bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changing health behaviour with rehabilitation in thoracic cancer: A systematic review and synthesis
Authors: Bayly Joanne , Wakefield Dominique , Hepgul Nilay , Wilcock Andrew , Higginson Irene J. , Maddocks Matthew 
Published: February 2018

AbstractObjectivesInternational guidelines recommend that rehabilitation be offered to people with thoracic cancer to improve symptoms, function, and quality of life. When rehabilitation interventions require a change in behaviour, the use of theory and behaviour change techniques (BCTs) enhance participation. Our objective was to systematically identify BCTs and examine their use in relation to the Capability, Opportunity, Motivation‐Behaviour model and known enablers and barriers to engagement in this population.MethodBibliographic databases and grey literature were searched for controlled trials of rehabilitation interventions for adults with lung cancer or mesothelioma, with no limits on language or date. Data on the application of behavioural change theory and BCTs were extracted, categorised using the BCT Taxonomy (v1) and described according to the “Capability, Opportunity, Motivation‐Behaviour” model.ResultsTwenty‐seven studies of exercise (n = 15) and symptom self‐management (n = 12) interventions were identified. Four studies reported use of behavioural change theory; one study used symptom theory. Across studies, a mean (range) of 7 (1‐18) BCTs were used, representing 26 of 93 possible BCTs included in the taxonomy. Most frequent enabling BCTs were “instructions on how to perform behaviours” (74%), “behavioural practice” (74%), and “action planning” (70%). BCTs to address barriers were less frequent and included “information about health consequences” (22%) and “verbal persuasion about capability” (7%) to change perceptions about benefits, burden, and harms.ConclusionThe application of behavioural change tools appears sub‐optimal in this group of patients. Explicit use of BCTs targeting behavioural components upon which outcomes depend may improve the uptake and effectiveness of rehabilitation interventions.
Cell‐Free DNA Blood Collection Tubes Are Appropriate for Clinical Proteomics: A Demonstration in Colorectal Cancer
Authors: Almazi Juhura G. , Pockney Peter , Gedye Craig , Smith Nathan D. , Hondermarck Hubert , Verrills Nicole M. , Dun Matthew D. 
Published: February 2018

BackgroundOptimized blood collection tubes (BCT) have been developed to expand the utility of plasma cell‐free DNA (cfDNA) and are in clinical use. The appropriateness of plasma collected and stored in these tubes for proteomic analysis is unknown.MethodsPaired blood samples were collected in BCT and traditional K3EDTA (EDTA) tubes from healthy controls and from colorectal cancer (CRC) patients before and after surgery, and stored for between 45 min and 48 h at room temperature. Plasma proteins were analyzed following high‐abundant plasma protein depletion in quantitative discovery and targeted proteomics by liquid chromatography tandem‐mass spectrometry (LC‐MS/MS).ResultsBCT reduced cellular protein contamination in healthy controls over time, and increased the number of high confident low‐abundant protein identifications in CRC blood samples compared to matched samples collected in EDTA tubes. The known CRC plasma protein biomarker, carcinoembryonic antigen (CEA), showed elevated levels across patients pre‐operatively when collected and stored in BCT compared to EDTA tubes. Emerging CRC biomarkers, Dickkopf‐3 (DKK3) and Gelsolin (GSN), showed elevated levels pre‐operatively when collected in BCT.ConclusionsOptimized BCT are appropriate for low‐abundant plasma protein analysis and can be used with confidence for clinical proteomics.
Nectar yeasts: a natural microcosm for ecology
Authors: Chappell Callie R. , Fukami Tadashi 
Published: February 2018

AbstractThe species of yeasts that colonize floral nectar can modify the mutualistic relationships between plants and pollinators by changing the chemical properties of nectar. Recent evidence supporting this possibility has led to increased interest among ecologists in studying these fungi as well as the bacteria that interact with them in nectar. Although not fully explored, nectar yeasts also constitute a promising natural microcosm that can be used to facilitate development of general ecological theory. We discuss the methodological and conceptual advantages of using nectar yeasts from this perspective, including simplicity of communities, tractability of dispersal, replicability of community assembly, and the ease with which the mechanisms of species interactions can be studied in complementary experiments conducted in the field and the laboratory. To illustrate the power of nectar yeasts as a study system, we discuss several topics in community ecology, including environmental filtering, priority effects, and metacommunity dynamics. An exciting new direction is to integrate metagenomics and comparative genomics into nectar yeast research to address these fundamental ecological topics.
Molecular diversity of tuliposide B-converting enzyme in tulip (Tulipa gesneriana): identification of the third isozyme with a distinct expression profile
Authors: Nomura Taiji , Kuchida Ryo , Kitaoka Naoki , Kato Yasuo 
Published: February 2018

Abstract
6-Tuliposide B (PosB), a major secondary metabolite that accumulates in tulip (Tulipa gesneriana), is converted to the antibacterial lactone, tulipalin B (PaB), by PosB-converting enzyme (TCEB). TgTCEB1 and TgTCEB-R, which encode TCEB, are specifically expressed in tulip pollen and roots, respectively, but are hardly expressed in other tissues (e.g. leaves) despite the presence of substantial PosB-converting activity, suggesting the existence of another TCEB isozyme. Here, we describe the identification of TgTCEB-L (“L” for leaf), a paralog of TgTCEB1 and TgTCEB-R, from leaves via native enzyme purification. The enzymatic characters of TgTCEB-L, including catalytic activity and subcellular localization, were substantially the same as those of TgTCEB1 and TgTCEB-R. However, TgTCEB-L did not exhibit tissue-specific expression. Identification of TgTCEB-L explains the PosB-converting activity detected in tissues where TgTCEB1 and TgTCEB-R transcripts could not be detected, indicating that tulip subtilizes the three TgTCEB isozymes depending on the tissue.
Relationship between skeletal muscle contractile properties and power production capacity in female Olympic rugby players
Authors: Valenzuela Pedro L. , Montalvo Zigor , Sánchez‐Martínez G. , Torrontegi Elaia , De La Calle‐Herrero J. , Domínguez‐castells R. , Maffiuletti Nicola A. , De La Villa Pedro 
Published: February 2018

AbstractThis study aimed to determine which contractile properties measured by tensiomyography (TMG) could better differentiate athletes with high‐ and low‐power values, as well as to analyse the relationship between contractile properties and power production capacity. The contractile properties of the vastus medialis (VM), rectus femoris (RF) and vastus lateralis (VL) of an Olympic women's Rugby Sevens team (n = 14) were analysed before a Wingate test in which their peak power output (PPO) was determined. Athletes were then divided into a high‐power (HP) and a low‐power (LP) group. HP presented an almost certainly higher PPO (9.8 ± 0.3 vs. 8.9 ± 0.4 W kg−1, ES = 3.00) than LP, as well as a very likely lower radial displacement (3.39 ± 1.16 vs. 5.65 ± 1.50 mm, ES = 1.68) and velocity of deformation (0.08 ± 0.02 vs. 0.13 ± 0.03 mm ms−1, ES = 1.87) of the VL. A likely lower time of delay was observed in HP for all analysed muscles (ES > 0.60). PPO was very largely related to the radial displacement (r = −0.75, 90% CI = −0.90 to −0.44) and velocity of deformation (r = −0.70, 90% CI = −0.87 to −0.34) of the VL. A large correlation was found between PPO and the time of delay of the VL (r = −0.61, 90% CI = −0.84 to −0.22). No correlations were found for the contractile properties of RF or VM. These results highlight the importance of VL contractile properties (but not so much those of RF and VM) for maximal power production and suggest TMG as a practical technique for its evaluation.
Isoform-level gene expression patterns in single-cell RNA-sequencing data
Authors: Vu Trung Nghia , Wills Quin F , Kalari Krishna R , Niu Nifang , Wang Liewei , Pawitan Yudi , Rantalainen Mattias 
Published: February 2018

AbstractMotivationRNA sequencing of single cells enables characterization of transcriptional heterogeneity in seemingly homogeneous cell populations. Single-cell sequencing has been applied in a wide range of researches fields. However, few studies have focus on characterization of isoform-level expression patterns at the single-cell level. In this study, we propose and apply a novel method, ISOform-Patterns (ISOP), based on mixture modeling, to characterize the expression patterns of isoform pairs from the same gene in single-cell isoform-level expression data.ResultsWe define six principal patterns of isoform expression relationships and describe a method for differential-pattern analysis. We demonstrate ISOP through analysis of single-cell RNA-sequencing data from a breast cancer cell line, with replication in three independent datasets. We assigned the pattern types to each of 16 562 isoform-pairs from 4929 genes. Among those, 26% of the discovered patterns were significant (P&lt;0.05), while remaining patterns are possibly effects of transcriptional bursting, drop-out and stochastic biological heterogeneity. Furthermore, 32% of genes discovered through differential-pattern analysis were not detected by differential-expression analysis. Finally, the effects of drop-out events and expression levels of isoforms on ISOP's performances were investigated through simulated datasets. To conclude, ISOP provides a novel approach for characterization of isoform-level preference, commitment and heterogeneity in single-cell RNA-sequencing data.Availability and implementationThe ISOP method has been implemented as a R package and is available at https://github.com/nghiavtr/ISOP under a GPL-3 license.Supplementary informationSupplementary data are available at Bioinformatics online.
Prediction of potential disease-associated microRNAs using structural perturbation method
Authors: Zeng Xiangxiang , Liu Li , Lü Linyuan , Zou Quan 
Published: February 2018

Abstract

Motivation
The identification of disease-related microRNAs (miRNAs) is an essential but challenging task in bioinformatics research. Similarity-based link prediction methods are often used to predict potential associations between miRNAs and diseases. In these methods, all unobserved associations are ranked by their similarity scores. Higher score indicates higher probability of existence. However, most previous studies mainly focus on designing advanced methods to improve the prediction accuracy while neglect to investigate the link predictability of the networks that present the miRNAs and diseases associations. In this work, we construct a bilayer network by integrating the miRNA–disease network, the miRNA similarity network and the disease similarity network. We use structural consistency as an indicator to estimate the link predictability of the related networks. On the basis of the indicator, a derivative algorithm, called structural perturbation method (SPM), is applied to predict potential associations between miRNAs and diseases.

Results
The link predictability of bilayer network is higher than that of miRNA–disease network, indicating that the prediction of potential miRNAs–diseases associations on bilayer network can achieve higher accuracy than based merely on the miRNA–disease network. A comparison between the SPM and other algorithms reveals the reliable performance of SPM which performed well in a 5-fold cross-validation. We test fifteen networks. The AUC values of SPM are higher than some well-known methods, indicating that SPM could serve as a useful computational method for improving the identification accuracy of miRNA‒disease associations. Moreover, in a case study on breast neoplasm, 80% of the top-20 predicted miRNAs have been manually confirmed by previous experimental studies.

Availability and implementation
https://github.com/lecea/SPM-code.git

Supplementary information
Supplementary data are available at Bioinformatics online.
Measuring the respiratory gas exchange by grazing cattle using an automated, open-circuit gas quantification system1
Authors: Gunter Stacey A , Beck Matthew R 
Published: February 2018

AbstractRuminants are a source of enteric CH4, which has been identified as an anthropogenic greenhouse gas that contributes to climate change. With interest in developing technologies to decrease enteric CH4 emissions, systems are currently being developed to measure CH4 emissions by cattle. An issue with grazing cattle is the ability to measure CH4 emissions in open-air environments. A scientific instrument for this task is an automated, open-circuit gas quantification system (GQS; C-Lock, Inc., Rapid City, SD). The GQS is a head chamber that grazing cattle occasionally visit (3 to 8 min/visit; 3 to 6 visits/d), and while the animal consumes a small portion of bait (0.5 to 1.0 kg/visit), the GQS captures the animal’s breath cloud by exhausting air through the GQS. The breath cloud is then analyzed for CH4, CO2, and O2 concentrations. Data are hourly uploaded to a server where it is processed using algorithms to determine total daily fluxes. Several factors affect emission estimates generated by the GQS including the animal’s visitation rate, length of sampling period, and airflow through the system. The location of the GQS is an important factor in determining the cattle’s willingness to visit. Further, cattle need to be trained to use the GQS, which normally requires 4 to 8 wk. Several researchers have shown that 30 or more visits are required to obtain high-quality estimates of gas fluxes. Once cattle are trained to use the GQS, the bait delivery rate has little effect on the animal’s willingness to use the system. Airflow through the GQS is an important factor, but as long as airflow is maintained above 26 L/s the breath-cloud capture seems nearly complete. There is great concern regarding circadian variation in the instantaneous production rates of CH4 because the GQS normally only spot-samples 2 to 4 times/d. Preliminary analysis has shown that variation in the instantaneous production rates of CH4 do not vary as greatly with grazing cattle compared with meal-fed cattle. It seems that increasing the visitation length decreases variation in estimated emissions, but there is a diminishing return to increasing visitation length. The GQS is a useful tool for researching the nutrition and emissions of grazing cattle, but great care must be taken to obtain the best quality data possible for use in this high-impact research.
TAG.ME: Taxonomic Assignment of Genetic Markers for Ecology
Authors: Valente Pires Douglas Eduardo , Oliveira Francislon Silva , Correa Felipe Borim , Morais Daniel Kumazawa , Fernandes Gabriel Rocha 
Published: February 2018

1.AbstractBackgroundSequencing of amplified genetic markers, such as the 16S rRNA gene, have been extensively used to characterize microbial community composition. Recent studies suggested that Amplicon Sequences Variants (ASV) should replace the Operational Taxonomic Units (OTU), given the arbitrary definition of sequence identity thresholds used to define units. Alignment-free methods are an interesting alternative for the taxonomic classification of the ASVs, preventing the introduction of biases from sequence identity thresholds.ResultsHere we present TAG.ME, a novel alignment-independent and amplicon-specific method for taxonomic assignment based on genetic markers. TAG.ME uses a multilevel supervised learning approach to create predictive models based on user-defined genetic marker genes. The predictive method can assign taxonomy to sequenced amplicons efficiently and effectively. We applied our method to assess gut and soil sample classification, and it outperformed alternative approaches, identifying a substantially larger proportion of species. Benchmark tests performed using the RDP database, and Mock communities reinforced the precise classification into deep taxonomic levels.ConclusionTAG.ME presents a new approach to assign taxonomy to amplicon sequences accurately. Our classification model, trained with amplicon specific sequences, can address resolution issues not solved by other methods and approaches that use the whole 16S rRNA gene sequence. TAG.ME is implemented as an R package and is freely available at http://gabrielrfernandes.github.io/tagme/
Intrinsic equivalence between developmental prosopagnosia questionnaires
Authors: Matsuyoshi Daisuke , Watanabe Katsumi 
Published: February 2018

AbstractThe 20-item prosopagnosia index (PI20) is a self-report measure of face recognition ability, which is aimed to assess the risk for developmental prosopagnosia (DP), developed by Shah, Gaule, Sowden, Bird, and Cook (2015). Although they validated PI20 in several ways and it may serve as a quick and cost-effective measure for estimating DP risk (Livingston & Shah, in press; Shah et al., 2015), they did not formally evaluate its validity against a pre-existing alternative questionnaire (Kennerknecht et al., 2008) even though they criticized the weak relationship of the pre-existing questionnaire to actual behavioral face recognition performance. Thus, we administered the questionnaires to a large population (N = 855) and found a very strong correlation (r = 0.82 [95% confidence interval: 0.80, 0.84]), a principal component that accounted for more than 90% of the variance, and comparable reliability between the questionnaires. These results show unidimensionality and equivalence between the two questionnaires, or at least, a very strong common latent factor underlying them. The PI20 may not be greater than the pre-existing questionnaire; the two questionnaires measured essentially the same trait. The intrinsic equivalence between the questionnaires necessitates a revision of the view that the PI20 overcomes the weakness of the pre-existing questionnaire. Because both questionnaires contained unreliable items, we suggest, instead of using either questionnaire alone, that selection of a set of items with high reliability may offer a more robust approach to capture face recognition ability.
Factors influencing gene family size variation among related species in a plant family
Authors: Wang Peipei , Moore Bethany M. , Panchy Nicholas L. , Meng Fanrui , Lehti-Shiu Melissa D. , Shiu Shin-Han 
Published: February 2018

AbstractGene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, we used the Solanaceae family as a model to investigate differences in gene family size and the likely factors contributing to these differences. We found that genes in highly variable families have high turnover rate and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high-and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggests that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.
Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging
Authors: Glaser Adam K. , Chen Ye , Yin Chengbo , Wei Linpeng , Barner Lindsey A. , Reder Nicholas P. , Liu Jonathan T.C. 
Published: February 2018

AbstractLight-sheet fluorescence microscopy (LSFM) has emerged as a powerful method for rapid and optically efficient 3D microscopy. Initial LSFM designs utilized a static sheet of light, termed selective plane illumination microscopy (SPIM), which exhibited shadowing artifacts and deteriorated contrast due to light scattering. These issues have been addressed, in part, by multidirectional selective plane illumination microscopy (mSPIM), in which rotation of the light sheet is used to mitigate shadowing artifacts, and digital scanned light-sheet microscopy (DSLM), in which confocal line detection is used to reject scattered light. Here we present a simple passive multidirectional digital scanned light-sheet microscopy (mDSLM) architecture that combines the benefits of mSPIM and DSLM. By utilizing an elliptical Gaussian beam with increased angular diversity in the imaging plane, mDSLM provides shadow-free contrast-enhanced imaging of fluorescently labeled samples.One Sentence SummaryGlaser et al. describe a light-sheet microscopy architecture that enables passive multidirectional illumination with confocal line detection to enable both uniform fluorescence excitation and contrast-enhanced imaging of fluorescently labeled samples.
Muscarinic M1 receptor modulation of synaptic plasticity in nucleus accumbens of wild-type and fragile X mice
Authors: Neuhofer Daniela , Lassalle Olivier , Manzoni Olivier J 
Published: February 2018

AbstractWe investigated how metabotropic Acetylcholine receptors control excitatory synaptic plasticity in the mouse nucleus accumbens core. Pharmacological and genetic approaches revealed that M1 mAChRs trigger multiple and interacting forms of synaptic plasticity. As previously described in the dorsal striatum, moderate pharmacological activation of M1 mAChR potentiated postsynaptic NMDARs. The M1-potentiation of NMDAR masked a previously unknown coincident TRPV1-mediated long-term depression (LTD). In addition, strong pharmacological activation of M1 mAChR induced canonical retrograde LTD, mediated by presynaptic CB1R. In the fmr1-/y mouse model of Fragile X, we found that CB1R but not TRPV1 M1-LTD was impaired. Finally, pharmacological blockade of the degradation of anandamide and 2-arachidonylglycerol, the two principal eCBs restored fmr1-/y LTD to wild type levels. These findings shed new lights on the complex influence of Acetylcholine on excitatory synapses in the nucleus accumbens core and identify new substrates of the synaptic deficits of Fragile X.