bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics in coastal RNA viruses and bacteriophages are driven by shifts in the community phylogenetic structure
Authors: Gustavsen Julia A. , Suttle Curtis A. 
Published: February 2019

AbstractMarine microbes including viruses are an essential part of the marine ecosystem that forms the base of the foodweb, and drives biogeochemical cycles. Marine viral communities display repeatable changes in abundance and community composition throughout time; however, whether these changes reflect shifts in dominance within evolutionarily related groups of viruses and their hosts is unexplored. To examine these dynamics, changes in the composition and phylogenetic makeup of two ecologically important groups of viruses, and their potential hosts, were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. Changes in the taxonomic composition within DNA bacteriophages related to T4-like viruses and marnavirus-like RNA viruses infecting eukaryotic phytoplankton, as well as bacteria and eukaryotes, were examined using amplicon sequencing of gene fragments encoding the major capsid protein (gp23), the RNA-dependent RNA polymerase (RdRp) and the 16S and 18S ribosomes, respectively. The results showed that for both viral marker genes, the dominant groups of phylogenetically-related viruses shifted over time and contained many transient taxa and few persistent taxa; yet, different community structures were observed in these different viral communities. Additionally, with strong lagged correlations between viral richness and community similarity of putative hosts, the results imply that viruses influence the composition of the host communities.ImportanceUsing high-throughput sequencing of coastal seawater collected every two weeks for one year, the dynamics of two groups of ecologically important groups of viruses were described in the context of their putative hosts and the environment. There was a large diversity of viruses and putative hosts in this study, and groups of phylogenetically-related viruses showed temporal dynamics in dominance. Examining the richness of viruses by phylogenetic groups showed different dynamics of either boom-bust or continued persistence. At the OTU-level, some members of these related groups persisted throughout time, while others were more ephemeral. These findings were put in context of potential quasispecies behaviour, and the dynamics of putative hosts. These results showed that temporal dynamics of viral communities have a phylogenetic signal which is important for understanding the ecology of these viruses since it elucidated one of the drivers of the community structure.
Transketolase is involved in the control of Sigma B during chronic infection byStaphylococcus aureus
Authors: Tan Xin , Ramond Elodie , Jamet Anne , Decaux-Tramoni Baptiste , Dupuis Marion , Euphrasie Daniel , Tros Fabiola , Nemazanyy Ivan , Ziveri Jason , Nassif Xavier , Charbit Alain , Coureuil Mathieu 
Published: February 2019

AbstractStaphylococcus aureusis a leading cause of both acute and chronic infections in humans. Its ability to persist within host cells is thought to play an important role in chronicity and treatment failures. The importance of the pentose phosphate pathway (PPP) duringS. aureuschronic infection is currently largely unexplored. Here, we focused on one key PPP enzyme, transketolase. We showed that inactivation of the unique gene encoding transketolase activity inS. aureusUSA300 (Δtkt) led to an impaired growth in broth. Using time-lapse video imaging, we correlated this phenotype with a defect in early intracellular proliferation compared to wild-type strain. As determined by metabolomic analysis,tktinactivation also had an important impact onS. aureusmetabolism. We then monitored long-term intracellular persistence over 10 days by counting of viable bacteria. Unexpectedly for such a slow-growing strain, the Δtktmutant was almost completely eliminated by endothelial cells after ten days, as opposed to a prototypical slow-growing ΔhemDBLmutant for which we recovered 1,000 fold more viable bacteria. We found that in infected cells, the transcriptional activity of the two master regulators Sigma B and RpiRc was drastically reduced in the Δtktmutant compared to wild-type strain. Concomitantly, RNAIII transcription was strongly increased. This transcriptional profile is likely to explain the inability of this slow-growing mutant to sustain long-term intracellular survival, suggesting that TKT -or a functional PPP-is required for intracellular bacteria to enable a transcriptional program geared towards persistence.ImportanceStaphylococcus aureusis a leading cause of severe bacterial infections. This bacterium is readily internalized by non-professional phagocytes and infected cells have been proposed to play an important role in chronic infections and treatment failures.Here, we show the importance of the unique transketolase TKT ofS. aureusUSA300 in bacterial adaptation during chronic intracellular infection. We show that TKT is mandatory for the metabolomic homeostasis ofS. aureusduring intracellular persistence. This work unravels the critical role of TKT in the transcriptional regulation of the master regulators Sigma B, RpiRc and RNAIII linking the pentose phosphate pathway to the control of chronicS. aureusinfections.
Differences in Long-Chained Cuticular Hydrocarbons between Males and Gynes inCataglyphisDesert Ants
Authors: Inbar Shani , Privman Eyal 
Published: February 2019

AbstractCuticualar hydrocarbons play an important role in chemical communication in social insects, serving, among other things, as nestmate, gender, dominance and fertility recognition cues. In ants, however, very little is known about the precopulatory signals cuticular hydrocarbons carry. These signals may serve as affecting sex pheromones and aphrodisiacs or as reliable signals for idiosyncratic traits, which indirectly affect sexual selection. In this study, we examined, for the first time, in theCataglyphisgenus, sex-specific variability in cuticular hydrocarbons. We focused on a species that exhibits split sex-ratio and found significant quantitative differences between virgin queens and their potential mates. In an analyses of both absolute amounts and relative amounts, we found different compounds to be significantly displayed on gynes and drones, suggesting absolute and relative amounts may carry different signals influencing mating behavior and mate choice. We discuss the possible signals advertised by the non-polar fraction of these hydrocarbon profiles.
Capabilities, strategies and firm performance in the United Kingdom
Authors: Parnell John , Brady Malcolm 
Published: February 2019

PurposeThe purpose of this paper is to investigate the influence of internal capabilities and environmental turbulence on market (e.g. cost leadership and differentiation) and nonmarket (e.g. political and social) strategies (NMS), and considers how these strategies impact financial and non-financial performance in firms in the United Kingdom.Design/methodology/approachA survey was administered online to 215 practicing managers in the UK. Measures for competitive strategy (i.e. cost leadership and differentiation), NMS, strategic capabilities, market turbulence and firm performance were adopted from or based on previous work. Hypotheses were tested via SmartPLS.FindingsFindings underscore the impact of market turbulence across all market and nonmarket strategy dimensions. Multiple links between capabilities and strategies were identified. Both cost leadership and differentiation were significantly linked to non-financial performance, but only differentiation was significantly linked to financial performance. An increased emphasis on social NMS was linked to higher financial performance, but not non-financial performance. Political NMS was linked to neither financial nor non-financial performance.Research limitations/implicationsThe sample included managers in multiple industries. Self-typing scales were utilized to measure market turbulence, emphasis on capabilities, strategic emphasis and firm performance.Practical implicationsEmphasis on social NMS can promote financial performance, but political NMS does not appear to drive either financial or non-financial performance.Originality/valueThis paper provides empirical support for a UK-based model linking market turbulence, strategic capabilities, market and nonmarket strategies, and both social and firm performance. It supports NMS as a key performance driver, but with caveats.
Designing and testing a network of passive seismic surveying and monitoring in Dehdasht (South Western Iran)
Authors: Salinas Victor , Ugalde Arantza , Kamayestani Ahmad , Jokar Mehrab , Gharibvand Mojtaba Moradi , Villaseñor Antonio , Heidari Ghasem 
Published: February 2019

ABSTRACTFrom August 2016 to July 2017, a passive seismic survey was conducted in South Western Iran as a part of a pilot project aimed to improve the imaging in geologically complex areas. Passive seismic methods have shown to be a useful tool to infer the physical properties of the underground geological structures where traditional hydrocarbon exploration methods are challenging. For this purpose, a dense passive seismic network consisting of 119 three‐component borehole seismic stations was deployed over an area of 400 km2 around the city of Dehdasht. This paper focuses on the details of the network design, which was devoted to high‐resolution seismological applications, including local earthquake tomography and seismic attenuation imaging. In this regard, we describe the instrument types and the station installation procedures used to obtain high‐quality data that were used to retrieve three‐dimensional models of P‐ and S‐wave velocity and P‐wave attenuation in the area using tomographic inversion techniques. We also assess the network performance in terms of the seismic ambient noise levels recorded at each station site, and we revise the horizontal orientation of the sensors using surface waves from teleseismic earthquakes.
Optimizing compaction calculation for improved probabilistic 2D mapping
Authors: Babak Olena , Liu Kun , Gallop Jeremy 
Published: February 2019

ABSTRACTIntegration of all available data in reservoir characterization is critically important. 2D mapping is a reliable and robust technique that allows integration of multiple secondary data, including geological and geophysical surfaces and maps, to generate realistic summaries of reservoir quality at each location in an area of interest with an associated measure of uncertainty. This is achieved in 2D mapping with a more straightforward implementation, requiring significantly less time and fewer resources than three‐dimensional modelling. In this paper, we propose an approach for the empirical calculation and optimization of differential compaction maps by leveraging existing well control for the use in 2D mapping. Success of the proposal is demonstrated through tests of accuracy, precision and fairness of the local uncertainty distributions for 100 new stratigraphical wells drilled in the Christina Lake and Kirby East area.
A Fatal Case of Acute Arsenic Poisoning
Authors: Lu Ping , Ma Jin‐Qi , Li Fan , Xu Guo‐Hui , Guo Wan , Zhou Hai‐Mei 
Published: February 2019

AbstractThis manuscript reported a case of fatal arsenic poisoning. A woman with schizophrenia took arsenic‐containing “pills,” which consisted of arsenic trioxide and realgar (arsenic (II) sulfide) and wrapped with gauze. The victim consumed 1.09 and 0.819 g arsenic on two occasions, respectively, with the interval between the two doses of 3 days. The woman died on the sixth day after the first dose without any treatment. In this case, pathological examination revealed fat degeneration of the liver rather than hepatomegaly, a rare finding in acute arsenic poisoning. Arsenic in tissue samples was measured, the total arsenic and inorganic arsenic in blood, liver, and gastric wall was 10.2 μg/mL (9.61 μg/mL), 23.1 μg/g (20.7 μg/g), and 32.3 μg/g (28.6 μg/g), respectively.
Predictive Model for Growth of Bacillus cereus at Temperatures Applicable to Cooling of Cooked Pasta
Authors: Juneja Vijay K. , Golden Chase E. , Mishra Abhinav , Harrison Mark A. , Mohr Tim B. 
Published: February 2019

AbstractA model was developed to predict the growth of Bacillus cereus from spores during cooling of cooked pasta. Cooked pasta was inoculated with a cocktail of four strains of heat‐shocked (80 °C/10 min) B. cereus spores to obtain a final spore concentration of approximately 2 log CFU/g. Thereafter, growth was determined at isothermal temperatures starting at 10 °C and every three degrees up to 49 °C. Samples were removed periodically and plated on mannitol egg yolk polymyxin agar. The plates were incubated for 24 hr at 30 °C. Baranyi, Huang, and modified Gompertz primary growth models were used to fit growth data. The modified Ratkowsky secondary model was used to fit growth rates determined by the primary growth models with respect to temperature. All three primary models fitted the growth data well. The modified Ratkowsky secondary model adequately fit growth rates generated by the three primary models (R2 values ranging from 0.96 to 0.98). After acceptable prediction zone (APZ) validation and goodness of fit statistical analyses, it was determined that the Baranyi primary growth model was best suited for these data. For both single‐rate exponential cooling and biphasic linear cooling model validation, all Baranyi model predictions (n = 24 and 28, respectively) fell within the APZ (−1.0 to 0.5 log CFU/g). The model will assist institutional food service settings to determine the safety of cooked pasta subjected to longer cooling times or stored at improper temperatures.Practical ApplicationPredictive model can be used to estimate extent of microbial growth during cooling of cooked pasta and in designing HACCP program and setting of critical control levels. Retail food industry would need fewer challenge studies to validate the safety of their products. The model will provide regulatory agencies and food industry with an objective means of assessing the microbial risk and ensuring that the public is not at risk of acquiring food poisoning.
Clinical significance of positive anti‐neutrophil cytoplasmic antibodies without evidence of anti‐neutrophil cytoplasmic antibodies‐associated vasculitis
Authors: Bornstein Gil , Ben‐Zvi Ilan , Furie Nadav , Grossman Chagai 
Published: February 2019

AbstractAimAnti‐neutrophil cytoplasmic antibodies (ANCA) have a role in the diagnostic workup of ANCA‐associated vasculitis. However, the clinical significance of positive ANCA in the absence of vasculitis is yet to be determined. Therefore, we sought to investigate the clinical spectrum and rate of patients with a positive ANCA without evidence of vasculitis.MethodsRetrospective analysis of patients positive for cytoplasmic ANCA (C‐ANCA) and proteinase 3 (PR3) or P‐ANCA and myeloperoxidase (MPO) between 2007 and 2016 in the Chaim Sheba Medical Center, Israel. The proportion of patients who had no evidence of vasculitis among all patients with a positive C‐ANCA/PR3 or P‐ANCA/MPO was calculated according to tertiles of enzyme‐linked immunosorbent assay (ELISA) antibody levels.ResultsAmong 113 patients who tested positive for C‐ANCA/PR3 or P‐ANCA/MPO, 68 (60.1%) had no evidence of vasculitis. ELISA antibody titers were significantly higher among patients with vasculitis than those without (6.2 vs 3.2, for C‐ANCA/PR3 and 5.4 vs 2.6 for P‐ANCA/MPO, P < 0.05). The proportion of patients without vasculitis among all patients with a positive C‐ANCA/PR3 and among all patients with a positive P‐ANCA/MPO declined in parallel to the increases in ELISA antibody level tertiles (96%, 57% and 22% in the 1st, 2nd and highest tertiles, respectively, for patients with C‐ANCA/PR3 patients and 100%, 66% and 20% in the 1st, 2nd and highest tertiles, respectively, for patients with P‐ANCA/MPO).ConclusionA significant proportion of patients with a positive C‐ANCA/PR3 or P‐ANCA/MPO do not have evidence of vasculitis, particularly those with low‐medium ELISA antibody titers. Using a higher threshold of ANCA titers may be required to improve specificity.
Mitochondrial NDUFA4L2 protein promotes the vitality of lung cancer cells by repressing oxidative stress
Authors: Meng Lifei , Yang Xuhui , Xie Xiao , Wang Mingsong 
Published: February 2019

BackgroundNon‐small cell lung cancer (NSCLC) accounts for a significant proportion of cancer‐related deaths and lacks an effective treatment strategy. NSCLC tissues are generally found in a low oxygen environment. The NDUFA4L2 protein, located in the mitochondria, is encoded by the nucleus genome and is considered a crucial mediator that regulates cell survival. A better understanding of the mechanism of NDUFA4L2 in NSCLC survival in hypoxic environments is essential to design new therapeutic methods.MethodsTwenty NSCLC and corresponding paired non‐tumorous lung tissue samples were collected. NSCLC cell lines were cultured in hypoxic conditions to investigate the mechanism of NDUFA4L2 in NSCLC. The role of NDUFA4L2 was confirmed by using Western blotting, reactive oxygen species measurement, flow cytometry, immunofluorescence analysis, and wound healing and colony formation assays.ResultsThe expression of HIF‐1α and mitochondrial NDUFA4L2 increased in NSCLC cell lines cultured in hypoxic conditions (1% O2). NDUFA4L2 was drastically overexpressed in human NSCLC tissues and cell lines cultured in hypoxic conditions. HIF‐1α regulated the expression of NDUFA4L2. Knockdown of NDUFA4L2 notably increased mitochondrial reactive oxygen species production, which suppressed the viability of NSCLC.ConclusionIn conclusion, overexpression of NDUFA4L2 is a key factor for maintaining NSCLC growth, suggesting that mitochondrial NDUFA4L2 may be a potential target for the treatment of lung cancer.
respR—An R package for the manipulation and analysis of respirometry data
Authors: Harianto Januar , Carey Nicholas , Byrne Maria 
Published: February 2019

AbstractRespirometry is a ubiquitous practice in experimental biology, but there is a lack of standard practices when analysing the resulting data, limiting transparency and reproducibility. As respirometry datasets become increasingly large and analytical approaches more complex, manipulating the data remains a challenge and often intractable with existing tools.Here we describe therespRRpackage, a collection of functions that implement a workflow‐based approach to automate the analysis and visualisation of respirometry data. The package can be used for closed, intermittent flow, flow‐through and open‐tank respirometry and uses well‐defined sets of rules to reliably and rapidly generate reproducible results.We demonstrate howrespRuses novel computing methods such as rolling regressions and kernel density estimates to reliably detect maximum, minimum and most linear sections of the data, and critical oxygen tension,.Although designed specifically with aquatic respirometry in mind, the object‐oriented approach of the package and the unit‐less nature of its analytical functions mean that parts of the package can easily be used to estimate linear relationships from a range of applications in many research disciplines.
Rules about smoking and vaping in the home: findings from the 2016 International Tobacco Control Four Country Smoking and Vaping Survey
Authors: Nahhas Georges J. , Braak David , Cummings K. Michael , Heckman Bryan W. , Alberg Anthony J. , Yong Hua‐Hie , Fong Geoffrey T. , Boudreau Christian , Hitchman Sara C. , McNeill Ann 
Published: February 2019

AbstractAimsTo examine rules about smoking and vaping in the home in relation to beliefs about the relative harm of second‐hand vapor (SHV) compared with second‐hand smoke (SHS) in four countries: Canada, United States, England and Australia.DesignData were available from 12 294 adults (18+) who participated in the 2016 (wave 1) International Tobacco Control Four Country Smoking and Vaping (ITC 4CV1) Survey.ParticipantsAll participants were current or recent former adult smokers.MeasurementsData were analyzed by weighted logistic regression on rules about smoking and vaping in the home; odds ratios and 95% confidence intervals were reported, adjusted for demographic and behavioral variables.FindingsOf all respondents, 37.4% allowed smoking inside their home. Among a subset who were current vapers (n = 6135), 60.4% allowed vaping in their homes. After controlling for demographic and behavioral characteristics, beliefs about the harm of SHV compared with SHS was not associated with allowing smoking in the home, but was associated with allowing vaping in the home [odds ratio (OR) = 2.86 in Canada, OR = 1.82 in the United States and OR = 1.68 in England]. Characteristics that were associated with rules about vaping inside the home included daily vaping (OR = 2.95, 2.04–4.26; OR = 7.00, 4.12–11.87; OR = 5.50, 3.40–8.88; OR = 7.78, 1.90–31.80), living with a spouse who vapes (OR = 2.48, 1.54–3.98; OR = 2.69, 1.42–5.11; OR = 4.67, 2.74–7.95; OR = 21.82, 2.16–220.9) and living with children aged under 18 years (OR = 0.50, 0.37–0.68; OR = 0.89, 0.48–1.65; OR = 0.76, 0.53–1.09; OR = 0.26, = 0.11–0.61) in Canada, the United States, England and Australia, respectively. Similar characteristics were associated with rules about smoking inside the home.ConclusionsAmong current and former smokers in 2016 in Canada, the United States, England and Australia, 37.4% allowed smoking in the home; 60.4% of current vapers allowed vaping. Both concurrent users and exclusive vapers were more likely to allow vaping than smoking inside the home. Allowing vaping inside the home was correlated with the belief that second‐hand vapor is less harmful than second‐hand smoke.
Predation of fruit and seed of Aloe pretoriensis – A little known effect on reproductive output in aloes
Authors: van den Bosch Kaylee , van Noort Simon , Cron Glynis V. 
Published: February 2019

AbstractThe effect of seed predation by phytophagous/parasitoid wasps on the reproductive output of aloes is relatively unknown. In this study, conducted at a nature reserve in Pretoria East, South Africa, the range of insects utilising Aloe pretoriensis (Asphodelaceae) fruits and/or seeds and the impact of this usage on its reproductive output were investigated. Using a GLMM, we explored the effects of morphological features (e.g. floral display size) and selected ecological factors (viz. distance between the aloes and conspecifics and other surrounding vegetation) on fruit utilisation and seed predation. A variety of insect visitors to A. pretoriensis (mainly bees and wasps) were identified including a number of seed predators and parasitoids. Evidence of phytophagy in dissected flowers showed increasing evidence of fruit utilisation and seed predation over an 8‐week period. Emergence boxes with infructescences revealed a range of insect phytophages (and their associated parasitoids) in the aloe fruits and seeds: the drosophilid fly, Apenthecia and six species of wasp – five of them associated with ultilisation of aloe fruits/seeds for the first time: Eurytoma aloineae (Chalcididae), Mesopolobus sp., Pteromalus sp., and c.f. Chlorocytus in the Pteromalidae, Bracon sp. (Braconidae) and Pediobius (Eulophidae). Fruit set ranged between 48% and 93%, with an average of 76%, while average percentage utilisation of fruits was 29%, ranging between 7% and 68%. Average seed set was 23 seeds per fruit and average percentage seed predation 21% (range: 0–51%). Fruit utilisation was found to be significantly negatively correlated with distance to the nearest flowering bush (usually Helichrysum kraussii), but display size did not significantly affect fruit utilisation, nor did distance to conspecifics. Aloe pretoriensis thus serves as host to a variety of phytophagous insects and their associated parasitoids, which impacts considerably on its reproductive output with possible implications for the future conservation of this aloe species.