamics.
Glyoxalase 1 gene improves the antistress capacity and reduces the immune inflammatory response
Authors: Du Fukuan , Li Yan , Shen Jing , Zhao Yueshui , Kaboli Parham Jabbarzadeh , Xiang Shixin , Wu Xu , Li Mingxing , Zhou Jiangyao , Zheng Yuan , Yi Tao , Li Xiang , Li Jing , Xiao Zhangang , Wen Qinglian 
Published: December 2019

AbstractBackgroundFish immunity is not only affected by the innate immune pathways but is also triggered by stress. Transport and loading stress can induce oxidative stress and further activate the immune inflammatory response, which cause tissue damage and sudden death. Multiple genes take part in this process and some of these genes play a vital role in regulation of the immune inflammatory response and sudden death. Currently, the key genes regulating the immune inflammatory response and the sudden death caused by stress inCoilia nasusare unknown.ResultsIn this study, we studied the effects of theGlo1gene on stress, antioxidant expression, and immune-mediated apoptosis inC. nasus. The full-length gene is 4356 bp, containing six exons and five introns. Southern blotting indicated thatGlo1is a single-copy gene in theC. nasusgenome. We found two single-nucleotide polymorphisms (SNPs) in theGlo1coding region, which affect the three-dimensional structure of Glo1 protein. An association analysis results revealed that the two SNPs are associated with stress tolerance. Moreover,Glo1mRNA and protein expression of the heterozygous genotype was significantly higher than that of the homozygous genotype. Na+and sorbitol also significantly enhancedGlo1mRNA and protein expression, improved the fish’s antioxidant capacity, and reduced the immune inflammatory response, thus sharply reducing the mortality caused by stress.ConclusionsGlo1 plays a potential role in the stress response, antioxidant capacity, and immune-mediated apoptosis inC. nasus.
Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes
Authors: Tamames Javier , Cobo-Simón Marta , Puente-Sánchez Fernando 
Published: December 2019

Abstract
Background
Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable.

Results
We have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles. Our results show that database completeness (the representation of diverse organisms and taxa in it) is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by metagenomic size, that in turn determines the completeness of the assembly (the percentage of read that were assembled).

Conclusions
Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a substantial number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.
Characterization of a wheat–tetraploid Thinopyrum elongatum 1E(1D) substitution line K17–841-1 by cytological and phenotypic analysis and developed molecular markers
Authors: Li Daiyan , Zhang Juwei , Liu Haijiao , Tan Binwen , Zhu Wei , Xu Lili , Wang Yi , Zeng Jian , Fan Xing , Sha Lina , Zhang Haiqin , Ma Jian , Chen Guoyue , Zhou Yonghong , Kang Houyang 
Published: December 2019

Abstract
Background
Tetraploid Thinopyrum elongatum (2n = 4x = 28) is a promising source of useful genes, including those related to adaptability and resistance to diverse biotic (Fusarium head blight, rust, powdery mildew, and yellow dwarf virus) and abiotic (cold, drought, and salt) stresses. However, gene transfer rates are low for this species and relatively few species-specific molecular markers are available.

Results
The wheat-tetraploid Th. elongatum line K17–841-1 derived from a cross between a hexaploid Trititrigia and Sichuan wheat cultivars was characterized based on sequential genomic and fluorescence in situ hybridizations and simple sequence repeat markers. We revealed that K17–841-1 is a 1E (1D) chromosomal substitution line that is highly resistant to stripe rust pathogen strains prevalent in China. By comparing the sequences generated during genotyping-by-sequencing (GBS), we obtained 597 specific fragments on the 1E chromosome of tetraploid Th. elongatum. A total of 235 primers were designed and 165 new Th. elongatum-specific markers were developed, with an efficiency of up to 70%. Marker validation analyses indicated that 25 specific markers can discriminate between the tetraploid Th. elongatum chromosomes and the chromosomes of other wheat-related species. An evaluation of the utility of these markers in a F2 breeding population suggested these markers are linked to the stripe rust resistance gene on chromosome 1E. Furthermore, 28 markers are unique to diploid Th. elongatum, tetraploid Th. elongatum, or decaploid Thinopyrum ponticum, which carry the E genome. Finally, 48 and 74 markers revealed polymorphisms between Thinopyrum E-genome- containing species and Thinopyrum bessarabicum (Eb) and Pseudoroegneria libanotica (St), respectively.

Conclusions
This new substitution line provide appropriate bridge–breeding–materials for alien gene introgression to improve wheat stripe rust resistance. The markers developed using GBS technology in this study may be useful for the high-throughput and accurate detection of tetraploid Th. elongatum DNA in diverse materials. They may also be relevant for investigating the genetic differences and phylogenetic relationships among E, Eb, St, and other closely-related genomes and for further characterizing these complex species.
ILC2 transfers to apolipoprotein E deficient mice reduce the lipid content of atherosclerotic lesions
Authors: Mantani Polyxeni T. , Dunér Pontus , Ljungcrantz Irena , Nilsson Jan , Björkbacka Harry , Fredrikson Gunilla Nordin 
Published: December 2019

Abstract
Background
Expansion of type 2 innate lymphoid cells (ILC2s) in hypercholesterolaemic mice protects against atherosclerosis while different ILC2 subsets have been described (natural, inflammatory) based on their suppression of tumorigenicity 2 (ST2) and killer-cell lectin like receptor G1 (KLRG1) expression. The aim of the current study is to characterize the interleukin 25 (IL25)-induced splenic ILC2 population (Lin−CD45+IL17RB+ICOS+IL7raintermediate) and address its direct role in experimental atherosclerosis by its adoptive transfer to hypercholesterolaemic apolipoprotein E deficient (apoE−/−) mice.

Results
Immunomagnetically enriched, FACS-sorted ILC2s from the spleens of IL-25 treated apoE−/− mice were stained for KLRG1 and ST2 directly upon cell obtainment or in vitro cell expansion for flow cytometric analysis. IL25-induced splenic ILC2s express high levels of both KLRG1 and ST2. However, both markers are downregulated upon in vitro cell expansion. In vitro expanded splenic ILC2s were intraperitoneally transferred to apoE−/− recipients on high fat diet. ApoE−/− mice that received in vitro expanded splenic ILC2s had decreased lipid content in subvalvular heart and brachiocephalic artery (BCA) plaques accompanied by increased peritoneal B1 cells, activated eosinophils and alternatively activated macrophages (AAMs) as well as anti-phosphorylcholine (PC) immunoglobulin (Ig) M in plasma.

Conclusions
With the current data we designate the IL25-induced ILC2 population to decrease the lipid content of atherosclerotic lesions in apoE−/− mice and we directly link the induction of B1 cells and the atheroprotective anti-PC IgM antibodies with ILC2s.
Localization of phosphotyrosine adaptor protein ShcD/SHC4 in the adult rat central nervous system
Authors: Robeson Hannah N. , Lau Hayley R. , New Laura A. , Lalonde Jasmin , Armstrong John N. , Jones Nina 
Published: December 2019

Abstract
Background
Mammalian Shc (Src homology and collagen) proteins comprise a family of four phosphotyrosine adaptor molecules which exhibit varied spatiotemporal expression and signaling functions. ShcD is the most recently discovered homologue and it is highly expressed in the developing central nervous system (CNS) and adult brain. Presently however, its localization within specific cell types of mature neural structures has yet to be characterized.

Results
In the current study, we examine the expression profile of ShcD in the adult rat CNS using immunohistochemistry, and compare with those of the neuronally enriched ShcB and ShcC proteins. ShcD shows relatively widespread distribution in the adult brain and spinal cord, with prominent levels of staining throughout the olfactory bulb, as well as in sub-structures of the cerebellum and hippocampus, including the subgranular zone. Co-localization studies confirm the expression of ShcD in mature neurons and progenitor cells. ShcD immunoreactivity is primarily localized to axons and somata, consistent with the function of ShcD as a cytoplasmic adaptor. Regional differences in expression are observed among neural Shc proteins, with ShcC predominating in the hippocampus, cerebellum, and some fiber tracts. Interestingly, ShcD is uniquely expressed in the olfactory nerve layer and in glomeruli of the main olfactory bulb.

Conclusions
Together our findings suggest that ShcD may provide a distinct signaling contribution within the olfactory system, and that overlapping expression of ShcD with other Shc proteins may allow compensatory functions in the brain.
Comparative transcriptome and histological analyses of wheat in response to phytotoxic aphid Schizaphis graminum and non-phytotoxic aphid Sitobion avenae feeding
Authors: Zhang Yong , Fu Yu , Fan Jia , Li Qian , Francis Frédéric , Chen Julian 
Published: December 2019

Abstract
Background
Infestation of the phytotoxic aphid Schizaphis graminum can rapidly induce leaf chlorosis in susceptible plants, but this effect is not observed with the nonphytotoxic aphid Sitobion avenae. However, few studies have attempted to identify the different defence responses induced in wheat by S. graminum and S. avenae feeding and the mechanisms underlying the activation of chlorosis by S. graminum feeding.

Results
S. graminum feeding significantly reduced the chlorophyll content of wheat leaves, and these effects were not observed with S. avenae. A transcriptomic analysis showed that the expression levels of genes involved in the salicylic acid, jasmonic acid and ethylene signalling defence pathways were significantly upregulated by both S. avenae and S. graminum feeding; however, more plant defence genes were activated by S. graminum feeding than S. avenae feeding. The transcript levels of genes encoding cell wall-modifying proteins were significantly increased after S. graminum feeding, but only a few of these genes were induced by S. avenae. Furthermore, various reactive oxygen species-scavenging genes, such as 66 peroxidase (POD) and 8 ascorbate peroxidase (APx) genes, were significantly upregulated after S. graminum feeding, whereas only 15 POD and one APx genes were induced by S. avenae feeding. The activity of four antioxidant enzymes was also significantly upregulated by S. graminum feeding. Cytological examination showed that S. graminum feeding induced substantial hydrogen peroxide (H2O2) accumulation in wheat leaves. The chlorosis symptoms and the loss of chlorophyll observed in wheat leaves after S. graminum feeding were reduced and inhibited by the scavenging of H2O2 by dimethylthiourea, which indicated that H2O2 plays important role in the induction of chlorosis by S. graminum feeding.

Conclusions
S. graminum and S. avenae feeding induces the JA, SA and ET signalling pathways, but S. graminum activated stronger plant defence responses than S. avenae. S. graminum feeding triggers strong ROS-scavenging activity and massive H2O2 production in wheat leaves, and the accumulation of H2O2 induced by S. graminum feeding is involved in the activation of chlorosis in wheat leaves. These results enhance our understanding of mechanisms underlying aphid-wheat interactions and provide clues for the development of aphid-resistant wheat varieties.
Cytological and transcriptome analyses reveal OsPUB73 defect affects the gene expression associated with tapetum or pollen exine abnormality in rice
Authors: Chen Lin , Deng Ruilian , Liu Guoqiang , Jin Jing , Wu Jinwen , Liu Xiangdong 
Published: December 2019

Abstract
Background
As one of the main crops in the world, sterility of rice (Oryza sativa L.) significantly affects the production and leads to yield decrease. Our previous research showed that OsPUB73, which encodes U-box domain-containing protein 73, may be associated with male sterility. However, little information is available on this gene that is required for anther development. In the present study, we knocked out OsPUB73 by using the CRISPR/Cas9 system and studied the cytological and transcriptome of the gene-defect associated with pollen development and sterility in the rice variety (Taichung 65).

Results
The sequence analysis indicated that OsPUB73 was comprised of 3 exons and 2 introns, of which CDS encoded 586 amino acids including a U-box domain. The expression pattern of OsPUB73 showed that it was highly expressed in the anther during meiosis stage. The ospub73 displayed low pollen fertility (19.45%), which was significantly lower than wild type (WT) (85.37%). Cytological observation showed tapetum vacuolated at the meiosis stage and pollen exine was abnormal at the bi-cellular pollen stage of ospub73. RNA-seq analysis detected 2240 down and 571 up-regulated genes in anther of ospub73 compared with WT during meiosis stage. Among of 2240 down-regulated genes, seven known genes were associated with tapetal cell death or pollen exine development, including CYP703A3 (Cytochrome P450 Hydroxylase703A3), CYP704B2 (Cytochrome P450 Hydroxylase704B2), DPW (Defective Pollen Wall), PTC1 (Persistant Tapetal Cell1), UDT1 (Undeveloped Tapetum1), OsAP37 (Aspartic protease37) and OsABCG15 (ATP binding cassette G15), which were validated by quantitative real-time polymerase chain reaction (qRT-PCR). These results suggested OsPUB73 may play an important role in tapetal or pollen exine development and resulted in pollen partial sterility.

Conclusion
Our results revealed that OsPUB73 plays an important role in rice male reproductive development, which provides valuable information about the molecular mechanisms of the U-box in rice male reproductive development.
General practitioners’ accounts of negotiating antibiotic prescribing decisions with patients: a qualitative study on what influences antibiotic prescribing in low, medium and high prescribing practices
Authors: van der Zande Marieke M. , Dembinsky Melanie , Aresi Giovanni , van Staa Tjeerd P. 
Published: December 2019

Abstract
Background
Antimicrobial resistance (AMR) is high on the UK public health policy agenda, and poses challenges to patient safety and the provision of health services. Widespread prescribing of antibiotics is thought to increase AMR, and mostly takes place in primary medical care. However, prescribing rates vary substantially between general practices. The aim of this study was to understand contextual factors related to general practitioners’ (GPs) antibiotic prescribing behaviour in low, high, and around the mean (medium) prescribing primary care practices.

Methods
Qualitative semi-structured interviews were conducted with 41 GPs working in North-West England. Participants were purposively sampled from practices with low, medium, and high antibiotic prescribing rates adjusted for the number and characteristics of patients registered in a practice. The interviews were analysed thematically.

Results
This study found that optimizing antibiotic prescribing creates tensions for GPs, particularly in doctor-patient communication during a consultation. GPs balanced patient expectations and their own decision-making in their communication. When not prescribing antibiotics, GPs reported the need for supportive mechanisms, such as regular practice meetings, within the practice, and in the wider healthcare system (e.g. longer consultation times). In low prescribing practices, GPs reported that increasing dialogue with colleagues, having consistent patterns of prescribing within the practice, supportive practice policies, and enough resources such as consultation time were important supports when not prescribing antibiotics.

Conclusions
Insight into GPs’ negotiations with patient and public health demands, and consistent and supportive practice-level policies can help support prudent antibiotic prescribing among primary care practices.
A longitudinal analysis of the association between the living arrangements and psychological well-being of older Chinese adults: the role of income sources
Authors: Zhou Zi , Cai Lun , Zhuang Meilan , Hong Y. Alicia , Fang Ya 
Published: December 2019

AbstractBackgroundUnderstanding how living arrangements may affect psychological well-being (PWB) is critical in China, a society with the largest older population in the world. However, few studies have examined the moderating effect of income sources on the relationship between living arrangements and PWB. Our aim was to examine whether living arrangements are associated with PWB and whether income sources moderate this association.MethodsThe data were drawn from the third (2002) to sixth (2011/2012) waves of the Chinese Longitudinal Healthy Longevity Survey (CLHLS). Six questions reflecting older adults’ well-being were used to measure PWB. Living arrangements were classified as follows: living alone, living with family and living in an institution. Income sources were categorized into financially independent, supported by children, and governmental support. We performed random-effects ordinal probit models to examine the association of living arrangements with PWB and the moderating effect of income sources on this relationship.ResultsWe included a total sample of 30,899 observations for 16,020 respondents aged 65 and over during 9-year follow-up. Older adults living with family (β = .29,p < .001) and those living in an institution (β = .34,p < .001) had stronger PWB than those living alone; moreover, support from children (β= −.24,p < .001) or from the government (β= −.08,p < .05) has a negative effect on PWB compared to the effect of financial self-support. Living in an institution with support from children (β= −.22,p < .05) led to lower PWB than living alone with financial self-support. The opposite result was observed for older adults living with their family and supported by the government (β = .16,p < .05).ConclusionsOur analysis provides a significant contribution to the existing literature on the relationship between living arrangements and PWB in China. We recognize that living with family or in an institution leads to better PWB than does living alone. In addition, financial support from the government can moderate this association.
Comparison of an in house and a commercial real-time polymerase chain reaction targeting Toxoplasma gondii RE gene using various samples collected from patients in Turkey
Authors: Döşkaya Mert , Pullukçu Hüsnü , Karakavuk Muhammet , Şahar Esra Atalay , Taşbakan Mehmet Sezai , Taşbakan Meltem Işıkgöz , Yılmaz Mümtaz , Can Hüseyin , Döşkaya Aysu Değirmenci , Gürüz Adnan Yüksel 
Published: December 2019

AbstractBackgroundToxoplasma gondiiis an opportunistic protozoan parasite that can infect all warm-blooded animals including humans and cause serious clinical manifestations. Toxoplasmosis can be diagnosed using histological, serological, and molecular methods. In this study, we aimed to detectT. gondiiRE gene in various human samples byin houseand commercial real time polymerase chain reactions.MethodsA total of 38 suspected cases of toxoplasmosis [peripheral blood (n:12), amnion fluid (n:11), tissue (n:9), cerebrospinal fluid (n:5), and intraocular fluid (n:1)] were included to the study. Anin houseand a commercial RT-PCR were applied to investigate theT. gondiiRE gene in these samples.ResultsThe compatibility rate of the two tests was 94.7% (37/38). When the commercial RT-PCR kit was taken as reference, the sensitivity and specificity ofin houseRT-PCR test was 87.5 and 100%. When thein houseRT-PCR test was taken as reference, the commercial RT-PCR kit has 100% sensitivity and 96.8% specificity. Incompatibility was detected in only in a buffy coat sample with high protein content.ConclusionsBoth the commercial andin houseRT-PCR tests can be used to investigateT. gondiiRE gene in various clinical specimens with their high sensitivity and specificity. In house RT-PCR assay can be favorable due to cost savings compared to using the commercial test.