bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of natural forest dynamics on vascular plant, bryophyte, and lichen diversity in primevalFagus sylvaticaforests and comparison with production forests
Authors: Kaufmann Stefan , Hauck Markus , Leuschner Christoph 
Published: March 2018

AbstractStand structure, mean tree age, deadwood amount and microclimate all change markedly in the course of natural forest dynamics. The last remaining primeval forests of the temperate forest biome are valuable study objects to investigate the effects of forest dynamics and management on forest structure and function as well as phytodiversity, which is not sufficiently understood.Three pairs ofFagus sylvaticaprimeval and production forests in eastern Slovakia were selected for studying the effects of natural forest development stages on vascular plant, bryophyte, and lichen species richness and composition. We further compared the diversity patterns in the initial, optimal and terminal stages of forest development with those of nearby production forests.The plot‐level species richness of epiphytic bryophytes and lichens increased from the initial to the terminal stage, but only lichens exhibited a significantly higher cumulative species richness (γ diversity) in the later (optimal and terminal) stages. No increase in species richness from the initial to the terminal stage was found for deadwood‐inhabiting epiphytes and the ground‐layer vascular plants. Canonical correspondence analyses identified characteristic bryophyte and lichen species for the different development stages, while the bulk of vascular ground layer species occurred across all stages with no stage preference.Stem diameter was an even more important driver of epiphyte diversity and species composition than the development stage. All stages of the primeval forests (including the initial) were more species‐rich in epiphytes and, when investigating larger plot numbers, also in vascular plants than the production forests.Synthesis. In primeval forests of European beech, plant species richness did not differ significantly between the consecutive forest development stages, while species composition did. This is attributable to the small‐scale mosaic structure of the forest, rapid gap closure by beech, and the continuity of deadwood across the stages, which reduces spatio‐temporal differences in microhabitat availability in the forest. Bryophytes and lichens are species‐richer, and vascular plants at least similarly rich, in the primeval as compared to the production forests, if the study area is sufficiently large.
The contribution of occupation to children’s experience of resilience: A qualitative descriptive study
Authors: Bowden Linda , Reed Kirk , Nicholson Ellen 
Published: March 2018

BackgroundThis qualitative descriptive study explored what occupations children aged 10–13 years participate in and how participation in occupation contributes to resilience from their perspective. Little is known about how occupations contribute to resilience, and less is known from children's perspectives. Exploring how participation in occupation contributes to resilience is important as children continue to face adverse situations; resilience may help protect their development against uncertainty.MethodsFollowing ethics approval eight participants were recruited through schools in a large New Zealand city. Data were collected through semi‐structured interviews and one focus group, these were audio recorded and transcribed. The six‐phase process of thematic analysis, developed by Braun and Clarke (), was utilised to analyse the data.FindingsThree main themes emerged from the data: what resilience is, occupations children do and how those occupations contribute to resilience and thirdly; building participation and resilience. The study revealed sophisticated descriptions of what resilience meant to the participants from their experience, which included the ideas of bouncing back and staying strong. The participants described what occupations they participate in and how these occupations connect to resilience. The participants also described their experience of how participation in their occupations helped build resilience by fostering support, letting go, experiencing distraction, and experiencing fun and happiness.ConclusionThe findings suggest that health professionals, policy makers and educators have much to learn from children. Specifically, the need for children to participate in occupations as a way to build resilience. This indicates that a child‐focussed approach is needed to incorporate children's perspectives in practice and policy development. The findings suggest that practitioners working with children should incorporate participation in occupation in social, health and education intervention plans with children, as well as use occupation based coping strategies when teaching children skills to manage challenges in life.
Long non‐coding RNA NEAT1 mediates the toxic of Parkinson's disease induced by MPTP/MPP+ via regulation of gene expression
Authors: Liu Ying , Lu Zuneng 
Published: March 2018

SummaryParkinson's disease (PD) is a result of the loss of dopaminergic neurons in the substantia nigra and is expected to increase the economic burden on patients’ families and societies. NEAT1, a long non‐coding RNA, is known as a cancer‐related gene, however, the role of it in PD remains unclear. The aims of this study are to detect the NEAT1‐mediated effects in PD and explore the mechanism of NEAT1 in PD. One group (n = 6) of C57BL/6 model mice were intraperitoneal injected with 1‐Methyl‐4‐phenyl‐2, 3, 6‐tetrahydropyridine (MPTP), while another group (n = 6) was treated with saline and served as control. Human neuroblastoma cell line SH‐SY5Y was pretreated with 1‐Methyl‐4‐phenylpyridinium (MPP+). Cell viability and apoptosis, as well as gene expression with different treatments were examined. Up‐regulated NEAT1 was found in MPTP‐induced PD mice. Moreover, the NEAT1 expression was positively correlated with the concentration of MPP+. In SH‐SY5Y cells stimulated by MPP+, NEAT1 knockdown dramatically promoted cell viability and suppressed cell apoptosis. Additionally, down‐regulation of NEAT1 also decreased the ratio of Bax/Bcl‐2, the activity of caspase‐3, as well as the expression of α‐synuclein. Moreover, α‐synuclein overexpression could significantly reverse the increase in cell viability and the decrease in cell apoptosis induced by NEAT1 knockdown. The results suggested that the knockdown of NEAT1 will have a protective effect on MPTP‐induced PD mice. The mechanism may be related to the dysregulation of α‐synuclein.
Patient characteristics associated with peglyated interferon alfa‐2a induced neutropenia in chronic hepatitis C patients
Authors: Hindi Nagham N , Saleh Mohammad I 
Published: March 2018

SummaryNeutropenia is a haematologic disorder commonly reported in patients with chronic hepatitis C virus (HCV) infection treated with pegylated interferon alfa‐2a (PEG‐IFN α‐2a). The objective of the present project is to identify patient characteristics associated with neutropenia in hepatitis C patients. Demographic, clinical, and genetic data from 715 patients with chronic HCV infection treated with PEG‐IFN α‐2a and ribavirin. The outcome variable was the development of grade 3 or 4 neutropenia, defined as the decrease in neutrophil counts below 1 109/L anytime during study. Predictors of neutropenia were identified using a 2‐stage approach. First, univariate analysis was performed to identify possible predictors of neutropenia. T test was used for continuous variables and Fisher's exact test was used for categorical variables. Second, multiple logistic regression with stepwise addition was then performed using predictors identified in the univariate analysis step to produce final model containing independent predictors at P < .05. Logistic regression identified female gender, absolute neutrophils counts, and cholesterol level as the main predictors of neutropenia. Female gender increases the odds of experiencing neutropenia by 86% compared to male gender. A 1 unit (mmol/L) increase in cholesterol level decreases the odds of developing neutropenia by 13%. A 55% reduction in the likelihood of developing neutropenia for a 1 unit (109/L) increase in the absolute neutrophils counts. Patients with high risk of developing neutropenia can be identified. Identification of this cohort allows early intervention to prevent neutropenia. Possible intervention is to administer drugs that raise neutrophil count such as filgrastim before neutropenia occurs.
Essential role of Rpd3‐dependent lysine modification in the growth, development and virulence of Beauveria bassiana
Authors: Cai Qing , Wang Zhi‐Kang , Shao Wei , Ying Sheng‐Hua , Feng Ming‐Guang 
Published: March 2018

SummaryRpd3 is a class I histone deacetylase that reverses lysine acetylation thus influencing cellular processes and functions. However, its role in fungal insect pathogens has not been explored yet. Here we show that Rpd3‐dependent lysine modification and gene expression orchestrate growth, conidiation and virulence in Beauveria bassiana. Deletion of Rpd3 resulted in severe growth defects on various carbon/nitrogen sources, 97% reduction in conidiation capacity and drastic attenuation in virulence. These phenotypes concurred with differential expression of 1479 proteins and hyperacetylation or hypoacetylation of 2227 lysine residues on 1134 proteins. Many of these proteins fell into carbon/nitrogen metabolism and cell rescue/defence/virulence, indicating vital roles of Rpd3‐dependent protein expression and lysine modification in the fungal growth and virulence. Intriguingly, lysine residues of four core histones (H2A, H2B, H3 and H4) and many histone acetyltransferases were also hyper‐ or hypoacetylated in Δrpd3, suggesting direct and indirect roles for Rpd3 in genome‐wide lysine modification. However, crucial development activators were transcriptionally repressed and not found in either proteome or acetylome. Single/double‐site‐directed H3K9/K14 mutations for hyper/hypoacetylation exerted significant impacts on conidiation and dimorphic transition crucial for fungal virulence. Altogether, Rpd3 mediates growth, asexual development and virulence through transcriptional/translational regulation and posttranslational lysine modification in B. bassiana.
The Myosin5‐mediated actomyosin motility system is required for Verticillium pathogenesis of cotton
Authors: Feng Zhidi , Tian Juan , Han Libo , Geng Yuan , Sun Jie , Kong Zhaosheng 
Published: March 2018

SummaryThe vascular wilt fungus Verticillium dahliae is one of the most destructive pathogens of cotton (Gossypium hirsutum) and many other economically important dicot plants. Fungal pathogens require Myosin‐mediated actomyosin motility system for colonization of their host plants; however, the mechanisms underlying this process have not been fully characterized for V. dahliae. Here, in a knock‐out experiment, we characterized the role of VdMyo5, a member of the Myosin V family, before and during infection of cotton and Arabidopsis thaliana. The VdMyo5 deletion mutant (ΔVdmyo5) fungi showed obvious defects in the development of conidia and the polarized elongation of vegetative hyphae, but no inhibition of host root penetration. Overall, the ΔVdmyo5 fungi exhibited dramatically reduced virulence in cotton and Arabidopsis, with almost no colonization in sections of host vascular tissue. We found labelled Myosin5‐GFP to be specifically enriched at the hyphal tip, co‐localized with FM4‐64 labelled Spitzenkörper, which is the vesicle supply centre in filamentous fungi. Comparative secretome analysis revealed that proteins associated with cell wall modification and degradation of reactive oxygen species were significantly altered in mutant strains. Our results indicate that Myosin5 is required for vegetative growth and full virulence, possibly by regulating vesicle transport. The findings provide important insight into the cellular mechanisms of Verticillium pathogenesis.
Nosema ceranae in Apis mellifera: a 12 years postdetection perspective
Authors: Martín‐Hernández Raquel , Bartolomé Carolina , Chejanovsky Nor , Le Conte Yves , Dalmon Anne , Dussaubat Claudia , García‐Palencia Pilar , Meana Aranzazu , Pinto M. Alice , Soroker Victoria , Higes Mariano 
Published: March 2018

SummaryNosema ceranae is a hot topic in honey bee health as reflected by numerous papers published every year. This review presents an update of the knowledge generated in the last 12 years in the field of N. ceranae research, addressing the routes of transmission, population structure and genetic diversity. This includes description of how the infection modifies the honey bee's metabolism, the immune response and other vital functions. The effects on individual honey bees will have a direct impact on the colony by leading to losses in the adult's population. The absence of clear clinical signs could keep the infection unnoticed by the beekeeper for long periods. The influence of the environmental conditions, beekeeping practices, bee genetics and the interaction with pesticides and other pathogens will have a direct influence on the prognosis of the disease. This review is approached from the point of view of the Mediterranean countries where the professional beekeeping has a high representation and where this pathogen is reported as an important threat.
Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis
Authors: Tsementzi Despina , Castro Gordillo Juan , Mahagna Mustafa , Gottlieb Yuval , Konstantinidis Konstantinos T. 
Published: March 2018

SummaryUnderstanding the symbiotic interaction between Coxiella‐like endosymbionts (CLE) and their tick hosts is challenging due to lack of isolates and difficulties in tick functional assays. Here we sequenced the metagenome of a CLE population from wild Rhipicephalus sanguineus ticks (CRs) and compared it to the previously published genome of its close relative, CLE of R. turanicus (CRt). The tick hosts are closely related sympatric species, and their two endosymbiont genomes are highly similar with only minor differences in gene content. Both genomes encode numerous pseudogenes, consistent with an ongoing genome reduction process. In silico flux balance metabolic analysis (FBA) revealed the excess production of L‐proline for both genomes, indicating a possible proline transport from Coxiella to the tick. Additionally, both CR genomes encode multiple copies of the proline/betaine transporter, proP gene. Modelling additional Coxiellaceae members including other tick CLE, did not identify proline as an excreted metabolite. Although both CRs and CRt genomes encode intact B vitamin synthesis pathway genes, which are presumed to underlay the mechanism of CLE‐tick symbiosis, the FBA analysis indicated no changes for their products. Therefore, this study provides new testable hypotheses for the symbiosis mechanism and a better understanding of CLE genome evolution and diversity.
Environmental microbiology to the rescue of planet earth
Authors: de Lorenzo Víctor 
Published: March 2018

SummaryEnvironmental Microbiology has undergone a dramatic transition from being a somewhat marginal branch of Life Sciences to becoming one of the most vibrant and visible areas of contemporary research. The homonymous journal has not only borne witness of the growing interest in environmental microbes that bloomed since the mid‐1980s but it has helped also to give visibility to the field and nucleate an active and influential community of authors and readers. During the past 20 years the focus has shifted from individual isolates to communities and microbiomes, from single genomes to metagenomes and from small/medium‐scale experimental systems to large/very large scenarios. New challenges that were somewhat marginal when the journal was founded have acquired an unanticipated relevance owing to their impact on the global Earth's homeostasis. They include the unacceptably high atmospheric levels of greenhouse gases, the worrying pollution of the oceans with very recalcitrant plastics and microplastics and the noxious effects of micropollutants on many ecosystems. Global problems ask for global solutions and the environmental microbiome – because of its dimension and its amazing activities – may end up being out best instrument to both counter the impact of industrial development and enable a new, sustainable partnership with Nature.
Reef invertebrate viromics: diversity, host specificity and functional capacity
Authors: Laffy Patrick W. , Wood‐Charlson Elisha M. , Turaev Dmitrij , Jutz Sabrina , Pascelli Cecilia , Botté Emmanuelle S. , Bell Sara C. , Peirce Tyler E. , Weynberg Karen D. , van Oppen Madeleine J. H. , Rattei Thomas , Webster Nicole S. 
Published: March 2018

SummaryRecent metagenomic analyses have revealed a high diversity of viruses in the pelagic ocean and uncovered clear habitat‐specific viral distribution patterns. Conversely, similar insights into the composition, host specificity and function of viruses associated with marine organisms have been limited by challenges associated with sampling and computational analysis. Here, we performed targeted viromic analysis of six coral reef invertebrate species and their surrounding seawater to deliver taxonomic and functional profiles of viruses associated with reef organisms. Sponges and corals' host species‐specific viral assemblages with low sequence identity to known viral genomes. While core viral genes involved in capsid formation, tail structure and infection mechanisms were observed across all reef samples, auxiliary genes including those involved in herbicide resistance and viral pathogenesis pathways such as host immune suppression were differentially enriched in reef hosts. Utilising a novel OTU based assessment, we also show a prevalence of dsDNA viruses belonging to the Mimiviridae, Caudovirales and Phycodnaviridae in reef environments and further highlight the abundance of ssDNA viruses belonging to the Circoviridae, Parvoviridae, Bidnaviridae and Microviridae in reef invertebrates. These insights into coral reef viruses provide an important framework for future research into how viruses contribute to the health and evolution of reef organisms.
Short‐term gains, long‐term losses? A diary study on literacy practices in Ghana
Authors: Stoffelsma Lieke 
Published: March 2018

BackgroundThis study explores the English literacy practices of students in Ghana, in particular their time spent on reading, the availability of reading resources and their use in the curriculum, and the importance of reading from the perspectives of students and lecturers.MethodsStudent diaries (6,364 reported hours) and interviews (12 students/ 14 lecturers) were used for data collection.ResultsStudents spend many hours on academic work, but little time on processing academic texts. Their low reading proficiency is maintained at university due to the following factors: little time spent on reading, the type of reading students engage in, institutional values and poor resources.ConclusionUniversal mechanisms that determine literacy practices from the more affluent Western world are prevalent in Ghana. These mechanisms, in combination with contextual factors, especially poor resources and low reading levels, make the Ghana case distinct.
Entrepreneurship and Social Capital: Examining the Association in Deprived Urban Neighbourhoods
Authors: Williams Nick , Huggins Robert , Thompson Piers 
Published: March 2018

AbstractSpatial approaches to examining entrepreneurship have increasingly built on theories of social capital. However, the nature and extent of local social capital in less successful deprived communities remains under researched and inadequately understood. This article examines the association between social capital and entrepreneurship in a deprived urban neighbourhood in the city of Leeds, UK as a means of contributing to an improved theoretical understanding of how space moderates this association. It is found that social capital has a strong association with patterns of entrepreneurship in deprived urban neighbourhoods, with the potential impacts being both positive and negative. The forms of social capital are found to differ from that found in more affluent localities, with a prevalence of bonding social capital as the key facilitator of entrepreneurship, which may help in the early stages of venture development, but which over time may become a constraint. Also, a lack of the bridging social capital associated with entrepreneurial success is found within the locality. From a policy perspective, it is recommended that policymakers responsible for entrepreneurship in deprived urban neighbourhoods should seek to enhance initiatives for developing social capital which incorporate local businesses, residents and local government agencies.
Urban Redevelopment Policies on the Move: Rethinking the Geographies of Comparison, Exchange and Learning
Authors: Ward Kevin 
Published: March 2018

AbstractRecent years have seen the emergence of two interrelated strands of work in the field of English‐speaking urban studies. The first has centred on rethinking notions of place along relational lines. The second centres on rethinking what an attention to the city in the world might mean for understanding the arriving at and making up of urban policy. Taking its cue from the intersection of these two strands, this article explores the forging of Edinburgh's tax increment financing (TIF) policy. It highlights how those in the city drew upon experiences from elsewhere (both relatively close to home and further afield) in assembling the policy and the particular ‘local’ politics over its translation/adoption/failed introduction. The article argues for an approach to urban policy mobility studies which is sensitive both to the ephemeral, indeterminate and open‐ended ways in which policies are arrived at and made up, and the segmented and structured contexts that inform how policies appear and reappear in multiple locations.
An evaluation of fetal heart rate characteristics associated with neonatal encephalopathy: a case‐control study
Authors: Frey HA , Liu X , Lynch CD , Musindi W , Samuels P , Rood KM , Thung SF , Bakk JM , Cheng W , Landon MB 
Published: March 2018

ObjectiveWe sought to identify fetal heart rate (FHR) characteristics that are associated with neonatal encephalopathy (NE).DesignRetrospective case‐control study.SettingA single medical centre in Shanghai, China, 2006–2015.SampleWomen delivering a singleton, non‐anomalous infant at ≥36 weeks’ gestation diagnosed with NE (cases, n = 109) were compared with a group of women with unaffected infants (controls, n = 233).MethodsTwo physicians blinded to the outcome independently reviewed FHR tracings during the last 30 minutes of tracing prior to delivery. FHR characteristics were compared in the two groups and multivariable logistic regression was used to adjust for confounding.Main outcome measuresAdjusted odds ratio (aOR) and 95% confidence interval (CI) for the presence of specific FHR categories and characteristics.ResultsCategory II FHR tracings were observed in 89% of women prior to delivery and were not independently associated with NE. Notably, a category III FHR was observed in 17.4% of women in the NE group compared with 0.9% of women in the control group (aOR 44.99, 95% CI 7.23–279.97). Bradycardia, minimal/absent variability, late decelerations and prolonged decelerations were independently associated with NE, whereas accelerations were protective. Similar findings were found when the cases were limited to NE with arterial cord pH <7.1 and in a subgroup analysis of women with category II tracings.ConclusionsCategory III tracings, while infrequent, are not uncommon prior to delivery among fetuses who develop NE. In contrast, most FHR tracings are category II prior to delivery; however, individual FHR characteristics within this category are associated with NE.FundingThis research was supported by the Interdisciplinary Programme of Shanghai Jiao Tong University.Tweetable abstractCategory III tracings are not uncommon prior to delivery among fetuses who develop neonatal encephalopathy.