bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translation Inhibition and Resource Balance in the Cell-Free Gene Expression System
Authors: Nagaraj Vijayalakshmi H. , Greene James M. , Sengupta Anirvan M. , Sontag Eduardo D. 
Published: May 2017

AbstractQuantifying the effect of vital resources on transcription and translation helps to understand the degree to which the concentration of each resource must be regulated for achieving homeostasis. Utilizing the synthetic transcription-translation (TX-TL) system, we study the impact of nucleotide triphosphates (NTPs) and magnesium (Mg2+), on gene expression. Recent observations of the counterintuitive phenomenon of suppression of gene expression at high NTP concentrations have led to the speculation that such suppression is due to the consumption of resources by transcription, hence leaving fewer resources for translation. In this work, we investigate an alternative hypothesis: direct suppression of the translation rate via stoichiometric mismatch in necessary reagents. We observe NTP-dependent suppression even in the early phase of gene expression, contradicting the resource limitation argument. To further decouple the contributions of transcription and translation, we performed gene expression experiments with purified mRNA. Simultaneously monitoring mRNA and protein abundances allowed us to extract a time-dependent translation rate. Measuring translation rates for different Mg2+and NTP concentrations, we observe a complex resource dependence. We demonstrate that translation is the rate-limiting process that is directly inhibited by high NTP concentrations. Additional Mg2+can partially reverse this inhibition. In several experiments, we observe two maxima of the translation rate viewed as a function of both Mg2+and NTP concentration, which can be explained in terms of an NTP-independent effect on the ribosome complex and an NTP-Mg2+titration effect. The non-trivial compensatory effects of abundance of different vital resources signals the presence of complex regulatory mechanisms to achieve optimal gene expression.
Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale
Authors: Foster Charles S. P. , Ho Simon Y. W. 
Published: June 2017

AbstractEvolutionary timescales can be inferred from molecular sequence data using a Bayesian phylogenetic approach. In these methods, the molecular clock is often calibrated using fossil data. The uncertainty in these fossil calibrations is important because it determines the limiting posterior distribution for divergence-time estimates as the sequence length tends to infinity. Here we investigate how the accuracy and precision of Bayesian divergence-time estimates improve with the increased clock-partitioning of genome-scale data into clock-subsets. We focus on a data set comprising plastome-scale sequences of 52 angiosperm taxa. There was little difference among the Bayesian date estimates whether we chose clock-subsets based on patterns of among-lineage rate heterogeneity or relative rates across genes, or by random assignment. Increasing the degree of clock-partitioning usually led to an improvement in the precision of divergence-time estimates, but this increase was asymptotic to a limit presumably imposed by fossil calibrations. Our clock-partitioning approaches yielded highly precise age estimates for several key nodes in the angiosperm phylogeny. For example, when partitioning the data into 20 clock-subsets based on patterns of among-lineage rate heterogeneity, we inferred crown angiosperms to have arisen 198–178 Ma. This demonstrates that judicious clock-partitioning can improve the precision of molecular dating based on phylogenomic data, but the meaning of this increased precision should be considered critically.
Precise timing of sensory modulations coupled to eye movements during active vision
Authors: Devia Christ , Montefusco-Siegmund Rodrigo , Egaña José Ignacio , Maldonado Pedro E. 
Published: June 2017

AbstractPerception is the result of ongoing brain activity combined with sensory stimuli. In natural vision, changes in the visual input typically occur as the result of self-initiated eye movements. Nonetheless, in most studies, stimuli are flashed, and natural eye movements are avoided or restricted. As a consequence, the neural sensory processing associated with active vision is poorly understood. Here, we show that occipital event-related potentials (ERP) to eye movements during free exploration of natural images exhibited different amplitudes, time course and motor dependency than that from the same flashed stimuli. We found that the ERP to visual fixations doubles in P1 magnitude and does not show a late component, which is classically seen with flashed stimuli1,2. In addition, we discovered that the ERP to the saccade onset was as large as the ERP to fixations onset, with an early component that preceded the visual input, suggesting that a motor modulation was associated with the saccades3. Furthermore, the use of different visual scenes revealed that both the ERP amplitude and time course were dependent on the type of image explored. Our results demonstrated that during active vision, the nervous system engages a mechanism of sensory modulation that is precisely timed to the self-initiated stimulus changes. This mechanism could help coordinate neural activity across different cortical areas and, by extension, serve as a general mechanism for the global coordination of neural networks.
Associations of prenatal and postnatal growth with insulin-like growth factor-I levels in pre-adolescence
Authors: Arathimos R , Macdonald-Wallis C , Bull CJ , Holly JMP , Oken E , Kramer MS , Gusina N , Bogdanovich N , Vilchuck K , Patel R , Martin R M , Tilling K 
Published: June 2017

ABSTRACTBackgroundRapid pre - and postnatal growth have been associated with later life adverse health outcomes, which could implicate (as a mediator) circulating insulin-like-growth-factor I (IGF-I), an important regulator of growth. We investigated associations of prenatal (birth weight and length) and postnatal growth in infancy and childhood with circulating IGF-I measured at 11.5 years of age.MethodsWe analysed 11.5-year follow-up data from 17,046 Belarusian children who participated in the Promotion of Breastfeeding Intervention Trial (PROBIT) since birth.ResultsComplete data were available for 5422 boys and 4743 girls (60%). We stratified the analyses by sex, as there was evidence of interaction between growth and sex in their associations with IGF-I. Weight and length/height velocity during childhood were positively associated with IGF-I at 11.5 years; associations increased with age at growth assessment and were stronger for length/height gain than for weight gain. The change in internal run-normalized IGF-I z-score at 11.5 years was 0.038 (95% CI -0.004,0.080) per standard deviation (SD) increase in length gain at 0-3 months amongst girls and 0.025 (95% CI - 0.011,0.060) amongst boys, increasing to 0.336 (95% CI 0.281,0.391;) and 0.211 (95% CI 0.165,0.256) for girls and boys, respectively, for growth during 6.5-11.5 years.ConclusionPostnatal growth velocities in childhood are positively associated with levels of circulating IGF-I in pre-adolescents. Future studies should focus on assessing whether IGF-I is on the causal pathway between early growth and later health outcomes, such as cancer and diabetes.
SCENIC: Single-cell regulatory network inference and clustering
Authors: Aibar Sara , González-Blas Carmen Bravo , Moerman Thomas , Wouters Jasper , Huynh-Thu Vân Anh , Imrichova Hana , Atak Zeynep Kalender , Hulselmans Gert , Dewaele Michael , Rambow Florian , Geurts Pierre , Aerts Jan , Marine Jean-Christophe , den Oord Joost van , Aerts Stein 
Published: June 2017

AbstractSingle-cell RNA-seq allows building cell atlases of any given tissue and infer the dynamics of cellular state transitions during developmental or disease trajectories. Both the maintenance and transitions of cell states are encoded by regulatory programs in the genome sequence. However, this regulatory code has not yet been exploited to guide the identification of cellular states from single-cell RNA-seq data. Here we describe a computational resource, called SCENIC (Single Cell rEgulatory Network Inference and Clustering), for the simultaneous reconstruction of gene regulatory networks (GRNs) and the identification of stable cell states, using single-cell RNA-seq data. SCENIC outperforms existing approaches at the level of cell clustering and transcription factor identification. Importantly, we show that cell state identification based on GRNs is robust towards batch-effects and technical-biases. We applied SCENIC to a compendium of single-cell data from the mouse and human brain and demonstrate that the proper combinations of transcription factors, target genes, enhancers, and cell types can be identified. Moreover, we used SCENIC to map the cell state landscape in melanoma and identified a gene regulatory network underlying a proliferative melanoma state driven by MITF and STAT and a contrasting network controlling an invasive state governed by NFATC2 and NFIB. We further validated these predictions by showing that two transcription factors are predominantly expressed in early metastatic sentinel lymph nodes. In summary, SCENIC is the first method to analyze scRNA-seq data using a network-centric, rather than cell-centric approach. SCENIC is generic, easy to use, and flexible, and allows for the simultaneous tracing of genomic regulatory programs and the mapping of cellular identities emerging from these programs. Availability: SCENIC is available as an R workflow based on three new R/Bioconductor packages:GENIE3, RcisTargetandAUCell.As scalable alternative to GENIE3, we also provideGRNboost,paving the way towards the network analysis across millions of single cells.
Learning and transfer of working memory gating policies
Authors: Bhandari Apoorva , Badre David 
Published: June 2017

AbstractAbstract knowledge about the tasks we encounter enables us to rapidly and flexibly adapt to novel task contexts. Previous research has focused primarily on abstract rules that leverage shared structure in stimulus-response (S-R) mappings as the basis of such task knowledge. Here we provide evidence that working memory (WM) gating policies – a type of control policy required for internal control of WM during a task – constitute a form of abstract task knowledge that can be transferred across contexts. In two experiments, we report specific evidence for the transfer of selective WM gating policies across changes of task context. We show that this transfer is not tied to shared structure in S-R mappings, but instead in the dynamic structure of the task. Collectively, our results highlight the importance of WM gating policies in particular, and control policies in general, as a key component of the task knowledge that supports flexible behavior and task generalization.
Market‐driven production of biospecimens and the role of NHS hospital‐led biobanks
Authors: Timmons Stephen , Vezyridis Paraskevas 
Published: May 2017

AbstractBiobanks are vital for biospecimen production in research, despite the regulatory, recruitment and commercial difficulties they face. We conducted interviews with clinicians, researchers, volunteers who recruit biobank participants, regulators and NHS managers about the integration of a biobank into an NHS hospital. We show that medical waste collected for biomedical research acquires its socio‐ethical and economic value from the level of integration (both technologically and organisationally) of the biobank into the NHS hospital. There is extensive investment in a range of intellectual and commercial relationships and labour among stakeholders involved in the production of biospecimens. It is not only the boundaries of research, clinical care and commercialisation of biospecimens that blur but also those of volunteerism and citizenship. Hospital‐led biobanks provide an opportunity to study the intertwining of biomedical innovation and healthcare.
Effect of temporal data aggregation on the perceived structure of a quantitative plant–floral visitor network
Authors: Sajjad Asif , Saeed Shafqat , Ali Mudssar , Khan Fawad Zafar Ahmad , Kwon Yong Jung , Devoto Mariano 
Published: May 2017

AbstractSeasonal turnover in plant and floral visitor communities changes the structure of the network of interactions they are involved in. Despite the dynamic nature of plant–visitor networks, a usual procedure is to pool year‐round interaction data into a single network which may result in a biased depiction of the real structure of the interaction network. The annual temporal dynamics and the effect of merging monthly data have previously been described for qualitative data (i.e. describing the occurrence of interactions) alone, while its quantitative aspect (i.e. the actual frequency with which interactions occur) remain little explored. For this, we built a set of 12 monthly networks describing year‐round plant–floral visitor interactions in a 30‐hectare planted forest and its adjacent agricultural landscape at Bahauddin Zakariya University Multan, Pakistan. A total of 80 plant and 162 insect species, which engaged in 1573 unique interactions, were recorded. Most network properties (particularly the number of plants, visitors and unique interactions) varied markedly during the year. Data aggregation showed that while animal species, plant species, unique interaction, weighted nestedness, interaction diversity and robustness increased, connectance and specialization decreased. The only metric which seemed relatively unaffected by data pooling was interaction evenness. In general, quantitative metrics were relatively less affected by temporal data aggregation than qualitative ones. Avoiding data aggregation not only gives a more realistic depiction of the dynamic nature of plant–visitor community networks, but also avoids biasing network metrics and, consequently, their expected response to disturbances such as the loss of species.
Isolation of Egg Yolk Granules as Low‐Cholesterol Emulsifying Agent in Mayonnaise
Authors: Motta‐Romero Hollman , Zhang Zhong , Tien Nguyen An , Schlegel Vicki , Zhang Yue 
Published: May 2017

AbstractEgg yolk is an essential ingredient for many food products due to its excellent functional properties such as emulsification. However, the consumers’ concern of its cholesterol level has led food industry to seek solutions for its replacement. Utilization of low‐fat egg yolk granules as emulsifier can be an alternative strategy. In this study, granules with low cholesterol content were separated from egg yolk by a simple method under easily scalable centrifugal conditions. The egg yolk granules isolated within 0.17 M NaCl solution achieved a 22.5% yield that was similar to that using higher centrifugation speeds and longer time. The yield of egg yolk granules increased from 25% to 32% when the yolk:water ratio was changed from 1:1 to 1:2. Mayonnaise was prepared to evaluate the emulsifying capacity of the egg yolk granules. It was found that egg yolk granules exhibited similar emulsifying activity as that of whole egg yolk, but a better emulsion stabilizing property that is evidenced by the higher viscosity of mayonnaise prepared with the granules. In addition, the viscosities of mayonnaise prepared by spray dried yolk and granules were slightly higher than the liquid counterpart, showing a further improvement by spray drying on the emulsion stabilizing properties. The mechanical spectra of mayonnaise samples by frequency sweep also suggested that granules favored the formation of stronger 3‐dimensional arrangements of oil droplets and therefore a more stable emulsion. Results suggest that granules isolated within 0.17 M NaCl solution present best emulsifying properties and can be applied as whole yolk replacer in food emulsions.
elementr: An R package for reducing elemental data from LA‐ICPMS analysis of biological calcified structures
Authors: Sirot Charlotte , Ferraton Franck , Panfili Jacques , Childs Amber‐Robyn , Guilhaumon François , Darnaude Audrey M. 
Published: May 2017

Abstract

Elemental analysis of biological calcified structures (e.g. fish otoliths, mollusc shelves, coral skeletons or fish and shark bones) provides invaluable information regarding ecological processes for many aquatic species. Despite this importance, the reduction of the raw data obtained through Laser‐ablation Inductively Coupled Plasma Mass Spectrometry (LA‐ICPMS) (i.e. the conversion of the machine raw signal into elemental concentrations) remains a challenge as the tools developed so far for carrying out this task have important limitations for aquatic ecologists.

Here, we introduce the elementr R‐package which provides a handy, reliable and transparent way to reduce elemental data acquired from spot or transect LA‐ICPMS analysis of biological calcified structures. This free and open‐source software, implemented based on state‐of‐the‐art literature, handles data from both standards and samples, allowing fast and simultaneous calculations of concentration for any chemical element, correction for potential machine drift, and realignment and averaging for sample replicates when needed.

The major attributes of elementr are: (i) its user‐friendly graphical interface which provides widgets to set all the reduction settings (i.e. no programming skills are required to run it), (ii) its reactivity whereby the software continuously observes any setting change made by the user, re‐calculates and displays all updated results, allowing therefore users to visually check the validity of their settings and to tune them if needed and (iii) an object oriented underlying that facilitates subsequent handling of LA‐ICPMS data in R.

Despite the elementr design being most suited to the needs of aquatic ecologists, its use could be broadened to other research fields (i.e. geology, material engineering) due to its flexibility. Moreover, the open‐source approach used for programming this software allows its expansion in order to refine calculation procedures or to add new functionalities.
An analysis of purchase price of legal and illicit cigarettes in urban retail environments in 14 low‐ and middle‐income countries
Authors: Brown Jennifer , Welding Kevin , Cohen Joanna E. , Cherukupalli Rajeev , Washington Carmen , Ferguson Jacqueline , Clegg Smith Katherine 
Published: May 2017

AbstractBackground/AimsTo estimate and compare price differences between legal and illicit cigarettes in 14 low‐ and middle‐income countries (LMIC).DesignA cross‐sectional census of all packs available on the market was purchased.SettingCigarette packs were purchased in formal retail settings in three major cities in each of 14 LMIC: Bangladesh, Brazil, China, Egypt, India, Indonesia, Mexico, Pakistan, the Philippines, Russia, Thailand, Turkey, Ukraine and Vietnam.ParticipantsA total of 3240 packs were purchased (range = 58 packs in Egypt to 505 in Russia). Packs were categorized as ‘legal’ or ‘illicit’ based on the presence of a health warning label from the country of purchase and existence of a tax stamp; 2468 legal and 772 illicit packs were in the analysis.MeasurementsDescriptive statistics stratified by country, city and neighborhood socio‐economic status were used to explore the association between price and legal status of cigarettes.FindingsThe number of illicit cigarettes in the sample setting was small (n < 5) in five countries (Brazil, Egypt, Indonesia, Mexico, Russia) and excluded from analysis. In the remaining nine countries, the median purchase price of legal cigarettes ranged from US$0.32 in Pakistan (n = 72) to US$3.24 in Turkey (n = 242); median purchase price of illicit cigarettes ranged from US$0.80 in Ukraine (n = 14) to US$3.08 in India (n = 41). The difference in median price between legal and illicit packs as a percentage of the price of legal packs ranged from 32% in Philippines to 455% in Bangladesh. Median purchase price of illicit cigarette packs was higher than that of legal cigarette packs in six countries (Bangladesh, India, Pakistan, Philippines, Thailand, Vietnam). Median purchase price of illicit packs was lower than that of legal packs in Turkey, Ukraine and China.ConclusionsThe median purchase price of illicit cigarettes is higher than that of legal cigarette packs in Bangladesh, India, Pakistan, Philippines, Thailand, and Vietnam, Brazil, Egypt, Indonesia, Mexico, Russia appear to have few or no illicit cigarettes for purchase from formal, urban retailers.
Association between smoking and alcohol‐related behaviours: a time–series analysis of population trends in England
Authors: Beard Emma , West Robert , Michie Susan , Brown Jamie 
Published: May 2017

AbstractAimsThis paper estimates how far monthly changes in prevalence of cigarette smoking, motivation to quit and attempts to stop smoking have been associated with changes in prevalence of high‐risk drinking, and motivation and attempts to reduce alcohol consumption in England.DesignData were used from the Alcohol and Smoking Toolkit Studies between April 2014 and June 2016. These involve monthly household face‐to‐face surveys of representative samples of ~1700 adults in England.MeasurementsAutoregressive Integrated Moving Average with Exogeneous Input (ARIMAX) modelling was used to assess the association over time between monthly prevalence of (a) smoking and high‐risk drinking; (b) high motivation to quit smoking and high motivation to reduce alcohol consumption; and (c) attempts to quit smoking and attempts to reduce alcohol consumption.FindingsMean smoking prevalence over the study period was 18.6% and high‐risk drinking prevalence was 13.0%. A decrease of 1% of the series mean smoking prevalence was associated with a reduction of 0.185% of the mean prevalence of high‐risk drinking 2 months later [95% confidence interval (CI) = 0.033 to 0.337, P = 0.017]. A statistically significant association was not found between prevalence of high motivation to quit smoking and high motivation to reduce alcohol consumption (β = 0.324, 95% CI = –0.371 to 1.019, P = 0.360) or prevalence of attempts to quit smoking and attempts to reduce alcohol consumption (β = −0.026, 95% CI = –1.348 to 1.296, P = 0.969).ConclusionBetween 2014 and 2016, monthly changes in prevalence of smoking in England were associated positively with prevalence of high‐risk drinking. There was no significant association between motivation to stop and motivation to reduce alcohol consumption, or attempts to quit smoking and attempts to reduce alcohol consumption.